U.S. patent application number 17/481243 was filed with the patent office on 2022-03-10 for predicting t cell epitopes useful for vaccination.
The applicant listed for this patent is BioNTech RNA Pharmaceuticals GmbH, TRON-Translationale Onkologie an der Universitatsmedizin der Johannes Gutenberg-. Invention is credited to Sebastian Boegel, Sebastian Kreiter, Martin Lower, Ugur Sahin, Barbara Schrors, Arbel D. Tadmor, Mathias Vormehr.
Application Number | 20220074948 17/481243 |
Document ID | / |
Family ID | 52469061 |
Filed Date | 2022-03-10 |
United States Patent
Application |
20220074948 |
Kind Code |
A1 |
Sahin; Ugur ; et
al. |
March 10, 2022 |
PREDICTING T CELL EPITOPES USEFUL FOR VACCINATION
Abstract
The present invention relates to methods for predicting T cell
epitopes useful for vaccination. In particular, the present
invention relates to methods for predicting whether modifications
in peptides or polypeptides such as tumor-associated neoantigens
are immunogenic and, in particular, useful for vaccination, or for
predicting which of such modifications are most immunogenic and, in
particular, most useful for vaccination. The methods of the
invention may be used, in particular, for the provision of vaccines
which are specific for a patient's tumor and thus, in the context
of personalized cancer vaccines.
Inventors: |
Sahin; Ugur; (Mainz, DE)
; Lower; Martin; (Mainz, DE) ; Tadmor; Arbel
D.; (Bodenheim, DE) ; Boegel; Sebastian;
(Obermoschel, DE) ; Schrors; Barbara; (Mainz,
DE) ; Vormehr; Mathias; (Mainz, DE) ; Kreiter;
Sebastian; (Mainz, DE) |
|
Applicant: |
Name |
City |
State |
Country |
Type |
BioNTech RNA Pharmaceuticals GmbH
TRON-Translationale Onkologie an der Universitatsmedizin der
Johannes Gutenberg- |
Mainz
Mainz |
|
DE
DE |
|
|
Family ID: |
52469061 |
Appl. No.: |
17/481243 |
Filed: |
September 21, 2021 |
Related U.S. Patent Documents
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Application
Number |
Filing Date |
Patent Number |
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15550286 |
Aug 10, 2017 |
11156617 |
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PCT/EP16/52684 |
Feb 9, 2016 |
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17481243 |
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Current U.S.
Class: |
1/1 |
Current CPC
Class: |
A61P 35/00 20180101;
G01N 33/505 20130101; G01N 33/6845 20130101; G01N 2500/04 20130101;
A61K 39/0011 20130101; G01N 2333/70539 20130101 |
International
Class: |
G01N 33/68 20060101
G01N033/68; G01N 33/50 20060101 G01N033/50; A61K 39/00 20060101
A61K039/00 |
Foreign Application Data
Date |
Code |
Application Number |
Feb 12, 2015 |
EP |
PCT/EP15/53021 |
Claims
1.-29. (canceled)
30. A method for predicting immunogenicity of an amino acid
modification, the method comprising steps of: a) ascertaining a
score for binding of a modified peptide comprising a fragment of a
modified protein to one or more MHC class II molecules ("its MHC
class II binding score"); b) ascertaining a score for expression or
abundance (its "abundance score") of the modified protein; and c)
predicting immunogenicity of the amino acid modification based on
the score for binding of the modified peptide to the one or more
MHC class II molecules and the score for expression or abundance of
the modified protein.
31. The method of claim 31, wherein predicting immunogenicity of an
amino acid modification comprises predicting whether a peptide
comprising an amino acid modification will be immunogenic.
32. A method for selecting and/or ranking immunogenic amino acid
modifications, the method comprising steps of: a) ascertaining a
score for binding of a modified peptide comprising a fragment of a
modified protein to one or more MHC class II molecules ("its MHC
class II binding score"); b) ascertaining a score for expression or
abundance (its "abundance score") of the modified protein; c)
performing steps a) and b) for two or more different immunogenic
amino acid modifications; and d) selecting and/or ranking the two
or more different immunogenic amino acid modifications by comparing
the MHC class II binding scores of the corresponding modified
peptide and the abundance scores for the corresponding modified
protein.
33. The method of claim 32, wherein selecting and/or ranking the
two or more different immunogenic amino acid modifications
comprises a selection and/or ranking of peptides comprising the two
or more different immunogenic amino acid modifications for their
immunogenicity.
34. The method of claim 32, wherein comparing the MHC class II
binding scores and the abundance scores comprises ranking the two
or more different amino acid modifications by their MHC class II
binding scores and removing amino acid modifications for which the
corresponding modified protein has an expression or abundance of
less than a given threshold.
35. The method of claim 30, wherein the modified protein comprises
a tumor-associated neoantigen of a patient.
36. The method of claim 35, wherein the tumor-associated neoantigen
is a peptide or protein comprising a tumor-specific amino acid
modification.
37. The method of claim 30, wherein the MHC class II binding score
reflects a probability for binding of the modified peptide to the
one or more MHC class II molecules.
38. The method claim 30, wherein the abundance score is based on a
score for level of expression of a protein to which the one or more
amino acid modifications are associated and a score for variant
allele frequency for the modified protein.
39. The method of claim 38, wherein the abundance score is
determined by multiplying the score for level of expression of the
protein to which the one or more amino acid modifications are
associated with the score for variant allele frequency of the
modified protein.
40. The method of claim 38, wherein the score for variant allele
frequency is determined from a sum of detected sequence reads
covering mutation site(s) corresponding to the amino acid
modification(s) and carrying the amino acid modification(s) divided
by a sum of all detected sequence reads covering the mutation
site(s).
41. The method of claim 38, wherein the score for variant allele
frequency is determined from a sum of mutated nucleotides detected
at the mutation site(s) corresponding to the one or more amino acid
modifications divided by a sum of all nucleotides detected at the
mutation site(s).
42. The method of claim 30, wherein two or more different amino
acid modifications are present in the same and/or in different
modified proteins.
43. The method of claim 30, further comprising performing step a)
on two or more different modified peptides, said two or more
different modified peptides comprising the same amino acid
modification(s).
44. The method of claim 43, wherein the two or more different
modified peptides comprising the same amino acid modification(s)
comprise different fragments of a modified protein, said different
fragments comprising the same amino acid modification(s) present in
the modified protein.
45. The method of claim 44, wherein the two or more different
modified peptides comprising the same amino acid modification(s)
comprise different potential MHC class II binding fragments of a
modified protein, said fragments comprising the same amino acid
modification(s) present in the modified protein.
46. The method of claim 43, further comprising selecting the
modified peptide(s) from the two or more different modified
peptides comprising the same amino acid modification(s) having a
probability or having the highest probability for binding to one or
more MHC class II molecules.
47. The method of claim 43, wherein the two or more different
modified peptides comprising the same amino acid modification(s)
differ in length and/or position of the amino acid
modification(s).
48. The method of claim 43, wherein a highest score for binding to
one or more MHC class II molecules of the two or more different
modified peptides comprising the same amino acid modification(s) is
assigned to the amino acid modification(s).
49. The method of claim 38, further comprising a step of
determining a score for level of expression (an "RNA expression
score") of the RNA encoding the protein to which the one or more
amino acid modifications are associated, wherein is determined by
measuring the level of expression of RNA encoding the protein.
50. The method of claim 38, further comprising a step of
determining a score for variant allele frequency (a "variant allele
frequency score") for the modified protein, wherein the score is
determined by measuring the level of expression of RNA encoding the
modified protein.
51. The method of claim 30, wherein the modified peptide comprises
a fragment of the modified protein, said fragment comprising the
amino acid modification(s) present in the modified protein.
52. The method of claim 30, further comprising identifying
non-synonymous mutations in one or more protein-coding regions of a
transcript corresponding to the modified protein.
53. The method claim 30, wherein amino acid modifications are
identified by partially or completely sequencing the genome, exome,
or transcriptome of one or more cells.
54. The method of claim 30, wherein mutation(s) corresponding to
the amino acid modification(s) are somatic mutation(s).
55. The method of claim 54, wherein said mutation(s) are cancer
mutation(s).
56. The method of claim 30, further comprising a step of
manufacturing a vaccine that delivers one or more peptides or
polypeptides comprising the one or more amino acid modifications
predicted as being immunogenic or more immunogenic, and/or one or
more modified peptides predicted as being immunogenic or more
immunogenic.
57. The method of claim 56, wherein the vaccine is a nucleic acid
vaccine comprising a nucleic acid encoding the one or more peptides
or polypeptides comprising the one or more amino acid modifications
predicted as being immunogenic or more immunogenic, and/or one or
more modified peptides predicted as being immunogenic or more
immunogenic.
58. The method of claim 56, wherein the vaccine is a peptide or
polypeptide vaccine comprising one or more peptides or polypeptides
comprising the one or more amino acid modifications predicted as
being immunogenic or more immunogenic, and/or one or more modified
peptides predicted as being immunogenic or more immunogenic.
59. The method of claim 58, wherein the step of manufacturing
comprises in vitro transcription to generate an RNA encoding the
one or more peptides or polypeptides comprising the one or more
amino acid modifications predicted as being immunogenic or more
immunogenic, and/or one or more modified peptides predicted as
being immunogenic or more immunogenic.
60. A method for manufacturing a vaccine, the method comprising
steps of: a) detecting a mutation corresponding to a non-synonymous
amino acid modification by partial or complete sequencing of the
genome, exome, or transcriptome of one or more cells from a
subject; b) predicting one or more immunogenic amino acid
modifications or one or more immunogenic modified peptides by the
method of claim 30; and c) manufacturing a vaccine comprising one
or more peptides or polypeptides comprising the one or more
immunogenic amino acid modifications predicted as being immunogenic
or more immunogenic or comprising the one or more immunogenic
modified peptides predicted as being immunogenic or more
immunogenic, or a nucleic acid encoding the one or more peptides or
polypeptides.
61. The method of claim 60, wherein the one or more peptides or
polypeptides comprises one or more neo-epitopes or T-cell
epitopes.
62. The method of claim 60, wherein the one or more neo-epitopes or
T-cell epitopes each comprises one or more tumor-specific amino
acid modifications.
63. The method of claim 60, wherein the one or more peptides or
polypeptides further comprises one or more epitopes that do not
comprise tumor-specific amino acid modifications.
64. The method of claim 62, wherein the one or more neo-epitopes or
T-cell epitopes are separated by linkers.
65. The method of claim 60, wherein the vaccine provides WIC class
II-presented epitopes that are capable of eliciting a CD4.sup.+
helper T cell response against cells expressing antigens from which
the WIC class II-presented epitopes are derived.
66. The method of claim 60, wherein the vaccine provides WIC class
I-presented epitopes that are capable of eliciting a CD8.sup.+ T
cell response against cells expressing antigens from which the WIC
class I-presented epitopes are derived.
67. The method of claim 60, wherein the nucleic acid is ribonucleic
acid (RNA).
68. The method of claim 67, wherein the RNA has been modified to
increase stability or expression.
69. A vaccine comprising: a peptide or polypeptide comprising one
or more amino acid modification(s) predicted as being immunogenic
or more immunogenic by the method of claim 30, or a nucleic acid
encoding said peptide or polypeptide.
70. The vaccine of claim 69, wherein the vaccine is specific for a
subject's tumor.
71. The vaccine of claim 69, wherein the peptide or polypeptide
comprises one or more neo-epitopes or T-cell epitopes.
72. The vaccine of claim 71, wherein the one or more neo-epitopes
or T-cell epitopes each comprise one or more tumor-specific amino
acid modifications.
73. The vaccine of claim 69, wherein the peptide or polypeptide
further comprises one or more epitopes that do not comprise
tumor-specific amino acid modifications.
74. The vaccine of claim 71, wherein the one or more neo-epitopes
or T-cell epitopes are separated by linkers.
75. The vaccine of claim 69, wherein the vaccine provides MHC class
II-presented epitopes that are capable of eliciting a CD4.sup.+
helper T cell response against cells expressing antigens from which
the MHC class II-presented epitopes are derived.
76. The vaccine of claim 69, wherein the vaccine provides MHC class
I-presented epitopes that are capable of eliciting a CD8.sup.+ T
cell response against cells expressing antigens from which the MHC
class I-presented epitopes are derived.
77. The vaccine of claim 69, wherein the nucleic acid is
ribonucleic acid (RNA).
78. The vaccine of claim 77, wherein the RNA has been modified to
increase stability or expression.
79. The vaccine of claim 69, wherein the vaccine further comprises
a pharmaceutically acceptable carrier.
80. The vaccine of claim 69, wherein the vaccine further comprises
one or more adjuvants or stabilizers.
81. A method for analyzing and selecting modified peptides for use
in producing a vaccine, the method comprising: employing a
computer-based analytical process comprising predicting, ranking,
and/or selecting one or more immunogenic amino acid modifications
in a protein by the method claim 30.
82. The method of claim 81, wherein the protein comprises a
tumor-associated neoantigen of a patient.
83. A method of manufacturing a vaccine, the method comprising: a)
performing the method of claim 82; and b) manufacturing a vaccine
comprising a peptide or polypeptide comprising the one or more
immunogenic amino acid modifications or modified peptides predicted
as being immunogenic or more immunogenic, or a nucleic acid
encoding the peptide or polypeptide.
84. A method for manufacturing a vaccine, the method comprising
steps of: a) detecting a mutation corresponding to a non-synonymous
amino acid modification by partial or complete sequencing of the
genome, exome, or transcriptome of one or more cells from a
subject; b) predicting one or more immunogenic amino acid
modifications in a protein comprising a tumor-associated neoantigen
by the method of claim 30; and c) manufacturing a vaccine
comprising a peptide or polypeptide comprising the one or more
immunogenic amino acid modifications or modified peptides predicted
as being immunogenic or more immunogenic, or a nucleic acid
encoding the peptide or polypeptide.
85. The method of claim 84, wherein the vaccine comprises a
synthetic mRNA vaccine encoding one or more neo-epitopes or T-cell
epitopes.
Description
CROSS REFERENCE TO RELATED APPLICATIONS
[0001] This application is a continuation of U.S. application Ser.
No. 15/550,286 filed Aug. 10, 2017, which is a National Stage Entry
patent application of PCT/EP2016/052684, filed on Feb. 9, 2016,
which claims foreign priority to International Patent Application
No. PCT/EP2015/053021, filed on Feb. 12, 2015, the disclosures of
each of which are hereby incorporated by reference in their
entirety.
SUBMISSION OF SEQUENCE LISTING ON ASCII TEXT FILE
[0002] The instant applications contains a Sequence Listing which
has been submitted electronically in ASCII format and is hereby
incorporated by reference in its entirety. Said ASCII copy, created
on Sep. 21, 2021 is named 2013237-0220_SL.txt and is 33,004 bytes
in size.
TECHNICAL FIELD OF THE INVENTION
[0003] The present invention relates to methods for predicting T
cell epitopes useful for vaccination. In particular, the present
invention relates to methods for predicting whether modifications
in peptides or polypeptides such as tumor-associated neoantigens
are immunogenic and, in particular, useful for vaccination, or for
predicting which of such modifications are most immunogenic and, in
particular, most useful for vaccination. The methods of the
invention may be used, in particular, for the provision of vaccines
which are specific for a patient's tumor and, thus, in the context
of personalized cancer vaccines.
BACKGROUND OF THE INVENTION
[0004] Mutations are regarded as ideal targets for cancer
immunotherapy. As neo-epitopes with strict lack of expression in
any healthy tissue, they are expected to be safe and could bypass
the central tolerance mechanisms. The systematic use of mutations
for vaccine approaches, however, is hampered by the uniqueness of
the repertoire of mutations ("the mutanome") in every patient s
tumor (Alexandrov, L. B., et al., Nature 500, 415 (2013)). We have
recently proposed a personalized immunotherapy approach targeting
the spectrum of individual mutations (Castle, J. C., et al., Cancer
Res 72, 1081 (2012)).
[0005] However, there is a need for a model to predict whether an
epitope, in particular a neo-epitope, will induce efficient
immunity and, thus, will be useful in vaccination.
[0006] Here we show in three independent murine tumor models that a
considerable fraction of non-synonymous cancer mutations is
immunogenic and that unexpectedly the immunogenic mutanome is
pre-dominantly recognized by CD4.sup.+ T cells ("the CD4+
immunome"). Vaccination with such CD4.sup.+ immunogenic mutations
confers strong anti-tumour activity. Encouraged by these findings
we set up a process comprising mutation detection by exome
sequencing, selection of vaccine targets by solely bioinformatical
prioritization of mutated epitopes predicted to be abundantly
expressed and good MHC class II binders and rapid production of
synthetic mRNA vaccines encoding multiple of these mutated
epitopes. We show that vaccination with such poly-neo-epitopic mRNA
vaccines induces potent tumor control and complete rejection of
established aggressively growing tumors in mice. Moreover, we
demonstrate that CD4.sup.+ T cell neo-epitope vaccination induces
CTL responses against an independent immunodominant antigen in
tumor bearing mice indicating orchestration of antigen spread.
Finally, we demonstrate by analyses of corresponding human cancer
types with the same bioinformatical algorithms the abundance of
mutations predicted to bind to MHC class II in human cancers as
well. Thus, the tailored immunotherapy approach introduced here may
be regarded as a universally applicable blueprint for comprehensive
exploitation of the huge neo-epitope target repertoire of cancers
enabling targeting of every patient s tumour with "just in time"
produced vaccines.
DESCRIPTION OF INVENTION
Summary of the Invention
[0007] In one aspect, the present invention relates to a method for
predicting immunogenic amino acid modifications, the method
comprising the steps:
a) ascertaining a score for binding of a modified peptide which is
a fragment of a modified protein to one or more MHC class II
molecules, and b) ascertaining a score for expression or abundance
of the modified protein.
[0008] In one embodiment, a score for binding to one or more MHC
class II molecules indicating binding to one or more MHC class II
molecules and a score for expression or abundance of the modified
protein indicating expression, high level of expression or
abundance of the modified protein indicates that the modification
or modified peptide is immunogenic.
[0009] In a further aspect, the present invention relates to a
method for selecting and/or ranking immunogenic amino acid
modifications, the method comprising the steps:
a) ascertaining a score for binding of a modified peptide which is
a fragment of a modified protein to one or more MHC class II
molecules, and b) ascertaining a score for expression or abundance
of the modified protein, wherein the method comprises performing
steps a) and b) on two or more different modifications.
[0010] In one embodiment, the different modifications are present
in the same and/or in different proteins.
[0011] In one embodiment, the method comprises comparing the scores
of said two or more different modifications. In one embodiment, the
scores of said two or more different modifications are compared by
ranking the different modifications by their MHC class II binding
scores and removing modifications with an expression or abundance
of less than a given threshold.
[0012] In one embodiment of all aspects of the invention, the score
for binding to one or more MHC class II molecules reflects a
probability for binding to one or more MHC class II molecules. In
one embodiment, the score for binding to one or more MHC class II
molecules is ascertained by a process comprising a sequence
comparison with a database of MHC class II-binding motifs.
[0013] In one embodiment of all aspects of the invention, the
method comprises performing step a) on two or more different
modified peptides, said two or more different modified peptides
comprising the same modification(s). In one embodiment, the two or
more different modified peptides comprising the same
modification(s) comprise different fragments of a modified protein,
said different fragments comprising the same modification(s)
present in the protein. In one embodiment, the two or more
different modified peptides comprising the same modification(s)
comprise different potential MHC class II binding fragments of a
modified protein, said fragments comprising the same
modification(s) present in the protein. In one embodiment, the
method further comprises selecting (the) modified peptide(s) from
the two or more different modified peptides comprising the same
modification(s) having a probability or having the highest
probability for binding to one or more MHC class II molecules. In
one embodiment, the two or more different modified peptides
comprising the same modification(s) differ in length and/or
position of the modification(s). In one embodiment, the best score
for binding to one or more MHC class II molecules of the two or
more different modified peptides comprising the same
modification(s) is assigned to the modification(s).
[0014] In one embodiment of all aspects of the invention,
ascertaining a score for expression or abundance of a modified
protein comprises determining the level of expression of the
protein to which the modification is associated and determining the
frequency of the modified protein among the protein to which the
modification is associated. In one embodiment, said determining the
level of expression of the protein to which the modification is
associated and/or determining the frequency of the modified protein
among the protein to which the modification is associated is
performed on the RNA level. In one embodiment, the frequency of the
modified protein among the protein to which the modification is
associated is determined by determining the variant allele
frequency. In one embodiment, the variant allele frequency is the
sum of detected sequences, in particular reads, covering the
mutation site and carrying the mutation divided by the sum of all
detected sequences, in particular reads, covering the mutation
site. In one embodiment, the variant allele frequency is the sum of
mutated nucleotides at the mutation site divided by the sum of all
nucleotides determined at the mutation site. In one embodiment, for
ascertaining a score for expression or abundance of a modified
protein a score for the level of expression of the protein to which
the modification is associated is multiplied with a score for the
frequency of the modified protein among the protein to which the
modification is associated.
[0015] In one embodiment of all aspects of the invention, the
modified peptide comprises a fragment of the modified protein, said
fragment comprising the modification present in the protein.
[0016] In one embodiment of all aspects of the invention, the
method further comprises identifying non-synonymous mutations in
one or more protein-coding regions.
[0017] In one embodiment of all aspects of the invention, amino
acid modifications are identified by partially or completely
sequencing the genome or transcriptome of one or more cells such as
one or more cancer cells and optionally one or more non-cancerous
cells and identifying mutations in one or more protein-coding
regions. In one embodiment, said mutations are somatic mutations.
In one embodiment, said mutations are cancer mutations.
[0018] In one embodiment of all aspects of the invention, the
method is used in the manufacture of a vaccine. In one embodiment,
the vaccine is derived from (a) modification(s) or (a) modified
peptide(s) predicted as immunogenic or more immunogenic by said
method.
[0019] In one embodiment, in particular in order to provide a
personalized vaccine for a patient such as a cancer patient, the
modification(s) are present in said patient and said ascertaining a
score for binding to one or more MHC class II molecules, and said
ascertaining a score for expression or abundance of the modified
protein is performed for said patient. Preferably, said one or more
MHC class II molecules are present in said patient (in this
embodiment the present invention may include determining the
partial or complete MHC class II expression pattern of the
patient). Preferably, said ascertaining a score for expression or
abundance of the modified protein is performed on a sample from
said patient such as a tumor specimen.
[0020] In a further aspect, the present invention relates to a
method for providing a vaccine comprising the step: [0021]
identifying (a) modification(s) or (a) modified peptide(s)
predicted as immunogenic or more immunogenic (than other
modification(s) or modified peptide(s) also analysed) by the method
of the invention. In one embodiment, the method further comprises
the step: [0022] providing a vaccine comprising a peptide or
polypeptide comprising the modification(s) or modified peptide(s)
predicted as immunogenic or more immunogenic, or a nucleic acid
encoding the peptide or polypeptide.
[0023] In a further aspect, the present invention provides a
vaccine which is obtainable using the methods according to the
invention. Preferred embodiments of such vaccines are described
herein.
[0024] A vaccine provided according to the invention may comprise a
pharmaceutically acceptable carrier and may optionally comprise one
or more adjuvants, stabilizers etc. The vaccine may in the form of
a therapeutic or prophylactic vaccine.
[0025] Another aspect relates to a method for inducing an immune
response in a patient, comprising administering to the patient a
vaccine provided according to the invention.
[0026] Another aspect relates to a method of treating a cancer
patient comprising the steps:
(a) providing a vaccine using the methods according to the
invention; and (b) administering said vaccine to the patient.
[0027] Another aspect relates to a method of treating a cancer
patient comprising administering the vaccine according to the
invention to the patient.
[0028] In further aspects, the invention provides the vaccines
described herein for use in the methods of treatment described
herein, in particular for use in treating or preventing cancer.
[0029] The treatments of cancer described herein can be combined
with surgical resection and/or radiation and/or traditional
chemotherapy.
[0030] Other features and advantages of the instant invention will
be apparent from the following detailed description and claims.
DETAILED DESCRIPTION OF THE INVENTION
[0031] Although the present invention is described in detail below,
it is to be understood that this invention is not limited to the
particular methodologies, protocols and reagents described herein
as these may vary. It is also to be understood that the terminology
used herein is for the purpose of describing particular embodiments
only, and is not intended to limit the scope of the present
invention which will be limited only by the appended claims. Unless
defined otherwise, all technical and scientific terms used herein
have the same meanings as commonly understood by one of ordinary
skill in the art.
[0032] In the following, the elements of the present invention will
be described. These elements are listed with specific embodiments,
however, it should be understood that they may be combined in any
manner and in any number to create additional embodiments. The
variously described examples and preferred embodiments should not
be construed to limit the present invention to only the explicitly
described embodiments. This description should be understood to
support and encompass embodiments which combine the explicitly
described embodiments with any number of the disclosed and/or
preferred elements. Furthermore, any permutations and combinations
of all described elements in this application should be considered
disclosed by the description of the present application unless the
context indicates otherwise.
[0033] Preferably, the terms used herein are defined as described
in "A multilingual glossary of biotechnological terms: (IUPAC
Recommendations)", H. G. W. Leuenberger, B. Nagel, and H. Kolbl,
Eds., (1995) Helvetica Chimica Acta, CH-4010 Basel,
Switzerland.
[0034] The practice of the present invention will employ, unless
otherwise indicated, conventional methods of biochemistry, cell
biology, immunology, and recombinant DNA techniques which are
explained in the literature in the field (cf., e.g., Molecular
Cloning: A Laboratory Manual, 2.sup.nd Edition, J. Sambrook et al.
eds., Cold Spring Harbor Laboratory Press, Cold Spring Harbor
1989). Throughout this specification and the claims which follow,
unless the context requires otherwise, the word "comprise", and
variations such as "comprises" and "comprising", will be understood
to imply the inclusion of a stated member, integer or step or group
of members, integers or steps but not the exclusion of any other
member, integer or step or group of members, integers or steps
although in some embodiments such other member, integer or step or
group of members, integers or steps may be excluded, i.e. the
subject-matter consists in the inclusion of a stated member,
integer or step or group of members, integers or steps. The terms
"a" and "an" and "the" and similar reference used in the context of
describing the invention (especially in the context of the claims)
are to be construed to cover both the singular and the plural,
unless otherwise indicated herein or clearly contradicted by
context. Recitation of ranges of values herein is merely intended
to serve as a shorthand method of referring individually to each
separate value falling within the range. Unless otherwise indicated
herein, each individual value is incorporated into the
specification as if it were individually recited herein.
