NZ790046A - Selecting neoepitopes as disease-specific targets for therapy with enhanced efficacy - Google Patents
Selecting neoepitopes as disease-specific targets for therapy with enhanced efficacy Download PDFInfo
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- NZ790046A NZ790046A NZ790046A NZ79004617A NZ790046A NZ 790046 A NZ790046 A NZ 790046A NZ 790046 A NZ790046 A NZ 790046A NZ 79004617 A NZ79004617 A NZ 79004617A NZ 790046 A NZ790046 A NZ 790046A
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Abstract
The present invention relates to methods for determining whether neoepitopes that are only expressed in or on diseased cells are suitable disease-specific targets, such that the diseased cell is less likely to be able to escape immune surveillance, and use of the neoepitopes in providing an immune response against diseased cells expressing the neoepitopes. esponse against diseased cells expressing the neoepitopes.
Description
SELECTING TOPES AS E-SPECIFIC
TARGETS FOR THERAPY WITH ENHANCED EFFICACY
This is a divisional application of NZ 750058, the entire contents of which are incorporated
herein by reference.
TECHNICAL FIELD OF THE INVENTION
The present invention relates to methods for determining the suitability of a disease-specific
neoepitope as a disease-specific target and the use of such identified le neoepitopes in
immunotherapy targeted specifically to a patient's diseased tissue, such as tumor tissue, which
expresses one or more of the identified suitable neoepitopes.
BACKGROUND OF THE INVENTION
Cancer is a primary cause of mortality, accounting for 1 in 4 of all deaths. The treatment of
cancer has traditionally been based on the law of averages - what works best for the largest
number of patients. However, owing to the molecular geneity in cancer, often less than
% of treated individuals profit from the approved ies. dualized medicine based
on tailored ent of patients is regarded as a potential solution to low efficacies and high
costs for innovation in drug development.
Personalized cancer immunotherapies are emerging as a potential breakthrough in cancer
treatment with the potential to transform the standard of care for the millions of cancer patients
yearly diagnosed world-wide. The g aspect of personalized cancer immunotherapies is
ng the immune system to target genetic abnormalities (mutations) unique to a patient’s
cancer. Such disease-specific mutations can encode for neoepitopes, which neoepitopes are
disease-specific targets. The most prevalent genetic abnormalities that plague cancer genomes
that can be used as disease-specific targets for personalized immunotherapies are
nonsynonymous single nucleotide ions (SNVs). Therefore, precise and exhaustive
identification of a patient’s SNVs in the coding regions of the genome is a critical step in the
process of producing personalized cancer immunotherapies.
However, as described herein, knowing the identity of the e-specific mutation is only part
of the picture. Rather, full genetic profiling of a mutation requires dge of the exact
number of copies of the gene ning the mutation in the diseased cell, e.g., in the tumor cell
(including both the wild-type and mutated alleles), the number of copies of the mutated allele
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in the tumor cell (referred to here as the zygosity of the mutation), and the degree of subclonality
of the mutation in a sample of diseased cells, such as a tumor sample. Indeed, copy number
variations occurring in diseased cells are an important component of genetic variation in the
diseased cells across most disease indications. Moreover, the extent of copy number variations,
the identity of genes affected by copy number variations and the precise genetic makeup of
copy number variations is unique to each individual and can vary widely from one individual
to another. See, generally, Shlien and Malkin, 2009, Genome Med. 1:62; Yang et al, 2013, Cell
153:919-929. Precise knowledge of these genetic es may be critical for selecting
mutations that when targeted would be immune to tumor escape, and therefore have the
potential to confer total tumor control.
In order to maximize the efficacy of personalized cancer immunotherapies and confer lasting
tumor control for the ty of d patients, therapies need to circumvent in some way the
ability of tumors to escape immune surveillance, for example by silencing expression of the
mutated target, e.g., by deleting the gene. Without addressing this problem, immunotherapies
run the risk of relapse since the therapy cannot target mutations if they are not
expressed, e.g., deleted from the genome. Selecting suitable neoepitopes that enhance tumor
control would benefit all personalized immunotherapy ches that target neoepitopes, no
matter how they are ented. Thus, there is a need in the art for ways in which to select
neoepitopes resulting from e-specific mutations that result in enhanced tumor control.
PTION OF INVENTION
SUMMARY OF THE INVENTION
The present invention provides ways to overcome the deficiencies in the state of the art by
providing methods for determining the suitability of a neoepitope resulting from a diseasespecific
on in a gene as a e-specific target from which a diseased tissue cannot
easily escape immune surveillance, which in the case of cancer will result in enhanced tumor
control. Once suitable neoepitopes have been identified, such suitable epitopes can be used as
disease-specific targets to induce a specific immune response in a patient having the disease.
