U.S. patent application number 16/993782 was filed with the patent office on 2021-02-18 for combination therapy with gold controlled transgenes.
This patent application is currently assigned to Chimera Bioengineering, Inc.. The applicant listed for this patent is Chimera Bioengineering, Inc.. Invention is credited to Scott Dylla, Benjamin Wang, Gusti Zeiner.
Application Number | 20210046117 16/993782 |
Document ID | / |
Family ID | 1000005100797 |
Filed Date | 2021-02-18 |
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United States Patent
Application |
20210046117 |
Kind Code |
A1 |
Wang; Benjamin ; et
al. |
February 18, 2021 |
Combination Therapy with Gold Controlled Transgenes
Abstract
Control Devices are disclosed including RNA destabilizing
elements (RDE) combined with transgenes, including Chimeric Antigen
Receptors (CARs) in eukaryotic cells. These RDEs can be used to
optimize expression of transgenes, e.g., CARs, in the eukaryotic
cells so that, for example, effector function is optimized. CARs
and transgene payloads can also be engineered into eukaryotic cells
so that the transgene payload is expressed and delivered at desired
times from the eukaryotic cell. Such CAR T-cells with transgene
payloads can be combined with the administrstion of other
molecules, e.g., other therapeutics such as anticancer
therapies.
Inventors: |
Wang; Benjamin; (Menlo Park,
CA) ; Dylla; Scott; (Portola Valley, CA) ;
Zeiner; Gusti; (Pacifica, CA) |
|
Applicant: |
Name |
City |
State |
Country |
Type |
Chimera Bioengineering, Inc. |
Menlo Park |
CA |
US |
|
|
Assignee: |
Chimera Bioengineering,
Inc.
Menlo Park
CA
|
Family ID: |
1000005100797 |
Appl. No.: |
16/993782 |
Filed: |
August 14, 2020 |
Related U.S. Patent Documents
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Application
Number |
Filing Date |
Patent Number |
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62888524 |
Aug 18, 2019 |
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62965569 |
Jan 24, 2020 |
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63054721 |
Jul 21, 2020 |
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Current U.S.
Class: |
1/1 |
Current CPC
Class: |
A61P 35/00 20180101;
C07K 14/70578 20130101; C07K 14/7156 20130101; A61K 35/17 20130101;
C07K 14/7155 20130101 |
International
Class: |
A61K 35/17 20060101
A61K035/17; C07K 14/715 20060101 C07K014/715; C07K 14/705 20060101
C07K014/705; A61P 35/00 20060101 A61P035/00 |
Claims
1. A method for delivering a payload, comprising the steps of:
exposing a cancer cell to a therapeutic agent; obtaining a primary
T-cell comprising a chimeric antigen receptor, and a heterologous
nucleic acid comprising a promoter operably linked to a
polynucleotide encoding the payload that is operably linked to a
polynucleotide encoding a RNA degradation element (RDE), wherein
the RDE is an AU rich element, wherein the heterologous nucleic
acid is transcribed to make a transcript encoding the transgene
operably linked to the RDE; exposing the primary T-cell to a ligand
for the chimeric antigen receptor wherein the ligand is associated
with the cancer cell, and wherein binding of the ligand by the
receptor activates the primary T-cell; and expressing the transgene
wherein the amount of polypeptide made from the transgene is
increased after the primary T-cell is activated.
2. The method of claim 1, wherein the therapeutic agent is an
unconjugated antibody, an immunoconjugate, a gene therapy, a
chemotherapeutic agent, a therapeutic peptide, a cytokine, a
localized radiation therapy, a radioconjugate, a surgery, an
interference RNA, a drug, or a toxin.
3. The method of claim 2, wherein the therapeutic agent is an
immunoconjugate and wherein the immunoconjugate binds to the same
ligand as the chimeric antigen receptor.
4. The method of claim 2, wherein the therapeutic agent is an
immunoconjugate and wherein the immunoconjugate binds to a
different ligand as the chimeric antigen receptor.
5. The method of claim 2, wherein the chemotherapeutic agent is a
mitotic inhibitor, an antitumor antibiotic, a plant alkaloid, an
alkylating agent, an antimetabolite, and/or a radionuclide.
6. The method of claim 1 wherein the transgene encodes a cytokine,
a FasL, an antibody, a growth factor, a chemokine, an enzyme that
cleaves a polypeptide or a polysaccharide, a granzyme, a perforin,
or a checkpoint inhibitor.
7. The method of claim 1, wherein the transgene encodes an IL-2,
and IL-12, an IL-15, an IL-18, an IFNg, a CD40L, or a
TNF-.alpha..
8. The method of claim 1, wherein the chimeric antigen receptor is
an anti-DLL3 chimeric antigen receptor.
9. The method of claim 8, wherein the ligand is a DLL3 found on a
tumor cell.
10. The method of claim 9, wherein the tumor cell is an IDH1mut
glioma cell, a melanoma cell, or a small cell lung cancer cell.
11. The method of claim 10, wherein the transgene encodes a
cytokine, a FasL, an antibody, a growth factor, a chemokine, an
enzyme that cleaves a polypeptide or a polysaccharide, a granzyme,
a perforin, or a checkpoint inhibitor.
12. The method of claim 11, wherein the wherein therapeutic agent
is an unconjugated antibody, an immunoconjugate, a gene therapy, a
chemotherapeutic agent, a therapeutic peptide, a cytokine, a
localized radiation therapy, a surgery, an interference RNA, a
drug, or a toxin.
13. The method of claim 11, wherein the therapeutic agent is an
immunoconjugate and wherein the immunoconjugate binds to a
DLL3.
14. The method of claim 1, wherein the chimeric antigen receptor is
an anti-TnMUC1 chimeric antigen receptor.
15. The method of claim 14, wherein the ligand is a TnMUC1 found on
a tumor cell.
16. The method of claim 15, wherein the tumor cell is a breast
cancer cell or a pancreatic cancer cell.
17. The method of claim 15, wherein the transgene encodes a
cytokine, a FasL, an antibody, a growth factor, a chemokine, an
enzyme that cleaves a polypeptide or a polysaccharide, a granzyme,
a perforin, or a checkpoint inhibitor, and wherein the wherein
therapeutic agent is an unconjugated antibody, an immunoconjugate,
a gene therapy, a chemotherapeutic agent, a therapeutic peptide, a
cytokine, a localized radiation therapy, a surgery, an interference
RNA, a drug, or a toxin.
18. The method of claim 1, wherein exposing the cancer cell to a
therapeutic agent is performed before exposing the primary T-cell
to a ligand for the chimeric antigen receptor.
19. The method of claim 1, wherein exposing the primary T-cell to a
ligand for the chimeric antigen receptor is performed before
exposing the cancer cell to a therapeutic agent.
20. The method of claim 1, wherein exposing the cancer cell to a
therapeutic agent is performed at the same time as exposing the
primary T-cell to a ligand for the chimeric antigen receptor.
Description
REFERENCE TO SEQUENCE LISTING, TABLE OR COMPUTER PROGRAM
[0001] The official copy of the Sequence Listing is submitted
concurrently with the specification as an ASCII formatted text file
via EFS-Web, with a file name of "CBIO046_ST25.txt", a creation
date of Jan. 24, 2020, and a size of 9 kilobytes. The Sequence
Listing filed via EFS-Web is part of the specification and is
incorporated in its entirety by reference herein.
BACKGROUND OF THE INVENTION
[0002] Chimeric Antigen Receptors are human engineered receptors
that may direct a T-cell to attack a target recognized by the CAR.
For example, CAR T cell therapy has been shown to be effective at
inducing complete responses against acute lymphoblastic leukemia
and other B-cell-related malignancies and has been shown to be
effective at achieving and sustaining remissions for
refractory/relapsed acute lymphoblastic leukemia (Maude et al.,
NEJM, 371:1507, 2014). However, dangerous side effects related to
cytokine release syndrome (CRS), tumor lysis syndrome (TLS), B-cell
aplasia and on-tumor, off-target toxicities have been seen in some
patients.
[0003] There are currently two extant strategies to control CAR
technology. The first is an inducible "kill switch." In this
approach, one or more "suicide" genes that initiate apoptotic
pathways are incorporated into the CAR construct (Budde et al.
PLoS1, 2013 doi:10.1371/journal.pone.0082742). Activation of these
suicide genes is initiated by the addition of AP1903 (also known as
rimiducid), a lipid-permeable tachrolimus analog that initiates
homodimerization of the human protein FKBP12 (Fv) to which the
apoptosis-inducing proteins are translationally fused In the ideal
scenario, these kill switches endeavor to sacrifice the long-term
surveillance benefit of CAR technology to safeguard against
toxicity. However, in vivo, these suicide switches are not likely
to realize this goal, as they are operating against powerful
selection pressures for CAR T-cells that do not respond to AP1903,
a situation worsened by the inimical error-prone retroviral copying
associated with the insertion of stable transgenes into patient
T-cells. In this scenario, non-responsive CAR T-cell clones will
continue to proliferate and kill target cells in an
antigen-dependent manner. Thus, kill switch technology is unlikely
to provide an adequate safeguard against toxicity.
[0004] The second CAR regulatory approach is transient CAR
expression, which can be achieved in several ways. In one approach,
T-cells are harvested from unrelated donors, the HLA genes are
deleted by genome-editing technology and CAR-encoding transgenes
are inserted into the genome of these cells. Upon adoptive
transfer, these CAR T-cells will be recognized by the recipient's
immune system as being foreign and destroyed, thus the CAR exposure
in this system is transient. In another transient CAR exposure
approach, mRNA of a CAR-encoding gene is introduced into harvested
patient T-cells (Beatty, G L 2014. Cancer Immunology Research 2
(2): 112-20. doi:10.1158/2326-6066.CIR-13-0170). As mRNA has a
short half-life and is not replicated in the cell or stably
maintained, there is no permanent alteration of the CAR-expressing
T-cell, thus the CAR expression and activity will be for a short
period of time. However, as with the kill-switch approach, these
transient CAR exposure approaches sacrifice the surveillance
benefit of CARs. Additionally, with these transient systems acute
toxicity can be difficult to control.
SUMMARY OF THE INVENTION
[0005] In an aspect, the description discloses new chimeric antigen
receptors (CARs) that use a knottin (an inhibitor cystine-knot
protein or cysteine knot protein) as the antigen recognition
portion of the CAR. Knottins can be engineered to recognize targets
of interest as knottins have a core structure (scaffold) with
peptide loops around the core structure which peptide loops can be
engineered to produce different binding properties and
specificities. Knottins can be small and so have the properties of
a small molecule with the binding affinity of a biologic (such as
an antibody). Knottins have high stability to pH, heat, and
enzymes.
[0006] In an aspect, the description discloses a eukaryotic cell
with a CAR, T-cell receptor, or other targeting polypeptide and a
transgene under the control of an RNA Destabilizing Element (RDE).
The RDE may control multiple transgenes or multiple RDEs may
control multiple transgenes. The multiple transgenes may be
arranged serially and/or as a concatemer and/or in other
arrangements. Multiple RDEs may be used to regulate a transgene,
and these multiple RDEs can be organized as a concatemer,
interspersed within a region of the transcript, or located in
different parts of the transcript. Multiple transgenes can be
regulated by an RDE or a combination of RDEs. The RDEs can be
localized in the 3'-UTR, the 5'-UTR and/or an intron. RDEs can
include, for example, the RDEs from AU 1 (CD40L), AU 2 (CSF2), AU 3
(CD247), AU 4 (CTLA4), AU 5 (EDN1), AU 6 (IL2RA), AU 7 (SLC2A1), AU
8 (TRAC), AU 9 (CD274), AU 10 (Myc), AU 11 (CD19), AU 12 (IL4), AU
13 (IL5), AU 14 (IL6), AU 15 (IL9), AU 16 (IL10), AU 17 (IL13), AU
18 (FOXP3), AU 19 (TMEM-219), AU 20 (TMEM-219snp), AU 21 (CCR7), AU
22 (SEM-A4D), AU 23 (CDC42-SE2), AU 24 (CD8), AU 27 (bGH), and/or
AU 101 (Interferon gamma or IFNg). Other RDEs are disclosed in the
following description. RDE control can also be combined with codon
optimization of the transgene to increase the GC content of the
wobble position (third position of the codon) in some or all of the
codons of the transgene. This codon optimization can increase
efficiency of expression (the on signal) by up to 100-fold. Such
codon optimized transgenes can be linked to an RDE and produce a
larger dynamic range of expression from the RDE control compared to
the transgene-RDE without codon optimization.
[0007] In an aspect, the RDE can be under the control of a RNA
control device. Such, Smart RDEs place the RDE control under the
regulation of the RNA control device which introduces ligand
control to the RDE. The RNA control device can disrupt the RDE when
ligand is bound (or not bound) resulting in loss of the RDE
control, and when ligand is added (or removed) the RNA control
device is inhibited and the RDE structure is available for
interaction with RNA binding proteins. The RNA control device could
also act upon a portion of the transcript that disrupts the RDE
(e.g., the portion of the transcript could form secondary
structures with the RDE that inhibit RNA binding proteins from
binding to the RDE), when the RNA control device binds (or is free
from ligand) the RNA control device disrupts the inhibitory portion
of the transcript so it is not available to interact with the RDE,
and the RDE is now available to interact with RNA binding proteins.
This RNA control device regulation allows the activity of the RDE
to be ligand controlled through the action of the RNA control
device.
[0008] In an aspect, a therapy utilizing a CAR T-lymphocyte with or
without an RDE controlled transgene(s) is combined or in an order
of succession with another therapy. The other therapy can include
any therapeutic molecule including, for example, a polypeptide,
lipid, carbohydrate, nucleic acid, small molecule drug, biological
drug, antibody, antibody-drug-conjugate, or combinations of the
foregoing. Suitable molecules are described below. The other
therapy can be administered to a subject at the same time as the
CAR therapy (with or without a RDE controlled transgene(s)), before
the administration of the CAR therapy (with or without a RDE
controlled transgene(s)), or after the administration of the CAR
therapy (with or without a RDA controlled transgene(s)). For
example, a subject could be treated with chemotherapy and/or an
immunotherapy (e.g., an antibody-drug conjugate), followed by
treatment with a CAR T-cell with optionally a RDE controlled
payload. The CAR T-cell treatment can be given the subject at
varying times after the chemotherapy and/or immunotherapy, e.g.,
one, two, three, four, five, or six weeks. The chemotherapy and/or
immunotherapy (e.g., ADC) can be cycled with the CAR T-cell
treatment for multiple cycles of treatment. Treatment with CAR
T-cells may also be boosted with target X peptide, or virus or
cells loaded with target X peptide (target X is the target bound by
the CAR).
[0009] In an aspect, an RDE, combination of RDEs, and/or modified
RDEs can be used to provide desired kinetic parameters to the
regulation of a gene product including, for example, amount of
expression, steady state concentration, C.sub.max (maximal
concentration of gene product obtained), T.sub.max (time to reach
C.sub.max), baseline expression, speed of induction (acceleration),
induction rate (velocity), dynamic range also known as fold
regulation (induced expression/basal expression), maximal dynamic
range (DR.sub.max), time to DR.sub.max, area under the curve (AUC),
etc. A RDE construct can be made that has a desired set of kinetic
parameters to provide the level, degree, temporal, and amount of
regulation that is desired. In addition, RDE concatemers can be
used to alter the kinetic performance of a construct.
[0010] Combinations of RDEs can be used to provide temporal
regulation between two or more transgenes. RDEs can be selected to
provide maximal rates of expression (and different amounts of
maximal expression) at different times following activation of a
cell (or induction of expression). This temporal control allows a
first transgene encoded polypeptide to alter the state of the cell
so that the cell is prepared to be acted upon by a second
polypeptide encoded by a second transgene with an RDE that provides
later in time expression. This temporal control can also be used to
time the expression of two, three or more transgenes following
activation of a cell. If the transgene encoded polypeptides are
secreted, they can act in a temporal fashion upon target cells. For
example, a first transgene polypeptide (with an early expression
RDE) could be secreted and act upon a target cell to change its
state (e.g., induce the expression of receptor). The second
transgene polypeptide is expressed at a later time (under the
control of a later expression RDE) and acts upon the target cell
with the changed state (e.g., the second protein can be a ligand
for the induced receptor).
[0011] In an aspect, the RDE can be engineered to increase or
decrease the binding affinity of RNA binding protein(s) that
interact with the RDE. Altering the affinity of the RNA binding
protein can change the timing and response of transgene expression
as regulated by the RNA binding protein. In an aspect, the RNA
binding protein binding at the RDE is altered by the metabolic
state of the cell and changing the binding affinity of the RDE for
the RNA binding protein alters the response to and/or timing of
transgene expression with the metabolic state of the cell. In an
aspect, the RNA binding protein binding at the RDE is altered by
the redox state of the cell and changing the binding affinity of
the RDE for the RNA binding protein alters the response to and/or
timing of transgene expression with the redox state of the
cell.
[0012] In an aspect, the CAR, T-cell receptor, B-cell receptor,
innate immunity receptor, or other targeting receptor or targeting
polypeptide recognizes an antigen at the target site (e.g., tumor
cell or other diseased tissue/cell) and this activates the cell.
The transgene can be another CAR that recognizes a second antigen
at the target site and activation of the cell by the first CAR,
T-cell receptor or other targeting polypeptide induces the second
CAR allowing the eukaryotic cell to recognize the target site by a
second antigen. In an aspect, the eukaryotic cell has a first CAR
that recognizes an antigen at a target site and this activates a
transgene (through an RDE) that encodes a polypeptide that directly
or indirectly reduces the activation state of the cell. For
example, the transgene may encode a second CAR that recognizes an
antigen on healthy tissue so that when the first CAR reacts with
antigen at a nontarget cell, the eukaryotic cell will be
de-activated by the second CAR interaction with the healthy cell
antigen (that is not present or is present in reduced amounts at
the target site).
[0013] In some aspects, the eukaryotic cell is an immune cell,
e.g., a T-cell, a natural killer cell, a B-cell, a macrophage, a
dendritic cell, or other antigen presenting cell. In these aspects,
activation of the cell by the CAR or changing the metabolic state
of the immune cell in other ways can induce expression of the
transgene through the RDE. The RDE that controls the transgene can
have microRNA binding sites and can be engineered to remove one or
more of these microRNA binding sites. The RDE can be bound by the
Hu Protein R (HuR). Without wishing to be bound by theory it is
expected that HuR can bind to some RDEs, and act to stabilize the
mRNA, leading to enhanced translation. Some RDEs can be tied to the
glycolytic state of the eukaryotic cell through the enzyme
glyceraldehyde 3-phosphate dehydrogenase (GAPDH), other
dehydrogenases, other oxidoreductases, or other glycolytic enzymes
that can bind to an RDE when the eukaryotic cell is not activated
(low glycolytic activity), quiescent, or at rest. When GAPDH or the
other enzymes bind to the RDE this can reduce half-life of the RNA
with the RDE. In this aspect, CAR activation of the eukaryotic cell
(e.g., T-lymphocyte) can induce glycolysis in the cell which
reduces GAPDH binding of the RNA, increases half-life of the RNA,
which produces increased expression of the transgene encoded in the
RNA and controlled by the RDE. Without wishing to be bound by
theory, as GAPDH vacates the RDE, HuR or other RDE binding proteins
may subsequently bind either the same RDE, or a previously
inaccessible RDE (sterically hindered by presence of GAPDH),
further stabilizing the mRNA, increasing half-life of the mRNA, and
producing further increased expression of the transgene encoded by
the RNA and controlled by said RDE. Thus, CAR activation can induce
expression of the transgene. In other aspects, other activation of
the immune cell can cause GAPDH to engage in glycolysis and so
induce expression of the transgene under the control of the RDE.
Examples of RDEs bound by GAPDH include, for example, AU 19
(TMEM-219), AU 20 (TMEM-219snp), AU 21 (CCR7), AU 22 (SEM-A4D), and
AU 23 (CDC42-SE2).
[0014] Expression from the transcript with the RDE(s) can respond
to the metabolic state of the cell. For example, the RDE can be
bound by metabolic or glycolytic enzymes which couples expression
of the transgene to the activation state of the cell through these
metabolic or glycolytic enzymes. Some metabolic or glycolytic
enzymes bind to RDEs in the transcript and degrade or target for
degradation the transcript. When those metabolic or glycolytic
enzymes become active, the enzymes no longer bind to the RDEs, the
transcripts are stable for a longer period of time, and the
transcripts can be translated for this longer period of time. Cells
expressing transgenes under the control of such RDEs can also be
engineered to express a CAR that can alter the metabolic state of
the cell at desired times resulting in expression of the transgene
at the desired time. Alternatively, other stimuli can be used to
alter the metabolic state of the eukaryotic cell resulting in
expression of the transgene. For example, the metabolic state of
the cell can be altered to cause transgene expression (or to
inhibit expression) by stimuli including, for example, small
molecules (e.g., PMA/ionomycin), cytokines, a TCR and costimulatory
domain engagement with ligand, oxygen levels, cellular stress,
temperature, or light/radiation.
[0015] GAPDH binding to the RDE can be increased by introducing
into the cell a small molecule that inhibits glycolysis such as,
for example, dimethylfumarate (DMF), rapamycin, 2-deoxyglucose,
3-bromophyruvic acid, iodoacetate, fluoride, oxamate, ploglitazone,
dichloroacetic acid, or other metabolism inhibitors such as, for
example, dehydroepiandrosterone. Other small molecules can be used
to reduce GAPDH binding to the RDE. Such small molecules may block
the RDE binding site of GAPDH including, for example, CGP 3466B
maleate or Heptelidic acid (both sold by Santa Cruz Biotechnology,
Inc.), pentalenolactone, or 3-bromopyruvic acid. Other small
molecules can be used to analogously inhibit other enzymes or
polypeptides from binding to RDEs. Other small molecules can be
used to change the redox state of GAPDH, leading to an altered
affinity of GAPDH for the RDE. Other small molecules known to
interact with GAPDH function, such as vitamin C, saframycin,
salicylic acid, insulin, vitamin d3, metformin, or suramin can
modify the binding of GAPDH for the RDE. Other molecules can modify
the binding of GAPDH for the RDE including trehalose, galactose and
other saccharides. Other molecules known to alter GAPDH structure
can modify the binding of GAPDH for the RDE including nitric oxide
and hydrogen sulfide.
[0016] GAPDH binding of RDEs can also be modified by acetyl-CoA.
GAPDH can be acetylated at a number of Lysines in the GAPDH
sequence. Bond et al, FASEB J. 31:2592-2602 (2017), which is
incorporated by reference in its entirety for all purposes.
Acetylation at Lysine 254 can increase GAPDH activity in response
to glucose. ATP citrate lyase (ACLY) can increase the level of
acetyl-CoA in a cell thereby increasing the acetylation of GAPDH.
ACLY can be expressed in eukaryotic cells (e.g., an immune cell
such as a T-cell) at a desired time which can increase acetylation
of GAPDH which can increase expression from RDE controlled
transcripts. For example, ACLY can be used as a payload regulated
by an RDE. In this example, a eukaryotic cell (e.g., an immune
cell) is activated and the RDE controlled ACLY is expressed. The
ACLY can increased acetylation of GAPDH which can cause more
expression from RDE controlled transcripts. In this example, if
another payload is under control of an RDE the increase in
expression that payload can be increased by the co-expression of
ACLY as acetylation reduces the GAPDH bound to RDEs.
[0017] In an aspect, alternative splicing is used to complement or
in lieu of RDE control to tie cell activation and/or change in
metabolic state to the expression of a transgene. For example
alternative splicing mediated by hnRNPLL can be used. hnRNPLL is
expressed when immune cells (e.g., T-cells or B-cells) are
activated. hnRNPLL binds to RNA transcripts and can cause the
retention or excision of introns and/or exons resulting in
alternative splicing of RNAs (e.g., mRNAs). hnRNPLL alternative
splicing control can be used alone or in combination with RDE
control to regulate the expression of transgenes. When a cell is
activated (e.g., by ligand binding at a receptor which can change a
cell's metabolic state) it can induce expression of hnRNPLL, which
can produce alternative splicing products in transcripts with
hnRNPLL binding sites. As discussed above and below, such cell
activation also induces expression in transcripts with RDE sites.
By combining RDE control with hnRNPLL control the dynamic range of
control for a transgene upon cell activation (e.g., receptor
binding of ligand) can be increased.
[0018] In an aspect, activation of the immune cell induces
expression of the transgene that can encode a payload to be
delivered at the target (activation) site. The transgene can encode
a payload for delivery at the site of CAR activation and/or immune
cell activation and/or other receptor activation. The payload can
be a cytokine, an antibody, a reporter (e.g., for imaging), a
receptor (such as a CAR), or other polypeptide that can have a
desired effect at the target site. The payload can remain in the
cell, or on the cell surface to modify the behavior of the cell.
The payload can be an intracellular protein such as a kinase,
phosphatase, metabolic enzyme, an epigenetic modifying enzyme, a
gene editing enzyme, etc. The payload can be a gene regulatory RNA,
such as, for example, siRNA, microRNAs (e.g., miR155), shRNA,
antisense RNA, ribozymes, and the like, or guide RNAs for use with
CRISPR systems. The payload can be a nucleic acid (e.g., a vector,
or a human artificial chromosome (HAC)). The payload can also be a
membrane bound protein such as GPCR, a transporter, etc. The
payload can be an imaging agent that allows a target site to be
imaged (target site has a desired amount of target antigen bound by
the CAR). The payload can be a checkpoint inhibitor, and the CAR
and/or other binding protein (e.g., T-cell receptor, antibody or
innate immunity receptor) can recognize a tumor associated antigen
so the eukaryotic cell preferentially delivers the checkpoint
inhibitor at a tumor. The payload can be a cytotoxic compound
including, for example, a granzyme, an apoptosis inducer, a
cytotoxic small molecule, or complement. The payload can be an
antibody, such as for example, an anti-4-1BB agonist antibody (an
anti-CD137 antibody), an anti-IL 1b antibody (anti-inflammatory),
anti-CD29/anti-VEGF antibody, an anti-CTLA4 antibody, a bispecific
antibody (e.g., BiTE), or an anti-CD11b antibody. The payload can
be an immune polypeptide, including for example, cytokines (e.g.,
IL-2, IL-12, IL-15, IL-18), chemokines (e.g., CXCL12), perforins,
granzymes, and other immune polypeptides. The payload can be an
enzyme including for example, hyaluronidase, or heparinase. The
payload can be a polypeptide including for example, ApoE (e.g.,
ApoE2, ApoE3 and ApoE4), NO synthase (e.g., iNOS, nNOS, eNOS),
HSV-thymidine kinase (HSV-TK), antagonists of CSF1 receptor, CCR2,
CCR4, a BiTE (activates immunosuppressed T-cells), soluble CD40
ligand, HSP70, and HSP60. The payload can be fused or associated
with Decorin, Biglycan, fibromodulaon/Lumican so that the payload
binds to the collagen near or in the target site. This strategy is
particularly useful for keeping cytotoxic payloads localized to the
target cells (e.g., a tumor). The payload can be a transgene(s)
which delivers a virus as a payload. For example, the RDE can
control a master control element that controls the expression of
the virus genes for replication and coat/envelope proteins.
Alternatively, the Rep and coat/envelope proteins can be placed
under the control of inducible promoters that are controlled by a
regulatory protein, and that regulatory protein can be controlled
by an RDE. Still alternatively, the Rep proteins of the virus can
be placed under the control of an RDE, and/or the coat/envelope
proteins of the virus can be placed under the control of an RDE. As
with other payloads this complex payload can use CAR T-cell
regulation or any other regulation that induces glycolysis in a
cell. Helper constructs in a T cell, or other delivery cell can
encode the genes needed for viral replication and viral
packaging.
[0019] In some aspects, the expression of CAR, DE-CAR and/or
Side-CAR polypeptide is controlled, at least in part, by an RDE
that interacts with a glycolytic enzyme with RDE binding activity,
e.g., GAPDH. The glycolytic enzyme can bind to the RDE and reduce
production of the CAR, DE-CAR, Side-CAR polypeptide, and/or other
transgene product. This reduction in polypeptide production can
occur because of an inhibition of translation and/or an increase in
the rate of mRNA degradation (RDE binding can shorten the half-life
of the mRNA). Some RDE binding proteins may reduce translation and
enhance degradation of RNA to reduce the level of polypeptide made.
The RDE can be an AU rich element from the 3' UTR of a transcript
(e.g., a transcript encoding IL-2 or IFN-.gamma.), or can be a
modified 3' UTR that has been engineered to remove one or more
microRNA sites (e.g., modified 3'-UTRs of IL-2 or IFN-.gamma.). In
an aspect, the expression of the transgene, CAR, DE-CAR and/or
Side-CAR polypeptide under the control of an RDE bound by a
glycolytic enzyme(s), e.g., GAPDH, is increased by increasing the
activity of the enzyme(s) in prosecuting glycolysis. The activity
of enzymes in glycolysis can be increased by providing the cell
with increased glucose in the cell medium, increasing triose
isomerase activity in the cell, or providing the cell with a
compound that increases glycolysis in the cell, e.g., tamoxifen or
glucose. The RDE can bind to Hu Protein R (HuR). Without wishing to
be bound by theory it is expected that HuR binds to some AU-rich
RDEs and U-rich RDEs, and can act to stabilize the mRNA, leading to
enhanced translation. Thus, cell conditions that result in
increased HuR expression can increase expression of transgenes with
appropriate AU-rich elements and/or U-rich elements, and conditions
that reduce HuR expression can decrease expression of these
transgenes. HuR interaction with the 3' UTR of the transgene (or
native genes) can also be altered by expressing a recombinant
transcript containing HuR binding sites. Expression of these
transcripts will reduce the amount of HuR available to bind to the
transgene transcript or native HuR regulated transcripts and reduce
the half-lives of these transcripts resulting in decreased
expression.
[0020] In an aspect, RDE control can be used to lower CAR
expression in a subject which can reduce the availability of CAR
polypeptide for immune reactions. This can lower the immunogenicity
of transgenic immune cells with the CAR. In part, this lower
immunogenicity occurs because the CAR peptide has lower exposure to
the immune system.
[0021] In an aspect, nucleic acids can be used to boost the
response of immune cells upon stimulation of the immune cell. For
example, the immune cell can produce higher amounts of immune
polypeptides (greater C.sub.max) with faster kinetics of
production. The immune polypeptides can include, for example,
cytokines, perforins, granzymes, apoptosis inducing polypeptides,
etc. The nucleic acids that boost the immune response can comprise
control regions operably linked to nucleic acids encoding RDEs for
selected RDE binding proteins, so that upon expression of the
nucleic acid into RNA the RDEs in the RNA bind the RDE binding
proteins that repress expression of a polypeptide, for example,
cytokines, perforins, granzymes, and other immune polypeptides. The
expression of the RNAs with the RDEs can poise the eukaryotic cell
for expression of polypeptide controlled by RDEs. For example, the
expression of RNAs with the RDEs may be done in immune cells to
poise the cell for expression of immune polypeptides upon
stimulation of the immune cell.
[0022] In an aspect, the CAR, DE-CAR, Side-CAR polypeptides, and/or
other receptor can be directed against antigens found on acute
myeloid leukemia (AML) cells including, for example, CD 33, CD 34,
CD 38, CD43, CD 44, CD 45, CD 45RA, CD 47, CD 64, CD 66, CD 123, CD
133, CD 157, CLL-1, CXCR4, LeY, PR1, RHAMM (CD 168), TIM-3, and/or
WT1. The monoclonal antibody 293C3-SDIE can be used as the
extracellular element for the CAR, DE-CAR and/or Side-CAR
polypeptides. (Rothfelder et al., 2015, at
ash.confex.com/ash/2015/webprogram/Paper81121.htmh which is
incorporated by reference in its entirety for all purposes) Other
antigens for AML are known in the art and may be the target of the
CAR, DE-CAR, Side-CAR, and/or other receptor. An onco-sialylated CD
43 has been associated with acute myeloid leukemia (AML) and this
onco-sialylated CD 43 is not found on normal cells and tissue. This
onco-sialylated CD 43 is bound by the monoclonal antibody AT14-013,
and the variable region of this antibody is used to make an
anti-onco sialylated CD 43 CAR. AT14-013 recognizes the unique
sialylation epitope found on this onco-sialylated CD 43. This CAR
is specific for AML and does not have side reactivity with normal
tissue in a subject. In an aspect, the CAR, DE-CAR, Side-CAR
polypeptides, and/or other receptor can be directed against
antigens found on diffuse large cell B-cell lymphoma (DLBCL) cells
including, for example, CD19, CD20, CD22, CD79a, CD5, CD10, and
CD43. Other antigens for DLBCL are known in the art and may be the
target of the CAR, DE-CAR, Side-CAR, and/or other receptor.
[0023] Other antigens that can be targeted by the CAR, DE-CAR,
side-CAR or other receptor include, for example, DLL3, HER2, PSCA,
CSPG4, EGFRvIII, MSLN (mesothelin), FAP, MUC16 (CA-125), CEA, CD133
(PROM1), IL13Ra, CD171 (L1CAM), CD123, (IL3R), CD33 (SIGLEC3), LeY,
GUCY2C, BCMA and/or EPHA2. Eukaryotic cells with CAR, DE-CAR,
side-CAR or other receptors targeting these antigens can include a
payload such as, for example, one or more of anti-4-1BB antibody,
anti-CD11b antibody, anti-CTLA4 antibody, anti-IL1b antibody, a
BiTE, CCL2, anti-CXCR4 antibody, anti-CXCL12 antibody, HAC,
heparinase, hyaluronidase, Hsp60, Hsp70, IL-2, IL-12, IL-15, IL-18,
INF.gamma., miRNA (e.g., mir155), CD40 ligand, ApoE3, ApoE4,
TNF.alpha., CCR2, CCR4/CXCL12, ACLY, antagonists of CSF1 receptor,
siRNA, other antisense RNAs, and/or anti-CD28 antibody (including
full length and fragments such as single chain antibodies). The
payload can be presented as a fusion protein with a Small Leucine
Rich Proteoglycans (SLRPs) such as Decorin, Biglycan and/or Lumican
(all of which can anchor the fusion protein to the cellular matrix
in or near the target site). Fusions with Decorin and/or Biglycan
can also bind TGF-beta in and around the target site which can
reduce immune suppression. Myeloid modifying payloads ("MM
payloads") which reduce immune suppression or inhibition caused by
myeloid cells may be delivered including, for example, ApoE3,
ApoE4, Hsp60, Hsp70, TNF.alpha., antagonists of CSF1 receptor,
CD40L (CD154) and/or IL-12. Two or more MM payloads can also be
delivered by the CAR, DE-CAR, side-CAR and/or other receptor cell
(e.g., T-cell) using RDEs that produce different pharmacokinetics
for delivery. For example, the different MM payloads could be
controlled by different RDEs so that the Cmax of delivery for the
different MM payloads occurs at different times.
[0024] AB toxins can be used to engineer fusion payloads that
deliver a desired protein product into a target cell. AB toxins
include, for example diphtheria toxin, tetanus toxin, exotoxin A of
P. aeruginosa, iota toxin Ia of C. perfringens, C2 toxin CI of C.
botulinum, ADP-ribosyltransferase of C. difficile, etc. The AB
toxin can be engineered to replace the catalytic (toxic) component
(A domain) of the AB toxin with the desired protein so that the
modified AB toxin binds its receptor and delivers the desired
protein into a target cell through the B domain of the AB toxin.
These B toxin fusions can also be engineered to replace the
receptor binding portion of the B domain with a binding domain
(e.g., ligand) that binds to a desired antigen and/or receptor on a
desired target cell. These modified B toxin fusions can deliver a
desired protein payload into a target cell using the B domain of
the toxin.
[0025] The CAR, DE-CAR, Side-CAR polypeptides, and/or other
receptor can be directed against antigens found on solid tumors
such as, for example, integrins such as .alpha.v.beta.6 (found on
numerous solid tumors (including, for example, oral squamous cell
cancer, colon cancer, pancreatic cancer, gastric cancer, breast
cancer, ovarian cancer, cervical cancer, lung cancer, etc.).
[0026] In an aspect, small molecules and other molecules that
affect the availability of GAPDH or other RDE binding proteins to
bind RDEs can be used to regulate gene expression by GAPDH, other
RDE binding glycolysis enzymes, and/or other RDE binding enzymes
involved in energy and cell metabolism. Molecules that increase
glycolysis in a cell can reduce the amount of GAPDH available for
binding to RDEs which can increase translation from transcripts
under GAPDH control. Similarly, other glycolysis enzymes and
metabolic enzymes can bind to RDEs and activating glycolysis and
other energy pathways in the cell can reduce the amount of these
enzymes that are available to bind their corresponding RDEs. This
reduced binding can increase translation from transcripts
controlled by these RDE binding proteins (enzyme binding to the RDE
decreases expression) or can decrease translation if enzyme binding
has a positive effect on expression. These molecules can also be
useful in the treatment of certain types of neural degeneration
associated with inflammation and/or autoimmune diseases. These
molecules can be used to alter the amount of GAPDH in immune cells
so that RDEs are bound and the immune cells reduce expression of
RDE regulated genes. Some genes under RDE control in immune cells
are associated with inflammation and so, molecules that increase
the amount of RDE binding proteins that inhibit the inflammatory
associated transcripts could reduce inflammation.
