U.S. patent application number 17/478133 was filed with the patent office on 2022-08-04 for anticancer combinations.
The applicant listed for this patent is City of Hope. Invention is credited to Don J. Diamond, Edwin Manuel.
Application Number | 20220241432 17/478133 |
Document ID | / |
Family ID | 1000006276920 |
Filed Date | 2022-08-04 |
United States Patent
Application |
20220241432 |
Kind Code |
A1 |
Diamond; Don J. ; et
al. |
August 4, 2022 |
ANTICANCER COMBINATIONS
Abstract
Provided herein, inter alia, are compositions and kits
comprising a bacterial cell and a tumor penetrating agent. Also
provided are methods of treating cancer in a subject including the
step of administering to the subject an effective amount of a
bacterial cell and a tumor penetrating agent. Provided are methods
of stimulating an immune system in a subject. The methods include
administering to the subject an effective amount of a bacterial
cell and a tumor penetrating agent. Also provided are methods of
enhancing delivery of an anti-cancer agent to a tumor cell
including the step of contacting the tumor cell with a bacterial
cell, a tumor penetrating agent and an anti-cancer agent.
Inventors: |
Diamond; Don J.; (Glendora,
CA) ; Manuel; Edwin; (Pomona, CA) |
|
Applicant: |
Name |
City |
State |
Country |
Type |
City of Hope |
Duarte |
CA |
US |
|
|
Family ID: |
1000006276920 |
Appl. No.: |
17/478133 |
Filed: |
September 17, 2021 |
Related U.S. Patent Documents
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Application
Number |
Filing Date |
Patent Number |
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14978590 |
Dec 22, 2015 |
11141492 |
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17478133 |
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PCT/US2014/045086 |
Jul 1, 2014 |
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14978590 |
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61842749 |
Jul 3, 2013 |
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Current U.S.
Class: |
1/1 |
Current CPC
Class: |
C12N 2320/32 20130101;
C12Y 302/01035 20130101; C12N 15/1137 20130101; A61K 48/0025
20130101; A61K 45/06 20130101; A61P 35/00 20180101; A61K 31/337
20130101; Y02A 50/30 20180101; A61K 35/74 20130101; C12N 2320/31
20130101; C12N 2310/11 20130101; A61K 31/713 20130101; A61K 31/7068
20130101; A61K 38/47 20130101 |
International
Class: |
A61K 48/00 20060101
A61K048/00; C12N 15/113 20060101 C12N015/113; A61K 38/47 20060101
A61K038/47; A61K 45/06 20060101 A61K045/06; A61K 35/74 20060101
A61K035/74; A61P 35/00 20060101 A61P035/00; A61K 31/337 20060101
A61K031/337; A61K 31/7068 20060101 A61K031/7068; A61K 31/713
20060101 A61K031/713 |
Claims
1. A method of treating cancer in a subject comprising
administering to the subject a combined effective amount of a
bacterial cell and a tumor penetrating agent, wherein
administration treats the cancer in the subject.
2. The method of claim 1, wherein the combined effective amount is
a combined synergistic amount.
3. A method of stimulating an immune system in a subject comprising
administering to the subject a combined effective amount of a
bacterial cell and a tumor penetrating agent, wherein
administration of the bacterial cell and the tumor penetrating
agent stimulates the immune system of the subject.
4. The method of claim 3, wherein the immune response is an
anti-cancer immune response.
5. The method of claim 1, further comprising administering to the
subject an anti-cancer agent.
6. (canceled)
7. A method of enhancing delivery of an anti-cancer agent to a
tumor cell comprising contacting the tumor cell with a bacterial
cell, a tumor penetrating agent and an anti-cancer agent, wherein
contacting the tumor cell with the bacterial cell and cell
penetrating agent enhances delivery of the anti-cancer agent.
8. The method of claim 7, wherein the anti-cancer agent is selected
from the group consisting of a small molecule, a nucleic acid, a
polypeptide, and an antibody.
9. The method of claim 1, wherein the bacterial cell is a
Salmonella bacterial cell.
10. (canceled)
11. The method of claim 9, wherein the Salmonella bacterial cell is
selected from the group consisting of YS1646 (ATCC #202165), RE88,
LH430, SL7207, .chi.8429, .chi.8431 an .chi.8468.
12. The method of claim 1, wherein the bacterial cell comprises an
antisense nucleic acid.
13. (canceled)
14. The method of claim 12, wherein the antisense nucleic acid
targets an immunosuppressive target.
15. The method of claim 14, wherein the immunosuppressive target is
STAT3, IDO1, IDO2, Arginase 1, iNOS, CTLA-4, TGF-.beta., IL-10,
pGE2 or VEGF.
16. (canceled)
17. (canceled)
18. The method of claim 12, wherein the antisense nucleic acid is
selected from the group consisting of SEQ ID NO:3-31.
19. The method of claim 1, wherein the tumor penetrating agent is a
hyaluronidase polypeptide.
20. (canceled)
21. (canceled)
22. (canceled)
23. (canceled)
24. A composition comprising a Salmonella bacterial cell and a
hyaluronidase polypeptide.
25. (canceled)
26. The composition of claim 24, wherein the Salmonella bacterial
cell is selected from the group consisting of YS1646 (ATCC
#202165), RE88, LH430, SL7207, .chi.8429, .chi.8431 an
.chi.8468.
27. The composition of claim 24, wherein the bacterial cell
comprises an antisense nucleic acid.
28. (canceled)
29. The composition of claim 27, wherein the antisense nucleic acid
targets an immunosuppressive target selected from STATS, IDO1,
IDO2, Arginase 1, iNOS, CTLA-4, TGF-.beta., IL-10, PGE2 and
VEGF.
30. (canceled)
31. (canceled)
32. (canceled)
33. The composition of claim 27, wherein the antisense nucleic acid
is selected from the group consisting of SEQ ID NO:3-31.
34. (canceled)
35. (canceled)
36. (canceled)
37. The composition of claim 24, further comprising an anti-cancer
agent.
38. (canceled)
39. (canceled)
40. (canceled)
41. (canceled)
Description
CROSS-REFERENCE TO RELATED APPLICATION
[0001] This application is a continuation of U.S. patent
application Ser. No. 14/978,590, filed Dec. 22, 2015, which is a
continuation of International Application No. PCT/US2014/045086,
filed Jul. 1, 2014, which claims priority to U.S. Provisional
Application No. 61/842,749, filed Jul. 3, 2013, which is
incorporated by reference herein in its entirety.
BACKGROUND OF THE INVENTION
[0002] Advanced pancreatic ductal adenocarcinoma (PDAC) is often
inoperable, and is only transiently responsive to existing
therapies. Overexpression of indoleamine 2,3-dioxygenase (IDO) in
PDAC plays a major role in accelerating disease progression by
suppressing antitumor immunity. Current IDO inhibitors inadequately
reverse immunosuppression while systemic off target effects
contribute to their toxicity. Thus, there is a need to provide
additional cancer therapies that target the immunosuppressive
mechanisms associated with tumors and the tumor microenvironment.
Provided herein are solutions to these and other problems in the
art.
BRIEF SUMMARY OF THE INVENTION
[0003] Provided herein are compositions and kits comprising a
bacterial cell and a tumor penetrating agent. Also provided are
methods of treating cancer in a subject including the step of
administering to the subject an effective amount of a bacterial
cell and a tumor penetrating agent. Provided are methods of
stimulating an immune system in a subject. The methods include
administering to the subject an effective amount of a bacterial
cell and a tumor penetrating agent. Also provided are methods of
enhancing delivery of an anti-cancer agent to a tumor cell
including the step of contacting the tumor cell with a bacterial
cell, a tumor penetrating agent and an anti-cancer agent.
BRIEF DESCRIPTION OF THE DRAWINGS
[0004] FIG. 1 shows a series of images demonstrating the effects of
shIDO-ST, PEGPH20.TM., and the combination of shIDO-ST and
PEGPH20.TM. in orthotopic KPC-luc model mice. Mice were imaged
using an intravital imaging system (IVIS) at the indicated time
points after tumor implantation. Tumor reduction was observed with
the combined treatment of shIDO-ST and PEGPH20.TM..
[0005] FIGS. 2A and 2B show a series of images demonstrating the
effects of the combined treatment with shIDO-ST and PEGPH20.TM.
under different dosing regimes. Mice were imaged using an
intravital imaging system (IVIS) at the indicated time points after
tumor implantation. The combination of shIDO-ST (5M cfu) and
PEGPH2.TM. (45 .mu.g) resulted in controlled tumor growth and in 2
of the 3 mice complete elimination of the KPC-luc pancreatic
tumors. The combination of PEGPH20.TM. and the control bacteria,
shScr-ST also showed significant tumor growth control at early time
points, but all mice eventually succumbed to tumor progression.
[0006] FIG. 3 is a graph showing quantitation of the IVIS for FIGS.
2A and 2B. Photons emitted from mice imaged in FIG. 2 were
quantitated. Tumors from mice treated with shIDO-ST and PEGPH20.TM.
at a specific dose of each are controlled significantly better than
all other groups.
[0007] FIG. 4 shows a series of images demonstrating the effects of
shIDO-ST and PEGPH20.TM., shScr-ST and PEGPH20.TM., gemcitabine and
PEGPH20.TM. and the agents alone on KPC-luc tumors. Significant
tumor reduction was observed in mice treated with shIDO-ST and
PEGPH20.TM., while all other treatment regimens were associated
with rapid tumor progression.
[0008] FIG. 5 is a graph showing quantitation of the IVIS for FIG.
4. Photons emitted from mice imaged in FIG. 4 were quantitated.
Tumors from mice treated with shIDO-ST and PEGPH20.TM. are
controlled significantly better than all other groups, and were
alive at the conclusion of the experiment.
[0009] FIG. 6 is a graph showing treatment does not significantly
change the weight of the mice. Mice in FIG. 4 were weighed at each
imaging point. No reductions were observed in mouse weight for any
group.
[0010] FIG. 7 shows a series of images demonstrating the effects of
PEGPH20.TM. in combination with shArg-ST or a control shScr-ST in
orthotopic KPC-luc model mice. Mice were imaged using an intravital
imaging system (IVIS) at the indicated time points after tumor
implantation. Tumor reduction was observed with the combined
treatment of shArg-ST and PEGPH20.TM. and the combined treatment of
shScr-ST and PEGPH20.TM..
[0011] FIG. 8 shows a series of images demonstrating the effects of
the combined treatment with shArg-ST and PEGPH20.TM. under a
different dosing regime. Mice were imaged using an intravital
imaging system (IVIS) at the indicated time points after tumor
implantation. The combination of shIDO-ST and PEGPH20.TM. resulted
in control of tumor growth. The combination of PEGPH20.TM. and the
control bacteria, shScr-ST, again showed attenuation of tumor
growth.
[0012] FIG. 9 shows a series of images demonostrating the effects
of the combined treatment of shIDO-AT and PEGPH20.TM.. Mice were
imaged using an intravital imaging system (IVIS) at the indicated
time points after tumor implantation. The combination of shIDO-ST
and PEGPH20.TM. resulted in tumor regression and prolonged survival
of the mice.
[0013] FIG. 10 is a graph of the quantitation of tumor burden at
different time points post tumor implantation. Specifically, the
photons emitted from IVIS imaging of the mouse groups represented
in FIG. 9 were quantitated. The combination of shIDO-ST and
PEGPH20.TM. resulted in statistically significant control of tumors
while all other groups exhibited no durable control.
[0014] FIG. 11 is a graph showing the weight of the mouse groups
represented in FIG. 9 at each time point indicated in the graph.
FIG. 11 shows that elimination of PDAC tumors using shIDO-ST and
PEGPH20.TM. combination therapy did not result in weight loss.
[0015] FIG. 12 shows images of hyaluronan (HA) staining of tumor
bearing mice treated with PEGPH20.TM.. Forty-eight hours after
treatment with PEGPH20.TM., a significant depletion of hyaluronan
was observed.
[0016] FIG. 13 shows images of open vessels in tumors in mice
treated with PEGPH20.TM.. Sections from 14 day tumors of mice
untreated or treated with PEGPH20.TM. were stained with anti-CD31
antibody to locate cross sections of vessels within the tumor mass.
Many more open vessels were observed in tumors of mice treated with
PEGPH20.TM..
[0017] FIG. 14 shows images of the influx of Salmonella typhimurium
(ST) and neutrophils (PMN) into tumors treated with shIDO-ST and
PEGPH20.TM. combination therapy.