[0035] All methods described herein can be performed in any
suitable order unless otherwise indicated herein or otherwise
clearly contradicted by context. The use of any and all examples,
or exemplary language (e.g., "such as"), provided herein is
intended merely to better illustrate the invention and does not
pose a limitation on the scope of the invention otherwise claimed.
No language in the specification should be construed as indicating
any non-claimed element essential to the practice of the
invention.
[0036] Several documents are cited throughout the text of this
specification. Each of the documents cited herein (including all
patents, patent applications, scientific publications,
manufacturer's specifications, instructions, etc.), whether supra
or infra, are hereby incorporated by reference in their entirety.
Nothing herein is to be construed as an admission that the
invention is not entitled to antedate such disclosure by virtue of
prior invention.
[0037] According to the present invention, the term "peptide"
refers to substances comprising two or more, preferably 3 or more,
preferably 4 or more, preferably 6 or more, preferably 8 or more,
preferably 10 or more, preferably 13 or more, preferably 16 more,
preferably 21 or more and up to preferably 8, 10, 20, 30, 40 or 50,
in particular 100 amino acids joined covalently by peptide bonds.
The term "polypeptide" or "protein" refers to large peptides,
preferably to peptides with more than 100 amino acid residues, but
in general the terms "peptide", "polypeptide" and "protein" are
synonyms and are used interchangeably herein.
[0038] According to the invention, the term "modification" with
respect to peptides, polypeptides or proteins relates to a sequence
change in a peptide, polypeptide or protein compared to a parental
sequence such as the sequence of a wildtype peptide, polypeptide or
protein. The term includes amino acid insertion variants, amino
acid addition variants, amino acid deletion variants and amino acid
substitution variants, preferably amino acid substitution variants.
All these sequence changes according to the invention may
potentially create new epitopes.
[0039] Amino acid insertion variants comprise insertions of single
or two or more amino acids in a particular amino acid sequence.
[0040] Amino acid addition variants comprise amino- and/or
carboxy-terminal fusions of one or more amino acids, such as 1, 2,
3, 4 or 5, or more amino acids.
[0041] Amino acid deletion variants are characterized by the
removal of one or more amino acids from the sequence, such as by
removal of 1, 2, 3, 4 or 5, or more amino acids.
[0042] Amino acid substitution variants are characterized by at
least one residue in the sequence being removed and another residue
being inserted in its place.
[0043] According to the invention, a modification or modified
peptide used for testing in the methods of the invention may be
derived from a protein comprising a modification.
[0044] The term "derived" means according to the invention that a
particular entity, in particular a particular peptide sequence, is
present in the object from which it is derived. In the case of
amino acid sequences, especially particular sequence regions,
"derived" in particular means that the relevant amino acid sequence
is derived from an amino acid sequence in which it is present.
[0045] A protein comprising a modification from which a
modification or modified peptide used for testing in the methods of
the invention may be derived may be a neoantigen.
[0046] According to the invention, the term "neoantigen" relates to
a peptide or protein including one or more amino acid modifications
compared to the parental peptide or protein. For example, the
neoantigen may be a tumor-associated neoantigen, wherein the term
"tumor-associated neoantigen" includes a peptide or protein
including amino acid modifications due to tumor-specific
mutations.
[0047] According to the invention, the term "tumor-specific
mutation" or "cancer-specific mutation" relates to a somatic
mutation that is present in the nucleic acid of a tumor or cancer
cell but absent in the nucleic acid of a corresponding normal, i.e.
non-tumorous or non-cancerous, cell. The terms "tumor-specific
mutation" and "tumor mutation" and the terms "cancer-specific
mutation" and "cancer mutation" are used interchangeably
herein.
[0048] The term "immune response" refers to an integrated bodily
response to a target such as an antigen and preferably refers to a
cellular immune response or a cellular as well as a humoral immune
response. The immune response may be
protective/preventive/prophylactic and/or therapeutic.
[0049] "Inducing an immune response" may mean that there was no
immune response before induction, but it may also mean that there
was a certain level of immune response before induction and after
induction said immune response is enhanced. Thus, "inducing an
immune response" also includes "enhancing an immune response".
Preferably, after inducing an immune response in a subject, said
subject is protected from developing a disease such as a cancer
disease or the disease condition is ameliorated by inducing an
immune response. For example, an immune response against a
tumor-expressed antigen may be induced in a patient having a cancer
disease or in a subject being at risk of developing a cancer
disease. Inducing an immune response in this case may mean that the
disease condition of the subject is ameliorated, that the subject
does not develop metastases, or that the subject being at risk of
developing a cancer disease does not develop a cancer disease.
[0050] The terms "cellular immune response" and "cellular response"
or similar terms refer to an immune response directed to cells
characterized by presentation of an antigen with class I or class
II MHC involving T cells or T-lymphocytes which act as either
"helpers" or "killers". The helper T cells (also termed CD4.sup.+ T
cells) play a central role by regulating the immune response and
the killer cells (also termed cytotoxic T cells, cytolytic T cells,
CD8.sup.+ T cells or CTLs) kill diseased cells such as cancer
cells, preventing the production of more diseased cells. In
preferred embodiments, the present invention involves the
stimulation of an anti-tumor CTL response against tumor cells
expressing one or more tumor-expressed antigens and preferably
presenting such tumor-expressed antigens with class I MHC.
[0051] An "antigen" according to the invention covers any
substance, preferably a peptide or protein, that is a target of
and/or induces an immune response such as a specific reaction with
antibodies or T-lymphocytes (T cells). Preferably, an antigen
comprises at least one epitope such as a T cell epitope.
Preferably, an antigen in the context of the present invention is a
molecule which, optionally after processing, induces an immune
reaction, which is preferably specific for the antigen (including
cells expressing the antigen). The antigen or a T cell epitope
thereof is preferably presented by a cell, preferably by an antigen
presenting cell which includes a diseased cell, in particular a
cancer cell, in the context of MHC molecules, which results in an
immune response against the antigen (including cells expressing the
antigen).
[0052] In one embodiment, an antigen is a tumor antigen (also
termed tumor-expressed antigen herein), i.e., a part of a tumor
cell such as a protein or peptide expressed in a tumor cell which
may be derived from the cytoplasm, the cell surface or the cell
nucleus, in particular those which primarily occur intracellularly
or as surface antigens of tumor cells. For example, tumor antigens
include the carcinoembryonal antigen, .alpha.1-fetoprotein,
isoferritin, and fetal sulphoglycoprotein, .alpha.2-H-ferroprotein
and .gamma.-fetoprotein. According to the present invention, a
tumor antigen preferably comprises any antigen which is expressed
in and optionally characteristic with respect to type and/or
expression level for tumors or cancers as well as for tumor or
cancer cells, i.e. a tumor-associated antigen. In one embodiment,
the term "tumor-associated antigen" relates to proteins that are
under normal conditions specifically expressed in a limited number
of tissues and/or organs or in specific developmental stages, for
example, the tumor-associated antigens may be under normal
conditions specifically expressed in stomach tissue, preferably in
the gastric mucosa, in reproductive organs, e.g., in testis, in
trophoblastic tissue, e.g., in placenta, or in germ line cells, and
are expressed or aberrantly expressed in one or more tumor or
cancer tissues. In this context, "a limited number" preferably
means not more than 3, more preferably not more than 2. The tumor
antigens in the context of the present invention include, for
example, differentiation antigens, preferably cell type specific
differentiation antigens, i.e., proteins that are under normal
conditions specifically expressed in a certain cell type at a
certain differentiation stage, cancer/testis antigens, i.e.,
proteins that are under normal conditions specifically expressed in
testis and sometimes in placenta, and germ line specific antigens.
Preferably, the tumor antigen or the aberrant expression of the
tumor antigen identifies cancer cells. In the context of the
present invention, the tumor antigen that is expressed by a cancer
cell in a subject, e.g., a patient suffering from a cancer disease,
is preferably a self-protein in said subject. In preferred
embodiments, the tumor antigen in the context of the present
invention is expressed under normal conditions specifically in a
tissue or organ that is non-essential, i.e., tissues or organs
which when damaged by the immune system do not lead to death of the
subject, or in organs or structures of the body which are not or
only hardly accessible by the immune system.
[0053] According to the invention, the terms "tumor antigen",
"tumor-expressed antigen", "cancer antigen" and "cancer-expressed
antigen" are equivalents and are used interchangeably herein.
[0054] The term "immunogenicity" relates to the relative
effectivity to induce an immune response that is preferably
associated with therapeutic treatments, such as treatments against
cancers. As used herein, the term "immunogenic" relates to the
property of having immunogenicity. For example, the term
"immunogenic modification" when used in the context of a peptide,
polypeptide or protein relates to the effectivity of said peptide,
polypeptide or protein to induce an immune response that is caused
by and/or directed against said modification. Preferably, the
non-modified peptide, polypeptide or protein does not induce an
immune response, induces a different immune response or induces a
different level, preferably a lower level, of immune response.
[0055] According to the invention, the term "immunogenicity" or
"immunogenic" preferably relates to the relative effectivity to
induce a biologically relevant immune response, in particular an
immune response which is useful for vaccination. Thus, in one
preferred embodiment, an amino acid modification or modified
peptide is immunogenic if it induces an immune response against the
target modification in a subject, which immune response may be
beneficial for therapeutic or prophylactic purposes.
[0056] The terms "major histocompatibility complex" and the
abbreviation "MHC" include MHC class I and MHC class II molecules
and relate to a complex of genes which occurs in all vertebrates.
MHC proteins or molecules are important for signaling between
lymphocytes and antigen presenting cells or diseased cells in
immune reactions, wherein the MHC proteins or molecules bind
peptides and present them for recognition by T cell receptors. The
proteins encoded by the MHC are expressed on the surface of cells,
and display both self antigens (peptide fragments from the cell
itself) and non-self antigens (e.g., fragments of invading
microorganisms) to a T cell.
[0057] The MHC region is divided into three subgroups, class I,
class II, and class III. MHC class I proteins contain an
.alpha.-chain and .beta.2-microglobulin (not part of the MHC
encoded by chromosome 15). They present antigen fragments to
cytotoxic T cells. On most immune system cells, specifically on
antigen-presenting cells, MHC class II proteins contain .alpha.-
and .beta.-chains and they present antigen fragments to T-helper
cells. MHC class III region encodes for other immune components,
such as complement components and some that encode cytokines.
[0058] The MHC is both polygenic (there are several MHC class I and
MHC class II genes) and polymorphic (there are multiple alleles of
each gene).
[0059] As used herein, the term "haplotype" refers to the HLA
alleles found on one chromosome and the proteins encoded thereby.
Haplotype may also refer to the allele present at any one locus
within the MHC. Each class of MHC is represented by several loci:
e.g., HLA-A (Human Leukocyte Antigen-A), HLA-B, HLA-C, HLA-E,
HLA-F, HLA-G, HLA-H, HLA-J, HLA-K, HLA-L, HLA-P and HLA-V for class
I and HLA-DRA, HLA-DRB1-9, HLA-, HLA-DQA1, HLA-DQB1, HLA-DPA1,
HLA-DPB1, HLA-DMA, HLA-DMB, HLA-DOA, and HLA-DOB for class II. The
terms "HLA allele" and "MHC allele" are used interchangeably
herein. The MHCs exhibit extreme polymorphism: within the human
population there are, at each genetic locus, a great number of
haplotypes comprising distinct alleles. Different polymorphic MHC
alleles, of both class I and class II, have different peptide
specificities: each allele encodes proteins that bind peptides
exhibiting particular sequence patterns.
[0060] In one preferred embodiment of all aspects of the invention
an MHC molecule is an HLA molecule.
[0061] According to the invention, MHC class II includes HLA-DM,
HLA-DO, HLA-DP, HLA-DQ and HLA-DR.
[0062] In the context of the present invention, the term "MHC
binding peptide" includes MEW class I and/or class II binding
peptides or peptides that can be processed to produce MHC class I
and/or class II binding peptides. In the case of class I
MHC/peptide complexes, the binding peptides are typically 8-12,
preferably 8-10 amino acids long although longer or shorter
peptides may be effective. In the case of class II MHC/peptide
complexes, the binding peptides are typically 9-30, preferably
10-25 amino acids long and are in particular 13-18 amino acids
long, whereas longer and shorter peptides may be effective.
[0063] If a peptide is to be presented directly, i.e., without
processing, in particular without cleavage, it has a length which
is suitable for binding to an MHC molecule, in particular a class I
MHC molecule, and preferably is 7-30 amino acids in length such as
7-20 amino acids in length, more preferably 7-12 amino acids in
length, more preferably 8-11 amino acids in length, in particular 9
or 10 amino acids in length.
[0064] If a peptide is part of a larger entity comprising
additional sequences, e.g. of a vaccine sequence or polypeptide,
and is to be presented following processing, in particular
following cleavage, the peptide produced by processing has a length
which is suitable for binding to an MHC molecule, in particular a
class I MHC molecule, and preferably is 7-30 amino acids in length
such as 7-20 amino acids in length, more preferably 7-12 amino
acids in length, more preferably 8-11 amino acids in length, in
particular 9 or 10 amino acids in length. Preferably, the sequence
of the peptide which is to be presented following processing is
derived from the amino acid sequence of an antigen or polypeptide
used for vaccination, i.e., its sequence substantially corresponds
and is preferably completely identical to a fragment of the antigen
or polypeptide.
[0065] Thus, an MHC binding peptide in one embodiment comprises a
sequence which substantially corresponds and is preferably
completely identical to a fragment of an antigen.
[0066] The term "epitope" refers to an antigenic determinant in a
molecule such as an antigen, i.e., to a part in or fragment of the
molecule that is recognized by the immune system, for example, that
is recognized by a T cell, in particular when presented in the
context of MHC molecules. An epitope of a protein such as a tumor
antigen preferably comprises a continuous or discontinuous portion
of said protein and is preferably between 5 and 100, preferably
between 5 and 50, more preferably between 8 and 30, most preferably
between 10 and 25 amino acids in length, for example, the epitope
may be preferably 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20,
21, 22, 23, 24, or 25 amino acids in length. It is particularly
preferred that the epitope in the context of the present invention
is a T cell epitope.
[0067] According to the invention an epitope may bind to MHC
molecules such as MHC molecules on the surface of a cell and thus,
may be a "MHC binding peptide".
[0068] As used herein the term "neo-epitope" refers to an epitope
that is not present in a reference such as a normal non-cancerous
or germline cell but is found in cancer cells. This includes, in
particular, situations wherein in a normal non-cancerous or
germline cell a corresponding epitope is found, however, due to one
or more mutations in a cancer cell the sequence of the epitope is
changed so as to result in the neo-epitope.
[0069] As used herein, the term "T cell epitope" refers to a
peptide which binds to a MHC molecule in a configuration recognized
by a T cell receptor. Typically, T cell epitopes are presented on
the surface of an antigen-presenting cell.
[0070] As used herein, the term "predicting immunogenic amino acid
modifications" refers to a prediction whether a peptide comprising
such amino acid modification will be immunogenic and thus useful as
epitope, in particular T cell epitope, in vaccination.
[0071] According to the invention, a T cell epitope may be present
in a vaccine as a part of a larger entity such as a vaccine
sequence and/or a polypeptide comprising more than one T cell
epitope. The presented peptide or T cell epitope is produced
following suitable processing.
[0072] T cell epitopes may be modified at one or more residues that
are not essential for TCR recognition or for binding to MHC. Such
modified T cell epitopes may be considered immunologically
equivalent.
[0073] Preferably a T cell epitope when presented by MHC and
recognized by a T cell receptor is able to induce in the presence
of appropriate co-stimulatory signals, clonal expansion of the T
cell carrying the T cell receptor specifically recognizing the
peptide/MHC-complex.
[0074] Preferably, a T cell epitope comprises an amino acid
sequence substantially corresponding to the amino acid sequence of
a fragment of an antigen. Preferably, said fragment of an antigen
is an MHC class I and/or class II presented peptide.
[0075] A T cell epitope according to the invention preferably
relates to a portion or fragment of an antigen which is capable of
stimulating an immune response, preferably a cellular response
against the antigen or cells characterized by expression of the
antigen and preferably by presentation of the antigen such as
diseased cells, in particular cancer cells. Preferably, a T cell
epitope is capable of stimulating a cellular response against a
cell characterized by presentation of an antigen with class I MHC
and preferably is capable of stimulating an antigen-responsive
cytotoxic T-lymphocyte (CTL).
[0076] "Antigen processing" or "processing" refers to the
degradation of a peptide, polypeptide or protein into procession
products, which are fragments of said peptide, polypeptide or
protein (e.g., the degradation of a polypeptide into peptides) and
the association of one or more of these fragments (e.g., via
binding) with MHC molecules for presentation by cells, preferably
antigen presenting cells, to specific T cells.
[0077] "Antigen presenting cells" (APC) are cells which present
peptide fragments of protein antigens in association with MHC
molecules on their cell surface. Some APCs may activate antigen
specific T cells.
[0078] Professional antigen-presenting cells are very efficient at
internalizing antigen, either by phagocytosis or by
receptor-mediated endocytosis, and then displaying a fragment of
the antigen, bound to a class II MHC molecule, on their membrane.
The T cell recognizes and interacts with the antigen-class II MHC
molecule complex on the membrane of the antigen-presenting cell. An
additional co-stimulatory signal is then produced by the
antigen-presenting cell, leading to activation of the T cell. The
expression of co-stimulatory molecules is a defining feature of
professional antigen-presenting cells.
[0079] The main types of professional antigen-presenting cells are
dendritic cells, which have the broadest range of antigen
presentation, and are probably the most important
antigen-presenting cells, macrophages, B-cells, and certain
activated epithelial cells. Dendritic cells (DCs) are leukocyte
populations that present antigens captured in peripheral tissues to
T cells via both MHC class II and I antigen presentation pathways.
It is well known that dendritic cells are potent inducers of immune
responses and the activation of these cells is a critical step for
the induction of antitumoral immunity. Dendritic cells are
conveniently categorized as "immature" and "mature" cells, which
can be used as a simple way to discriminate between two well
characterized phenotypes. However, this nomenclature should not be
construed to exclude all possible intermediate stages of
differentiation. Immature dendritic cells are characterized as
antigen presenting cells with a high capacity for antigen uptake
and processing, which correlates with the high expression of
Fc.gamma. receptor and mannose receptor. The mature phenotype is
typically characterized by a lower expression of these markers, but
a high expression of cell surface molecules responsible for T cell
activation such as class I and class II MHC, adhesion molecules
(e.g. CD54 and CD11) and costimulatory molecules (e.g., CD40, CD80,
CD86 and 4-1 BB). Dendritic cell maturation is referred to as the
status of dendritic cell activation at which such
antigen-presenting dendritic cells lead to T cell priming, while
presentation by immature dendritic cells results in tolerance.
Dendritic cell maturation is chiefly caused by biomolecules with
microbial features detected by innate receptors (bacterial DNA,
viral RNA, endotoxin, etc.), pro-inflammatory cytokines (TNF, IL-1,
IFNs), ligation of CD40 on the dendritic cell surface by CD40L, and
substances released from cells undergoing stressful cell death. The
dendritic cells can be derived by culturing bone marrow cells in
vitro with cytokines, such as granulocyte-macrophage
colony-stimulating factor (GM-CSF) and tumor necrosis factor
alpha.
[0080] Non-professional antigen-presenting cells do not
constitutively express the MHC class II proteins required for
interaction with naive T cells; these are expressed only upon
stimulation of the non-professional antigen-presenting cells by
certain cytokines such as IFN.gamma..
[0081] Antigen presenting cells can be loaded with MHC class I
presented peptides by transducing the cells with nucleic acid,
preferably RNA, encoding a peptide or polypeptide comprising the
peptide to be presented, e.g. a nucleic acid encoding an antigen or
polypeptide used for vaccination.
[0082] In some embodiments, a pharmaceutical composition or vaccine
comprising a nucleic acid delivery vehicle that targets a dendritic
or other antigen presenting cell may be administered to a patient,
resulting in transfection that occurs in vivo. In vivo transfection
of dendritic cells, for example, may generally be performed using
any methods known in the art, such as those described in WO
97/24447, or the gene gun approach described by Mahvi et al.,
Immunology and cell Biology 75: 456-460, 1997.
[0083] According to the invention, the term "antigen presenting
cell" also includes target cells.
[0084] "Target cell" shall mean a cell which is a target for an
immune response such as a cellular immune response. Target cells
include cells that present an antigen, i.e. a peptide fragment
derived from an antigen, and include any undesirable cell such as a
cancer cell. In preferred embodiments, the target cell is a cell
expressing an antigen as described herein and preferably presenting
said antigen with class I MHC.
[0085] The term "portion" refers to a fraction. With respect to a
particular structure such as an amino acid sequence or protein the
term "portion" thereof may designate a continuous or a
discontinuous fraction of said structure. Preferably, a portion of
an amino acid sequence comprises at least 1%, at least 5%, at least
10%, at least 20%, at least 30%, preferably at least 40%,
preferably at least 50%, more preferably at least 60%, more
preferably at least 70%, even more preferably at least 80%, and
most preferably at least 90% of the amino acids of said amino acid
sequence. Preferably, if the portion is a discontinuous fraction
said discontinuous fraction is composed of 2, 3, 4, 5, 6, 7, 8, or
more parts of a structure, each part being a continuous element of
the structure. For example, a discontinuous fraction of an amino
acid sequence may be composed of 2, 3, 4, 5, 6, 7, 8, or more,
preferably not more than 4 parts of said amino acid sequence,
wherein each part preferably comprises at least 5 continuous amino
acids, at least 10 continuous amino acids, preferably at least 20
continuous amino acids, preferably at least 30 continuous amino
acids of the amino acid sequence.
[0086] The terms "part" and "fragment" are used interchangeably
herein and refer to a continuous element. For example, a part of a
structure such as an amino acid sequence or protein refers to a
continuous element of said structure. A portion, a part or a
fragment of a structure preferably comprises one or more functional
properties of said structure. For example, a portion, a part or a
fragment of an epitope, peptide or protein is preferably
immunologically equivalent to the epitope, peptide or protein it is
derived from. In the context of the present invention, a "part" of
a structure such as an amino acid sequence preferably comprises,
preferably consists of at least 10%, at least 20%, at least 30%, at
least 40%, at least 50%, at least 60%, at least 70%, at least 80%,
at least 85%, at least 90%, at least 92%, at least 94%, at least
96%, at least 98%, at least 99% of the entire structure or amino
acid sequence.
[0087] The term "immunoreactive cell" in the context of the present
invention relates to a cell which exerts effector functions during
an immune reaction. An "immunoreactive cell" preferably is capable
of binding an antigen or a cell characterized by presentation of an
antigen or a peptide fragment thereof (e.g. a T cell epitope) and
mediating an immune response. For example, such cells secrete
cytokines and/or chemokines, secrete antibodies, recognize
cancerous cells, and optionally eliminate such cells. For example,
immunoreactive cells comprise T cells (cytotoxic T cells, helper T
cells, tumor infiltrating T cells), B cells, natural killer cells,
neutrophils, macrophages, and dendritic cells. Preferably, in the
context of the present invention, "immunoreactive cells" are T
cells, preferably CD4.sup.+ and/or CD8.sup.+ T cells.
[0088] Preferably, an "immunoreactive cell" recognizes an antigen
or a peptide fragment thereof with some degree of specificity, in
particular if presented in the context of MHC molecules such as on
the surface of antigen presenting cells or diseased cells such as
cancer cells. Preferably, said recognition enables the cell that
recognizes an antigen or a peptide fragment thereof to be
responsive or reactive. If the cell is a helper T cell (CD4.sup.+ T
cell) bearing receptors that recognize an antigen or a peptide
fragment thereof in the context of MHC class II molecules such
responsiveness or reactivity may involve the release of cytokines
and/or the activation of CD8.sup.+ lymphocytes (CTLs) and/or
B-cells. If the cell is a CTL such responsiveness or reactivity may
involve the elimination of cells presented in the context of MHC
class I molecules, i.e., cells characterized by presentation of an
antigen with class I MHC, for example, via apoptosis or
perforin-mediated cell lysis. According to the invention, CTL
responsiveness may include sustained calcium flux, cell division,
production of cytokines such as IFN-.gamma. and TNF-.alpha.,
up-regulation of activation markers such as CD44 and CD69, and
specific cytolytic killing of antigen expressing target cells. CTL
responsiveness may also be determined using an artificial reporter
that accurately indicates CTL responsiveness. Such CTL that
recognize an antigen or an antigen fragment and are responsive or
reactive are also termed "antigen-responsive CTL" herein. If the
cell is a B cell such responsiveness may involve the release of
immunoglobulins.
[0089] The terms "T cell" and "T lymphocyte" are used
interchangeably herein and include T helper cells (CD4+ T cells)
and cytotoxic T cells (CTLs, CD8+ T cells) which comprise cytolytic
T cells.
[0090] T cells belong to a group of white blood cells known as
lymphocytes, and play a central role in cell-mediated immunity.
They can be distinguished from other lymphocyte types, such as B
cells and natural killer cells by the presence of a special
receptor on their cell surface called T cell receptor (TCR). The
thymus is the principal organ responsible for the maturation of T
cells. Several different subsets of T cells have been discovered,
each with a distinct function.
[0091] T helper cells assist other white blood cells in immunologic
processes, including maturation of B cells into plasma cells and
activation of cytotoxic T cells and macrophages, among other
functions. These cells are also known as CD4+ T cells because they
express the CD4 protein on their surface. Helper T cells become
activated when they are presented with peptide antigens by MHC
class II molecules that are expressed on the surface of antigen
presenting cells (APCs). Once activated, they divide rapidly and
secrete small proteins called cytokines that regulate or assist in
the active immune response.