[0027] A nucleic acid construct encoding a transcript with selected
RDEs can be expressed in an immune cell, for example, a
T-lymphocyte. The recombinant transcript with the selected RDEs can
bind to and deplete the levels of RDE binding proteins in the
T-lymphocyte so that transcripts encoding polypeptides regulated by
the depleted RDE binding proteins are expressed at different
threshold points of activation for other cellular signals. The use
of the RDE constructs can increase the kinetics of expression
and/or the Cmax of expression of the polypeptides whose expression
is controlled by the RDE.
[0028] In an aspect, CAR T-lymphocytes are modified to reduce or
prevent graft versus host reactions. This is done by knocking out
the ability of the T-cell receptors to activate the T-lymphocyte.
When a dominant CD3 epsilon chain mutant is introduced to the
T-lymphocyte it can knockout the ability of the T-cell receptors to
activate the T-lymphocyte. One such CD3 epsilon mutant is a double
mutant that replaces the Cysteine residues of the C-X-X-C motif
with Serine residues (a C119S and C122S mutant). This mutant CD3
epsilon chain disrupts signaling from the T-cell receptor and
prevents ligand induced activation of the T-lymphocyte through the
T-cell receptor. By expressing an excess of the CD3 epsilon
C119S/C122S mutant in a T-lymphocyte, the T-lymphocyte will not
activate in response to host antigens binding to the T-lymphocyte
receptor of the CAR T-lymphocytes. This allows the use of allogenic
CAR T-lymphocytes in a subject with reduced graft versus host
reactions.
[0029] In an aspect, an expression vector has a CAR cassette and a
CD3 epsilon mutant (a dominant mutant such as C119S/C122S)
cassette. These two expression cassettes are operably linked to a
strong promoter (e.g., with a strong enhancer active in
T-lymphocytes). The two cassettes can have different promoters or
can be expressed from the same promoter. The expression construct
can also include a transgene under control of a different promoter,
which transgene is operably linked to a RDE that activates
transgene expression upon stimulation of the cell by the CAR.
[0030] In an aspect, Tox expression in a T-lymphocyte or T-cell is
regulated to produce either an effector state (low Tox) or an
exhausted state (T.sub.ex with high Tox). Tox can be down regulated
in activated T-lymphocytes with a miRNA, siRNA or antisense RNA
targeted at Tox. The Tox locus in an engineered T-lymphocyte can
also be knocked out so that it does not produce a functional
product. Conversely, Tox can be expressed in an engineered
T-lymphocyte to exhaust the cell and turn it off (an off
switch).
BRIEF DESCRIPTION OF THE DRAWINGS
[0031] FIG. 1 shows a diagram for optimal CAR activity where the
three variables are CAR copy number, target epitope copy number and
CAR binding affinity.
[0032] FIG. 2 shows a graph for the bioluminescence from T-cells
with luciferase controlled by an RDE following activation of the
T-cell by Raji target cells (activate CAR) or by CD3/CD28 beads
(activate TCR) as compared to bioluminescence of T-cells at
resting.
[0033] FIG. 3 shows a graph for bioluminescence from T-cells with
luciferase controlled by the RDEs Gold1, Gold2, or Gold3 following
activation of the T-cell by Raji target cells (activate CAR) as
compared to bioluminescence of T-cells at resting.
[0034] FIG. 4 shows a graph for the IL-12 expression from T-cells
with IL-12 expression controlled by an RDE following activation of
the T-cell by Raji target cells (activate CAR) as compared to IL-12
expression of T-cells at resting.
[0035] FIG. 5 shows basal luciferase expression and activated
luciferase expression for luciferase constructs utilizing different
RDEs as control elements in Jurkat cells.
[0036] FIG. 6 shows basal luciferase expression and activated
luciferase expression for luciferase constructs utilizing different
RDEs as control elements in primary T-cells.
[0037] FIG. 7 shows activated luciferase/basal luciferase
expression after 1, 3, 6, and 8 days for luciferase constructs
utilizing different RDEs as control elements.
[0038] FIG. 8 shows basal luciferase expression and activated
luciferase expression for luciferase constructs utilizing different
RDEs as control elements.
[0039] FIG. 9 shows the dynamic range (activated luciferase/basal
luciferase) measured 1, 3/4, 6, and 8 days after activation for
luciferase constructs utilizing different RDEs as control
elements.
[0040] FIG. 10 shows the dynamic range (activated luciferase/basal
luciferase) measured 1, 3/4, 6, and 8 days after activation for
luciferase constructs utilizing different RDEs as control
elements.
[0041] FIG. 11 shows the impact on luciferase expression for
luciferase constructs utilizing an RDE as a control element in the
presence of glucose and galactose.
DETAILED DESCRIPTION OF THE INVENTION
[0042] Before the various embodiments are described, it is to be
understood that the teachings of this disclosure are not limited to
the particular embodiments described, and as such can, of course,
vary. It is also to be understood that the terminology used herein
is for the purpose of describing particular embodiments only, and
is not intended to be limiting, since the scope of the present
teachings will be limited only by the appended claims.
[0043] Unless defined otherwise, all technical and scientific terms
used herein have the same meaning as commonly understood by one of
ordinary skill in the art to which this disclosure belongs.
Although any methods and materials similar or equivalent to those
described herein can also be used in the practice or testing of the
present teachings, some exemplary methods and materials are now
described.
[0044] It must be noted that as used herein and in the appended
claims, the singular forms "a", "an", and "the" include plural
referents unless the context clearly dictates otherwise. It is
further noted that the claims can be drafted to exclude any
optional element. As such, this statement is intended to serve as
antecedent basis for use of such exclusive terminology as "solely,"
"only" and the like in connection with the recitation of claim
elements, or use of a "negative" limitation. Numerical limitations
given with respect to concentrations or levels of a substance are
intended to be approximate, unless the context clearly dictates
otherwise. Thus, where a concentration is indicated to be (for
example) 10 .mu.g, it is intended that the concentration be
understood to be at least approximately or about 10 .mu.g.
[0045] As will be apparent to those of skill in the art upon
reading this disclosure, each of the individual embodiments
described and illustrated herein has discrete components and
features which can be readily separated from or combined with the
features of any of the other several embodiments without departing
from the scope or spirit of the present teachings. Any recited
method can be carried out in the order of events recited or in any
other order which is logically possible.
Definitions
[0046] In reference to the present disclosure, the technical and
scientific terms used in the descriptions herein will have the
meanings commonly understood by one of ordinary skill in the art,
unless specifically defined otherwise. Accordingly, the following
terms are intended to have the following meanings.
[0047] As used herein, an "actuator element" is defined to be a
domain that encodes the system control function of the RNA control
device. The actuator domain can optionally encode the
gene-regulatory function.
[0048] As used herein, an "antibody" is defined to be a protein
functionally defined as a ligand-binding protein and structurally
defined as comprising an amino acid sequence that is recognized by
one of skill as being derived from the variable region of an
immunoglobulin. An antibody can consist of one or more polypeptides
substantially encoded by immunoglobulin genes, fragments of
immunoglobulin genes, hybrid immunoglobulin genes (made by
combining the genetic information from different animals), or
synthetic immunoglobulin genes. The recognized, native,
immunoglobulin genes include the kappa, lambda, alpha, gamma,
delta, epsilon and mu constant region genes, as well as myriad
immunoglobulin variable region genes and multiple D-segments and
J-segments. Light chains are classified as either kappa or lambda.
Heavy chains are classified as gamma, mu, alpha, delta, or epsilon,
which in turn define the immunoglobulin classes, IgG, IgM, IgA, IgD
and IgE, respectively. Antibodies exist as intact immunoglobulins,
as a number of well characterized fragments produced by digestion
with various peptidases, or as a variety of fragments made by
recombinant DNA technology. Antibodies can derive from many
different species (e.g., rabbit, sheep, camel, human, or rodent,
such as mouse or rat), or can be synthetic. Antibodies can be
chimeric, humanized, or humaneered. Antibodies can be monoclonal or
polyclonal, multiple or single chained, fragments or intact
immunoglobulins.
[0049] As used herein, an "antibody fragment" is defined to be at
least one portion of an intact antibody, or recombinant variants
thereof, and refers to the antigen binding domain, e.g., an
antigenic determining variable region of an intact antibody, that
is sufficient to confer recognition and specific binding of the
antibody fragment to a target, such as an antigen. Examples of
antibody fragments include, but are not limited to, Fab, Fab',
F(ab').sub.2, and Fv fragments, scFv antibody fragments, linear
antibodies, single domain antibodies such as sdAb (either VL or
VH), camelid VHH domains, and multi-specific antibodies formed from
antibody fragments. The term "scFv" is defined to be a fusion
protein comprising at least one antibody fragment comprising a
variable region of a light chain and at least one antibody fragment
comprising a variable region of a heavy chain, wherein the light
and heavy chain variable regions are contiguously linked via a
short flexible polypeptide linker, and capable of being expressed
as a single chain polypeptide, and wherein the scFv retains the
specificity of the intact antibody from which it is derived. Unless
specified, as used herein an scFv may have the VL and VH variable
regions in either order, e.g., with respect to the N-terminal and
C-terminal ends of the polypeptide, the scFv may comprise
VL-linker-VH or may comprise VH-linker-VL.
[0050] As used herein, an "antigen" is defined to be a molecule
that provokes an immune response. This immune response may involve
either antibody production, or the activation of specific
immunologically-competent cells, or both. The skilled artisan will
understand that any macromolecule, including, but not limited to,
virtually all proteins or peptides, including glycosylated
polypeptides, phosphorylated polypeptides, and other
post-translation modified polypeptides including polypeptides
modified with lipids, can serve as an antigen. Furthermore,
antigens can be derived from recombinant or genomic DNA. A skilled
artisan will understand that any DNA, which comprises a nucleotide
sequences or a partial nucleotide sequence encoding a protein that
elicits an immune response therefore encodes an "antigen" as that
term is used herein. Furthermore, one skilled in the art will
understand that an antigen need not be encoded solely by a full
length nucleotide sequence of a gene. It is readily apparent that
the present invention includes, but is not limited to, the use of
partial nucleotide sequences of more than one gene and that these
nucleotide sequences are arranged in various combinations to encode
polypeptides that elicit the desired immune response. Moreover, a
skilled artisan will understand that an antigen need not be encoded
by a "gene" at all. It is readily apparent that an antigen can be
synthesized or can be derived from a biological sample, or can be a
macromolecule besides a polypeptide. Such a biological sample can
include, but is not limited to a tissue sample, a tumor sample, a
cell or a fluid with other biological components.
[0051] As used herein, the terms "Chimeric Antigen Receptor" and
the term "CAR" are used interchangeably. As used herein, a "CAR" is
defined to be a fusion protein comprising antigen recognition
moieties and cell-activation elements.
[0052] As used herein, a "CAR T-cell" or "CAR T-lymphocyte" are
used interchangeably, and are defined to be a T-cell containing the
capability of producing CAR polypeptide, regardless of actual
expression level. For example a cell that is capable of expressing
a CAR is a T-cell containing nucleic acid sequences for the
expression of the CAR in the cell.
[0053] As used herein, a "costimulatory element" or "costimulatory
signaling domain" or "costimulatory polypeptide" are defined to be
the intracellular portion of a costimulatory polypeptide. A
costimulatory polypeptide can be represented in the following
protein families: TNF receptor proteins, Immunoglobulin-like
proteins, cytokine receptors, integrins, signaling lymphocytic
activation molecules (SLAM proteins), and activating natural killer
cell receptors. Examples of such polypeptides include CD27, CD28,
4-1BB (CD137), OX40, GITR, CD30, CD40, ICOS, BAFFR, HVEM,
lymphocyte function-associated antigen-1 (LFA-1), CD2, CD7, LIGHT,
NKG2C, SLAMF7, NKp80, CD160, B7-H3, MyD88, and the like.
[0054] As used herein, a "Cmax" is defined to mean the maximum
concentration of a polypeptide produced by a cell after the cell is
stimulated or activated to produce the polypeptide.
[0055] As used herein, a "cytokine C.sub.max" is defined to mean
the maximum concentration of cytokine produced by an immune cell
after stimulation or activation to produce the cytokine.
[0056] As used herein, a "cytotoxic polypeptide C.sub.max" is
defined to mean the maximum concentration of cytotoxic polypeptide
produced by an immune cell after stimulation or activation to
produce the cytotoxic polypeptide.
[0057] As used herein, an "effective amount" or "therapeutically
effective amount" are used interchangeably, and defined to be an
amount of a compound, formulation, material, or composition, as
described herein effective to achieve a particular biological
result.
[0058] As used herein, an "epitope" is defined to be the portion of
an antigen capable of eliciting an immune response, or the portion
of an antigen that binds to an antibody. Epitopes can be a protein
sequence or subsequence that is recognized by an antibody.
[0059] As used herein, an "expression vector" and an "expression
construct" are used interchangeably, and are both defined to be a
plasmid, virus, or other nucleic acid designed for protein
expression in a cell. The vector or construct is used to introduce
a gene into a host cell whereby the vector will interact with
polymerases in the cell to express the protein encoded in the
vector/construct. The expression vector and/or expression construct
may exist in the cell extrachromosomally or integrated into the
chromosome. When integrated into the chromosome the nucleic acids
comprising the expression vector or expression construct will be an
expression vector or expression construct.
[0060] As used herein, an "extracellular element" is defined as the
antigen binding or recognition element of a Chimeric Antigen
Receptor.
[0061] As used herein, a "hematopoietic cell" is defined to be a
cell that arises from a hematopoietic stem cell. This includes but
is not limited to myeloid progenitor cells, lymphoid progenitor
cells, megakaryocytes, erythrocytes, mast cells, myeloblasts,
basophils, neutrophils, eosinophils, macrophages, thrombocytes,
monocytes, natural killer cells, T lymphocytes, B lymphocytes and
plasma cells.
[0062] As used herein, "heterologous" is defined to mean the
nucleic acid and/or polypeptide are not homologous to the host
cell. For example, a construct is heterologous to a host cell if it
contains some homologous sequences arranged in a manner not found
in the host cell and/or the construct contains some heterologous
sequences not found in the host cell.
[0063] As used herein "hnRNPLL" is defined to mean heterogeneous
nuclear ribonucleoprotein L like.
[0064] As used herein, an "intracellular element" is defined as the
portion of a Chimeric Antigen Receptor that resides on the
cytoplasmic side of the eukaryotic cell's cytoplasmic membrane, and
transmits a signal into the eukaryotic cell. The "intracellular
signaling element" is that portion of the intracellular element
which transduces the effector function signal which directs the
eukaryotic cell to perform a specialized function.
[0065] As used herein, a "knottin" or "inhibitor cystine-knots" or
"cysteine-knot" are a structural family of ultra-stable peptides
with diverse functions. Knottins contain three disulfide bonds
connected in a particular arrangement that endows these peptides
with high thermal, proteolytic, and chemical stability. Knottins
have a core scaffold structure with peptide loops that can confer
binding specificity to the peptide. Knottins have been engineered
to introduce diversity into the loops to create binding specificity
for desired targets.
[0066] As used herein, "RNA destabilizing element" or "RDE" are
used interchangeably and both are defined as a nucleic acid
sequence in an RNA that is bound by proteins and which protein
binding changes the stability and/or translation of the RNA.
Examples of RDEs include Class I AU rich elements (ARE), Class II
ARE, Class III ARE, U rich elements, GU rich elements, and
stem-loop destabilizing elements (SLDE). Without wishing to be
bound by theory, RDE's may also bind RNA stabilizing polypeptides
like HuR.
[0067] As used herein, a "single chain antibody" (scFv) is defined
as an immunoglobulin molecule with function in antigen-binding
activities. An antibody in scFv (single chain fragment variable)
format consists of variable regions of heavy (VH) and light (VL)
chains, which are joined together by a flexible peptide linker.
[0068] As used herein, a "T-lymphocyte" or T-cell" is defined to be
a hematopoietic cell that normally develops in the thymus.
T-lymphocytes or T-cells include, but are not limited to, natural
killer T cells, regulatory T cells, helper T cells, cytotoxic T
cells, memory T cells, gamma delta T cells and mucosal invariant T
cells.
[0069] As used herein, "Tox" is defined to mean thymocyte selection
associated high mobility group box.
[0070] As used herein, "transfected" or "transformed" or
"transduced" are defined to be a process by which exogenous nucleic
acid is transferred or introduced into a host cell. A "transfected"
or "transformed" or "transduced" cell is one which has been
transfected, transformed or transduced with exogenous nucleic acid.
The cell includes the primary subject cell and its progeny.
[0071] As used herein, a "transmembrane element" is defined as the
element between the extracellular element and the intracellular
element. A portion of the transmembrane element exists within the
cell membrane.
[0072] Combination Therapies
[0073] This disclosure provides compositions and methods for
providing a CAR T-lymphocyte expressing a transgene under the
control of an RDE in combination or in an order of succession with
another therapy. The other therapy can include, for example, a
chemotherapeutic, an antibody, and antibody-drug conjugate, a
radiotherapy, an alkylating agent, a plant alkaloid, an antitumor
antibiotic, an antimetabolite, a topoisomerase inhibitor, and/or an
anti-neoplastic. For example, the other therapy can be an antibody
drug conjugate that has the same or different specificity as the
CAR T-lymphocyte.
[0074] Antibodies and antibody-drug conjugates (ADC) can bind to a
tumor associated antigen, including, for example, any of the tumor
associate antigens described herein as targets for a CAR. The drug
component of the ADC can be, for example, a chemotherapeutic, a
radionucleotide, an alkylating agent, a plant alkaloid, an
antitumor antibiotic, an antimetabolite, a topoisomerase inhibitor,
and/or an anti-neoplastic. The drug component of the ADC can be
attached to the antibody through a linker which can be cleavable or
non-cleavable in nature.
[0075] Alkylating agents can include, for example, mustard gas
derivatives (e.g., mechlorethamine, cyclophosphamide, chlorambucil,
melphalan, or ifosfamide), ethylenimines (e.g., thiotepa or
hexamethylmelamine), alkylsulfonates (e.g., busulfan), hydrazines
and triazines (e.g., altretamine, procarbazine, dacarbazine, or
temozolomide), nitrosoureas (e.g., carmustine, lomustine or
streptozocin), and metal salts (e.g., carboplatin, cisplatin, or
oxaliplatin). Plant alkaloids can include, for example, Vinca
alkaloids (e.g., vincristine, vinblastine, or vinorelbine), taxanes
(e.g., paclitaxel or docetaxel), podophyllotoxins (e.g., etoposide
or tenisopide), and camptothecan analogs (e.g., irinotecan or
topotecan). Antitumor antibiotics can include, for example,
anthracyclines (e.g., doxorubicin, daunorubicin, epirubicin,
mixoantrone, or idarubicin), and chromomycins (e.g., dactinomycin
or plicamycin). Antimetabolites can include, for example, folic
acid antagonists (e.g., methotrexate), pyrimidine antagonists
(e.g., 5-flurouracil, foxuridine, cytarabine, capecitabine, or
gemcitabine), purine antagonists (e.g., 6-mercaptopurine or
6-thioguanine), and adenosine deaminase inhibitors (e.g.,
cladribine, fludarabine, nelarabine, or pentostatin). Topoisomerase
inhibitors can include, for example, topoisomerase I inhibitors
(e.g., irinotecan or topotecan) and topoisomerase II inhibitors
(e.g., amsacrine, etoposide, etoposide phosphate, or teniposide).
Anti-neoplastics can include, for example, ribonucleotide reductase
inhibitors (e.g., hydroxyurea), adrenocortical steroid inhibitors
(e.g., mitotane), enzymes (e.g., asparaginase or pegaspargase),
antimicrotubule agents (e.g., estramustine), and retinoids (e.g.,
bexarotene, isotretinoin, or tretinoin).
[0076] The drug component can also be an anthracycline, a
camptothecin, a tubulin inhibitor, a maytansinoid, a calicheamycin,
a pyrrolobenzodiazepine dimer (PBD), an auristatin, a nitrogen
mustard, an ethylenimine derivative, an alkyl sulfonate, a
nitrosourea, a triazene, a folic acid analog, a taxane, a COX-2
inhibitor, a pyrimidine analog, a purine analog, an antibiotic, an
enzyme inhibitor, an epipodophyllotoxin, a platinum coordination
complex, a vinca alkaloid, a substituted urea, a methyl hydrazine
derivative, an adrenocortical suppressant, a hormone antagonist, an
antimetabolite, an alkylating agent, an antimitotic, an
anti-angiogenic agent, a tyrosine kinase inhibitor, an mTOR
inhibitor, a heat shock protein (HSP90) inhibitor, a proteosome
inhibitor, an HDAC inhibitor, a pro-apoptotic agent, and a
combination thereof.
[0077] Specific drugs of use may be selected from the group
consisting of 5-fluorouracil, afatinib, aplidin, azaribine,
anastrozole, anthracyclines, axitinib, AVL-101, AVL-291,
bendamustine, bleomycin, bortezomib, bosutinib, bryostatin-1,
busulfan, calicheamycin, camptothecin, carboplatin,
10-hydroxycamptothecin, carmustine, celecoxib, chlorambucil,
cisplatinum, COX-2 inhibitors, irinotecan (CPT-11), SN-38,
carboplatin, cladribine, camptothecans, crizotinib,
cyclophosphamide, cytarabine, dacarbazine, dasatinib, dinaciclib,
docetaxel, dactinomycin, daunorubicin, DM1, DM3, DM4, doxorubicin,
2-pyrrolinodoxorubicine (2-PDox), a pro-drug form of 2-PDox
(pro-2-PDox), cyano-morpholino doxorubicin, doxorubicin
glucuronide, endostatin, epirubicin glucuronide, erlotinib,
estramustine, epidophyllotoxin, erlotinib, entinostat, estrogen
receptor binding agents, etoposide (VP16), etoposide glucuronide,
etoposide phosphate, exemestane, fingolimod, floxuridine (FUdR),
3',5'-O-dioleoyl-FudR (FUdR-dO), fludarabine, flutamide,
farnesyl-protein transferase inhibitors, flavopiridol,
fostamatinib, ganetespib, GDC-0834, GS-1101, gefitinib,
gemcitabine, hydroxyurea, ibrutinib, idarubicin, idelalisib,
ifosfamide, imatinib, lapatinib, lenolidamide, leucovorin, LFM-A13,
lomustine, mechlorethamine, melphalan, mercaptopurine,
6-mercaptopurine, methotrexate, mitoxantrone, mithramycin,
mitomycin, mitotane, monomethylauristatin F (MMAF),
monomethylauristatin D (MMAD), monomethylauristatin E (MMAE),
navelbine, neratinib, nilotinib, nitrosurea, olaparib, plicomycin,
procarbazine, paclitaxel, PCI-32765, pentostatin, PSI-341,
raloxifene, semustine, SN-38, sorafenib, streptozocin, SU11248,
sunitinib, tamoxifen, temazolomide, transplatinum, thalidomide,
thioguanine, thiotepa, teniposide, topotecan, uracil mustard,
vatalanib, vinorelbine, vinblastine, vincristine, vinca alkaloids
and ZD1839. Preferably, the drug is SN-38.
[0078] In an aspect the combination therapy is a protein conjugate.
The protein conjugate can carry a payload that can be a
therapeutic, diagnostic, or a reporter. A single molecule of the
therapeutic, diagnostic or reporter may be present or two or more
molecules may be present. The therapeutic can be a chemotherapeutic
including, for example, any of those described herein such as a
radionucleotide, an alkylating agent, a plant alkaloid, an
antitumor antibiotic, an antimetabolite, a topoisomerase inhibitor,
and/or an anti-neoplastic. The payload of the conjugate can be any
one or more of these therapeutics, diagnostics and/or reporters.
The protein can be a fragment, a monomer, a dimer, or a multimeric
protein. The protein can be an antibody, an antibody fragment or
derivative, a single chain antibody, an enzyme, cytokine,
chemokine, receptor, blood factor, peptide hormone, toxin, and/or
transcription factor.
[0079] Many conjugating reagents can be used to conjugate a payload
to a protein. Such reagents may contain at least one functional
group capable of reacting with a protein or peptide. For example,
the conjugating reagent may comprise a functional group capable of
reacting with at least one electrophile or, especially,
nucleophile, present in the protein, the functional group being
attached to the payload via the linker. Any type of known
conjugation reaction may be used to form the conjugate. For
example, the reaction can be carried out using the known methods of
thiol bonding, amine conjugation, or click chemistry. The reagent
may contain a maleimide group, an N-hydroxysuccinimide group, a
click-chemistry group, for example an azide or alkyne group, an
amine group, a carboxyl group, a carbonyl group, or an active ester
group. Other possible approaches include the use of proteins that
have been recombinantly engineered with an amino acid specifically
for conjugation such as engineered cysteines or non-natural amino
acids, and enzymatic conjugation through a specific enzymatic
reaction such as with transglutaminase. The reaction site on the
protein may be either nucleophilic or electrophilic in nature.
Common protein conjugation sites are at lysine or cysteine amino
acid residues or carbohydrate moieties. Alternatively, conjugation
may occur at a polyhistidine tag which has been attached to a
binding protein.
[0080] A conjugating reagent can be advantageously capable of
reacting with a nucleophile in a protein and hence becoming
chemically bonded thereto. In these examples, the conjugating
reagent typically includes at least one leaving group which is lost
on reaction with a nucleophile. The conjugating reagent may, for
example, include two or more leaving groups. The conjugating
reagent can be capable of reacting with two nucleophiles. The
conjugating reagent can comprise at least two leaving groups. When
two or more leaving groups are present, these may be the same or
different. Alternatively, a conjugating reagent may contain a
single group which is chemically equivalent to two leaving groups
and which single group is capable of reacting with two
nucleophiles. Nucleophilic groups include, for example, sulfur
atoms and amine groups, and nucleophilic groups in proteins are for
example provided by cysteine, lysine or histidine residues.
Nucleophilic groups can be a sulfur atom present in a cysteine
residue of a protein. Such structures may be obtained by reduction
of a disulfide bond in the protein. The nucleophilic group may be
an imidazole group in a histidine residue of the protein, e.g., as
present in a polyhistidine tag.
[0081] The conjugates can contain a linker which connects the
therapeutic, diagnostic or labelling agent to the protein or
peptide in the conjugate. The backbone of the linker can be a
continuous chain of atoms which runs from the therapeutic,
diagnostic or labelling agent at one end to the protein or peptide
at the other end. The linker may contain a degradable group, i.e.
it may contain a group which breaks under physiological conditions,
separating the payload from the protein to which it is, or will be,
bonded. Alternatively, the linker is not cleavable under
physiological conditions. Where a linker breaks under physiological
conditions, it is preferably cleavable under intracellular
conditions. Where the target is intracellular, preferably the
linker is substantially insensitive to extracellular conditions
(i.e. so that delivery to the intracellular target of a sufficient
dose of the therapeutic agent is not prohibited).
[0082] Where the linker contains a degradable group, this is
generally sensitive to hydrolytic conditions, for example it may be
a group which degrades at certain pH values (e.g. acidic
conditions). Hydrolytic/acidic conditions may for example be found
in endosomes or lysosomes. Examples of groups susceptible to
hydrolysis under acidic conditions include hydrazones,
semicarbazones, thiosemicarbazones, cis-aconitic amides,
orthoesters and ketals. The degradable linker can also be an
acid-cleavable linker or a reducible linker. The reducible linker
may comprise a disulfide group. The linker may also contain a group
which is susceptible to enzymatic degradation, for example it may
be susceptible to cleavage by a protease (e.g. a lysosomal or
endosomal protease) or peptidase. For example, it may contain a
peptidyl group comprising at least one, for example at least two,
or at least three amino acid residues (e.g. Phe-Leu,
Gly-Phe-Leu-Gly, Val-Ala, Val-Cit, Phe-Lys, Glu-Glu-Glu). For
example, it may include an amino acid chain having from 1 to 5, for
example 2 to 4, amino acids. The enzyme cleavable linker can also
comprise a chemical group which can be cleaved or degraded by one
or more lysosomal enzymes. Suitable groups include, for example, a
valine-citrulline dipeptide group, a phenylalanine-lysine dipeptide
group, and a .beta.-glucuronide group.
[0083] When the protein in the protein conjugate is an antibody
(e.g., full length, fragment, and/or single chain) one end of the
first linker can be covalently attached to the antibody. The
antibody-reactive end of the linker can be a site that is capable
of conjugation to the antibody through a cysteine thiol or lysine
amine group on the antibody, and so can be a thiol-reactive group
such as a double bond (as in maleimide) or a leaving group such as
a chloro, bromo, or iodo, or an R-sulfanyl group, or an
amine-reactive group such as a carboxyl group.
[0084] The CAR therapy (e.g., with a GOLD-controlled transgene) and
the other therapy can be provided to a subject at the same time, or
one can be provided to the subject before the other, or the CAR
therapy and the other therapy can be provided in alternating
cycles, or the CAR therapy together with the other therapy can be
provided in cycles, or other combinations of administration can be
used. The CAR therapy can be combined with an antibody conjugate
(ADC) therapy where the CAR and the ADC bind to the same antigen or
bind to different antigens. When the CAR and ADC bind to the same
antigen, the CAR and the ADC can bind to the same or different
epitopes on the antigen. One of the ADC or the CAR therapy can be
provided to the subject first, and followed by the other after a
period of treatment with the first. The ADC, either alone or in
combination with another approved therapy (e.g. chemotherapy and/or
immume checkpoint inhibitors) can be provided to the subject first
to reduce the tumor burden in the subject prior to the
administration of the CAR therapy. Alternatively, the ADC and CAR
therapy can be provided to the subject at the same time. Or the CAR
therapy can be provided first followed by the ADC therapy.
RNA Destabilizing Elements
[0085] RNA destabilizing elements (RDE) are nucleic acids that
affect or maintain the stability of an RNA molecule or the
translation kinetics of an RNA molecule. Some RDEs are bound by
polypeptides which destabilize (e.g., cleave) the RNA, or prevent
translation, leading to loss of function for the RNA. Some RDE
binding polypeptide stabilizes the RNA increasing the half-life of
the RNA. RDEs can be used to control the expression of a transgene,
e.g., a transgene encoding a chimeric antigen receptors. RDEs can
be used with RNA control devices, DEs, and/or Side CARs to regulate
the expression of a transgene. The RDEs can also be used to control
expression of transgenes encoding polypeptides other than a CAR.
Other transgenes may encode, for example, a cytokine, an antibody,
a checkpoint inhibitor, a granzyme, an apoptosis inducer,
complement, a cytotoxic small molecule, other cytotoxic compounds,
a polypeptide for imaging, or other polypeptide that can have a
desired effect. The RDE can control the delivery of a transgene
payload. Examples of RDEs include, for example, AU rich elements, U
rich elements, GU rich elements, and certain stem-loop elements.
Exemplary RDEs are described in Kovarik et al., Cytokine 89:21-26
(2017); Ray et al., Nature 499:172-177 (2013); Castello et al.,
Cell 149:1393-1406 (2012); Vlasova et al., Molc. Cell. 29:263-270
(2008); Barreau et al., Nucl. Acids Res. vol 33,
doi:10.1093/nar/gki1012 (2006); Meisner et al., ChemBioChem
5:1432-1447 (2004); Guhaniyogi et al., Gene 265:11-23 (2001), all
of which are incorporated by reference in their entirety for all
purposes.
[0086] The RDE can be a Class I AU rich element (dispersed AUUUA
(SEQ ID NO:1) in U rich context), a Class II AU rich element
(overlapping (AUUUA).sub.n), a Class III AU rich element (U-rich
stretch), a stem-loop destabilizing element (SLDE), a cytokine 3'
UTR (e.g., INF-.gamma., IL-2, T-cell receptor .alpha. chain,
TNF.alpha., IL-6, IL-8, GM-CSF, G-CSF etc.), and a sequence of
AUUUAUUUAUUUA (SEQ ID NO: 2). Khabar, WIREs RNA 2016, doi:
10.1002/wrna.1368 (2016); Palanisamy et al, J. Dent. Res.
91:651-658 (2012), both of which are incorporated by reference in
their entirety for all purposes. The RDE can also be a GU rich
element comprised of one or more of, for example, UUGUU (SEQ ID NO:
3), UGGGGAU (SEQ ID NO: 4), or GUUUG (SEQ ID NO: 5). The RDE can be
a U-rich element comprised of one or more of, for example, UUUGUUU
(SEQ ID NO: 6), U (SEQ ID NO: 7), UUUAUUU (SEQ ID NO: 8), UUUGUUU
(SEQ ID NO: 9), UUAGA (SEQ ID NO: 10), or AGUUU (SEQ ID NO: 11). In
some aspects, multiple RDEs can be combined to make a regulatory
unit, for example, multiple RDEs that have the same sequence can be
arranged in a concatemer or can be arranged with intervening
sequence in between some or all of the RDEs. The RDE sequence can
be modified to increase or decrease the affinity of an RNA binding
protein(s) for the RDE. For example, an AU rich RDE can be changed
to alter the affinity of glyceraldehyde phosphate dehydrogenase
(GAPDH) to the RDE. This change in affinity can alter the
GAPDH-activation threshold for expression of a transgene regulated
by the RDE to which GAPDH binds.
[0087] The disclosure assigns AU# designations to some RDEs and
these RDEs can be referred to by the AU# or the gene name from
which the RDE is derived. Some AU#s and the corresponding gene from
which the RDE is derived include, for example, AU 1 (CD40LG), AU 2
(CSF2), AU 3 (CD247), AU 4 (CTLA4), AU 5 (EDN1), AU 6 (IL2RA), AU 7
(SLC2A1), AU 8 (TRAC), AU 9 (CD274), AU 10 (Myc), AU 11 (CD19), AU
12 (IL4), AU 13 (IL5), AU 14 (IL6), AU 15 (IL9), AU 16 (IL10), AU
17 (IL13), AU 18 (FOXP3), AU 19 (TMEM-219), AU 20 (TMEM-219snp), AU
21 (CCR7), AU 22 (SEM-A4D), AU 23 (CDC42-SE2), AU 24 (CD8), AU 27
(bGH), and AU 101 (IFNg).
[0088] The RDE can be from the 3' UTR of a gene encoding, for
example, IL-1, IL-2, IL-3, IL-4, IL-6, IL-8, IL-10, GM-CSF, G-CSF,
VEGF, PGE.sub.2, COX-2, MMP (matrix metalloproteinases), bFGF,
c-myc, c-fos, betal-AR, PTH, interferon-gamma, MyoD, p21, Cyclin A,
Cyclin B1, Cyclin D1, PAI-2, NOS HANOS, TNF-alpha,
interferon-alpha, bc1-2, interferon-beta, c-jun, GLUT1, p53,
Myogenin, NF-M, or GAP-43, lymphocyte antigen 96, SUPV3L1, SFtPA2,
BLOC1S2, OR10A6, OR8D1, TRPT1,CIP29, EP400, PLE2, H3ST3A1, ZNF571,
PPP1R14A, SPAG4L, OR10A6 and KIR3DL. Other RDEs are found in, for
example, the 3'-UTRs from GLMN, AMY2B, AMY2A, AMY2A, AMY1A, TRIM33,
TRIM33, TRIM33, CSRP1, PPP1R12B, KCNH1, Reticulon 4, MRPL30,
Nav1.2, Tissue_factor_pathway_inhibitor, EEF1B2, CRYGB, ARMC9,
RPL15, EAF2, MRPS22, MRPS22, COPB2, PDCD10,
RE1-silencing_transcription_factor, Amphiregulin, AP1AR, TLR3,
SKP2, Peptidylglycine_alpha-amidating_monooxygenase, TNFAIP8,
Interleukin 9, PCDHA2, PCDHA12,
Aldehyde_dehydrogenase_5_family,_member_A1, KCNQ5, COX7A2,
Monocarboxylate_transporter_10, MLLT4, PHF10, PTPN12,
MRNA_(guanine-N7-)-methyltransferase, WHSC1L1,
Tricho-rhino-phalangeal_syndrome_Type_1, Interferon_alpha-1,
ZCCHC6, Retinitis_pigmentosa_GTPase_regulator, MED14, CLCN5, DNA2L,
OR52D1, NELL1, SLC22A25, SLC22A10, TRPC6, CACNA2D4, EPS8, CT2
(gene), Mitochondrial_ribosomal_protein_L42, TAOK3, NUPL1,
Endothelin_receptor_type_B,
Survival_of_motor_neuron_protein-interacting_protein 1, POLE2,
Hepatic_lipase, TPSG1, TRAP1, RPS15A, HS3ST3A1, CROP_(gene),
Apolipoprotein_H, GRB2, CEP76, VPS4B, Interleukin 28B, IZUMO1,
FGF21, PPP1R15A, LIN7B, hnRNPLL, Tox, and
CDC45-related_protein.