[0018] FIG. 15 shows images of surgically removed tumors analyzed
for PMN 96 hours after treatment with PEGPH20.TM./shScr-ST or
PEGPH20.TM./shIDO-ST.
[0019] FIG. 16 shows images showing necrosis of tumor cells in the
core of shIDO-ST/PEGPH20.TM. combination therapy treated
tumors.
[0020] FIG. 17 shows an image of spleen and pancreas taken from
normal BL/6 mice or KPC-Brca1 mice treated with
shIDO-ST/PEGPH20.TM. combination therapy at 12 weeks.
[0021] FIG. 18 shows a schematic of treatments of KPC-Brca1 mice to
determine if shIDO-ST/PEGPH20.TM. combination therapy has efficacy
in controlling spontaneous pancreatic tumors.
[0022] FIG. 19 shows images of the pancreas from mice treated with
PEGPH20.TM./shScr-ST or PEGPH20.TM./shIDO-ST or control
littermates.
DETAILED DESCRIPTION OF THE INVENTION
[0023] Provided herein are compositions and kits comprising a
bacterial cell and a tumor penetrating agent. Also provided are
methods of treating cancer in a subject including the step of
administering to the subject an effective amount of a bacterial
cell and a tumor penetrating agent, wherein administration treats
the cancer in the subject.
[0024] Provided are methods of stimulating an immune system in a
subject. The methods include administering to the subject an
effective amount of a bacterial cell and a tumor penetrating agent,
wherein administration stimulates the immune system in the subject.
Also provided are methods of enhancing delivery of an anti-cancer
agent to a tumor cell including the step of contacting the tumor
cell with a bacterial cell, a tumor penetrating agent and an
anti-cancer agent, wherein contacting the tumor cell with the
bacterial cell and tumor penetrating agent enhances delivery of the
anti-cancer agent to the tumor cell.
[0025] As used herein, the term "tumor penetrating agent" refers to
an agent that is capable of penetrating a tumor and/or a tumor
cell. Thus, a tumor penetrating agent can penetrate a tumor cell
itself or penetrates the area surrounding tumor cells, e.g., the
extracellular matrix. By way of example, a tumor penetrating agent
penetrates a tumor by breaking down or degrading the extracellular
matrix surrounding tumor cells. Alternatively, a tumor penetrating
agent penetrates a tumor by entering the tumor cell itself.
Examples of tumor penetrating agents for use in the provided
compositions and methods include, but are not limited to,
hyaluronidase polypeptides, pirfenidone, Saridegib (IPI-926),
nanoparticles, albumin nanoparticles, dextrans, liposomes, and cell
penetrating peptides. Such tumor penetrating agents including
methods of making and using the agents are known and are described
in, for example, U.S. Pat. Nos. 7,767,429; 7,829,081; 7,846,431;
7,871,607; 8,105,586; 8,202,517; 8,257,699; 8,431,380; and U.S.
Pat. No. 8,450,470; Kozono et al., Cancer Res. 73(7):2345-56
(2013); Olive et al., Science 324(5933):1457-61 (2009); Marrache,
et al., Curr. Med. Chem. 20(28):3500-14 (2013); Jung, et al., Curr.
Med. Chem. 20(28):3488-3499 (2013); Mattheolabakis et al.,
Nanomedicine (London) 7(10):1577-1590 (2012); Malam, et al., Trends
Pharmacol. Sci., 30(11):592-599 (2009); Varshoaz, Expert Opin. Drug
Deliv., 9(5):509-23 (2012); MacEwan and Chilkoti, Wiley Interdiscip
Rev Nanomed Nanobiotechnol., 5(1):31-48 (2013), which are
incorporated by reference herein in their entireties. Optionally,
the hyaluronidase polypeptide comprises SEQ ID NO:1 or SEQ ID NO:2
or a fragment thereof. Optionally, the hyaluronidase polypeptide is
a modified hyaluronidase polypeptide. Optionally, the hyaluronidase
polypeptide is pegylated. Optionally, the hyaluronidase polypeptide
is PEGPH20.TM. (Halozyme, Inc., San Diego, Calif.).
[0026] "Nucleic acid" refers to deoxyribonucleotides or
ribonucleotides and polymers thereof in either single- or
double-stranded form, and complements thereof. The term encompasses
nucleic acids containing known nucleotide analogs or modified
backbone residues or linkages, which are synthetic, naturally
occurring, and non-naturally occurring, which have similar binding
properties as the reference nucleic acid, and which are metabolized
in a manner similar to the reference nucleotides. Examples of such
analogs include, without limitation, phosphorothioates,
phosphoramidates, methyl phosphonates, chiral-methyl phosphonates,
2-O-methyl ribonucleotides, peptide-nucleic acids (PNAs).
[0027] Unless otherwise indicated, a particular nucleic acid
sequence also implicitly encompasses conservatively modified
variants thereof (e.g., degenerate codon substitutions) and
complementary sequences, as well as the sequence explicitly
indicated. Specifically, degenerate codon substitutions may be
achieved by generating sequences in which the third position of one
or more selected (or all) codons is substituted with mixed-base
and/or deoxyinosine residues (Batzer et al., Nucleic Acid Res.
19:5081 (1991); Ohtsuka et al., J. Biol. Chem. 260:2605-2608
(1985); Rossolini et al., Mol. Cell. Probes 8:91-98 (1994)). The
term nucleic acid is used interchangeably with gene, cDNA, mRNA,
oligonucleotide, and polynucleotide.
[0028] A particular nucleic acid sequence also implicitly
encompasses "splice variants." Similarly, a particular protein
encoded by a nucleic acid implicitly encompasses any protein
encoded by a splice variant of that nucleic acid. "Splice
variants," as the name suggests, are products of alternative
splicing of a gene. After transcription, an initial nucleic acid
transcript may be spliced such that different (alternate) nucleic
acid splice products encode different polypeptides. Mechanisms for
the production of splice variants vary, but include alternate
splicing of exons. Alternate polypeptides derived from the same
nucleic acid by read-through transcription are also encompassed by
this definition. Any products of a splicing reaction, including
recombinant forms of the splice products, are included in this
definition. An example of potassium channel splice variants is
discussed in Leicher, et al., J. Biol. Chem. 273(52):35095-35101
(1998).
[0029] Nucleic acid is "operably linked" when it is placed into a
functional relationship with another nucleic acid sequence. For
example, DNA for a presequence or secretory leader is operably
linked to DNA for a polypeptide if it is expressed as a preprotein
that participates in the secretion of the polypeptide; a promoter
or enhancer is operably linked to a coding sequence if it affects
the transcription of the sequence; or a ribosome binding site is
operably linked to a coding sequence if it is positioned so as to
facilitate translation. Generally, "operably linked" means that the
DNA sequences being linked are near each other, and, in the case of
a secretory leader, contiguous and in reading phase. However,
enhancers do not have to be contiguous. Linking is accomplished by
ligation at convenient restriction sites. If such sites do not
exist, the synthetic oligonucleotide adaptors or linkers are used
in accordance with conventional practice.
[0030] The terms "identical" or percent "identity," in the context
of two or more nucleic acids or polypeptide sequences, refer to two
or more sequences or subsequences that are the same or have a
specified percentage of amino acid residues or nucleotides that are
the same (i.e., about 60% identity, preferably 65%, 70%, 75%, 80%,
85%, 90%, 91%, 92%, 93%, 94%, 95%, 96%, 97%, 98%, 99%, or higher
identity over a specified region, when compared and aligned for
maximum correspondence over a comparison window or designated
region) as measured using a BLAST or BLAST 2.0 sequence comparison
algorithms with default parameters described below, or by manual
alignment and visual inspection (see, e.g., NCBI web site or the
like). Such sequences are then said to be "substantially
identical." This definition also refers to, or may be applied to,
the compliment of a test sequence. The definition also includes
sequences that have deletions and/or additions, as well as those
that have substitutions. As described below, the preferred
algorithms can account for gaps and the like. Preferably, identity
exists over a region that is at least about 25 amino acids or
nucleotides in length, or more preferably over a region that is
50-100 amino acids or nucleotides in length.
[0031] For sequence comparison, typically one sequence acts as a
reference sequence, to which test sequences are compared. When
using a sequence comparison algorithm, test and reference sequences
are entered into a computer, subsequence coordinates are
designated, if necessary, and sequence algorithm program parameters
are designated. Preferably, default program parameters can be used,
or alternative parameters can be designated. The sequence
comparison algorithm then calculates the percent sequence
identities for the test sequences relative to the reference
sequence, based on the program parameters.
[0032] A "comparison window," as used herein, includes reference to
a segment of any one of the number of contiguous positions selected
from the group consisting of from 20 to 600, usually about 50 to
about 200, more usually about 100 to about 150 in which a sequence
may be compared to a reference sequence of the same number of
contiguous positions after the two sequences are optimally aligned.
Methods of alignment of sequences for comparison are well-known in
the art. Optimal alignment of sequences for comparison can be
conducted, e.g., by the local homology algorithm of Smith &
Waterman, Adv. Appl. Math. 2:482 (1981), by the homology alignment
algorithm of Needleman & Wunsch, J. Mol. Biol. 48:443 (1970),
by the search for similarity method of Pearson & Lipman, Proc.
Nat'l. Acad. Sci. USA 85:2444 (1988), by computerized
implementations of these algorithms (GAP, BESTFIT, FASTA, and
TFASTA in the Wisconsin Genetics Software Package, Genetics
Computer Group, 575 Science Dr., Madison, Wis.), or by manual
alignment and visual inspection (see, e.g., Current Protocols in
Molecular Biology (Ausubel et al., eds. 1995 supplement)).
[0033] A preferred example of algorithm that is suitable for
determining percent sequence identity and sequence similarity are
the BLAST and BLAST 2.0 algorithms, which are described in Altschul
et al., Nuc. Acids Res. 25:3389-3402 (1977) and Altschul et al., J.
Mol. Biol. 215:403-410 (1990), respectively. BLAST and BLAST 2.0
are used, with the parameters described herein, to determine
percent sequence identity for the nucleic acids and proteins.
Software for performing BLAST analyses is publicly available
through the National Center for Biotechnology Information, as known
in the art. This algorithm involves first identifying high scoring
sequence pairs (HSPs) by identifying short words of length W in the
query sequence, which either match or satisfy some positive-valued
threshold score T when aligned with a word of the same length in a
database sequence. T is referred to as the neighborhood word score
threshold (Altschul et al., supra). These initial neighborhood word
hits act as seeds for initiating searches to find longer HSPs
containing them. The word hits are extended in both directions
along each sequence for as far as the cumulative alignment score
can be increased. Cumulative scores are calculated using, for
nucleotide sequences, the parameters M (reward score for a pair of
matching residues; always >0) and N (penalty score for
mismatching residues; always <0). For amino acid sequences, a
scoring matrix is used to calculate the cumulative score. Extension
of the word hits in each direction are halted when: the cumulative
alignment score falls off by the quantity X from its maximum
achieved value; the cumulative score goes to zero or below, due to
the accumulation of one or more negative-scoring residue
alignments; or the end of either sequence is reached. The BLAST
algorithm parameters W, T, and X determine the sensitivity and
speed of the alignment. The BLASTN program (for nucleotide
sequences) uses as defaults a wordlength (W) of 11, an expectation
(E) of 10, M=5, N=-4 and a comparison of both strands. For amino
acid sequences, the BLASTP program uses as defaults a wordlength of
3, and expectation (E) of 10, and the BLOSUM62 scoring matrix (see
Henikoff & Henikoff, Proc. Natl. Acad. Sci. USA 89:10915
(1989)) alignments (B) of 50, expectation (E) of 10, M=5, N=-4, and
a comparison of both strands.