For e, the disease can be cancer and ially the primary tumor as well as tumor
metastases expressing the le neoepitope can be targeted for a more effective treatment.
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The present invention relates to a method for determining the suitability of a tope
resulting from a disease-specific mutation at an allele in a gene (mutated allele) as a diseasespecific
target comprising determining, in a diseased cell or population of diseased cells, the
copy number of the mutated allele encoding the neoepitope. As used herein, copy number can
also be referred to as zygosity such that, for example, where the copy number of the d
allele is 4, the mutated allele has a ty of 4. As used herein, an allele is a site in the genome
having a specific tide identity, which identity can be the same on both the maternal and
paternal copies of the genome (homozygous genotype) or the identity can be different on the
maternal and paternal copies of the genome ozygous pe). A mutated allele is an
allele, which due to a disease-specific mutation, has a different identity from that site in a
corresponding normal genome, e.g., a genome from a non-diseased cell of the same individual
(matched genome), preferably from a non-diseased cell of the same tissue type as the diseased
cell. A neoepitope suitable as a e-specific target (suitable neoepitope) as used herein is a
neoepitope, which when targeted by the immune system, is less likely to have its expression
down-regulated or silenced (e.g., due to deletion) by the diseased tissue such that the diseased
tissue is less likely to be able to escape a response, preferably an immunological se
generated against the neoepitope by, for e, vaccination against the neoepitope or
administering immune cells that are able to target (bind) the neoepitope. In an embodiment, the
copy number of the mutated allele can be the same as the copy number of the gene comprising
the mutated allele such that the present invention also relates to a method for ining the
suitability of a neoepitope resulting from a disease-specific mutation in a gene as a diseasespecific
target comprising determining, in a diseased cell or population of diseased cells, the
copy number of the gene having the disease-specific mutation.
In one embodiment, a high copy number of the mutated allele or gene having the diseasespecific
mutation indicates the ility of the neoepitope as a disease-specific target, such
that the higher the copy number of the mutated allele or gene having the disease-specific
mutation, the higher the suitability of the neoepitope as a disease-specific target. In one
embodiment, where the copy number of the mutated allele or gene having the disease-specific
mutation in the diseased cell is greater than 2, this indicates the ility of the neoepitope as
a e-specific target. In one ment, where the copy number of the gene having the
disease-specific mutation is greater than 3, 4, 5, 6, 7, 8, 9, 10, 20, 30, 40, 50, 60, 70, 80, 90, or
is greater than 100, this indicates the suitability of the neoepitope as a disease-specific target.
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In cases where not all copies of the gene, in which at least one copy has the d , have
the mutation, it is preferable that many copies of the gene have the d allele, i. e., it is
preferable that a higher rather than lower fraction of the copies of the gene has the mutated
allele (higher rather than lower fractional zygosity). Thus, in certain embodiments, the mutated
allele is found in a high fraction of copies of the gene of which at least one copy has the mutated
allele (fractional zygosity), where the fractional zygosity is the ratio of the copy number of the
mutated allele (zygosity of the mutated allele) over the total number of copies of the tide
site to which the mutated allele maps, in particular to a reference genome or a corresponding
wild-type genome or a matched genome, i.e., wild-type genome from the same individual. The
higher the onal ty of copies of the mutated allele, the higher the suitability of the
neoepitope as a disease-specific target. Preferably, the fractional zygosity can be greater than
0.2, 0.3, 0.4, 0.5, 0.6, 0.7, 0.8, 0.9, 0.95, and most preferably the fractional zygosity is 1, i.e.,
that all the copies of the gene in the diseased cell have the mutated allele. In cases where the
fractional zygosity is 1, there are no wild-type copies of the gene such that the diseased cell
cannot revert back to expressing the corresponding wild-type epitope. As used herein, a fraction
of 1 is where the hypothesis that the genetic configuration of the d allele/gene, e.g., the
copy number, zygosity, is the same cannot be refuted by the data, i.e., is statistically tent.