[0089] Still other RDEs can be found in, for example, the 3'UTRs of
SCFD1, MAL2, KHSRP, IQCB1, CAMP_responsive_element_modulator,
MFAP5, SBF2, FKBP2, PDCD10, UBE2V2, NDUFAB1,
Coiled-Coil_Domain_Containing_Protein, ALG13, TPTE, Enaptin,
Thymopoietin, Delta-like 1, C11orf30, Actinin_alpha_4, TMEM59,
SP110, Dicer, TARDBP, IFNA17, IFNA16, IFNA14, ZMYM3,
Interleukin_9,_type_I, OPN1SW, THSD1, ERGIC2, CAMK2B, WDR8, FXR1,
Thymine-DNA_glycosylase, Parathyroid_hormone-related_protein,
OSBPL3, Ran, GYPE, AKAP4, LOC642658, L2HGDH, AKAP1,
Zinc_finger_protein_334, TC2N, FKBPL, GRB14, CXorf67, CXorf66,
CEP76, Gastricsin, CEP70, CYP26A1, NAA35,
Aryl_hydrocarbon_receptor_nuclear_translocator, KLC4, GPR112,
LARP4, NOVA1, UBE2D3, ITGA6, GPR18, MGST_type_A,
RE1-silencing_transcription_factor, ASPM, ZNF452, KIR2DS4, AHSA1,
TMTC4, VSX1, P16, MRPL19, CCL20, TRPT1, Hepatic_lipase, PDLIM5,
CCDCl53,'CCDCl55, GAPVD1, HOXB2, KCNQ5, BRCC3, GTF2IRD1, CDK5RAP3,
Transcription_factor_II_B, ZEB1, IRGM, SLC39A6, RHEB, PSIP1,
RPS6KA5, Urokinase_receptor, GFM1, DNAJC7,
Phosphoinositide-dependent_kinase-1, LMOD3, TTC35, RRP12, ATXN2,
ACSM3, SOAT1, FGF8, HNRPH3, CTAGE5, POLG2, DYRK3, POLK,
Cyclin-dependent_kinase_inhibitor_1C, CD137, Calmodulin_1, ZNF571,
CNOT2, CRYZL1, SMC3, SMC4, SLC36A1, Decorin, HKR1, ERC1, S100A6,
RIMS1, TMEM67, Mitochondrial_ribosomal_protein_L42, MECP2, RNF111,
SULT1A1, MYLK3, TINAG, PRKAR1A, RGPD5, UBE2V1, SAR1B, SLC27A6,
ZNF638, RAB33A, TRIOBP, MUCL1, CADPS2, MCF2L, TBCA, SLC17A3, LEO1,
IFNA21, RUNX1T1, PRKD2, ATP11B, MORC2, RBM6, KLRD1, MED31, PPHLN1,
HMGB2, DNA_repair_and_recombination_protein_RAD54-like, RBM9',
ARL11, HuD, SPEF2, CBLL1, SLC38A1, `Caspase 1`, S100G, CA1_, CELA1,
PTS, ITM2B, Natriuretic_peptide_precursor_C, TRPP3, IMPDH2, DPYS,
CDCA3, EFCAB6, SLIT2, SIPA1L1, FIP1L1, ATP6V1B2, HSD17B4, HSD17B7,
NDUFC1, CROP, CD48, APPBP1, CD44, CD46,
Histone_deacetylase_2_type_XI, Interleukin 4,
Tricho-rhino-phalangeal_syndrome_Type_1, SEC61G, TR1P12, PLEKHO1,
SEC61B, ST6GALNAC1, CPVL, E2F7, UTP20, E2F5, PARD3, EXOC7, HEXB,
Caspase_recruitment_domain-containing_protein 8, MBD4, PPP4C,
Helicase, Phosducin, SPG11, CGGBP1, PSKH1, Cathepsin_S, orexin,
IMMP2L, C2orf28, Laminin, EIF3S6, LRRC41_type_XII, Cathepsin_C,
HPS6, ARAF, Zinc_finger_and_BTB_domain-containing_protein_16,
Sex_hormone-binding_globulin, FBLN2,
Suppressor_of_cytokine_signaling_1, TMEM0126A, DOM3Z, TSFM
POLQ-like, DYNLT3, CDH9, EAF2, MIPEP, NDUFA12, HDAC8, MKKS, FGG,
IL36G, CDCA7, CRISPLD2, Olfactomedin-like_2b, MRPL32, MRPL33, AHI1,
SMARCAL1, UTP14A, SSH2, Dystonin, Contactin_6, PPFIBP1, THOC1,
CNOT1, RHCE, SLC41A3, SLC2A9, SNAP23, RFX3, GNG4, MRPL40, LSR,
Angiogenin, TRIP4, VRK1, COUP-TFII, FOXP2, SNX2, Nucleoporin_85,
RPL37A, RPL27A, SEC62,
Calcium-activated_potassium_channel_subunit_alpha-1, SMARCE1,
RPL17, CEP104, CEP290, VPS29, ANXA4, Zinc_finger_protein 737,
DDX59, SAP30, NEK3, Exosome_component_9,
Receptor_for_activated_C_kinase_1, Peptidylprolyl_isomerase_A,
TINP1, CEACAM1, DISC1, LRRTM1, POP1_Lamin_B1,
SREBP_cleavage-activating_protein, COX6C, TLR_1, ARID2, LACTB,
MMS22L, UBE2E3, DAP3, ZNF23, SKP2, GPR113, IRF9 Ghrelin
O-acyltransferase, NEIL3, EEF1E1, COX17, ESD_,
Dentin_sialophosphoprotein, HDAC9, RFC4, CYLD, RPLP0, EIF2B3,
UGT2A1, FABP7, TRIP11, PLA2G4A, AKR1C3, INTS12, MYH1, ZBTB17, MYH4,
NLRP2, MECOM, MYH8, Thermogenin_receptor_2, IFI16, THYN1, RAB17,
ETFA, Cystic_fibrosis_transmembrane_conductance_regulator, F13B,
RAB6A, ST8SIA1, SATB2, SATB1, HMG20B, UHRF1, CNOT3, Prostaglandin
EP2 receptor, FAM65B,
Peroxisome_proliferator-activated_receptor_gamma, KvLQT2, GRIK5,
SHOC2, Cortactin, FANCI, KIAA1199, Kynureninase, Decoy_receptor_1,
NEU3, PHF10, Methyl-CpG-binding_domain_protein 2, RABGAP1, CEP55,
SF3B1, MSH5, MSH6, CREB-binding_protein, LIMS1, SLC5A4, CCNB1IP1,
RNF34, SORBS2, UIMC1, SOX5, YWHAZ, ICOSLG, NOP58,
Zinc_finger_protein 679, PHKB, MED13, ABCB7, COQ9, C14orf104,
Zinc_finger_protein 530, KLRC2, LSM8, NBR1, PRKCD,
Long-chain-aldehyde_dehydrogenase, MTSS1, Somatostatin,
Ubiquitin_carboxyl-terminal_hydrolase_L5, WDR72, FERMT3, Nuclear
receptor related-1_protein, Citrate_synthase, VPS11, KIZ, ZFYVE27,
BCKDHB, Hypocretin, CACNG2, PTCH1, Carbonic_anhydrase_4,
Nucleoporin_107, LDL_receptor, LEKTI, FBXO11, NDUFB3, FCHO2, CEP78,
RAPGEF6, PPIL3, NIN, RAPGEF2, Growth_hormone_1, Growth_hormone_2,
MNAT1, Nav1, MAP3K8, SUGT1, LAIR1,
Hyaluronan-mediated_motility_receptor, MAP3K2, MPP2, TFB2M, CRB3,
MPP5, CACNA1G, DLGAP2, INHBA, MAGI2, CIP29, SETDB1, Cytochrome_b5,
TRPV2, Interleukin_1_receptor, HOXD8, TIMM10, ATXN2L, CLCN2, CREB1,
TNIP1, CBLB, Factor_V, USP33, SON, RBBP8, SLC22A18, PTPN12, ADCY8,
MYLK, KIF23, REXO2, BST1, TOP3B, COPB1, AXIN2, COPB2, TNRC6B,
Guanidinoacetate N-methyltransferase, Acyl-CoA_thioesterase_9,
C4orf21, TSHB, FRS3, EPB41, Cyclin_T2, LAIR2, Nucleoporin_43,
APLP2, TNFRSF19, Death-associated_protein_6,
Epithelial_cell_adhesion_molecule, CLEC7A, Gephyrin, CLDND1,
VPS37A, PCDHAC2, Bone_morphogenetic_protein_4, NVL, RBM33, RNF139,
Sperm_associated_antigen_5, PLCB1,
Glial_cell_line-derived_neurotrophic_factor, PARP4, PARP1, MAN2A1,
Bone_morphogenetic_protein 1, PAX4, BCCIP, MMPI, Decoy_receptor_3,
RAMP2, NCAPD3, LRRC37A, RWDD3, UBE2A, UBE2C, SLC3A1, MRPS22,
CDC14A, ITSN1, POLE2, MYC-induced_nuclear_antigen, TMLHE,
Glutamate_carboxypeptidase_II, GPR177, PPP2R5C, KIAA1333, RPP38,
MYO1F, Farnesoid_X_receptor, Caldesmon, FBXO4, FBXO5, OPN1MW, PIGN,
ARNTL2, BCAS3, C6orf58, PHTF2, SEC23A, NUFIP2, OAZ1,
Osteoprotegerin, ANAPC4, ATP6V0A2, SPAM1, PSMA6, TAS2R30, RABEP1,
DPM3, SLC6A15, RPS26, RPS27, RPS24, RPS20, RPS21, ARHGAP24,
Catechol-O-methyl transferase, ERCC5,
Transcription_initiation_protein_SPT3 homolog, OR1E1, ZNRF1, GMEB1,
CCT2_GNAQ, Mucin_6, Mucin_4, LRP5, PDE9A, C2orf3, EZH2,
Epidermal_growth_factor_receptor, TMTC2, PDE4A, EPH_receptor_A4,
PPIB, DENND4A, ANTXR1, ANTXR2, Nucleoporin_88, SLCO1B3, COG8,
RBMS1, MAP7, HIST2H2BE, AEBP2, DCLRE1A, RPL24, HNRPA2B1, RPL21,
RPL23, MAPKAP1, NIPBL, ATG7, SERPINI2, GYLTL1B, ATP5G2, DIP2A,
AMY2A, CEP63, TDRD7, PIEZO1, CLDN20, GRXCR1, PMEL, NIF3L1, MCC_,
PCNX, TMBIM4, DUSP12, ZMYND8, GOSR1, Interferon_gamma_receptor_1,
LDB3, PON3, C1D, ABCC8, COQ7, COQ6, AMELY, HAVCR1, PICALM,
Sjogren_syndrome_antigen_B, PLK4, HBB, AKT1, PCDHGB7, C6orf10,
UBR1, Retinoblastoma-like_protein 1, GRK6, WWC2, GRK4, INPP4B,
SLC34A1, GOLGA2, MYCBP2, PTP4A2, NUCB2, MAGOH, RPP40,
Alpha-2A_adrenergic_receptor, SPAG11B, Nucleoporin_205, COG1,
Motile_sperm_domain_containing_3, KCNMB3,
Motile_sperm_domain_containing_1, KLHL7, KCNN2, TSPAN8, GPR21,
Translocator_protein, HNRNPLL, ABHD5, CAB39L, Amphiregulin, GPR1,
Interleukin_18, EIF4G3, Interleukin_15, CCDCl80, CD2AP, NFS1, GRB2,
ULBP2, Vascular_endothelial_growth_factor_C, RPS3, TLR8,
BCL2-related_protein_A1, RHOT1, Collagen, Centromere_protein E,
STMN2, HESX1, RPL7, Kalirin, PCMT1, HLA-F, SUMO2, NOX3, EP400,
DNM3, EED, NGLY1, NPRL2, PLAC1,
Baculoviral_IAP_repeat-containing_protein_3, C7orf31, TUBA1C,
HAUS3, IFNA10, MYST4, DCHS1, SIRT4, EFEMP1, ARPC2, MED30, IFT74,
PAK1IP1, DYNC1LI2, POLR2B, POLR2H, KIF3A, PRDM16, PLSCR5, PEX5,
Parathyroid_hormone_1_receptor, CDC23, RBPMS, MAST1, NRD1, BAT5,
BAT2, Dock11, GCSH, POF1B, USP15, POT1, MUTYH, CYP2E1, FAM122C,
A1_polypeptide, Flavin_containing_monooxygenase_3, HPGD, LGALS13,
MTHFD2L, Survival_motor_neuron_domain_containing_1, PSMA3, MRPS35,
MHC_class_I_polypeptide-related_sequence_A, SGCE, REPS1, PPP1R12A,
PPP1R12B, PABPC1, MAPK8, PDCD5, Phosphoglucomutase_3, Ubiquitin_C,
GABPB2, Mitochondrial_translational_release_factor_1, PFDN4, NUB1,
SLC13A3, ZFP36L1, Galectin-3, CC2D2A, GCA,
Tissue_factor_pathway_inhibitor, UCKL1, ITFG3, SOS1, WWTR1, GPR84,
HSPA14, GJC3, TCF7L1, Matrix_metallopeptidase_12, ISG20, LILRA3,
Serum_albumin, Phosducin-like, RPS13, UTP6, HP1BP3, IL12A,
HtrA_serine_peptidase_2, LATS1, BMF_, Thymosin_beta-4,
B-cell_linker, BCL2L11, Coagulation_factor_XIII, BCL2L12, PRPF19,
SFRS5, Interleukin_23_subunit_alpha, NRAP,
60S_ribosomal_protein_L14, C9orf64, Testin, VPS13A, DGKD, PTPRB,
ATP5C1, KCNJ16, KARS, GTF2H2, AMBN, USP13, ADAMTSL1, TRO_, RTF1,
ATP6V1C2, SSBP1, SNRPN_upstream_reading_frame_protein, RPS29,
SNRPG, ABCC10, PTPRU, APPL1, TINF2, TMEM22, UNC45A, RPL30, PCDH7,
Galactosamine-6 sulfatase, UPF3A, ACTL6A, ACTL6B, IL3RA, SDHB,
Cathepsin L2, TAS2R7, Cathepsin_L1,
Pituitary_adenylate_cyclase-activating_peptide, RPN2, DYNLL1,
KLK13, NDUFB3, PRPF8, SPINT2, AHSA1, Glutamate_carboxypeptidase_II,
DRAP1, RNASE1, Olfactomedin-like_2b, VRK1, IKK2, ERGIC2, TAS2R16,
CAMK2G, CAMK2B, Estrogen_receptor_beta, NADH_dehydrogenase, RPL19,
NUCB2, KCTD13, ubiquinone, H2AFY, CEP290, PABPC1, HLA-F, DHX38,
KIAA0922, MPHOSPH8, DDX59, MD32, ZBP1, C16orf4, UACA, C6orf142,
MRPL39, Cyclin-dependent_kinase_7,
Far_upstream_element-binding_protein_1, SGOL1, GTF2IRD1, ATG10,
Dermcidin, EPS8L2, Decorin, Nicotinamide_phosphoribosyltransferase,
CDCl20, MYB, WNTSA, RBPJ, DEFB103A, RPS15A, ATPSH, RPS3, FABP1,
SLC4A8, Serum_amyloid_P_component, ALAS1, MAPK1, PDCD5, SULT1A1,
CHRNA3, ATXN10, MNAT1, ALG13, Ataxin_3, LRRC39, ADH7,
Delta-sarcoglycan, TACC1, IFNA4, Thymic_stromal_lymphopoietin,
LGTN, KIAA1333, MSH6, MYOT, RIPK5, BCL2L11, RPL27, Rnd1,
Platelet_factor_4, HSD17B7, LSM8, CEP63, INTS8, CTNS, ASAHL,
CELA3A, SMARCAL1, HEXB, SLC16A5, MAP3K12, FRMD6.
[0090] Additional RDEs are found in the 3'-UTRs of long noncoding
RNAs, or primary transcripts encoding miRNAs. For example, RDEs
from the 3'-UTR of THRIL (linc 1992), NIKILA lncRNA, SeT lncRNA,
lncRNAs uc.197, RP11-172E9.2, LINC00598, lncRNAs LOC100128098,
RP11-150012.3, and the primary transcripts encoding miR-146a,
miR-let7e, miR-181c, miR-155, miR-125b, and miR-16.
[0091] A class of RDEs includes those which are bound by glycolytic
enzymes such as glyceraldehyde phosphate dehydrogenase (GAPDH).
This group of RDEs includes, for example, AU 19 (TMEM-219), AU 20
(TMEM-219snp), AU 21 (CCR7), AU 22 (SEM-A4D), and AU 23
(CDCl42-SE2).
[0092] The RDE can be a Class I AU rich element that arises from
the 3' UTR of a gene encoding, for example, c-myc, c-fos, betal-AR,
PTH, interferon-gamma, MyoD, p21, Cyclin A, Cyclin B1, Cyclin D1,
PAI-2, or NOS HANOS. The RDE can also be a Class II AU rich element
and arises from the 3' UTR of a gene encoding, for example, GM-CSF,
TNF-alpha, interferon-alpha, COX-2, IL-2, IL-3, bc1-2,
interferon-beta, or VEG-F. The RDE can be a Class III AU rich
element that arises from the 3' UTR of a gene encoding, for
example, c-jun, GLUT1, p53, hsp 70, Myogenin, NF-M, or GAP-43.
Other RDEs may be obtained from the 3'-UTRs of a T-cell receptor
subunit (.alpha., .beta., .gamma., or .delta. chains), cytotoxic
T-lymphocyte-associated antigen 4 (CTLA4), programmed cell death
protein (PD-1), Killer-cell Immunoglobulin-like Receptors (KIR),
and Lymphocyte Activation Gene-3 (LAG3), and other checkpoint
inhibitors. Still other RDEs may be obtained from the 3'-UTRs of
senescence-associated secretory phenotype genes disclosed in Coppe
et al., Ann. Rev. Pathol 5:99-118 (2010), which is incorporated by
reference in its entirety for all purposes (e.g., see Table 1).
[0093] The RDE can be bound by certain polypeptides including, for
example, ARE poly(U) binding/degradation factor (AUF-1),
tristetraprolin (TTP), human antigen-related protein (HuR),
butyrate response factor 1 (BRF-1), butyrate response factor 2
(BRF-2), T-cell restricted intracellular antigen-1 (TIA-1), TIA-1
related protein (TIAR), CUG triplet repeat, RNA binding protein 1
(CUGBP-1), CUG triplet repeat, RNA binding protein 2 (CUGBP-2),
human neuron specific RNA binding protein (Hel-N1, Hel-N2), RNA
binding proteins HuA, HuB and HuC, KH-type splicing regulatory
protein (KSRP), 3-methylglutaconyl-CoA hydratase (AUH),
glyceraldehyde 3-phosphate dehydrogenase (GAPDH), heat shock
protein 70 (Hsp70), heat shock protein 10 (Hsp10), heterogeneous
nuclear ribonucleoprotein A1 (hnRNP A1), heterogeneous nuclear
ribonucleoprotein A2 (hnRNP A2), heterogeneous nuclear
ribonucleoprotein A3 (hnRNP A3), heterogeneous nuclear
ribonucleoprotein C (hnRNP C), heterogeneous nuclear
ribonucleoprotein L (hnRNP L), Bc1-2 AU-rich element RNA binding
protein (TINO), Poly(A) Binding Protein Interacting Protein 2
(PAIP2), IRP1, pyruvate kinase, lactate dehydrogenase, enolase, and
aldolase. The RDE binding protein also can be an enzyme involved in
glycolysis or carbohydrate metabolism, such as, for example,
Glyceraldehyde Phosphate Dehydrogenase (GAPDH), enolase (ENO1 or
ENO3), Phosphoglycerate Kinase (PGK1), Triosephosphate Isomerase
(TPI1), Aldolase A (ALDOA), Phosphoglycerate Mutase (PGAM1),
Hexokinase (HK-2), or Lactate Dehydrogenase (LDH). The RDE binding
protein can be an enzyme involved in the Pentose Phosphate Shunt,
including for example, Transketolase (TKT) or Triosephosphate
Isomerase (TPI1). Additional exemplary RNA binding proteins are
those described in Castello et al., Molc. Cell 63:696-710 (2016);
Kovarik et al., Cytokine 89:21-26 (2017); Ray et al., Nature
499:172-177 (2013); Castello et al., Cell 149:1393-1406 (2012);
Vlasova et al., Molc. Cell. 29:263-270 (2008); Barreau et al.,
Nucl. Acids Res. vol 33, doi:10.1093/nar/gki1012 (2006); Meisner et
al., ChemBioChem 5:1432-1447 (2004); Guhaniyogi et al., Gene
265:11-23 (2001), all of which are incorporated by reference in
their entirety for all purposes.
[0094] The RDE binding protein can be TTP which can bind to RDEs
including for example, one or more of UUAUUUAUU (SEQ ID NO: 12) and
AUUUA (SEQ ID NO: 1), or KSRP which binds AU-rich RDEs, or Auf1
which binds RDEs including for example, one or more of UUGA (SEQ ID
NO: 13), AGUUU (SEQ ID NO: 11), or GUUUG (SEQ ID NO: 5), or CELF-1
which binds RDEs including for example, one or more of UUGUU (SEQ
ID NO: 3), or HuR which binds RDEs including for example, one or
more of UUUAUUU (SEQ ID NO: 8), UUUAUUU (SEQ ID NO: 9), or UUUGUUU
(SEQ ID NO: 6), or ESRP1 or ESRP2 which binds RDEs including for
example, one or more of UGGGGAU (SEQ ID NO: 14), or ELAV which
binds RDEs including for example, one or more of UUUGUUU (SEQ ID
NO: 6). The RDE binding protein can be an enzyme involved in
glycolysis, including for example, GAPDH which binds AU rich
elements including for example, one or more of AUUUA (SEQ ID NO: 1)
elements, or ENO3/ENO1 which binds RDEs including for example, one
or more of CUGCUGCUG (SEQ ID NO: 15), or ALDOA which binds RDEs
including for example, one or more of AUUGA (SEQ ID NO: 16).
[0095] In an aspect, the RDE can be combined with an RNA control
device to make the regulation by the RDE ligand inducible. For
example, an RDE can be operably linked to an RNA control device
where ligand binding by the RNA control device activates the
regulatory element (e.g., a ribozyme or riboswitch) which inhibits
the RDE (e.g., a ribozyme cleaves the RDE so RDE binding proteins
no longer bind, or the riboswitch alters secondary structure). This
places transcripts with the RDE and RNA control device under two
types of control from the RDE, first the RDE can regulate the
transcript subject to binding of RDE binding proteins as governed
by conditions in the cell, and second, the RDE control can be
removed by inducing the RNA control device with ligand. When ligand
is added, the RNA control device renders the RDE unavailable for
binding and RDE regulation is removed. When ligand is removed, new
transcripts that are transcribed can be under the control of the
RDE (as the RNA control device will not be activated).
Alternatively, an RDE can be operable linked to an RNA control
device where ligand binding turns off the regulatory element (e.g.,
a ribozyme). In this example, the presence of ligand inhibits the
RNA control device and transcripts can be regulated by the RDE.
When ligand is removed, the RNA control device renders the RDE
unavailable for binding to RDE binding proteins and RDE regulation
of the transcript is removed. The RNA control device could also
cleave a polynucleotide that binds to the RDE to form a structure
(e.g., a helix) that inhibits RDE proteins from binding to the RDE.
In this example, the RNA control device can cleave the inhibitory
polynucleotide which then does not bind or is inhibited for binding
to the RDE. This cleavage by the RNA control device can be
stimulated by ligand binding or inhibited by ligand binding.
[0096] Different RDEs have different kinetic parameters such as,
for example, different steady expression levels, different
T.sub.max (time to maximal expression level), different C.sub.max
(maximum expression level), different dynamic range
(expression/basal expression), different AUC, different kinetics of
induction (acceleration of expression rate and velocity of
expression rate), amount of expression, baseline expression,
maximal dynamic range (DR.sub.max), time to DR.sub.max, area under
the curve (AUC), etc. In addition, these kinetic properties of the
RDEs can be altered by making concatemers of the same RDE, or
combining different RDEs into regulatory units. Placing RDEs under
the control of an operably linked RNA control device can also alter
the kinetic properties of the RDE, RDE concatemer, or RDE
combinations. Also, small molecules and other molecules that affect
the availability of RDE binding proteins for binding RDEs can be
used to alter the kinetic response of an RDE, RDE concatemer,
and/or RDE combinations. The kinetic response of RDEs, RDE
concatemers, and/or RDE combinations can be changed using
constructs that express competitive RDEs in a transcript. Such
transcripts with one or more competing RDEs can compete for RDE
binding proteins and so alter the regulation of the desired gene by
an RDE, RDE concatemer, and/or RDE combination. These competitive
RDE transcripts can bind to RDE binding proteins reducing the
amount of RDE binding protein available for binding to the RDE, RDE
concatemer, and/or RDE combination. Thus, RDEs, RDE concatemers,
and/or RDE combinations can be selected and/or combined with other
conditions (discussed above) to provide a desired kinetic response
to the expression of a transgene.
[0097] Table 2 in Example 20 shows that different RDEs (e.g., AU
elements) provided different kinetics of expression. For example,
different RDEs (e.g., AU elements) reached maximal induction
(maximal dynamic range also known as fold induction) at different
time points. The RDEs AU 2 and AU 101 reached maximal dynamic range
(DR.sub.max) at day 1 and then the dynamic range (DR) decreased
showing reduced expression compared to basal expression. The RDEs
AU 5 and AU 21 had a DR.sub.max at day 3/4 and this expression was
maintained out to day 8. The RDEs AU 3, AU 7, AU 10, AU 20 and AU
23 had a DR.sub.max on day 6 and expression decreased on day 8. The
RDEs AU 19 and AU 22 had DR.sub.max on day 8. The RDEs (e.g., AU
elements) also had differences in the amount of expression covering
a range of about 5500 fold comparing the expression of AU 7 to AU
10 (see Table 1). Thus, RDEs (AU elements) can be selected to
provide maximal rates of expression at a desired time point and to
provide a desired amount of polypeptide at that time point.
[0098] Some RNA binding proteins increase the rate of RNA
degradation after binding to the RDE. Some RNA binding proteins
decrease the rate of degradation of the RNA after binding to the
RDE. More than one RNA binding protein binds can bind to an RDE. In
some RDE regulatory units, more than one RNA binding protein binds
to more than one RDE. Binding of one or more of the RNA binding
proteins to the one or more RDEs can increase the degradation rate
of the RNA. Binding of one or more of the RNA binding proteins can
decrease the degradation rate of the RNA. RNA binding proteins that
increase degradation may compete for binding to an RDE with RNA
binding proteins that decrease degradation, so that the stability
of the RNA is dependent of the relative binding of the two RNA
binding proteins. Other proteins can bind to the RDE binding
proteins and modulate the effect of the RNA binding protein on the
RNA with the RDE. Binding of a protein to the RNA binding protein
can increases RNA stability or decrease RNA stability. An RNA can
have multiple RDEs that are bound by the proteins HuR and TTP. The
HuR protein can stabilize the RNA and the TTP protein can
destabilize the RNA. An RNA can have at least one RDE that
interacts with the proteins KSRP, TTP and/or HuR. KSRP can
destabilize the RNA and compete for binding with the HuR protein
that can stabilize the RNA. The KSRP protein can bind to the RDE
and destabilizes the RNA and the TTP protein can bind to KSRP and
prevent degradation of the RNA. Different proteins may be bound to
the same transcript and may have competing effects on degradation
and stabilization rates. Different proteins may be bound to the
same transcript and may have cooperative effects on degradation and
stabilization rates. Different proteins may be bound to the same
transcript at different times, conferring different effects on
degradation and stabilization.
[0099] The RDE can be a Class II AU rich element, and the RNA
binding protein can be GAPDH. The Class II AU rich element bound by
GAPDH can be AUUUAUUUAUUUA (SEQ ID NO: 2). The Class II AU rich
element and GADPH can be used to control the expression of a
transgene, a CAR, Smart CAR (RNA control device--CAR), DE-CAR
(destabilizing element--CAR), Smart-DE-CAR, and/or Side-CAR. The
Class II AU rich element and GADPH also can be used to effect the
expression of a transgene and/or a CAR in a T-lymphocyte. The Class
II AU rich element and GADPH can be used to effect the expression
of a transgene and/or a CAR in a CD8+ T-lymphocyte. The Class II AU
rich element and GADPH can be used to effect the expression of a
transgene and/or a CAR in a CD4+ T-lymphocyte. The Class II AU rich
element and GADPH can be used to effect the expression of a
transgene and/or a CAR in a natural killer cell.
[0100] The RDE may have microRNA binding sites. The RDE can be
engineered to remove one or more of these microRNA binding sites.
The removal of the microRNA binding sites can increase the on
expression from a construct with an RDE by at least 5, 10, 15, 20,
50 or 100 fold. The RDE with the microRNA sites can be an RDE that
is bound by GAPDH. The removal of microRNA sites from the RDE bound
by GAPDH can increase the on expression of a construct with the
GAPDH sensitive RDE by at least 5-10 fold. This GAPDH control
through the RDE can be used to deliver a payload at a target site.
The GAPDH control can be tied to activation of the eukaryotic cell
by a CAR that recognizes an antigen found preferentially at the
target site.
[0101] The RDE can be the 3'-UTR of IL-2 or IFN-.gamma., and
removal of micro-RNA sites can increase the rate of expression
and/or the dynamic range of expression from a transgene RNA with
the RDE. The RDE can be the 3'-UTR of IL-2 and the removed
micro-RNA sites can be the MIR-186 sites which deletion increases
the kinetics of expression and increases the dynamic range of
expression by about 50-fold. The RDE also can be the 3'-UTR of
IFN-.gamma. and the micro-RNA sites removed can be the MIR-125
sites.
[0102] The dynamic range of expression (control) with an RDE can be
increased by optimizing the codons of the transgene controlled by
the RDE. By increasing the GC content of the wobble position of the
codons in a transgene the efficiency of translation can be
increased by 1-2 logs (10-100 fold). The increased efficiency of
translation means the amount of expression in the "on" state with
the RDE is increased. If the "off" state expression rate is not
changed or changed less, the overall dynamic range of control with
the RDE is increased.
[0103] New RDEs can be obtained from synthetic libraries made by
combinatorially mixing and matching parts of known RDEs by applying
techniques such as molecular breeding and/or directed evolution to
the 3'-UTRs of genes known to have an RDE. For example, multiple
3'-UTRs with different RDEs are fragmented and assembled into
synthetic 3'-UTRs that are then screened or selected for RDE
activity. RDEs with desired properties can be discovered from such
libraries using positive and/or negative selections.
Alternative Splicing
[0104] Alternative splicing can link a change in metabolic state in
a cell to the splicing of a pre-mRNA transcript into a mRNA that
encodes and is translated into a desired polypeptide. For example,
following a change in metabolic state of a cell, a pre-mRNA
transcript can undergo alternative splicing to produce a payload in
the cell. Prior to the alternative splicing the pre-mRNA transcript
can be spliced into a transcript encoding a nonsense polypeptide or
into an mRNA encoding a different polypeptide product.
[0105] hnRNPLL (heterogeneous nuclear ribonucleoprotein L like) is
a RNA binding polypeptide that is made when immune cells (e.g.,
T-cells and B-cells) are activated (change in metabolic state).
hnRNPLL is a master regulator of activation-induced alternative
splicing in lymphocytes, including T cells and B-cells. In T-cells,
hnRNPLL effects the splicing of a variety of transcripts including
CD45, a tyrosine phosphatase essential for T-cell development and
activation.
[0106] hnRNPLL binds to CA repeats and also to C rich motifs, A
rich motifs, and T rich motifs including, for example,
CACACA(CA).sub.n, CTTCCt/c, CATt/a, CATT, and TTTAt/aA. When
hnRNPLL binding sites are in the 3'-UTRs of a transcript, binding
of hnRNPLL to the site can stabilize the transcript. When hnRNPLL
binding sites are within about 1 kilobase on the 5' side of an
exon, hnRNPLL binding promotes inclusion of the exon during
splicing. When hnRNPLL binding sites are within about 1 kilobase on
the 3' side of an exon, hnRNPLL binding promotes exclusion of the
exon. When hnRNPLL binds to a transcript it can alter the splicing
pattern of the transcript resulting in a new mRNA transcript and
new noncoding excision products (excised introns or introns plus
exons). This alternative splicing pattern can produce an
alternatively spliced mRNA that now encodes a desired polypeptide
(e.g., a payload), and/or the new noncoding excision products can
encode a miRNA or siRNA that is only produced upon alternative
splicing.
[0107] hnRNPLL alternative splicing can be used alone or in
combination with other regulatory signals such as RDEs. Together
hnRNPLL alternative splicing and RDEs can control expression of a
payload upon activation of a cell (change in metabolic state) when
it reaches a target site having a ligand that binds to a CAR,
T-cell receptor (TCR), or other receptor expressed on the cell.
Binding of ligand to the receptor (e.g., CAR or TCR) activates the
cell, increases expression of a payload by RDE mechanisms, and
produces alternative splicing following hnRNPLL expression.
Together the RDE control and alternative splicing produce desired
amounts of a payload or other transgene.
[0108] hnRNPLL alternative splicing can also be used to turn off a
gene that is being expressed while the cell is quiescent. When the
quiescent cell is activated by ligand binding to a receptor (e.g.,
CAR or TCR) this changes the metabolic state of the cell and
hnRNPLL is expressed. If a gene being expressed while the cell is
quiescent has hnRNPLL binding sites the binding of hnRNPLL can
alter the splicing of the transcript so that the mRNA no longer
encodes the gene product. For example, a cell (e.g., T-cell or
B-cell) can be engineered to express a stemness factor (e.g., Tox
and/or TCF7) while the cell is quiescent. The nucleic acid encoding
Tox and/or TCF7 can include intron(s) with hnRNPLL binding sites so
that in the absence of hnRNPLL the transcripts are spliced to make
the Tox and/or TCF7 polypeptides, but upon cell activation and
expression of hnRNPLL these transcripts now undergo alternative
splicing and no longer produce transcripts encoding Tox and/or
TCF7.
[0109] hnRNPLL alternative splicing also produces new "introns" or
noncoding excision products as well as new mRNAs. The new introns
can encode active RNAs (e.g., miRNA, siRNA, etc.) that are only
expressed in the new introns. This adds yet another level of
control to hnRNPLL alternative splicing as the miRNAs or siRNAs can
turn off genes in the activated cells that are detrimental to the
effector state of the cell including, for example, Tox, SCF7, and
other exhaustion factors. miRNAs and siRNAs that could be
controlled in this manner include, for example, miR155, mIR-192,
mIR-34a, miR-133a, miR-138-5p, miR-342-5p, miR-491-5p, miR-541-3p,
hsa-mir-26b-5p (MIRT030248), and hsa-mir-223-3p (MIRT054680).
Chimeric Antigen Receptors
[0110] Chimeric antigen receptors (CARs) can be fused proteins
comprising an extracellular antigen-binding/recognition element, a
transmembrane element that anchors the receptor to the cell
membrane and at least one intracellular element. These CAR elements
are known in the art, for example as described in patent
application US20140242701, which is incorporated by reference in
its entirety for all purposes herein. The CAR can be a recombinant
polypeptide expressed from a construct comprising at least an
extracellular antigen binding element, a transmembrane element and
an intracellular signaling element comprising a functional
signaling element derived from a stimulatory molecule. The
stimulatory molecule can be the zeta chain associated with the T
cell receptor complex. The cytoplasmic signaling element may
further comprise one or more functional signaling elements derived
from at least one costimulatory molecule. The costimulatory
molecule can be chosen from 4-1BB (i.e., CD137), CD27 and/or CD28.
The CAR may be a chimeric fusion protein comprising an
extracellular antigen recognition element, a transmembrane element
and an intracellular signaling element comprising a functional
signaling element derived from a stimulatory molecule. The CAR may
comprise a chimeric fusion protein comprising an extracellular
antigen recognition element, a transmembrane element and an
intracellular signaling element comprising a functional signaling
element derived from a co-stimulatory molecule and a functional
signaling element derived from a stimulatory molecule. The CAR may
be a chimeric fusion protein comprising an extracellular antigen
recognition element, a transmembrane element and an intracellular
signaling element comprising two functional signaling elements
derived from one or more co-stimulatory molecule(s) and a
functional signaling element derived from a stimulatory molecule.