[0034] An "inhibitory nucleic acid" is a nucleic acid (e.g. DNA,
RNA, polymer of nucleotide analogs) that is capable of binding to a
target nucleic acid (e.g. an mRNA translatable into PTPRS) and
reducing transcription of the target nucleic acid (e.g. mRNA from
DNA) or reducing the translation of the target nucleic acid (e.g.
mRNA) or altering transcript splicing (e.g. single stranded
morpholino oligo) relative to the absence of the inhibitory nucleic
acid. A "morpholino oligo" may be alternatively referred to as a
"morphlino nucleic acid" and refers to morpholine-containing
nucleic acid nucleic acids commonly known in the art (e.g.
phosphoramidate morpholinio oligo or a "PMO"). See Marcos, P.,
Biochemical and Biophysical Research Communications 358 (2007)
521-527. In some embodiments, the "inhibitory nucleic acid" is a
nucleic acid that is capable of binding (e.g. hybridizing) to a
target nucleic acid (e.g. an mRNA translatable into an RPTPS) and
reducing translation of the target nucleic acid. The target nucleic
acid is or includes one or more target nucleic acid sequences to
which the inhibitory nucleic acid binds (e.g. hybridizes). Thus, an
inhibitory nucleic acid typically is or includes a sequence (also
referred to herein as an "antisense nucleic acid sequence") that is
capable of hybridizing to at least a portion of a target nucleic
acid at a target nucleic acid sequence. An example of an inhibitory
nucleic acid is an antisense nucleic acid. Another example of an
inhibitory nucleic acid is siRNA or RNAi (including their
derivatives or pre-cursors, such as nucleotide analogs). Further
examples include shRNA, miRNA, shmiRNA, or certain of their
derivatives or pre-cursors. In some embodiments, the inhibitory
nucleic acid is single stranded. In other embodiments, the
inhibitory nucleic acid is double stranded.
[0035] An "antisense nucleic acid" is a nucleic acid (e.g. DNA, RNA
or analogs thereof) that is at least partially complementary to at
least a portion of a specific target nucleic acid (e.g. a target
nucleic acid sequence), such as an mRNA molecule (e.g. a target
mRNA molecule) (see, e.g., Weintraub, Scientific American, 262:40
(1990)), for example antisense, siRNA, shRNA, shmiRNA, miRNA
(microRNA). Thus, antisense nucleic acids are capable of
hybridizing to (e.g. selectively hybridizing to) a target nucleic
acid (e.g. target mRNA). In some embodiments, the antisense nucleic
acid hybridizes to the target nucleic acid sequence (e.g. mRNA)
under stringent hybridization conditions. In some embodiments, the
antisense nucleic acid hybridizes to the target nucleic acid (e.g.
mRNA) under moderately stringent hybridization conditions.
Antisense nucleic acids may comprise naturally occurring
nucleotides or modified nucleotides such as, e.g.,
phosphorothioate, methylphosphonate, and -anomeric sugar-phosphate,
backbone modified nucleotides. An "anti-PTPRS antisense nucleic
acid" is an antisense nucleic acid that is at least partially
complementary to at least a portion of a target nucleic acid
sequence, such as an mRNA molecule, that codes at least a portion
of the PTPRS. In some embodiments, an antisense nucleic acid is a
morpholino oligo. In some embodiments, a morpholino oligo is a
single stranded antisense nucleic acid, as is known in the art. In
some embodiments, a morpholino oligo decreases protein expression
of a target, reduces translation of the target mRNA, reduces
translation initiation of the target mRNA, or modifies transcript
splicing. In some embodiments, the morpholino oligo is conjugated
to a cell permeable moiety (e.g. peptide). Antisense nucleic acids
may be single or double stranded nucleic acids.
[0036] In the cell, the antisense nucleic acids may hybridize to
the target mRNA, forming a double-stranded molecule. The antisense
nucleic acids, interfere with the translation of the mRNA, since
the cell will not translate a mRNA that is double-stranded. The use
of antisense methods to inhibit the in vitro translation of genes
is well known in the art (Marcus-Sakura, Anal. Biochem., 172:289,
(1988)). Antisense molecules which bind directly to the DNA may be
used.
[0037] Inhibitory nucleic acids can be delivered to the subject
using any appropriate means known in the art, including by
injection, inhalation, or oral ingestion. Another suitable delivery
system is a colloidal dispersion system such as, for example,
macromolecule complexes, nanocapsules, microspheres, beads, and
lipid-based systems including oil-in-water emulsions, micelles,
mixed micelles, and liposomes. An example of a colloidal system of
this invention is a liposome. Liposomes are artificial membrane
vesicles which are useful as delivery vehicles in vitro and in
vivo. Nucleic acids, including RNA and DNA within liposomes and be
delivered to cells in a biologically active form (Fraley, et al.,
Trends Biochem. Sci., 6:77, 1981). Liposomes can be targeted to
specific cell types or tissues using any means known in the art.
Inhibitory nucleic acids (e.g. antisense nucleic acids, morpholino
oligos) may be delivered to a cell using cell permeable delivery
systems (e.g. cell permeable peptides). In some embodiments,
inhibitory nucleic acids are delivered to specific cells or tissues
using viral vectors or viruses.
[0038] An "siRNA" refers to a nucleic acid that forms a double
stranded RNA, which double stranded RNA has the ability to reduce
or inhibit expression of a gene or target gene when the siRNA is
present (e.g. expressed) in the same cell as the gene or target
gene. The siRNA is typically about 5 to about 100 nucleotides in
length, more typically about 10 to about 50 nucleotides in length,
more typically about 15 to about 30 nucleotides in length, most
typically about 20-30 base nucleotides, or about 20-25 or about
24-29 nucleotides in length, e.g., 20, 21, 22, 23, 24, 25, 26, 27,
28, 29, or 30 nucleotides in length. siRNA molecules and methods of
generating them are described in, e.g., Bass, 2001, Nature, 411,
428-429; Elbashir et al., 2001, Nature, 411, 494-498; WO 00/44895;
WO 01/36646; WO 99/32619; WO 00/01846; WO 01/29058; WO 99/07409;
and WO 00/44914. A DNA molecule that transcribes dsRNA or siRNA
(for instance, as a hairpin duplex) also provides RNAi. DNA
molecules for transcribing dsRNA are disclosed in U.S. Pat. No.
6,573,099, and in U.S. Patent Application Publication Nos.
2002/0160393 and 2003/0027783, and Tuschl and Borkhardt, Molecular
Interventions, 2:158 (2002). Small or short hairpin RNA molecules
(shRNA) are generated by such DNA molecules, e.g., within cells by
transcription. ShRNAs typically include two complementary RNA
sequences linked by a short loop of nucleotides similar to the
hairpin found in naturally occurring miRNA. Typically, shRNA
molecules are about 20-30 base nucleotides, or about 19-22, or
about 20-25 or about 24-29 nucleotides in length, e.g., 20, 21, 22,
23, 24, 25, 26, 27, 28, 29, or 30 nucleotides in length, with the
short loop of nucleotides forming the hairpin being about 4, 5, 6,
7, 8, 9, 10, 11, or 12 nucleotides in length.
[0039] The siRNA can be administered directly or siRNA expression
vectors can be used to induce RNAi that have different design
criteria. A vector can have inserted two inverted repeats separated
by a short spacer sequence and ending with a string of T's which
serve to terminate transcription.
[0040] The terms "polypeptide," "peptide," and "protein" are used
interchangeably herein to refer to a polymer of amino acid
residues. The terms apply to amino acid polymers in which one or
more amino acid residue is an artificial chemical mimetic of a
corresponding naturally occurring amino acid, as well as to
naturally occurring amino acid polymers and non-naturally occurring
amino acid polymer.
[0041] The term "amino acid" refers to naturally occurring and
synthetic amino acids, as well as amino acid analogs and amino acid
mimetics that function in a manner similar to the naturally
occurring amino acids. Naturally occurring amino acids are those
encoded by the genetic code, as well as those amino acids that are
later modified, e.g., hydroxyproline, .gamma.-carboxyglutamate, and
O-phosphoserine. Amino acid analogs refers to compounds that have
the same basic chemical structure as a naturally occurring amino
acid, i.e., an a carbon that is bound to a hydrogen, a carboxyl
group, an amino group, and an R group, e.g., homoserine,
norleucine, methionine sulfoxide, methionine methyl sulfonium. Such
analogs have modified R groups (e.g., norleucine) or modified
peptide backbones, but retain the same basic chemical structure as
a naturally occurring amino acid. Amino acid mimetics refers to
chemical compounds that have a structure that is different from the
general chemical structure of an amino acid, but that functions in
a manner similar to a naturally occurring amino acid.
[0042] Amino acids may be referred to herein by either their
commonly known three letter symbols or by the one-letter symbols
recommended by the IUPAC-IUB Biochemical Nomenclature Commission.
Nucleotides, likewise, may be referred to by their commonly
accepted single-letter codes.
[0043] "Conservatively modified variants" applies to both amino
acid and nucleic acid sequences. With respect to particular nucleic
acid sequences, conservatively modified variants refers to those
nucleic acids which encode identical or essentially identical amino
acid sequences, or where the nucleic acid does not encode an amino
acid sequence, to essentially identical sequences. Because of the
degeneracy of the genetic code, a large number of functionally
identical nucleic acids encode any given protein. For instance, the
codons GCA, GCC, GCG and GCU all encode the amino acid alanine.
Thus, at every position where an alanine is specified by a codon,
the codon can be altered to any of the corresponding codons
described without altering the encoded polypeptide. Such nucleic
acid variations are "silent variations," which are one species of
conservatively modified variations. Every nucleic acid sequence
herein which encodes a polypeptide also describes every possible
silent variation of the nucleic acid. One of skill will recognize
that each codon in a nucleic acid (except AUG, which is ordinarily
the only codon for methionine, and TGG, which is ordinarily the
only codon for tryptophan) can be modified to yield a functionally
identical molecule. Accordingly, each silent variation of a nucleic
acid which encodes a polypeptide is implicit in each described
sequence with respect to the expression product, but not with
respect to actual probe sequences.
[0044] As to amino acid sequences, one of skill will recognize that
individual substitutions, deletions or additions to a nucleic acid,
peptide, polypeptide, or protein sequence which alters, adds or
deletes a single amino acid or a small percentage of amino acids in
the encoded sequence is a "conservatively modified variant" where
the alteration results in the substitution of an amino acid with a
chemically similar amino acid. Conservative substitution tables
providing functionally similar amino acids are well known in the
art. Such conservatively modified variants are in addition to and
do not exclude polymorphic variants, interspecies homologs, and
alleles.
[0045] The following eight groups each contain amino acids that are
conservative substitutions for one another: 1) Alanine (A), Glycine
(G); 2) Aspartic acid (D), Glutamic acid (E); 3) Asparagine (N),
Glutamine (Q); 4) Arginine (R), Lysine (K); 5) Isoleucine (I),
Leucine (L), Methionine (M), Valine (V); 6) Phenylalanine (F),
Tyrosine (Y), Tryptophan (W); 7) Serine (S), Threonine (T); and 8)
Cysteine (C), Methionine (M) (see, e.g., Creighton, Proteins
(1984)).
[0046] The phrase "stringent hybridization conditions" refers to
conditions under which a probe will hybridize to its target
subsequence, typically in a complex mixture of nucleic acids, but
to no other sequences. Stringent conditions are sequence-dependent
and will be different in different circumstances. Longer sequences
hybridize specifically at higher temperatures. An extensive guide
to the hybridization of nucleic acids is found in Tijssen,
Techniques in Biochemistry and Molecular Biology--Hybridization
with Nucleic Probes, "Overview of principles of hybridization and
the strategy of nucleic acid assays" (1993). Generally, stringent
conditions are selected to be about 5-10.degree. C. lower than the
thermal melting point (Tm) for the specific sequence at a defined
ionic strength pH. The Tm is the temperature (under defined ionic
strength, pH, and nucleic concentration) at which 50% of the probes
complementary to the target hybridize to the target sequence at
equilibrium (as the target sequences are present in excess, at Tm,
50% of the probes are occupied at equilibrium). Stringent
conditions may also be achieved with the addition of destabilizing
agents such as formamide. For selective or specific hybridization,
a positive signal is at least two times background, preferably 10
times background hybridization. Exemplary stringent hybridization
conditions can be as following: 50% formamide, 5.times.SSC, and 1%
SDS, incubating at 42.degree. C., or, 5.times.SSC, 1% SDS,
incubating at 65.degree. C., with wash in 0.2.times.SSC, and 0.1%
SDS at 65.degree. C.
[0047] Nucleic acids that do not hybridize to each other under
stringent conditions are still substantially identical if the
polypeptides which they encode are substantially identical. This
occurs, for example, when a copy of a nucleic acid is created using
the maximum codon degeneracy permitted by the genetic code. In such
cases, the nucleic acids typically hybridize under moderately
stringent hybridization conditions. Exemplary "moderately stringent
hybridization conditions" include a hybridization in a buffer of
40% formamide, 1 M NaCl, 1% SDS at 37.degree. C., and a wash in
1.times.SSC at 45.degree. C. A positive hybridization is at least
twice background. Those of ordinary skill will readily recognize
that alternative hybridization and wash conditions can be utilized
to provide conditions of similar stringency. Additional guidelines
for determining hybridization parameters are provided in numerous
reference, e.g., and Current Protocols in Molecular Biology, ed.