It is known that diseased tissue, such as tumors, can be heterogeneous in their genetic make-up
and gene expression such that it is possible that not all of the diseased cells in the diseased tissue
have the same copy number of a gene and/or of the gene of which at least one copy has the
mutated allele (total copy number of the gene) and/or copies of the gene having the mutated
allele, much less the disease-specific on . Therefore, it is preferable that the copy
number, e.g., of the d allele and/or the fractional zygosity and/or the total number of
copies of the nucleotide site to which the d allele maps is found to be the same or similar
in a high fraction of diseased cells rather than a low fraction of diseased cells in the diseased
tissue (a high rather than a low clonal fraction). The higher the fraction of diseased cells having
the same or similar copy number, e.g., of the mutated allele and/or the fractional zygosity and/or
the total number of copies of the nucleotide site to which the mutated allele maps, the higher
the suitability of the neoepitope as a disease-specific target. For example, the clonal fraction
can be at least 0.3, 0.4, 0.5, 0.6, 0.7, 0.8, or at least 0.9. In a preferred embodiment, all of the
diseased cells in the diseased tissue have the same or similar copy numbers, i.e., the clonal
fraction is 1, i.e., is statistically consistent. As used herein, the same or similar copy number
encompasses the same copy number or a copy number within 30%, 25%, 20%, 15%, 10%, 5%,
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4%; 3%, 2% or less of the copy number, e.g., copy number or absolute copy number with or
without error correction.
ably, a clonal fraction of a mutation can be given by the fraction of ed cells that
have the same or r genetic configuration of the mutation, wherein a genetic configuration
of the mutation comprises the total number of copies of the nucleotide site to which the mutation
maps and the copy number of the mutated allele. A characteristic is said to be fixed in the
tion of diseased cells if the characteristic is present in all diseased cells to a degree that
cannot be statistically refuted by available data. Preferably, a clonal fraction of 1 means that the
genetic configuration of the mutation is fixed in the population of diseased cells. Preferably,
the genetic configuration of a mutation is fixed in the population of diseased cells if the mutation
is fixed in the population of diseased cells and the CNV affecting the site encoding the mutation
is fixed in the population of diseased cells. Preferably, if a mutation for which the total number
of copies of the nucleotide site to which the mutation maps is 2 and is in a balanced region of
the diseased (tumor) genome, is determined to be fixed in the population of diseased cells, then
the genetic uration of the mutation is fixed.
The gene in which the disease-specific mutation is found can be potentially in any gene in the
genome. A preferred type of gene in which a mutation that results in a suitable neoepitope is
found is a gene whose expression results in transformation of the cell into a cancerous
ype or whose lack of expression results in a cancerous cell losing its cancerous
ype, i.e., a gene whose expression contributes to tumor progression. Such genes are
known as driver genes. Examples of driver genes for many type of tumors are well known. For
example, a list of 291 high-confidence cancer driver genes acting on 3,205 tumors from 12
different cancer types is disclosed in Tamborero et al., 2013, Comprehensive identification of
onal cancer driver genes across 12 tumor types, Scientific Reports 3:2650. Further driver
genes have been identified using the s disclosed in Youn et al., 2011, Identifying cancer
driver genes in tumor genome sequencing studies, ormatics 27(2):175-181, in Sakopamig
et al, 2015, Identification of constrained cancer driver genes based on mutation timing, PFoS
Comput. Biol. 1 l(l):el004027, and in Forbes et al, 2008, t protocols in human genetics
-11. The disease-specific mutation in the driver gene may or may not contribute to the
cancerous phenotype. Preferably, every copy of the driver gene found in the diseased cell has
the disease-specific mutation. Also preferably, all cells in the ed tissue are diseased cells
in which every copy of the driver gene has the disease-specific mutation.
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Another preferred type of gene is an ial gene. In an embodiment, an essential gene is a
gene, which when silenced or its expression is reduced (e.g., by being deleted), at least results
in impaired growth or reduced s of the cell, preferably a diseased cell. Such genes are
termed herein essential genes. In one embodiment, an ial gene is a gene in which there is
an at least 10% ion in growth or d fitness of the diseased cell where the gene is
silenced or has its expression reduced compared to a cell in which the gene is not silenced nor
reduced expression. In one embodiment, the ion in growth or reduced fitness is at least
%, 30%, 40%, 50%, 60%, 75%, 80%, 90%, or at least 95%, most preferably the silencing or
reduced expression of the essential gene results in ity of the diseased cell. Preferably,
every copy of the essential gene found in the diseased cell has the disease-specific mutation.
Essential genes are well known in the art, for example, a list of essential genes in humans (e.g.,
in human cell lines or inferred from other organisms) is disclosed in Liao et al, 2008, Proc.
Nat. Acad. Sci. USA 105: 6987-6992 and in Georgi etal, 2013, PLoS Genetics 9 (5):el003484,
as well as corresponding orthologs in other otic organisms such as mouse (Liao et al,
2007, Trends Genet. 23:378-381), fruit fly ling et al, 1999, Genetics 153:135-177), C.
elegans (Kamath et al, 2003, Nature 421:231-237), zebrafish (Amsterdam et al, 2004, Proc.