The CAR may comprise a chimeric fusion protein comprising an
extracellular antigen recognition element, a transmembrane element
and an intracellular signaling element comprising at least two
functional signaling elements derived from one or more
co-stimulatory molecule(s) and a functional signaling element
derived from a stimulatory molecule. The CAR may comprise an
optional leader sequence at the amino-terminus (N-term) of the CAR
fusion protein. The CAR may further comprise a leader sequence at
the N-terminus of the extracellular antigen recognition element,
wherein the leader sequence is optionally cleaved from the antigen
recognition element (e.g., a scFv) during cellular processing and
localization of the CAR to the cellular membrane.
Chimeric Antigen Receptor--Extracellular Element
[0111] Exemplary extracellular elements useful in making CARs are
described, for example, in U.S. patent application Ser. No.
15/070,352 filed on Mar. 15, 2016, and U.S. patent application Ser.
No. 15/369,132 filed Dec. 5, 2016, both of which are incorporated
by reference in their entirety for all purposes.
[0112] The extracellular element(s) can be obtained from the
repertoire of antibodies obtained from the immune cells of a
subject that has become immune to a disease, such as for example,
as described in U.S. patent application Ser. No. 15/070,352 filed
on Mar. 15, 2016, and U.S. patent application Ser. No. 15/369,132
filed Dec. 5, 2016, both of which are incorporated by reference in
their entirety for all purposes.
[0113] The extracellular element may be obtained from any of the
wide variety of extracellular elements or secreted proteins
associated with ligand binding and/or signal transduction as
described in U.S. patent application Ser. No. 15/070,352 filed on
Mar. 15, 2016, U.S. patent application Ser. No. 15/369,132 filed
Dec. 5, 2016, U.S. Pat. Nos. 5,359,046, 5,686,281 and 6,103,521,
all of which are incorporated by reference in their entirety for
all purposes.
[0114] The extracellular element can also be obtained from a
variety of scaffold protein families which share the common feature
of a protein scaffold core with protein loops that can confer
binding specificity and which loops can be altered to provide
different binding specificities. Knottins are one such scaffold
protein that has peptide loops which can be engineered to produce
different binding specificities. For example, knottins can be
engineered to have high affinity for specific integrin peptides.
See for example, Silverman et al., J. Mol. Biol. 385:1064-75 (2009)
and Kimura et al, Proteins 77:359-69 (2009), which are incorporated
by reference in their entirety for all purposes. Some cancers
overexpress certain integrin peptides and such cancers can be
targeted by CARs that have an extracellular element that is a
knottin specific for the overexpressed integrin. One such integrin
is the integrin .alpha.v.beta.6 which is upregulated in multiple
solid tumors such as those derived from colon, lung, breast,
cervix, ovary/fallopian tubes, pancreas, and head and neck. See for
example, Whilding et al., Biochem. Soc. Trans. 44:349-355 (2016),
which is incorporated by reference in its entirety for all
purposes.
[0115] The extracellular element can also be derived from knottins,
which are a family of peptides containing a disulfide bonded core
that confers outstanding proteolytic resistance and thermal
stability. Knottins, which naturally function as protease
inhibitors, antimicrobials, and toxins, are composed of several
loops that possess diverse sequences amongst family members.
Knottins can be engineered to include additional diversity of
sequence in the loops to increase and create new binding
specificities. Engineered knottins can be made to bind desired
targets (e.g., desired antigens) with a desired specificity. Some
Knottins bind with nM specificity to integrins and can be used to
target a CAR to a certain integrins (e.g.,
.alpha.v.beta.3/.alpha.v.beta.5,
.alpha.v.beta.3/.alpha.v.beta.5/.alpha.5.beta.1, or .alpha.v.beta.6
integrins). Integrins such as .alpha.v.beta.6 can be upregulated on
solid tumors and so can be suitable targets for a CAR. Such
.alpha.v.beta.6 integrin specific CARs can be made using a knottin
specific for the .alpha.v.beta.6 integrin as the extracellular
element of the CAR. Activation of an engineered cell (e.g., a
T-cell) through the .alpha.v.beta.6 knottin-CAR can be used to
deliver a pay load to a solid tumor under the control of an RDE
that causes expression of the payload upon CAR cell activation.
[0116] In an aspect, the extracellular domain can be an antibody or
other binding molecule that binds specifically to an
onco-sialylated CD43 that is widely found on AML and MDS blasts.
See Hazenberg et al., European Hematology Associate abstracts, Abst
5511 (2016), which is incorporated by reference in its entirety for
all purposes. The antibody AT14-013 binds a specific sialylated
epitope on the onco-sialylated CD43 which epitope is not found on
CD43 associated with normal cells and tissue. See WO 2016/209079
and WO 2015/093949, both of which are incorporated by reference in
their entirety for all purposes. This antibody or antibodies or
other binding molecules which compete for onco-sialylated CD43
binding with AT14-013 are used to make anti-onco sialylated CD43
CARs. For example, the variable regions of the heavy and light
chain of AT14-013 can be taken and reformatted as a single chain
antibody for use as the extracellular domain of a CAR. Such an
extracellular domain on a CAR directs the CAR cell (e.g., anti-onco
sialylated CD43 CAR T-lymphocyte) to the AML and/or MDS cells
targeting them for cell killing or modification by the CAR
cell.
[0117] Other tumor associated antigens that can be the target of
the CAR include, for example, c-Met (e.g., NSCLC), gpNMB (e.g.,
melanoma, breast cancer, other solid tumors), TRAP-2 (e.g.,
epithelial tumors and other solid tumors), CEACAMS (e.g.,
colorectal cancer), CD56 (e.g., SCLC), CD25 (e.g., hematological
cancers), guanyl cyclase C (e.g., pancreatic cancer), CAG (e.g.,
solid tumors), LIV-1 (e.g., breast cancer), PTK7 (e.g., lung
cancer, colorectal cancer, breast cancer, and ovarian cancer),
LAMP-1 (e.g., colorectal cancer, melanoma, laryngeal cancer),
P-cadherin 3 (e.g., epithelial tumors), HER-3 (e.g., breast
cancer), CD133 (e.g., hepatocellular carcinoma, pancreatic cancer,
colorectal cancer, cholangiocarcinoma), BCMA (e.g., multiple
myeloma), CD138 (e.g., multiple myeloma), Ig kappa light chain
(e.g., leukemia, lymphoma, NHL, and multiple myeloma), CD30 (e.g.,
NHL, HD), IL13Ra2 (e.g., glioblastoma), and ligands for NKG2D
(e.g., using the NKG2D receptor as the binding domain for, e.g.,
AML, MDS, and MM).
[0118] Other tumor associated antigens that can be the target of
the CAR include, for example, mesothelin, disialoganglioside (GD2),
Her-2, MUC1, GPC3, EGFRVIII, CEA, CD19, EGFR, PSMA, GPC2, folate
receptor .beta., IgG Fc receptor, PSCA, PD-L1, EPCAM, Lewis Y
Antigen, L1CAM, FOLR, CD30, CD20, EPHA2, PD-1, C-MET, ROR1,
CLDN18.2, NKG2D, CD133, TSHR, CD70, ERBB, AXL, Death Receptor 5,
VEGFR-2, CD123, CD80, CD86, TSHR, ROR2, CD147, kappa IGG, IL-13,
MUC16, IL-13R, NY-ESO-1, IL13RA2, DLL3, FAP, LMP1, TSHR, BCMA,
NECTIN-4, MG7, AFP (alpha-fetoprotein), GP100, B7-H3, Nectin-4,
MAGE-A1, MAGE-A4, MART-1, HBV, MAGE-A3, TAA, GP100, Thyroglobulin,
EBV, HPV E6, PRAME, HERV-E, WT1, GRAS G12V, p53, TRAIL, MAGE-A10,
HPV-E7, KRAS G12D, MAGE-A6, CD19, BCMA, CD22, CD123, CD20, CD30,
CD33, CD138, CD38, CD7, SLAMF7, IGG FC, MUC1, Lewis Y Antigen,
CD133, ROR1, FLT3, NKG2D, Kappa light chain, CD34, CLL-1, TSLP,
CD10, PD-L1, CD44V6, EBV, CD5, GPC3, CD56, integrin B7, CD70, MUCL,
CKIT, CLDN18.2, TRBC1, TAC1, CD56, and CD4.
[0119] Still other tumor associated antigens that can be the target
of the CAR include, for example, CD2, CD18, CD27, CD37, CD72,
CD79A, CD79B, CD83, CD117, CD172, ERBB3, ERBB4, DR5, HER2, CS1,
IL-1RAP, ITGB7, SLC2A14, SLC4A1, SLC6A11, SLC7A3, SLC13A5, SLC19A1,
SLC22A12, SLC34A1, slc45A3, SLC46A2, Fra, IL-13Ra2, ULBP3, ULBP1,
CLD18, NANOG, CEACAM8, TSPAN16, GLRB, DYRK4, SV2C, SIGLEC8, RBMXL3,
HIST1HIT, CCR8, CCNB3, ALPPL2, ZP2, OTUB2, LILRA4, GRM2, PGG1,
NBIF3, GYPA, ALPP, SPATA19, FCRLI, FCRLA, CACNG3, UPK3B, 12UMO4,
MUC12, HEPACAM, BPI, ATP6V0A4, HMMR, UPK1A, ADGRV1, HERC5, C3AR1,
FASLG, NGB, CELSR3, CD3G, CEACAM3, TNFRSFBC, MS4AB, S1PR5, EDNRB,
SCN3A, ABCC8, ABCB1, ANO1, KCND2, HTR4, CACNB4, HTR4, CNR2, 26LRB,
EXOC1, ENTPP1, ICAM3, ABCGB, SCN4B, SPN, CD68, ITGAL, ITGAM, SCTR,
CYYR1, CLCN2, SLARA3, and JAG3.
Intracellular Element
[0120] The intracellular element can be a molecule that can
transmit a signal into a cell when the extracellular element of the
Smart CAR (RNA control device--CAR), DE-CAR (destabilizing
element--CAR), RDE-CAR, Smart-DE-CAR, Smart-RDE-CAR, DE-RDE-CAR,
Smart-DE-RDE-CAR, and/or Side-CAR (collectively "CARS") binds to
(interacts with) an antigen. The intracellular signaling element
can be generally responsible for activation of at least one of the
normal effector functions of the immune cell in which the CAR(s)
has been introduced. The term "effector function" refers to a
specialized function of a cell. Effector function of a T cell, for
example, may be cytolytic activity or helper activity including the
secretion of cytokines. Thus the term "intracellular signaling
element" refers to the portion of a protein which transduces the
effector function signal and directs the cell to perform a
specialized function. While the entire intracellular signaling
domain can be employed, in many cases the intracellular element or
intracellular signaling element need not consist of the entire
domain. To the extent that a truncated portion of the intracellular
signaling domain is used, such truncated portion may be used as
long as it transduces the effector function signal. The term
intracellular signaling element is thus also meant to include any
truncated portion of the intracellular signaling domain sufficient
to transduce the effector function signal. Examples of
intracellular signaling elements for use in the Smart CAR, DE-CAR,
RDE-CAR, Smart-DE-CAR, Smart-RDE-CAR, DE-RDE-CAR, Smart-DE-RDE-CAR,
and/or Side-CAR of the invention include the cytoplasmic sequences
of the T cell receptor (TCR) and co-receptors that act in concert
to initiate signal transduction following antigen receptor
engagement, as well as any derivative or variant of these sequences
and any recombinant sequence that has the same functional
capability.
[0121] Intracellular elements and combinations of polypeptides
useful with or as intracellular elements are described, for
example, in U.S. patent application Ser. No. 15/070,352 filed on
Mar. 15, 2016, and U.S. patent application Ser. No. 15/369,132
filed Dec. 5, 2016, both of which are incorporated by reference in
their entirety for all purposes.
Transmembrane Element and Spacer Element
[0122] The CAR, and/or RDE-CAR may comprise a transmembrane
element. The transmembrane element can be attached to the
extracellular element of CAR, and/or RDE-CAR. The transmembrane
element can include one or more additional amino acids adjacent to
the transmembrane region, e.g., one or more amino acid associated
with the extracellular region of the protein from which the
transmembrane was derived (e.g., 1, 2, 3, 4, 5, 6, 7, 8, 9, 10 up
to 15 amino acids of the extracellular region) and/or one or more
additional amino acids associated with the intracellular region of
the protein from which the transmembrane protein is derived (e.g.,
1, 2, 3, 4, 5, 6, 7, 8, 9, 10 up to 15 amino acids of the
intracellular region). The transmembrane element can be associated
with one of the other elements used in the CAR, and/or RDE-CAR. The
transmembrane element can be selected or modified by amino acid
substitution to avoid binding of such elements to the transmembrane
elements of the same or different surface membrane proteins, e.g.,
to minimize interactions with other members of the receptor
complex. The transmembrane element can be modified to remove
cryptic splice sites (e.g., CARS made with a CD8 transmembrane
domain can be engineered to remove a cryptic splice site) and/or a
transmembrane element can be used in the CAR construct that does
not have cryptic splice sites. The transmembrane element can be
capable of homodimerization with another CAR, and/or RDE-CAR on the
cell surface. The amino acid sequence of the transmembrane element
may be modified or substituted so as to minimize interactions with
the binding elements of the native binding partner present in the
same cell.
[0123] Transmembrane elements useful in the present invention are
described, for example, in U.S. patent application Ser. No.
15/070,352 filed on Mar. 15, 2016, and U.S. patent application Ser.
No. 15/369,132 filed Dec. 5, 2016, both of which are incorporated
by reference in their entirety for all purposes.
Chimeric Antigen Receptors: Side-CARs
[0124] Side CARs, selection of Side CARs, and their use with or
without a tether are described, for example, in U.S. patent
application Ser. No. 15/070,352 filed on Mar. 15, 2016, and U.S.
patent application Ser. No. 15/369,132 filed Dec. 5, 2016, both of
which are incorporated by reference in their entirety for all
purposes.
Receptors
[0125] CARS may be used as the receptor with the cell and the
RDE-transgene. CARS are described above. In addition to CARS, other
receptors may be used to activate or otherwise change conditions in
a cell so that a transgene under the control of an RDE is
expressed. Receptors that recognize and respond to a chemical
signal can be coupled to expression of the transgene through the
RDE. For example, ion channel-linked (ionotropic) receptors, G
protein-linked (metabotropic) receptors, and enzyme-linked
receptors can be coupled to the expression of the transgene.
[0126] One class of receptor that can be coupled to transgene
expression are immune receptors such as, for example, T-cell
receptors, B-cell receptors (aka antigen receptor or immunoglobulin
receptor), and innate immunity receptors.
[0127] T-cell receptors are heterodimers of two different
polypeptide chains. In humans, most T cells have a T-cell receptor
made of an alpha (a) chain and a beta (.beta.) chain have a T-cell
receptor made of gamma and delta (.gamma./.delta.) chains (encoded
by TRG and TRD, respectively). Techniques and primers for
amplifying nucleic acids encoding the T-cell receptor chains from
lymphocytes are well known in the art and are described in, for
example, SMARTer Human TCR a/b Profiling Kits sold commercially by
Clontech, Boria et al., BMC Immunol. 9:50-58 (2008); Moonka et al.,
J. Immunol. Methods 169:41-51 (1994); Kim et al., PLoS ONE 7:e37338
(2012); Seitz et al., Proc. Natl Acad. Sci. 103:12057-62 (2006),
all of which are incorporated by reference in their entirety for
all purposes. The TCR repertoires can be used as separate chains to
form an antigen binding domain. The TCR repertoires can be
converted to single chain antigen binding domains. Single chain
TCRs can be made from nucleic acids encoding human alpha and beta
chains using techniques well-known in the art including, for
example, those described in U.S. Patent Application Publication No.
US2012/0252742, Schodin et al., Mol. Immunol. 33:819-829 (1996);
Aggen et al., "Engineering Human Single-Chain T Cell Receptors,"
Ph.D. Thesis with the University of Illinois at Urbana-Champaign
(2010) a copy of which is found at
ideals.illinois.edu/bitstream/handle/2142/18585/Aggen
David.pdf?sequence=1, all of which are incorporated by reference in
their entirety for all purposes.
[0128] B-cell receptors include an immunoglobulin that is membrane
bound, a signal transduction moiety, CD79, and an ITAM. Techniques
and primers for amplifying nucleic acids encoding human antibody
light and heavy chains are well-known in the art, and described in,
for example, ProGen's Human IgG and IgM Library Primer Set, Catalog
No. F2000; Andris-Widhopf et al., "Generation of Human Fab Antibody
Libraries: PCR Amplification and Assembly of Light and Heavy Chain
Coding Sequences," Cold Spring Harb. Protoc. 2011; Lim et al., Nat.
Biotechnol. 31:108-117 (2010); Sun et al., World J. Microbiol.
Biotechnol. 28:381-386 (2012); Coronella et al., Nucl. Acids. Res.
28:e85 (2000), all of which are incorporated by reference in their
entirety for all purposes. Techniques and primers for amplifying
nucleic acids encoding mouse antibody light and heavy chains are
well-known in the art, and described in, for example, U.S. Pat. No.
8,143,007; Wang et al., BMC Bioinform. 7(Suppl):S9 (2006), both of
which are incorporated by reference in their entirety for all
purposes. The antibody repertoires can be used as separate chains
in antigen binding domains, or converted to single chain antigen
binding domains. Single chain antibodies can be made from nucleic
acids encoding human light and heavy chains using techniques
well-known in the art including, for example, those described in
Pansri et al., BMC Biotechnol. 9:6 (2009); Peraldi-Roux, Methods
Molc. Biol. 907:73-83 (2012), both of which are incorporated by
reference in their entirety for all purposes. Single chain
antibodies can be made from nucleic acids encoding mouse light and
heavy chains using techniques well-known in the art including, for
example, those described in Imai et al., Biol. Pharm. Bull.
29:1325-1330 (2006); Cheng et al., PLoS ONE 6:e27406 (2011), both
of which are incorporated by reference in their entirety for all
purposes.
[0129] Innate immunity receptors include, for example, the
CD94/NKG2 receptor family (e.g., NKG2A, NKG2B, NKG2C, NKG2D, NKG2E,
NKG2F, NKG2H), the 2B4 receptor, the NKp30, NKp44, NKp46, and NKp80
receptors, the Toll-like receptors (e.g., TLR1, TLR2, TLR3, TLR4,
TLR5, TLR6, TLR7, TLR8, TLR9, TLR10, RP105).
[0130] G-protein linked receptors also known as seven-transmembrane
domain receptors are a large family of receptors that couple
receptor binding of ligand to cellular responses through G
proteins. These G-proteins are trimers of .alpha., .beta., and
.gamma. subunits (known as G.alpha., G.beta., and G.gamma.,
respectively) which are active when bound to GTP and inactive when
bound to GDP. When the receptor binds ligand it undergoes a
conformational change and allosterically activates the G-protein to
exchange GTP for bound GDP. After GTP binding the G-protein
dissociates from the receptor to yield a G.alpha.-GTP monomer and a
G.beta..gamma. dimer. G-protein linked receptors have been grouped
together into classes which include, for example, Rhodopsin-like
receptors, secretin receptors, metabotropic glutamate/pheromone
receptors, fungal mating pheromone receptors, cyclic AMP receptors,
and frizzled/smoothened receptors. G-protein receptors are used in
a wide variety of physiological processes including detection of
electromagnetic radiation, gustatory sense (taste), sense of smell,
neurotransmission, immune system regulation, growth, cell density
sensing, etc.
[0131] Enzyme linked receptors also known as a catalytic receptor,
is a transmembrane receptor, where the binding of an extracellular
ligand causes enzymatic activity on the intracellular side. Enzyme
linked receptors have two domains joined together by a
transmembrane portion (or domain) of the polypeptide. The two
terminal domains are an extracellular ligand binding domain and an
intracellular domain that has a catalytic function. There are
multiple families of enzyme linked receptors including, for
example, the Erb receptor family, the glial cell-derived
neurotrophic factor receptor family, the natriuretic peptide
receptor family, the trk neurotrophin receptor family, and the
toll-like receptor family.
[0132] Ion channel linked receptors also known as ligand-gated ion
channels are receptors that allow ions such as, for example,
Na.sup.+, K.sup.+, Ca.sup.2+ and Cl.sup.- to pass through the
membrane in response to the binding of a ligand to the receptor.
There are multiple families of ligand-gated ion channels including,
for example, cationic cys-loop receptors, anionic cys-loop
receptors, ionotropic glutamate receptors (AMPA receptors, NMDA
receptors), GABA receptors, 5-HT receptors, ATP-gated channels, and
PIP2-gated channels.
Eukaryotic Cells
[0133] Various eukaryotic cells can be used as the eukaryotic cell.
The eukaryotic cells can be animal cells. The eukaryotic cells can
be mammalian cells, such as mouse, rat, rabbit, hamster, porcine,
bovine, feline, or canine. The mammalian cells can be cells of
primates, including but not limited to, monkeys, chimpanzees,
gorillas, and humans. The mammalians cells can be mouse cells, as
mice routinely function as a model for other mammals, most
particularly for humans (see, e.g., Hanna, J. et al., Science
318:1920-23, 2007; Holtzman, D. M. et al., J Clin Invest.
103(6):R15-R21, 1999; Warren, R. S. et al., J Clin Invest. 95:
1789-1797, 1995; each publication is incorporated by reference in
its entirety for all purposes). Animal cells include, for example,
fibroblasts, epithelial cells (e.g., renal, mammary, prostate,
lung), keratinocytes, hepatocytes, adipocytes, endothelial cells,
and hematopoietic cells. The animal cells can be adult cells (e.g.,
terminally differentiated, dividing or non-dividing) or embryonic
cells (e.g., blastocyst cells, etc.) or stem cells. The eukaryotic
cell also can be a cell line derived from an animal or other
source.
[0134] The eukaryotic cells can be stem cells. A variety of stem
cells types are known in the art and can be used as the eukaryotic
cell, including for example, embryonic stem cells, inducible
pluripotent stem cells, hematopoietic stem cells, neural stem
cells, epidermal neural crest stem cells, mammary stem cells,
intestinal stem cells, mesenchymal stem cells, olfactory adult stem
cells, testicular cells, and progenitor cells (e.g., neural,
angioblast, osteoblast, chondroblast, pancreatic, epidermal, etc.).
The stem cells can be stem cell lines derived from cells taken from
a subject.
[0135] The eukaryotic cell can be a cell found in the circulatory
system of a mammal, including humans. Exemplary circulatory system
cells include, among others, red blood cells, platelets, plasma
cells, T-cells, natural killer cells, B-cells, macrophages,
neutrophils, or the like, and precursor cells of the same. As a
group, these cells are defined to be circulating eukaryotic cells
of the invention. The eukaryotic cell can be derived from any of
these circulating eukaryotic cells. Transgenes may be used with any
of these circulating cells or eukaryotic cells derived from the
circulating cells. The eukaryotic cell can be a T-cell or T-cell
precursor or progenitor cell. The eukaryotic cell can be a helper
T-cell, a cytotoxic T-cell, a memory T-cell, a regulatory T-cell, a
natural killer T-cell, a mucosal associated invariant T-cell, a
gamma delta T cell, or a precursor or progenitor cell to the
aforementioned. The eukaryotic cell can be a natural killer cell,
or a precursor or progenitor cell to the natural killer cell. The
eukaryotic cell can be a B-cell, or a B-cell precursor or
progenitor cell. The eukaryotic cell can be a neutrophil or a
neutrophil precursor or progenitor cell. The eukaryotic cell can be
a megakaryocyte or a precursor or progenitor cell to the
megakaryocyte. The eukaryotic cell can be a macrophage or a
precursor or progenitor cell to a macrophage.
[0136] The eukaryotic cells can be obtained from a subject. The
subject may be any living organisms. The cells can be derived from
cells obtained from a subject. Examples of subjects include humans,
dogs, cats, mice, rats, and transgenic species thereof. T cells can
be obtained from a number of sources, including peripheral blood
mononuclear cells, bone marrow, lymph node tissue, cord blood,
thymus tissue, tissue from a site of infection, ascites, pleural
effusion, spleen tissue, and tumors. Any number of T cell lines
available in the art also may be used. T-cells can be obtained from
a unit of blood collected from a subject using any number of
techniques known to the skilled artisan, such as Ficoll separation.
Cells from the circulating blood of an individual can be obtained
by apheresis. The apheresis product typically contains lymphocytes,
including T cells, monocytes, granulocytes, B cells, other
nucleated white blood cells, red blood cells, and platelets. The
cells collected by apheresis may be washed to remove the plasma
fraction and to place the cells in an appropriate buffer or media
for subsequent processing steps. The cells can be washed with
phosphate buffered saline (PBS). In an alternative aspect, the wash
solution lacks calcium and may lack magnesium or may lack many if
not all divalent cations. Initial activation steps in the absence
of calcium can lead to magnified activation.
[0137] Enrichment of a T cell population by negative selection can
be accomplished with a combination of antibodies directed to
surface markers unique to the negatively selected cells. Cells can
be enriched by cell sorting and/or selection via negative magnetic
immunoadherence or flow cytometry using a cocktail of monoclonal
antibodies directed to cell surface markers present on the cells.
For example, to enrich for CD4+ cells, a monoclonal antibody
cocktail typically includes antibodies to CD14, CD20, CD11b, CD16,
HLA-DR, and CD8. It may be desirable to enrich for regulatory T
cells which typically express CD4+, CD25+, CD62Lhi, GITR+, and
FoxP3+. Alternatively, in certain aspects, T regulatory cells are
depleted by anti-C25 conjugated beads or other similar method of
selection.
[0138] T cells may be activated and expanded generally using
methods as described, for example, in U.S. Pat. Nos. 6,352,694;
6,534,055; 6,905,680; 6,692,964; 5,858,358; 6,887,466; 6,905,681;
7,144,575; 7,067,318; 7,172,869; 7,232,566; 7,175,843; 5,883,223;
6,905,874; 6,797,514; 6,867,041; and U.S. Patent Application
Publication No. 20060121005, each of which is incorporated by
reference in its entirety for all purposes.
[0139] NK cells may be expanded in the presence of a myeloid cell
line that has been genetically modified to express membrane bound
IL-15 and 4-1BB ligand (CD137L). A cell line modified in this way
which does not have WIC class I and II molecules is highly
susceptible to NK cell lysis and activates NK cells. For example,
K562 myeloid cells can be transduced with a chimeric protein
construct consisting of human IL-15 mature peptide fused to the
signal peptide and transmembrane domain of human CD8a and GFP.
Transduced cells can then be single-cell cloned by limiting
dilution and a clone with the highest GFP expression and surface
IL-15 selected. This clone can then be transduced with human
CD137L, creating a K562-mb15-137L cell line. To preferentially
expand NK cells, peripheral blood mononuclear cell cultures
containing NK cells are cultured with a K562-mb15-137L cell line in
the presence of 10 IU/mL of IL-2 for a period of time sufficient to
activate and enrich for a population of NK cells. This period can
range from 2 to 20 days, preferably about 5 days. Expanded NK cells
may then be transduced with the anti-CD19-BB-.xi. chimeric
receptor.
Modification of CD3 Epsilon in T-lymphocytes
[0140] T-lymphocytes can be modified to reduce graft versus host
reactions. For example, allogenic T-lymphocytes can be modified so
that upon transplantation graft versus host reactions are reduced.
The allogenic T-lymphocytes can be used in a CAR therapy and/or can
carry other transgenes for delivery by the T-lymphocyte at a target
site. The T-lymphocytes can be modified by introducing a mutant
that has a dominant effect on T-cell receptor function. For
example, the mutant can knock out the T-cell receptor, or can
disrupt signaling from the T-cell receptor. Mutations of the CD3
epsilon chain can have such dominant negative effects on T-cell
receptor signaling. An example of a negative dominant mutant of CD3
epsilon is a C119S/C122S double mutant that alters the C-X-X-C
motif in the CD3 epsilon to S-X-X-S. This double mutant is
defective for signal transduction from an activated T-cell receptor
and so binding of host antigens by a T-lymphocyte (e.g., an
allogenic T-lymphocyte) does not activate the T-lymphocyte reducing
graft versus host disease.
[0141] The CD3 epsilon double mutant (C119S/C122S) can be
introduced into the T-lymphocyte by integrating it to the CD3
epsilon locus of the T-lymphocyte, or because this double mutant is
a negative dominant it can be introduced at other sites in the
T-lymphocyte genome or can be transiently transfected/transduced
into the T-lymphocyte. Transient transfection can produce
T-lymphocytes with CD3 epsilon double mutant associated with the
T-cell receptors of the T-lymphocytes prior to activation by
binding of a CAR (or other receptor) at the target site. If the
transient expression has ended when the T-lymphocyte reaches target
and interacts with its CAR, the CAR T-lymphocytes can kill through
CAR reactions and through graft versus host/tumor cell reactions
through the allogenic T-cell receptors.
[0142] In an example, T-lymphocytes are obtained from a host (e.g.,
an allogenic host) and activated with CD3/CD28 beads. These
activated T-lymphocytes are transfected with a construct encoding a
CAR (and/or other desired transgene) and a double mutant CD3
epsilon (C119S/C122S). T-lymphocytes transfected/transduced with
the CAR are isolated (e.g., by affinity isolation with the CAR or a
selection against active T-lymphocytes with active TCRs can be
done) and administered to a subject.
[0143] Another mutation of CD3 epsilon can make deletions of one or
more of the ITAM portions of the polypeptide. These ITAM deletions
reduce the signaling capacity of CARS made with these ITAM mutants.
The CD3 epsilon of the CAR can be engineered to have ITAM deletions
of one or more ITAM sequences. T-cells engineered with a CAR and
these CD3 epsilon genes with the AITAM(s) can be used with payloads
under control of an RDE. When these T-cells are activated by the
CAR the payload is expressed. The AITAMs reduce the responsiveness
of the cell to the CAR (a crippled CAR) which can reduce or prevent
T-cell exhaustion. This allows the T-cell to produce the transgene
payload for a longer period of time.
Nucleic Acids
[0144] Also described in this disclosure are nucleic acids that
encode, at least in part, the individual peptides, polypeptides,
proteins, RDEs, and other post-transcriptional control devices
described herein. The nucleic acids may be natural, synthetic or a
combination thereof. The nucleic acids of the invention may be RNA,
mRNA, DNA or cDNA.
[0145] The nucleic acids of the invention also include expression
vectors, such as plasmids, or viral vectors, or linear vectors, or
vectors that integrate into chromosomal DNA. Expression vectors can
contain a nucleic acid sequence that enables the vector to
replicate in one or more selected host cells. Such sequences are
well known for a variety of cells. The origin of replication from
the plasmid pBR322 is suitable for most Gram-negative bacteria. In
eukaryotic host cells, e.g., mammalian cells, the expression vector
can be integrated into the host cell chromosome and then replicate
with the host chromosome. Similarly, vectors can be integrated into
the chromosome of prokaryotic cells.
[0146] Expression vectors also generally contain a selection gene,
also termed a selectable marker. Selectable markers are well-known
in the art for prokaryotic and eukaryotic cells, including host
cells of the invention. Generally, the selection gene encodes a
protein necessary for the survival or growth of transformed host
cells grown in a selective culture medium. Host cells not
transformed with the vector containing the selection gene will not
survive in the culture medium. Typical selection genes encode
proteins that (a) confer resistance to antibiotics or other toxins,
e.g., ampicillin, neomycin, methotrexate, or tetracycline, (b)
complement auxotrophic deficiencies, or (c) supply critical
nutrients not available from complex media, e.g., the gene encoding
D-alanine racemase for Bacilli. An exemplary selection scheme can
utilize a drug to arrest growth of a host cell. Those cells that
are successfully transformed with a heterologous gene produce a
protein conferring drug resistance and thus survive the selection
regimen. Other selectable markers for use in bacterial or
eukaryotic (including mammalian) systems are well-known in the
art.
[0147] An example of a promoter that is capable of expressing a
Smart CAR, DE-CAR, RDE-CAR, Smart-DE-CAR, Smart-RDE-CAR,
DE-RDE-CAR, Smart-DE-RDE-CAR, and/or Side-CAR transgene in a
mammalian T cell is the EF1a promoter. The native EF1a promoter
drives expression of the alpha subunit of the elongation factor-1
complex, which is responsible for the enzymatic delivery of
aminoacyl tRNAs to the ribosome. The EF1a promoter has been
extensively used in mammalian expression plasmids and has been
shown to be effective in driving CAR expression from transgenes
cloned into a lentiviral vector. See, e.g., Milone et al., Mol.
Ther. 17(8): 1453-1464 (2009), which is incorporated by reference
in its entirety for all purposes. Another example of a promoter is
the immediate early cytomegalovirus (CMV) promoter sequence. This
promoter sequence is a strong constitutive promoter sequence
capable of driving high levels of expression of any polynucleotide
sequence operatively linked thereto. Other constitutive promoter
sequences may also be used, including, but not limited to the
simian virus 40 (SV40) early promoter, mouse mammary tumor virus
promoter (MMTV), human immunodeficiency virus (HIV) long terminal
repeat (LTR) promoter, MoMuLV promoter, phosphoglycerate kinase
(PGK) promoter, MND promoter (a synthetic promoter that contains
the U3 region of a modified MoMuLV LTR with myeloproliferative
sarcoma virus enhancer, see, e.g., Li et al., J. Neurosci. Methods
vol. 189, pp. 56-64 (2010) which is incorporated by reference in
its entirety for all purposes), an avian leukemia virus promoter,
an Epstein-Barr virus immediate early promoter, a Rous sarcoma
virus promoter, as well as human gene promoters such as, but not
limited to, the actin promoter, the myosin promoter, the elongation
factor-1a promoter, the hemoglobin promoter, and the creatine
kinase promoter. Further, the invention is not limited to the use
of constitutive promoters.
[0148] Inducible or repressible promoters are also contemplated for
use in this disclosure. Examples of inducible promoters include,
but are not limited to a Nuclear Factor of Activated T-cell
inducible promoter (NFAT), a metallothionein promoter, a
glucocorticoid promoter, a progesterone promoter, a tetracycline
promoter, a c-fos promoter, the T-REx system of ThermoFisher which
places expression from the human cytomegalovirus immediate-early
promoter under the control of tetracycline operator(s), and
RheoSwitch promoters of Intrexon. Macian et al., Oncogene
20:2476-2489 (2001); Karzenowski, D. et al., BioTechiques
39:191-196 (2005); Dai, X. et al., Protein Expr. Purif 42:236-245
(2005); Palli, S. R. et al., Eur. J. Biochem. 270:1308-1515 (2003);
Dhadialla, T. S. et al., Annual Rev. Entomol. 43:545-569 (1998);
Kumar, M. B, et al., J. Biol. Chem. 279:27211-27218 (2004);
Verhaegent, M. et al., Annal. Chem. 74:4378-4385 (2002); Katalam,
A. K., et al., Molecular Therapy 13:S103 (2006); and Karzenowski,
D. et al., Molecular Therapy 13:S194 (2006), U.S. Pat. Nos.
8,895,306, 8,822,754, 8,748,125, 8,536,354, all of which are
incorporated by reference in their entirety for all purposes.
Inducible promoter also include promoters with heat shock elements
that respond to mild hyperthermia. Heat shock elements are made of
multiple inverted repeats of the consensus sequence 5'-nGAAn-3'
located upstream of a promoter such as, for example, a promoter
from a heat shock gene (e.g., HSPB1).
[0149] Expression vectors typically have promoter elements, e.g.,
enhancers, to regulate the frequency of transcriptional initiation.
Typically, these are located in the region 30-110 bp upstream of
the start site, although a number of promoters have been shown to
contain functional elements downstream of the start site as well.
The spacing between promoter elements frequently is flexible, so
that promoter function is preserved when elements are inverted or
moved relative to one another. In the thymidine kinase (tk)
promoter, the spacing between promoter elements can be increased to
50 bp apart before activity begins to decline. Depending on the
promoter, it appears that individual elements can function either
cooperatively or independently to activate transcription.
[0150] The expression vector may be a bi-cistronic construct or
multiple cistronic construct. The two cistrons may be oriented in
opposite directions with the control regions for the cistrons
located in between the two cistrons. When the construct has more
than two cistrons, the cistrons may be arranged in two groups with
the two groups oriented in opposite directions for transcription.
Exemplary bicistronic constructs are described in Amendola et al.,
Nat. Biotechnol. 23:108-116 (2005), which is incorporated by
reference in its entirety for all purposes. The control region for
one cistron may be capable of high transcription activity and the
other may have low transcriptional activity under conditions of
use. One or both control regions may be inducible. Examples of high
transcription activity control regions include, for example, MND,
EF1-alpha, PGK1, CMV, ubiquitin C, SV40 early promoter,
tetracycline-responsive element promoter, cell-specific promoters,
human beat-actin promoter, and CBG (chicken beta-globin),
optionally including the CMV early enhancer. Examples of low
transcription activity control regions include, for example, TRE3G
(commercially sold by Clontech, a tetracycline-responsive element
promoter with mutations that reduce basal expression), T-REx.TM.