Ausubel, et al., John Wiley & Sons.
[0048] For PCR, a temperature of about 36.degree. C. is typical for
low stringency amplification, although annealing temperatures may
vary between about 32.degree. C. and 48.degree. C. depending on
primer length. For high stringency PCR amplification, a temperature
of about 62.degree. C. is typical, although high stringency
annealing temperatures can range from about 50.degree. C. to about
65.degree. C., depending on the primer length and specificity.
Typical cycle conditions for both high and low stringency
amplifications include a denaturation phase of 90.degree. C. to
95.degree. C. for 30 seconds to 2 minutes, an annealing phase
lasting 30 seconds to 2 minutes, and an extension phase of about
72.degree. C. for 1 to 2 minutes. Protocols and guidelines for low
and high stringency amplification reactions are provided, e.g., in
Innis et al. (1990) PCR Protocols, A Guide to Methods and
Applications, Academic Press, Inc. N.Y.).
[0049] A "control" sample or value refers to a sample that serves
as a reference, usually a known reference, for comparison to a test
sample. For example, a test sample can be taken from a test
condition, e.g., in the presence of a test agent, and compared to
samples from known conditions, e.g., in the absence of the test
agent (negative control), or in the presence of a known agent
(positive control). A control can also represent an average value
gathered from a number of tests or results. One of skill in the art
will recognize that controls can be designed for assessment of any
number of parameters. For example, a control can be devised to
compare therapeutic benefit based on pharmacological data (e.g.,
half-life) or therapeutic measures (e.g., comparison of side
effects). One of skill in the art will understand which controls
are valuable in a given situation and be able to analyze data based
on comparisons to control values. Controls are also valuable for
determining the significance of data. For example, if values for a
given parameter are widely variant in controls, variation in test
samples will not be considered as significant.
[0050] As used herein, the term "cancer" refers to all types of
cancer, neoplasm, or malignant tumors found in mammals, including
leukemia, carcinomas and sarcomas. Exemplary cancers include cancer
of the brain, breast, cervix, colon, head & neck, liver,
kidney, lung, non-small cell lung, melanoma, mesothelioma, ovary,
sarcoma, stomach, uterus and Medulloblastoma. Additional examples
include, Hodgkin's Disease, Non-Hodgkin's Lymphoma, multiple
myeloma, neuroblastoma, ovarian cancer, rhabdomyosarcoma, primary
thrombocytosis, primary macroglobulinemia, primary brain tumors,
cancer, malignant pancreatic insulanoma, malignant carcinoid,
urinary bladder cancer, premalignant skin lesions, testicular
cancer, lymphomas, thyroid cancer, neuroblastoma, esophageal
cancer, genitourinary tract cancer, malignant hypercalcemia,
endometrial cancer, adrenal cortical cancer, neoplasms of the
endocrine and exocrine pancreas, and prostate cancer.
[0051] The term "leukemia" refers broadly to progressive, malignant
diseases of the blood-forming organs and is generally characterized
by a distorted proliferation and development of leukocytes and
their precursors in the blood and bone marrow. Leukemia is
generally clinically classified on the basis of (1) the duration
and character of the disease-acute or chronic; (2) the type of cell
involved; myeloid (myelogenous), lymphoid (lymphogenous), or
monocytic; and (3) the increase or non-increase in the number
abnormal cells in the blood-leukemic or aleukemic (subleukemic).
The P388 leukemia model is widely accepted as being predictive of
in vivo anti-leukemic activity. It is believed that a compound that
tests positive in the P388 assay will generally exhibit some level
of anti-leukemic activity in vivo regardless of the type of
leukemia being treated. Accordingly, the present application
includes a method of treating leukemia, and, preferably, a method
of treating acute nonlymphocytic leukemia, chronic lymphocytic
leukemia, acute granulocytic leukemia, chronic granulocytic
leukemia, acute promyelocytic leukemia, adult T-cell leukemia,
aleukemic leukemia, a leukocythemic leukemia, basophylic leukemia,
blast cell leukemia, bovine leukemia, chronic myelocytic leukemia,
leukemia cutis, embryonal leukemia, eosinophilic leukemia, Gross'
leukemia, hairy-cell leukemia, hemoblastic leukemia,
hemocytoblastic leukemia, histiocytic leukemia, stem cell leukemia,
acute monocytic leukemia, leukopenic leukemia, lymphatic leukemia,
lymphoblastic leukemia, lymphocytic leukemia, lymphogenous
leukemia, lymphoid leukemia, lymphosarcoma cell leukemia, mast cell
leukemia, megakaryocytic leukemia, micromyeloblastic leukemia,
monocytic leukemia, myeloblastic leukemia, myelocytic leukemia,
myeloid granulocytic leukemia, myelomonocytic leukemia, Naegeli
leukemia, plasma cell leukemia, multiple myeloma, plasmacytic
leukemia, promyelocytic leukemia, Rieder cell leukemia, Schilling's
leukemia, stem cell leukemia, subleukemic leukemia, and
undifferentiated cell leukemia.
[0052] The term "sarcoma" generally refers to a tumor which is made
up of a substance like the embryonic connective tissue and is
generally composed of closely packed cells embedded in a fibrillar
or homogeneous substance. Sarcomas which can be treated with a
combination of antineoplastic thiol-binding mitochondrial oxidant
and an anticancer agent include a chondrosarcoma, fibrosarcoma,
lymphosarcoma, melanosarcoma, myxosarcoma, osteosarcoma, Abemethy's
sarcoma, adipose sarcoma, liposarcoma, alveolar soft part sarcoma,
ameloblastic sarcoma, botryoid sarcoma, chloroma sarcoma, chorio
carcinoma, embryonal sarcoma, Wilms' tumor sarcoma, endometrial
sarcoma, stromal sarcoma, Ewing's sarcoma, fascial sarcoma,
fibroblastic sarcoma, giant cell sarcoma, granulocytic sarcoma,
Hodgkin's sarcoma, idiopathic multiple pigmented hemorrhagic
sarcoma, immunoblastic sarcoma of B cells, lymphoma, immunoblastic
sarcoma of T-cells, Jensen's sarcoma, Kaposi's sarcoma, Kupffer
cell sarcoma, angiosarcoma, leukosarcoma, malignant mesenchymoma
sarcoma, parosteal sarcoma, reticulocytic sarcoma, Rous sarcoma,
serocystic sarcoma, synovial sarcoma, and telangiectaltic
sarcoma.
[0053] The term "melanoma" is taken to mean a tumor arising from
the melanocytic system of the skin and other organs. Melanomas
which can be treated with a combination of antineoplastic
thiol-binding mitochondrial oxidant and an anticancer agent
include, for example, acral-lentiginous melanoma, amelanotic
melanoma, benign juvenile melanoma, Cloudman's melanoma, S91
melanoma, Harding-Passey melanoma, juvenile melanoma, lentigo
maligna melanoma, malignant melanoma, nodular melanoma, subungal
melanoma, and superficial spreading melanoma.
[0054] The term "carcinoma" refers to a malignant new growth made
up of epithelial cells tending to infiltrate the surrounding
tissues and give rise to metastases. Exemplary carcinomas which can
be treated with a combination of antineoplastic thiol-binding
mitochondrial oxidant and an anticancer agent include, for example,
acinar carcinoma, acinous carcinoma, adenocystic carcinoma, adenoid
cystic carcinoma, carcinoma adenomatosum, carcinoma of adrenal
cortex, alveolar carcinoma, alveolar cell carcinoma, basal cell
carcinoma, carcinoma basocellulare, basaloid carcinoma,
basosquamous cell carcinoma, bronchioalveolar carcinoma,
bronchiolar carcinoma, bronchogenic carcinoma, cerebriform
carcinoma, cholangiocellular carcinoma, chorionic carcinoma,
colloid carcinoma, comedo carcinoma, corpus carcinoma, cribriform
carcinoma, carcinoma en cuirasse, carcinoma cutaneum, cylindrical
carcinoma, cylindrical cell carcinoma, duct carcinoma, carcinoma
durum, embryonal carcinoma, encephaloid carcinoma, epiermoid
carcinoma, carcinoma epitheliale adenoides, exophytic carcinoma,
carcinoma ex ulcere, carcinoma fibrosum, gelatiniforni carcinoma,
gelatinous carcinoma, giant cell carcinoma, carcinoma
gigantocellulare, glandular carcinoma, granulosa cell carcinoma,
hair-matrix carcinoma, hematoid carcinoma, hepatocellular
carcinoma, Hurthle cell carcinoma, hyaline carcinoma, hypemephroid
carcinoma, infantile embryonal carcinoma, carcinoma in situ,
intraepidermal carcinoma, intraepithelial carcinoma, Krompecher's
carcinoma, Kulchitzky-cell carcinoma, large-cell carcinoma,
lenticular carcinoma, carcinoma lenticulare, lipomatous carcinoma,
lymphoepithelial carcinoma, carcinoma medullare, medullary
carcinoma, melanotic carcinoma, carcinoma molle, mucinous
carcinoma, carcinoma muciparum, carcinoma mucocellulare,
mucoepidermoid carcinoma, carcinoma mucosum, mucous carcinoma,
carcinoma myxomatodes, nasopharyngeal carcinoma, oat cell
carcinoma, carcinoma ossificans, osteoid carcinoma, papillary
carcinoma, periportal carcinoma, preinvasive carcinoma, prickle
cell carcinoma, pultaceous carcinoma, renal cell carcinoma of
kidney, reserve cell carcinoma, carcinoma sarcomatodes,
schneiderian carcinoma, scirrhous carcinoma, carcinoma scroti,
signet-ring cell carcinoma, carcinoma simplex, small-cell
carcinoma, solanoid carcinoma, spheroidal cell carcinoma, spindle
cell carcinoma, carcinoma spongiosum, squamous carcinoma, squamous
cell carcinoma, string carcinoma, carcinoma telangiectaticum,
carcinoma telangiectodes, transitional cell carcinoma, carcinoma
tuberosum, tuberous carcinoma, verrucous carcinoma, and carcinoma
villosum.
[0055] ShIDO-ST is a Salmonella typhimurium (ST) cell that
expresses a small hairpin (sh)RNA to specifically silence
indoleamine-pyrrole 2,3-dioxygenase (IDO) with decreased toxicity.
Specifically, shIDO-ST is composed of an attenuated Salmonella
typhimurium strain known as YS1646 (ATCC Accession No. 202165, also
referred to herein as VNP20009) expressing a small hairpin RNA
targeted to IDO comprising SEQ ID NO:8. This cell based therapy has
been described in, for example, WO2012/149364, which is
incorporated by reference herein in its entirety. As described in
the examples below, the combination of pegylated recombinant human
hyaluronidase PH20 (PEGPH20.TM., Halozyme Inc., San Diego, Calif.),
which depletes hyaluronan abundant in tissue and increases vascular
permeability, and shIDO-ST resulted in effective control of and, in
some cases, complete elimination of established pancreatic tumors
in autochthonous and orthotopic models. Further, it was observed
that ST containing a control small hairpin RNA in combination with
PEGPH20.TM. was also able to control tumor growth when tumors were
of smaller size. Recombinant human hyaluronidase PH20 and the
pegylated form of PH20 are known and described in, for example,
Bookbinder et al., Journal of Controlled Release, 114:230-241
(2006) and Thompson et al., Mol. Cancer Ther. 9:3052-3064 (2010),
which are incorporated by reference herein in their entireties.
[0056] Thus, provided are compositions comprising a bacterial cell
and a tumor penetrating agent. Optionally, the composition further
comprises an anti-cancer agent. The anti-cancer agent can be
selected from the group consisting of a small molecule, a nucleic
acid, a polypeptide and an antibody. Examples of tumor penetrating
agents include, but are not limited to, hyaluronidase polypeptides,
pirfenidone, Saridegib (IPI-926), nanoparticles, albumin
nanoparticles, dextrans, liposomes, and cell penetrating peptides.