Natl. Acad. Sci. USA 101:12792-12797), Arabidopsis thaliana ir et al, 2004, Plant
Physiol. 135:1206-1220), yeast (Kim et al, 2010, Nat. Biotechnol. 28:617-623) and so on. A
list of essential genes derived from human cancer cell lines is disclosed in Wang et al, 2015,
Science 350:1096-1101, and a list of essential genes can be found at the database of essential
genes, DEG5.0 (Zhang et al, 2009, Nucleic Acids Res. 37:D455-D458).
Additionally, a list of essential genes whose deletion/silencing significantly reduces the fitness
of a cohort of cell lines can be generated empirically from multiple healthy tissues and/or cancer
cell lines, which cell lines can be derived from donors or from the patient. Deletion/silencing
of genes can be performed experimentally using various molecular biology techniques such as
CRISPR technology, RNA interference, and so on, where the survival or fitness of the cell is
ined with and without expression of the putative essential gene. A list of essential genes
also can be experimentally ined from cells or from a cell line or a list of essential genes
can be obtained by bioinformatic approaches. The cells or cell lines can be diseased cells or cell
lines (tumor cells or cell lines) or non-diseased hy/normal) cells or cell lines, and can be
obtained from donors or the patient having the disease. Preferably, the non-diseased cells or
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cell lines are from the same tissue type as the diseased cell, and more preferably from the same
patient. In embodiments where the disease is cancer, the cells or cell lines can be obtained from
the primary tumor or from any metastases, if present. Further, a list of essential genes can be
essentially the same as the minimal set of genes expressed in a wide variety of tissues in the
body. For example, an essential gene is a gene that is expressed in a wide y of ent
tissues and is expressed with a RPKM (minimum reads per kilobase of transcript per n
mapped reads) old greater than 0, preferably, greater than 0.1, 0.5, 1, 2, 3, 4, 5, 10, 20,
. Such a list of essential genes can be obtained by analyzing the RNA expression data, (e.g.,
RNAseq) obtained from a panel of cell samples obtained from at least 5, 6, 7, 8, 9, 10, 15, 20,
or more different tissues. Moreover, if a tumor cell line from the patient is available, genes
in which all copies contain a on encoding a neoepitope can be deleted one at a time and
the growth rates of each modified cell line measured. Such measurement/analysis can be
performed by high-throughput methods known in the art, which allows for the screening of at
least one gene at a time, preferably many genes at a time, in order to assess its effect on the
fitness of a diseased or non-diseased cell. Such s also allow for the ion of synthetic
sick or lethal combination of genes, discussed below. y, a library of cell lines, each cell
line missing one gene, can be used to test the deletion of one or more candidate genes such that
the effect on the cell of the deletion of the genes can be determined.
The present invention further relates to a method for determining the suitability of a tope
resulting from a disease-specific mutation in a gene as a disease-specific target comprising
determining, in a diseased cell or population of diseased cells, the copy number of the gene,
i.e., determining the copy number of a gene in which at least one copy of the gene has a disease-
specific mutation. In cases where a gene has a high copy number in a diseased cell such as a
tumor cell, e.g., due to focal amplification, the chances are very good that the gene may be a
driver gene. Thus, a high copy number of a gene indicates the suitability of the neoepitope as a
disease-specific target, and the higher the copy number of the gene, the higher the suitability of
the neoepitope as a disease-specific target. For e, a high copy number can be a copy
number greater than 2, 5, 10, 20, 30, 40, 50, 60, 70, 80, 90, or greater than 100. A high copy
number can also be a copy number that is at least 50% greater than the copy number of the gene
in a corresponding non-diseased cell. A high copy number can also be where the copy number
of the gene in which at least one copy has the disease-specific mutation is at least 2x, 3x, 5x,
lOx, 15x, 20x, 25x, 30x, 40x, 50x, 60x, 70x, 80x, 90x, or at least lOOx greater than the copy
number of the gene in a corresponding non-diseased cell. Due to copy number variations that
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can also be present in the normal genome, the copy number of the gene in the normal genome
is not necessarily two. Moreover, it is known that focal amplifications are more often observed
in certain diseases than , such as in glioblastoma where the mal growth factor
receptor gene is often focally amplified, thus this embodiment is well suited to use in those
diseases.