(commercially sold by ThermoFisher), and a minimal TATA promoter
(Kiran et al., Plant Physiol. 142:364-376 (2006), which is
incorporated by reference in its entirety for all purposes), HSP68,
and a minimal CMV promoter. Examples of inducible control regions
include, for example, NFAT control regions (Macian et al, Oncogene
20:2476-2489 (2001)), and the inducible control regions described
above.
[0151] The bi-cistronic construct may encode a CAR and a
polypeptide that is a payload (or makes a payload) to be delivered
at a target site. Exemplary payloads are described above and below.
The nucleic acid encoding the CAR can be operably linked to a
strong promoter, a weak promoter, and/or an inducible promoter, and
optionally, operably linked to a RNA control device, DE, RDE, or
combination of the foregoing. The CAR can be encoded by nucleic
acids in a Side-CAR format. The nucleic acid encoding the
polypeptide can be operably linked to a strong promoter, a weak
promoter, and/or an inducible promoter. The nucleic acid encoding
the polypeptide that is a payload (or makes the payload) can be
under the control of an RDE. The RDE may be one that responds to
the activation state of the cell through, for example, glycolytic
enzymes such as, for example, glyceraldehyde phosphate
dehydrogenase (GAPDH), enolase (ENO1 or ENO3), phosphoglycerate
kinase (PGK1), triose phosphate isomerase (TPI1), aldolase A
(ALDOA), or phosphoglycerate mutase (PGAM1). The RDE may also be
bound and regulated by other energy metabolism enzymes such as, for
example, transketolase (TKT), malate dehydrogenase (MDH2), succinyl
CoA Synthetase (SUGLG1), ATP citrate lyase (ACLY), or isocitrate
dehydrogenase (IDH1/2). The host cell can express a CAR that binds
to its antigen at a target site in a subject. This binding of
antigen at the target site activates the cell causing the cell to
increase glycolysis which induces expression of the nucleic acid
encoding the polypeptide under the control of the RDE (bound by
glycolytic or other energy metabolism enzymes).
[0152] The multicistronic constructs can have three or more
cistrons with each having control regions (optionally inducible)
and RDEs operably linked to some or all of the transgenes. These
cassettes may be organized into two groups that are transcribed in
opposite directions on the construct. Two or more transgenes can be
transcribed from the same control region and the two or more
transgenes may have IRES (internal ribosome entry site) sequences
operably linked to the downstream transgenes. Alternatively, the
two or more transgenes are operably linked together by 2A elements
as described in Plasmids 101: Multicistronic Vectors found at
blog.addgene.org/plasmids-101-multicistrnic-vectors. Commonly used
2A sequences include, for example, EGRGSLLTCGDVEENPGP (T2A) (SEQ ID
NO: 17), ATNFSLLKQAGDVEENPGP (P2A) (SEQ ID NO: 18);
QCTNYALLKLAGDVESNPGP (E2A) (SEQ ID NO: 19); and
VKQTLNFDLLKLAGDVESNPGP (F2A) (SEQ ID NO: 20) all of which can
optionally include the sequence GSG at the amino terminal end. This
allows multiple transgenes to be transcribed onto a single
transcript that is regulated by a 3'-UTR with an RDE (or multiple
RDEs).
[0153] The bicistronic/multicistronic vector can increase the
overall expression of the two or more cistrons (versus introducing
the cistrons on separate constructs). The
bicistronic/multicistronic construct can be derived from a
lenti-virus vector. The bicistronic/multicistronic construct can
encode a CAR and a polypeptide(s) that is encoded on a transgene(s)
(e.g., a payload), and the bicistronic construct may increase
expression of the polypeptide encoded by the transgene(s) when the
cell is activated by the CAR.
[0154] Expression constructs can be modified to remove an RNA
splice site in a 5'-LTR of the construct so as to increase the
transduction frequency of the expression construct. Many lentiviral
transduction constructs have a residual splice site in the 5'-LTR
that can reduce transduction frequency through splicing events with
this site that alter the nucleic acids to be introduced. For
example, lentiviral vectors represented by the pCDH vectors (System
Biosciences), the lentiviral vectors pLVTH, pRRLSIN, pWPI, and
pWPXL, as well as other lentiviral vectors contain a portion of the
HIV 5'-LTR that includes a splice acceptor site. Removal of this
splice site from the vectors increases transduction frequencies
with the modified vectors (compared to the non-modified vectors).
The splice donor site in the residual HIV 5'-LTR segment can be
disrupted by making two nucleotide changes, G290C and U291A
(numbering the HIV splice site according to Keane et al., Science
348:917-921 (2015), which is incorporated by reference in its
entirety for all purposes). Other changes in this splice donor site
could also be made to knock out this splice site. Other
transduction vectors also include residual splice sites that can
disrupt the desired sequence after transduction/transfection and
removal of these splice sites should increase
transduction/transfection frequencies with these vectors.
[0155] It may be desirable to modify polypeptides described herein.
One of skill will recognize many ways of generating alterations in
a given nucleic acid construct to generate variant polypeptides
Such well-known methods include site-directed mutagenesis, PCR
amplification using degenerate oligonucleotides, exposure of cells
containing the nucleic acid to mutagenic agents or radiation,
chemical synthesis of a desired oligonucleotide (e.g., in
conjunction with ligation and/or cloning to generate large nucleic
acids) and other well-known techniques (see, e.g., Gillam and
Smith, Gene 8:81-97, 1979; Roberts et al., Nature 328:731-734,
1987, which is incorporated by reference in its entirety for all
purposes). The recombinant nucleic acids encoding the polypeptides
of the invention can be modified to provide preferred codons which
enhance translation of the nucleic acid in a selected organism.
[0156] The polynucleotides can also include polynucleotides
including nucleotide sequences that are substantially equivalent to
other polynucleotides described herein. Polynucleotides can have at
least about 80%, more typically at least about 90%, and even more
typically at least about 95%, sequence identity to another
polynucleotide. The nucleic acids also provide the complement of
the polynucleotides including a nucleotide sequence that has at
least about 80%, more typically at least about 90%, and even more
typically at least about 95%, sequence identity to a polynucleotide
encoding a polypeptide recited herein. The polynucleotide can be
DNA (genomic, cDNA, amplified, or synthetic) or RNA. Methods and
algorithms for obtaining such polynucleotides are well known to
those of skill in the art and can include, for example, methods for
determining hybridization conditions which can routinely isolate
polynucleotides of the desired sequence identities.
[0157] Nucleic acids which encode protein analogs or variants
(i.e., wherein one or more amino acids are designed to differ from
the wild type polypeptide) may be produced using site directed
mutagenesis or PCR amplification in which the primer(s) have the
desired point mutations. For a detailed description of suitable
mutagenesis techniques, see Sambrook et al., Molecular Cloning: A
Laboratory Manual, Cold Spring Harbor Laboratory Press, Cold Spring
Harbor, N.Y. (1989) and/or Current Protocols in Molecular Biology,
Ausubel et al., eds, Green Publishers Inc. and Wiley and Sons, N.Y
(1994), each of which is incorporated by reference in its entirety
for all purposes. Chemical synthesis using methods well known in
the art, such as that described by Engels et al., Angew Chem Intl
Ed. 28:716-34, 1989 (which is incorporated by reference in its
entirety for all purposes), may also be used to prepare such
nucleic acids.
[0158] Amino acid "substitutions" for creating variants are
preferably the result of replacing one amino acid with another
amino acid having similar structural and/or chemical properties,
i.e., conservative amino acid replacements. Amino acid
substitutions may be made on the basis of similarity in polarity,
charge, solubility, hydrophobicity, hydrophilicity, and/or the
amphipathic nature of the residues involved. For example, nonpolar
(hydrophobic) amino acids include alanine, leucine, isoleucine,
valine, proline, phenylalanine, tryptophan, and methionine; polar
neutral amino acids include glycine, serine, threonine, cysteine,
tyrosine, asparagine, and glutamine; positively charged (basic)
amino acids include arginine, lysine, and histidine; and negatively
charged (acidic) amino acids include aspartic acid and glutamic
acid.
[0159] Also disclosed herein are nucleic acids encoding a
transgene, including a transgene encoding a CARS. The nucleic acid
encoding the transgene can be easily prepared from an amino acid
sequence of the specified CAR combined with the sequence of the RNA
control device by a conventional method. A base sequence encoding
an amino acid sequence can be obtained from the aforementioned NCBI
RefSeq IDs or accession numbers of GenBenk for an amino acid
sequence of each element, and the nucleic acid of the present
invention can be prepared using a standard molecular biological
and/or chemical procedure. For example, based on the base sequence,
a nucleic acid can be synthesized, and the nucleic acid of the
present invention can be prepared by combining DNA fragments which
are obtained from a cDNA library using a polymerase chain reaction
(PCR).
[0160] The nucleic acids can be linked to another nucleic acid so
as to be expressed under control of a suitable promoter. The
nucleic acid can be also linked to, in order to attain efficient
transcription of the nucleic acid, other regulatory elements that
cooperate with a promoter or a transcription initiation site, for
example, a nucleic acid comprising an enhancer sequence, a polyA
site, or a terminator sequence. In addition to the nucleic acid of
the present invention, a gene that can be a marker for confirming
expression of the nucleic acid (e.g. a drug resistance gene, a gene
encoding a reporter enzyme, or a gene encoding a fluorescent
protein) may be incorporated.
[0161] When the nucleic acid is introduced into a cell ex vivo, the
nucleic acid of may be combined with a substance that promotes
transference of a nucleic acid into a cell, for example, a reagent
for introducing a nucleic acid such as a liposome or a cationic
lipid, in addition to the aforementioned excipients. Alternatively,
a vector carrying the nucleic acid of the present invention is also
useful. Particularly, a composition in a form suitable for
administration to a living body which contains the nucleic acid of
the present invention carried by a suitable vector is suitable for
in vivo gene therapy.
Introducing Nucleic Acids into Eukaryotic Cells
[0162] A process for producing a cell expressing a transgene
includes a step of introducing the nucleic acid encoding the
transgene described herein into a eukaryotic cell. This step can be
carried out ex vivo. Exemplary methods for introducing nucleic
acids to eukaryotic cells are described, for example, in U.S.
patent application Ser. No. 15/070,352 filed on Mar. 15, 2016, and
U.S. patent application Ser. No. 15/369,132 filed Dec. 5, 2016,
both of which are incorporated by reference in their entirety for
all purposes.
Virus Payloads
[0163] Viruses can be used to deliver transgenes to target cells.
Viruses can carry nucleic acid constructs (e.g., transfer plasmids)
as payloads and so deliver to a target cell desired nucleic acids
for modification of the target cell genotype and/or phenotype
(transiently or stably). In many of these transduction
applications, the nucleic acid carried by the virus does not
include all of the viral genome, and often includes the viral
genome signals needed for packaging the nucleic acid construct into
the virus without most or all of the rest of the viral genome. For
example, lentiviral helper plasmid and transfer plasmids systems
for transduction of target cells are available from addgene. Other
helper and transfer plasmid systems are commercially available form
a number of sources (e.g., Clontech/Takara).
[0164] When used as a payload, synthesis of viral capsids,
packaging of payload nucleic acids, and release of virus with
payload nucleic acids can be restricted to the target site by
timing the expression of the virus genes for replication and coat
proteins to binding of ligand by a receptor at the target site.
Such control can be achieved using RDEs that induce expression when
the cell undergoes a change in metabolic state (e.g., activation of
glycolysis after receptor binding to target). This RDE control can
regulate expression of master switch factors for expression of the
virus genes. For example, a transcription regulatory factor can be
placed under the control of a suitable RDE, and the viral genes for
replication, coat proteins etc can be placed under the control of
this transcription factor. When the host cell binds to ligand at
the target site through an appropriate receptor (e.g., a CAR) this
activates the cell, induces expression of the transcription factor
with the appropriate RDE leading to expression of the viral
replication proteins, coat proteins, etc.
Transduction with a Viral Vector
[0165] Transduction can be accomplished with a virus vector such as
a retrovirus vector (including an oncoretrovirus vector, a
lentivirus vector, and a pseudo type vector), an adenovirus vector,
an adeno-associated virus (AAV) vector, a simian virus vector, a
vaccinia virus vector or a sendai virus vector, an Epstein-Barr
virus (EBV) vector, and a HSV vector can be used. The virus vector
can lack replicating ability so as not to self-replicate in an
infected cell.
[0166] When a retrovirus vector is used to transduce the host cell,
the process can be carried out by selecting a suitable packaging
cell based on a LTR sequence and a packaging signal sequence
possessed by the vector and preparing a retrovirus particle using
the packaging cell. Examples of the packaging cell include PG13
(ATCC CRL-10686), PA317 (ATCC CRL-9078), GP+E-86 and GP+envAm-12
(U.S. Pat. No. 5,278,056, which is incorporated by reference in its
entirety for all purposes), and Psi-Crip (Proceedings of the
National Academy of Sciences of the United States of America, vol.
85, pp. 6460-6464 (1988), which is incorporated by reference in its
entirety for all purposes). A retrovirus particle can also be
prepared using a 293 cell or a T cell having high transfection
efficiency. Many kinds of retrovirus vectors produced based on
retroviruses and packaging cells that can be used for packaging of
the retrovirus vectors are widely commercially available from many
companies.
[0167] A number of viral based systems have been developed for gene
transfer into mammalian cells. A selected gene can be inserted into
a vector and packaged in viral particles using techniques known in
the art. The recombinant virus can then be isolated and delivered
to cells of the subject either in vivo or ex vivo. A number of
viral systems are known in the art. Adenovirus vectors can be used.
A number of adenovirus vectors are known in the art and can be
used. In addition, lentivirus vectors can be used.
[0168] A viral vector derived from a RNA virus can be used to
introduce to a cell a RDE-CAR, Smart-RDE-CAR, DE-RDE-CAR,
Smart-DE-RDE-CAR, and/or transgene-RDE encoding polynucleotides.
The RNA virus vector can encode the reverse complement or antisense
strand of the polynucleotide encoding the RNA control device and
CAR construct (the complementary strand encodes the sense strand
for the RNA control device, DE, RDE, CAR and/or Side-CAR
construct). Thus, the RNA control device should not be active in
the single stranded, RNA virus vector. The sense strand of the RNA
virus construct encoding the RNA control device, DE, RDE, CAR,
Side-CAR, and/or transgene can be used, and the viral vector with
the RNA control device, DE, RDE, CAR and/or Side-CAR construct is
maintained and replicated in the presence (or absence) of ligand
for the sensor element of the RNA control device (or under
conditions where the RDE is stable) to prevent cleavage of the RNA.
The viral vector encoding the sense strand of the RNA control
device, DE, RDE, CAR, Side-CAR, and/or transgene construct in the
viral vector can then be maintained and replicated with (or
without) ligand for the sensor element. Transduction efficiency can
be increased by cryopreservation of packaged constructs prior to
thawing and transduction. Increased efficiency ranged from about
10% to about 70%.
Pharmaceutical Compositions
[0169] Pharmaceutical compositions of the present invention may
comprise a CARS and/or transgene-RDE expressing cell, e.g., a
plurality of CARS and/or transgene-RDE expressing cells, as
described herein, in combination with one or more pharmaceutically
or physiologically acceptable carriers, diluents or excipients.
Such compositions may comprise buffers such as neutral buffered
saline, phosphate buffered saline and the like; carbohydrates such
as glucose, mannose, sucrose or dextrans, mannitol; proteins;
polypeptides or amino acids such as glycine; antioxidants;
chelating agents such as EDTA or glutathione; adjuvants (e.g.,
aluminum hydroxide); and preservatives. Compositions of the present
invention are in one aspect formulated for intravenous
administration.
[0170] Pharmaceutical compositions may be administered in a manner
appropriate to the disease to be treated (or prevented). The
quantity and frequency of administration will be determined by such
factors as the condition of the patient, and the type and severity
of the patient's disease, although appropriate dosages may be
determined by clinical trials.
[0171] Suitable pharmaceutically acceptable excipients are well
known to a person skilled in the art. Examples of the
pharmaceutically acceptable excipients include phosphate buffered
saline (e.g. 0.01 M phosphate, 0.138 M NaCl, 0.0027 M KCl, pH 7.4),
an aqueous solution containing a mineral acid salt such as a
hydrochloride, a hydrobromide, a phosphate, or a sulfate, saline, a
solution of glycol or ethanol, and a salt of an organic acid such
as an acetate, a propionate, a malonate or a benzoate. An adjuvant
such as a wetting agent or an emulsifier, and a pH buffering agent
can also be used. The pharmaceutically acceptable excipients
described in Remington's Pharmaceutical Sciences (Mack Pub. Co.,
N.J. 1991) (which is incorporated herein by reference in its
entirety for all purposes) can be appropriately used. The
composition can be formulated into a known form suitable for
parenteral administration, for example, injection or infusion. The
composition may comprise formulation additives such as a suspending
agent, a preservative, a stabilizer and/or a dispersant, and a
preservation agent for extending a validity term during
storage.
[0172] A composition comprising the eukaryotic cells described
herein as an active ingredient can be administered for treatment
of, for example, a cancer (blood cancer (leukemia), solid tumor
(ovarian cancer) etc.), an inflammatory disease/autoimmune disease
(pemphigus vulgaris, lupus erythematosus, rheumatoid arthritis,
asthma, eczema), hepatitis, and an infectious disease the cause of
which is a virus such as influenza and HIV, a bacterium, or a
fungus, for example, a disease such as tuberculosis, MRSA, VRE, or
deep mycosis, depending on an antigen to which a CAR, DE-CAR,
and/or Side-CAR polypeptide binds.
[0173] The administration of the subject compositions may be
carried out in any convenient manner, including by aerosol
inhalation, injection, ingestion, transfusion, implantation or
transplantation. The compositions described herein may be
administered to a patient trans arterially, subcutaneously,
intradermally, intratumorally, intranodally, intramedullary,
intramuscularly, intranasally, intraarterially, intratumorally,
into an afferent lymph vessel, by intravenous (i.v.) injection, or
intraperitoneally. In one aspect, the T cell compositions of the
present invention are administered to a patient by intradermal or
subcutaneous injection. In one aspect, the T-cell compositions of
the present invention are administered by i.v. injection. The
compositions of T-cells may be injected directly into a tumor,
lymph node, or site of infection. The administration can be done by
adoptive transfer.
[0174] When "an immunologically effective amount," "an anti-tumor
effective amount," "a tumor-inhibiting effective amount," or
"therapeutic amount" is indicated, the precise amount of the
compositions of the present invention to be administered can be
determined by a physician with consideration of individual
differences in age, weight, tumor size, extent of infection or
metastasis, and condition of the patient (subject). A
pharmaceutical composition comprising the eukaryotic cells
described herein may be administered at a dosage of 10.sup.4 to
10.sup.9 cells/kg body weight, in some instances 10.sup.5 to
10.sup.6 cells/kg body weight, including all integer values within
those ranges. A eukaryotic cell composition may also be
administered multiple times at these dosages. Eukaryotic cells can
also be administered by using infusion techniques that are commonly
known in immunotherapy (see, e.g., Rosenberg et al., New Eng. J. of
Med. 319:1676, 1988, which is incorporated by reference in its
entirety for all purposes).
[0175] Uses of Eukaryotic Cells
[0176] Nucleic acids encoding CARS and/or transgene-RDE(s) can be
used to express CAR, DE-CAR, Side-CAR, and/or transgene
polypeptides in eukaryotic cells. The eukaryotic cell can be a
mammalian cell, including for example human cells or murine cells.
The eukaryotic cells may also be, for example, hematopoietic cells
including, e.g., T-cells, natural killer cells, B-cells, or
macrophages.
[0177] T-cells (e.g., CD4+ or CD8+) or natural killer cells can be
engineered with a polynucleotide encoding a CAR. Ligand for the RNA
control device, DE, or Side CAR is added to the T-cells (e.g., CD4+
or CD8+) or natural killer cells can be added in increasing amounts
to obtain a desired amount of effector function. The desired amount
of effector function can be an optimized amount of effector
function with a known amount (and/or density) of target antigen on
target cells. Effector function can be target cell killing,
activation of host immune cells, cytokine secretion, production of
granzymes, production of apoptosis inducing ligands, production of
other ligands that modulate the immune system, etc. The effector
function can be secretion of cytokines such as, for example, IL-2,
IFN-.gamma., TNF-.alpha., TGF-.beta., and/or IL-10. Effector
function can be the killing of target cells. Target cells can be
killed with granzymes. Target cells can be induced to undergo
apoptosis. Eukaryotic cells with CARs can kill target cells through
apoptosis and granzymes.
[0178] The RDE, DE, RNA control device, or Side CAR regulatory
element can be used to control expression of a transgene. This
transgene expression can deliver a payload at a target site. These
transgenes can also be carried by viral constructs, or viruses when
the payload is a virus. Expression of the transgene can cause a
desired change in the eukaryotic cell. An RDE regulated by GAPDH
can be used for payload delivery, and the eukaryotic cell (e.g.,
T-cell, natural killer cell, B-cell, macrophage, dendritic cell, or
other antigen presenting cell) can be activated (e.g., by a CAR)
when it reaches the target site. Upon activation of the eukaryotic
cell at the target site through the CAR, the cell induces
glycolysis and the GAPDH releases from the RDE allowed payload
expression and delivery. The target site can be a tumor or
infection and the transgene could encode a cytokine, a chemokine,
an antibody, a checkpoint inhibitor, a granzyme, an apoptosis
inducer, complement, an enzyme for making a cytotoxic small
molecule, an enzyme that cleaves peptides or saccharides (e.g., for
digesting a biofilm), other cytotoxic compounds, or other
polypeptides that can have a desired effect at the target site.
Checkpoint inhibitors include agents that act at immune checkpoints
including, for example, cytotoxic T-lymphocyte-associated antigen 4
(CTLA4), programmed cell death protein (PD-1), Killer-cell
Immunoglobulin-like Receptors (KIR), and Lymphocyte Activation
Gene-3 (LAG3). Examples of checkpoint inhibitors that may be used
as payloads include, for example, Nivolumab (Opdivo.RTM.),
Pembrolizumab (Keytruda.RTM.), Cemiplimab (Libtayo.RTM.),
Atezolizumab (Tecentriq.RTM.), Avelumab (Bavencio.RTM.), Durvalumab
(Imfinzi.RTM.), Ipilimumab (Yervoy.RTM.), Lirilumab, and
BMS-986016. Nivolumab, Atezolizumab and Pembrolizumab act at the
checkpoint protein PD-1 and inhibit apoptosis of anti-tumor immune
cells. Some checkpoint inhibitors prevent the interaction between
PD-1 and its ligand PD-L1. Ipilimumab acts at CTLA4 and prevents
CTLA4 from downregulating activated T-cells in the tumor. Lirilumab
acts at KIR and facilitates activation of Natural Killer cells.
BMS-986016 acts at LAG3 and activates antigen-specific
T-lymphocytes and enhances cytotoxic T cell-mediated lysis of tumor
cells.
[0179] The payload can be one or more of an anti-IL33 antibody,
anti-LAG3 antibody, anti-TIM3 antibody, anti-TIGIT antibody,
anti-MARCO antibody, anti-VISTA antibody, anti-CD39 antibody,
anti-41BB antibody, IL-15, IL-21, IL-12, CD40L, and/or Leptin. The
IL-33 receptor is upregulated in T.sub.regs (regulatory T-cells)
and anti-IL33 antibody reduces proliferation and activation of
T.sub.regs. Anti-LAG3 antibody can also decrease activity of
T.sub.regs. Anti-Il33 antibody and anti-LAG3 antibody can be used
alone or together to reduce the activity of T.sub.regs which can
reduce the suppression of CAR T-cells and other anti-cancer
T-cells. Anti-TIM-3 antibody allows co-localization of CD8+ T-cells
and DC-1 cells (which improves anti-tumor response). MARCO is
expressed on macrophages and in the tumor microenvironment this can
be suppressive to T-cells. Anti-MARCO antibody prevents this tumor
suppression by macrophages. Anti-VISTA antibody reduces the amount
of neutrophils in the tumor microenvironment. A high neutrophil to
T-cell ratio in the tumor microenvironment correlates with poor
patient outcomes. Decreasing the neutrophils in the tumor can
improve patient outcomes and tumor cell killing. IL-15 and Il-21
increase the expansion of natural killer cells and Il-15 can rescue
CD8+ T-cells and may prevent T-cell exhaustion. CD40L plays a
central role in priming, co-stimulation and activation of T-cells
in an immune response. Anti-CD39 antibody can reduce adenosine
levels in the tumor microenvironment. High levels of adenosine in
the tumor microenvironment can induce immunosuppression. Anti-CD39
antibody can reduce this immunosuppression. Anti-41BB antibody can
prevent T-cells from undergoing apoptosis and can also cause tumor
cells to upregulate expression of PD1 (so can be combined with
anti-PD1 therapies).
[0180] Cytokines can include, for example, IL-2, IL-12, IL-15,
IL-18, IL-21, IFN-.gamma., TNF-.alpha., TGF-.beta., and/or IL-10.
Cytotoxic agents can include, for example, granzymes, apoptosis
inducers, complement, or a cytotoxic small molecule. The payload
can be a gene regulatory RNA, such as, for example, siRNA,
microRNAs (e.g., miR155), shRNA, antisense RNA, ribozymes, and the
like, or guide RNAs for use with CRISPR systems. The payload can be
an anti-4-1BB antibody, anti-CD11b antibody, anti-CTLA4 antibody,
anti-IL1b antibody,anti-IL33 antibody, anti-LAG3 antibody,
anti-TIM3 antibody, anti-TIGIT antibody, anti-MARCO antibody,
anti-VISTA antibody, anti-CD39 antibody, PGC-alpha, Leptin, a BiTE,
CCL2, anti-CXCR4 antibody, anti-CXCL12 antibody, HAC, heparinase,
hyaluronidase, Hsp60, Hsp70, IL-2, IL-15, IL-18, INF.gamma., miRNA
(e.g., mir155), CD40 ligand, ApoE3, ApoE4, TNF.alpha., CCR2,
CCR4/CXCL12, CXCR3+CXCL9, CXCL9, ACLY, antagonists of CSF1
receptor, Ox40-41BB, miRNA for Tox (e.g., hsa-mir-26b-5p
(MIRT030248) hsa-mir-223-3p (MIRT054680)), miRNA for TCF-7 (e.g.,
mIR-192, mIR-34a, miR-133a, miR-138-5p, miR-342-5p, miR-491-5p,
miR-541-3p), anti-CD28 antibody (including full length and
fragments such as single chain antibodies), IL-21, Leptin, GOT2,
NAMPT, CD56, IL-2 superkine, anti-REGNASE-1 payloads (e.g., miRNA),
C-jun, cysteinase enzyme, cystinase enzyme, PCBP1 (poly(RC) binding
protein 1), complement (one or more of B, C1-C9, D, C5b, C3b, C4b,
C2a), BMP-1, anti-TGFb agents (e.g., anti-TGFb antibody, soluble
TGFbR, anti-avB6 integrin antibody, natural TGFb binding proteins,
small molecules such as GW788388, Tranilast, Losartan, HMG CoA
reductase inhibitors, Imatinib mesylate, PPAR-g agonists,
rosiglitazone, Pirfenidone, Halofuginone), IL7 combined with CCL19
(e.g., IL7-t2A-CCL19), dnTNFR2, dnTGFBR2, DCN, DKK1, OKT3, NOS2,
CCL5, anti-4-1BB agonist Antibody, anti-CD11b, anti-CD28 agonist
Ab, anti-CD29/anti-VEGF, anti-CTLA4 Ab, anti-IL1b Ab, BiTE, CCR2,
CCR4/CXCL12 disruption, HAC, heparinase, HSP60, HSP70,
hyaluronidase, IL-12, IL15, IL18, IL2, anti-CSF1R and anti-IGF1,
anti-IL4, IL4 receptor antagonists, IL4 binders (e.g., soluble
IL4R), soluble CD40 ligand (e.g., secreted ecto-CD40L), membrane
CD40 ligand, a TGFBR antagonist, and/or 4-1BB ligand. The payloads
can also include those found in US20190183932, which is
incorporated by reference in its entirety for all purposes. The
payload delivered at a target site (e.g., non-tumor target site)
can be a factor that protects the target site such as, for example,
an anti-inflammatory, a factor that attracts T-regulatory cells to
the site, or cytokines or other factors that cause suppression and
reduction in immune activity. The payload can be an enzyme that
cleaves peptides or saccharides, for example hyaluronidase,
heparanase, metalloproteinases and other proteinases which can be
used, for example, to digest an undesired biofilm. Myeloid
modifying payloads ("MM payloads") which reduce immune suppression
or inhibition caused by myeloid cells may be delivered including,
for example, ApoE3, ApoE4, Hsp60, Hsp70, TNF.alpha., antagonists of
CSF1 receptor, CD40L (CD154) and/or IL-12. Two or more MM payloads
can also be delivered by the CAR, DE-CAR, side-CAR and/or other
receptor cell (e.g., T-cell) using RDEs that produce different
pharmacokinetics for delivery. For example, the different MM
payloads could be controlled by different RDEs so that the Cmax of
delivery for the different MM payloads occurs at different times.
For example, Myeloid modifying payloads can promote activated M1
macrophages that are proinflammatory and tumoricidal. A MM payload
that promotes M1 phenotypes are antagonists of CSF1R (antagonists
that block and do not activate the CSF1 receptor and agents that
bind CSF1 and prevent it from interacting with the CSF1R). Such
antagonists of CSF1R include, for example, small-molecule
inhibitors, PLX3397 (Pexidartinib, Plexxikon), PLX7486 (Plexxikon),
ARRY-332 (Array Biopharma), JNJ-40346527 (Johnson & Johnson),
and BLZ945 (Novartis). Exemplary antibodies which are antagonists
of CSF include, for example, Emactuzumab (Roche), AMG820 (Amgen),
IMC-CS4 (LY3022855, Eli Lilly), and MCS110 (Novartis). Cannarile et
al, J. Immunotherp. Cancer 5:53 (2017) which is incorporated by
reference in its entirety for all purposes. The payload can be
localized to the target cell (e.g., tumor site) by fusing or
associating the payload with a Small Leucine Rich Proteoglycans
(SLRPs) such as Decorin, Biglycan, or fibromodulaon/Lumican. The
Decorin, Biglycan, or Lumican can bind to the collagen near the
target cell and this binding will localize the payload at or near
the target site. This strategy is particularly useful for keeping
cytotoxic payloads localized to the target cells (e.g., a tumor).
Decorin and Biglycan can also bind to TGF-beta at or near the
target site and reduce suppression of the engineered T-cell, and so
these can be used as a payload themselves to reduce TGFb. A
Decorin, Biglycan, and/or lumican payload can also be
constitutively expressed, or expressed under the control of an RDE
with a moderate level of baseline expression (mimicking low level
constitutive expression coupled with increased expression upon cell
activation). The payload can be one or more of any of the above.
The payload can be an imaging agent that allows the target site to
be imaged. The payload may be a polypeptide that can be imaged
directly, or it can be a polypeptide that interacts with a
substrate to make a product that can be imaged, imaging
polypeptides include, for example, thymidine kinase (PET), dopamine
D2 (D2R) receptor, sodium iodide transporter (NIS), dexoycytidine
kinase, somatostatin receptor subtype 2, norepinephrine transporter
(NET), cannabinoid receptor, glucose transporter (Glut1),
tyrosinase, sodium iodide transporter, dopamine D2 (D2R) receptor,
modified haloalkane dehalogenase, tyrosinase, .beta.-galactosidase,
and somatostatin receptor 2. These reporter payloads can be imaged
using, for example, optical imaging, ultrasound imaging, computed
tomography imaging, optical coherence tomography imaging,
radiography imaging, nuclear medical imaging, positron emission
tomography imaging, tomography imaging, photo acoustic tomography
imaging, x-ray imaging, thermal imaging, fluoroscopy imaging,
bioluminescent imaging, and fluorescent imaging. These imaging
methods include Positron Emission Tomography (PET) or Single Photon
Emission Computed Tomography (SPECT).
[0181] AB toxins can be used to engineer fusion payloads that
deliver a desired protein product into a target cell. AB toxins
include, for example diphtheria toxin, tetanus toxin, exotoxin A of
P. aeruginosa, iota toxin Ia of C. perfringens, C2 toxin CI of C.
botulinum, ADP-ribosyltransferase of C. difficile, etc. The AB
toxin can be engineered to replace the catalytic (toxic) component
(A domain) of the AB toxin with the desired protein so that the
modified AB toxin binds its receptor and delivers the desired
protein into a target cell through the B domain of the AB toxin.
The B domain of AB toxins generally includes a receptor binding
portion that binds to a feature on the target cell, and a
transmembrane domain portion that forms a pore and interacts with
target cell proteins to transport the A domain into the target
cell. The B toxin fusions replace the A domain with a desired
protein that the B domain will transport into the target cell
through the B domain pore utilizing the cytosolic translocation
factor complex (CTF) from the target cell.
[0182] These B toxin fusions can also be engineered to replace the
receptor binding portion of the B domain with a binding domain
(e.g., ligand) that binds to a desired antigen and/or receptor on a
desired target cell. These modified B toxin fusions now bind to a
desired target cell and then transport the desired protein into the
target cell using the B domain pore and the CTF of the target cell.
For example, the B toxin fusion could be engineered to bind to the
antigen target of a CAR so that the B toxin fusion delivers payload
from a CAR cell into a target cell (e.g., a tumor cell). The
transgene payload can encode a cell penetrating peptide. The cell
penetrating peptide can be fused to another protein to make a
chimeric protein (aka fusion protein) in which the CPP portion
guides the chimeric protein to the cytoplasm of a target cell.
[0183] Multiple systems are envisioned for use that can kill target
cells directly. These include, for example, the introduction of a
viral or a bacterial gene into target cells. This approach turns a
non-toxic pro-drug to a toxic one. There are systems that have been
extensively investigated: the cytosine deaminase gene ("CD") of
Escherichia coli, which converts the pro-drug 5-Fluorocytosine
("5-FC") to 5-Fluorouracil ("5-FU"); and the herpes simplex virus
thymidine kinase gene ("HSV-tk"), which converts ganciclovir
("GCV") to ganciclovir monophosphate, converted by the cancer
cells' enzymes to ganciclovir triphosphate. The HSV-tk/GCV system
useful in killing tumor cells directly, involves adenoviral
transfer of HSV-tk to tumor cells, with the subsequent
administration of ganciclovir. Specifically, recombinant
replication-defective adenovirus is employed to transfer the
thymidine, HSV-tk, into hepatocellular carcinoma ("HCC") cells to
confer sensitivity to ganciclovir. Three useful HCC cell lines
include, for example, Hep3B, PLC/PRF/5 and HepG2, which can
efficiently infect, in vitro, by a recombinant adenovirus carrying
lacZ reporter gene ("Ad-CMVlacZ"). Expression of HSV-tk in HCC
cells infected with a recombinant adenovirus carrying HSV-tk gene
("AdCMVtk") induces sensitivity to ganciclovir in a dose-dependent
manner (Qian et al., Induction of sensitivity to ganciclovir in
human hepatocellular carcinoma cells by adenovirus-mediated gene
transfer of herpes simplex virus thymidine kinase, Hepatology,
22:118-123 (1995)) doi.org/10.1002/hep.1840220119.
[0184] When the payload is a gene regulatory RNA, such as, for
example, siRNAs, shRNAs, and/or microRNAs (e.g., miR155), the
regulatory RNA (e.g., mir155) can be the transgene or can be
included in an intron of a transgene encoding a polypeptide. For
example, a mir155 cassette as described in Du et al., FEBs J.
273:5421-27 (2006) and Chung et al., Nucl Acids Res. 34:e53 (2006)
can be used as the payload or be engineered into an intron of a
transgene that is used as the payload. The mir155 cassette (or
cassette for other regulatory RNA) can be engineered into a
transgene as an intron or the transgene can be the mir155 cassette,
optionally with additional nucleotides. The regulatory RNA
transgene (or transgene with regulatory RNA as an intron) can be
placed under the control of an RDE. RDEs can impact RNA processing
and stability in the nucleus. After the transgene encoding the
regulatory RNA (e.g., mir155) or encoding a transgene with a
regulatory RNA (e.g., mir155) intron is transcribed, the transcript
can be processed in the nucleus by the nuclear microprocessor
complex or other nuclear components to make the nucleotide
stem-loop precursor regulatory RNA (e.g., pre-mir155). The
pre-regulatory RNA (e.g., pre-mir155) stem-loop is exported out of
the nucleus where it is processed by Dicer to form a short RNA
duplex. The short RNA duplex(es) are bound by Argonaute (Ago) to
form the core of the multi-subunit complex called the RNA-induced
silencing complex (RISC). By operably linking a RDE to the
transgene encoding the regulatory RNA (e.g., mir155) or the
transgene with the regulatory RNA (e.g., mir155) intron, the
expression of regulatory RNA (e.g., mir155) can be regulated by the
RDE. Different RDEs can be operably linked to the regulatory RNA
(e.g., mir155) transgene or transgene with regulatory RNA (e.g.,
mir155) intron to provide different timing and kinetics of
expression following activation of a eukaryotic cell (e.g.,
activation of a T-cell by the TCR or a CAR). RDEs can be used that
produce expression quickly after activation of the cell (e.g., AU2
or AU101), produce high expression 72-96 hours after activation
(e.g., AU5 or AU21), or produce increasing expression through 192
hours after expression (e.g., AU19 or AU22). RDEs can also be
selected that will produce continuous expression of regulatory RNA
(e.g., mir155) or that will produce expression for a period of time
after activation of the cell followed by reduced expression.