In certain embodiments, the tumor penetrating agent is a
hyaluronidase polypeptide. Optionally, the bacterial cell and
hyaluronidase polypeptide are present in an effective amount, e.g.,
a synergistic effective amount. Optionally, the bacterial cell is a
Salmonella bacterial cell. Thus, provided are compositions
comprising a Salmonella bacterial cell and a hyaluronidase
polypeptide.
[0057] Hyaluronidases are a group of neutral- and acid-active
enzymes generally grouped in three different classes,
mammalian-type hyaluronidases, bacterial hyaluronidases and
hyaluronidases from leeches, other parasites and crustaceans.
Mammalian-type hyaluronidases are endo-beta-N-acetylhexosaminidases
that have both hydrolytic and transglycosidase activities, and can
be further divided into two groups, neutral active and acid active
enzymes. There are six hyaluronidase-like genes in the human
genome, HYAL1, HYAL2, HYAL3 HYAL4 HYALP1 and PH20/SPAM1, which can
degrade hyaluronan and chondroitin sulfates (CS), specifically C4-S
and C6-S. Hyaluronan is found in the extracellular matrix of many
cells and plays a key role in biological phenomena associated with
cell mobility including tumorigenesis. Hyaluronidase polypeptides
suitable for use in the provided methods and compositions include
mammalian hyaluronidases, for example, PH-20 hyaluronidase.
Optionally, the hyaluronidase polypeptide comprises SEQ ID NO:1 or
SEQ ID NO:2 or a fragment thereof. As used throughout, the term
"hyaluronidase polypeptide" includes domains, fragments, and
variants thereof. Thus, as described herein, the hyaluronidase
polypeptide can comprise a fragment of SEQ ID NO:1 or SEQ ID NO:2
as long as the fragment remains catalytically active, e.g., the
polypeptide retains the ability to degrade hyaluron and/or
chondroitin sulfate. Further, the hyaluronidase polypeptide can
comprise SEQ ID NO:1 or SEQ ID NO:2 or a fragment of SEQ ID NO:1 or
SEQ ID NO:2 with one or more amino acid substitutions again as long
as the hyaluronidase polypeptide remains catalytically active.
Optionally, the amino acid substitution is a conservative amino
acid substitution as described in more detail above. By way of an
example, the hyaluronidase polypeptide can include a fragment of
SEQ ID NO:1, e.g., amino acids 35-464 of SEQ ID NO:1 or the entire
sequence of amino acids set forth in SEQ ID NO:1. Exemplary nucleic
acid sequences of hyaluronidases can be found, for example, at
GenBank Accession Nos. NM_003117 and NM_153189.2 and exemplary
polypeptide sequences of hyaluronidases can be found, for example,
at GenBank Accession Nos. NP_003108 and NP_694859. Hyaluronidase
polypeptides suitable for use in the provided compositions, kits
and methods are described in U.S. Pat. Nos. 7,767,429; 7,829,081;
7,846,431; 7,871,607; 8,105,586; 8,202,517; 8,257,699; 8,431,380;
and 8,450,470, each of which are incorporated by reference herein
in their entirety. Optionally, the hyaluronidase polypeptide is a
chemically modified hyaluronidase polypeptide, i.e., the
polypeptide has been modified to include one or more glycosylated
and/or pegylated moieties. Optionally, the hyaluronidase
polypeptide is pegylated. Optionally, the hyaluronidase polypeptide
is PEGPH20.TM. (Halozyme, Inc., San Diego, Calif.), which is used
in the examples below. PEGPH20.TM. (Halozyme, Inc., San Diego,
Calif.), is recombinant human hyaluronidase PH-20 (SEQ ID NO:1)
that has been modified by pegylation. Thus, PEGPH20.TM. (Halozyme,
Inc., San Diego, Calif.), is pegylated recombinant human
hyaluronidase PH-20.
[0058] As used herein, the terms peptide, polypeptide, or protein
are used broadly to mean two or more amino acids linked by a
peptide bond. Protein, peptide, and polypeptide are also used
herein interchangeably to refer to amino acid sequences. It should
be recognized that the term polypeptide is not used herein to
suggest a particular size or number of amino acids comprising the
molecule and that a peptide of the invention can contain up to
several amino acid residues or more. It is understood that the
nucleic acids that can encode those peptide, polypeptide, or
protein sequences, variants and fragments thereof are also
disclosed. This would include all degenerate sequences related to a
specific polypeptide sequence, i.e. all nucleic acids having a
sequence that encodes one particular polypeptide sequence as well
as all nucleic acids, including degenerate nucleic acids, encoding
the disclosed variants and derivatives of the polypeptide
sequences. Thus, while each particular nucleic acid sequence may
not be written out herein, it is understood that each and every
sequence is in fact disclosed and described herein through the
disclosed polypeptide sequence.
[0059] As with all peptides, polypeptides, and proteins, including
fragments thereof, it is understood that additional modifications
in the amino acid sequence of the provided agents that are
polypeptides can occur that do not alter the nature or function of
the peptides, polypeptides, or proteins. Thus, modification of the
hyaluronidase polypeptide can be made as long as the hyaluronidase
polypeptide remains catalytically active, e.g., the polypeptide
retains the ability to degrade hyaluron and/or chondroitin sulfate.
Such modifications include, for example, conservative amino acids
substitutions. Thus, the provided agents comprising polypeptides or
nucleic acids can be further modified and varied so long as the
desired function is maintained. It is understood that one way to
define any known modifications and derivatives or those that might
arise, of the disclosed nucleic acid sequences and proteins herein
is through defining the modifications and derivatives in terms of
identity to specific known sequences. Specifically disclosed are
polypeptides which have at least 70, 71, 72, 73, 74, 75, 76, 77,
78, 79, 80, 81, 82, 83, 84, 85, 86, 87, 88, 89, 90, 91, 92, 93, 94,
95, 96, 97, 98, 99 percent identity to the polypeptides provided
herein. Those of skill in the art readily understand how to
determine the identity of two polypeptides as discussed in more
detail above.
[0060] Bacterial cells useful in the provided composition, kits and
methods include, but are not limited to Salmonella bacterial cells,
Bifidobacteria bacterial cells, Listeria monocytogenes bacterial
cells, Clostridium histolyticus bacterial cells, Clostridium novyi
bacterial cells, Vibrio cholera bacterial cells, Shigella bacterial
cells, Streptococcus bacterial cells, Mycobacterium bovis bacterial
cells, Yersinia enterocolitica bacterial cells, Bacillus anthracis
bacterial cells, Lactobacillus bacterial cells, Staphylococcus
bacterial cells, E. coli bacterial cells. Optionally, the
Streptococcus bacterial cells are Streptococcus pyrogenes bacterial
cells or Streptococcus gordonii bacterial cells. Suitable bacterial
cells include bacterial cells described in International
Publication No. WO 2012/149364, which is incorporated by reference
herein in its entirety. Optionally, the Salmonella bacterial cell
is an attenuated attenuated Salmonella strain, for example, any
serovar or Salmonella enterica, including, but not limited to,
Salmonella typhimurium, Salmonella enteritidis or Salmonella typhi.
Optionally, the Salmonella bacterial cell is an attenuated strain
of Salmonella typhimurium. Attenuated Salmonella typhimurium
strains include, but are not limited to, YS1646, RE88, LH430,
SL7207, .chi.8429, .chi.8431 or .chi.8468. Optionally, the
attenuated Salmonella typhimurium strain is a YS1646 Salmonella
typhimurium strain (ATCC Accession No. 202165, also referred to
herein as VNP20009), which is the strain used in the examples below
and used to generate shIDO-ST.
[0061] Optionally, the bacterial cells provided herein comprise one
or more molecules suitable for the treatment of a disease or
disorder. Optionally, the disease or disorder is cancer. Thus, the
bacterial cell can comprise one or more agents capable of blocking,
inhibiting or suppressing target gene expression or a target
protein activity including, but not limited to, antibodies or
functional fragments thereof, small molecules, aptamers, nucleic
acids and RNA interference molecules (e.g., small interfering RNA
(siRNA), microRNA (miRNA) and small hairpin RNA (shRNA)).
Optionally, the bacterial cell comprises a functional nucleic acid,
e.g., an antisense nucleic acid.
[0062] Functional nucleic acids are nucleic acid molecules that
have a specific function, such as binding a target molecule or
catalyzing a specific reaction. Functional nucleic acid molecules
can interact with any macromolecule, such as DNA, RNA,
polypeptides, or carbohydrate chains. Thus, functional nucleic
acids can interact with a target molecule directly. Often
functional nucleic acids are designed to interact with other
nucleic acids based on sequence homology between the target
molecule and the functional nucleic acid molecule.
[0063] Antisense nucleic acids or antisense oligonucleotides (ASOs)
are designed to interact with a target nucleic acid molecule
through either canonical or non-canonical base pairing. The
interaction of the antisense molecule and the target molecule is
designed to promote the destruction of the target molecule through,
for example, RNAseH mediated RNA-DNA hybrid degradation.
Alternatively the antisense molecule is designed to interrupt a
processing function that normally would take place on the target
molecule, such as transcription or replication. Antisense molecules
can be designed based on the sequence of the target molecule.
Numerous methods for optimization of antisense efficiency by
finding the most accessible regions of the target molecule exist.
See for example, Vermeulen et al., RNA 13: 723-730 (2007) and in
WO2007/095387 and WO 2008/036825; Yue, et al., Curr. Genomics,
10(7):478-92 (2009) and Lennox Gene Ther. 18(12):1111-20 (2011),
which are incorporated by reference herein in their entireties.
Optionally, the antisense nucleic acid is a short haripin RNA,
which is a sequence of RNA that makes a tight hairpin turn.
Optionally, the antisense nucleic acid is an siRNA or an miRNA.
Antisense nucleic acid can be designed and made using standard
nucleic acid synthesis techniques or obtained from a commercial
entity, e.g., Sigma-Aldrich (St. Louis, Mo.) or Regulus
Therapeutics (San Diego, Calif.).
[0064] Optionally, the backbone of the antisense nucleic acid is
modified by various chemical modifications to improve the in vitro
and in vivo stability and to improve the in vivo delivery of
antisense molecules. Modifications of antisense molecules include,
but are not limited to, 2'-O-methyl modifications, 2'-O-methyl
modified ribose sugars with terminal phosphorothioates and a
cholesterol group at the 3' end, 2'-O-methoxyethyl (2'-MOE)
modifications, 2'-fluoro modifications, and 2',4' methylene
modifications (referred to as "locked nucleic acids" or LNAs).
Thus, inhibitory nucleic acids include, for example, modified
oligonucleotides (2'-O-methylated or 2'-O-methoxyethyl), locked
nucleic acids (LNA; see, e.g, Valoczi et al., Nucleic Acids Res.
32(22):e175 (2004)), morpholino oligonucleotides (see, e.g,
Kloosterman et al., PLoS Biol 5(8):e203 (2007)), peptide nucleic
acids (PNAs), PNA-peptide conjugates, and LNA/2'-O-methylated
oligonucleotide mixmers (see, e.g., Fabiani and Gait, RNA 14:336-46
(2008)).
[0065] Optionally, the antisense nucleic acid targets a metabolic
enzyme, an immunosuppressive target or a cancer target. Optionally,
the antisense nucleic acid targets an immunosuppressive target and
the immunosuppressive target is STAT3, IDO1, IDO2, Arginase 1,
iNOS, CTLA-4, TGF-.beta., IL-10, pGE2 or VEGF. Optionally, the
immunosuppressive target is IDO1.