Further, it is preferable that the copy number of the gene is found to be the same or similar in a
high on of diseased cells rather than a low fraction of diseased cells, such that the higher
the fraction of diseased cells having the same or similar copy number, the higher the suitability
of the neoepitope as a e-specific target. In a preferred embodiment, all of the ed
cells in the diseased tissue have the same or r copy number of the gene in which at least
one copy has the e-specific mutation, i.e., the clonal fraction is 1. As used herein, the
same or similar copy number encompasses the same copy number or a copy number within
%, 25%, 20%, 15%, 10%, 5%, 4%; 3%, 2% or less of the copy number, e.g., copy number
or absolute copy number with or without error correction.
er, the gene having a high copy number, in which at least one copy has a disease-specific
mutation resulting in a neoepitope, preferably can be a gene whose expression results in
transformation of the cell into a cancerous phenotype or whose lack of expression results in a
ous cell losing its cancerous phenotype, i.e., a driver gene such as those driver genes
known in the art, or can be an essential gene, e.g., a gene which when silenced or its expression
is reduced, at least results in impaired growth or reduced fitness of the diseased cell.
The present invention also relates to a method for determining the ility of a neoepitope
resulting from a disease-specific mutation in a gene as a disease-specific target comprising
determining, in a diseased cell or population of diseased cells, whether the gene having the
disease-specific mutation is an essential gene. In one embodiment, the essential gene is a gene
which when silenced or its expression is d {e.g., by deletion of the gene), at least s
in impaired growth or reduced fitness of the diseased cell. In this embodiment, where the gene
is an essential gene and all copies of the essential gene have the disease-specific mutation
(fractional zygosity of 1) indicates the suitability of the neoepitope as a preferable diseasespecific
target. In an embodiment, an ial gene is a gene that is expressed in a wide variety
of ent tissues and is expressed with a RPKM (minimum reads per kilobase of transcript
per million mapped reads) threshold greater than 0, preferably, greater than 0.1, 0.5, 1, 2, 3, 4,
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, 10, 20, 25. Preferably, all copies of the ial gene n the mutation. Further, it is
preferable that a high fraction of ed cells contain copies of the essential gene in which all
copies of the essential gene have the disease-specific mutation (a high rather than low clonal
fraction), such that the higher the fraction of diseased cells containing copies of the essential
gene in which all copies of the essential gene have the disease-specific mutation, the higher the
suitability of the neoepitope as a disease-specific target. In a more preferred embodiment, all of
the diseased cells in the diseased tissue have the essential gene in which all copies of the
essential gene have the disease-specific mutation, i.e., the clonal fraction is 1.
It is known that certain genes, when individually silenced or where their expression is
individually reduced, may have only a small , if any, on the fitness or the growth ability
of the diseased cell. However, it has been observed that when two of such genes both of which
have been silenced or where each of their expression has been reduced can result in a much
stronger growth ment, up to ity. Such genetic combinations are referred to as
tic lethal or synthetic sick/impaired. See Nijman, 2011, Synthetic lethality: General
principles, utility and detection using genetic s in human cells, FEES Lett. 585:1-6 for a
discussion on synthetic lethal and synthetic sick genes and methods for identifying such genes.
Since both genes are required for the cell to survive, it is unlikely that the cell will silence or
reduce sion of both of the genes. Thus, a suitable combination of neoepitopes as diseasespecific
targets can result from disease-specific mutations in at least two genes, which genes
er are synthetically lethal or synthetically sick. In view thereof, the present invention
r relates to a method for determining the suitability of a combination of at least two
neoepitopes resulting from disease-specific mutations in at least two genes as a combination of
disease-specific targets comprising determining r a combination of the at least two genes
each having a disease-specific mutation are synthetic lethal or synthetic sick genes. When the
ation of the at least two genes results in a synthetic lethal or synthetic sick phenotype,
this indicates that the resulting neoepitopes are a suitable combination of disease-specific
targets. In a preferred embodiment, tic sick results in at least a greater effect on cell
growth/fitness that what would be expected from the additive effect of on/reduced
expression of each gene individually. This approach is favored where there is a high number of
suitable neoepitopes since the higher the number of neoepitopes, the greater the number of
combinations that could be synthetic sick or lethal. For example, 10 mutations corresponds to
45 possible combinations, 100 mutations corresponds to 4950 combinations, and 1000
ons corresponds to about 500,000 combinations. In certain embodiments, the at least two
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genes each have a higher rather than lower fractional zygosity, preferably a fractional zygosity
of 1, and/or each have a higher rather than lower clonal on, preferably a clonal fraction of
1, both in the diseased cells and diseased cells in the diseased tissue. As used herein, each
tope found in a combination of suitable topes is each considered to be a suitable
neoepitope for the purposes of the present ion.