[0092] Cytotoxic T cells destroy virally infected cells and tumor
cells, and are also implicated in transplant rejection. These cells
are also known as CD8+ T cells since they express the CD8
glycoprotein at their surface. These cells recognize their targets
by binding to antigen associated with MHC class I, which is present
on the surface of nearly every cell of the body.
[0093] A majority of T cells have a T cell receptor (TCR) existing
as a complex of several proteins. The actual T cell receptor is
composed of two separate peptide chains, which are produced from
the independent T cell receptor alpha and beta (TCR.alpha. and
TCR.beta.) genes and are called .alpha.- and .beta.-TCR chains.
.gamma..delta. T cells (gamma delta T cells) represent a small
subset of T cells that possess a distinct T cell receptor (TCR) on
their surface. However, in .gamma..delta. T cells, the TCR is made
up of one .gamma.-chain and one .delta.-chain. This group of T
cells is much less common (2% of total T cells) than the
.alpha..beta. T cells.
[0094] The first signal in activation of T cells is provided by
binding of the T cell receptor to a short peptide presented by the
MHC on another cell. This ensures that only a T cell with a TCR
specific to that peptide is activated. The partner cell is usually
an antigen presenting cell such as a professional antigen
presenting cell, usually a dendritic cell in the case of naive
responses, although B cells and macrophages can be important
APCs.
[0095] According to the present invention, a molecule is capable of
binding to a target if it has a significant affinity for said
predetermined target and binds to said predetermined target in
standard assays. "Affinity" or "binding affinity" is often measured
by equilibrium dissociation constant (K.sub.D). A molecule is not
(substantially) capable of binding to a target if it has no
significant affinity for said target and does not bind
significantly to said target in standard assays.
[0096] Cytotoxic T lymphocytes may be generated in vivo by
incorporation of an antigen or a peptide fragment thereof into
antigen-presenting cells in vivo. The antigen or a peptide fragment
thereof may be represented as protein, as DNA (e.g. within a
vector) or as RNA. The antigen may be processed to produce a
peptide partner for the MHC molecule, while a fragment thereof may
be presented without the need for further processing. The latter is
the case in particular, if these can bind to MHC molecules. In
general, administration to a patient by intradermal injection is
possible. However, injection may also be carried out intranodally
into a lymph node (Maloy et al. (2001), Proc Natl Acad Sci USA
98:3299-303). The resulting cells present the complex of interest
and are recognized by autologous cytotoxic T lymphocytes which then
propagate.
[0097] Specific activation of CD4+ or CD8+ T cells may be detected
in a variety of ways. Methods for detecting specific T cell
activation include detecting the proliferation of T cells, the
production of cytokines (e.g., lymphokines), or the generation of
cytolytic activity. For CD4+ T cells, a preferred method for
detecting specific T cell activation is the detection of the
proliferation of T cells. For CD8+ T cells, a preferred method for
detecting specific T cell activation is the detection of the
generation of cytolytic activity.
[0098] By "cell characterized by presentation of an antigen" or
"cell presenting an antigen" or similar expressions is meant a cell
such as a diseased cell, e.g. a cancer cell, or an antigen
presenting cell presenting the antigen it expresses or a fragment
derived from said antigen, e.g. by processing of the antigen, in
the context of MHC molecules, in particular MHC Class I molecules.
Similarly, the terms "disease characterized by presentation of an
antigen" denotes a disease involving cells characterized by
presentation of an antigen, in particular with class I MHC.
Presentation of an antigen by a cell may be effected by
transfecting the cell with a nucleic acid such as RNA encoding the
antigen.
[0099] By "fragment of an antigen which is presented" or similar
expressions is meant that the fragment can be presented by MHC
class I or class II, preferably MHC class I, e.g. when added
directly to antigen presenting cells. In one embodiment, the
fragment is a fragment which is naturally presented by cells
expressing an antigen.
[0100] The term "immunologically equivalent" means that the
immunologically equivalent molecule such as the immunologically
equivalent amino acid sequence exhibits the same or essentially the
same immunological properties and/or exerts the same or essentially
the same immunological effects, e.g., with respect to the type of
the immunological effect such as induction of a humoral and/or
cellular immune response, the strength and/or duration of the
induced immune reaction, or the specificity of the induced immune
reaction. In the context of the present invention, the term
"immunologically equivalent" is preferably used with respect to the
immunological effects or properties of a peptide used for
immunization. For example, an amino acid sequence is
immunologically equivalent to a reference amino acid sequence if
said amino acid sequence when exposed to the immune system of a
subject induces an immune reaction having a specificity of reacting
with the reference amino acid sequence.
[0101] The term "immune effector functions" in the context of the
present invention includes any functions mediated by components of
the immune system that result, for example, in the killing of tumor
cells, or in the inhibition of tumor growth and/or inhibition of
tumor development, including inhibition of tumor dissemination and
metastasis. Preferably, the immune effector functions in the
context of the present invention are T cell mediated effector
functions. Such functions comprise in the case of a helper T cell
(CD4.sup.+ T cell) the recognition of an antigen or an antigen
fragment in the context of MHC class II molecules by T cell
receptors, the release of cytokines and/or the activation of
CD8.sup.+ lymphocytes (CTLs) and/or B-cells, and in the case of CTL
the recognition of an antigen or an antigen fragment in the context
of MHC class I molecules by T cell receptors, the elimination of
cells presented in the context of MHC class I molecules, i.e.,
cells characterized by presentation of an antigen with class I MHC,
for example, via apoptosis or perforin-mediated cell lysis,
production of cytokines such as IFN-.gamma. and TNF-.alpha., and
specific cytolytic killing of antigen expressing target cells.
[0102] According to the invention, the term "score" relates to a
result, usually expressed numerically, of a test or examination.
Terms such as "score better" or "score best" relate to a better
result or the best result of a test or examination.
[0103] According to the invention, modified peptides are scored
according to their predicted ability to bind to MHC class II and
according to the expression or abundance of the modified proteins
from which the modified peptides are derived. In general, a peptide
with a predicted higher ability to bind to MHC class II is scored
better than a peptide with a predicted lower ability to bind to MHC
class II. Furthermore, a peptide with higher expression or
abundance of the corresponding modified protein is scored better
than a peptide with lower expression or abundance of the
corresponding modified protein.
[0104] Terms such as "predict", "predicting" or "prediction" relate
to the determination of a likelihood.
[0105] According to the invention, ascertaining a score for binding
of a peptide to one or more MHC class II molecules includes
determining the likelihood of binding of a peptide to one or more
MHC class II molecules.
[0106] A score for binding of a peptide to one or more MHC class II
molecules may be ascertained by using any peptide:MHC binding
predictive tools. For example, the immune epitope database analysis
resource (IEDB-AR: http://tools.iedb.org) may be used.
[0107] Predictions are usually made against a set of MHC class II
molecules such as a set of different MHC class II alleles such as
all possible MHC class II alleles or a set or subset of MHC class
II alleles found in a patient. Preferably, the patient has the
modification(s) the immunogenicity of which is to be determined
according to the invention or which are to be selected and/or
ranked according to their predicted immunogenicity according to the
invention. Preferably, the vaccine described herein is to be
provided ultimately for said patient. Accordingly, the present
invention may also include determining the MHC class II expression
pattern of a patient.
[0108] The present invention also may comprise performing the
method of the invention on different peptides comprising the same
modification(s) and/or different modifications.
[0109] The term "different peptides comprising the same
modification(s)" in one embodiment relates to peptides comprising
or consisting of different fragments of a modified protein, said
different fragments comprising the same modification(s) present in
the protein but differing in length and/or position of the
modification(s). If a protein has a modification at position x, two
or more fragments of said protein each comprising a different
sequence window of said protein covering said position x are
considered different peptides comprising the same
modification(s).
[0110] The term "different peptides comprising different
modifications" in one embodiment relates to peptides either of the
same and/or differing lengths comprising different modifications of
either of the same and/or different proteins. If a protein has
modifications at positions x and y, two fragments of said protein
each comprising a sequence window of said protein covering either
position x or position y are considered different peptides
comprising different modifications.
[0111] The present invention also may comprise breaking of protein
sequences having modifications the immunogenicity of which is to be
determined according to the invention or which are to be selected
and/or ranked according to their predicted immunogenicity according
to the invention into appropriate peptide lengths for MHC binding
and ascertaining scores for binding to one or more MHC class II
molecules of different modified peptides comprising the same and/or
different modifications of either the same and/or different
proteins. Outputs may be ranked and may consist of a list of
peptides and their predicted scores, indicating their likelihood of
binding.
[0112] The step of ascertaining a score for expression or abundance
of the modified protein may be performed with all different
modifications, a subset thereof, e.g. those modifications scoring
best for binding to one or more MHC class II molecules, or only
with the modification scoring best for binding to one or more MHC
class II molecules.
[0113] Following said further step, the results may be ranked and
may consist of a list of peptides and their predicted scores,
indicating their likelihood of being immunogenic.
[0114] According to the invention, ascertaining a score for
expression or abundance of the modified protein may be performed
for a patient such as a cancer patient, for example, on a tumor
specimen of a patient such as a cancer patient.
[0115] According to the invention, ascertaining a score for
expression or abundance of a modified protein may comprises
determining the level of expression of the protein to which the
modification is associated and/or determining the level of
expression of RNA encoding the protein to which the modification is
associated (which again may be indicative for the level of
expression of the protein to which the modification is associated)
and determining the frequency of the modified protein among the
protein to which the modification is associated and/or determining
the frequency of RNA encoding the modified protein among the RNA
encoding the protein to which the modification is associated.
[0116] The frequency of the modified protein among the protein to
which the modification is associated and/or the frequency of RNA
encoding the modified protein among the RNA encoding the protein to
which the modification is associated may be considered the
proportion of the modified protein within the protein to which the
modification is associated and/or the proportion of RNA encoding
the modified protein within the RNA encoding the protein to which
the modification is associated.
[0117] According to the invention, the term "protein to which the
modification is associated" relates to the protein which may
comprise the modification and includes the protein in its
unmodified as well as modified state.
[0118] According to the invention, the term "level of expression"
may refer to an absolute or relative amount.
[0119] The amino acid modifications the immunogenicity of which is
to be determined according to the present invention or which are to
be selected and/or ranked according to their predicted
immunogenicity according to the invention may result from mutations
in the nucleic acid of a cell. Such mutations may be identified by
known sequencing techniques.
[0120] In one embodiment, the mutations are cancer specific somatic
mutations in a tumor specimen of a cancer patient which may be
determined by identifying sequence differences between the genome,
exome and/or transcriptome of a tumor specimen and the genome,
exome and/or transcriptome of a non-tumorigenous specimen.
[0121] According to the invention a tumor specimen relates to any
sample such as a bodily sample derived from a patient containing or
being expected of containing tumor or cancer cells. The bodily
sample may be any tissue sample such as blood, a tissue sample
obtained from the primary tumor or from tumor metastases or any
other sample containing tumor or cancer cells. Preferably, a bodily
sample is blood and cancer specific somatic mutations or sequence
differences are determined in one or more circulating tumor cells
(CTCs) contained in the blood. In another embodiment, a tumor
specimen relates to one or more isolated tumor or cancer cells such
as circulating tumor cells (CTCs) or a sample containing one or
more isolated tumor or cancer cells such as circulating tumor cells
(CTCs).
[0122] A non-tumorigenous specimen relates to any sample such as a
bodily sample derived from a patient or another individual which
preferably is of the same species as the patient, preferably a
healthy individual not containing or not being expected of
containing tumor or cancer cells. The bodily sample may be any
tissue sample such as blood or a sample from a non-tumorigenous
tissue.
[0123] The invention may involve the determination of the cancer
mutation signature of a patient. The term "cancer mutation
signature" may refer to all cancer mutations present in one or more
cancer cells of a patient or it may refer to only a portion of the
cancer mutations present in one or more cancer cells of a patient.
Accordingly, the present invention may involve the identification
of all cancer specific mutations present in one or more cancer
cells of a patient or it may involve the identification of only a
portion of the cancer specific mutations present in one or more
cancer cells of a patient. Generally, the methods of the invention
provides for the identification of a number of mutations which
provides a sufficient number of modifications or modified peptides
to be included in the methods of the invention.
[0124] Preferably, the mutations identified according to the
present invention are non-synonymous mutations, preferably
non-synonymous mutations of proteins expressed in a tumor or cancer
cell.
[0125] In one embodiment, cancer specific somatic mutations or
sequence differences are determined in the genome, preferably the
entire genome, of a tumor specimen. Thus, the invention may
comprise identifying the cancer mutation signature of the genome,
preferably the entire genome of one or more cancer cells. In one
embodiment, the step of identifying cancer specific somatic
mutations in a tumor specimen of a cancer patient comprises
identifying the genome-wide cancer mutation profile.
[0126] In one embodiment, cancer specific somatic mutations or
sequence differences are determined in the exome, preferably the
entire exome, of a tumor specimen. Thus, the invention may comprise
identifying the cancer mutation signature of the exome, preferably
the entire exome of one or more cancer cells. In one embodiment,
the step of identifying cancer specific somatic mutations in a
tumor specimen of a cancer patient comprises identifying the
exome-wide cancer mutation profile.
[0127] In one embodiment, cancer specific somatic mutations or
sequence differences are determined in the transcriptome,
preferably the entire transcriptome, of a tumor specimen. Thus, the
invention may comprise identifying the cancer mutation signature of
the transcriptome, preferably the entire transcriptome of one or
more cancer cells. In one embodiment, the step of identifying
cancer specific somatic mutations in a tumor specimen of a cancer
patient comprises identifying the transcriptome-wide cancer
mutation profile.
[0128] In one embodiment, the step of identifying cancer specific
somatic mutations or identifying sequence differences comprises
single cell sequencing of one or more, preferably 2, 3, 4, 5, 6, 7,
8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20 or even more
cancer cells. Thus, the invention may comprise identifying a cancer
mutation signature of said one or more cancer cells. In one
embodiment, the cancer cells are circulating tumor cells. The
cancer cells such as the circulating tumor cells may be isolated
prior to single cell sequencing.
[0129] In one embodiment, the step of identifying cancer specific
somatic mutations or identifying sequence differences involves
using next generation sequencing (NGS).
[0130] In one embodiment, the step of identifying cancer specific
somatic mutations or identifying sequence differences comprises
sequencing genomic DNA and/or RNA of the tumor specimen.
[0131] To reveal cancer specific somatic mutations or sequence
differences the sequence information obtained from the tumor
specimen is preferably compared with a reference such as sequence
information obtained from sequencing nucleic acid such as DNA or
RNA of normal non-cancerous cells such as germline cells which may
either be obtained from the patient or a different individual.
[0132] In one embodiment, normal genomic germline DNA is obtained
from peripheral blood mononuclear cells (PBMCs)
[0133] The term "genome" relates to the total amount of genetic
information in the chromosomes of an organism or a cell.
[0134] The term "exome" refers to part of the genome of an organism
formed by exons, which are coding portions of expressed genes. The
exome provides the genetic blueprint used in the synthesis of
proteins and other functional gene products. It is the most
functionally relevant part of the genome and, therefore, it is most
likely to contribute to the phenotype of an organism. The exome of
the human genome is estimated to comprise 1.5% of the total genome
(Ng, P C et al., PLoS Gen., 4(8): 1-15, 2008).
[0135] The term "transcriptome" relates to the set of all RNA
molecules, including mRNA, rRNA, tRNA, and other non-coding RNA
produced in one cell or a population of cells. In context of the
present invention the transcriptome means the set of all RNA
molecules produced in one cell, a population of cells, preferably a
population of cancer cells, or all cells of a given individual at a
certain time point.
[0136] A "nucleic acid" is according to the invention preferably
deoxyribonucleic acid (DNA) or ribonucleic acid (RNA), more
preferably RNA, most preferably in vitro transcribed RNA (IVT RNA)
or synthetic RNA. Nucleic acids include according to the invention
genomic DNA, cDNA, mRNA, recombinantly produced and chemically
synthesized molecules. According to the invention, a nucleic acid
may be present as a single-stranded or double-stranded and linear
or covalently circularly closed molecule. A nucleic acid can,
according to the invention, be isolated. The term "isolated nucleic
acid" means, according to the invention, that the nucleic acid (i)
was amplified in vitro, for example via polymerase chain reaction
(PCR), (ii) was produced recombinantly by cloning, (iii) was
purified, for example, by cleavage and separation by gel
electrophoresis, or (iv) was synthesized, for example, by chemical
synthesis. A nucleic can be employed for introduction into, i.e.
transfection of, cells, in particular, in the form of RNA which can
be prepared by in vitro transcription from a DNA template. The RNA
can moreover be modified before application by stabilizing
sequences, capping, and polyadenylation.
[0137] The term "genetic material" refers to isolated nucleic acid,
either DNA or RNA, a section of a double helix, a section of a
chromosome, or an organism's or cell's entire genome, in particular
its exome or transcriptome.
[0138] The term "mutation" refers to a change of or difference in
the nucleic acid sequence (nucleotide substitution, addition or
deletion) compared to a reference. A "somatic mutation" can occur
in any of the cells of the body except the germ cells (sperm and
egg) and therefore are not passed on to children. These alterations
can (but do not always) cause cancer or other diseases. Preferably
a mutation is a non-synonymous mutation. The term "non-synonymous
mutation" refers to a mutation, preferably a nucleotide
substitution, which does result in an amino acid change such as an
amino acid substitution in the translation product.
[0139] According to the invention, the term "mutation" includes
point mutations, Indels, fusions, chromothripsis and RNA edits.
[0140] According to the invention, the term "Indel" describes a
special mutation class, defined as a mutation resulting in a
colocalized insertion and deletion and a net gain or loss in
nucleotides. In coding regions of the genome, unless the length of
an indel is a multiple of 3, they produce a frameshift mutation.
Indels can be contrasted with a point mutation; where an Indel
inserts and deletes nucleotides from a sequence, a point mutation
is a form of substitution that replaces one of the nucleotides.
[0141] Fusions can generate hybrid genes formed from two previously
separate genes. It can occur as the result of a translocation,
interstitial deletion, or chromosomal inversion. Often, fusion
genes are oncogenes. Oncogenic fusion genes may lead to a gene
product with a new or different function from the two fusion
partners. Alternatively, a proto-oncogene is fused to a strong
promoter, and thereby the oncogenic function is set to function by
an upregulation caused by the strong promoter of the upstream
fusion partner. Oncogenic fusion transcripts may also be caused by
trans-splicing or read-through events.
[0142] According to the invention, the term "chromothripsis" refers
to a genetic phenomenon by which specific regions of the genome are
shattered and then stitched together via a single devastating
event.
[0143] According to the invention, the term "RNA edit" or "RNA
editing" refers to molecular processes in which the information
content in an RNA molecule is altered through a chemical change in
the base makeup. RNA editing includes nucleoside modifications such
as cytidine (C) to uridine (U) and adenosine (A) to inosine (I)
deaminations, as well as non-templated nucleotide additions and
insertions. RNA editing in mRNAs effectively alters the amino acid
sequence of the encoded protein so that it differs from that
predicted by the genomic DNA sequence.
[0144] The term "cancer mutation signature" refers to a set of
mutations which are present in cancer cells when compared to
non-cancerous reference cells.
[0145] According to the invention, a "reference" may be used to
correlate and compare the results obtained in the methods of the
invention from a tumor specimen. Typically the "reference" may be
obtained on the basis of one or more normal specimens, in
particular specimens which are not affected by a cancer disease,
either obtained from a patient or one or more different
individuals, preferably healthy individuals, in particular
individuals of the same species. A "reference" can be determined
empirically by testing a sufficiently large number of normal
specimens.
[0146] Any suitable sequencing method can be used according to the
invention for determining mutations, Next Generation Sequencing
(NGS) technologies being preferred. Third Generation Sequencing
methods might substitute for the NGS technology in the future to
speed up the sequencing step of the method. For clarification
purposes: the terms "Next Generation Sequencing" or "NGS" in the
context of the present invention mean all novel high throughput
sequencing technologies which, in contrast to the "conventional"
sequencing methodology known as Sanger chemistry, read nucleic acid
templates randomly in parallel along the entire genome by breaking
the entire genome into small pieces. Such NGS technologies (also
known as massively parallel sequencing technologies) are able to
deliver nucleic acid sequence information of a whole genome, exome,
transcriptome (all transcribed sequences of a genome) or methylome
(all methylated sequences of a genome) in very short time periods,
e.g. within 1-2 weeks, preferably within 1-7 days or most
preferably within less than 24 hours and allow, in principle,
single cell sequencing approaches. Multiple NGS platforms which are
commercially available or which are mentioned in the literature can
be used in the context of the present invention e.g. those
described in detail in Zhang et al. 2011: The impact of
next-generation sequencing on genomics. J. Genet Genomics 38 (3),
95-109; or in Voelkerding et al. 2009: Next generation sequencing:
From basic research to diagnostics. Clinical chemistry 55, 641-658.
Non-limiting examples of such NGS technologies/platforms are [0147]
1) The sequencing-by-synthesis technology known as pyrosequencing
implemented e.g. in the GS-FLX 454 Genome Sequencer.TM. of
Roche-associated company 454 Life Sciences (Branford, Conn.), first
described in Ronaghi et al. 1998: A sequencing method based on
real-time pyrophosphate". Science 281 (5375), 363-365. This
technology uses an emulsion PCR in which single-stranded DNA
binding beads are encapsulated by vigorous vortexing into aqueous
micelles containing PCR reactants surrounded by oil for emulsion
PCR amplification. During the pyrosequencing process, light emitted
from phosphate molecules during nucleotide incorporation is
recorded as the polymerase synthesizes the DNA strand. [0148] 2)
The sequencing-by-synthesis approaches developed by Solexa (now
part of Illumina Inc., San Diego, Calif.) which is based on
reversible dye-terminators and implemented e.g. in the
Illumina/Solexa Genome Analyzer.TM. and in the Illumina HiSeq 2000
Genome Analyzer.TM.. In this technology, all four nucleotides are
added simultaneously into oligo-primed cluster fragments in
flow-cell channels along with DNA polymerase. Bridge amplification
extends cluster strands with all four fluorescently labeled
nucleotides for sequencing. [0149] 3) Sequencing-by-ligation
approaches, e.g. implemented in the SOLid.TM. platform of Applied
Biosystems (now Life Technologies Corporation, Carlsbad, Calif.).
In this technology, a pool of all possible oligonucleotides of a
fixed length are labeled according to the sequenced position.
Oligonucleotides are annealed and ligated; the preferential
ligation by DNA ligase for matching sequences results in a signal
informative of the nucleotide at that position. Before sequencing,
the DNA is amplified by emulsion PCR. The resulting bead, each
containing only copies of the same DNA molecule, are deposited on a
glass slide. As a second example, he Polonator.TM. G.007 platform
of Dover Systems (Salem, N.H.) also employs a
sequencing-by-ligation approach by using a randomly arrayed,
bead-based, emulsion PCR to amplify DNA fragments for parallel
sequencing. [0150] 4) Single-molecule sequencing technologies such
as e.g. implemented in the PacBio RS system of Pacific Biosciences
(Menlo Park, Calif.) or in the HeliScope.TM. platform of Helicos
Biosciences (Cambridge, Mass.). The distinct characteristic of this
technology is its ability to sequence single DNA or RNA molecules
without amplification, defined as Single-Molecule Real Time (SMRT)
DNA sequencing. For example, HeliScope uses a highly sensitive
fluorescence detection system to directly detect each nucleotide as
it is synthesized. A similar approach based on fluorescence
resonance energy transfer (FRET) has been developed from Visigen
Biotechnology (Houston, Tex.). Other fluorescence-based
single-molecule techniques are from U.S. Genomics (GeneEngine.TM.)
and Genovoxx (AnyGene.TM.). [0151] 5) Nano-technologies for
single-molecule sequencing in which various nanostructures are used
which are e.g. arranged on a chip to monitor the movement of a
polymerase molecule on a single strand during replication.
Non-limiting examples for approaches based on nano-technologies are
the GridON.TM. platform of Oxford Nanopore Technologies (Oxford,
UK), the hybridization-assisted nano-pore sequencing (HANS.TM.)
platforms developed by Nabsys (Providence, R.I.), and the
proprietary ligase-based DNA sequencing platform with DNA nanoball
(DNB) technology called combinatorial probe-anchor ligation
(cPAL.TM.). [0152] 6) Electron microscopy based technologies for
single-molecule sequencing, e.g. those developed by LightSpeed
Genomics (Sunnyvale, Calif.) and Halcyon Molecular (Redwood City,
Calif.) [0153] 7) Ion semiconductor sequencing which is based on
the detection of hydrogen ions that are released during the
polymerisation of DNA. For example, Ion Torrent Systems (San
Francisco, Calif.) uses a high-density array of micro-machined
wells to perform this biochemical process in a massively parallel
way. Each well holds a different DNA template. Beneath the wells is
an ion-sensitive layer and beneath that a proprietary Ion
sensor.
[0154] Preferably, DNA and RNA preparations serve as starting
material for NGS. Such nucleic acids can be easily obtained from
samples such as biological material, e.g. from fresh, flash-frozen
or formalin-fixed paraffin embedded tumor tissues (FFPE) or from
freshly isolated cells or from CTCs which are present in the
peripheral blood of patients. Normal non-mutated genomic DNA or RNA
can be extracted from normal, somatic tissue, however germline
cells are preferred in the context of the present invention.
Germline DNA or RNA may be extracted from peripheral blood
mononuclear cells (PBMCs) in patients with non-hematological
malignancies. Although nucleic acids extracted from FFPE tissues or
freshly isolated single cells are highly fragmented, they are
suitable for NGS applications.