Multiple regulatory RNA (e.g., mir155) constructs (e.g., with
mir155 as the transgene or a transgene with a mir155 intron) with
different RDEs can be used to provide continuous expression of
regulatory RNA (e.g., mir155) following activation of a cell (e.g.,
T-cell) by using RDEs that provide different pharmacokinetic
profiles of expression which together produce continuous expression
(e.g., see Example 11). Alternatively, select RDEs or combinations
of RDEs or combinations of regulatory RNA (e.g., mir155) with
different RDEs can be used to provide a desired expression profile
of the regulatory RNA (e.g., mir155).
[0185] Upregulation of mir155 has been associated with activated
CD8+ T-cells and the formation of memory T-cells after an
immunological challenge. Upregulation of mir155 expression during
activation of T-cells (e.g., CAR T-cells activated by target
antigens) will potentiate the CAR T-cell response against target
cells. Placing mir155 under control of a heterologous RDE (e.g., an
RDE that responds to GAPDH) ties upregulation of mir155 to
activation of the T-cell so that mir155 is upregulated in activated
T-cells (e.g., CD8+, CAR T-cells). This upregulation can increase
proliferation of activated T-cells. The upregulation can also
decrease T-cell exhaustion and senescence. The upregulation can
also potentiate T-cell effector functions resulting in increased
target cell killing.
[0186] Effector function of T-cells can also be enhanced by
downregulating TCF7 and/or Tox expression and/or by upregulating
IL-15 expression. TCF7 is a member of the T-cell factor/lymphoid
enhancer-binding factor family of high mobility group (HMG) box
transcriptional activators. This gene is expressed predominantly in
T-cells and plays a critical role in natural killer cell and innate
lymphoid cell development. HMG box protein TCF7 can be a regulator
in the switch between self-renewal and differentiation. TCF7 can
have a dual role in promoting the expression of genes
characteristic of self-renewing CD34+ cells while repressing genes
activated in partially differentiated CD34- state. TCF7 can
regulate a network of transcription factors that switch cells from
a naive, undifferentiated state to a differentiated, effector cell
state. When TCF7 is expressed cells adopt a self-renewal state that
is more naive and less differentiated. TCF7 can be downregulated
using miRNAs such as, for example, mIR-192, mIR-34a, miR-133a,
miR-138-5p, miR-342-5p, miR-491-5p, and/or miR-541-3p. In an
example, one of more of these miRNAs can be encoded in one or more
introns of a payload that are spliced out when the transcript is
bound by hnRNPLL (see above), and when the payload is expressed in
an activated cell making hnRNPLL these miRNAs will downregulate
TCF7. Alternatively, a transgene encoding TCF7 can be used as an
off switch for activated CAR T-cells. If TCF7 is expressed after
the effector, CAR T-cell has killed the target cancer cells, this
should push the CAR T-cell into a naive, undifferentiated state (an
off state for the CAR T-cell). The transgene encoding TCF7 could be
placed under the control of an inducible promoter (e.g., an
inducible promoter that is ligand inducible) or it could be placed
under control of an RDE that results in expression after eight days
or more of cell activation (e.g., see Example 11). Expression of
TCF7 can be turned off by removal of ligand (or other inducing
factors for the inducible promoter), and/or the RDE control will
turn off expression. This can return the CAR T-cell to state where
it can be reactivated by binding to target ligand at other cancer
cells.
[0187] Thymocyte selection-associated high mobility group box (TOX)
protein is a member of a small subfamily of proteins (TOX2, TOX3,
and TOX4) that share almost identical HMG-box sequences. TOX can be
induced by high antigen stimulation of the T cell receptor and TOX
can be a central regulator of T.sub.EX (exhausted T-cells). Robust
TOX expression can result in commitment to development of the
T.sub.EX cell type. TOX exhaustion may counteract and balance
T-cell overstimulation and activation-induced cell death in
settings of chronic antigen stimulation. Effector T-cells (e.g.,
activated CD8+ T-cells) can have low Tox, whereas higher levels of
Tox pushes the effector cells to become T.sub.EX cells. TEX cells
have reduced effector function but are still effective against low
level infections or small numbers of cancer cells.
[0188] Effector function of T-cells can be enhanced by including a
payload encoding an miRNA for Tox (e.g., hsa-mir-26b-5p
(MIRT030248) hsa-mir-223-3p (MIRT054680)) under regulation of an
RDE. Following activation of the T-cell, the RDE control will
result in expression of the miRNA for Tox. This miRNA will lower
levels of Tox in the T-cell inhibiting T.sub.EX formation by the
activated T-cells resulting in more active, effector T-cells
against a target. In addition, a payload can be Tox itself, used as
on off-switch that pushes the activated T-cells into a T.sub.EX
phenotype at a desired time. When used as an off-switch, Tox
expression can be under control of an inducible promoter that can
be induced to express Tox at a desired time (e.g., by adding an
appropriate ligand), Tox can be controlled by an RNA control device
or a DE (ligand can induce expression), or Tox can be placed under
control of an RDE that produces expression at late time intervals
after activation of the cell (e.g., see Example 11). Functional
state and type of T-cell can tailored by treating T-cells with
electromagnetic radiation. Electromagnetic radiation in the UV
range can condition T-cells to become Treg cells. For example, a
dose of UVA/UVB can induce formation of Tregs. Electromagnetic
radiation in the blue light range can activate T-cells.
[0189] An exemplary payload is a transgene encoding ApoE (e.g.,
ApoE2, ApoE3 and/or APoE4) which is secreted from the cell. ApoE
can bind to receptors (e.g., LRP8) on Myeloid Derived Suppressor
Cells (MDSC) and reduce the survival of MDSCs. MDSCs are a
heterogeneous population of suppressive innate immune cells that
can expand in certain disease states. In some cancers (e.g.,
melanoma, lung, breast and ovarian cancers) MDSC levels can
substantially rise in the tumor(s) and in the plasma of patients.
Such patients with high levels of circulating MDSCs can respond
poorly to checkpoint blockade. MDSCs can mediate immunosuppression
in these patients and induce angiogenesis. Payload expression of
ApoE (e.g., ApoE4) can reduce the number of MDSCs in tumors and
circulating in the serum, and result in suppression of tumor
progression and metastatic colonization. The reduction in MDSCs in
the tumor also enables other immune cells (e.g., CAR T-cells) to
more efficiently kill tumor cells. The ApoE payload can also act
directly on myeloid malignancies that express the LRP8 receptor. In
such examples, the payload delivery of ApoE to a myeloid cancer
cell can suppress and/or kill the cancer cell. Thus, ApoE can be a
payload for delivery to myeloid malignancies that are LRP8+,
including LRP8+ AML. Delivery of the ApoE payload by a eukaryotic
cell (e.g., primary T-cell) can be combined with another
therapeutic agent such as, for example, an anti-cancer agent (e.g.,
a CAR T-cell, a chemotherapeutic, radiation, a checkpoint
inhibitor, or any of the anti-cancer therapeutics described
herein). The ApoE effect on MDSCs can potentiate the action of the
other anti-cancer agent.
[0190] Another exemplary payload is a transgene encoding
NO-synthase (e.g., iNOS, nNOS and eNOS). NO synthase can bind to
GAPDH and can sequester the GAPDH allowing RDE (which are bound by
GAPDH) controlled transgenes (or native genes) to be expressed, or
increasing expression from RDE (which are bound by GAPDH, e.g., AU
19 (TMEM-219), AU 20 (TMEM-219snp), AU 21 (CCR7), AU 22 (SEM-A4D),
and AU 23 (CDC42-SE2)) controlled transgenes (or native genes) once
the cell is activated and glycolysis is induced. Expression of NO
synthase can induce RDE (which are bound by GAPDH) controlled
expression (through binding to GAPDH) and/or can potentiate RDE
(which are bound by GAPDH) controlled expression by decreasing the
amount of GAPDH that can bind RDEs and/or increasing the time over
which GAPDH cannot bind to RDEs. When NO synthase is used to
increase the RDE (which are bound by GAPDH) response to cell
activation, a transgene encoding NO synthase can be placed under
control of an RDE so that when the cell is activated, expression
from the transgene encoding the NO synthase is induced. When NO
synthase is used to induce expression from RDE (which are bound by
GAPDH) controlled genes, the NO synthase can be placed under
inducible control (e.g., inducible promoters, RNA control devices,
or destabilizing elements as disclosed in U.S. Pat. No. 9,777,064,
which is hereby incorporated by reference in its entirety for all
purposes) and induction of NO synthase expression induces
expression from the RDE (which are bound by GAPDH) controlled
genes.
[0191] An exemplary payload is a transgene encoding HSV-Thymidine
Kinase (HSV-TK). HSV-TK can be used as an adjuvant, and/or as a
super antigen that induces an inflammatory response in the patient.
When used in this manner, a cell secretes the HSV-TK payload at the
target site inducing an inflammatory response. The transgene
encoding the HSV-TK can also be used as a kill switch to eliminate
the engineered cells (e.g., CAR T-cells with or without a RDE
controlled payload). When used as a kill switch, the HSV-TK can be
controlled by a late expressing RDE so the HSV-TK is expressed
after the CAR T-cell has acted at the target site, or the transgene
expressing the HSV-TK can be controlled by a ligand inducible
control means so that the HSV-TK protein is expressed in response
to the ligand which is introduced at a desired time. In the
kill-switch application, ganciclovir can be provided to the cells
and the HSV-TK converts the ganciclovir to GCV-triphosphate which
kills the cell by a cytotoxic effect. A transgene expressing HSV-TK
can also be included in a viral payload so that when the virus
infects target cells the target cells express HSV-TK. Ganciclovir
is provided to the target cells which use the HSV-TK to convert the
ganciclovir to GCV-triphosphate which is toxic to the target
cells.
[0192] Thymidine kinase can be used with PET reporter probes such
as, for example,
[.sup.18F]9-(4-[.sup.18F]-fluoro-3-hydroxymethylbutyl)-guanine, a
fluorine-18-labelled penciclovir analogue, which when
phosphorylated by thymidine kinase (TK) becomes retained
intracellularly, or is 5-(76) Br-bromo-2'-fluoro-2'-deoxyuridine.
The relevant reporter probes for each of the PET reporters are well
known to the skilled artisan. An exemplary reporter probe for
dopamine D2 (D2R) receptor is 3-(2'-[.sup.18F]fluoroethyl)spiperone
(FESP) (MacLaren et al., Gene Ther. 6(5):785-91 (1999)). An
exemplary reporter probe for the sodium iodide transporter is
.sup.124I, which is retained in cells following transport by the
transporter. An exemplary reporter probe for deoxycytidine kinase
is 2'-deoxy-2'-.sup.18F-5-ethyl-1-.beta.-d-arabinofuranosyluracil
(.sup.18F-FEAU). An exemplary reporter probe for somatostatin
receptor subtype 2 is .sup.99m/94mTc-, .sup.90Y-, or
.sup.177Lu-labeled octreotide analogues, for example .sup.90Y-, or
.sup.177Lu-labeled DOTATOC (Zhang et al., J Nucl Med. 50(suppl
2):323 (2009)); .sup.68Ga-DOTATATE; and .sup.111In-DOTABASS (see.
e.g., Brader et al., J Nucl Med. 54(2):167-172 (2013), incorporated
herein by reference). An exemplary reporter probe for
norepinephrine transporter is .sup.11C-m-hydroxyephedrine (Buursma
et al., J Nucl Med. 46:2068-2075 (2005)). An exemplary reporter
probe for the cannabinoid receptor is .sup.11C-labeled CB2 ligand,
.sup.11C-GW405833 (Vandeputte et al., J Nucl Med. 52(7):1102-1109
(2011)). An exemplary reporter probe for the glucose transporter is
[.sup.18F]fluoro-2-deoxy-d-glucose (Herschman, H. R., Crit Rev
Oncology/Hematology 51:191-204 (2004)). An exemplary reporter probe
for tyrosinase is
N-(2-(diethylamino)ethyl)-.sup.18F-5-fluoropicolinamide (Qin et
al., Sci Rep. 3:1490 (2013)). Other reporter probes are described
in the art, for example, in Yaghoubi et al., Theranostics
2(4):374-391 (2012), incorporated herein by reference.
[0193] An exemplary photoacoustic reporter probe for
.beta.-galactosidase is
5-bromo-4-chloro-3-indolyl-.beta.-D-galactoside (X-gal) (Li et al.,
J Biomed Opt. 12(2):020504 (2007)). Exemplary X-ray reporter
includes, among others, somatostatin receptor 2, or other types of
receptor based binding agents. The reporter probe can have a
radiopaque label moiety that is bound to the reporter probe and
imaged, for example, by X-ray or computer tomography. Exemplary
radiopaque label is iodine, particularly a polyiodinated chemical
group (see, e.g., U.S. Pat. No. 5,141,739), and paramagnetic labels
(e.g., gadolinium), which can be attached to the reporter probe by
conventional means. Optical imaging agents include, for example, a
fluorescent polypeptide. Fluorescent polypeptides include, for
example, green fluorescent protein from Aequorea victoria or
Renilla reniformis, and active variants thereof (e.g., blue
fluorescent protein, yellow fluorescent protein, cyan fluorescent
protein, etc.); fluorescent proteins from Hydroid jellyfishes,
Copepod, Ctenophora, Anthrozoas, and Entacmaea quadricolor, and
active variants thereof; and phycobiliproteins and active variants
thereof. The optical imaging agent can also be a bioluminescent
polypeptide. These include, for example, aequorin (and other
Ca.sup.+2 regulated photoproteins), luciferase based on luciferin
substrate, luciferase based on Coelenterazine substrate (e.g.,
Renilla, Gaussia, and Metridina), and luciferase from Cypridina,
and active variants thereof.
[0194] CARS and/or universal-CARs can be designed to include
receptors against antigens that are of bacterial, fungal or viral
origin. Because CARS can be utilized to fight infections, which are
a source of toxicity in immunocompromised patients, such
anti-pathogen CARS can be used in conjunction with CARS T-cell
therapy specific for a TAA.
[0195] A eukaryotic cell can bind to a specific antigen via the
CAR, DE-CAR, and/or Side-CAR polypeptide causing the CAR, DE-CAR,
and/or Side-CAR polypeptide to transmit a signal into the
eukaryotic cell, and as a result, the eukaryotic cell can be
activated and so express an appropriate RDE-transgene. The
activation of the eukaryotic cell expressing the CARS is varied
depending on the kind of a eukaryotic cell and the intracellular
element of the CARS. The eukaryotic cell can express a RDE
transcript that poises the cell for effector function upon
stimulation of the eukaryotic cell through a CARS.
[0196] A eukaryotic cell expressing the RDE-transgene or RDE
transcript, and optionally, a CARS, T-cell receptor, B-cell
receptor, innate immunity receptor and/or other receptor or
targeting polypeptide can be used as a therapeutic agent to treat a
disease. The therapeutic agent can comprise the eukaryotic cell
expressing the RDE-transgene or RDE transcript, and optionally, a
CARS, T-cell receptor, B-cell receptor, innate immunity receptor
and/or other receptor or targeting polypeptide as an active
ingredient, and may further comprise a suitable excipient. Examples
of the excipient include pharmaceutically acceptable excipients for
the composition. The disease against which the eukaryotic cell
expressing the RDE-transgene or RDE transcript, and optionally, a
CARS, T-cell receptor, B-cell receptor, innate immunity receptor
and/or other receptor or targeting polypeptide is administered is
not particularly limited as long as the disease shows sensitivity
to the eukaryotic cell and/or the product of the RDE-transgene.
[0197] Examples of diseases that can be treated include a cancer
(blood cancer (leukemia), solid tumor (ovarian cancer) etc.), an
inflammatory disease/autoimmune disease (asthma, eczema),
hepatitis, and an infectious disease, the cause of which is a virus
such as influenza and HIV, a bacterium, or a fungus, for example,
tuberculosis, MRSA, VRE, and deep mycosis, other immune mediated
diseases such as neurodegenerative diseases like Alzheimer's or
Parkinson's, and metabolic diseases like diabetes. A receptor
(e.g., a CAR) can target the eukaryotic cell to the diseased
cell(s) and when the receptor binds to its target at the diseased
cell(s) the receptor can send a signal into the eukaryotic cell
leading to expression of the RDE-transgene. The RDE-transgene
encodes a polypeptide that is useful in treating or killing the
diseased cell(s). A cancer and/or solid tumor can be treated with a
eukaryotic cell expressing receptor that binds to a tumor
associated (or cancer associated) antigen, such as those described
above. When the receptor binds to the tumor associated antigen the
receptor sends a signal into the cell that causes the RDE-transgene
to be expressed (e.g., the signal effects an RDE binding protein
leading to expression of the RDE-transcript). The RDE-transcript
can encode a polypeptide that activates the eukaryotic cell so that
the eukaryotic cell treats the cancer and/or the RDE-transcript
encodes a polypeptide that itself treats the cancer (e.g., a
cytotoxic polypeptide).
[0198] An autoimmune disease (e.g., pemphigus vulgaris, lupus
erythematosus, rheumatoid arthritis, multiple sclerosis, Crohn's
disease) can be treated with a eukaryotic cell expressing a
RDE-transgene or RDE transcript, and optionally, a CARS, T-cell
receptor, B-cell receptor, innate immunity receptor and/or other
receptor or targeting polypeptide that binds to the immune proteins
associated with the autoimmune disease. The receptor or targeting
polypeptide can trigger expression of the RDE-transgene that
encodes a polypeptide useful in treating the autoimmune disease
(e.g., the polypeptide can regulate the cells causing the
autoimmune disease or kill these cells). The eukaryotic cell
expressing the RDE-transgene or RDE transcript, and receptor or
targeting polypeptide can target cells that make an antibody
involved with the autoimmune disease (e.g., the RDE-transgene can
encode a polypeptide that kills the antibody producing cells or
that inhibits the production of antibody by these cells). The
eukaryotic cell expressing the RDE-transgene or RDE transcript, and
receptor or targeting polypeptide can target T-lymphocytes involved
with the autoimmune disease (e.g., the RDE-transgene can encode a
polypeptide that kills the target T-lymphocytes or that regulates
the activity of the T-lymphocytes).
[0199] Eukaryotic cells expressing the RDE-transgene or RDE
transcript, and optionally, a CARS, T-cell receptor, B-cell
receptor, innate immunity receptor and/or other receptor or
targeting polypeptide can be used as a therapeutic agent to treat
an allergy. Examples of allergies that can be treated include, for
example, allergies to pollen, animal dander, peanuts, other nuts,
milk products, gluten, eggs, seafood, shellfish, and soy. The
eukaryotic cell expressing the RDE-transgene or RDE transcript, and
receptor or targeting polypeptide can target cells that make an
antibody which causes the allergic reaction against, for example,
pollen, animal dander, peanuts, other nuts, milk products, gluten,
eggs, seafood, shellfish, and soy. The targeted cells can be one or
more of B-cells, memory B-cells, plasma cells, pre-B-cells, and
progenitor B-cells. Targeted cells can also include T-lymphocytes
which cause the allergic reaction against, for example, pollen,
animal dander, peanuts, other nuts, milk products, gluten, eggs,
seafood, shellfish, and soy. Eukaryotic cells expressing the
RDE-transgene or RDE transcript, and receptor or targeting
polypeptide can bind to the idiotypic determinant of the antibody
or T-cell receptor.
[0200] The eukaryotic cell expressing the RDE-transgene or RDE
transcript, and optionally, a CARS, T-cell receptor, B-cell
receptor, innate immunity receptor and/or other receptor or
targeting polypeptide can be administered for treatment of a
disease or condition. For example, the eukaryotic cell can be
utilized to treat an infectious disease. The eukaryotic cell can
express a receptor or targeting polypeptide that binds to an
antigen found on the infectious disease causing agent or a cell
infected with such an agent. The receptor or targeting polypeptide
binds the antigen associated with the infectious disease and sends
a signal into the eukaryotic cell that leads to expression of the
RDE-transgene. The RDE-transgene encodes a product that can
activate the eukaryotic cell for treating the infectious disease
(e.g., the eukaryotic cell can produce a cytotoxic polypeptide or a
cytokine that activates immune cells). The RDE-transgene can also
encode a polypeptide that itself is a cytotoxic polypeptide or a
cytokine. The eukaryotic cell can also be utilized for prevention
of an infectious disease (used prophylactically), for example,
after bone marrow transplantation or exposure to radiation, donor
lymphocyte transfusion for the purpose of remission of recurrent
leukemia, and the like.
[0201] The therapeutic agent comprising the eukaryotic cell
expressing the CARS, T-cell receptor, B-cell receptor, innate
immunity receptor and/or other receptor or targeting polypeptide as
an active ingredient can be administered intradermally,
intramuscularly, subcutaneously, intraperitoneally, intranasally,
intraarterially, intravenously, intratumorally, or into an afferent
lymph vessel, by parenteral administration, for example, by
injection or infusion, although the administration route is not
limited.
[0202] The RDE-transgene or RDE transcript, and optionally, CARS,
T-cell receptor, B-cell receptor, innate immunity receptor and/or
other receptor or targeting polypeptide can be used with a
T-lymphocyte that has aggressive anti-tumor properties, such as
those described in Pegram et al, CD28z CARs and armored CARs, 2014,
Cancer J. 20(2):127-133, which is incorporated by reference in its
entirety for all purposes. The RDE transcript can encode a
polypeptide that causes aggressive anti-tumor properties in the
T-lymphocyte.
[0203] A transgene, a CAR, DE-CAR, and/or Side CAR polypeptides can
be controlled by an RDE from the 3'-UTR of the gene encoding IL-2
or the 3'-UTR of IFN-.gamma.. These RDEs can be modified to
inactivate microRNA sites found in the RDE. Using these control
elements makes expression of the CAR, DE-CAR, Side-CAR, and/or
transgene sensitive to changes in the glycolytic state of the host
cell through the interaction of the RDE with
glyceraldehyde-3-phosphate dehydrogenase (GAPDH). When the host
cell is in a quiescent state a large proportion of the GAPDH is not
involved in glycolysis and is able to bind to the RDE resulting in
reduced translation of the transcript encoding the CAR, DE-CAR,
Side-CAR, and/or transgene polypeptides. When the host cell is
induced to increase glycolysis, e.g., by providing the host cells
with glucose, or other small molecules that will increase
glycolytic activity, GAPDH becomes enzymatically active and is not
able to bind to the RDE. The reduction in GAPDH binding to the RDE
increases translation of the transcripts (e.g., by increasing
half-life of the transcript and/or by increasing the translation
rate) encoding the CAR, DE-CAR, Side-CAR, or other transgene. The
glycolytic activity of GAPDH can be increased by increasing the
amount and/or activity of triose isomerase. The host cell can be
induced to over-express a recombinant triose isomerase, and this
over-expression increases the glycolytic activity of GAPDH. A
glycolysis inhibitor can be added to decrease expression of the
transcript with the RDE. Such glycolysis inhibitors include for
example, dimethylfumarate (DMF), rapamycin, 2-deoxyglucose,
3-bromophyruvic acid, iodoacetate, fluoride, oxamate, ploglitazone,
dichloroacetic acid, quinones (e.g., chloroquine,
hydroxychloroquine, etc.), or other metabolism inhibitors such as,
for example, dehydroepiandrosterone. Expression from the RDE
controlled transcript can be increased by the addition of GAPDH (or
other RDE binding protein) inhibitor that inhibits binding of the
RDE by GAPDH (or other RDE binding protein). Such GAPDH inhibitors
include, for example, CGP 3466B maleate or Heptelidic acid (both
sold by Santa Cruz Biotechnology, Inc.), pentalenolactone, or
3-bromopyruvic acid. Quinones such as, for example, chloroquine and
hydroxychloroquine, can de-acidify the endosome impairing antigen
processing by APCs, decrease signaling from toll-like receptors,
reduces T-cell proliferation, T-cell metabolic activity, T-cell
cytokine secretion, interferes with IL-2 production, and interferes
with T-cell response to IL-2.
[0204] Constructs encoding transcripts with RDEs can be expressed
in eukaryotic cells to bind to RDE binding proteins and so reduce
the ability of those RDE binding proteins to interact with native
transcripts in the cell. The recombinant transcripts can compete
for binding of RDE binding proteins and this can reduce the
inhibition and/or activation of native transcripts within the
eukaryotic cell by the RDE binding proteins. The constructs
encoding transcripts with the RDEs can be used in this way to
change when and how native transcripts are expressed in the
eukaryotic cell. The eukaryotic cell can be a T-cell, natural
killer cell, or B-cell and the recombinant transcript has RDEs that
are shared with cytokine or cytotoxic transcripts (e.g., in their
3' untranslated regions). The recombinant transcript can compete
for binding with the RDE binding proteins (e.g., GAPDH and/or other
glycolytic enzymes described above) that regulate expression of the
cytokine or cytotoxic polypeptide and change the threshold (e.g.,
glycolysis activity for GAPDH) needed to express the cytokine or
cytotoxic polypeptide. This can be used to create super T-cell (aka
Angry T-cells or Hornet T-cells) that will secrete higher amounts
of cytokines and/or cytotoxic proteins (greater C.sub.max) in
response to stimulation of the immune cell (e.g., through a CAR or
T-cell receptor). T-cells can be reprogrammed with a recombinant
transcript encoding an RDE from an IL-2 transcript so that when the
T-cell is stimulated by its T-cell receptor it produces more IL-2
and other effector polypeptides with faster kinetics. These
reprogrammed T-cells can also produce other inflammatory cytokines
and cytotoxic polypeptides (e.g., granzymes and/or perforins) in
larger amounts and with faster kinetics. Reprogramming T-cells and
natural killer cells into such Angry/Hornet states can be useful
for treating disease and disorders, including, for example, tumors,
other cancers, and infectious diseases.
[0205] RDEs can be used to reduce CAR expression in immune cells
until those immune cells are activated by target or at a desired
time. This can result in expression of the CAR at desired times for
therapeutic effect while reducing the systemic exposure of a
subject to the CAR. The reduced systemic exposure can reduce and/or
inhibit the development of an immune response against the CAR as
the subject's immune system will see less CAR over time.
[0206] Control of receptor (e.g., CAR and/or TCR) expression can be
used to modulate the PK-PD axis of an immunotherapy. The amount of
receptor expressed on the surface of cell can be modulated with the
strength of a promoter, the inducibility of the promoter, the use
of bicistronic constructs with different promoter strengths
expressing the two cistrons, RDEs (selection of RDE impacts dynamic
range and timing of expression), GC3 content of the transcript, RNA
control devices, degrons and/or Side-CARs. These control elements
used singly or in combination change the amount of receptor on the
surface of the cell which changes the input signal (e.g., amount of
ligand for the receptor) needed to activate the cell so that it
produces an output (e.g., payload delivery or target cell killing).
Using this control, the input signal needed for the receptor cells
can be optimized for a given target, compartment of the body,
reduction of side effects, etc. as desired. RDEs can also be used
to change the timing of the output from the cell after activation
at the receptor (e.g., CAR and/or TCR).
[0207] Some neural degenerative diseases and syndromes are
associated with inflammation, as are a number of other non-neural
diseases and syndromes. Such inflammation associated diseases can
be treated, at least in part, by providing a subject with small
molecules (or other molecules) that increase the availability of
inhibitory RDE binding proteins within immune cells. Such small
molecules include, for example, glycolysis inhibitors (e.g.,
dimethylfumarate (DMF), rapamycin, 2-deoxyglucose, 3-bromophyruvic
acid, iodoacetate, fluoride, oxamate, ploglitazone, dichloroacetic
acid), other metabolic inhibitors (e.g., dehydroepiandrosterone),
etc. For example, glycolytic inhibitors reduce glycolysis in the
cell and can increase the amount of free GAPDH (not involved in
glycolysis) for binding to RDEs reducing the expression of these
transcripts. A number of inflammatory gene products in immune cells
(e.g., gene products that activate the immune system) are regulated
by RDEs that can bind GAPDH. Decreasing glycolysis increases the
amount of free GAPDH for RDE binding, increases the amount of GAPDH
bound to the RDEs of these inflammatory genes and reduces the
expression of these inflammatory genes. Inflammatory genes include
proinflammatory cytokines such as, for example, IL-1, TNF-.alpha.,
INF-g, and GM-CSF. These cytokines have 3'-UTRs with RDEs that can
bind RDE binding proteins, including GAPDH, to regulate their
expression. The increased GAPDH can bind to these RDEs and decrease
the expression of these proinflammatory cytokines. Reduced
expression of proinflammatory cytokines could reduce activity of
the immune system in these subjects reducing inflammation. The
reduction in inflammation can have positive therapeutic effects
alleviating symptoms and/or treating the underlying disease state
in these inflammation related neural diseases, as well as in other
inflammation associated diseases and syndromes.
[0208] RDEs (e.g., AU elements) can be selected to provide maximal
expression at a desired time point and to provide a desired amount
of polypeptide at that time point. RDEs can also be selected to
provide a desired area under the curve for a polypeptide. As shown
in Table 2 of Example 20, different RDEs (e.g., AU elements)
reached maximal rates of expression at different times. Also as
shown in Table 1, different RDEs provided different amounts of
expression with different profiles over time providing different
AUC. Using these RDEs in combination with different transgenes
allows temporal programming of when the different transgenes reach
maximal rates of expression in relation to one another following
activation of a cell. In addition, using different RDEs one can
program the transgenes to express a desired amount of transgene
encoded polypeptide and/or a desired amount of AUC or exposure to
the polypeptide encoded by the transgene. Thus, RDEs can be used to
provide control that produces desired amounts of different
transgene polypeptides at a different (or the same) desired
times.
[0209] This temporal control can be used to provide desired timing
for the production of different transgene polypeptides within a
cell. Using this temporal control, a cell can be programmed to
express a first transgene that alters the state of the cell so that
is prepared to be affected by the polypeptide of a second transgene
that is expressed at a later time. For example, the first expressed
polypeptide could induce the cell to make and store cytotoxic
polypeptides (e.g., granzymes and/or perforins) and the second
expressed polypeptide could be involved in the release of the
cytotoxic polypeptides. Another example of temporal expression
involves it use to program a cell to undergo changes (e.g.,
differentiation or changing a state of the cell) that requires
temporal expression of two or more gene products. RDEs can be used
to mimic this temporal expression allowing one to control when the
cell changes its state or differentiates (e.g., programmed
differentiation of stem cells). In a stem cell example, the
temporal and induction control can be used to program a stem cell
to differentiate when (and where) it is desired to have the stem
cell differentiate into a desired cell type.
[0210] The temporal control can also be used to provide desired
timing of the production of different transgene polypeptides
outside of the cell. Using this temporal control, a cell can be
activated and secrete a first transgene polypeptide that conditions
and/or alters a target cell so that the target cell is prepared to
be acted upon by a polypeptide expressed at later time from a
second transgene. For example, the first polypeptide could induce a
target cell to express a receptor on the target cell surface (e.g.,
FasR, Her2, CD20, CTLA-4, PD-L1, etc.) or a polypeptide in the
cell. The first transgene could also induce the cell to secrete a
factor that induces the target cell to change its state (e.g., the
first transgene could induce the cell to secrete CpG which causes
the target cell to express OX40 on the target cell surface). The
second transgene that reaches maximal rate of expression at a later
time can encode a polypeptide that acts on the induced surface
receptor (e.g., FasL, Herceptin, Rituximab, Ipilimumab, Nivolumab,
anti-OX40 antibody, etc.). The temporal and induction control can
also be used to change the state or differentiation of a target
cell by providing to the target cell polypeptides in a timed manner
where the first polypeptide induces the target cell to alter its
state (e.g., differentiation) so that it can be acted upon by the
second polypeptide (etc. for additional transgene polypeptides
which reach maximal rate of expression at later times).
[0211] Autoimmune diseases and other disease states involving an
overactive immune system (e.g., SARS-CoV-2 infection) can be
treated with a AITAM CAR T-cell targeted against autoimmune disease
antigen(s). The AITAM CAR T-cell can include a payload of IL-4,
IL-10 or other immunosuppressive. The AITAM CAR T-cell with or
without a payload can induce the formation of Tregs that can
inhibit the autoimmune disease and/or reduce the toxicity caused by
over-stimulation or chronic stimulation of the immune system.
[0212] Some examples of diseases and payloads that can be treated
using RDEs (Gold elements) with different kinetic parameters (e.g.,
an RDE that gives rapid expression early after activation of the
cell followed by a rapid decline in expression or an RDE that
delays expression after cell activation for 2-3 days) include the
following: DLL3 positive cancers (such as IDH1mut gliomas,
melanoma, and SCLC) using an anti-DLL3 CAR and a payload of one or
more of anti-4-1BB antibody, anti-CD11b antibody, anti-CTLA4
antibody, anti-IL1b antibody, a BiTE, CCL2, anti-CXCR4 antibody,
anti-CXCL12 antibody, HAC, heparinase, hyaluronidase, Hsp60, Hsp70,
IL-2, IL-12, IL-15, IL-18, INF.gamma., miRNA (e.g., mir155), CD40
ligand, ApoE3, ApoE4, TNF.alpha., CCR2, CCR4/CXCL12, CXCR3+CXCL9,
CXCL9, ACLY, antagonists of CSF1 receptor, miRNA for Tox (e.g.,
hsa-mir-26b-5p (MIRT030248) hsa-mir-223-3p (MIRT054680)), miRNA for
TCF-7 (e.g., mIR-192, mIR-34a, miR-133a, miR-138-5p, miR-342-5p,
miR-491-5p, miR-541-3p), and/or anti-CD28 antibody (including full
length and fragments such as single chain antibodies). Optionally,
the anti-DLL3 CAR with an RDE controlled payload is combined or
administered in succession with another therapy as described above.
The combined or sequenced therapy can be an ADC where the antibody
binds to a tumor associate antigen, e.g., DLL3. The combination
therapy can be provided to a subject prior to, at the same time, or
after the administration of the anti-DLL3 CAR with an RDE
controlled payload. CD19 positive lymphomas (e.g., NHL) using an
anti-CD19 CAR and a payload of IL-12, or one or more of anti-4-1BB
antibody, anti-CD11b antibody, anti-CTLA4 antibody, anti-IL1b
antibody, a BiTE, CCL2, anti-CXCR4 antibody, anti-CXCL12 antibody,
HAC, heparinase, hyaluronidase, Hsp60, Hsp70, IL-2, IL-15, IL-18,
INF.gamma., miRNA (e.g., mir155), CD40 ligand, ApoE3, ApoE4,
TNF.alpha., CCR2, CCR4/CXCL12, CXCR3+CXCL9, CXCL9, ACLY,
antagonists of CSF1 receptor, miRNA for Tox (e.g., hsa-mir-26b-5p
(MIRT030248) hsa-mir-223-3p (MIRT054680)), miRNA for TCF-7 (e.g.,
mIR-192, mIR-34a, miR-133a, miR-138-5p, miR-342-5p, miR-491-5p,
miR-541-3p), and/or anti-CD28 antibody (including full length and
fragments such as single chain antibodies). Optionally, the
anti-CD19 CAR with an RDE controlled payload is combined or
administered in succession with another therapy as described above.
The combined or sequenced therapy can be an ADC where the antibody
binds to a tumor associate antigen, e.g., CD19. The combination
therapy can be provided to a subject prior to, at the same time, or
after the administration of the anti-CD19 CAR with an RDE
controlled payload. AML with onco-CD43 (sialylation mutant) using
an anti-onco-CD43 CAR that recognizes the mutated sialylation and a
payload of one or more of anti-CXCL12 antibody, anti-anti-CXCR4
antibody, or IL-12, and/or one or more of anti-4-1BB antibody,
anti-CD11b antibody, anti-CTLA4 antibody, anti-IL1b antibody, a
BiTE, CCL2, HAC, heparinase, hyaluronidase, Hsp60, Hsp70, IL-2,
IL-15, IL-18, INF.gamma., miRNA (e.g., mir155), CD40 ligand, ApoE3,
ApoE4, TNF.alpha., CCR2, CCR4/CXCL12, CXCR3+CXCL9, CXCL9, ACLY,
antagonists of CSF1 receptor, miRNA for Tox (e.g., hsa-mir-26b-5p
(MIRT030248) hsa-mir-223-3p (MIRT054680)), miRNA for TCF-7 (e.g.,
mIR-192, mIR-34a, miR-133a, miR-138-5p, miR-342-5p, miR-491-5p,
miR-541-3p), and/or anti-CD28 antibody (including full length and
fragments such as single chain antibodies). Optionally, the
anti-onco-CD43 CAR with an RDE controlled payload is combined or
administered in succession with another therapy as described above.