As referred to herein, the copy number of the gene, either in the diseased or non-diseased cell,
can be the relative copy number, but is preferably the absolute copy number, and more
preferably is the absolute copy number normalized against a ploidy, e.g., the ploidy of the
genome of the diseased cell, i.e., the copy number of the genome. Even more preferably, the
relative, absolute and normalized copy number is error ted.
When estimating te copy number, for example of a mutated allele or gene or its zygosity
the tion may be rate and correcting the absolute copy number to take into t
sources of error is desirous. In embodiments where next generation sequencing is used to obtain
sequence information from genomes and exomes, s of error can include: a bias in the
estimated purity of the sample of diseased tissue such as a tumor sample, a bias in any estimated
parameter required in order to derive the purity and/or absolute copy numbers, stochastic errors
due to the finite coverage of the sample being sequenced, limited detection capability due to a
low purity, a low clonal fraction, and so on.
In an embodiment where absolute copy number is determined using ed heterozygous
segments ning a heterozygous SNP, such as that disclosed in International PCT Patent
Application entitled “Tumor Modeling Based on Primary Balanced Heterozygous Segments”
filed on even date herewith, the disclosure of which is incorporated by nce herein in its
ty, an error in the absolute copy number of a segment can propagate to other estimated
parameters, such as the absolute copy number of the mutated allele, e.g., a SNY, encoding a
neoepitope, the zygosity of the mutated allele, the clonal fraction and so on. Since such
downstream estimated parameters have clinical implications for determining the suitability of
a neoepitope as a disease specific target for a patient as described herein, is it desirable to correct
errors in the absolute copy number to obtain to most accurate value of the absolute copy number.
Moreover, since the mutations encoding the neoepitopes can be prioritized for their suitability
to be ed in a vaccine to be given to the patient using the criteria discussed herein, and
because a fraction zygosity of 1 is qualitatively better than a on zygosity smaller than 1,
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in particular when the gene containing the mutation is an essential gene, it is beneficial to have
the most accurate tes of absolute copy numbers and any parameter derived f from.
In a preferred ment, the absolute copy number of a mutated allele, e.g., a SNV, and/or
the zygosity of a SNV can be error corrected. In an embodiment, the absolute copy number of
a SNV is first error corrected, and then the zygosity of the SNV is corrected to reflect the error
corrected absolute copy number of the SNV. Once the absolute copy number of the SNV and/or
zygosity of the SNV are error corrected, the estimation of the clonal fraction can be also
corrected to reflect the error corrected absolute copy numbers, including the determination if
the clonal fraction is statistically consistent with a value of 1.
The absolute copy number of a SNV is preferably given by the absolute copy number of the
segment to which the SNV maps. The absolute copy numbers of all segments in the diseased,
e.g, tumor genome can be error corrected, including the absolute copy number of the SNV.
Once the absolute copy numbers of all segments in a genome are error corrected, an error
ted ploidy can be calculated based on the error ted absolute copy numbers of
segments in the diseased, e.g, tumor genome.
In a specific embodiment, if the absolute copy number of a SNV is error corrected such that the
new te copy number differs from the original absolute copy number this can be taken as
an indication that the estimated absolute copy number of the SNV is not reliable.
One example of error correction of absolute copy numbers of segments is parity error
correction, comprising correcting an odd te copy number of a segment to an even
absolute copy number if the segment is in a ed region. A balanced region is a region of
the diseased, e.g, tumor genome wherein the maternal and paternal alleles within the region
underwent equal ced) amplification, or both maternal and paternal alleles did not undergo
any amplification at all.
The decision to error correct the odd te copy number of the segment to the closest higher
even absolute copy number or the closest lower even absolute copy number can depend on the
e reads and normal reads mapping to the segment, and comparison to the ted
boundaries defining the te copy number of a segment. Wherein a normal read is a read
pertaining to the sequenced normal sample, and a disease read is a read pertaining to the
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sequenced diseased sample. In particular, when the disease is cancer, a tumor read is a read
pertaining to the sequenced tumor sample.
For example, in a parity error correction of the first kind, if is the absolute copy number
in the diseased genome of the segment to which the on maps, the absolute copy number
of a segment predicted to have a value of CNmut, can be corrected to CNmut + 1 if r > pth,
and to CNmut — 1 if r < pth, where r is the disease over normal t read count ratio (the
ratio of the number of disease, e.g., tumor reads mapping to the segment over the number of
normal reads mapping to the segment), wherein pth is the predicted decision boundary, the
value of which depends also on the purity of the disease tissue sample, e.g., tumor sample.