[0155] Several targeted NGS methods for exome sequencing are
described in the literature (for review see e.g. Teer and Mullikin
2010: Human Mol Genet 19 (2), R145-51), all of which can be used in
conjunction with the present invention. Many of these methods
(described e.g. as genome capture, genome partitioning, genome
enrichment etc.) use hybridization techniques and include
array-based (e.g. Hodges et al. 2007: Nat. Genet. 39, 1522-1527)
and liquid-based (e.g. Choi et al. 2009: Proc. Natl. Acad. Sci USA
106, 19096-19101) hybridization approaches. Commercial kits for DNA
sample preparation and subsequent exome capture are also available:
for example, Illumina Inc. (San Diego, Calif.) offers the
TruSeq.TM. DNA Sample Preparation Kit and the Exome Enrichment Kit
TruSeq.TM. Exome Enrichment Kit.
[0156] In order to reduce the number of false positive findings in
detecting cancer specific somatic mutations or sequence differences
when comparing e.g. the sequence of a tumor sample to the sequence
of a reference sample such as the sequence of a germ line sample it
is preferred to determine the sequence in replicates of one or both
of these sample types. Thus, it is preferred that the sequence of a
reference sample such as the sequence of a germ line sample is
determined twice, three times or more. Alternatively or
additionally, the sequence of a tumor sample is determined twice,
three times or more. It may also be possible to determine the
sequence of a reference sample such as the sequence of a germ line
sample and/or the sequence of a tumor sample more than once by
determining at least once the sequence in genomic DNA and
determining at least once the sequence in RNA of said reference
sample and/or of said tumor sample. For example, by determining the
variations between replicates of a reference sample such as a germ
line sample the expected rate of false positive (FDR) somatic
mutations as a statistical quantity can be estimated. Technical
repeats of a sample should generate identical results and any
detected mutation in this "same vs. same comparison" is a false
positive. In particular, to determine the false discovery rate for
somatic mutation detection in a tumor sample relative to a
reference sample, a technical repeat of the reference sample can be
used as a reference to estimate the number of false positives.
Furthermore, various quality related metrics (e.g. coverage or SNP
quality) may be combined into a single quality score using a
machine learning approach. For a given somatic variation all other
variations with an exceeding quality score may be counted, which
enables a ranking of all variations in a dataset.
[0157] In the context of the present invention, the term "RNA"
relates to a molecule which comprises at least one ribonucleotide
residue and preferably being entirely or substantially composed of
ribonucleotide residues. "Ribonucleotide" relates to a nucleotide
with a hydroxyl group at the 2'-position of a
.beta.-D-ribofuranosyl group. The term "RNA" comprises
double-stranded RNA, single-stranded RNA, isolated RNA such as
partially or completely purified RNA, essentially pure RNA,
synthetic RNA, and recombinantly generated RNA such as modified RNA
which differs from naturally occurring RNA by addition, deletion,
substitution and/or alteration of one or more nucleotides. Such
alterations can include addition of non-nucleotide material, such
as to the end(s) of a RNA or internally, for example at one or more
nucleotides of the RNA. Nucleotides in RNA molecules can also
comprise non-standard nucleotides, such as non-naturally occurring
nucleotides or chemically synthesized nucleotides or
deoxynucleotides. These altered RNAs can be referred to as analogs
or analogs of naturally-occurring RNA.
[0158] According to the present invention, the term "RNA" includes
and preferably relates to "mRNA". The term "mRNA" means
"messenger-RNA" and relates to a "transcript" which is generated by
using a DNA template and encodes a peptide or polypeptide.
Typically, an mRNA comprises a 5'-UTR, a protein coding region, and
a 3'-UTR. mRNA only possesses limited half-life in cells and in
vitro. In the context of the present invention, mRNA may be
generated by in vitro transcription from a DNA template. The in
vitro transcription methodology is known to the skilled person. For
example, there is a variety of in vitro transcription kits
commercially available.
[0159] According to the invention, the stability and translation
efficiency of RNA may be modified as required. For example, RNA may
be stabilized and its translation increased by one or more
modifications having a stabilizing effects and/or increasing
translation efficiency of RNA. Such modifications are described,
for example, in PCT/EP2006/009448 incorporated herein by reference.
In order to increase expression of the RNA used according to the
present invention, it may be modified within the coding region,
i.e. the sequence encoding the expressed peptide or protein,
preferably without altering the sequence of the expressed peptide
or protein, so as to increase the GC-content to increase mRNA
stability and to perform a codon optimization and, thus, enhance
translation in cells.
[0160] The term "modification" in the context of the RNA used in
the present invention includes any modification of an RNA which is
not naturally present in said RNA.
[0161] In one embodiment of the invention, the RNA used according
to the invention does not have uncapped 5'-triphosphates. Removal
of such uncapped 5'-triphosphates can be achieved by treating RNA
with a phosphatase.
[0162] The RNA according to the invention may have modified
ribonucleotides in order to increase its stability and/or decrease
cytotoxicity. For example, in one embodiment, in the RNA used
according to the invention 5-methylcytidine is substituted
partially or completely, preferably completely, for cytidine.
Alternatively or additionally, in one embodiment, in the RNA used
according to the invention pseudouridine is substituted partially
or completely, preferably completely, for uridine.
[0163] In one embodiment, the term "modification" relates to
providing an RNA with a 5'-cap or 5'-cap analog. The term "5'-cap"
refers to a cap structure found on the 5'-end of an mRNA molecule
and generally consists of a guanosine nucleotide connected to the
mRNA via an unusual 5' to 5' triphosphate linkage. In one
embodiment, this guanosine is methylated at the 7-position. The
term "conventional 5'-cap" refers to a naturally occurring RNA
5'-cap, preferably to the 7-methylguanosine cap (m.sup.7G). In the
context of the present invention, the term "5'-cap" includes a
5'-cap analog that resembles the RNA cap structure and is modified
to possess the ability to stabilize RNA and/or enhance translation
of RNA if attached thereto, preferably in vivo and/or in a
cell.
[0164] Providing an RNA with a 5'-cap or 5'-cap analog may be
achieved by in vitro transcription of a DNA template in presence of
said 5'-cap or 5'-cap analog, wherein said 5'-cap is
co-transcriptionally incorporated into the generated RNA strand, or
the RNA may be generated, for example, by in vitro transcription,
and the 5'-cap may be attached to the RNA post-transcriptionally
using capping enzymes, for example, capping enzymes of vaccinia
virus.
[0165] The RNA may comprise further modifications. For example, a
further modification of the RNA used in the present invention may
be an extension or truncation of the naturally occurring poly(A)
tail or an alteration of the 5'- or 3'-untranslated regions (UTR)
such as introduction of a UTR which is not related to the coding
region of said RNA, for example, the exchange of the existing
3'-UTR with or the insertion of one or more, preferably two copies
of a 3'-UTR derived from a globin gene, such as alpha2-globin,
alpha1-globin, beta-globin, preferably beta-globin, more preferably
human beta-globin.
[0166] RNA having an unmasked poly-A sequence is translated more
efficiently than RNA having a masked poly-A sequence. The term
"poly(A) tail" or "poly-A sequence" relates to a sequence of adenyl
(A) residues which typically is located on the 3'-end of a RNA
molecule and "unmasked poly-A sequence" means that the poly-A
sequence at the 3' end of an RNA molecule ends with an A of the
poly-A sequence and is not followed by nucleotides other than A
located at the 3' end, i.e. downstream, of the poly-A sequence.
Furthermore, a long poly-A sequence of about 120 base pairs results
in an optimal transcript stability and translation efficiency of
RNA.
[0167] Therefore, in order to increase stability and/or expression
of the RNA used according to the present invention, it may be
modified so as to be present in conjunction with a poly-A sequence,
preferably having a length of 10 to 500, more preferably 30 to 300,
even more preferably 65 to 200 and especially 100 to 150 adenosine
residues. In an especially preferred embodiment the poly-A sequence
has a length of approximately 120 adenosine residues. To further
increase stability and/or expression of the RNA used according to
the invention, the poly-A sequence can be unmasked.
[0168] In addition, incorporation of a 3'-non translated region
(UTR) into the 3'-non translated region of an RNA molecule can
result in an enhancement in translation efficiency. A synergistic
effect may be achieved by incorporating two or more of such 3'-non
translated regions. The 3'-non translated regions may be autologous
or heterologous to the RNA into which they are introduced. In one
particular embodiment the 3'-non translated region is derived from
the human .beta.-globin gene.
[0169] A combination of the above described modifications, i.e.
incorporation of a poly-A sequence, unmasking of a poly-A sequence
and incorporation of one or more 3'-non translated regions, has a
synergistic influence on the stability of RNA and increase in
translation efficiency.
[0170] The term "stability" of RNA relates to the "half-life" of
RNA. "Half-life" relates to the period of time which is needed to
eliminate half of the activity, amount, or number of molecules. In
the context of the present invention, the half-life of an RNA is
indicative for the stability of said RNA.
[0171] The half-life of RNA may influence the "duration of
expression" of the RNA. It can be expected that RNA having a long
half-life will be expressed for an extended time period.
[0172] Of course, if according to the present invention it is
desired to decrease stability and/or translation efficiency of RNA,
it is possible to modify RNA so as to interfere with the function
of elements as described above increasing the stability and/or
translation efficiency of RNA.
[0173] The term "expression" is used according to the invention in
its most general meaning and comprises the production of RNA and/or
peptides, polypeptides or proteins, e.g. by transcription and/or
translation. With respect to RNA, the term "expression" or
"translation" relates in particular to the production of peptides,
polypeptides or proteins. It also comprises partial expression of
nucleic acids. Moreover, expression can be transient or stable.
[0174] According to the invention, the term expression also
includes an "aberrant expression" or "abnormal expression".
"Aberrant expression" or "abnormal expression" means according to
the invention that expression is altered, preferably increased,
compared to a reference, e.g. a state in a subject not having a
disease associated with aberrant or abnormal expression of a
certain protein, e.g., a tumor antigen. An increase in expression
refers to an increase by at least 10%, in particular at least 20%,
at least 50% or at least 100%, or more. In one embodiment,
expression is only found in a diseased tissue, while expression in
a healthy tissue is repressed.
[0175] The term "specifically expressed" means that a protein is
essentially only expressed in a specific tissue or organ. For
example, a tumor antigen specifically expressed in gastric mucosa
means that said protein is primarily expressed in gastric mucosa
and is not expressed in other tissues or is not expressed to a
significant extent in other tissue or organ types. Thus, a protein
that is exclusively expressed in cells of the gastric mucosa and to
a significantly lesser extent in any other tissue, such as testis,
is specifically expressed in cells of the gastric mucosa. In some
embodiments, a tumor antigen may also be specifically expressed
under normal conditions in more than one tissue type or organ, such
as in 2 or 3 tissue types or organs, but preferably in not more
than 3 different tissue or organ types. In this case, the tumor
antigen is then specifically expressed in these organs. For
example, if a tumor antigen is expressed under normal conditions
preferably to an approximately equal extent in lung and stomach,
said tumor antigen is specifically expressed in lung and
stomach.
[0176] In the context of the present invention, the term
"transcription" relates to a process, wherein the genetic code in a
DNA sequence is transcribed into RNA. Subsequently, the RNA may be
translated into protein. According to the present invention, the
term "transcription" comprises "in vitro transcription", wherein
the term "in vitro transcription" relates to a process wherein RNA,
in particular mRNA, is in vitro synthesized in a cell-free system,
preferably using appropriate cell extracts. Preferably, cloning
vectors are applied for the generation of transcripts. These
cloning vectors are generally designated as transcription vectors
and are according to the present invention encompassed by the term
"vector". According to the present invention, the RNA used in the
present invention preferably is in vitro transcribed RNA (IVT-RNA)
and may be obtained by in vitro transcription of an appropriate DNA
template. The promoter for controlling transcription can be any
promoter for any RNA polymerase. Particular examples of RNA
polymerases are the T7, T3, and SP6 RNA polymerases. Preferably,
the in vitro transcription according to the invention is controlled
by a T7 or SP6 promoter. A DNA template for in vitro transcription
may be obtained by cloning of a nucleic acid, in particular cDNA,
and introducing it into an appropriate vector for in vitro
transcription. The cDNA may be obtained by reverse transcription of
RNA.
[0177] The term "translation" according to the invention relates to
the process in the ribosomes of a cell by which a strand of
messenger RNA directs the assembly of a sequence of amino acids to
make a peptide, polypeptide or protein.
[0178] Expression control sequences or regulatory sequences, which
according to the invention may be linked functionally with a
nucleic acid, can be homologous or heterologous with respect to the
nucleic acid. A coding sequence and a regulatory sequence are
linked together "functionally" if they are bound together
covalently, so that the transcription or translation of the coding
sequence is under the control or under the influence of the
regulatory sequence. If the coding sequence is to be translated
into a functional protein, with functional linkage of a regulatory
sequence with the coding sequence, induction of the regulatory
sequence leads to a transcription of the coding sequence, without
causing a reading frame shift in the coding sequence or inability
of the coding sequence to be translated into the desired protein or
peptide.
[0179] The term "expression control sequence" or "regulatory
sequence" comprises, according to the invention, promoters,
ribosome-binding sequences and other control elements, which
control the transcription of a nucleic acid or the translation of
the derived RNA. In certain embodiments of the invention, the
regulatory sequences can be controlled. The precise structure of
regulatory sequences can vary depending on the species or depending
on the cell type, but generally comprises 5'-untranscribed and 5'-
and 3'-untranslated sequences, which are involved in the initiation
of transcription or translation, such as TATA-box,
capping-sequence, CAAT-sequence and the like. In particular,
5'-untranscribed regulatory sequences comprise a promoter region
that includes a promoter sequence for transcriptional control of
the functionally bound gene. Regulatory sequences can also comprise
enhancer sequences or upstream activator sequences.
[0180] Preferably, according to the invention, RNA to be expressed
in a cell is introduced into said cell. In one embodiment of the
methods according to the invention, the RNA that is to be
introduced into a cell is obtained by in vitro transcription of an
appropriate DNA template.
[0181] According to the invention, terms such as "RNA capable of
expressing" and "RNA encoding" are used interchangeably herein and
with respect to a particular peptide or polypeptide mean that the
RNA, if present in the appropriate environment, preferably within a
cell, can be expressed to produce said peptide or polypeptide.
Preferably, RNA according to the invention is able to interact with
the cellular translation machinery to provide the peptide or
polypeptide it is capable of expressing.
[0182] Terms such as "transferring", "introducing" or
"transfecting" are used interchangeably herein and relate to the
introduction of nucleic acids, in particular exogenous or
heterologous nucleic acids, in particular RNA into a cell.
According to the present invention, the cell can form part of an
organ, a tissue and/or an organism. According to the present
invention, the administration of a nucleic acid is either achieved
as naked nucleic acid or in combination with an administration
reagent. Preferably, administration of nucleic acids is in the form
of naked nucleic acids. Preferably, the RNA is administered in
combination with stabilizing substances such as RNase inhibitors.
The present invention also envisions the repeated introduction of
nucleic acids into cells to allow sustained expression for extended
time periods.
[0183] Cells can be transfected with any carriers with which RNA
can be associated, e.g. by forming complexes with the RNA or
forming vesicles in which the RNA is enclosed or encapsulated,
resulting in increased stability of the RNA compared to naked RNA.
Carriers useful according to the invention include, for example,
lipid-containing carriers such as cationic lipids, liposomes, in
particular cationic liposomes, and micelles, and nanoparticles.
Cationic lipids may form complexes with negatively charged nucleic
acids. Any cationic lipid may be used according to the
invention.
[0184] Preferably, the introduction of RNA which encodes a peptide
or polypeptide into a cell, in particular into a cell present in
vivo, results in expression of said peptide or polypeptide in the
cell. In particular embodiments, the targeting of the nucleic acids
to particular cells is preferred. In such embodiments, a carrier
which is applied for the administration of the nucleic acid to a
cell (for example, a retrovirus or a liposome), exhibits a
targeting molecule. For example, a molecule such as an antibody
which is specific for a surface membrane protein on the target cell
or a ligand for a receptor on the target cell may be incorporated
into the nucleic acid carrier or may be bound thereto. In case the
nucleic acid is administered by liposomes, proteins which bind to a
surface membrane protein which is associated with endocytosis may
be incorporated into the liposome formulation in order to enable
targeting and/or uptake. Such proteins encompass capsid proteins of
fragments thereof which are specific for a particular cell type,
antibodies against proteins which are internalized, proteins which
target an intracellular location etc.
[0185] The term "cell" or "host cell" preferably is an intact cell,
i.e. a cell with an intact membrane that has not released its
normal intracellular components such as enzymes, organelles, or
genetic material. An intact cell preferably is a viable cell, i.e.
a living cell capable of carrying out its normal metabolic
functions. Preferably said term relates according to the invention
to any cell which can be transformed or transfected with an
exogenous nucleic acid. The term "cell" includes according to the
invention prokaryotic cells (e.g., E. coli) or eukaryotic cells
(e.g., dendritic cells, B cells, CHO cells, COS cells, K562 cells,
HEK293 cells, HELA cells, yeast cells, and insect cells). The
exogenous nucleic acid may be found inside the cell (i) freely
dispersed as such, (ii) incorporated in a recombinant vector, or
(iii) integrated into the host cell genome or mitochondrial DNA.
Mammalian cells are particularly preferred, such as cells from
humans, mice, hamsters, pigs, goats, and primates. The cells may be
derived from a large number of tissue types and include primary
cells and cell lines. Specific examples include keratinocytes,
peripheral blood leukocytes, bone marrow stem cells, and embryonic
stem cells. In further embodiments, the cell is an
antigen-presenting cell, in particular a dendritic cell, a
monocyte, or macrophage.
[0186] A cell which comprises a nucleic acid molecule preferably
expresses the peptide or polypeptide encoded by the nucleic
acid.
[0187] The term "clonal expansion" refers to a process wherein a
specific entity is multiplied. In the context of the present
invention, the term is preferably used in the context of an
immunological response in which lymphocytes are stimulated by an
antigen, proliferate, and the specific lymphocyte recognizing said
antigen is amplified. Preferably, clonal expansion leads to
differentiation of the lymphocytes.
[0188] Terms such as "reducing" or "inhibiting" relate to the
ability to cause an overall decrease, preferably of 5% or greater,
10% or greater, 20% or greater, more preferably of 50% or greater,
and most preferably of 75% or greater, in the level. The term
"inhibit" or similar phrases includes a complete or essentially
complete inhibition, i.e. a reduction to zero or essentially to
zero.
[0189] Terms such as "increasing", "enhancing", "promoting" or
"prolonging" preferably relate to an increase, enhancement,
promotion or prolongation by about at least 10%, preferably at
least 20%, preferably at least 30%, preferably at least 40%,
preferably at least 50%, preferably at least 80%, preferably at
least 100%, preferably at least 200% and in particular at least
300%. These terms may also relate to an increase, enhancement,
promotion or prolongation from zero or a non-measurable or
non-detectable level to a level of more than zero or a level which
is measurable or detectable.
[0190] The present invention provides vaccines such as cancer
vaccines designed on the basis of amino acid modifications or
modified peptides predicted as being immunogenic by the methods of
the present invention.
[0191] According to the invention, the term "vaccine" relates to a
pharmaceutical preparation (pharmaceutical composition) or product
that upon administration induces an immune response, in particular
a cellular immune response, which recognizes and attacks a pathogen
or a diseased cell such as a cancer cell. A vaccine may be used for
the prevention or treatment of a disease. The term "personalized
cancer vaccine" or "individualized cancer vaccine" concerns a
particular cancer patient and means that a cancer vaccine is
adapted to the needs or special circumstances of an individual
cancer patient.
[0192] In one embodiment, a vaccine provided according to the
invention may comprise a peptide or polypeptide comprising one or
more amino acid modifications or one or more modified peptides
predicted as being immunogenic by the methods of the invention or a
nucleic acid, preferably RNA, encoding said peptide or
polypeptide.
[0193] The cancer vaccines provided according to the invention when
administered to a patent provide one or more T cell epitopes
suitable for stimulating, priming and/or expanding T cells specific
for the patient's tumor. The T cells are preferably directed
against cells expressing antigens from which the T cell epitopes
are derived. Thus, the vaccines described herein are preferably
capable of inducing or promoting a cellular response, preferably
cytotoxic T cell activity, against a cancer disease characterized
by presentation of one or more tumor-associated neoantigens with
class I WIC. Since a vaccine provided according to the present
invention will target cancer specific mutations it will be specific
for the patient's tumor.
[0194] A vaccine provided according to the invention relates to a
vaccine which when administered to a patent preferably provides one
or more T cell epitopes, such as 2 or more, 5 or more, 10 or more,
15 or more, 20 or more, 25 or more, 30 or more and preferably up to
60, up to 55, up to 50, up to 45, up to 40, up to 35 or up to 30 T
cell epitopes, incorporating amino acid modifications or modified
peptides predicted as being immunogenic by the methods of the
invention. Such T cell epitopes are also termed "neo-epitopes"
herein. Presentation of these epitopes by cells of a patient, in
particular antigen presenting cells, preferably results in T cells
targeting the epitopes when bound to WIC and thus, the patient's
tumor, preferably the primary tumor as well as tumor metastases,
expressing antigens from which the T cell epitopes are derived and
presenting the same epitopes on the surface of the tumor cells.
[0195] The methods of the invention may comprise the further step
of determining the usability of the identified amino acid
modifications or modified peptides for cancer vaccination. Thus
further steps can involve one or more of the following: (i)
assessing whether the modifications are located in known or
predicted MHC presented epitopes, (ii) in vitro and/or in silico
testing whether the modifications are located in MHC presented
epitopes, e.g. testing whether the modifications are part of
peptide sequences which are processed into and/or presented as MHC
presented epitopes, and (iii) in vitro testing whether the
envisaged modified epitopes, in particular when present in their
natural sequence context, e.g. when flanked by amino acid sequences
also flanking said epitopes in the naturally occurring protein, and
when expressed in antigen presenting cells are able to stimulate T
cells such as T cells of the patient having the desired
specificity. Such flanking sequences each may comprise 3 or more, 5
or more, 10 or more, 15 or more, 20 or more and preferably up to
50, up to 45, up to 40, up to 35 or up to 30 amino acids and may
flank the epitope sequence N-terminally and/or C-terminally.
[0196] Modified peptides determined according to the invention may
be ranked for their usability as epitopes for cancer vaccination.
Thus, in one aspect, the method of the invention comprises a manual
or computer-based analytical process in which the identified
modified peptides are analyzed and selected for their usability in
the respective vaccine to be provided. In a preferred embodiment,
said analytical process is a computational algorithm-based process.
Preferably, said analytical process comprises determining and/or
ranking epitopes according to a prediction of their capacity of
being immunogenic.
[0197] The neo-epitopes identified according to the invention and
provided by a vaccine of the invention are preferably present in
the form of a polypeptide comprising said neo-epitopes such as a
polyepitopic polypeptide or a nucleic acid, in particular RNA,
encoding said polypeptide. Furthermore, the neo-epitopes may be
present in the polypeptide in the form of a vaccine sequence, i.e.
present in their natural sequence context, e.g. flanked by amino
acid sequences also flanking said epitopes in the naturally
occurring protein. Such flanking sequences each may comprise 5 or
more, 10 or more, 15 or more, 20 or more and preferably up to 50,
up to 45, up to 40, up to 35 or up to 30 amino acids and may flank
the epitope sequence N-terminally and/or C-terminally. Thus, a
vaccine sequence may comprise 20 or more, 25 or more, 30 or more,
35 or more, 40 or more and preferably up to 50, up to 45, up to 40,
up to 35 or up to 30 amino acids. In one embodiment, the
neo-epitopes and/or vaccine sequences are lined up in the
polypeptide head-to-tail.
[0198] In one embodiment, the neo-epitopes and/or vaccine sequences
are spaced by linkers, in particular neutral linkers. The term
"linker" according to the invention relates to a peptide added
between two peptide domains such as epitopes or vaccine sequences
to connect said peptide domains. There is no particular limitation
regarding the linker sequence. However, it is preferred that the
linker sequence reduces steric hindrance between the two peptide
domains, is well translated, and supports or allows processing of
the epitopes. Furthermore, the linker should have no or only little
immunogenic sequence elements. Linkers preferably should not create
non-endogenous neo-epitopes like those generated from the junction
suture between adjacent neo-epitopes, which might generate unwanted
immune reactions. Therefore, the polyepitopic vaccine should
preferably contain linker sequences which are able to reduce the
number of unwanted MHC binding junction epitopes. Hoyt et al. (EMBO
J. 25(8), 1720-9, 2006) and Zhang et al. (J. Biol. Chem., 279(10),
8635-41, 2004) have shown that glycine-rich sequences impair
proteasomal processing and thus the use of glycine rich linker
sequences act to minimize the number of linker-contained peptides
that can be processed by the proteasome. Furthermore, glycine was
observed to inhibit a strong binding in MHC binding groove
positions (Abastado et al., J. Immunol. 151(7), 3569-75, 1993).
Schlessinger et al. (Proteins, 61(1), 115-26, 2005) had found that
amino acids glycine and serine included in an amino acid sequence
result in a more flexible protein that is more efficiently
translated and processed by the proteasome, enabling better access
to the encoded neo-epitopes. The linker each may comprise 3 or
more, 6 or more, 9 or more, 10 or more, 15 or more, 20 or more and
preferably up to 50, up to 45, up to 40, up to 35 or up to 30 amino
acids. Preferably the linker is enriched in glycine and/or serine
amino acids. Preferably, at least 50%, at least 60%, at least 70%,
at least 80%, at least 90%, or at least 95% of the amino acids of
the linker are glycine and/or serine. In one preferred embodiment,
a linker is substantially composed of the amino acids glycine and
serine. In one embodiment, the linker comprises the amino acid
sequence (GGS).sub.a(GSS).sub.b(GGG).sub.c(SSG).sub.d(GSG).sub.e
wherein a, b, c, d and e is independently a number selected from 0,
1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19,
or 20 (SEQ ID NO: 91) and wherein a+b+c+d+e are different from 0
and preferably are 2 or more, 3 or more, 4 or more or 5 or more. In
one embodiment, the linker comprises a sequence as described herein
including the linker sequences described in the examples such as
the sequence GGSGGGGSG (SEQ ID NO: 92).