The combined or sequenced therapy can be an ADC where the antibody
binds to a tumor associated antigen, e.g., onco-CD43. The
combination therapy can be provided to a subject prior to, at the
same time, or after the administration of the anti-onco-CD43 CAR
with an RDE controlled payload. PSCA positive prostate cancer,
bladder cancer or pancreatic cancer using an anti-PSCA CAR and a
payload of heparinase or IL-12, and/or one or more of anti-4-1BB
antibody, anti-CD11b antibody, anti-CTLA4 antibody, anti-IL1b
antibody, a BiTE, CCL2, anti-CXCR4 antibody, anti-CXCL12 antibody,
HAC, hyaluronidase, Hsp60, Hsp70, IL-2, IL-15, IL-18, INF.gamma.,
miRNA (e.g., mir155), CD40 ligand, ApoE3, ApoE4, TNF.alpha., CCR2,
CCR4/CXCL12, CXCR3+CXCL9, CXCL9, ACLY, antagonists of CSF1
receptor, miRNA for Tox (e.g., hsa-mir-26b-5p (MIRT030248)
hsa-mir-223-3p (MIRT054680)), miRNA for TCF-7 (e.g., mIR-192,
mIR-34a, miR-133a, miR-138-5p, miR-342-5p, miR-491-5p, miR-541-3p),
and/or anti-CD28 antibody (including full length and fragments such
as single chain antibodies). Optionally, the anti-PSCA CAR with an
RDE controlled payload is combined or administered in succession
with another therapy as described above. The combined or sequenced
therapy can be an ADC where the antibody binds to a tumor
associated antigen, e.g., PSCA. The combination therapy can be
provided to a subject prior to, at the same time, or after the
administration of the anti-PSCA CAR with an RDE controlled payload.
Triple negative breast cancer with a CAR that recognizes cancer
testis antigen, misfolded or mutant EGFR (associated with triple
negative breast cancer), and/or folate receptor alpha peptide and a
payload of IL-12 and/or one or more of anti-4-1BB antibody,
anti-CD11b antibody, anti-CTLA4 antibody, anti-IL1b antibody, a
BiTE, CCL2, anti-CXCR4 antibody, anti-CXCL12 antibody, HAC,
heparinase, hyaluronidase, Hsp60, Hsp70, IL-2, IL-15, IL-18,
INF.gamma., miRNA (e.g., mir155), CD40 ligand, ApoE3, ApoE4,
TNF.alpha., CCR2, CCR4/CXCL12, CXCR3+CXCL9, CXCL9, ACLY,
antagonists of CSF1 receptor, miRNA for Tox (e.g., hsa-mir-26b-5p
(MIRT030248) hsa-mir-223-3p (MIRT054680)), miRNA for TCF-7 (e.g.,
mIR-192, mIR-34a, miR-133a, miR-138-5p, miR-342-5p, miR-491-5p,
miR-541-3p), and/or anti-CD28 antibody (including full length and
fragments such as single chain antibodies). Optionally, the
anti-cancer testis antigen CAR, anti-misfolded or mutant EGFR CAR,
or anti-folate receptor alpha CAR with an RDE controlled payload is
combined or administered in succession with another therapy as
described above. The combined or sequenced therapy can be an ADC
where the antibody binds to a tumor associated antigen, e.g.,
cancer testis antigen, misfolded or mutant EGFR (associated with
triple negative breast cancer), and/or folate receptor alpha
peptide. The combination therapy can be provided to a subject prior
to, at the same time, or after the administration of the
anti-cancer testis antigen CAR, anti-misfolded or mutant EGFR CAR,
or anti-folate receptor alpha CAR with an RDE controlled payload.
SEZ6 positive small cell lung cancer (SCLC), neuroendocrine cancers
(e.g., medullary thyroid cancer), large cell lung cancer (LCLC),
and malignant pheochromocytoma with a CAR that recognizes SEZ6 and
a payload of IL-12 and/or one or more of anti-4-1BB antibody,
anti-CD11b antibody, anti-CTLA4 antibody, anti-IL1b antibody, a
BiTE, CCL2, anti-CXCR4 antibody, anti-CXCL12 antibody, HAC,
heparinase, hyaluronidase, Hsp60, Hsp70, IL-2, IL-15, IL-18,
INF.gamma., miRNA (e.g., mir155), CD40 ligand, ApoE3, ApoE4,
TNF.alpha., CCR2, CCR4/CXCL12, CXCR3+CXCL9, CXCL9, ACLY,
antagonists of CSF1 receptor, miRNA for Tox (e.g., hsa-mir-26b-5p
(MIRT030248) hsa-mir-223-3p (MIRT054680)), miRNA for TCF-7 (e.g.,
mIR-192, mIR-34a, miR-133a, miR-138-5p, miR-342-5p, miR-491-5p,
miR-541-3p), and/or anti-CD28 antibody (including full length and
fragments such as single chain antibodies). Optionally, the
anti-SEZ6 CAR with an RDE controlled payload is combined or
administered in succession with another therapy as described above.
The combined or sequenced therapy can be an ADC where the antibody
binds to a tumor associated antigen, e.g., SEZ6. The combination
therapy can be provided to a subject prior to, at the same time, or
after the administration of the anti-SEZ6 CAR with an RDE
controlled payload. RNF43 positive colorectal cancer, colon cancer,
and endometrial cancers with a CAR that recognizes RNF43 and a
payload of IL-12 and/or one or more of anti-4-1BB antibody,
anti-CD11b antibody, anti-CTLA4 antibody, anti-IL1b antibody, a
BiTE, CCL2, anti-CXCR4 antibody, anti-CXCL12 antibody, HAC,
heparinase, hyaluronidase, Hsp60, Hsp70, IL-2, IL-15, IL-18,
INF.gamma., miRNA (e.g., mir155), CD40 ligand, ApoE3, ApoE4,
TNF.alpha., CCR2, CCR4/CXCL12, CXCR3+CXCL9, CXCL9, ACLY,
antagonists of CSF1 receptor, miRNA for Tox (e.g., hsa-mir-26b-5p
(MIRT030248) hsa-mir-223-3p (MIRT054680)), miRNA for TCF-7 (e.g.,
mIR-192, mIR-34a, miR-133a, miR-138-5p, miR-342-5p, miR-491-5p,
miR-541-3p), and/or anti-CD28 antibody (including full length and
fragments such as single chain antibodies). Optionally, the
anti-RNF43 CAR with an RDE controlled payload is combined or
administered in succession with another therapy as described above.
The combined or sequenced therapy can be an ADC where the antibody
binds to a tumor associated antigen, e.g., RNF43. The combination
therapy can be provided to a subject prior to, at the same time, or
after the administration of the anti-RNF43 CAR with an RDE
controlled payload. TnMUC1 positive breast cancer or pancreatic
cancer with a CAR that recognizes TnMUC1 and a payload of IL-12
and/or one or more of anti-4-1BB antibody, anti-CD11b antibody,
anti-CTLA4 antibody, anti-IL1b antibody, a BiTE, CCL2, anti-CXCR4
antibody, anti-CXCL12 antibody, HAC, heparinase, hyaluronidase,
Hsp60, Hsp70, IL-2, IL-15, IL-18, INF.gamma., miRNA (e.g., mir155),
CD40 ligand, ApoE3, ApoE4, TNF.alpha., CCR2, CCR4/CXCL12,
CXCR3+CXCL9, CXCL9, ACLY, antagonists of CSF1 receptor, miRNA for
Tox (e.g., hsa-mir-26b-5p (MIRT030248) hsa-mir-223-3p
(MIRT054680)), miRNA for TCF-7 (e.g., mIR-192, mIR-34a, miR-133a,
miR-138-5p, miR-342-5p, miR-491-5p, miR-541-3p), and/or anti-CD28
antibody (including full length and fragments such as single chain
antibodies). Optionally, the anti-TnMUC1 CAR with an RDE controlled
payload is combined or administered in succession with another
therapy as described above. The combined or sequenced therapy can
be an ADC where the antibody binds to a tumor associated antigen,
e.g., TnMUC1. The combination therapy can be provided to a subject
prior to, at the same time, or after the administration of the
anti-TnMUC1 CAR with an RDE controlled payload. Nectin4 positive
urothelial cancer, NSCLC, breast cancer, ovarian cancer, bladder
cancer, pancreatic cancer, and other solid tumors with a CAR that
recognizes Nectin4 and a payload of IL-12 and/or one or more of
anti-4-1BB antibody, anti-CD11b antibody, anti-CTLA4 antibody,
anti-IL1b antibody, a BiTE, CCL2, anti-CXCR4 antibody, anti-CXCL12
antibody, HAC, heparinase, hyaluronidase, Hsp60, Hsp70, IL-2,
IL-15, IL-18, INF.gamma., miRNA (e.g., mir155), CD40 ligand, ApoE3,
ApoE4, TNF.alpha., CCR2, CCR4/CXCL12, CXCR3+CXCL9, CXCL9, ACLY,
antagonists of CSF1 receptor, miRNA for Tox (e.g., hsa-mir-26b-5p
(MIRT030248) hsa-mir-223-3p (MIRT054680)), miRNA for TCF-7 (e.g.,
mIR-192, mIR-34a, miR-133a, miR-138-5p, miR-342-5p, miR-491-5p,
miR-541-3p), and/or anti-CD28 antibody (including full length and
fragments such as single chain antibodies). Optionally, the
anti-Nectin4 CAR with an RDE controlled payload is combined or
administered in succession with another therapy as described above.
The combined or sequenced therapy can be an ADC where the antibody
binds to a tumor associated antigen, e.g., Nectin4. The combination
therapy can be provided to a subject prior to, at the same time, or
after the administration of the anti-Nectin4 CAR with an RDE
controlled payload. EFNA4 positive triple negative breast cancer,
ovarian cancer, colorectal cancer, liver cancer, lung cancer, and
other solid tumors with a CAR that recognizes EFNA4 and a payload
of IL-12 and/or one or more of anti-4-1BB antibody, anti-CD11b
antibody, anti-CTLA4 antibody, anti-IL1b antibody, a BiTE, CCL2,
anti-CXCR4 antibody, anti-CXCL12 antibody, HAC, heparinase,
hyaluronidase, Hsp60, Hsp70, IL-2, IL-15, IL-18, INF.gamma., miRNA
(e.g., mir155), CD40 ligand, ApoE3, ApoE4, TNF.alpha., CCR2,
CCR4/CXCL12, CXCR3+CXCL9, CXCL9, ACLY, antagonists of CSF1
receptor, miRNA for Tox (e.g., hsa-mir-26b-5p (MIRT030248)
hsa-mir-223-3p (MIRT054680)), miRNA for TCF-7 (e.g., mIR-192,
mIR-34a, miR-133a, miR-138-5p, miR-342-5p, miR-491-5p, miR-541-3p),
and/or anti-CD28 antibody (including full length and fragments such
as single chain antibodies). Optionally, the anti-EFNA4 CAR with an
RDE controlled payload is combined or administered in succession
with another therapy as described above. The combined or sequenced
therapy can be an ADC where the antibody binds to a tumor
associated antigen, e.g., EFNA4. The combination therapy can be
provided to a subject prior to, at the same time, or after the
administration of the anti-EFNA4 CAR with an RDE controlled
payload. GPC3 positive hepatocellular carcinoma, lung cancer and
other solid tumors with a CAR that recognizes GPC3 and a payload of
IL-12 and/or one or more of anti-4-1BB antibody, anti-CD11b
antibody, anti-CTLA4 antibody, anti-IL1b antibody, a BiTE, CCL2,
anti-CXCR4 antibody, anti-CXCL12 antibody, HAC, heparinase,
hyaluronidase, Hsp60, Hsp70, IL-2, IL-15, IL-18, INF.gamma., miRNA
(e.g., mir155), CD40 ligand, ApoE3, ApoE4, TNF.alpha., CCR2,
CCR4/CXCL12, CXCR3+CXCL9, CXCL9, ACLY, antagonists of CSF1
receptor, miRNA for Tox (e.g., hsa-mir-26b-5p (MIRT030248)
hsa-mir-223-3p (MIRT054680)), miRNA for TCF-7 (e.g., mIR-192,
mIR-34a, miR-133a, miR-138-5p, miR-342-5p, miR-491-5p, miR-541-3p),
and/or anti-CD28 antibody (including full length and fragments such
as single chain antibodies). Optionally, the anti-GPC3 CAR with an
RDE controlled payload is combined or administered in succession
with another therapy as described above. The combined or sequenced
therapy can be an ADC where the antibody binds to a tumor
associated antigen, e.g., GPC3. The combination therapy can be
provided to a subject prior to, at the same time, or after the
administration of the anti-GPC3 CAR with an RDE controlled
payload.
[0213] In general, any of the above CAR cells with or without an
RDE controlled transgene(s) can be used in combination or
administered in succession with another molecule (e.g., another
therapy). For example, the other molecule can be a polypeptide,
lipid, carbohydrate, nucleic acid, small molecule drug, antibody,
antibody-drug-conjugate, biological drug, or any combination of the
foregoing. The antibody drug conjugate (ADC) includes those
described herein. The ADC can bind to the same antigen as the CAR
or it can bind to a different antigen. When the ADC and CAR bind to
the same antigen, they may bind to the same or different epitopes
on the same antigen. The ADC and CAR therapy (with or without a RDE
controlled payload) can be provided at the same time, or one can be
administered to a subject before the other. For example, the ADC
and CAR can target a tumor associate antigen and the ADC can be
administered the subject first to reduce the tumor burden, and then
the CAR therapy is administered to clear the remaining cancer
cells.
[0214] The inventions disclosed herein will be better understood
from the experimental details which follow. However, one skilled in
the art will readily appreciate that the specific methods and
results discussed are merely illustrative of the inventions as
described more fully in the claims which follow thereafter. Unless
otherwise indicated, the disclosure is not limited to specific
procedures, materials, or the like, as such may vary. It is also to
be understood that the terminology used herein is for the purpose
of describing particular embodiments only and is not intended to be
limiting.
EXAMPLES
Example 1. Control of T-Cell Effector Activity with an RDE-CAR
[0215] A RDE Car is made using the third generation anti-CD19 CAR
cassette described in WO 2012/079000, which is hereby
incorporated-by-reference in its entirety for all purposes), and
the 3'-UTR of the gene encoding IL-2 (NCBI Reference Sequence
Number: NM 000586.3), which is hereby incorporated by reference in
its entirety for all purposes). A nucleic acid encoding the IL-2
3'-UTR is engineered into the anti-CD19 CAR cassette in an
appropriate expression vector. The IL-2, 3'-UTR sequence used
was:
TABLE-US-00001 (SEQ ID NO: 21)
taattaagtgatcccacttaaaacatatcaggccttctATTTATTTAaat
ATTTAaattttatATTTAttgttgaatgtatggtttgctacctattgtaa
ctattattcttaatcttaaaactataaatatggatcttttatgattcttt
ttgtaagccctaggggctctaaaatggtttcacttATTTAtcccaaaatA
TTTAttattatgttgaatgttaaatatagtatctatgtagattggttagt
aaaactATTTAataaatttgataaatataaa
[0216] The anti-CD19 RDE CAR and anti-CD19 CAR constructs are
transfected by routine methods into different populations of
T-cells (primary human T-cells), and stable populations of T-cells
are selected using appropriate antibiotics (or other selection
schemes). T-cell populations with anti-CD19 RDE CARs
(CD19.sup.-/CD22.sup.-/CD3.sup.+) and T-cell populations with
anti-CD19 CARs (CD19.sup.-/CD22.sup.-/CD3.sup.+) are activated by
co-incubation with anti-CD3/CD28 beads and allowed to return to
quiescent state after debeading.
[0217] Quiescent anti-CD19 RDE CAR T-cells are co-cultured with
CD19.sup.+/CD22.sup.+/CD3.sup.- Raji target cells at RDE CAR
T-cell:Raji target ratios of 2:1, 5:1, and 10:1. The glycolysis
activator glucose is added to the culture medium at concentrations
in the range of 1.0 mM to 10 mM (1 mM, 2 mM, 3 mM, 4 mM, 5 mM, 7.5
mM and 10 mM). The RDE-CAR T-cells and the Raji cells are grown
together for 24 hours. Cultures are washed, and then stained with
anti-CD22 and anti-CD3 reagents, followed by counting of CD22.sup.+
(Raji target cells) and CD3.sup.+ cells (Smart CAR T-cells). These
measurements will identify the target cell killing rate (e.g.,
half-life) and the proliferation rate of the RDE-CAR T-cells at
different levels of RDE-CAR expression.
[0218] Activated anti-CD19 RDE CAR T-cells are co-cultured with
CD19.sup.+/CD22.sup.+/CD3.sup.- Raji target cells at RDE CAR
T-cell:Raji target ratios of 2:1, 5:1, and 10:1. The glycolysis
activator glucose is added to the culture medium at concentrations
in the range of 1.0 mM to 10 mM (1 mM, 2, mM, 3 mM, 4 mM, 5 mM, 7.5
mM and 10 mM). The RDE-CAR T-cells and the Raji cells are grown
together for 24 hours. Samples from culture media are taken and
tested for IL-2 by ELISA.
[0219] As a control activated anti-CD19 CAR T-cells are co-cultured
with CD19.sup.+/CD22.sup.+/CD3.sup.- Raji target cells at CAR
T-cell:Raji target ratios of 2:1, 5:1, and 10:1. The glycolysis
activator glucose is added to the culture medium at concentrations
in the range of 1.0 mM to 10 mM (1 mM, 2 mM, 3 mM, 4 mM, 5 mM, 7.5
mM and 10 mM). The CAR T-cells and the Raji cells are grown
together for 24 hours. Cultures are washed, and then stained with
anti-CD22 and anti-CD3 reagents, followed by counting of CD22.sup.+
(Raji target cells) and CD3.sup.+ cells (CAR T-cells).
[0220] As a control, activated anti-CD19 CAR T-cells are
co-cultured with CD19.sup.+/CD22.sup.+/CD3.sup.- Raji target cells
at CAR T-cell:Raji target ratios of 2:1, 5:1, and 10:1. The
glycolysis activator glucose is added to the culture medium at
concentrations in the range of 1.0 mM to 10 mM (1 mM, 2 mM, 3 mM, 4
mM, 5 mM, 7.5 mM and 10 mM). The CAR T-cells and the Raji cells are
grown together for 48 hours. Samples from culture media are taken
and tested for IL-2 by ELISA.
Example 2: Removal of MicroRNA Binding Sites from an RDE
[0221] The AU-rich element from the 3'-UTR of IL-2 has mir-181 and
mir 186 microRNA binding sites. Different combinations of the
microRNA sites were removed from the 3'-UTR of IL-2. When the
MIR186 micro-RNA sites were removed from the 3'-UTR of IL-2 the
dynamic range of expression from constructs with this UTR increased
50 fold. The modified IL-2, 3'-UTR replaces CTT in the sequence
with GAA and is shown below (the new GAA is underlined in the
sequence):
TABLE-US-00002 (SEQ ID NO: 22)
taattaagtgatcccacttaaaacatatcaggccttctATTTATTTAaat
ATTTAaattttatATTTAttgttgaatgtatggtttgctacctattgtaa
ctattattcttaatcttaaaactataaatatggatcttttatgattGAAt
ttgtaagccctaggggctctaaaatggtttcacttATTTAtcccaaaatA
TTTAttattatgttgaatgttaaatatagtatctatgtagattggttagt
aaaactATTTAataaatttgataaatataaa
[0222] The AU-rich element from the 3'UTR of IFNg also has
micro-RNA binding sites characterized as mir-125. The sequence of
the IFNg RDE is:
TABLE-US-00003 (SEQ ID NO: 23)
tggttgtcctgcctgcaatatttgaattttaaatctaaatctATTTAtta
atATTTAacattATTTAtatggggaatatatttttagactcatcaatcaa
ataagtATTTAtaatagcaacttttgtgtaatgaaaatgaatatctatta
atatatgtattATTTAtaattcctatatcctgtgactgtctcacttaatc
ctttgttttctgactaattaggcaaggctatgtgattacaaggetttatc
tcaggggccaactaggcagccaacctaagcaagatcccatgggttgtgtg
tttatttcacttgatgatacaatgaacacttataagtgaagtgatactat
ccagttactgccggtttgaaaatatgcctgcaatctgagccagtgcttta
atggcatgtcagacagaacttgaatgtgtcaggtgaccctgatgaaaaca
tagcatctcaggagatttcatgcctggtgcttccaaatattgttgacaac
tgtgactgtacccaaatggaaagtaactcatttgttaaaattatcaatat
ctaatatatatgaataaagtgtaagttcacaacta
[0223] Different combinations of the micro-RNA sites were removed
from the 3'UTR of IFNg and tested for increased expression. When
the mir125 micro-RNA sites were removed from the 3'-UTR of
IFN-.gamma. the expression rate from constructs with this UTR is
increased.
[0224] Expression of GFP in T-cells, transfected with the RDE-GFP
plus the microRNA sites, is compared to expression of GFP in
T-cells with the RDE-GFP in which the microRNA sites have been
removed, following activation with CD3/CD28 beads for 24 hours. The
removal of the microRNA sites increased expression of the GFP by a
factor of between 2-5 after 24 hours, relative to the cells with
microRNA sites.
Example 3: Payload Delivery to DLBCL Using an Anti-CD19 CAR
T-Cell
[0225] The anti-CD19 Smart CAR T-lymphocytes and anti-CD19 CAR
T-cell lymphocytes of Example 6 are used in this example. These CAR
T-lymphocytes are further engineered to include a construct
encoding a PD-1 inhibitor under the control of the 3'-UTR of IL2
that has been modified by removal of the MIR186 sites. PD-1
inhibitors expressed by the construct include, for example,
Pembrolizumab (Keytruda.RTM.), Nivolumab (Opdivo.RTM.), Cemiplimab
(Libtayo.RTM.), Atezolizumab (Tecentriq.RTM.), Avelumab
(Bavencio.RTM.), Durvalumab (Imfinzi.RTM.), BMS-936558,
Lambrolizumab, or polypeptides derived from these drugs. Other PD-1
inhibitors that may be expressed by the construct include those
disclosed in Herbst et al., J Clin Oncol., 31:3000 (2013); Heery et
al., J Clin Oncol., 32:5s, 3064 (2014); Powles et al., J Clin
Oncol, 32:5s, 5011(2014); Segal et al., J Clin Oncol., 32:5s, 3002
(2014), or U.S. Pat. Nos. 8,735,553; 8,617,546; 8,008,449;
8,741,295; 8,552,154; 8,354,509; 8,779,105; 7,563,869; 8,287,856;
8,927,697; 8,088,905; 7,595,048; 8,168,179; 6,808,710; 7,943,743;
8,246,955; and 8,217,149.
[0226] T-cell populations with anti-CD19 Smart CARs/PD-1
(CD19-/CD22-/CD3+) and T-cell populations with anti-CD19 CARs/PD-1
(CD19-/CD22-/CD3+) are activated by co-incubation with
anti-CD3/CD28 beads. T-cells with anti-CD19 Smart CARs/PD-1
inhibitor or anti-CD19 CARs/PD-1 inhibitor were incubated with
theophylline at 0, 75 and 250 .mu.M for 72 hours. Activated
anti-CD19 Smart CAR/PD-1 T-cells or anti-CD19 CAR/PD-1 T-cells were
co-cultured with CD19.sup.+/CD22.sup.+/CD3- Raji target cells at
Smart CAR/PD-1 T-cell:Raji target ratios of 2:1, 5:1, and 10:1.
Ligand for the RNA control device, theophylline is maintained in
the culture medium at concentrations of 0 .mu.M, 75 .mu.M, and 250
.mu.M. The Smart-CAR/PD-1 T-cells or CAR/PD-1 T-cells and the Raji
cells are grown together for 18 hours. Cultures are washed, and
then stained with anti-CD22 and anti-CD3 reagents, followed by
counting of CD22+(Raji target cells) and CD3+ cells (Smart CAR
T-cells). Samples from culture media are also taken at 6, 12 and 18
hours, and tested for PD-1 inhibitor by ELISA.
Example 4: Payload Delivery to AML Using an Anti-CD133 CAR
T-Cell
[0227] A CAR is made using the anti-CD20 CAR cassette described in
Budde 2013 (Budde et al. PLoS1, 2013
doi:10.1371/journal.pone.0082742, which is hereby
incorporated-by-reference in its entirety for all purposes), with
the anti-CD133 mAb 293C3-SDIE is used for the extracellular element
(Rothfelder et al., 2015,
ash.confex.com/ash/2015/webprogram/Paper81121.html, which is
incorporated by reference in its entirety for all purposes)
replacing the anti-CD20 extracellular domain. The anti-CD133 CAR
also can encode the RNA control device, 3XL2bulge9 (Win and Smolke
2007 Proc. Natl Acad. Sci. 104 (36): 14283-88, which is hereby
incorporated by reference in its entirety for all purposes). A
nucleic acid encoding the anti-CD20 CAR cassette is engineered to
replace the anti-CD20 extracellular domain with the anti-CD133
element, and optionally the RNA control device is also engineered
into the cassette. The anti-CD133 CAR with or without the RNA
control device are cloned into appropriate expression vectors.
[0228] These anti-CD133 CAR and anti-CD133 Smart CAR constructs are
transfected by routine methods into T-lymphocytes (Jurkat cells
and/or primary human T-lymphocytes), and stable populations of
T-lymphocytes are selected using appropriate antibiotics (or other
selection schemes).
[0229] These CAR T-lymphocytes are further engineered to include a
construct encoding a PD-1 inhibitor under the control of the RDE
from the 3'-UTR of IL2 that has been modified by removal of a
MIR186 site. PD-1 inhibitors expressed by the construct include,
for example, Pembrolizumab (Keytruda.RTM.), Nivolumab
(Opdivo.RTM.), Cemiplimab (Libtayo.RTM.), Atezolizumab
(Tecentriq.RTM.), Avelumab (Bavencio.RTM.), Durvalumab
(Imfinzi.RTM.), BMS-936558, Lambrolizumab, or polypeptides derived
from these drugs. Other PD-1 inhibitors that may be expressed by
the construct include those disclosed in Herbst et al., J Clin
Oncol., 31:3000 (2013); Heery et al., J Clin Oncol., 32:5s, 3064
(2014); Powles et al., J Clin Oncol, 32:5s, 5011(2014); Segal et
al., J Clin Oncol., 32:5s, 3002 (2014), or U.S. Pat. Nos.
8,735,553; 8,617,546; 8,008,449; 8,741,295; 8,552,154; 8,354,509;
8,779,105; 7,563,869; 8,287,856; 8,927,697; 8,088,905; 7,595,048;
8,168,179; 6,808,710; 7,943,743; 8,246,955; and 8,217,149.
[0230] T-lymphocyte populations with anti-CD133 CAR/PD-1 inhibitor
or anti-CD133 Smart CAR/PD-1 inhibitor
(CD20.sup.-/CD22.sup.-/CD3.sup.+) are activated by co-incubation
with anti-CD3/CD28 beads.
[0231] Activated anti-CD133 CAR/PD-1 inhibitor or anti-CD133 Smart
CAR/PD-1 inhibitor T-lymphocytes are co-cultured with
CD133.sup.+/CD3.sup.- AML target cells (e.g., U937, MV4-11,
MOLM-14, HL-60 and/or KG1a) at anti-CD133 CAR and/or anti-CD133
Smart CAR T-lymphocyte:AML target ratios of 2:1, 5:1, and 10:1.
Ligand for the RNA control device, theophylline, is added to the
culture medium at concentrations in the range of 500 .mu.M to 1 mM
(lower or greater concentrations can be used to titrate Smart-CAR
activity to the desired level). The anti-CD133 CAR/PD-1 inhibitor
and/or anti-CD133 Smart CAR/PD-1 inhibitor T-lymphocytes and the
AML cells are grown together for 48 hours. Cultures are washed, and
then stained with anti-CD133 and anti-CD3 reagents, followed by
counting of CD133.sup.+ (AML target cells) and CD3.sup.+ cells
(anti-CD133 CAR, anti-CD133 DE-CAR, anti-CD133 Smart CAR, and/or
the anti-CD133 DE-Smart CAR T-lymphocytes). These measurements will
identify the target cell killing rate (e.g., half-life) and the
proliferation rate of the anti-CD133 CAR/PD-1 inhibitor and/or
anti-CD133 Smart CAR/PD-1 inhibitor T-lymphocytes at different
levels of CAR expression. Samples from culture media are also taken
at 12, 24, 26 and 48 hours, and tested for PD-1 inhibitor by
ELISA.
Example 5: An RDE Construct for Expressing a Second Transgene
[0232] Constructs were made using an anti-CD19 CAR cassette as
described in WO 2012/079000, which is hereby
incorporated-by-reference in its entirety for all purposes), and a
GFP-RDE1 (3'-UTR from IFNg) insert. These two inserts/cassettes
were placed in the same lenti virus construct. The anti-CD19 CAR
cassette and the insert with the GFP-RDE are transcribed in
opposite directions, and the control regions for each are located
in between the two insert/cassettes. The control region for the
GFP-RDE insert was MinP and the RDE was the endogenous 3'-UTR of
IFNg. The control region of the anti-CD19 CAR cassette was MND (as
described above). CD4+ T-cells were transduced with the bicistronic
construct.
[0233] The transduced T cells were allowed to return to resting
state, and then were tested after stimulation as follows. For the
`no stimulation` set, transduced T-cells were incubated for 24h
alone in medium. For the `Raji co-culture` set and the "CD3/CD28
Beads" set, CD19+ Raji B cells or anti-CD.sup.3/anti-CD28 beads
were incubated with the transduced T cells for 24h. At 24h, the T
cells were stained for CD25 and CD69, which are activation markers,
and subject to flow cytometry to measure these markers and GFP
expression in the T cells.
[0234] The transduced T-cells showed an increase in fluorescence
when cultured with Raji target cells (activate CAR) of 1.0% to 6.5%
(about 6.5 fold), and increase in fluorescence when cultured with
CD3/CD28 beads (activate TCR) of 1.0% to 4.4% (about 4.4 fold). The
transformed T-cells showed a change in activated cells in the
population when cultured with Raji cells of 0.9% to 84.8%, and when
cultured with CD3/CD28 beads of 0.9% to 90.8%.
Example 6: A Modified RDE2 Construct for Expressing a Second
Transgene
[0235] Constructs were made using an anti-CD19 CAR cassette as
described in Examples 11 and 12, and a GFP-RDE2.1 (IL-2 RDE)
insert. The RDE2.1 was modified to remove the MIR186 microRNA
sites, altering nucleotides from the 3'-UTR of IL-2 which was used
as RDE2.
[0236] These two inserts/cassettes were placed in the same lenti
virus construct. The anti-CD19 CAR cassette and the insert with the
GFP-RDE are transcribed in opposite directions, and the control
regions for each are located in between the two insert/cassettes.
The control region for the GFP-RDE insert was a MinP. The control
region of the anti-CD19 CAR cassette in was MND (as described
above). CD4+ T-cells were transduced with the bicistronic
construct.
[0237] The transduced T cells were allowed to return to resting
state, and then were tested after stimulation as follows. For the
`no stimulation` set, transduced T-cells were incubated for 24h
alone in medium. For the `Raji co-culture` set and the "CD3/CD28
Beads" set, CD19+ Raji B cells or anti-CD.sup.3/anti-CD28 beads
were incubated with the transduced T cells for 24h. At 24h, the T
cells were stained for CD25 and CD69, which are activation markers,
and subject to flow cytometry to measure these markers and GFP
expression in the T cells.
[0238] The transduced T-cells showed a change in activated cells in
the population when cultured with Raji cells of 3.9% to 12.1%, and
when cultured with CD3/CD28 beads of 3.9% to 11.1%.
Example 7: An RDE Construct for Expressing a Luciferase
Transgene
[0239] Constructs were made using an anti-CD19 CAR cassette as
described in WO 2012/079000, which is hereby
incorporated-by-reference in its entirety for all purposes), and a
Luciferase-RDE1 (3'-UTR of IFNg, Gold1) insert or a
Luciferase-3'-UTR (a 3'-UTR that does not confer differential
transgene translation in response to metabolic state of the cell,
3'-UTR). The anti-CD19 CAR cassette and the insert with the
luciferase-RDE1 are transcribed in opposite directions, and the
control regions for each are located in between the two
insert/cassettes. The control region for the Luciferase-RDE1 insert
and Luciferase-3'-UTR were either a MinP promoter or an NFAT
promoter having the sequences of:
TABLE-US-00004 (MinP) SEQ ID NO: 24
TAGAGGGTATATAATGGAAGCTCGACTTCCAG (NEAT) SEQ ID NO: 25
GGAGGAAAAACTGTTTCATACAGAAGGCGTGGAGGAAAAACTGTTTCATA
CAGAAGGCGTGGAGGAAAAACTGTTTCATACAGAAGGCGTAGATCTAGAC
TCTAGAGGGTATATAATGGAAGCTCGAATTC
The control region of the anti-CD19 CAR cassette was the MND
promoter. CD4+ T-cells were transduced with the bicistronic
construct.
[0240] The transduced T cells were allowed to return to resting
state, and then were tested after stimulation as follows. For the
`no stimulation` set, transduced T-cells were incubated for 24h
alone in medium. For the `Raji co-culture` set and the "CD3/CD28
Beads" set, CD19+ Raji B cells or anti-CD.sup.3/anti-CD28 beads
were incubated with the transduced T cells for 24h. At 24h, the T
cells were stained for CD25 and CD69, which are activation markers,
and subject to flow cytometry to measure these markers and
luciferase expression in the T cells.
[0241] FIG. 2 shows that the transduced T-cells had an increase in
bioluminescence when cultured with Raji target cells (activate CAR)
or when cultured with CD3/CD28 beads (activate TCR) as compared to
bioluminescence of T-cells at resting. The T-cells with a NFAT
promoter and the 3'-UTR of IFNg (Gold1) showed a larger on-off
response from CAR stimulation versus TCR stimulation. Under all
conditions, T-cells with Gold1 had lower amounts of bioluminescence
than T-cells under the same conditions (and same promoter) with
Luciferase that was not controlled by the 3'UTR of IFNg
(3'-UTR).
Example 8: Comparison of RDEs Controlling Luciferase
[0242] Constructs were made using an anti-CD19 CAR cassette as
described in WO 2012/079000, which is hereby
incorporated-by-reference in its entirety for all purposes), and a
Luciferase-RDE1 (3' UTR of IFNg, Gold1) insert, a Luciferase-RDE2
(3'-UTR of IL-2, Gold2) insert, a Luciferase-RDE3 (3'-UTR of IL-2
modified as described above to remove the mir186 sites, Gold3), or
a Luciferase-3'-UTR (a 3'-UTR that does not confer differential
transgene translation in response to metabolic state of the cell,
3'-UTR). Combinations of these inserts/cassettes shown in FIG. 3
were placed in the similar lenti virus constructs. The anti-CD19
CAR cassette and the insert with the luciferase-RDE are transcribed
in opposite directions, and the control regions for each are
located in between the two insert/cassettes. The control region for
the Luciferase-RDE insert and Luciferase-3'-UTR were either a MinP
promoter or an NFAT promoter. The control region of the anti-CD19
CAR cassette was the MND promoter, and CD4+ T-cells were transduced
with the bicistronic construct.
[0243] The transduced T cells were allowed to return to resting
state, and then were tested after stimulation as follows. For the
`no stimulation` set, transduced T-cells were incubated for 24h
alone in medium. For the `Raji co-culture` set CD19+ Raji B cells
were incubated with the transduced T cells for 24h. At 24h, the T
cells were stained for CD25 and CD69, which are activation markers,
and subject to flow cytometry to measure these markers and
luciferase expression in the T cells.
[0244] FIG. 3 shows that the transduced T-cells had an increase in
bioluminescence when cultured with Raji target cells (activate CAR)
as compared to bioluminescence of T-cells at resting for constructs
with RDE1 (Gold1), RDE2 (Gold2), or RDE3 (Gold3). The T-cells with
a NFAT promoter and the RDE1 showed a larger on-off response than
T-cells with a MinP promoter and the corresponding RDE. Under all
conditions, T-cells with an RDE controlling luciferase had lower
amounts of bioluminescence than T-cells with luciferase cassettes
that were not controlled by an RDE. Combined with the MinP
promoter, RDE1 gave a 4.1-fold increase in bioluminescence with CAR
stimulation, RDE2 gave a 1.8-fold increase in bioluminescence, and
RDE3 gave a 1.4-fold increase. Combined with the NFAT promoter,
RDE1 gave a 8.5-fold increase in bioluminescence with CAR
stimulation, RDE2 gave a 3.1-fold increase in bioluminescence, and
RDE3 gave a 1.3-fold increase. With either promoter, the RDE3
construct gave the highest amount of bioluminescence, the RDE1
construct gave the lowest amount of bioluminescence, and the RDE2
construct gave an amount of bioluminescence between RDE3 and
RDE1.