An allele specific copy number of a segment is the number of copies in the diseased genome of
either the maternal allele or al allele of the segment. When the segment contains a
heterozygous SNP (heterozygous segment), the heterozygous SNP can be used to determine the
allele specific copy number of the segment. A heterozygous segment can be assigned to a
preferred node, wherein a node can be defined to be a unique combination of an te copy
number of the heterozygous segment and an allele specific copy number of heterozygous
segment. Even nodes are a subset of nodes for which the te copy number of the t
is even. If a heterozygous segment contains more than one heterozygous SNP, the group of two
or more heterozygous SNPs can be represented by either a single member of the group, or the
allele frequencies of all members of the group can be averaged, or a median can be taken, so
long as the allele frequency of each zygous SNP is calculated consistently for either the
allele having the higher or lower number of copies in the diseased genome.
A parity error correction of the first kind of a zygous segment can involve finding the
most likely even node to correspond to the heterozygous segment, for example, based on a
maximum likelihood framework given the measured disease {e.g., tumor) reads and normal
reads mapping to the segment.
In a parity error tion of the second kind, the nearest upstream and downstream segments
that do not require parity error correction are identified, preferably within 10Mb, 5Mb, 1Mb of
the segment containing the SNV. If the absolute copy number of both nearest upstream and
ream segments are identical, then the absolute copy number of the segment containing
the SNV is changed to the absolute copy number of the nearest segment. Generally, parity error
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tion of the second kind is preferred to parity error correction of the first kind, unless it
cannot be implemented e suitable neighboring segments cannot be identified, in which
case parity error correction of the first kind can be applied.
Other forms of error correction of an absolute copy number of a segment can also be introduced
instead of or in addition to parity error correction. For example, methods considering the
absolute copy number of ts in the immediate vicinity of the gene containing the mutation
in the diseased genome, wherein the absolute copy number of the t ning the SNV
is changed to the mode of the absolute copy numbers of neighboring segments, preferably if
the change in absolute copy number is not more than 3, 2 and preferably 1, and preferably if
most of the neighboring segments (50%, 60%, 70%, 80%, 90%, 100%) have an absolute copy
number equal to the mode.
ent error correction schemes for the absolute copy numbers can be combined. In a
preferred ment, first parity error correction is applied as first layer of error tion,
on top of which onal error correction methods can be applied.
As used herein, a segment can be a predetermined region of the genome, e.g., predetermined
based on a reference genome. A segment can span a gene, e.g., as defined in a reference genome
that the reads are aligned to. A segment can also be a fragment of a gene, an exon, a union of
exons, or the union of exons associated within a given gene. A segment can also be another set
of predetermined regions in a reference genome (with or without introns), or another set of
predetermined regions in a reference genome based on the normal genome. In specific
embodiments, a segment can be a region of the nce genome with a given constant copy
number and/or a given allele specific copy number in the diseased, e.g., tumor, genome or
alternatively a fragment of a gene with a given nt copy number and/or allele specific copy
number in the diseased, e.g., tumor genome. A segment can be defined to e or to exclude
A number of copies of a segment in a given genome (e.g., in the normal genome, or in the tumor
genome) can be defined as how often in total the nucleotide sequence of the segment occurs in
the genome, ignoring variations caused by SNPs and/or SNVs and/or other cancer-associated
changes such as, but not limited to, mutation, insertions, deletions and/or other cancer-related
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genetic variants. Preferably the different copies of the segment in the given genome have the
same length or nearly the same length.
The number of copies of a segment in a genome can mean the number of physical copies of the
segment in a cell containing the . An absolute copy number of a segment in the normal
genome can be defined as the number of physical copies of the given segment in a healthy cell.
An absolute copy number of a segment in the diseased, e.g., tumor, genome can be defined as
the number of physical copies of the given segment in a diseased, e.g., tumor, cell. The number
of copies of a segment in the genome can be referred to as the absolute copy number of the
segment in the said genome. A copy number can mean an te copy number.
In a specific embodiment, if only a part of a segment is ied or deleted in a genome, then
such a partial copy of the segment can either be d as a copy of the t or not counted
as a copy of the segment. In a red embodiment, copies of the segment spanning less than
90%, 80%, 70%, 60%, 50%, 40%, 30%, 20%, 10% or 5% of the segment length can be ignored.
A reference genome is used for mapping reads and providing a nate system for the normal
genome and the diseased, e.g., tumor, genome, wherein a coordinate system can comprise
providing a chromosome number, a nucleotide position in the chromosome, as well as
directionality of the read, where the position in the chromosome ted by the line.