[0199] In one particularly preferred embodiment, a polypeptide
incorporating one or more neo-epitopes such as a polyepitopic
polypeptide according to the present invention is administered to a
patient in the form of a nucleic acid, preferably RNA such as in
vitro transcribed or synthetic RNA, which may be expressed in cells
of a patient such as antigen presenting cells to produce the
polypeptide. The present invention also envisions the
administration of one or more multiepitopic polypeptides which for
the purpose of the present invention are comprised by the term
"polyepitopic polypeptide", preferably in the form of a nucleic
acid, preferably RNA such as in vitro transcribed or synthetic RNA,
which may be expressed in cells of a patient such as antigen
presenting cells to produce the one or more polypeptides. In the
case of an administration of more than one multiepitopic
polypeptide the neo-epitopes provided by the different
multiepitopic polypeptides may be different or partially
overlapping. Once present in cells of a patient such as antigen
presenting cells the polypeptide according to the invention is
processed to produce the neo-epitopes identified according to the
invention. Administration of a vaccine provided according to the
invention preferably provides MHC class II-presented epitopes that
are capable of eliciting a CD4+ helper T cell response against
cells expressing antigens from which the MHC presented epitopes are
derived. Administration of a vaccine provided according to the
invention may also provide MHC class I-presented epitopes that are
capable of eliciting a CD8+ T cell response against cells
expressing antigens from which the MHC presented epitopes are
derived. Furthermore, administration of a vaccine provided
according to the invention may provide one or more neo-epitopes
(including known neo-epitopes and neo-epitopes identified according
to the invention) as well as one or more epitopes not containing
cancer specific somatic mutations but being expressed by cancer
cells and preferably inducing an immune response against cancer
cells, preferably a cancer specific immune response. In one
embodiment, administration of a vaccine provided according to the
invention provides neo-epitopes that are MHC class II-presented
epitopes and/or are capable of eliciting a CD4+ helper T cell
response against cells expressing antigens from which the MHC
presented epitopes are derived as well as epitopes not containing
cancer-specific somatic mutations that are MHC class I-presented
epitopes and/or are capable of eliciting a CD8+ T cell response
against cells expressing antigens from which the MHC presented
epitopes are derived. In one embodiment, the epitopes not
containing cancer-specific somatic mutations are derived from a
tumor antigen. In one embodiment, the neo-epitopes and epitopes not
containing cancer-specific somatic mutations have a synergistic
effect in the treatment of cancer. Preferably, a vaccine provided
according to the invention is useful for polyepitopic stimulation
of cytotoxic and/or helper T cell responses.
[0200] The vaccine provided according to the invention may be a
recombinant vaccine.
[0201] The term "recombinant" in the context of the present
invention means "made through genetic engineering". Preferably, a
"recombinant entity" such as a recombinant polypeptide in the
context of the present invention is not occurring naturally, and
preferably is a result of a combination of entities such as amino
acid or nucleic acid sequences which are not combined in nature.
For example, a recombinant polypeptide in the context of the
present invention may contain several amino acid sequences such as
neo-epitopes or vaccine sequences derived from different proteins
or different portions of the same protein fused together, e.g., by
peptide bonds or appropriate linkers.
[0202] The term "naturally occurring" as used herein refers to the
fact that an object can be found in nature. For example, a peptide
or nucleic acid that is present in an organism (including viruses)
and can be isolated from a source in nature and which has not been
intentionally modified by man in the laboratory is naturally
occurring.
[0203] Agents, compositions and methods described herein can be
used to treat a subject with a disease, e.g., a disease
characterized by the presence of diseased cells expressing an
antigen and presenting a fragment thereof. Particularly preferred
diseases are cancer diseases. Agents, compositions and methods
described herein may also be used for immunization or vaccination
to prevent a disease described herein.
[0204] According to the invention, the term "disease" refers to any
pathological state, including cancer diseases, in particular those
forms of cancer diseases described herein.
[0205] The term "normal" refers to the healthy state or the
conditions in a healthy subject or tissue, i.e., non-pathological
conditions, wherein "healthy" preferably means non-cancerous.
[0206] "Disease involving cells expressing an antigen" means
according to the invention that expression of the antigen in cells
of a diseased tissue or organ is detected. Expression in cells of a
diseased tissue or organ may be increased compared to the state in
a healthy tissue or organ. An increase refers to an increase by at
least 10%, in particular at least 20%, at least 50%, at least 100%,
at least 200%, at least 500%, at least 1000%, at least 10000% or
even more. In one embodiment, expression is only found in a
diseased tissue, while expression in a healthy tissue is repressed.
According to the invention, diseases involving or being associated
with cells expressing an antigen include cancer diseases.
[0207] According to the invention, the term "tumor" or "tumor
disease" refers to an abnormal growth of cells (called neoplastic
cells, tumorigenous cells or tumor cells) preferably forming a
swelling or lesion. By "tumor cell" is meant an abnormal cell that
grows by a rapid, uncontrolled cellular proliferation and continues
to grow after the stimuli that initiated the new growth cease.
Tumors show partial or complete lack of structural organization and
functional coordination with the normal tissue, and usually form a
distinct mass of tissue, which may be either benign, pre-malignant
or malignant.
[0208] Cancer (medical term: malignant neoplasm) is a class of
diseases in which a group of cells display uncontrolled growth
(division beyond the normal limits), invasion (intrusion on and
destruction of adjacent tissues), and sometimes metastasis (spread
to other locations in the body via lymph or blood). These three
malignant properties of cancers differentiate them from benign
tumors, which are self-limited, and do not invade or metastasize.
Most cancers form a tumor but some, like leukemia, do not.
Malignancy, malignant neoplasm, and malignant tumor are essentially
synonymous with cancer.
[0209] Neoplasm is an abnormal mass of tissue as a result of
neoplasia. Neoplasia (new growth in Greek) is the abnormal
proliferation of cells. The growth of the cells exceeds, and is
uncoordinated with that of the normal tissues around it. The growth
persists in the same excessive manner even after cessation of the
stimuli. It usually causes a lump or tumor. Neoplasms may be
benign, pre-malignant or malignant.
[0210] "Growth of a tumor" or "tumor growth" according to the
invention relates to the tendency of a tumor to increase its size
and/or to the tendency of tumor cells to proliferate.
[0211] For purposes of the present invention, the terms "cancer"
and "cancer disease" are used interchangeably with the terms
"tumor" and "tumor disease".
[0212] Cancers are classified by the type of cell that resembles
the tumor and, therefore, the tissue presumed to be the origin of
the tumor. These are the histology and the location,
respectively.
[0213] The term "cancer" according to the invention comprises
carcinomas, adenocarcinomas, blastomas, leukemias, seminomas,
melanomas, teratomas, lymphomas, neuroblastomas, gliomas, rectal
cancer, endometrial cancer, kidney cancer, adrenal cancer, thyroid
cancer, blood cancer, skin cancer, cancer of the brain, cervical
cancer, intestinal cancer, liver cancer, colon cancer, stomach
cancer, intestine cancer, head and neck cancer, gastrointestinal
cancer, lymph node cancer, esophagus cancer, colorectal cancer,
pancreas cancer, ear, nose and throat (ENT) cancer, breast cancer,
prostate cancer, cancer of the uterus, ovarian cancer and lung
cancer and the metastases thereof. Examples thereof are lung
carcinomas, mamma carcinomas, prostate carcinomas, colon
carcinomas, renal cell carcinomas, cervical carcinomas, or
metastases of the cancer types or tumors described above. The term
cancer according to the invention also comprises cancer metastases
and relapse of cancer.
[0214] By "metastasis" is meant the spread of cancer cells from its
original site to another part of the body. The formation of
metastasis is a very complex process and depends on detachment of
malignant cells from the primary tumor, invasion of the
extracellular matrix, penetration of the endothelial basement
membranes to enter the body cavity and vessels, and then, after
being transported by the blood, infiltration of target organs.
Finally, the growth of a new tumor, i.e. a secondary tumor or
metastatic tumor, at the target site depends on angiogenesis. Tumor
metastasis often occurs even after the removal of the primary tumor
because tumor cells or components may remain and develop metastatic
potential. In one embodiment, the term "metastasis" according to
the invention relates to "distant metastasis" which relates to a
metastasis which is remote from the primary tumor and the regional
lymph node system.
[0215] The cells of a secondary or metastatic tumor are like those
in the original tumor. This means, for example, that, if ovarian
cancer metastasizes to the liver, the secondary tumor is made up of
abnormal ovarian cells, not of abnormal liver cells. The tumor in
the liver is then called metastatic ovarian cancer, not liver
cancer.
[0216] The term "circulating tumor cells" or "CTCs" relates to
cells that have detached from a primary tumor or tumor metastases
and circulate in the bloodstream. CTCs may constitute seeds for
subsequent growth of additional tumors (metastasis) in different
tissues. Circulating tumor cells are found in frequencies in the
order of 1-10 CTC per mL of whole blood in patients with metastatic
disease. Research methods have been developed to isolate CTC.
Several research methods have been described in the art to isolate
CTCs, e.g. techniques which use of the fact that epithelial cells
commonly express the cell adhesion protein EpCAM, which is absent
in normal blood cells. Immunomagnetic bead-based capture involves
treating blood specimens with antibody to EpCAM that has been
conjugated with magnetic particles, followed by separation of
tagged cells in a magnetic field. Isolated cells are then stained
with antibody to another epithelial marker, cytokeratin, as well as
a common leukocyte marker CD45, so as to distinguish rare CTCs from
contaminating white blood cells. This robust and semi-automated
approach identifies CTCs with an average yield of approximately 1
CTC/mL and a purity of 0.1% (Allard et al., 2004: Clin Cancer Res
10, 6897-6904). A second method for isolating CTCs uses a
microfluidic-based CTC capture device which involves flowing whole
blood through a chamber embedded with 80,000 microposts that have
been rendered functional by coating with antibody to EpCAM. CTCs
are then stained with secondary antibodies against either
cytokeratin or tissue specific markers, such as PSA in prostate
cancer or HER2 in breast cancer and are visualized by automated
scanning of microposts in multiple planes along three dimensional
coordinates. CTC-chips are able to identifying
cytokerating-positive circulating tumor cells in patients with a
median yield of 50 cells/ml and purity ranging from 1-80% (Nagrath
et al., 2007: Nature 450, 1235-1239). Another possibility for
isolating CTCs is using the CellSearch.TM. Circulating Tumor Cell
(CTC) Test from Veridex, LLC (Raritan, N.J.) which captures,
identifies, and counts CTCs in a tube of blood. The CellSearch.TM.
system is a U.S. Food and Drug Administration (FDA) approved
methodology for enumeration of CTC in whole blood which is based on
a combination of immunomagnetic labeling and automated digital
microscopy. There are other methods for isolating CTCs described in
the literature all of which can be used in conjunction with the
present invention.
[0217] A relapse or recurrence occurs when a person is affected
again by a condition that affected them in the past. For example,
if a patient has suffered from a tumor disease, has received a
successful treatment of said disease and again develops said
disease said newly developed disease may be considered as relapse
or recurrence. However, according to the invention, a relapse or
recurrence of a tumor disease may but does not necessarily occur at
the site of the original tumor disease. Thus, for example, if a
patient has suffered from ovarian tumor and has received a
successful treatment a relapse or recurrence may be the occurrence
of an ovarian tumor or the occurrence of a tumor at a site
different to ovary. A relapse or recurrence of a tumor also
includes situations wherein a tumor occurs at a site different to
the site of the original tumor as well as at the site of the
original tumor. Preferably, the original tumor for which the
patient has received a treatment is a primary tumor and the tumor
at a site different to the site of the original tumor is a
secondary or metastatic tumor.
[0218] By "treat" is meant to administer a compound or composition
as described herein to a subject in order to prevent or eliminate a
disease, including reducing the size of a tumor or the number of
tumors in a subject; arrest or slow a disease in a subject; inhibit
or slow the development of a new disease in a subject; decrease the
frequency or severity of symptoms and/or recurrences in a subject
who currently has or who previously has had a disease; and/or
prolong, i.e. increase the lifespan of the subject. In particular,
the term "treatment of a disease" includes curing, shortening the
duration, ameliorating, preventing, slowing down or inhibiting
progression or worsening, or preventing or delaying the onset of a
disease or the symptoms thereof.
[0219] By "being at risk" is meant a subject, i.e. a patient, that
is identified as having a higher than normal chance of developing a
disease, in particular cancer, compared to the general population.
In addition, a subject who has had, or who currently has, a
disease, in particular cancer, is a subject who has an increased
risk for developing a disease, as such a subject may continue to
develop a disease. Subjects who currently have, or who have had, a
cancer also have an increased risk for cancer metastases.
[0220] The term "immunotherapy" relates to a treatment involving
activation of a specific immune reaction. In the context of the
present invention, terms such as "protect", "prevent",
"prophylactic", "preventive", or "protective" relate to the
prevention or treatment or both of the occurrence and/or the
propagation of a disease in a subject and, in particular, to
minimizing the chance that a subject will develop a disease or to
delaying the development of a disease. For example, a person at
risk for a tumor, as described above, would be a candidate for
therapy to prevent a tumor.
[0221] A prophylactic administration of an immunotherapy, for
example, a prophylactic administration of a vaccine of the
invention, preferably protects the recipient from the development
of a disease. A therapeutic administration of an immunotherapy, for
example, a therapeutic administration of a vaccine of the
invention, may lead to the inhibition of the progress/growth of the
disease. This comprises the deceleration of the progress/growth of
the disease, in particular a disruption of the progression of the
disease, which preferably leads to elimination of the disease.
[0222] Immunotherapy may be performed using any of a variety of
techniques, in which agents provided herein function to remove
diseased cells from a patient. Such removal may take place as a
result of enhancing or inducing an immune response in a patient
specific for an antigen or a cell expressing an antigen.
[0223] Within certain embodiments, immunotherapy may be active
immunotherapy, in which treatment relies on the in vivo stimulation
of the endogenous host immune system to react against diseased
cells with the administration of immune response-modifying agents
(such as polypeptides and nucleic acids as provided herein).
[0224] The agents and compositions provided herein may be used
alone or in combination with conventional therapeutic regimens such
as surgery, irradiation, chemotherapy and/or bone marrow
transplantation (autologous, syngeneic, allogeneic or
unrelated).
[0225] The term "immunization" or "vaccination" describes the
process of treating a subject with the purpose of inducing an
immune response for therapeutic or prophylactic reasons.
[0226] The term "in vivo" relates to the situation in a
subject.
[0227] The terms "subject", "individual", "organism" or "patient"
are used interchangeably and relate to vertebrates, preferably
mammals. For example, mammals in the context of the present
invention are humans, non-human primates, domesticated animals such
as dogs, cats, sheep, cattle, goats, pigs, horses etc., laboratory
animals such as mice, rats, rabbits, guinea pigs, etc. as well as
animals in captivity such as animals of zoos. The term "animal" as
used herein also includes humans. The term "subject" may also
include a patient, i.e., an animal, preferably a human having a
disease, preferably a disease as described herein.
[0228] The term "autologous" is used to describe anything that is
derived from the same subject. For example, "autologous transplant"
refers to a transplant of tissue or organs derived from the same
subject. Such procedures are advantageous because they overcome the
immunological barrier which otherwise results in rejection.
[0229] The term "heterologous" is used to describe something
consisting of multiple different elements. As an example, the
transfer of one individual's bone marrow into a different
individual constitutes a heterologous transplant. A heterologous
gene is a gene derived from a source other than the subject.
[0230] As part of the composition for an immunization or a
vaccination, preferably one or more agents as described herein are
administered together with one or more adjuvants for inducing an
immune response or for increasing an immune response. The term
"adjuvant" relates to compounds which prolongs or enhances or
accelerates an immune response. The composition of the present
invention preferably exerts its effect without addition of
adjuvants. Still, the composition of the present application may
contain any known adjuvant. Adjuvants comprise a heterogeneous
group of compounds such as oil emulsions (e.g., Freund's
adjuvants), mineral compounds (such as alum), bacterial products
(such as Bordetella pertussis toxin), liposomes, and
immune-stimulating complexes. Examples for adjuvants are
monophosphoryl-lipid-A (MPL SmithKline Beecham). Saponins such as
QS21 (SmithKline Beecham), DQS21 (SmithKline Beecham; WO 96/33739),
QS7, QS17, QS18, and QS-L1 (So et al., 1997, Mol. Cells 7:
178-186), incomplete Freund's adjuvants, complete Freund's
adjuvants, vitamin E, montanid, alum, CpG oligonucleotides (Krieg
et al., 1995, Nature 374: 546-549), and various water-in-oil
emulsions which are prepared from biologically degradable oils such
as squalene and/or tocopherol.
[0231] Other substances which stimulate an immune response of the
patient may also be administered. It is possible, for example, to
use cytokines in a vaccination, owing to their regulatory
properties on lymphocytes. Such cytokines comprise, for example,
interleukin-12 (IL-12) which was shown to increase the protective
actions of vaccines (cf. Science 268:1432-1434, 1995), GM-CSF and
IL-18.
[0232] There are a number of compounds which enhance an immune
response and which therefore may be used in a vaccination. Said
compounds comprise co-stimulating molecules provided in the form of
proteins or nucleic acids such as B7-1 and B7-2 (CD80 and CD86,
respectively).
[0233] According to the invention, a bodily sample may be a tissue
sample, including body fluids, and/or a cellular sample. Such
bodily samples may be obtained in the conventional manner such as
by tissue biopsy, including punch biopsy, and by taking blood,
bronchial aspirate, sputum, urine, feces or other body fluids.
According to the invention, the term "sample" also includes
processed samples such as fractions or isolates of biological
samples, e.g. nucleic acid or cell isolates.
[0234] The agents such as vaccines and compositions described
herein may be administered via any conventional route, including by
injection or infusion. The administration may be carried out, for
example, orally, intravenously, intraperitoneally, intramuscularly,
subcutaneously or transdermally. In one embodiment, administration
is carried out intranodally such as by injection into a lymph node.
Other forms of administration envision the in vitro transfection of
antigen presenting cells such as dendritic cells with nucleic acids
described herein followed by administration of the antigen
presenting cells.
[0235] The agents described herein are administered in effective
amounts. An "effective amount" refers to the amount which achieves
a desired reaction or a desired effect alone or together with
further doses. In the case of treatment of a particular disease or
of a particular condition, the desired reaction preferably relates
to inhibition of the course of the disease. This comprises slowing
down the progress of the disease and, in particular, interrupting
or reversing the progress of the disease. The desired reaction in a
treatment of a disease or of a condition may also be delay of the
onset or a prevention of the onset of said disease or said
condition.
[0236] An effective amount of an agent described herein will depend
on the condition to be treated, the severeness of the disease, the
individual parameters of the patient, including age, physiological
condition, size and weight, the duration of treatment, the type of
an accompanying therapy (if present), the specific route of
administration and similar factors. Accordingly, the doses
administered of the agents described herein may depend on various
of such parameters. In the case that a reaction in a patient is
insufficient with an initial dose, higher doses (or effectively
higher doses achieved by a different, more localized route of
administration) may be used.
[0237] The pharmaceutical compositions described herein are
preferably sterile and contain an effective amount of the
therapeutically active substance to generate the desired reaction
or the desired effect.
[0238] The pharmaceutical compositions described herein are
generally administered in pharmaceutically compatible amounts and
in pharmaceutically compatible preparation. The term
"pharmaceutically compatible" refers to a nontoxic material which
does not interact with the action of the active component of the
pharmaceutical composition. Preparations of this kind may usually
contain salts, buffer substances, preservatives, carriers,
supplementing immunity-enhancing substances such as adjuvants, e.g.
CpG oligonucleotides, cytokines, chemokines, saponin, GM-CSF and/or
RNA and, where appropriate, other therapeutically active compounds.
When used in medicine, the salts should be pharmaceutically
compatible. However, salts which are not pharmaceutically
compatible may used for preparing pharmaceutically compatible salts
and are included in the invention. Pharmacologically and
pharmaceutically compatible salts of this kind comprise in a
non-limiting way those prepared from the following acids:
hydrochloric, hydrobromic, sulfuric, nitric, phosphoric, maleic,
acetic, salicylic, citric, formic, malonic, succinic acids, and the
like. Pharmaceutically compatible salts may also be prepared as
alkali metal salts or alkaline earth metal salts, such as sodium
salts, potassium salts or calcium salts.
[0239] A pharmaceutical composition described herein may comprise a
pharmaceutically compatible carrier. The term "carrier" refers to
an organic or inorganic component, of a natural or synthetic
nature, in which the active component is combined in order to
facilitate application. According to the invention, the term
"pharmaceutically compatible carrier" includes one or more
compatible solid or liquid fillers, diluents or encapsulating
substances, which are suitable for administration to a patient. The
components of the pharmaceutical composition of the invention are
usually such that no interaction occurs which substantially impairs
the desired pharmaceutical efficacy.
[0240] The pharmaceutical compositions described herein may contain
suitable buffer substances such as acetic acid in a salt, citric
acid in a salt, boric acid in a salt and phosphoric acid in a
salt.
[0241] The pharmaceutical compositions may, where appropriate, also
contain suitable preservatives such as benzalkonium chloride,
chlorobutanol, paraben and thimerosal.
[0242] The pharmaceutical compositions are usually provided in a
uniform dosage form and may be prepared in a manner known per se.
Pharmaceutical compositions of the invention may be in the form of
capsules, tablets, lozenges, solutions, suspensions, syrups,
elixirs or in the form of an emulsion, for example.
[0243] Compositions suitable for parenteral administration usually
comprise a sterile aqueous or nonaqueous preparation of the active
compound, which is preferably isotonic to the blood of the
recipient. Examples of compatible carriers and solvents are Ringer
solution and isotonic sodium chloride solution. In addition,
usually sterile, fixed oils are used as solution or suspension
medium.
[0244] The present invention is described in detail by the figures
and examples below, which are used only for illustration purposes
and are not meant to be limiting. Owing to the description and the
examples, further embodiments which are likewise included in the
invention are accessible to the skilled worker.
FIGURES
[0245] FIG. 1. Non synonymous cancer-associated mutations are
frequently immunogenic and pre-dominantly recognized by CD4.sup.+ T
cells. a, For immunogenicity testing, mice (n=5 for b and c, n=3
for d) were vaccinated with either synthetic peptides and poly
(I:C) as adjuvant (b) or antigen-encoding RNA (c, d) representing
the mutated epitopes (two mutations per mouse). Splenocytes were
restimulated ex vivo with the mutated peptide or an irrelevant
control peptide and tested by IFN.gamma. Elispot (see exemplarily
FIG. 2a) and intracellular cytokine and CD4/CD8 surface staining to
assess subtype of elicited immune responses. b-c, T cell responses
obtained by vaccinating C57BL/6 mice with epitopes mutated in the
B16F10 tumor model. Left, prevalence of non-immunogenic, MHC class
I or class 11 restricted mutated epitopes. Right, examples for
detection and typing of mutation-specific T cells (see Table 1 for
data on individual epitopes). d prevalence of non-immunogenic, MHC
class I or class II restricted mutated epitopes discovered in the
CT26 model. Right, MHC restriction of immunogenic mutated epitopes
prioritized based on predicted MHC class I binding and selected
based on either good (0.1-2.1) or poor (>3.9) binding scores.
See Table 2 for data on individual epitopes. Sequences in a
("Sequence analysis and mutation identification"): TTCAGGACCCA (SEQ
ID NO: 93); TTCAGGACCCACACGA (SEQ ID NO: 94);
TTCAGGACCCACACGACGGGAAGACAA (SEQ ID NO: 95);
TTCAGGACCAACACGACGGGAAGACAAGT (SEQ ID NO: 96);
CAGGACCCACACGACGGGTAGACAAGT (SEQ ID NO: 97); ACCCACACGACGGGTAG
ACAAGT (SEQ ID NO: 98); ACCCACACGAGCCCTAGACAAGT (SEQ ID NO: 99);
GACGGGAAGACAAGT (SEQ ID NO: 100). Sequences in b and c: B16-M27
(SEQ ID NO: 10); B16-M30 (SEQ FD NO: 13).
[0246] FIG. 2. Efficient tumor control and survival benefit in
B16F10 melanoma by immunization with an RNA vaccine encoding a
single mutated CD4.sup.+ T cell epitope. a, Splenocytes of mice
(n=5) vaccinated with B16-M30 RNA were tested by ELISpot for
recognition of synthetic peptides. Left, the mutated (B16-M30)
versus the corresponding wild type (B16-WT30) sequence. Right,
definition of the minimal epitope by testing for recognition of
truncated variants of B16-M30 (mean.+-.SEM). b, The mean.+-.SEM
tumor growth (left) and survival (right) of C57BL/6 mice (n=10)
inoculated subcutaneously with B16F10 tumors cells and left
untreated (control) or immunized IV with B16-M30 encoding RNA
(B16-M30) with or without administration of CD4 or CD8 depleting
antibodies. c, B6 albino mice (n=10) developing lung metastases
upon IV injection of luciferase transgenic B16F10 tumor cells
(B16F10-Luc) were treated with B16-M30 encoding RNA (B16-M30) or
irrelevant control RNA. Median tumor growth was determined by BLI.
d, Single cell suspensions of B16F10 tumors of untreated (control,
n=x) or B16-M30 RNA immunized mice (n=4) were restimulated with
B16-M30 peptide, medium or irrelevant peptide (VSV-NP.sub.52-59)
and tested in an IFN.gamma. ELISpot assay (mean.+-.SEM). e, Flow
cytometric characterization of tumor infiltrating leucocytes in
B16-M30 RNA vaccinated mice. Depicted is the frequency of
CD4.sup.+, CD8.sup.+ or FoxP3.sup.+/CD4.sup.+ T cells among
CD45.sup.+ cells and Gr-1.sup.+/CD11b.sup.+ cells (MDSCs) of
untreated (control) or Mut30 RNA vaccinated C57BL/6 mice (n=3)
inoculated subcutaneously with B16F10 tumors cells. Sequences in a:
B16-M30 (SEQ ID NO: 13); DWENVSPELNSTDQP (SEQ ID NO: 80); DWE
NVSPELNSTDQ (SEQ ID NO: 81); DWENVSPELNSTD (SEQ ID NO: 82);
DWENVSPELNS T (SEQ ID NO: 83); DWENVSPELNS (SEQ ID NO: 84);
WENVSPELNSTDQP (SEQ ID NO: 85); WENVSPELNSTD (SEQ ID NO: 86);
WENVSPELNST (SEQ ID NO: 87); ENVSPELNS TDQP (SEQ ID NO: 88);
NVSPELNSTDQP (SEQ ID NO: 89); VSPELNSTDQP (SEQ ID NO: 90).