[0066] Suppression, inhibition or blockade of the immunosuppressive
target gene or protein ultimately results in disruption of
tumor-derived immunosuppression within the tumor microenvironment
through direct or indirect mechanisms. Thus, the agent may be an
antisense nucleic acid that targets STAT3, IDO1, IDO2, Arginase 1
(Arg1), iNOS, CTLA-4, IL-10, VEGF, pEGF2, or TGF-.beta.. These
targets including their amino acid and nucleic acid sequences are
known and, as is known and described herein, the nucleic acid
sequences of these targets can be used to generate inhibitory
nucleic acid molecules including antisense oligonucleotides and
short hairpin RNA using known methods. By way of example, the
bacterial cells can comprise one or more of any of the following
antisense nucleic acids of SEQ ID NOs: 3-31. Thus, the antisense
nucleic acid can target STAT3 and can be short hairpin RNA
comprising shSTAT3 #58: AGTTCCTGGCACCTTGGATTGAGAGTCAA (SEQ ID
NO:3), shSTAT3 #59: ACTGGATAACTTCATTAGCAGAATCTCAA (SEQ ID NO:4),
shSTAT3 #60: CATCAATCCTGTGGTATAACATGCTGACC (SEQ ID NO:5), or
shSTAT3 #61: ACCTGAAGACCAAGTTCATCTGTGTGACA (SEQ ID NO:6). The
antisense nucleic acid can target IDO1 and can be short hairpin RNA
comprising shIDO1-8: CCTCGCAATAGTAGATACT (SEQ ID NO:7), shIDO1-9:
CGTCTCTCTATTGGTGGAA (SEQ ID NO:8), shIDO1-10: GCAAAGAATCTCCTGCAGA
(SEQ ID NO:9), shIDO1-11: GCCCATGACATACGAGAAC (SEQ ID NO:10), or
shIDO1-12: CCAGTCCGTGAGTTTGTCA (SEQ ID NO:11). The antisense
nucleic acid can target Arg1 and can be short hairpin RNA
comprising shArg1-5: GCAGTTCCTTTCTGGTATG (SEQ ID NO:12), shArg1-6:
GCCTTTGTTGATGTCCCT (SEQ ID NO:13), shArg1-7: CCAGGGACTGACTACCTTA
(SEQ ID NO:14), shArg1-8: GCCAAAGACATCGTGTACA (SEQ ID NO:15), or
shArg1-9: TCTCTACATCACAGAAGA (SEQ ID NO:16). The antisense nucleic
acid can target iNOS and can be short hairpin RNA comprising
shiNOS-43: GTATTGTACTATTGTGGACTA (SEQ ID NO:17), shiNOS-44:
CCAGTATTATGGCTCCTTTAA (SEQ ID NO:18), shiNOS-45:
GCCACAGCAATATAGGCTCAT (SEQ ID NO:19), shiNOS-46:
CCTATCTCCATTCTACTACTA (SEQ ID NO:20), or shiNOS-47:
GCTGTAACAAAGGAAATAGAA (SEQ ID NO:21). The antisense nucleic acid
can target IDO2 and can be short hairpin RNA comprising
CGCAGTTATGAGCTTTCTTAA (SEQ ID NO:22), CCGCAGTTATGAGCTTTCTTA (SEQ ID
NO:23), CCTGGGATAAAGGCTCTTGTT (SEQ ID NO:24), GAAAGCTATCACATATCTGAA
(SEQ ID NO:25), CTTTGGAAAGCTATCACATAT (SEQ ID NO:26),
CCATTGTCTTTGGAAAGCTAT (SEQ ID NO:27), CTTCTTCCAGATTCTCTGAAA (SEQ ID
NO:28), GCTTCAAGCTCATGTGGACAA (SEQ ID NO:29), CAAGGAATCTTGCCCTTCCAT
(SEQ ID NO:30), GCAGTGCCATTGTCTTTGGAA (SEQ ID NO:31). As discussed
above, antisense molecules can be readily designed and obtained
using the nucleic acid sequence of a known target using known
methods. For example, antisense molecules can be designed and made
using standard nucleic acid synthesis techniques or obtained from a
commercial entity, e.g., Regulus Therapeutics (San Diego,
Calif.).
[0067] The agents capable of blocking, inhibiting or suppressing
target gene expression or a target protein activity, e.g.,
antisense nucleic acids, can be expressed from an expression vector
or cassette in the bacterial cell. Suitable expression vectors,
e.g., plasmids, and their methods of use are known.
[0068] Provided herein are compositions including the agents
provided herein. Provided compositions can include a single agent,
e.g., a bacterial cell or more than one agent, e.g., a bacterial
cell and tumor penetrating agent. The provided compositions are,
optionally, suitable for formulation and administration in vitro or
in vivo. Optionally, the compositions comprise one or more of the
provided agents and a pharmaceutically acceptable carrier. Suitable
carriers and their formulations are described in Remington: The
Science and Practice of Pharmacy, 21st Edition, David B. Troy, ed.,
Lippicott Williams & Wilkins (2005). By pharmaceutically
acceptable carrier is meant a material that is not biologically or
otherwise undesirable, i.e., the material is administered to a
subject without causing undesirable biological effects or
interacting in a deleterious manner with the other components of
the pharmaceutical composition in which it is contained. If
administered to a subject, the carrier is optionally selected to
minimize degradation of the active ingredient and to minimize
adverse side effects in the subject.
[0069] The term "pharmaceutically acceptable salts" or
"pharmaceutically acceptable carrier" is meant to include salts of
the active agents which are prepared with relatively nontoxic acids
or bases, depending on the particular substituents found on the
agents described herein. When agents of the present application
contain relatively acidic functionalities, base addition salts can
be obtained by contacting the neutral form of such agents with a
sufficient amount of the desired base, either neat or in a suitable
inert solvent. Examples of pharmaceutically acceptable base
addition salts include sodium, potassium, calcium, ammonium,
organic amino, or magnesium salt, or a similar salt. When agents of
the present application contain relatively basic functionalities,
acid addition salts can be obtained by contacting the neutral form
of such agents with a sufficient amount of the desired acid, either
neat or in a suitable inert solvent. Examples of pharmaceutically
acceptable acid addition salts include those derived from inorganic
acids like hydrochloric, hydrobromic, nitric, carbonic,
monohydrogencarbonic, phosphoric, monohydrogenphosphoric,
dihydrogenphosphoric, sulfuric, monohydrogensulfuric, hydriodic, or
phosphorous acids and the like, as well as the salts derived from
relatively nontoxic organic acids like acetic, propionic,
isobutyric, maleic, malonic, benzoic, succinic, suberic, fumaric,
lactic, mandelic, phthalic, benzenesulfonic, p-tolylsulfonic,
citric, tartaric, methanesulfonic, and the like. Also included are
salts of amino acids such as arginate and the like, and salts of
organic acids like glucuronic or galactunoric acids and the like
(see, e.g., Berge et al., Journal of Pharmaceutical Science 66:1-19
(1977)). Other pharmaceutically acceptable carriers known to those
of skill in the art are suitable for compositions of the present
application.
[0070] The agents are administered in accord with known methods,
such as intravenous administration, e.g., as a bolus or by
continuous infusion over a period of time, by intramuscular,
intraperitoneal, intracerobrospinal, subcutaneous, intra-articular,
intrasynovial, intrathecal, intracavity, transdermal, oral,
topical, intratumoral, parenteral, or inhalation routes. Thus, the
compositions are administered in a number of ways depending on
whether local or systemic treatment is desired, and on the area to
be treated.
[0071] The compositions for administration will commonly comprise
an agent as described herein dissolved in a pharmaceutically
acceptable carrier, preferably an aqueous carrier. A variety of
aqueous carriers can be used, e.g., buffered saline and the like.
These solutions are sterile and generally free of undesirable
matter. These compositions may be sterilized by conventional, well
known sterilization techniques. The compositions may contain
pharmaceutically acceptable auxiliary substances as required to
approximate physiological conditions such as pH adjusting and
buffering agents, toxicity adjusting agents and the like, for
example, sodium acetate, sodium chloride, potassium chloride,
calcium chloride, sodium lactate and the like. The concentration of
active agent in these formulations can vary widely, and will be
selected primarily based on fluid volumes, viscosities, body weight
and the like in accordance with the particular mode of
administration selected and the subject's needs.
[0072] Solutions of the active agents as free base or
pharmacologically acceptable salt can be prepared in water suitably
mixed with a surfactant, such as hydroxypropylcellulose.
Dispersions can also be prepared in glycerol, liquid polyethylene
glycols, and mixtures thereof and in oils. Under ordinary
conditions of storage and use, these preparations can contain a
preservative to prevent the growth of microorganisms.
[0073] Oral formulations can include excipients as, for example,
pharmaceutical grades of mannitol, lactose, starch, magnesium
stearate, sodium saccharine, cellulose, magnesium carbonate and the
like. These compositions take the form of solutions, suspensions,
tablets, pills, capsules, sustained release formulations or
powders. In some embodiments, oral pharmaceutical compositions will
comprise an inert diluent or assimilable edible carrier, or they
may be enclosed in hard or soft shell gelatin capsule, or they may
be compressed into tablets, or they may be incorporated directly
with the food of the diet. For oral therapeutic administration, the
active agents may be incorporated with excipients and used in the
form of ingestible tablets, buccal tablets, troches, capsules,
elixirs, suspensions, syrups, wafers, and the like. Such
compositions and preparations should contain at least 0.1% of
active agent. The percentage of the compositions and preparations
may, of course, be varied and may conveniently be between about 2
to about 75% of the weight of the unit, or preferably between
25-60%. The amount of active agents in such compositions is such
that a suitable dosage can be obtained
[0074] For parenteral administration in an aqueous solution, for
example, the solution should be suitably buffered and the liquid
diluent first rendered isotonic with sufficient saline or glucose.
Aqueous solutions, in particular, sterile aqueous media, are
especially suitable for intravenous, intramuscular, subcutaneous
and intraperitoneal administration. For example, one dosage could
be dissolved in 1 ml of isotonic NaCl solution and either added to
1000 ml of hypodermoclysis fluid or injected at the proposed site
of infusion
[0075] Sterile injectable solutions can be prepared by
incorporating the active agents or constructs in the required
amount in the appropriate solvent followed by filtered
sterilization. Generally, dispersions are prepared by incorporating
the various sterilized active ingredients into a sterile vehicle
which contains the basic dispersion medium. Vacuum-drying and
freeze-drying techniques, which yield a powder of the active
ingredient plus any additional desired ingredients, can be used to
prepare sterile powders for reconstitution of sterile injectable
solutions. The preparation of more, or highly, concentrated
solutions for direct injection is also contemplated. DMSO can be
used as solvent for extremely rapid penetration, delivering high
concentrations of the active agents to a small area.
[0076] The formulations of agents can be presented in unit-dose or
multi-dose sealed containers, such as ampules and vials. Thus, the
composition can be in unit dosage form. In such form the
preparation is subdivided into unit doses containing appropriate
quantities of the active component. Thus, the compositions can be
administered in a variety of unit dosage forms depending upon the
method of administration. For example, unit dosage forms suitable
for oral administration include, but are not limited to, powder,
tablets, pills, capsules and lozenges.
[0077] The compositions and agents as described herein are useful
for both prophylactic and therapeutic treatment. For prophylactic
use, a therapeutically effective amount of the agents described
herein are administered to a subject prior to or during early onset
(e.g., upon initial signs and symptoms of cancer). Therapeutic
treatment involves administering to a subject a therapeutically
effective amount of the agents described herein after diagnosis or
development of disease.
[0078] Provided herein is a method of treating cancer in a subject
comprising administering to the subject an effective amount, e.g.,
a combined effective amount, of a bacterial cell and a tumor
penetrating agent, wherein administration treats the cancer in the
subject. Optionally, the effective amount or combined effective
amount is a synergistic amount or combined synergistic effective
amount. Also provided is a method of stimulating an immune system
in a subject comprising administering to the subject an effective
amount of a bacterial cell and a tumor penetrating agent, wherein
administration of the bacterial cell and the tumor penetrating
agent stimulates the immune system of the subject. Optionally, the
immune response is an anti-cancer immune response. Optionally, the
provided methods further include administering to the subject an
anti-cancer agent. Optionally, the anti-cancer agent is
administered subsequent to administration of the bacterial cell and
tumor penetrating agent.
[0079] Further provided is a method of enhancing delivery of an
anti-cancer agent to a tumor cell comprising contacting the tumor
cell with a bacterial cell, a tumor penetrating agent and an
anti-cancer agent, wherein administration of the bacterial cell and
cell penetrating agent enhances delivery of the anti-cancer
agent.
[0080] Anti-cancer agent can be selected from the group consisting
of a small molecule, a nucleic acid, a polypeptide, and an
antibody. Anti-cancer agents are known to those of skill in the
art. See, e.g., Physician's Drug Handbook, 12.sup.th Edition,
Lippincott, Williams & Wilkins, (2007) or Physician's Cancer
Chemotherapy Drug Manual 2013, by Chu and DeVita, Jones &
Bartlett Learning, LLC, (2013). Optionally, the anti-cancer agent
is a chemotherapeutic agent. Chemotherapeutic agents are agents
which may inhibit the growth of tumors. Such agents, include, but
are not limited to 5-fluorouracil; gemcitabine; mitomycin C;
methotrexate; hydroxyurea; cyclophosphamide; dacarbazine;
mitoxantrone; anthracyclins (epirubicin and doxurubicin);
antibodies to receptors, such as herceptin; etoposide; pregnasome;
hormone therapies such as tamoxifen and anti-estrogens;
interferons; aromatase inhibitors; progestational agents; and LHRH
analogs.