Example 9: An RDE Construct for Expressing IL-12
[0245] Constructs were made using an anti-CD19 CAR cassette as
described in WO 2012/079000, which is hereby
incorporated-by-reference in its entirety for all purposes), and an
IL-12-RDE1 (3'-UTR of IFNg) insert or an IL-12 3'-UTR (a 3'-UTR
that does not confer differential transgene translation in response
to metabolic state of the cell). The anti-CD19 CAR cassette and the
insert with the IL-12-RDE1 are transcribed in opposite directions,
and the control regions for each are located in between the two
insert/cassettes. The control region for the IL-12-RDE1 insert and
IL-12 3'-UTR were either a minP promoter or an NFAT promoter. The
control region of the anti-CD19 CAR cassette was the MND promoter.
CD4+ T-cells were transduced with the bicistronic construct.
[0246] The transduced T cells were allowed to return to resting
state, and then were tested after stimulation as follows. For the
`no stimulation` set, transduced T-cells were incubated for 24h
alone in medium. For the `Raji co-culture` set, CD19+ Raji B cells
were incubated with the transduced T cells for 24h. At 24h, the T
cells were stained for CD25 and CD69, which are activation markers,
and subject to flow cytometry to measure these markers. IL-12
expression in the T cells was measured by ELISA.
[0247] FIG. 4 shows that the transduced T-cells had an increase in
IL-12 expression when cultured with Raji target cells (activate
CAR) as compared to IL-12 expression of T-cells at resting using
constructs controlled by the MinP promoter or NFAT promoter.
T-cells with the NFAT promoter and RDE1 (Gold1) showed a 168-fold
change in IL-12 expression form resting to CAR stimulation. T-cells
with the NFAT promoter and a 3'-UTR (not responsive to CAR
stimulation, 3'-UTR) showed a 50-fold change in expression, and a
minP promoter with RDE1 (Gold1) showed a 6.3 fold change in
expression.
Example 10: AU Elements and Steady State Expression
[0248] Constructs were made with different RDEs operably linked to
a nucleic acid encoding luciferase. The different RDEs used were AU
4 (CTLA4), AU 13 (IL-5), AU 14 (IL-6), AU 15 (IL-9), AU 16 (IL-10),
AU 17 (IL-13), and AU 101 (IFNg). These luciferase-AU constructs
were transduced into primary T-cells. After the cells returned to
the resting stage they were plated and sham induced (basal) or
induced with anti-CD3 and anti-CD28 antibody (activated). At 24
hours post activation the amount of luciferase units in each was
measured. These amounts are plotted in the bar graph of FIG. 5.
[0249] The AU elements in this example had different basal
expression levels, different induced expression levels (at 24
hours), and different levels of fold induction. The AU constructs
showed different amounts of basal expression, different amounts of
induced expression and different amounts of fold induction (or
dynamic range).
Example 11: AU Elements and Expression Parameters
[0250] Constructs were made with different RDEs operably linked to
a nucleic acid encoding luciferase. The different RDEs used were AU
2 (CSF2), AU 3 (CD247), AU 5 (EDN1), AU 7 (SLC2A1), AU 10 (Myc), AU
19 (TMEM-219), AU 20 (TMEM-219snp), AU 21 (CCR7), AU 22 (SEM-A4D),
AU 23 (CDC42-SE2), and AU 101 (IFNg). These luciferase-AU
constructs were transduced into primary T-cells. After the cells
returned to the resting stage they were plated and either not
treated (basal) or activated with anti-CD3 and anti-CD28 antibody
(activated). At 24 hours post activation the amount of luciferase
units in each was measured. These amounts are plotted in the bar
graph of FIG. 6. Alternatively, after the cells returned to resting
stage they were plated into 96-well plates in quadruplicate for
measuring at each time point: 1 day, 3 days, 6 days and 8 days. The
cells were either not treated or activated with anti-CD3 and
anti-CD28 antibody, and luciferase activity was measured at 1 day,
3 days, 6 days and 8 days. These results are plotted in the bar
graph of FIG. 7, and shown in Table 1 below. FIG. 8 shows selected
data plotted in a bar graph. The numbers in parentheses in Table 1
below are the Luciferase Units on Days 3, 6, and 8 divided by the
Luciferase Units of Day 1.
TABLE-US-00005 TABLE 1 Luciferase Units AU Construct Day 1 Day 3
Day 6 Day 8 AU 2 (CSF2) 60051 306035 (5) 578305 (10) 591953 (10) AU
101 (IFNg) 85816 473395 (6) 724129 (8) 817447 (10) AU 5 (EDN1)
69391 613921 (9) 838040 (12) 1023000 (15) AU 3 (CD247) 44939 595753
(13) 961839 (21) 1116000 (25) AU 20 (TMEM-219snp) 1135000 10750000
(9) 21020000 (19) 25480000 (22) AU 10 (Myc) 1233000 16020000 (13)
26780000 (22) 27800000 (23) AU 7 (SLC2A1) 4914 80906 (16) 132974
(27) 136537 (28) AU 21 (CCR7) 27128 465140 (17) 604016 (22) 692715
(26) AU 23 (CDC42-SE2) 71105 1215000 (17) 2012000 (28) 2110000 (30)
AU 22 (SEM-A4D) 226815 2829000 (12) 6106000 (27) 7396000 (33) AU 19
(TMEM-219) 833146 11260000 (14) 22560000 (27) 27500000 (33)
[0251] The AU elements in FIG. 6, FIG. 7 and Table 1 had different
basal expression levels, different induced expression levels (at 24
hours), and different levels of fold induction. The basal
expression levels differed over an about 2000 fold range for these
AU elements (AU 7 to AU 20), and the induced expression levels
differed over an about 5500 fold range (AU 7 to AU 10). Basal
expression for the constructs ranged from 1390 for AU 7 (SLC2A1) to
2,927,000 for AU 20 (TMEM-219snp). Activated expression ranged from
4914 for AU 7 (day 1) to 27,800,0000 for AU 10 (day 8). FIG. 8 and
Table 1 show that some AU elements had lower levels of output, for
example, AU 101 (IFNg), AU 2 (CSF2), AU 5 (EDN1), AU 7 (SLC2A1), AU
21 (CCR7), and AU 23 (CDC42-SE2). Some AU elements had intermediate
amounts of output: AU 19 (TMEM-219) and AU 22 (SEM-A4D). And some
AU element had high output: AU 20 (TMEM-219snp) and AU 10
(Myc).
[0252] The Luciferase data was also analyzed for dynamic range
(fold induction or luciferase activated/luciferase basal) of each
luciferase-AU construct. The dynamic range (fold induction) for
each AU construct at Days 1, 3/4 (activated expression was measured
on Day 3 and basal expression was measured on Day 4), 6 and 8. This
data is shown below in Table 2, and plotted in bar graphs in FIG. 9
and FIG. 10.
TABLE-US-00006 TABLE 2 Fold Induction AU Construct Day 1 Day 3/4*
Day 6 Day 8 AU 2 9.3 9.3 8.1 5.8 AU 101 16.9 14.6 12.3 10.5 AU 5
5.7 11.9 10.1 9.4 AU 21 5.6 27.3 28.6 29.6 AU 3 1.8 6.7 8.1 6.8 AU
20 3.1 7.3 9.3 8.7 AU 10 3.7 13.2 14.1 10.2 AU 7 3.5 12.3 13.1 10.6
AU 23 2.6 12.8 15.1 12.2 AU 19 2.3 9.3 12.9 13.8 AU 22 1.2 4.6 6.9
7.1 *Induction was measured on Day 3 and basal was measured on Day
4.
[0253] At Day 1 dynamic range (fold induction=activated/basal)
ranged from about 1 (AU 22) to about 17 (AU 101). At Day 3/4,
dynamic range varied from about 4.5 (AU 22) to about 27 (AU21). At
Day 6, dynamic range varies from about 7 (AU 22) to about 29 (AU
21). On Day 8, dynamic range varied from about 7 (AU22) to about 30
(AU 21). The AU constructs showed a number of related patterns. AU
2 and AU 101 showed a rapid increase in dynamic range on Day 1, and
then the dynamic range decreased on days 6 and 8. AU 5 and AU 21
show increasing dynamic range from day 0 to day 3/4, and then the
dynamic range is maintained through days 6 and 8. AU 3, AU 20, AU
10, AU 7 and AU 23 showed rising dynamic range from day 0 to day 6,
and then the dynamic range decreased on day 8. AU 19, and AU 22,
showed rising dynamic ranges from day 0 to day 8.
[0254] AU 21 and AU 23 showed accelerating dynamic range and these
AU constructs also had low basal expression (day 1=4865 and 27363,
respectively). AU 2 and AU 101 showed decreasing dynamic range from
24 hours to 72 hours and these AU elements also had low basal
expression. AU 5 and AU 20 also showed decreasing dynamic range
from day 1 to day 3/4 (though more expression than AU 2 and AU 101)
and AU 5 had low basal expression whereas AU 20 had high basal
expression. AU 10, AU 19 and AU 22 showed consistent dynamic range
from day 1 to day 3/4 and had high basal levels of expression. AU 3
and AU 7 also had consistent dynamic range from day 1 to day 3/4
and had low basal expression levels.
[0255] The above data shows that different AU elements have
different temporal effects on expression from days 1-8. Some AU
elements show accelerating dynamic range over different portions of
the time range. The AU elements show different amounts of total
expression (C.sub.max) and different times to maximum expression
(T.sub.max). The AU elements also show different maximum dynamic
ranges and time to reach these maximums. These differing kinetics
of expression can be used to provide customized basal, C.sub.max,
T.sub.max, dynamic range, and time to max dynamic range for a
desired transgene. These differing kinetics can also be used to
provide temporally distinct expression for two transgenes in a cell
after activation of the cell.
Example 12: AU Element Control with Glucose and Galactose
[0256] Constructs were made with different RDEs operably linked to
a nucleic acid encoding luciferase. The RDE was an AU element
responsive to glycolytic state of the cell. The AU
element--luciferase constructs were transduced into T-cells. After
the cells reached the resting state, they were split into wells and
fed media including either glucose or galactose. Luciferase
activity was measured on days 3 and 5. These results are shown in
the bar graph of FIG. 11. The results show that glucose increased
expression of luciferase compared to galactose and the amount of
expression increased from days 3 to 5. On day 3 the glucose treated
cells had 15.times. more expression of luciferase than the
galactose treated cells and on day 5 this had grown to 27.times.
more expression.
Example 13: Delivery and Design of a Viral Payload
[0257] A Smart Car is made using the third generation anti-CD19 CAR
cassette described in WO 2012/079000, which is hereby
incorporated-by-reference in its entirety for all purposes), and
the RNA control device, 3XL2bulge9 (Win and Smolke 2007 Proc. Natl
Acad. Sci. 104 (36): 14283-88, which is hereby incorporated by
reference in its entirety for all purposes). A nucleic acid
encoding the 3XL2bulge9 control device is engineered into the
anti-CD19 CAR cassette in an appropriate expression vector. The
anti-CD19 Smart CAR and anti-CD19 CAR constructs are transfected by
routine methods into different populations of T-cells (Jurkat cells
and/or primary human T-cells), and stable populations of T-cells
are selected using appropriate antibiotics (or other selection
schemes). T-cell populations with anti-CD19 Smart CARs
(CD19.sup.-/CD22.sup.-/CD3.sup.+) and T-cell populations with
anti-CD19 CARs (CD19.sup.-/CD22.sup.-/CD3.sup.+) are activated by
co-incubation with anti-CD3/CD28 beads.
[0258] Third generation Lentiviral packaging, envelope, and
transfer plasmids are obtained from addgene. The Rev encoding
packaging plasmid is engineered to include the AU101 (INFg) RDE in
the 3'-UTR of Rev. The modified Rev packaging plasmid, the Gag Pol
packaging plasmid, and the envelope plasmid are transfected into
anti-CD19 T-lymphocyte cells. A transfer plasmid is engineered to
include GFP as the transgene in the transfer plasmid. This transfer
plasmid is also transfected into the anti-CD19 CAR T-lymphocyte
cells.
[0259] Anti-CD19 Smart CAR T-lymphocytes are co-cultured with
CD19.sup.+/CD22.sup.+/CD3-Ramos target cells at Smart CAR
T-lymphocyte:Raji target ratios of 2:1, 5:1, and 10:1. Ligand for
the RNA control device, theophylline is added to the culture medium
at concentrations in the range of 2 .mu.M to 2 mM (2 .mu.M, 10
.mu.M, 20 .mu.M, 100 .mu.M, 200 .mu.M, 1 mM, and 2 mM). The
Smart-CAR T-cells and the Raji cells are grown together for 48
hours.
[0260] At the end of the incubation period, the culture media is
separated from the T-lymphocytes and Raji cells. Viral titer in the
supernatant is measured using an ELISA with anti-lentivirus
antibody reagents. Infectivity and payload delivery by the viruses
is tested by infecting HEK 293 cells with the virus, and after a
suitable incubation time measuring GFP fluorescence from the
transduced HEK 293 cells.
Example 14: Payload Delivery Using Gold in a Mouse Lymphoma
Model
[0261] Constructs were made using an anti-CD19 CAR cassette as
described in WO 2012/079000, which is hereby
incorporated-by-reference in its entirety for all purposes, and a
Luciferase-AU (3' UTR of IL-6) insert. These constructs were placed
in a bicistronic lenti virus construct. The anti-CD19 CAR cassette
and the insert with the luciferase-RDE are transcribed in opposite
directions on the bicistronic vector, and the control regions for
each are located in between the two insert/cassettes. The control
region for the Luciferase-RDE insert was a MinP promoter. The
control region of the anti-CD19 CAR cassette was the MND promoter.
CD4+ T-cells were transduced with the bicistronic construct.
[0262] A second construct was made using the anti-CD19 CAR cassette
described above and a Luciferase insert (without the RDE element so
that expression was constitutive). Both constructs were separately
transduced into different groups of T-cells.
[0263] The transduced T cells were allowed to return to resting
state, and then were tested after stimulation as follows. For the
`no stimulation` set, transduced T-cells were incubated for 24h
alone in medium. For the `Raji co-culture` set CD19+ Raji B cells
were incubated with the transduced T cells for 24h. At 24h, the T
cells were stained for CD25 and CD69, which are activation markers,
and subject to flow cytometry to measure these markers and
luciferase expression in the T cells. These in vitro results showed
that the anti-CD19 CAR T-cells made luciferase after activation of
the T-cells through the CAR.
[0264] These anti-CD19 CAR T-cells with the luciferase-RDE were
also tested in a mouse model for lymphoma. CD19+ Raji cells were
implanted in the flanks of NSG mice. After tumor formation, the
anti-CD19 CAR T-cells were injected into the mice and the mice were
scanned for luminescence. Imaging of the mice showed luminescence
at the tumor sites from anti-CD19 CAR T-cells that have been
activated by the CD19 positive tumor. The amount of luminescence
increased over time as more T-cells were activated. In contrast,
the anti-CD19 CAR T-cells with constitutive expression of
luciferase should luminescence throughout the mice as well as at
the site of the tumors in the flanks of the mice.
Example 15: Payload Delivery to .alpha.v.beta.6 Positive Solid
Tumor
[0265] A nucleic acid encoding a knottin as described in Silverman
et al., J. Mol. Biol. 385:1064-75 (2009) and Kimura et al, Proteins
77:359-69 (2009), which are incorporated by reference in their
entirety for all purposes is operably linked to a nucleic acid
encoding the CAR components
aCD43z,CD8Hinge,CD8transmembrane,41BB(CD28 or other costim),and
CD3z to make a nucleic acid encoding an anti-.alpha.v.beta.6
CAR.
[0266] The nucleic acid encoding the anti-.alpha.v.beta.6 CAR is
transfected by routine methods into T-cells (Jurkat cells and/or
primary human T-cells), and stable populations of T-cells are
selected using appropriate antibiotics (or other selection
schemes). T-cell populations with anti-.alpha.v.beta.6 CARs are
activated by co-incubation with anti-CD3/CD28 beads. These cells
are also engineered with an expression cassette encoding IL-12
operably linked to the Gold element from INFg or AU 21 (CCR7) is
placed under the control of the promoter Min P.
[0267] The anti-.alpha.v.beta.6 CAR T-cells are incubated in wells
with .alpha.v.beta.6 tumor cells. After incubation, the wells are
tested for secretion of IL-12 from the anti-.alpha.v.beta.6 CAR
T-cells. anti-.alpha.v.beta.6 CAR T-cells secrete IL-12 when
incubated with .alpha.v.beta.6 tumor cells, and the controls show
low or no secretion when the CAR T-cell is not stimulated.
Example 16: An Anti-Onco CD 43 CAR for AML
[0268] A single chain antibody for onco-sialylated CD 43 was made
using an anti-onco-sialylated CD 43 antibody. The nucleic acid
encoding this single-chain antibody was combined with a nucleic
acid encoding the CAR components
aCD43z,CD8Hinge,CD8transmembrane,41BB(CD28 or other costim),and
CD3z to make a nucleic acid encoding an anti-onco-sialylated CD 43
CAR.
[0269] The nucleic acid encoding the anti-onco-sialylated CD 43 CAR
is transfected by routine methods into T-cells (Jurkat cells and/or
primary human T-cells), and stable populations of T-cells are
selected using appropriate antibiotics (or other selection
schemes). T-cell populations with anti-onco-sialylated CD 43 CARs
are activated by co-incubation with anti-CD3/CD28 beads.
Example 17: Payload Delivery to CD 43 Positive AML
[0270] An expression cassette encoding IL-12 operably linked to the
Gold element from INFg or AU 21 (CCR7) is placed under the control
of the promoter Min P, and engineered into the anti-onco-sialylated
CD 43 CAR T-cell.
[0271] The anti-onco-sialylated CD 43 CAR T-cells are incubated in
wells with AML cells. After incubation, the wells are tested for
secretion of IL-12 from the anti-onco-sialylated CD 43 CAR T-cells.
Anti-onco-sialylated CD 43 CAR T-cells secrete IL-12 when incubated
with AML cells, and the controls show low or no secretion when the
CAR T-cell is not stimulated.
Example 18: miRNA as a Payload
[0272] A payload transgene encoding IL-12 is engineered to have an
artificial intron encoding a mir155 cassette as disclosed in Du et
al., FEBs Journal 273:5421-5427 (2006) or Chung et al., Nucl Acids
Res 34:e53 (2006). The mir155 cassette is engineered to include an
AU element such as, for example, AU101 (IFNg) or AU14 (IL-6),
operably linked to it, and the transgene is also engineered with an
AU element such as AU101 or AU14. This transgene with the mir155
intron is engineered into primary T-cells. An anti-CD19 CAR as
described in Example 14 is also engineered into the primary
T-cells.
[0273] The anti-CD19 CAR T cells with the IL-12 payload are allowed
to return to resting state, and then are tested after stimulation
as follows. For the `no stimulation` set, transduced T-cells are
incubated for 24h alone in medium. For the `Raji co-culture` set
CD19+ Raji B cells are incubated with the transduced T cells for
24h. At 24h, the T cells are stained for CD25 and CD69, which are
activation markers, and subject to flow cytometry to measure these
markers. The cells are also tested for expression of the payload
IL-12.
[0274] These anti-CD19 CAR T-cells with the IL-12 payload are also
tested in a mouse model for lymphoma. CD19+ Raji cells are
implanted in the flanks of NSG mice. After tumor formation, the
anti-CD19 CAR T-cells with the IL-12 payload are injected into the
mice. At every third day starting at day 4 after administration,
tumor killing in the mice is measured using calipers.
Example 19: IL-12 Payload Delivery
[0275] A construct with an anti-CD19 CAR as described in Example 14
was made. A construct with the NFAT promoter operably linked to a
nucleic acid encoding IL-12 followed by AU101 (the RDE from INFg)
was also made. The IL-12 transcript made from the construct
operably links the coding sequence for IL-12 to the AU101 RDE. A
second IL-12 construct was made that provided constitutive
expression of IL-12. A third construct placed Luciferase under
control of an AU14 (IL-6).
[0276] The constructs were transduced into primary T-cells which
were then allowed to return to a resting state. This produced
anti-CD19 CAR T-cells with payloads of IL-12 (RDE controlled or
constitutive) or luciferase.
[0277] The primary T-cells with the anti-CD19 CAR and IL-12 payload
(RDE controlled or constitutive) or luciferase payload were
administered to mice bearing CD19+ tumors in their flanks. Killing
of tumor cells was monitored over 42 days. The mice which received
T-cells with the anti-CD19 CAR and luciferase payload showed a
moderate amount of tumor cell killing (about 3 logs). The mice
receiving the IL-12 payloads had a large amount of tumor cell
killing (6-7 logs). A comparison of IL-12 serum levels in the mice
receiving the constitutive or AU101 controlled IL-12 had 10-fold
differences in the systemic IL-12 levels with the AU101 controlled
payload having 10 times lower amounts of IL-12 than the
constitutive IL-12 payload.
[0278] The RDE control of IL-12 expression lowered systemic IL-12
levels in the mice but gave localized concentrations of IL-12 that
improved tumor cell killing. After the activated CAR T-cells kill
the tumor cells these CAR T-cells can migrate from the tumor site
to lymph nodes and/or the spleen where they can educate other
T-cells and form memory T-cells.
Example 20: Payload Delivery to DLL3+ Cancer Cells
[0279] CAR constructs are made using an anti-DLL3 antibody domain
such as described in US20170137533 (which is incorporated by
reference in its entirety for all purposes) as SC16.15. This
anti-DLL3 antibody domain is made into a single chain antibody
(scFv), and the anti-DLL3 scFv is combined with the transmembrane
and intracellular portions of a CAR (such as those described in WO
2012/079000, which is hereby incorporated-by-reference in its
entirety for all purposes) to make an anti-DLL3 CAR.
[0280] Payload constructs are made by engineering a transgene with
an RDE so that when the transgene is transcribed the transcript for
the transgene operably links the transgene to the RDE. The payload
transgene can encode an anti-4-1BB antibody, an anti-CD11b
antibody, an anti-CTLA4 antibody, an anti-IL1b antibody, a BiTE, a
CCL2, an anti-CXCR4 antibody, an anti-CXCL12 antibody, a HAC, a
heparinase, a hyaluronidase, a Hsp60, a Hsp70, an IL-2, an IL-12,
an IL-15, an IL-18, an INF.gamma., a miRNA (e.g., mir155), a CD40
ligand, an ApoE3, an ApoE4, an antagonists of CSF1 receptor, a
TNF.alpha., and/or an anti-CD28 antibody. The RDE can be AU101
(INFg) or AU14 (IL-6).
[0281] The constructs are transduced into primary T-cells which are
then allowed to return to a resting state. This produced anti-DLL3
CAR T-cells with one or more of the payloads: anti-CXCL12 antibody,
anti-CXCR4 antibody, IL-12, anti-4-1BB antibody, anti-CD11b
antibody, anti-CTLA4 antibody, anti-IL1b antibody, a BiTE, CCL2,
HAC, heparinase, hyaluronidase, Hsp60, Hsp70, IL-2, IL-15, IL-18,
INF.gamma., miRNA (e.g., mir155), CD40 ligand, ApoE3, ApoE4,
TNF.alpha., CCR2, CCR4/CXCL12, CXCR3+CXCL9, CXCL9, ACLY,
antagonists of CSF1 receptor, miRNA for Tox (e.g., hsa-mir-26b-5p
(MIRT030248) hsa-mir-223-3p (MIRT054680)), miRNA for TCF-7 (e.g.,
mIR-192, mIR-34a, miR-133a, miR-138-5p, miR-342-5p, miR-491-5p,
miR-541-3p), and/or anti-CD28 antibody (including full length and
fragments such as single chain antibodies).
[0282] An NSG mouse model from Jackson Laboratories is used to
establish cancer xenografts of human melanoma, human small cell
lung cancer (SCLC), and human IDH1mut glioma. After the cancer
xenograft is established in the mice, the mice are treated with the
primary T-cells with the anti-DLL3 CAR and one of the payloads.
Cancer xenograft killing is then compared between the different
payloads of the DLL3-CAR T-cells.
Example 21: B Toxin Fusion Payload Delivery to Target Cell
[0283] CAR T-cells are made as described in Example 19, except that
the IL-12 payload is replaced with a modified B Toxin fusion as
described below.
[0284] The B Toxin fusion is made using tetanus toxin as described
in Toivonen et al., Toxins 2:2622-44 (2010) and fusing the B domain
of tetanus toxin to the payload encoding luciferase from Gaussia
princeps (a secreted luciferase). This B Toxin payload is modified
to provide for targeting to the CD19 antigen by replacing the
tetanus B domain receptor binding portion with the anti-CD19 CAR
portion which binds to CD19 (e.g., an anti-CD19 scFv). This can be
done as described in Kelley et al., Proc. Natl Acad. Sci.
85:3980-84 (1988) for the B domain of diphtheria toxin.
[0285] The primary T-cells with the anti-CD19 CAR and modified B
Toxin payload (RDE controlled or constitutive) are administered to
mice bearing CD19+ tumors in their flanks. Killing of tumor cells
and adverse responses are monitored in the treated mice. The mice
treated with the CAR T-cells with RDE controlled, modified B Toxin
payload show increased tumor cell killing.
Example 22: hnRNPLL Control of Payload Expression
[0286] A nucleic acid encoding GFP is engineered to have extra
introns and an extra exon at the 3'end of the coding region. The
nucleic acids encoding GFP are followed by intron 1 from
betaglobin, exon 4 of CD45 (has hnRNPLL binding sites) and another
intron of betaglobin (engineered to have hnRNPLL CA repeat binding
sites). This engineered GFP encoding nucleic acid is operably
linked to a constitutive promoter.
[0287] The expression cassette with the nucleic acid encoding this
engineered GFP is transduced into primary T-cells which are then
allowed to express the GFP in a quiescent state. This should
produce a GFP protein with the amino acids of exon 4 of CD45 on
carboxyl terminal end. This fusion polypeptide should have reduced
GFP activity. The primary T-cells with the expression cassette for
GFP are then activated with anti-CD3/CD28 beads. These activated
cells should produce hnRNPLL which should lead to exclusion of exon
4 of CD45 from the GFP transcript which now encodes active GFP.
Translation of this transcript produces active GFP that can be
detected.
Example 23: Coordinated Delivery of CXCL9 and an Anti-PD1 Therapy
to DLL3+ Cancer Cells
[0288] An anti-DLL3 CAR is made as described in Example 20. This
CAR construct is engineered into T-cells also as described in
Example 20.
[0289] Two payload cassettes are made for delivery by the anti-DLL3
CAR T-cell. First, a construct is made that encodes CXCL9 as a
secreted payload operably linked to an RDE with an early expression
profile (early maximal expression after activation of the cell)
such as AU2 (CSF-2, maximal fold induction on day 1), AU101 (IFNg,
maximal fold induction on day 1), or AU5 (EDN1, maximal fold
induction on day 3/4). Second, a construct is made that encodes an
anti-PD1 antibody (e.g., Pembrolizumab (Keytruda.RTM.)) as a
secreted payload operably linked to an RDE with a late expression
profile (late maximal expression after activation of the cell) such
as AU22 (SEM-A4D, maximal fold induction on day 8) or AU19
(TMEM-219, maximal fold induction on day 8). The two payloads can
be placed into a bicistronic construct, placed on the same
construct, or the payloads can be expressed from separate
constructs. The payload construct(s) are engineered into the
anti-DLL3 CAR T-cell as described above in Example 20.
[0290] When this engineered CAR T-cell is administered to NSG mouse
model as described in Example 20. The CAR T-cells are activated by
DLL3 at the tumor target, and the RDE constructs with the CXCL9
express this payload first, and then at a later time the anti-PD1
antibody payload is expressed. The AU2, AU5 or AU101 RDE of the
CXCL9 construct has an early maximal expression of about 1 day
after activation of the cell by DLL3 at a cancer target. The CXCL9
can be secreted early after activation of the T-cell by DLL3 and
the CXCL9 can potentiate the T-cell responses to tumors treated
with anti-PD1 antibodies. After CXCL9 secretion, anti-PD1 is
maximally secreted at a later time (about 8 days) and the effect of
this antibody can be increased by the pretreatment with CXCL9.
[0291] The early expression of CXCL9 potentiates the activity and
cancer killing from the anti-PD1 antibody.
Example 24: Combination Therapy
[0292] CAR constructs are made using an anti-DLL3 antibody domain
such as described in US20170137533 (which is incorporated by
reference in its entirety for all purposes) as SC16.15 or SC16.25.
This anti-DLL3 antibody domain is made into a single chain antibody
(scFv), and the anti-DLL3 scFv is combined with the transmembrane
and intracellular portions of a CAR (such as those described in WO
2012/079000, which is hereby incorporated-by-reference in its
entirety for all purposes) to make an anti-DLL3 CAR.
[0293] Payload constructs are made by engineering a transgene with
an RDE so that when the transgene is transcribed the transcript for
the transgene operably links the transgene to the RDE. The payload
transgene can encode an anti-4-1BB antibody, an anti-CD11b
antibody, an anti-CTLA4 antibody, an anti-IL1b antibody, a BiTE, a
CCL2, an anti-CXCR4 antibody, an anti-CXCL12 antibody, a HAC, a
heparinase, a hyaluronidase, a Hsp60, a Hsp70, an IL-2, an IL-12,
an IL-15, an IL-18, an INF.gamma., a miRNA (e.g., mir155), a CD40
ligand, an ApoE3, an ApoE4, an antagonists of CSF1 receptor, a
TNF.alpha., and/or an anti-CD28 antibody. The RDE can be AU101
(INFg) or AU14 (IL-6).
[0294] The constructs are transduced into primary T-cells which are
then allowed to return to a resting state. This produced anti-DLL3
CAR T-cells with one or more of the payloads: anti-CXCL12 antibody,
anti-CXCR4 antibody, IL-12, anti-4-1BB antibody, anti-CD11b
antibody, anti-CTLA4 antibody, anti-IL1b antibody, a BiTE, CCL2,
HAC, heparinase, hyaluronidase, Hsp60, Hsp70, IL-2, IL-15, IL-18,
INF.gamma., miRNA (e.g., mir155), CD40 ligand, ApoE3, ApoE4,
TNF.alpha., CCR2, CCR4/CXCL12, CXCR3+CXCL9, CXCL9, ACLY,
antagonists of CSF1 receptor, miRNA for Tox (e.g., hsa-mir-26b-5p
(MIRT030248) hsa-mir-223-3p (MIRT054680)), miRNA for TCF-7 (e.g.,
mIR-192, mIR-34a, miR-133a, miR-138-5p, miR-342-5p, miR-491-5p,
miR-541-3p), and/or anti-CD28 antibody (including full length and
fragments such as single chain antibodies).
[0295] An antibody drug conjugate (ADC) is made between an
anti-DLL3 antibody such as described in US20170137533 (which is
incorporated by reference in its entirety for all purposes) as
SC16.15 or SC16.25. This anti-DLL3 antibody domain is converted to
an appropriate format (e.g., a Fab, F(ab')2 or full-length IgG) and
conjugated to one or more drugs (e.g., etoposide, irinotecan,
cisplatin and/or carboplatin).
[0296] An NSG mouse model from Jackson Laboratories is used to
establish cancer xenografts of human melanoma, human small cell
lung cancer (SCLC), and human IDH1mut glioma. After the cancer
xenograft is established in the mice, the mice are treated with the
primary T-cells with the anti-DLL3 CAR and one of the payloads,
anti-DLL3 ADC, or primary T-cells with the anti-DLL3 CAR and one of
the payloads and the anti-DLL3 ADC. Cancer xenograft killing is
then compared between the ADC, different payloads of the DLL3-CAR
T-cells, and the different payloads of the DLL3 CAR T-cells with
the anti-DLL3 ADC.
[0297] All publications, patents and patent applications discussed
and cited herein are incorporated herein by reference in their
entireties. It is understood that the disclosed invention is not
limited to the particular methodology, protocols and materials
described as these can vary. It is also understood that the
terminology used herein is for the purposes of describing
particular embodiments only and is not intended to limit the scope
of the present invention which will be limited only by the appended
claims.
[0298] Those skilled in the art will recognize, or be able to
ascertain using no more than routine experimentation, many
equivalents to the specific embodiments of the invention described
herein. Such equivalents are intended to be encompassed by the
following claims.
Sequence CWU 1
1
2515RNAArtificial SequenceAU repeat element 1auuua
5213RNAArtificial SequenceAU rich element 2auuuauuuau uua
1335RNAArtificial SequenceGU rich repeat element 3uuguu
547RNAArtificial SequenceGU rich repeat element 4uggggau
755RNAArtificial SequenceU rich repeat element 5guuug
567RNAArtificial SequenceGU rich element 6uuuguuu 779RNAArtificial
SequenceU rich elementmisc_feature(1)..(2)n is a, c, g, or
umisc_feature(5)..(6)n is a, c, g, or u 7nnuunnuuu 987RNAArtificial
SequenceU rich element 8uuuauuu 797RNAArtificial SequenceU rich
element 9uuuuuuu 7105RNAArtificial SequenceRDE element 10uuaga
5115RNAArtificial SequenceRDE element 11aguuu 5129RNAArtificial
SequenceRDE element 12uuauuuauu 9134RNAArtificial SequenceRDE
element 13uuga 4147RNAArtificial SequenceRDE element 14uggggau
7159RNAArtificial SequenceRDE element 15cugcugcug 9165RNAArtificial
SequenceRDE element 16auuga 51718PRTThoseaasigna virus 2A 17Glu Gly
Arg Gly Ser Leu Leu Thr Cys Gly Asp Val Glu Glu Asn Pro1 5 10 15Gly
Pro1819PRTPorcine teschovirus-1 18Ala Thr Asn Phe Ser Leu Leu Lys
Gln Ala Gly Asp Val Glu Glu Asn1 5 10 15Pro Gly Pro1920PRTEquine
rhinitis A virus 19Gln Cys Thr Asn Tyr Ala Leu Leu Lys Leu Ala Gly
Asp Val Glu Ser1 5 10 15Asn Pro Gly Pro 202022PRTfoot and mouth
disease virus 20Val Lys Gln Thr Leu Asn Phe Asp Leu Leu Lys Leu Ala
Gly Asp Val1 5 10 15Glu Ser Asn Pro Gly Pro 2021282DNAHomo sapiens
21taattaagtg cttcccactt aaaacatatc aggccttcta tttatttaaa tatttaaatt
60ttatatttat tgttgaatgt atggtttgct acctattgta actattattc ttaatcttaa
120aactataaat atggatcttt tatgattctt tttgtaagcc ctaggggctc
taaaatggtt 180tcacttattt atcccaaaat atttattatt atgttgaatg
ttaaatatag tatctatgta 240gattggttag taaaactatt taataaattt
gataaatata aa 28222282DNAHomo sapiens 22taattaagtg cttcccactt
aaaacatatc aggccttcta tttatttaaa tatttaaatt 60ttatatttat tgttgaatgt
atggtttgct acctattgta actattattc ttaatcttaa 120aactataaat
atggatcttt tatgattgaa tttgtaagcc ctaggggctc taaaatggtt
180tcacttattt atcccaaaat atttattatt atgttgaatg ttaaatatag
tatctatgta 240gattggttag taaaactatt taataaattt gataaatata aa
28223585DNAHomo sapiens 23tggttgtcct gcctgcaata tttgaatttt
aaatctaaat ctatttatta atatttaaca 60ttatttatat ggggaatata tttttagact
catcaatcaa ataagtattt ataatagcaa 120cttttgtgta atgaaaatga
atatctatta atatatgtat tatttataat tcctatatcc 180tgtgactgtc
tcacttaatc ctttgttttc tgactaatta ggcaaggcta tgtgattaca
240aggctttatc tcaggggcca actaggcagc caacctaagc aagatcccat
gggttgtgtg 300tttatttcac ttgatgatac aatgaacact tataagtgaa
gtgatactat ccagttactg 360ccggtttgaa aatatgcctg caatctgagc
cagtgcttta atggcatgtc agacagaact 420tgaatgtgtc aggtgaccct
gatgaaaaca tagcatctca ggagatttca tgcctggtgc 480ttccaaatat
tgttgacaac tgtgactgta cccaaatgga aagtaactca tttgttaaaa
540ttatcaatat ctaatatata tgaataaagt gtaagttcac aacta
5852432DNAArtificial SequenceMinP promoter 24tagagggtat ataatggaag
ctcgacttcc ag 3225131DNAArtificial SequenceNFAT promoter
25ggaggaaaaa ctgtttcata cagaaggcgt ggaggaaaaa ctgtttcata cagaaggcgt
60ggaggaaaaa ctgtttcata cagaaggcgt agatctagac tctagagggt atataatgga
120agctcgaatt c 131
* * * * *