[0247] FIG. 3. Immunization with RNA pentatopes induces T cell
responses against the individual mutated epitopes and confers
disease control and significant survival benefit in mouse tumor
models. a, Engineering of a poly-neo-epitope RNA vaccine. The RNA
pentatope contains five 27mer sequences connected by gly/ser
linkers inserted into the pST1-Sp-MITD-2hBgUTR-A120 backbone. (UTR,
untranslated region; sp, signal peptide; MITD, WIC class I
trafficking domain). b, BALB/c mice (n=5) were vaccinated either
with pentatope RNA (35 .mu.g) or the corresponding mixture of five
RNA monotopes (7 .mu.g each). T cell responses in peptide
stimulated splenocytes of mice were measured ex vivo on day 19 in
an IFN.gamma. ELISpot assay (medium control subtracted
mean.+-.SEM). c, BALB/c mice (n=10) developing lung metastases upon
IV injection of CT26-Luc cells were treated simultaneously with a
mixture of two RNA pentatopes or left untreated (control). The
median tumor growth by BLI (left), survival data (mid) and lungs
from treated animals (right) are shown. d, CD3 stained tissue
sections from the lungs of pentatope1+2 treated animals (upper
panel). The left side of each panel shows the analyzed sections,
the right side the magnifications (scale bar: scan: 1000 .mu.m,
upper pictures: 100 .mu.m, lower pictures: 50 .mu.m). CD3.sup.+,
CD4.sup.+, FoxP3.sup.+ and CD8.sup.+ (calculated by CD3.sup.+
area-CD4.sup.+ area) areas in consecutive immunohistochemical lung
tissue sections of control (n=6) or RNA pentatope (CD3: n=14; CD4,
CD8, FoxP3: n=12) treated animals were quantified and proportions
of tumor were calculated. The right figure depicts a comparison of
tumor area in sections of control (n=18) and Pentatope 1+2 (n=39)
treated animals (tumor free animals of pentatope1+2 treatment group
were excluded). Depicted are mean.+-.SEM. Sequences in a ("Cloning
of template"): GGAAACTTTC (SEQ ID NO: 105).
[0248] FIG. 4. RNA pentatope vaccines with mutations selected for
in silico predicted favorable MHC class II binding properties and
abundant expression confer potent antitumor control. a, Comparison
of MHC II binding scores of immunogenic and non-immunogenic
mutations (medians shown). b, Mutations with high expression levels
were selected with (`ME` mutations) or without (`E` mutations)
considering MHC class II binding score. See also Table 4. Ten
mutations out of each category represented by two pentatopes each
were used for vaccination of CT26-Luc lung tumor bearing mice.
Tumor growth curves (left), area under the curve (mid) and ink
treated lungs (right) are shown. c, Mice (5 per group) were
analyzed for T cell responses against the vaccinated pentatopes by
restimulation with RNA electroporated syngeneic BMDC in an
IFN.gamma. ELISpot assay. Each dot represents the mean spot count
of one mouse subtracted by an irrelevant RNA control (mean.+-.SEM).
d, Tumor nodules per lung of BALB/c mice (n=10) inoculated IV with
CT26 tumor cells and left untreated or injected with irrelevant
RNA, pentatope1, pentatope2 or CT26-M19 RNA. e, T cell responses
against gp70.sub.423-431 (gp70-AH1) were determined via IFN.gamma.
ELISpot assay in blood (pooled from 5 mice, day 20 after tumor
inoculation) and spleen (n=5). (Background (no peptide control)
subtracted mean.+-.SEM depicted). f, Somatic mutation and RNA-Seq
data for individual human cancer samples (black dots) from The
Cancer Genome Atlas (TCGA) was employed to identify genomic (upper
panel) and expressed (mid panel) non-synonymous single nucleotide
variations (nsSNVs). (lower panel) Neo-epitopes predicted to bind
to the patients' HLA-DRB1 alleles (percentile rank <10%) are
shown (SKCM, skin cutaneous melanoma; COAD, colon adenocarcinoma;
BRCA, breast invasive carcinoma).
[0249] FIG. 5: Calculation of variant allele frequency (VAF). The
figure shows an idealized gene as a combination of exons on a piece
of genomic DNA (upper part) and example read sequences aligned to
this locus (lower part, in a higher zoom level). The site of the
mutation event ("mutation site") is shown by a dashed line (upper
part) or box (lower part). The mutant nucleotides are colored red,
the wild type nucleotides are colored green. Also the sums of those
nucleotides in the VAF formula are colored accordingly. Sequences
in a: TGCAAGAACGCGT ACTTATTCGCCGCCATGATTATGACCAGTGTTTCCAGTC (SEQ ID
NO: 101); CAAGAA CGCGTACTTATTCGCCACCATGATTATGACCAGTGTTTCCAG (SEQ ID
NO: 102); AAC GCGTACTTATTCGCCACCATGATTATGACCAGTGTTTCCAGTC (SEQ ID
NO: 103); TG CAAGAACGCGTACTTATTCGCCGCCATGATTATGACCAGTGTTT (SEQ ID
NO: 104).
[0250] FIG. 6: Influence of the expression of mutated allele on the
prediction performance of MHC II-scores. 185 selected mutations
from the murine tumor models 4T1, CT26 and B16F10 were tested for
their antigenicity. The predictive performance of the calculated
MHC II-scores was deduced from the area under the receiver
operating characteristic curve (AUC, open circle). This value was
subsequently recalculated after applying different thresholds for
the total mRNA expression (left panel) and the expression of the
mutated allele (right panel, mRNA expression*mutated allele
frequency, closed circles). The maximum AUC values are indicated.
The expression of the mutated allele contributes more to the
improvement of the prediction performance.
[0251] FIG. 7: Comparison of receiver operating characteristic
(ROC) curves with and without threshold on the expression. The ROC
curves indicate the performance of the antigenicity prediction for
all 185 selected mutations from the murine tumor models 4T1, CT26
and B16F10 (dotted curves) and for those mutations, for which the
mRNA expression was .gtoreq.6 RPKM (left panel, solid curve) or the
expression of the mutated allele was .gtoreq.4 RPKM (right panel,
solid curve). The selected thresholds achieved the maximum AUC
values (see FIG. 6).
EXAMPLES
[0252] The techniques and methods used herein are described herein
or carried out in a manner known per se and as described, for
example, in Sambrook et al., Molecular Cloning: A Laboratory
Manual, 2.sup.nd Edition (1989) Cold Spring Harbor Laboratory
Press, Cold Spring Harbor, N.Y. All methods including the use of
kits and reagents are carried out according to the manufacturers'
information unless specifically indicated.
Example 1: Materials and Methods
[0253] Samples. Female 8-12 week old C57BL/6, BALB/c mice (Janvier
Labs) and C57BL/6BrdCrHsd-Tyr.sup.c mice (B6 albino, Harlan) were
kept in accordance with federal policies on animal research at the
University of Mainz. B16F10 melanoma cell line, CT26 colon
carcinoma cell line and 4T1-luc2-tdtomato (4T1-Luc) cells were
purchased in 2010, 2011 and 2011 respectively (ATCC CRL-6475 lot
#58078645, ATCC CRL-2638 lot #58494154, Caliper 125669 lot #101648)
and maintained as suggested by the supplier. Firefly luciferase
expressing CT26-Luc and B16F10-Luc cells were lentivirally
transduced. Master and working cell banks were generated, of which
third and fourth passages were used for tumor experiments.
[0254] Next generation sequencing and data processing was described
previously (Castle, J. C., et al., Cancer Res 72, 1081 (2012);
Castle, J. C., et al., BMC Genomics 15, 190 (2014)). In brief,
exome capture from mouse tumor cells and tail tissue samples of
BALB/c or C57BL/6 mice were sequenced in triplicate (4T1-Luc in
duplicate). Oligo(dT) based RNA sequencing libraries for gene
expression profiling were prepared in triplicate. Libraries were
sequenced on an Illumina HiSeq2000 to generate 50 nucleotide
single-end (B16F10) or 100 nucleotide paired-end (CT26, 4T1-Luc)
reads, respectively. Gene expression values were determined by
counting reads overlapping transcript exons and junctions, and
normalizing to RPKM expression units (Reads which map per kilobase
of transcript length per million mapped reads). Mutation expression
was determined by normalization of mutated RNA reads to the total
mapped read counts multiplied by 100 million (normalized variant
read counts; NVRC).
[0255] Mutation selection, validation and prioritization was
described previously (Castle, J. C., et al., Cancer Res 72, 1081
(2012); Castle, J. C., et al., BMC Genomics 15, 190 (2014); Lower,
M., et al., PLoS Comput Biol 8, e1002714 (2012)). Mutations to be
pursued were selected based on following criteria: (i) present in
the respective tumor cell line sequencing triplicates and absent in
the corresponding healthy tissue sample triplicates, (ii) occur in
a RefSeq transcript, and (iii) cause non-synonymous changes.
Further criteria were occurrence in expressed genes of tumor cell
lines (median RPKM across replicates). For validation, mutations
were amplified from DNA of B16F10, CT26 or 4T1-Luc cells and
C57BL/6 or BALB/c tail tissue and subjected to Sanger sequencing.
DNA-derived mutations were classified as validated if confirmed by
either Sanger sequencing or the RNASeq reads. No confirmation via
Sanger sequencing and immunogenicity testing was performed for
experiments shown in FIG. 4. For experiments shown in FIG. 1
mutated epitopes were prioritized according to their predicted MHC
class I binding based on the consensus method (version 2.5) of the
Immune Epitope Database (Vita, R., et al., Nucleic Acids Res 38,
D854-D862 (2010)). Mutations targeted in the experiment shown in
FIG. 4b-e were selected based on either their expression (NVRC)
alone or together with their predicted MHC class II peptide binding
capability (IEDB consensus method version 2.5). Retrospective
analysis of MHC II binding prediction shown in FIG. 4a was
determined with IEDB consensus method version 2.12. For analysis of
mutations in human tumors, DNA sequencing data of skin cutaneous
melanoma (SKCM, n=308), colon adenocarcinoma (COAD, n=192) or
breast invasive carcinoma (BRCA, n=872) retrieved from The Cancer
Genome Atlas (TCGA) (august 2014) was filtered to obtain genomic
non-synonymous point mutations (nsSNVs). RNA-Seq data (TCGA) of
tumor samples with identified genomic mutations was used to define
expressed nsSNVs. In order to predict MHC II binding expressed
neo-epitopes seq2HLA was employed to identify the patients' 4-digit
HLA class II (HLA-DQA1, HLA-DQB1, HLA-DRB1) type. The IEDB
consensus binding prediction (version 2.12) was used to predict MHC
class II binding from a 27mer peptide and the patients HLA-DRB1
alleles. As recommended from IEDB, neo-eptiopes with a percentile
rank below 10% were considered as binders.
[0256] Synthetic RNA and synthetic peptides. Identified
non-synonymous mutations were studied in the context of the
respective 27mer amino acid epitope with the mutated amino acid in
the center (position 14). Either of these mutated peptides were
synthesized together with control peptides (vesiculo-stomatitis
virus nucleo-protein (VSV-NP.sub.52-59), gp70-AH1
(gp70.sub.423-431) and tyrosinase-related protein 2
(Trp2.sub.180-188) by JPT Peptide Technologies GmbH. Alternatively,
sequences encoding mutated 27mer peptides were cloned into the
pST1-Sp-MITD-2hBgUTR-A120 backbone (Holtkamp, S., et al., Blood
108, 4009 (2006)) featuring sequence elements for pharmacologically
optimized synthetic RNA in terms of translation efficiency and MHC
class I/II processing of epitopes either as monotopes or as
pentatopes fused to each other by sequences encoding 10 amino acid
long glycine-serine linker in between. Linearization of these
plasmid constructs, in vitro translation (IVT) of these templates
and purification are described in detail elsewhere (Holtkamp, S.,
et al., Blood 108, 4009 (2006)).
[0257] Mouse Models.
[0258] For experiments investigating the immunogenicity of mutated
epitopes age-matched female C57BL/6 or BALB/c mice were vaccinated
on day 0, 3, 7 and 14 (immunization with RNA) or day 0 and 7
(immunization with peptide), the read out was performed five to six
days after the last immunization. Vaccination was performed either
by retro-orbital injection of 200 .mu.l (20 .mu.g per mutation for
B16F10, 40 .mu.g per mutation for CT26) RNA complexed with cationic
lipids (manuscript in preparation) or subcutaneous injection of 100
.mu.g synthetic peptide and 50 .mu.g poly (I:C) formulated in PBS
(200 .mu.L total volume) into the lateral flank. Two mutations per
mouse were tested (n=5 for B16F10, n=3 for CT26). For confirmation
of immunogenic mutations and subtyping, mice were vaccinated
against a single mutation (n=5).
[0259] For therapeutic tumor experiments C57BL/6 mice were
inoculated subcutaneously with 1.times.10.sup.5 B16F10 melanoma
cells into the right flank and randomly distributed into treatment
groups. Tumor volume was measured unblinded with a caliper and
calculated using the formula (AxB.sup.2)/2 (A as the largest and B
the smallest diameter of the tumor). In lung metastasis experiments
5.times.10.sup.5 CT26-Luc or 2.times.10.sup.5 CT26 cells were
injected into the tail vein of BALB/c mice or 1.5.times.10.sup.5
B16F10-Luc tumor cells into B6 albino mice to obtain lung tumors.
Tumor growth of luciferase transgenic cells was traced unblinded by
bioluminescence imaging after i.p. injection of an aqueous solution
of D-luciferin (250 .mu.l, 1.6 mg, BD Bioscience) on an IVIS Lumina
(Caliper Life Sciences). Five minutes after injection emitted
photons were quantified. In vivo bioluminescence in regions of
interest (ROI) were quantified as total flux (photons/sec) using
IVIS Living Image 4.0 software. Mice were randomized based on their
total flux values (ANOVA-P method, Daniel's XL Toolbox V6.53). CT26
lung tumor burden was quantified unblinded after tracheal Ink (1:10
diluted in PBS) injection and fixation with Fekete's solution (5 mL
70% EtOH, 0.5 mL formalin, and 0.25 mL glacial acetic acid). In
therapeutic experiments mice were administered repeated doses of
either monotope (40 .mu.g), pentatope RNA (in total 40 .mu.g) or
equimolar amounts of irrelevant RNA. For mechanistic studies
repeated doses of CD8 depleting (clone YTS191, BioXcell), CD4
depleting (clone YTS169.1, BioXcell) or CD40L blocking (clone MR1,
kind gift of Prof. Stephen Schoenberger) antibodies were
administered intraperitoneally as indicated in the figure (200
.mu.g/mouse in 2004, PBS).
[0260] Enzyme-linked immunospot (ELISpot) has been previously
described (Kreiter, S., et al., Cancer Res 70, 9031 (2010)). In
brief, 5.times.10.sup.5 splenocytes were cultured over night at
37.degree. C. in anti-INF-y (10 .mu.g/mL, clone AN18, Mabtech)
coated Multiscreen 96-well plates (Millipore) and cytokine
secretion was detected with an anti-IFN-.gamma. antibody (1
.mu.g/mL, clone R4-6A2, Mabtech). For stimulation either 2 .mu.g/mL
peptide was added or spleen cells were coincubated with
5.times.10.sup.4 syngeneic bone marrow-derived dendritic cells
(BMDC) transfected with RNA. For analysis of tumor infiltrating
lymphocytes, single cell suspensions of lung metastasis were rested
overnight to get rid of living tumor cells via plastic adherence.
Viable cells were separated via density gradient centrifugation.
All retrieved cells were added to the ELISpot plate. For analysis
of T cell responses in peripheral blood, PBMC were isolated via
density gradient centrifugation, counted and restimulated by
addition of peptide and syngeneic BMDC. Subtyping of T cell
responses was performed by addition of a WIC class II blocking
antibody (20 .mu.g/ml, clone M5/114, BioXcell). All samples were
tested in duplicates or triplicates.
[0261] Flow cytometric analysis was used to determine the subtype
of mutation reactive T cells. In the presence of Brefeldin A
(Sigma-Aldrich) 2.times.10.sup.6 splenocytes were stimulated with
2.times.10.sup.5 RNA transfected BMDC or 2 .mu.g/mL peptide. As a
positive control splenocytes were treated with phorbol 12-myristate
13-acetate (PMA, 0.5 .mu.g/ml, Sigma-Aldrich) and Ionomycin (1
.mu.g/ml, Sigma-Aldrich). Cells were incubated 5 h at 37.degree. C.
and subsequently stained for CD4.sup.+ and CD8.sup.+ cell surface
marker. Cells were permeabilized and fixated using BD
Cytofix/Cytoperm according to the manufacturer's protocol and
thereafter stained for INF-.gamma., TNF-.alpha. and IL-2 cytokines
(BD Biosciences). Cytokine secretion among CD4.sup.+ or CD8.sup.+ T
cells in stimulated samples was compared to control samples
(medium, irrelevant RNA or irrelevant peptide) in order to
determine the responding T cell subtype (n=5). Tumor infiltrating
leucocytes were prepared from subcutaneous B16F10 tumors as
described previously (PMID:2071934). The resulting cell suspension
was stained for CD4, CD8, Gr-1 and CD11b surface marker.
Intracellular FoxP3 staining was performed according to the
manufacturer's protocol (Mouse Foxp3 Buffer Set, BD). Samples were
acquired on a BD FACSCanto II.
[0262] Immune histochemistry. Lungs of CT26 tumor bearing mice were
fixated overnight in 4% phosphate buffered formaldehyde solution
(Carl Roth) and embedded in paraffin. 50 .mu.m consecutive sections
(3 per mouse) were stained for CD3 (clone SP7, Abcam), CD4 (clone
1, cat #50134-M08H, Sino Biologinal) and FoxP3 (polyclonal, cat
#NB100-39002, Novus Biologicals) following detection by a
HRP-conjugated antibody (Poly-HRP-anti-rabbit IgG, ImmunoLogic) and
the corresponding peroxidase substrate (Vector Nova Red, Vector
Laboratories) and counterstained with hematoxylin. CD3.sup.+,
CD4.sup.+, FoxP3.sup.+ and tumor areas were captured on an Axio
Scan.Z1 (Zeiss) and manually pre-defined tumor and lung regions
were quantified via computerized image analysis software (Tissue
Studio 3.6.1, Definiens).
[0263] Immunofluorescence staining. Cryoconserved organs were cut
in 8 .mu.m sections and attached on Superfrost slides. Sections
were dried overnight at room temperature (RT) and fixed in 4%
para-formaldehyde (PFA) for 10 min at RT in the dark. Sections were
washed 3 times with PBS and blocked using PBS supplemented with 1%
BSA, 5% mouse serum, 5% rat serum and 0.02% Nonident for 1 h at RT
in the dark. Fluorescent labeled antibodies (FoxP3, clone FJK-16s,
eBioscience; CD8, clone 53-6.7, BD; CD4, clone RM4-5, BD) were
diluted in staining buffer (PBS supplemented with 1% BSA, 5% mouse
serum and 0.02% Nonident) and sections were stained overnight at
4.degree. C. After washing twice with washing buffer (PBS
supplemented with 1% BSA and 0.02% Nonident) and once with PBS,
slides were stained for 3 min with Hoechst (Sigma), washed 3 times
with PBS, once with distilled water and mounted using Mounting
Medium Flouromount G (eBioscience). Immunofluorescence images were
acquired using an epifluorescence microscope (ApoTome, Zeiss).
Tumor, CD4, CD8 and FoxP3 stained areas were quantified within
manually pre-defined tumor regions via computerized image analysis
software (Tissue Studio 3.6.1., Definiens)
[0264] Statistics. Means were compared by using Student's t-test
for two groups. For comparison of means in more than two groups
one-way ANOVA with Tukey's test was applied. The area under the
curve (AUC) for comparison of tumor growth dynamics was determined
for single mice per group and was displayed as median. Statistical
differences in medians between two groups were calculated with a
nonparametric Mann-Whitney U test. Survival benefit was determined
with the log-rank test. All analyses were two-tailed and carried
out using GraphPad Prism 5.03. ns: P>0.05, *: P.ltoreq.0.05, **:
P.ltoreq.0.01, ***: P.ltoreq.0.001. Grubb's test was used for
identification of outliers (alpha=0.05).
Example 2: MHC Class II Restricted T Cell Epitopes in Neo-Epitope
Vaccines
[0265] A. Characterization of T Cell Subtypes Reactive Against
Mutated Epitopes
[0266] Recently, we described a workflow for comprehensive mapping
of non-synonymous mutations of the B16F10 tumor by NGS (FIG. 1a)
(Castle, J. C., et al., Cancer Res 72, 1081 (2012)). Tumor-bearing
C57BL/6 mice were immunized with synthetic 27mer peptides encoding
the mutated epitope (mutation in position 14), resulting in T cell
responses which conferred in vivo tumor control. In continuation of
that work, we now characterized the T cell responses against the
mutated epitopes starting with those with a high likelihood of MEW
I binding. Mice were vaccinated with synthetic 27mer mutated
epitope peptides (FIG. 1b upper right). Their splenocytes were
tested in IFN-.gamma. ELISpot to identify immunogenic mutations for
further analysis of subtype and cytokine expression (FIG. 1a).
About 30% of mutated epitopes were found to induce mutation
reactive cytokine secreting T cells in mice (FIG. 1b).
Surprisingly, responses against nearly all mutated epitopes (
16/17, 95%) were of CD4.sup.+ T cell type (FIG. 1b, Table 1).
TABLE-US-00001 TABLE 1 Immunogenic B16F10 mutations. B16F10
mutations determined to be immunogenic upon peptide or RNA
immunization (as described in FIG. 1). (WT, wild type; AA#, number
of mutated amino acid; Mut, Mutation) Substi- Response tution
Reactive MHC I score after Mu- Mutated sequence (WT, AA#, T cell
(best pre- vaccination with tation Gene used for vaccination Mut)
subtype diction) Peptide RNA B16-M05 Eef2
FVVKAYLPVNESFAFTADLRSNTGGQA G795A CD4.sup.+ 1.1 X (SEQ ID NO: 1)
B16-M08 Ddx23 ANFESGKHKYRQTAMFTATMPPAVERL V602A CD4.sup.+ 1.3 X
(SEQ ID NO: 2) B16-M12 Gnas TPPPEEAMPFEFNGPAQGDHSQPPLQV S111G
CD4.sup.+ 1.2 X (SEQ ID NO: 3) B16-M17 Tnpo3
VVDRNPQFLDPVLAYLMKGLCEKPLAS G504A CD4.sup.+ 1.0 X (SEQ ID NO: 4)
B16-M20 Tubb3 FRRKAFLHWYTGEAMDEMEFTEAESNM G402A CD4.sup.+ 1.9 X
(SEQ ID NO: 5) B16-M21 Alp11a SSPDEVALVEGVQSLGFTYLRLKDNYM R552S
CD4.sup.+ 0.1 X (SEQ ID NO: 6) B16-M22 Asf1b
PKPDFSQLQRNILPSNPRVTRFHINWD A141P CD4.sup.+ 1.7 X (SEQ ID NO: 7)
B16-M24 Dag1 TAVITPPTTTTKKARVSTPKPATPSTD P425A CD4.sup.+ 2.2 X (SEQ
ID NO: 8) B16-M25 Plod1 STANYNTSHLNNDVWQIFENPVDWKEK F530V CD4.sup.+
0.1 X X (SEQ ID NO: 9) B16-M27 Obsl1 REGVELCPGNKYEMRRHGTTHSLVIHD
T1764M CD8.sup.+ 2.3 X X (SEQ ID NO: 10) B16-M28 Ppp1r7
NIEGIDKLTQLKKPFLVNNKINKIENI L170P CD4.sup.+ 3.2 X X (SEQ ID NO: 11)
B16-M29 Mthfd1I IPSGTTILNCFHDVLSGKLSGGSPGVP F294V CD4.sup.+ 1.7 X
(SEQ ID NO: 12) B16-M30 Kif18b PSKPSFQEFVDWENVSPELNSTDQPFL K739N
CD4.sup.+ 1.2 X X (SEQ ID NO: 13) B16-M33 Pbk
DSGSPFPAAVILRDALHMARGLKYLHQ V146D CD8.sup.+ 0.1 X (SEQ ID NO: 14)
B16-M36 Tm9sf3 CGTAFFINFIAIYHHASRAIPFGTMVA Y382H CD4.sup.+ 0.2 X
(SEQ ID NO: 15) B16-M44 Cpsf3I EFKHIKAFDRTFANNPGPMVVFATPGM D314N
CD4.sup.+ 0.5 X X (SEQ ID NO: 16) B16-M45 Mkm1
ECRITSNFVIPSEYWVEEKEEKQKLIQ N346Y CD4.sup.+ 1.4 X (SEQ ID NO: 17)
B16-M46 Actn4 NHSGLVTFQAFIDVMSRETTDTDTADQ F835V CD4.sup.+ 0.2 X X
(SEQ ID NO: 18) B16-M47 Rpl13a GRGHLLGRLAAIVGKQVLLGRKVVVVR A24G
CD4.sup.+ 0.5 X (SEQ ID NO: 19) B16-M48 Def8
SHCHWNDLAVIPAGVVHNWDFEPRKVS R255G CD4.sup.+ 3.8 X X (SEQ ID NO: 20)
B16-M50 Sema3b GFSQPLRRLVIHVVSAAQAERLARAEE L663V CD4.sup.+ 2.9 X X
(SEQ ID NO: 21)
[0267] To exclude any bias associated with a peptide-based vaccine
format, this experiment was repeated using in vitro transcribed
(IVT) mRNA encoding the mutated epitopes (FIG. 1c upper graph right
hand side). T cell reactivities determined with these RNA monotopes
were largely comparable to the data obtained with synthetic
peptides (FIG. 1c, Table 1), with somewhat lower numbers of
immunogenic epitopes (about 25%). Importantly, also in this setting
the majority of mutation-specific immune responses ( 10/12,
.about.80%) were conferred by CD4.sup.+ T cells.