[0081] Optionally, in the provided methods the tumor penetrating
agent is administered prior to the bacterial cell. When the methods
include administration of an anti-cancer agent, the anti-cancer
agent can be administered after administration of the bacterial
cell and/or tumor penetrating agent. Thus, combinations of agents
or compositions can be administered either concomitantly (e.g., as
a mixture), separately but simultaneously (e.g., via separate
intravenous lines) or sequentially (e.g., one agent is administered
first followed by administration of the second agent). Thus, the
term combination is used to refer to concomitant, simultaneous or
sequential administration of two or more agents or
compositions.
[0082] In the provided methods, the bacterial cell and
hyaluronidase polypeptide are, optionally, present in an effective
amount, e.g., a synergistic effective amount. Optionally, the
bacterial cell is a Salmonella bacterial cell. Optionally, the
tumor penetrating agent is a hyaluronidase polypeptide. Optionally,
the hyaluronidase polypeptide comprises SEQ ID NO:1 or SEQ ID NO:2
or a fragment thereof. Hyaluronidase polypeptides suitable for use
in the provided compositions, kits and methods are described in
U.S. Pat. Nos. 7,767,429; 7,829,081; 7,846,431; 7,871,607;
8,105,586; 8,202,517; 8,257,699; 8,431,380; and 8,450,470, each of
which are incorporated by reference herein in their entirety.
Optionally, the hyaluronidase polypeptide is a modified
hyaluronidase polypeptide. Optionally, the hyaluronidase
polypeptide is pegylated. Optionally, the hyaluronidase polypeptide
is PEGPH20.TM. (Halozyme, Inc., San Diego, Calif.).
[0083] Optionally, the tumor penetrating agent is selected from the
group consisting of pirfenidone (Kozono et al., Cancer Res.
73(7):2345-56 (2013)), IPI-929 (Olive et al., Science
324(5933):1457-61 (2009)), nanoparticles, albumin nanoparticles,
dextrans, liposomes, and cell penetrating peptides.
[0084] Bacterial cells useful in the provided methods include, but
are not limited to, Salmonella bacterial cells, Bifidobacteria
bacterial cells, Listeria monocytogenes bacterial cells,
Clostridium histolyticus bacterial cells, Clostridium novyi
bacterial cells, Vibrio cholera bacterial cells, Shigella bacterial
cells, Streptococcus bacterial cells, Mycobacterium bovis bacterial
cells, Yersinia enterocolitica bacterial cells, Bacillus anthracis
bacterial cells, Lactobacillus bacterial cells, Staphylococcus
bacterial cells, E. coli bacterial cells. Optionally, the
Streptococcus bacterial cells are Streptococcus pyrogenes bacterial
cells or Streptococcus gordonii bacterial cells. Suitable bacterial
cells include bacterial cells described in International
Publication No. WO 2012/149364, which is incorporated by reference
herein in its entirety. Optionally, the Salmonella bacterial cell
is an attenuated Salmonella strain. Optionally, the Salmonella
bacterial cell is a Salmonella choleraesuis bacterial cells.
Optionally, the Salmonella bacterial cell is an attenuated strain
of Salmonella typhimurium. Attenuated Salmonella typhimurium
strains include, but are not limited to, YS1646, RE88, LH430,
SL7207, .chi.8429, .chi.8431 or .chi.8468. Optionally, the
attenuated Salmonella typhimurium strain is an YS1646 Salmonella
typhimurium strain (ATCC Accession No. 202165, also referred to
herein as VNP20009). Optionally, Toxoplasma gondii cells can be
used in the provided compositions, kits and methods.
[0085] Optionally, the bacterial cells provided herein comprise one
or more molecules suitable for the treatment of a disease or
disorder. Thus, the bacterial cell can comprise one or more agents
capable of blocking, inhibiting or suppressing target gene
expression or a target protein activity including, but not limited
to, antibodies or functional fragments thereof, small molecules,
aptamers, nucleic acids and RNA interference molecules (e.g., small
interfering RNA (siRNA), microRNA (miRNA) and small hairpin RNA
(shRNA)). Optionally, the bacterial cell comprises a functional
nucleic acid, e.g., an antisense nucleic acid. Optionally, the
antisense nucleic acid targets a metabolic enzyme, an
immunosuppressive target or a cancer target. Optionally, the
antisense nucleic acid targets an immunosuppressive target and the
immunosuppressive target is STAT3, IDOL IDO2, Arginase 1, iNOS,
CTLA-4, TGF-.beta., IL-10, pGE2 or VEGF. Optionally, the
immunosuppressive target is IDO1. Optionally, the antisense nucleic
acid is selected from the group consisting of SEQ ID NOs:3-31.
[0086] By "effective dose or amount" herein is meant a dose that
produces effects for which it is administered. By "combined
effective dose or amount" herein is meant a dose of two or more
agents administered concomitantly (e.g., as a mixture), separately
but simultaneously (e.g., via separate intravenous lines) or
sequentially (e.g., one agent is administered first followed by
administration of the second agent), that produces effects for
which it is administered. For example, therapeutically effective
amount or combined effect amount includes that amount of an agent
or combination of agents sufficient to reduce or ameliorate one or
more symptoms of a disease or disorder. For example, for the given
parameter, an effective amount will show an increase or decrease of
at least 5%, 10%, 15%, 20%, 25%, 40%, 50%, 60%, 75%, 80%, 90%, or
at least 100%. Efficacy can also be expressed as "-fold" increase
or decrease. For example, a therapeutically effective amount can
have at least a 1.2-fold, 1.5-fold, 2-fold, 5-fold, or more effect
over a control. The exact dose and formulation will depend on the
purpose of the treatment, and will be ascertainable by one skilled
in the art using known techniques (see, e.g., Lieberman,
Pharmaceutical Dosage Forms (vols. 1-3, 1992); Lloyd, The Art,
Science and Technology of Pharmaceutical Compounding (1999);
Remington: The Science and Practice of Pharmacy, 20th Edition,
Gennaro, Editor (2003), and Pickar, Dosage Calculations
(1999)).
[0087] The terms "synergistic," "synergistic effect," "synergistic
therapeutic effect," "synergistically effective amount" and the
like in the context of co-administration of agents described herein
refer to a more than additive (e.g., supra-additive) response
(e.g., biological response) when two or more agents are
administered with respect to the summed effects upon administration
of each agent in the absence of the other agent or agents. For
example, if two agents provide a synergistic therapeutic effect,
then the therapeutic effect observed upon co-administration of both
agents is greater than the summed observed therapeutic effects when
either agent is administered in the absence of the other agent.
Likewise, a first amount of a first agent and a second amount of a
second agent together provide a synergistically effective amount
where the therapeutic effect observed upon co-administration of
both agents is greater than the summed observed therapeutic effects
when either agent is administered in the absence of the other
agent.
[0088] As used herein the terms treatment, treat, or treating
refers to a method of reducing the effects of one or more symptoms
of a disease or condition characterized by expression of the
protease or symptom of the disease or condition characterized by
expression of the protease. Thus in the disclosed method, treatment
can refer to a 10%, 20%, 30%, 40%, 50%, 60%, 70%, 80%, 90%, or 100%
reduction in the severity of an established disease, condition, or
symptom of the disease or condition. For example, a method for
treating a disease is considered to be a treatment if there is a
10% reduction in one or more symptoms of the disease in a subject
as compared to a control. Thus the reduction can be a 10%, 20%,
30%, 40%, 50%, 60%, 70%, 80%, 90%, 100%, or any percent reduction
in between 10% and 100% as compared to native or control levels. It
is understood that treatment does not necessarily refer to a cure
or complete ablation of the disease, condition, or symptoms of the
disease or condition. Further, as used herein, references to
decreasing, reducing, or inhibiting include a change of 10%, 20%,
30%, 40%, 50%, 60%, 70%, 80%, 90% or greater as compared to a
control level and such terms can include but do not necessarily
include complete elimination.
[0089] A "subject," "individual," or "patient," is used
interchangeably herein, which refers to a vertebrate, preferably a
mammal, more preferably a human. Mammals include, but are not
limited to, murines, simians, humans, farm animals, sport animals,
and pets. Tissues, cells and their progeny of a biological entity
obtained in vitro or cultured in vitro are also encompassed.
[0090] Provided herein are kits comprising one or more of the
provided compositions. Thus, provided are kits comprising a
bacterial cell and a tumor penetrating agent. Optionally, the
bacterial cell and tumor penetrating agent are present in an
effective amount, e.g., a synergistic effective amount. Optionally,
the kits comprise a first composition comprising a Salmonella
bacterial cell and a second composition comprising a hyaluronidase
polypeptide. Optionally, the Salmonella bacterial cell and
hyaluronidase polypeptide are present in an effective amount, e.g.,
a synergistic effective amount. Optionally, the compositions are
present in a container such as a vial or packet. Optionally, the
kit comprises one or more additional agents. Thus, for example, the
kit further includes an additional therapeutic agent, e.g., an
anti-cancer agent. The additional therapeutic agent may be included
in a composition comprising the bacterial cell and/or tumor
penetrating agent or formulated as a separate composition.
Optionally, the kit comprises a means of administering the
compositions, such as, for example, a syringe, needle, tubing,
catheter, patch, and the like. The kit may also comprise
formulations and/or materials requiring sterilization and/or
dilution prior to use. Optionally, the provided kits include
instructions for use.
[0091] Disclosed are materials, compositions, and components that
can be used for, can be used in conjunction with, can be used in
preparation for, or are products of the disclosed methods and
compositions. These and other materials are disclosed herein, and
it is understood that when combinations, subsets, interactions,
groups, etc. of these materials are disclosed that while specific
reference of each various individual and collective combinations
and permutations of these agents may not be explicitly disclosed,
each is specifically contemplated and described herein. For
example, if a method is disclosed and discussed and a number of
modifications that can be made to a number of molecules including
the method are discussed, each and every combination and
permutation of the method, and the modifications that are possible
are specifically contemplated unless specifically indicated to the
contrary. Likewise, any subset or combination of these is also
specifically contemplated and disclosed. This concept applies to
all aspects of this disclosure including, but not limited to, steps
in methods using the disclosed compositions. Thus, if there are a
variety of additional steps that can be performed, it is understood
that each of these additional steps can be performed with any
specific method steps or combination of method steps of the
disclosed methods, and that each such combination or subset of
combinations is specifically contemplated and should be considered
disclosed.
[0092] Publications cited herein and the material for which they
are cited are hereby specifically incorporated by reference in
their entireties.
[0093] A number of embodiments have been described. Nevertheless,
it will be understood that various modifications may be made.
Accordingly, other embodiments are within the scope of the
claims.
Example
Example 1. Combination of shIDO-ST and PEGPH20.TM. for Cancer
Treatment
[0094] To determine the effects of shIDO-ST and PEGPH20.TM., nine
C57BL/6 mice were injected orthotopically (in the pancreas) with
5.times.10.sup.5 KPC-luc cells. Three small groups (n=3) were
created: shIDO-ST alone, PEGPH20.TM. alone, and shIDO-ST with
PEGPH20.TM.. The shIDO-ST alone group received shIDO-ST at a dose
of 5.times.10.sup.6 cfu/mouse through intravenous (i.v.) injection
on days 8 and 12. PEGPH20.TM. alone group received PEGPH20.TM. at a
dose of 4.5 mg/kg HO (.about.90 ug/mouse) on day 7 through i.v.
injection. The combination (PEGPH20.TM. with shIDO-ST) group
received PEGPH20.TM. at 4.5 mg/kg on day 7 followed by treatment
with shIDO-ST on day 8 at 5.times.10.sup.6 cfu/mouse. Mice were
imaged using an intravital imaging system (IVIS) at indicated time
points after tumor cell implantation. Mice were injected with
D-luciferin at indicated days and imaged 5-10 minutes
post-injection. Exposure time was 2 seconds for all time points. In
both the shIDO-ST group and combination group, mice exhibited signs
of sickness due to toxicity of the shIDO-ST, which was likely a
result of too high a dose. Tumor reduction in the combination
group, and to a lesser degree in the shIDO-ST alone group, was
observed. Mice in the PEGPH20.TM. group were euthanized due to
significantly large tumors which caused problems with mobility in
all cases and sickness in two of the three mice.