[0268] We extended our study to the chemically induced colon
carcinoma model CT26 (Griswold, D. P. and Corbett, T. H., Cancer
36, 2441 (1975)) in BALB/c mice, in which we recently identified
over 1680 non-synonymous mutations (Castle, J. C., et al., BMC
Genomics 15, 190 (2014)). We selected 96 mutations based on their
predicted MHC class I binding properties. In analogy to the B16F10
study, half of the candidates were good binders (`low score`
0.1-2.1). The other half was deliberately chosen for poor MHC I
binding (`high score`>3.9). In total, about 20% of mutated
epitopes were immunogenic in mice immunized with the respective RNA
monotopes (FIG. 1d pie chart, Table 2). It is noteworthy that in
the `low` MHC I score subgroup a couple of CD8.sup.+ T cells
inducing epitopes were identified, which was not the case in the
`high` score subgroup (FIG. 1d right). This apparently did not bias
against MHC class II restricted epitopes, as these were represented
in similar frequency in both subgroups constituting the majority of
CT26 immunogenic mutations ( 16/21, 80%).
TABLE-US-00002 TABLE 2 Immunogenic CT26 mutations. CT26 mutations
determined to be immunogenic upon RNA immunization (as described in
FIG. 1). (WT, wild type; AA#, number of mutated amino acid; Mut,
Mutation) Reactive MHC I score Mutated sequence Substitution T cell
(best pre- Mutation Gene used for vaccination (WT, AA#, Mut)
subtype diction) CT26-M03 Slc20a1 DKPLRRNNSYTSYIMAICGMPLDSFRA T425I
CD4.sup.+ 0.3 (SEQ ID NO: 22) CT26-M12 Gpc1
YRGANLHLEETLAGFWARLLERLFKQL E165G CD8.sup.+ 1.9 (SEQ ID NO: 23)
CT26-M13 Nphp3 AGTQCEYWASRALDSEHSIGSMIQLPQ G234D CD4.sup.+ 0.1 (SEQ
ID NO: 24) CT26-M19 Tmem87a QAIVRGCSMPGPWRSGRLLVSRRWSVE G63R
CD8.sup.+ 0.7 (SEQ ID NO: 25) CT26-M20 Slc4a3
PLLPFYPPDEALEIGLELNSSALPPTE T373I CD4.sup.+ 0.9 (SEQ ID NO: 26)
CT26-M24 Cxcr7 MKAFIFKYSAKTGFTKLIDASRVSETE L340F CD4.sup.+ 1.8 (SEQ
ID NO: 27) CT26-M26 E2f8 VILPQAPSGPSYATYLQPAQAQMLTPP I522T
CD8.sup.+ 0.1 (SEQ ID NO: 28) CT26-M27 Agxt2I2
EHIHRAGGLFVADAIQVGFGRIGKHFW E247A CD4.sup.+ 0.2 (SEQ ID NO: 29)
CT26-M35 Nap1I4 HTPSSYIETLPKAIKRRINALKQLQVR V63I CD4.sup.+ 0.7 (SEQ
ID NO: 30) CT26-M37 Dhx35 EVIQTSKYYMRDVIAIESAWLLELAPH T646I
CD4.sup.+ 0.1 (SEQ ID NO: 31) CT26-M39 Als2
GYISRVTAGKDSYIALVDKNIMGYIAS L675I CD8.sup.+ 0.2 (SEQ ID NO: 32)
CT26-M42 Deptor SHDSRKSTSFMSVNPSKEIKIVSAVRR S253N CD4.sup.+ 0.3
(SEQ ID NO: 33) CT26-M43 Tdg AAYKGHHYPGPGNYFWKCLFMSGLSEV H169Y
CD4.sup.+ 0.3 (SEQ ID NO: 34) CT26-M55 Dkk2
EGDPCLRSSDCIDEFCCARHFWTKICK G192E CD4.sup.+ 9.7 (SEQ ID NO: 35)
CT26-M58 Rpap2 CGYPLCQKKLGVISKQKYRISTKTNKV P113S CD4.sup.+ 11.3
(SEQ ID NO: 36) CT26-M68 Steap2 VTSIPSVSNALNWKEFSFIQSTLGYVA R388K
CD4.sup.+ 6.8 (SEQ ID NO: 37) CT26-M75 Usp26
KTTLSHTQDSSQSLQSSSDSSKSSRCS S715L n.d. 5.8 (SEQ ID NO: 38) CT26-M78
Nbea PAPRAVLTGHDHEIVCVSVCAELGLVI V576I CD4.sup.+ 6.3 (SEQ ID NO:
39) CT26-M90 Aldh18a1 LHSGQNHLKEMAISVLEARACAAAGQS P154S CD4.sup.+
8.3 (SEQ ID NO: 40) CT26-M91 Zc3h14 NCKYDTKCTKADCLFTHMSRRASILTP
P497L CD4.sup.+ 8.8 (SEQ ID NO: 41) CT26-M93 Drosha
LRSSLVNNRTQAKIAEELGMQEYAITN V1189I CD4.sup.+ 9.9 (SEQ ID NO:
42)
[0269] On a similar note, when analyzing all immune responses to
RNA monotopes representing all 38 mutations we identified in the
4T1 mammary carcinoma model, nearly 70% of the recognized epitopes
were recognized by CD4.sup.+ T cells (data not shown; Table 3).
TABLE-US-00003 TABLE 3 Immunogenic 4T1 mutations. 4T1 mutations
determined to be immunogenic upon RNA immunization (as described in
FIG. 1). (WT, wild type; AA#, number of mutated amino acid; Mut,
Mutation) Reactive Mutated sequence Substitution T cell Mutation
Gene used for vaccination (WT, AA#, Mut) subtype 4T1-M2 Gen1
IPHNPRVAVKTTNNLVMKNSVCLERDS K707N CD4 (SEQ ID NO: 43) 4T1-M3 Polr2a
LAAQSLGEPATQITLNTFHYAGVSAKN M1102I CD4 (SEQ ID NO: 44) 4T1-M8 Tmtc2
QGVTVLAVSAVYDIFVFHRLKMKQILP V201I CD8 (SEQ ID NO: 45) 4T1-M14 Zfr
AHIRGAKHQKVVTLHTKLGKPIPSTEP K411T CD4 (SEQ ID NO: 46) 4T1-M16
Cep120 ELAWEIDRKVLHQNRLQRTPIKLQCFA H68N CD4 (SEQ ID NO: 47) 4T1-M17
Malt1 FLKDRLLEDKKIAVLLDEVAEDMGKCH T534A CD4 (SEQ ID NO: 48) 4T1-M20
Wdr11 NDEPDLDPVQELIYDLRSQCDAIRVTK T340I CD8 (SEQ ID NO: 49) 4T1-M22
Kbtbd2 DAAALQMIIAYAYRGNLAVNDSTVEQL T91R CD4 (SEQ ID NO: 50) 4T1-M25
Adamts9 KDYTAAGFSSFQKLRLDLTSMQIITTD I623L CD4 (SEQ ID NO: 51)
4T1-M26 Pzp AVKEEDSLHWQRPEDVQKVKALSFYQP G1199E CD8 (SEQ ID NO: 52)
4T1-M27 Gprc5a FAICFSCLLAHALNLIKLVRGRKPLSW F119L CD8 (SEQ ID NO:
53) 4T1-M30 Enho MGAAISQGAIIAIVCNGLVGFLL L10I CD4 (SEQ ID NO: 54)
4T1-M31 Dmrta2 EKYPRTPKCARCGNHGVVSALKGHKRY R73G CD4 (SEQ ID NO: 55)
4T1-M32 Rragd SHRSCSHQTSAPSPKALAHNGTPRNAI L263P CD4 (SEQ ID NO: 56)
4T1-M35 Zzz3 KELLQFKKLKKQNLQQMQAESGFVQHV K311N CD8 (SEQ ID NO: 57)
4T1-M39 Ilkap RKGEREEMQDAHVSLNDITQECNPPSS 127S CD4 (SEQ ID NO: 58)
4T1-M40 Cenpf RVEKLQLESELNESRTECITATSQMTA D1327E CD4 (SEQ ID NO:
59)
[0270] Thus, we have found in three independent mouse tumor models
on different MHC backgrounds that a considerable fraction of
non-synonymous cancer mutations are immunogenic and that quite
unexpectedly the immunogenic mutanome is pre-dominantly recognized
by CD4.sup.+ T cells.
[0271] B. MHC Class II Restricted Cancer Mutations as Vaccine
Targets
[0272] To investigate whether MHC class II restricted cancer
mutations are good vaccine targets in vivo, we proceeded to use
synthetic RNA as vaccine format. Antigen-encoding synthetic RNA is
emerging as promising vaccine technology due to its advantages
including its capability to deliver more than one epitope, its
selective uptake by antigen presenting cells (APC) and its
intrinsic adjuvanticity (Diken, M., et al., Gene Ther 18, 702
(2011); Kreiter, S., et al., Curr Opin Immunol 23, 399 (2011);
Pascolo, S., Handb Exp Pharmacol, 221 (2008); Sahin, U., et al.,
Nat Rev Drug Discov 13, 759 (2014); Van, L. S., et al., Hum Vaccin
Immunother 9 (2013)). Our group has developed pharmacologically
optimized RNA (stabilizing elements in RNA sequence and liposomal
formulation), which meanwhile has reached the stage of clinical
testing (NCT01684241) (Holtkamp, S., et al., Blood 108, 4009
(2006); Kreiter, S., et al., J Immunol 180, 309 (2008); Kuhn, A.
N., et al. Gene Ther 17, 961 (2010)). We engineered RNA encoding
B16-M30, one of the epitopes identified in the B16F10 tumor model.
B16-M30 elicited strong CD4.sup.+ T cell responses, which did not
recognize the wild type peptide (FIG. 2a left) as the mutated amino
acid was shown to be essential for T cell recognition (FIG. 2a
right). When B16F10 tumor-bearing C57BL/6 mice were repeatedly
vaccinated with the B16-Mt30 RNA monotope, tumor growth was
profoundly retarded (FIG. 2b). Half of the B16-M30 RNA treated mice
were still alive 120 days after tumor vaccination, while all the
control RNA treated mice died within 65 days.
[0273] Similarly, repeated vaccination in a lung metastasis model
with luciferase transduced B16F10 cells revealed efficient
eradication of metastases with B16-M30 RNA but not control
synthetic RNA in the vast majority of mice as shown by
bioluminescence imaging (BLI) (FIG. 2c). Consistently, tumor
infiltrating leukocytes purified from B16F10 tumors of B16-M30 RNA
immunized mice showed strong reactivity against B16-M30 (FIG.
2d).
[0274] Taking together, these data establish B16-M30 as a novel
major rejection antigen in B16F10 tumors. They also exemplify that
immunizing with RNA encoding a single immunogenic mutated epitope
may give rise to functional T cells. These cells appear to be
capable to target into the cancer lesion triggering control and
even cure in murine tumor models. Our findings are in agreement
with recent reports supporting the pivotal role of CD4.sup.+ T cell
immunity in the control of cancer (Schumacher, T., et al., Nature
512, 324 (2014); Tran, E., et al., Science 344, 641 (2014)).
[0275] As the vast majority of mutations are unique to the
individual patient, tapping the mutanome as a source for vaccine
antigens requires an actively individualized approach (Britten, C.
M., et al., Nat Biotechnol 31, 880 (2013)). In this respect, one of
the major challenges is instant manufacturing of a tailored
on-demand vaccine. This can be viably addressed by RNA vaccine
technology. RNA manufacturing based on in vitro transcription
usually takes a few days (FIG. 3a). At present, the GMP-grade
material could be made ready for release within three weeks and
this process is continuously being optimized to reduce the
duration. On another note, though we have shown tumor eradication
in mouse models with a single mutation, one would ideally prefer to
combine several mutations in a poly-neo-epitope vaccine. This would
allow us to address several factors that counteract the clinical
success of vaccines in humans such as tumor heterogeneity and
immunoediting (Gerlinger, M., et al., N Engl J Med 366, 883 (2012);
Koebel, C. M., et al., Nature 450, 903 (2007)).
[0276] In light of these considerations, we explored how to use our
insights on immunogenic epitopes to develop a cancer vaccine
concept which we call "mutanome engineered RNA immunotherapy"
(MERIT) (FIG. 3a). To test this concept, we selected four MHC class
II (CT26-M03, CT26-M20, CT26-M27, CT26-M68) and one MHC class I
(CT26-M19) restricted mutations that were derived from the CT26
model (see Table 2) and engineered RNA monotopes encoding each of
them. In addition, a synthetic RNA pentatope was engineered
encoding all five mutated epitopes connected by 10 mer
non-immunogenic glycine/serine linkers to avoid the generation of
junctional epitopes (FIG. 3a). By immunizing naive BALB/c mice we
found that the quantity of IFN-producing T cells elicited by the
pentatope was comparable to that evoked by the respective monotope
for three of these mutations (FIG. 3b). However, for two of these
mutations the pentatope RNA was significantly superior in robustly
expanding mutations-specific T cells.
[0277] We assessed the anti-tumour efficacy of immune responses
elicited by RNA pentatope vaccines in a lung metastasis model of
CT26 luciferase transfectant (CT26-Luc) tumors. Tumor-bearing
BALB/c mice were vaccinated repeatedly with a mixture of two RNA
pentatopes (3 MHC class I and 7 class II restricted epitopes)
including the mutations tested in the previous experiment. Tumor
growth in vaccinated mice was significantly inhibited as measured
by BLI of the lung (FIG. 3c left). At day 32 all mice in the RNA
pentatope group were alive whereas 80% of the control mice had
already died (FIG. 3c mid). Post mortem macroscopic (FIG. 3c
right), histological (FIG. 3d right) and computerized image
analysis (data not shown) of tissue sections revealed significantly
lower tumor load in the vaccinated mice as compared to untreated
controls. Tumor lesions of pentatope RNA vaccinated mice were
briskly infiltrated with CD3.sup.+ T cells, whereas the number of
CD3+ T cells was significantly lower in their surrounding lung
tissues. Tumors of untreated controls displayed CD3.sup.+ cells
staining which was not much different to that of the surrounding
lung tissue in terms of quantity and mainly at the tumor border but
not within the tumor. (FIG. 3d).
[0278] Altogether, these findings indicate that T cells against
each single epitope are elicited with a MERIT approach employing a
poly-neo-epitope encoding RNA vaccine. These T cells target tumor
lesions, recognize their mutated targets and result in efficient
tumor control in vivo.
[0279] C. Selection of Mutations Having Anti-Tumor Immunity
[0280] One of the key questions is how to select the mutations with
the highest probability of inducing efficient anti-tumor immunity.
We (FIG. 1d right) and others (Matsushita, H., et al., Nature 482,
400 (2012); Robbins, P. F., et al., Nat Med 19, 747 (2013); van, R.
N., et al., J Clin Oncol 31, e439-e442 (2013)) have shown that MHC
class I binding scores enable enrichment for mutated epitope
candidates which elicit CD8.sup.+ responses and tumor rejection
(Duan, F., et al., J Exp Med 211, 2231 (2014)). Our findings
described above indicate that MHC class II presented mutated
epitopes may even be of higher interest for a MERIT approach. In
fact, a correlation analysis revealed that immunogenic mutations
have a significantly better MHC class II binding score as compared
to non-immunogenic ones (FIG. 4a). Most cancers lack MHC class II
expression. Effective recognition of neo-epitopes by CD4.sup.+ T
cells in MHC class II negative tumors should depend on release of
tumor antigens to be taken up and presented by antigen presenting
cells (APCs). This should be most efficient for antigens with
highly abundant expression. To test this hypothesis, we implemented
an algorithm combining good MEW class II binding with abundant
expression of the mRNA encoding the mutated epitope. For the latter
we used confirmed mutated RNA sequencing reads normalized to the
overall read count (NVRC: normalized variant read counts). We
ranked CT26 mutanome data with this algorithm and selected the top
ten mutations (`ME` mutations in Table 4) predicted to be good MEW
class II binders among the most abundant candidate epitopes (NVRC
.gtoreq.60). As control we chose ten mutations based on abundant
expression only (`E` mutations in Table 4). Most importantly, these
epitopes were used without any further pre-validation or
immunogenicity testing to engineer two RNA pentatopes for each
group (P.sub.ME and P.sub.E pentatopes). When mice with established
CT26-Luc lung tumors were vaccinated with these epitopes, P.sub.ME
as compared to P.sub.E pentatopes induced a much stronger T cell
response (FIG. 4c). Established lung metastases were completely
rejected in almost all mice whereas P.sub.E pentatopes were not
able to confer tumor growth control (FIG. 4b).
TABLE-US-00004 TABLE 4 In silico prediction of CT26 mutations with
abundant expression and favorable MHC class II binding properties.
CT26 mutations selected for high expression with (ME) or without
(E) consideration of the MHC II percentile rank (IEDB consensus
version 2.5). (WT, wild type; AA#, number of mutated amino acid;
Mut, Mutation) MHC II score Mutated sequence Substitution
Expression (best pre- Mutation Gene used for vaccination (WT, AA#,
Mut) (NVRC) diction) CT2-E16 Asns DSVVIFSGEGSDEFTQGYIYFHKAPSP L370F
1428.05 45.45 (SEQ ID NO: 60) CT26-E2 Cd34
PQTSPTGILPTTSNSISTSEMTWKSSL D120N 1150.85 23.76 (SEQ ID NO: 61)
CT26-E3 Actb WIGGSILASLSTFHQMWISKQEYDESG Q353H 974.16 8.30 (SEQ ID
NO: 62) CT26-E4 Tmbim6 SALGSLALMIWLMTTPHSHETEQKRLG A73T 825.51 2.96
(SEQ ID NO: 63) CT26-E5 Glud1 DLRTAAYVNAIEKIFKVYNEAGVTFT V5461
619.54 8.04 (SEQ ID NO: 64) CT26-E16 Eif4g2
KLCLELLNVGVESNLILKGVILLIVDK K108N 327.79 20.99 (SEQ ID NO: 65)
CT26-E17 Sept7 NVHYENYRSRKLATVTYNGVDNNKNKG A314T 316.98 6.47 (SEQ
ID NO: 66) CT26-E18 Fn1 YTVSVVALHDDMENQPLIGIQSTAIPA S1710N 303.62
17.41 (SEQ ID NO: 67) CT26-E19 Brd2 KPSTLRELERYVLACLRKKPRKPYTIR
S703A 301.83 7.86 (SEQ ID NO: 68) CT26-E20 Uchl3
KFMERDPDELRFNTIALSAA A224T 301.78 9.75 (SEQ ID NO: 69) CT26-ME1
Aldh18a1 LHSGQNHLKEMAISVLEARACAAAGQS P154S 67.73 0.05 (SEQ ID NO:
70) CT26-ME2 Ubqln1 DTLSAMSNPRAMQVLLQIQQGLQTLAT A62V 84.08 0.24
(SEQ ID NO: 71) CT26-ME3 Ppp6r1 DGQLELLAQGALDNALSSMGALHALRP D309N
139.80 0.44 (SEQ ID NO: 72) CT26-ME4 Trip12
WKGGPVKIDPLALMQAIERYLVVRGYG V1328M 83.09 0.49 (SEQ ID NO: 73)
CT26-ME5 Pcdhgc3 QDINDNNPSFPTGKMKLEISEALAPGT E139K 86.16 0.54 (SEQ
ID NO: 74) CT26-ME6 Cad SDPRAAYFRQAENDMYIRMALLATVLG G2139D 152.86
0.55 (SEQ ID NO: 75) CT26-ME7 Smarcd1 MDLLAFERKLDQTVMRKRLDIQEALKR
I161V 125.85 0.60 (SEQ ID NO: 76) CT26-ME8 Ddx27
ITTCLAVGGLDVKFQEAALRAAPDILI S297F 61.82 0.62 (SEQ ID NO: 77)
CT26-ME9 Snx5 KARLKSKDVKLAEAHQQECCQKFEQLS T341A 120.27 0.73 (SEQ ID
NO: 78) CT26-ME10 Lin7c GEVPPQKLQALQRALQSEFCNAVREVY V41A 71.24 1.09
(SEQ ID NO: 79)
[0281] Antigen specific T.sub.H cells promote the cross-priming of
tumor specific CTL responses by CD40 ligand mediated licensing of
dendritic cells. This may result in antigen spread if T.sub.H cells
recognize their antigen on the same APC that cross-presents an
unrelated CTL epitope (Bennett, S. R., et al., Nature 393, 478
(1998); Schoenberger, S. P., et al., Nature 393, 480 (1998)).
Congruently, in the blood and spleen of mice immunized with
P.sub.ME but not P.sub.E pentatopes we detected strong CD8.sup.+ T
cell responses against gp70-AH1, a well characterized
immunodominant CTL epitope derived from the endogenous murine
leukemia virus-related cell surface antigen (FIG. 4d). This
indicates that cancer neo-epitope specific T.sub.H cells, in
analogy to viral neo-antigen specific T cells (Croxford, J. L., et
al., Autoimmun Rev 1, 251 (2002)), may exert their anti-tumour
function by antigen spreading and augmentation of CTL responses
[0282] D. Summary
[0283] In summary, our data indicate that MHC class II restricted T
cell epitopes are abundant in the cancer mutanome and can be used
to customize RNA-based poly-neo-epitope vaccines with substantial
therapeutic effect in mouse tumor models.
[0284] The mechanism responsible for the high rate of CD4.sup.+ T
cell recognition of mutations is unclear yet. A simple explanation
may be the longer and variable size of peptides presented on MHC
class II molecules as compared to MHC class I epitopes increasing
the likelihood that a mutation is covered by the respective
peptide. T cell epitopes presented by MHC class I molecules are
typically peptides between 8 and 11 amino acids in length with
well-defined N- and C-termini. MHC class II molecules present
longer peptides of 13-17 amino acids in length with a 9 amino acid
MHC II core binding region and variable number of additional
flanking amino acids both contributing to the recognition by
CD4.sup.+ T cells (Arnold, P. Y., et al., J Immunol 169, 739
(2002)).
[0285] While the first evidence of the spontaneous CD8.sup.+ and
CD4.sup.+ T-cell responses directed against mutated gene-products
in cancer patients was generated in the 1990s (Dubey, P., et al., J
Exp Med 185, 695 (1997); Lennerz, V., et al., Proc Natl Acad Sci
USA 102, 16013 (2005); Wolfel, T., et al., Science 269, 1281
(1995)), only the recent high level publications have created broad
acceptance for the enormous potential of mutation-specific T cells
to confer anti-tumor activity in cancer patients (Lu, Y. C., et
al., J Immunol 190, 6034 (2013); Schumacher, T., et al., Nature
512, 324 (2014); Tran, E., et al., Science 344, 641 (2014)). To
assess whether the principles we unraveled in the mouse models for
melanoma, colon and breast cancer are true in the human setting, we
analyzed mutation and RNA-Seq data in the same three human cancer
types provided by The Cancer Genome Atlas (TCGA). For all three
human cancer types we confirmed the abundance of mutations
predicted to bind to MHC class II we revealed in mouse models (FIG.
4.e). The MERIT approach we presented here integrates advances in
the field of next generation sequencing, computational immunology
and synthetic genomics and thereby provides the integrated
technology for comprehensive exploitation of the neo-epitope target
repertoire. Targeting multiple mutations at once may at least in
theory pave the way to solve critical problems in current cancer
drug development such as clonal heterogeneity and antigen escape
(Kroemer, G. and Zitvogel, L., Oncoimmunology 1, 579 (2012);
Mittal, D., et al., Curr Opin Immunol 27, 16 (2014)).
[0286] Meanwhile, based on this study and our prior work clinical
translation has been initiated and a first-in-concept trial in
melanoma patients (Castle, J. C., et al., Cancer Res 72, 1081
(2012); Castle, J. C., et al., Sci Rep 4, 4743 (2014); Lower, M.,
et al., PLoS Comput Biol 8, e1002714 (2012)) is actively recruiting
(NCT02035956) and confirms that "just in time" production of a
poly-neo-epitope mRNA cancer vaccine is in fact feasible.
Example 3: Selection of Mutations Having Anti-Tumor Immunity
[0287] For selecting/ranking amino acid sequence modifications one
may proceed as follows: [0288] 1. Within a given list of
non-synonymous point mutations, compute a peptide sequence which
has the mutated amino acid in the middle and is flanked by up to 13
amino acids on the N and C-terminal end, respectively; this will be
called 27mer in the following text (the length for each flanking
sequence may be smaller than 13 amino acids when the mutation is
close to the N or C-terminus of the whole protein) [0289] 2.