[0095] Titration of combination treatment with shIDO-ST and
PEGPH20.TM. was performed to reduce the toxicity observed in
initial experiment (FIG. 2). Three groups, representing three
different dose combinations of shIDO-ST and PEGPH20.TM., were
generated to determine optimal doses that would continue to control
tumor growth with little to no toxicity. Groups consisted of full
dose of PEGPH20.TM. (.about.90 ug) with half dose of shIDO-ST
(2.5.times.10.sup.6 cfu/mouse, i.e. 2.5 million (2.5M)), half dose
of PEGPH20.TM. with full dose of shIDO-ST, or half doses of both. A
control group was added that consisted of full dose of PEGPH20.TM.
and full dose of the scrambled (shScr-ST) control that is not
specific to any gene target. As before, mice received PEGPH20.TM.
on day 7 and shIDO-ST or shScr-ST on day 8. In this experiment, no
mice were observed to become ill due to treatment using the
mentioned doses. Mice receiving the full dose of PEGPH20.TM. with a
half dose of shIDO-ST controlled tumors initially, but tumors
rebounded quickly, resulting in euthanization of the group due to
large tumors. The group receiving a half dose of PEGPH20.TM. and
full dose of shIDO-ST significantly controlled tumors and in 2 of 3
mice resulted in complete cure of KPC-luc over 80 days post tumor
injection. In 1 of 3 mice where tumor was still apparent, a second
treatment at the same dose was given on day 56-57. Although some
regression of tumor signal occurred, the tumor continued to grow as
evidenced by continual increase in photon signal (FIG. 3). KPC-luc
tumors in mice given half the dose of both PEGPH20.TM. and shIDO-ST
showed no significant tumor growth control (compare to the
PEGPH20.TM. only group in FIG. 1). The combination of PEGPH20.TM.
with shScr-ST resulted in transient but measurable tumor growth
control, however, tumors rebounded rapidly in 2 of 3 mice, and no
mice were cured of KPC-luc as all mice still had tumors on day 45.
Photons emitted from mice imaged in FIG. 2 were quantitated using
Living Image.RTM. software. Tumors from 45 ug PEGPH20.TM. (PEG) and
5M shIDO-ST treated mice are controlled significantly better than
all other groups (FIG. 3).
[0096] Due to the sensitivity of 7 day KPC-luc tumors to the
combination PEGPH20.TM. and shScr-ST treatment (FIG. 2), treatment
of implanted KPC-luc tumors was delayed to day 14. This allowed
greater establishment of tumors to better compare the efficacy of
shIDO-ST versus shScr-ST in combination with PEGPH20.TM.. This
experiment consisted of 6 treatment groups: 3 groups treated with
PEGPH20.TM. and shScr-ST, shIDO-ST, or gemcitabine (GEM, at 100
mg/kg). The other 3 groups were also treated with either shScr-ST,
shIDO-ST, or GEM, but with no PEGPH20.TM.. Doses (previously
determined from titration studies described in FIG. 2) consisted of
45 ug of PEGPH20.TM. followed by 5.times.10.sup.6 cfu/mouse of
shIDO-ST or shScr-ST. As mentioned previously, mice were started on
treatment on day 14 (with PEGPH20.TM. or vehicle control). Mice
then received a single dose of therapy on day 15. Tumor growth was
visualized longitudinally by IVIS. The images are shown in FIG. 4.
All groups, except for the PEGPH20.TM. and shIDO-ST combination
group were euthanized by day 30 due to significantly large tumors
causing mobility issues or illness in mice. Again, significant
reduction in tumor growth was observed in 2 of 3 mice in the
PEGPH20.TM. and shIDO-ST combination group on days 21 and 30.
Although not as significant, the third mouse also exhibited tumor
control which will extend survival. Tumors reappeared in mice by
day 37. Therefore, a second treatment was administered to these
mice to determine if this could induce further tumor regression. We
saw modest tumor reduction through day 44. Photons emitted from
mice imaged in FIG. 4 were quantitated using Living Image.RTM.
software. Tumors from PEGPH20.TM. (PEG)+shIDO-ST treated mice are
controlled significantly better than all other groups. See FIG. 5.
Further, mice in FIG. 4 were weighed at each imaging point. There
were no significant changes in mouse weight for any group. See FIG.
6.
Example 2. Combination of shArg-ST and PEGPH20.TM. for Cancer
Treatment
[0097] To determine the effects of shArg-ST combined with
PEGPH20.TM., five mice were orthotopically implanted with
5.times.10.sup.5 KPC-luc tumor cells. Two mice were used for the
control group consisting of treatment with PEGPH20.TM. and a
Salmonella (ST) therapy (shScr-ST) carrying an shRNA plasmid that
does not target any known genes (Scr=scrambled). Three mice were
used for the experimental group receiving PEGPH20.TM. and shArg-ST.
All groups received PEGPH20 (90 ug/mouse intravenously) on day 7
and ST therapy on days 8 and 11 (5.times.10.sup.6 cfu/mouse,
intravenously). ShScr-ST control treatment as well as shArg-ST
treatment in combination with PEGPH20.TM. resulted in attenuation
of tumor growth. However, some toxicity was observed. The results
are shown in FIG. 7.
[0098] The doses used for the combination treatment with shIDO-ST
and PEGPH20.TM. were changed to reduce the toxicity observed in the
initial experiment (FIG. 7). Two groups (n=4) with orthotopic
KPC-luc tumors were generated and received PEGPH20.TM. treatment
with either shScr-ST or shArg-ST. PEGPH20.TM. was administered at
45 ug/mouse (half the dose than used previously) at a later time
point, day 9 (as opposed to day 7 in the previous experiment), for
both groups, followed by treatment with shScr-ST or shArg-ST on
days 10 and 13 (at full dose, 5.times.10.sup.6 cfu). Fifty percent
of mice in the control group were still cured of tumor, with the
experimental group working marginally better. Mice receiving
shArg-ST treatment still showed some signs of toxicity. The results
are shown in FIG. 8.
Example 3. Efficacy of shIDO-ST/PEGPH20.TM. Combination Therapy
[0099] To further evaluate the efficacy of shIDO-ST/PEGPH20.TM.
combination therapy, groups of mice were orthotopically implanted
with 0.5 million KPC (KrasLSL.G12D/+; p53R172H/+; PdxCretg/+) cells
expressing luciferase (KPC-luc cells). Fourteen days after
implantation, all mice were treated with indicated therapies
according to the schedule outlined in Table 1.
TABLE-US-00001 TABLE 1 Dose and Schedule of Administered PEGPH20
.TM. and Therapeutics. Dose Schedule Route PEGPH20 .TM. 45
.mu.g/mouse (1X)d0* Intravenous shIDO-ST 5X10.sup.6 cfu/mouse
(3X)d1-d3 Intravenous shScr-ST 5X10.sup.6 cfu/mouse (3X)d1-d3
Intravenous Gemcitabine 100 mg/kg (5X)d1-d5 Intraperitoneal
Abraxane 120 mg/kg (3X)d1, d4, d7 Intravenous *d = day. Day 0 of
treatment corresponds to day 14 post-tumor implantation. shScr-ST
is a Salmonella control that carries a scrambled shRNA sequence
with no specificity.
[0100] At each indicated timepoint, groups were injected with
D-luciferin 5 minutes prior to imaging by intravital imaging using
a Xenogen 100 machine. As shown in FIG. 9, based on the imaging
results, 100% of mice treated with PEGPH20.TM./shIDO-ST were
observed to have substantial tumor regression with nearly 75% of
mice showing remarkable elimination of tumors and indefinite
survival (>1Y) comparable to that of healthy, tumor-free mice.
No other treatment combinations were nearly as effective.
[0101] For statistical analyses, the photons emitted from IVIS
imaging of mouse groups represented in FIG. 9 were quantitated. As
shown in FIG. 10, quantitation of luciferase signal shows that only
mice treated with PEGPH20.TM.+shIDO-ST have statistically
significant control of tumors (p<0.01, ANOVA) compared to all
tested combinations of standard chemotherapies with
PEGPH20.TM..
[0102] Mouse groups represented in FIG. 9 were weighed at each time
point indicated. As shown in FIG. 11, elimination of PDAC tumors
using PEGPH20.TM./shIDO-ST combination therapy was not associated
with any significant toxicity (weight loss). Overall, no treatment
group had any associated weight loss.
[0103] Fourteen day orthotopic tumors from mice untreated or
treated with PEGPH20.TM. were fixed using a modified method
(superior to standard 10% formalin fixation) that utilizes 10% acid
formalin and 70% ethanol for greater intensity staining of
hyaluronan (Lin et al., J Histochem Cytochem 1997). As shown in
FIG. 12, the staining reveals that KPC-luc tumors 14 days after
implantation express significant amounts of hyaluronan. Forty-eight
hours after treatment with PEGPH20.TM., significant depletion of
hyaluronan in sections of KPC-luc tumor tissue was observed (FIG.
12).
[0104] Sections from 14 day tumors of mice untreated or treated
with PEGPH20 were stained with anti-CD31 antibody to locate cross
sections of vessels within the tumor mass. FITC-conjugated
secondary specific to CD31 primary and DAPI staining were
visualized by fluorescence microscopy. As shown in FIG. 13, the
images represent a majority of closed vessels in untreated tumors
and many more open vessels in tumors of mice treated with
PEGPH20.TM..
[0105] Tumor and neutrophils in indicated treatment groups were
imaged over the span of 72 hours after beginning treatment with
Salmonella. Time points represent hours after treatment with
Salmonella (i.e. PEGPH20.TM. was given at -24 hour time point). As
shown in FIG. 14, remarkable migration of neutrophils specifically
into tumor was observed, resulting in regions of overlap, and only
occurs in mice treated with PEGPH20.TM./shIDO-ST. Mice treated with
PEGPH20.TM./shIDO-ST showed dramatic tumor regression coincident
with PMN influx (note 72 hour time point).
[0106] The tumors represented in FIG. 14 for PEGPH20.TM./shScr-ST
and PEGPH20.TM./shIDO-ST mice were resected 96 hours after
Salmonella treatment to confirm presence of PMN specifically within
tumor mass. Mice were injected with near infrared imaging agent
(specific for PMN) 1 hour prior to tumor resection. As seen in FIG.
15, tumor resected from the PEGPH20.TM./shIDO-ST treated mouse
(right) was observed to have significantly more PMN infiltration
compared to PEGPH20/shScr-ST control treated mouse (left).
[0107] Control tumor and tumors represented in FIG. 15 were
sectioned for immunofluorescence staining of Salmonella, PMN, and
intact nuclei (DAPI). Only mice treated with PEGPH20.TM./shIDO-ST
were observed to have dramatic influx of Salmonella and PMN (FIG.
16). PMN were observed to have significant knock down of IDO mRNA
by quantitative PCR. Considerable necrosis of tumor cells (absence
of DAPI staining) is visualized in core of PEGPH20.TM./shIDO-ST
treated tumors (FIG. 16).
[0108] To further explore the effects of PEGPH20.TM./shIDO-ST
combination treatment, a genetically engineered mouse model (GEMM)
that incorporates Kras, p53, and Brca1 mutations conditionally
expressed in the presence of Cre (KPC-Brca1) specifically in the
pancreas, resulting in spontaneous pancreatic cancer, was treated.
Spleen and pancreas on the left were extracted from a 12 week old
normal C57BL/6 mouse, whereas the spleen and pancreas to the right
were taken from a KPC-Brca1 mouse which was treated at 7 weeks old
with PEGPH20.TM./shIDO-ST. The treatment schedule is outlined in
FIG. 18. The treated KPC-Brca1 mouse was euthanized 5 weeks later
(at 12 weeks of age). As shown in FIG. 17, the KPC-Brca1 mouse was
observed to have a significantly smaller pancreas when compared to
a normal sized pancreas.
[0109] Additional experiments were then performed in KPC-Brca1 mice
with appropriate control treated mice (i.e. PEGPH20.TM./shScr-ST).
Male and female KPC-Brca1 mice were treated with PEGPH20.TM. and
either shScr-ST or shIDO-ST using the treatment schedule outlined
in FIG. 18. Again, significant control/reduction in tumor size in
mice treated with PEGPH20.TM./shIDO-ST compared to those treated
with PEGPH20.TM./shScr-ST, indicating efficacy in a rigorous
autochthonous/spontaneous model (FIG. 19).
* * * * *