Compute MHC class II binding prediction consensus scores (e.g.
using the IEDB T-cell prediction tools [Wang P, et al. (2010) BMC
Bioinformatics. 11:568. PMID: 21092157.
http://tools.immuneepitope.org/mhcii/]) for each overlapping 15 nt
long subsequence of each 27mer; the best (=lowest) score is
assigned to the whole 27mer [0290] 3. Compute the expression
(preferably in RPKM units [Ali Mortazavi, et al. (2008) Nature
Methods 5, 621-628]) of the genes to which the 27mers are
associated [0291] 4. Compute the variant allele frequency (VAF) of
each mutation in the RNA: [0292] input are short read alignments of
an RNA-Seq experiment done with the same tumor sample as used for
mutation detection [0293] look up the alignments and reads
overlapping the mutation site [0294] tally the nucleotides mapped
to the mutation site using the reads aggregated a step before
[0295] compute the sum of mutant-allele nucleotides divided by the
sum of all nucleotides mapped to the genomic site of the mutation
(FIG. 5) [0296] 5. Multiply the respective gene expression with the
VAF to get the mutation expression (preferably in RPKM units)
[0297] 6. Rank all 27mers by the MHC binding score (as computed in
step 2, lowest score is best) and remove 27mers with an associated
mutation expression of less than a given threshold
[0298] Application to Murine Data Set:
[0299] For testing the algorithm, 185 mutations were selected from
the murine tumor models 4T1, CT26 and B16F10 were tested for their
antigenicity. Then we first tried to test the influence of the
level of gene and mutation expression on the predictive performance
of the algorithm (FIG. 6). Here we can observe that the maximum
area under the curve of the receiver operating characteristic (ROC
AUC [Fawcett T., Pattern Recogn Lett. 2006; 27:861-874. doi:
10.1016/j.patrec.2005.10.010]) is higher when the mutation
expression is filtered instead of the gene expression (FIG. 6 left
(gene expression) vs. right (mutation expression) plot).
[0300] FIG. 7 shows the ROC curves for the optimum thresholds,
indicating a pronounced influence of the mutation expression for
binders with only a mediocre relative binding affinity (FIG. 7,
right panel, values between a false positive rate of about 0.3 and
0.6).
Sequence CWU 1
1
105127PRTArtificial SequenceEpitope 1Phe Val Val Lys Ala Tyr Leu
Pro Val Asn Glu Ser Phe Ala Phe Thr1 5 10 15Ala Asp Leu Arg Ser Asn
Thr Gly Gly Gln Ala 20 25227PRTArtificial SequenceEpitope 2Ala Asn
Phe Glu Ser Gly Lys His Lys Tyr Arg Gln Thr Ala Met Phe1 5 10 15Thr
Ala Thr Met Pro Pro Ala Val Glu Arg Leu 20 25327PRTArtificial
SequenceEpitope 3Thr Pro Pro Pro Glu Glu Ala Met Pro Phe Glu Phe
Asn Gly Pro Ala1 5 10 15Gln Gly Asp His Ser Gln Pro Pro Leu Gln Val
20 25427PRTArtificial SequenceEpitope 4Val Val Asp Arg Asn Pro Gln
Phe Leu Asp Pro Val Leu Ala Tyr Leu1 5 10 15Met Lys Gly Leu Cys Glu
Lys Pro Leu Ala Ser 20 25527PRTArtificial SequenceEpitope 5Phe Arg
Arg Lys Ala Phe Leu His Trp Tyr Thr Gly Glu Ala Met Asp1 5 10 15Glu
Met Glu Phe Thr Glu Ala Glu Ser Asn Met 20 25627PRTArtificial
SequenceEpitope 6Ser Ser Pro Asp Glu Val Ala Leu Val Glu Gly Val
Gln Ser Leu Gly1 5 10 15Phe Thr Tyr Leu Arg Leu Lys Asp Asn Tyr Met
20 25727PRTArtificial SequenceEpitope 7Pro Lys Pro Asp Phe Ser Gln
Leu Gln Arg Asn Ile Leu Pro Ser Asn1 5 10 15Pro Arg Val Thr Arg Phe
His Ile Asn Trp Asp 20 25827PRTArtificial SequenceEpitope 8Thr Ala
Val Ile Thr Pro Pro Thr Thr Thr Thr Lys Lys Ala Arg Val1 5 10 15Ser
Thr Pro Lys Pro Ala Thr Pro Ser Thr Asp 20 25927PRTArtificial
SequenceEpitope 9Ser Thr Ala Asn Tyr Asn Thr Ser His Leu Asn Asn
Asp Val Trp Gln1 5 10 15Ile Phe Glu Asn Pro Val Asp Trp Lys Glu Lys
20 251027PRTArtificial SequenceEpitope 10Arg Glu Gly Val Glu Leu
Cys Pro Gly Asn Lys Tyr Glu Met Arg Arg1 5 10 15His Gly Thr Thr His
Ser Leu Val Ile His Asp 20 251127PRTArtificial SequenceEpitope
11Asn Ile Glu Gly Ile Asp Lys Leu Thr Gln Leu Lys Lys Pro Phe Leu1
5 10 15Val Asn Asn Lys Ile Asn Lys Ile Glu Asn Ile 20
251227PRTArtificial SequenceEpitope 12Ile Pro Ser Gly Thr Thr Ile
Leu Asn Cys Phe His Asp Val Leu Ser1 5 10 15Gly Lys Leu Ser Gly Gly
Ser Pro Gly Val Pro 20 251327PRTArtificial SequenceEpitope 13Pro
Ser Lys Pro Ser Phe Gln Glu Phe Val Asp Trp Glu Asn Val Ser1 5 10
15Pro Glu Leu Asn Ser Thr Asp Gln Pro Phe Leu 20
251427PRTArtificial SequenceEpitope 14Asp Ser Gly Ser Pro Phe Pro
Ala Ala Val Ile Leu Arg Asp Ala Leu1 5 10 15His Met Ala Arg Gly Leu
Lys Tyr Leu His Gln 20 251527PRTArtificial SequenceEpitope 15Cys
Gly Thr Ala Phe Phe Ile Asn Phe Ile Ala Ile Tyr His His Ala1 5 10
15Ser Arg Ala Ile Pro Phe Gly Thr Met Val Ala 20
251627PRTArtificial SequenceEpitope 16Glu Phe Lys His Ile Lys Ala
Phe Asp Arg Thr Phe Ala Asn Asn Pro1 5 10 15Gly Pro Met Val Val Phe
Ala Thr Pro Gly Met 20 251727PRTArtificial SequenceEpitope 17Glu
Cys Arg Ile Thr Ser Asn Phe Val Ile Pro Ser Glu Tyr Trp Val1 5 10
15Glu Glu Lys Glu Glu Lys Gln Lys Leu Ile Gln 20
251827PRTArtificial SequenceEpitope 18Asn His Ser Gly Leu Val Thr
Phe Gln Ala Phe Ile Asp Val Met Ser1 5 10 15Arg Glu Thr Thr Asp Thr
Asp Thr Ala Asp Gln 20 251927PRTArtificial SequenceEpitope 19Gly
Arg Gly His Leu Leu Gly Arg Leu Ala Ala Ile Val Gly Lys Gln1 5 10
15Val Leu Leu Gly Arg Lys Val Val Val Val Arg 20
252027PRTArtificial SequenceEpitope 20Ser His Cys His Trp Asn Asp
Leu Ala Val Ile Pro Ala Gly Val Val1 5 10 15His Asn Trp Asp Phe Glu
Pro Arg Lys Val Ser 20 252127PRTArtificial SequenceEpitope 21Gly
Phe Ser Gln Pro Leu Arg Arg Leu Val Leu His Val Val Ser Ala1 5 10
15Ala Gln Ala Glu Arg Leu Ala Arg Ala Glu Glu 20
252227PRTArtificial SequenceEpitope 22Asp Lys Pro Leu Arg Arg Asn
Asn Ser Tyr Thr Ser Tyr Ile Met Ala1 5 10 15Ile Cys Gly Met Pro Leu
Asp Ser Phe Arg Ala 20 252327PRTArtificial SequenceEpitope 23Tyr
Arg Gly Ala Asn Leu His Leu Glu Glu Thr Leu Ala Gly Phe Trp1 5 10
15Ala Arg Leu Leu Glu Arg Leu Phe Lys Gln Leu 20
252427PRTArtificial SequenceEpitope 24Ala Gly Thr Gln Cys Glu Tyr
Trp Ala Ser Arg Ala Leu Asp Ser Glu1 5 10 15His Ser Ile Gly Ser Met
Ile Gln Leu Pro Gln 20 252527PRTArtificial SequenceEpitope 25Gln
Ala Ile Val Arg Gly Cys Ser Met Pro Gly Pro Trp Arg Ser Gly1 5 10
15Arg Leu Leu Val Ser Arg Arg Trp Ser Val Glu 20
252627PRTArtificial SequenceEpitope 26Pro Leu Leu Pro Phe Tyr Pro
Pro Asp Glu Ala Leu Glu Ile Gly Leu1 5 10 15Glu Leu Asn Ser Ser Ala
Leu Pro Pro Thr Glu 20 252727PRTArtificial SequenceEpitope 27Met
Lys Ala Phe Ile Phe Lys Tyr Ser Ala Lys Thr Gly Phe Thr Lys1 5 10
15Leu Ile Asp Ala Ser Arg Val Ser Glu Thr Glu 20
252827PRTArtificial SequenceEpitope 28Val Ile Leu Pro Gln Ala Pro
Ser Gly Pro Ser Tyr Ala Thr Tyr Leu1 5 10 15Gln Pro Ala Gln Ala Gln
Met Leu Thr Pro Pro 20 252927PRTArtificial SequenceEpitope 29Glu
His Ile His Arg Ala Gly Gly Leu Phe Val Ala Asp Ala Ile Gln1 5 10
15Val Gly Phe Gly Arg Ile Gly Lys His Phe Trp 20
253027PRTArtificial SequenceEpitope 30His Thr Pro Ser Ser Tyr Ile
Glu Thr Leu Pro Lys Ala Ile Lys Arg1 5 10 15Arg Ile Asn Ala Leu Lys
Gln Leu Gln Val Arg 20 253127PRTArtificial SequenceEpitope 31Glu
Val Ile Gln Thr Ser Lys Tyr Tyr Met Arg Asp Val Ile Ala Ile1 5 10
15Glu Ser Ala Trp Leu Leu Glu Leu Ala Pro His 20
253227PRTArtificial SequenceEpitope 32Gly Tyr Ile Ser Arg Val Thr
Ala Gly Lys Asp Ser Tyr Ile Ala Leu1 5 10 15Val Asp Lys Asn Ile Met
Gly Tyr Ile Ala Ser 20 253327PRTArtificial SequenceEpitope 33Ser
His Asp Ser Arg Lys Ser Thr Ser Phe Met Ser Val Asn Pro Ser1 5 10
15Lys Glu Ile Lys Ile Val Ser Ala Val Arg Arg 20
253427PRTArtificial SequenceEpitope 34Ala Ala Tyr Lys Gly His His
Tyr Pro Gly Pro Gly Asn Tyr Phe Trp1 5 10 15Lys Cys Leu Phe Met Ser
Gly Leu Ser Glu Val 20 253527PRTArtificial SequenceEpitope 35Glu
Gly Asp Pro Cys Leu Arg Ser Ser Asp Cys Ile Asp Glu Phe Cys1 5 10
15Cys Ala Arg His Phe Trp Thr Lys Ile Cys Lys 20
253627PRTArtificial SequenceEpitope 36Cys Gly Tyr Pro Leu Cys Gln
Lys Lys Leu Gly Val Ile Ser Lys Gln1 5 10 15Lys Tyr Arg Ile Ser Thr
Lys Thr Asn Lys Val 20 253727PRTArtificial SequenceEpitope 37Val
Thr Ser Ile Pro Ser Val Ser Asn Ala Leu Asn Trp Lys Glu Phe1 5 10
15Ser Phe Ile Gln Ser Thr Leu Gly Tyr Val Ala 20
253827PRTArtificial SequenceEpitope 38Lys Thr Thr Leu Ser His Thr
Gln Asp Ser Ser Gln Ser Leu Gln Ser1 5 10 15Ser Ser Asp Ser Ser Lys
Ser Ser Arg Cys Ser 20 253927PRTArtificial SequenceEpitope 39Pro
Ala Pro Arg Ala Val Leu Thr Gly His Asp His Glu Ile Val Cys1 5 10
15Val Ser Val Cys Ala Glu Leu Gly Leu Val Ile 20
254027PRTArtificial SequenceEpitope 40Leu His Ser Gly Gln Asn His
Leu Lys Glu Met Ala Ile Ser Val Leu1 5 10 15Glu Ala Arg Ala Cys Ala
Ala Ala Gly Gln Ser 20 254127PRTArtificial SequenceEpitope 41Asn
Cys Lys Tyr Asp Thr Lys Cys Thr Lys Ala Asp Cys Leu Phe Thr1 5 10
15His Met Ser Arg Arg Ala Ser Ile Leu Thr Pro 20
254227PRTArtificial SequenceEpitope 42Leu Arg Ser Ser Leu Val Asn
Asn Arg Thr Gln Ala Lys Ile Ala Glu1 5 10 15Glu Leu Gly Met Gln Glu
Tyr Ala Ile Thr Asn 20 254327PRTArtificial SequenceEpitope 43Ile
Pro His Asn Pro Arg Val Ala Val Lys Thr Thr Asn Asn Leu Val1 5 10
15Met Lys Asn Ser Val Cys Leu Glu Arg Asp Ser 20
254427PRTArtificial SequenceEpitope 44Leu Ala Ala Gln Ser Leu Gly
Glu Pro Ala Thr Gln Ile Thr Leu Asn1 5 10 15Thr Phe His Tyr Ala Gly
Val Ser Ala Lys Asn 20 254527PRTArtificial SequenceEpitope 45Gln
Gly Val Thr Val Leu Ala Val Ser Ala Val Tyr Asp Ile Phe Val1 5 10
15Phe His Arg Leu Lys Met Lys Gln Ile Leu Pro 20
254627PRTArtificial SequenceEpitope 46Ala His Ile Arg Gly Ala Lys
His Gln Lys Val Val Thr Leu His Thr1 5 10 15Lys Leu Gly Lys Pro Ile
Pro Ser Thr Glu Pro 20 254727PRTArtificial SequenceEpitope 47Glu
Leu Ala Trp Glu Ile Asp Arg Lys Val Leu His Gln Asn Arg Leu1 5 10
15Gln Arg Thr Pro Ile Lys Leu Gln Cys Phe Ala 20
254827PRTArtificial SequenceEpitope 48Phe Leu Lys Asp Arg Leu Leu
Glu Asp Lys Lys Ile Ala Val Leu Leu1 5 10 15Asp Glu Val Ala Glu Asp
Met Gly Lys Cys His 20 254927PRTArtificial SequenceEpitope 49Asn
Asp Glu Pro Asp Leu Asp Pro Val Gln Glu Leu Ile Tyr Asp Leu1 5 10
15Arg Ser Gln Cys Asp Ala Ile Arg Val Thr Lys 20
255027PRTArtificial SequenceEpitope 50Asp Ala Ala Ala Leu Gln Met
Ile Ile Ala Tyr Ala Tyr Arg Gly Asn1 5 10 15Leu Ala Val Asn Asp Ser
Thr Val Glu Gln Leu 20 255127PRTArtificial SequenceEpitope 51Lys
Asp Tyr Thr Ala Ala Gly Phe Ser Ser Phe Gln Lys Leu Arg Leu1 5 10
15Asp Leu Thr Ser Met Gln Ile Ile Thr Thr Asp 20
255227PRTArtificial SequenceEpitope 52Ala Val Lys Glu Glu Asp Ser
Leu His Trp Gln Arg Pro Glu Asp Val1 5 10 15Gln Lys Val Lys Ala Leu
Ser Phe Tyr Gln Pro 20 255327PRTArtificial SequenceEpitope 53Phe
Ala Ile Cys Phe Ser Cys Leu Leu Ala His Ala Leu Asn Leu Ile1 5 10
15Lys Leu Val Arg Gly Arg Lys Pro Leu Ser Trp 20
255423PRTArtificial SequenceEpitope 54Met Gly Ala Ala Ile Ser Gln
Gly Ala Ile Ile Ala Ile Val Cys Asn1 5 10 15Gly Leu Val Gly Phe Leu
Leu 205527PRTArtificial SequenceEpitope 55Glu Lys Tyr Pro Arg Thr
Pro Lys Cys Ala Arg Cys Gly Asn His Gly1 5 10 15Val Val Ser Ala Leu
Lys Gly His Lys Arg Tyr 20 255627PRTArtificial SequenceEpitope
56Ser His Arg Ser Cys Ser His Gln Thr Ser Ala Pro Ser Pro Lys Ala1
5 10 15Leu Ala His Asn Gly Thr Pro Arg Asn Ala Ile 20
255727PRTArtificial SequenceEpitope 57Lys Glu Leu Leu Gln Phe Lys
Lys Leu Lys Lys Gln Asn Leu Gln Gln1 5 10 15Met Gln Ala Glu Ser Gly
Phe Val Gln His Val 20 255827PRTArtificial SequenceEpitope 58Arg
Lys Gly Glu Arg Glu Glu Met Gln Asp Ala His Val Ser Leu Asn1 5 10
15Asp Ile Thr Gln Glu Cys Asn Pro Pro Ser Ser 20
255927PRTArtificial SequenceEpitope 59Arg Val Glu Lys Leu Gln Leu
Glu Ser Glu Leu Asn Glu Ser Arg Thr1 5 10 15Glu Cys Ile Thr Ala Thr
Ser Gln Met Thr Ala 20 256027PRTArtificial SequenceEpitope 60Asp
Ser Val Val Ile Phe Ser Gly Glu Gly Ser Asp Glu Phe Thr Gln1 5 10
15Gly Tyr Ile Tyr Phe His Lys Ala Pro Ser Pro 20
256127PRTArtificial SequenceEpitope 61Pro Gln Thr Ser Pro Thr Gly
Ile Leu Pro Thr Thr Ser Asn Ser Ile1 5 10 15Ser Thr Ser Glu Met Thr
Trp Lys Ser Ser Leu 20 256227PRTArtificial SequenceEpitope 62Trp
Ile Gly Gly Ser Ile Leu Ala Ser Leu Ser Thr Phe His Gln Met1 5 10
15Trp Ile Ser Lys Gln Glu Tyr Asp Glu Ser Gly 20
256327PRTArtificial SequenceEpitope 63Ser Ala Leu Gly Ser Leu Ala
Leu Met Ile Trp Leu Met Thr Thr Pro1 5 10 15His Ser His Glu Thr Glu
Gln Lys Arg Leu Gly 20 256426PRTArtificial SequenceEpitope 64Asp
Leu Arg Thr Ala Ala Tyr Val Asn Ala Ile Glu Lys Ile Phe Lys1 5 10
15Val Tyr Asn Glu Ala Gly Val Thr Phe Thr 20 256527PRTArtificial
SequenceEpitope 65Lys Leu Cys Leu Glu Leu Leu Asn Val Gly Val Glu
Ser Asn Leu Ile1 5 10 15Leu Lys Gly Val Ile Leu Leu Ile Val Asp Lys
20 256627PRTArtificial SequenceEpitope 66Asn Val His Tyr Glu Asn
Tyr Arg Ser Arg Lys Leu Ala Thr Val Thr1 5 10 15Tyr Asn Gly Val Asp
Asn Asn Lys Asn Lys Gly 20 256727PRTArtificial SequenceEpitope
67Tyr Thr Val Ser Val Val Ala Leu His Asp Asp Met Glu Asn Gln Pro1
5 10 15Leu Ile Gly Ile Gln Ser Thr Ala Ile Pro Ala 20
256827PRTArtificial SequenceEpitope 68Lys Pro Ser Thr Leu Arg Glu
Leu Glu Arg Tyr Val Leu Ala Cys Leu1 5 10 15Arg Lys Lys Pro Arg Lys
Pro Tyr Thr Ile Arg 20 256920PRTArtificial SequenceEpitope 69Lys
Phe Met Glu Arg Asp Pro Asp Glu Leu Arg Phe Asn Thr Ile Ala1 5 10
15Leu Ser Ala Ala 207027PRTArtificial SequenceEpitope 70Leu His Ser
Gly Gln Asn His Leu Lys Glu Met Ala Ile Ser Val Leu1 5 10 15Glu Ala
Arg Ala Cys Ala Ala Ala Gly Gln Ser 20 257127PRTArtificial
SequenceEpitope 71Asp Thr Leu Ser Ala Met Ser Asn Pro Arg Ala Met
Gln Val Leu Leu1 5 10 15Gln Ile Gln Gln Gly Leu Gln Thr Leu Ala Thr
20 257227PRTArtificial SequenceEpitope 72Asp Gly Gln Leu Glu Leu
Leu Ala Gln Gly Ala Leu Asp Asn Ala Leu1 5 10 15Ser Ser Met Gly Ala
Leu His Ala Leu Arg Pro 20 257327PRTArtificial SequenceEpitope
73Trp Lys Gly Gly Pro Val Lys Ile Asp Pro Leu Ala Leu Met Gln Ala1
5 10 15Ile Glu Arg Tyr Leu Val Val Arg Gly Tyr Gly 20
257427PRTArtificial SequenceEpitope 74Gln Asp Ile Asn Asp Asn Asn
Pro Ser Phe Pro Thr Gly Lys Met Lys1 5 10 15Leu Glu Ile Ser Glu Ala
Leu Ala Pro Gly Thr 20 257527PRTArtificial SequenceEpitope 75Ser
Asp Pro Arg Ala Ala Tyr Phe Arg Gln Ala Glu Asn Asp Met Tyr1 5 10
15Ile Arg Met Ala Leu Leu Ala Thr Val Leu Gly 20
257627PRTArtificial SequenceEpitope 76Met Asp Leu Leu Ala Phe Glu
Arg Lys Leu Asp Gln Thr Val Met Arg1 5 10 15Lys Arg Leu Asp Ile Gln
Glu Ala Leu Lys Arg 20 257727PRTArtificial SequenceEpitope 77Ile
Thr Thr Cys Leu Ala Val Gly Gly Leu Asp Val Lys Phe Gln Glu1 5 10
15Ala Ala Leu Arg Ala Ala Pro Asp Ile Leu Ile 20
257827PRTArtificial SequenceEpitope 78Lys Ala Arg Leu Lys Ser Lys
Asp Val Lys Leu Ala Glu Ala His Gln1 5 10 15Gln Glu Cys Cys Gln Lys
Phe Glu Gln
Leu Ser 20 257927PRTArtificial SequenceEpitope 79Gly Glu Val Pro
Pro Gln Lys Leu Gln Ala Leu Gln Arg Ala Leu Gln1 5 10 15Ser Glu Phe
Cys Asn Ala Val Arg Glu Val Tyr 20 258015PRTArtificial
SequenceEpitope 80Asp Trp Glu Asn Val Ser Pro Glu Leu Asn Ser Thr
Asp Gln Pro1 5 10 158114PRTArtificial SequenceEpitope 81Asp Trp Glu
Asn Val Ser Pro Glu Leu Asn Ser Thr Asp Gln1 5 108213PRTArtificial
SequenceEpitope 82Asp Trp Glu Asn Val Ser Pro Glu Leu Asn Ser Thr
Asp1 5 108312PRTArtificial SequenceEpitope 83Asp Trp Glu Asn Val
Ser Pro Glu Leu Asn Ser Thr1 5 108411PRTArtificial SequenceEpitope
84Asp Trp Glu Asn Val Ser Pro Glu Leu Asn Ser1 5
108514PRTArtificial SequenceEpitope 85Trp Glu Asn Val Ser Pro Glu
Leu Asn Ser Thr Asp Gln Pro1 5 108612PRTArtificial SequenceEpitope
86Trp Glu Asn Val Ser Pro Glu Leu Asn Ser Thr Asp1 5
108711PRTArtificial SequenceEpitope 87Trp Glu Asn Val Ser Pro Glu
Leu Asn Ser Thr1 5 108813PRTArtificial SequenceEpitope 88Glu Asn
Val Ser Pro Glu Leu Asn Ser Thr Asp Gln Pro1 5 108912PRTArtificial
SequenceEpitope 89Asn Val Ser Pro Glu Leu Asn Ser Thr Asp Gln Pro1
5 109011PRTArtificial SequenceEpitope 90Val Ser Pro Glu Leu Asn Ser
Thr Asp Gln Pro1 5 109115PRTArtificial SequenceLinker
SequenceREPEAT(1)..(3)Portion of sequence repeated a times, wherein
a is independently a number selected from 0, 1, 2, 3, 4, 5, 6, 7,
8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, or
20REPEAT(4)..(6)Portion of sequence repeated b times, wherein b is
independently a number selected from 0, 1, 2, 3, 4, 5, 6, 7, 8, 9,
10, 11, 12, 13, 14, 15, 16, 17, 18, 19, or 20REPEAT(7)..(9)Portion
of sequence repeated c times, wherein c is independently a number
selected from 0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15,
16, 17, 18, 19, or 20REPEAT(10)..(12)Portion of sequence repeated d
times, wherein d is independently a number selected from 0, 1, 2,
3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, or
20REPEAT(13)..(15)Portion of sequence repeated e times, wherein e
is independently a number selected from 0, 1, 2, 3, 4, 5, 6, 7, 8,
9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, or
20MISC_FEATURE(1)..(15)a + b + c + d + e are different from 0 and
preferably are 2 or more, 3 or more, 4 or more or 5 or more 91Gly
Gly Ser Gly Ser Ser Gly Gly Gly Ser Ser Gly Gly Ser Gly1 5 10
15929PRTArtificial SequenceLinker Sequence 92Gly Gly Ser Gly Gly
Gly Gly Ser Gly1 59311DNAMus musculus 93ttcaggaccc a 119416DNAMus
musculus 94ttcaggaccc acacga 169527DNAMus musculus 95ttcaggaccc
acacgacggg aagacaa 279629DNAMus musculus 96ttcaggacca acacgacggg
aagacaagt 299727DNAMus musculus 97caggacccac acgacgggta gacaagt
279823DNAMus musculus 98acccacacga cgggtagaca agt 239923DNAMus
musculus 99acccacacga gccctagaca agt 2310015DNAMus musculus
100gacgggaaga caagt 1510152DNAArtificial SequenceIdealized Gene
101tgcaagaacg cgtacttatt cgccgccatg attatgacca gtgtttccag tc
5210248DNAArtificial SequenceIdealized Gene 102caagaacgcg
tacttattcg ccaccatgat tatgaccagt gtttccag 4810346DNAArtificial
SequenceIdealized Gene 103aacgcgtact tattcgccac catgattatg
accagtgttt ccagtc 4610446DNAArtificial SequenceIdealized Gene
104tgcaagaacg cgtacttatt cgccgccatg attatgacca gtgttt
4610510DNAArtificial SequenceSynthetic Construct 105ggaaactttc
10
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References