A reference genome can be based on the genome of one or more members from the same species
as a subject providing the sample of diseased tissue, or can be based on the normal genome of
the subject.
A sample of diseased tissue, such as a tumor sample, also can comprise contamination from the
normal genome, in particular the normal genome of the same patient from which the sample
was taken, and/or in case of intratumor geneity, also comprise more than one tumor
genome. The purity, tumor sample purity, tumor purity, and sample purity are all taken to be
equivalent terms, preferably meaning the fraction of tumor cells t in a tumor sample.
Normal contamination preferably means the fraction of normal cells present in the tumor
sample, and can be given by one minus the purity.
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Normalizing against the ploidy of the cell controls for the presence of copies of a gene due to
genome ation events. In an embodiment, the absolute copy number can be normalized
against the ploidy of the genome, which ploidy is the average of the absolute copy number of
all segments in a given genome is a given cell weighted by the length of each segment. In an
embodiment, the absolute copy number can be normalized against the ploidy of the
chromosome which contains the mutated gene of interest (comprising the mutation), which
ploidy is the average of the te copy number of all segments on the given chromosome in
a given cell weighted by the length of each segment on the chromosome. In an embodiment,
the absolute copy number can be normalized against the ploidy of a neighboring region of the
chromosome which contains the mutated gene of interest, which ploidy is the average of each
segment in the given region in a given cell weighted by the length of each segment in the region.
The neighboring region can be within a predetermined distance of the gene having the diseasespecific
mutation, e.g., within 100 megabases (Mb), 75 Mb, 50 Mb, 25 Mb, 10 Mb, 5 Mb, 4
Mb, 3 Mb, 2 Mb, or 1 Mb of the gene having the e-specific mutation. The copy number
of a segment can be calculated routinely by methods known in the art, both experimentally and
computationally. For example, EP Patent Nos. 2 198 292 B1 and EP 2 002 016 B1 se
methods for determining relative copy number and copy number ncy of nucleic acid
sequences, tively. r, EP Patent Application Publication No. 2 835 752 A and
International Patent Application Publication Nos. WO 14497 and
se methods for determining copy number ions. See also, Machado et al, 2013, Copy
Number Variation of Fc Gamma Receptor Genes in HIV-Infected and berculosis Co-
Infected Individuals in Sub-Saharan Africa, PLoS, 8(1 l):e78165. Other methods include the
use of FACS, FISH or other fluorescent-based methods, spectral karyotyping (SKY), and digital
PCR. A segment can also be a gene.
The disease-specific mutation can be any mutation that results in the expression of a neo epitope,
preferably on the surface of the diseased cell. In particular, the mutation can be an indel or genefusion
event or can be a single nucleotide variation (point mutation). Preferably, the diseasespecific
mutations are a nonymous mutations, preferably non-synonymous mutations of
proteins expressed in a tumor or cancer cell. Any method known in the art for determining
disease-specific mutations can be used, and in particular methods using next generation
sequencing data to detennine any changes between the /exome of diseased cells
compared to the genome/exome of corresponding non-diseased, wild-type cells is preferred.
For example, Carter et al, 2012, Absolute quantification of c DNA alterations in human
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, Nature Biotechnology 30:413-421; Cibulskis et a/., 2013, Sensitive ion of somatic
point mutations in impure and heterogeneous cancer samples, Nature Biotechnology 31:213-
219; and Li and Li, 2014, A general framework for analyzing tumor subclonality using SNP
array and DNA sequencing data, Genome Biology 15:473-495 se methods not only for
identifying disease-specific ons, but also disclose s for determining gene copy
number, fractional zygosity and fractional nality of the zygosity and fractional zygosity.
Another method for determining copy , such as absolute copy number, concerns the use
of segments of the genome, each segment containing at least one zygous single nucleotide
polymorphism (SNP), and which segments are balanced (equal number of each version of the
heterozygous SNP) and share a common number of copies (primary copy number) which
preferably is the most frequently observed absolute copy number of all the balanced segments
of the genome, as disclosed in International PCX Patent Application entitled “Tumor Modeling
Based on Primary ed Heterozygous Segments” filed on even date herewith, the
disclosure of which is incorporated by reference herein in its entirety. Moreover, in additional
to determining absolute copy number, this application can also determine zygosity, fractional
zygosity, and nality of the mutated allele or the gene of which at least one copy comprises
the mutated allele. Further, the methodology therein also performs error correction for absolute
copy numbers, which improves the accuracy of absolute copy numbers and zygosities and
parameters derived therein, such as subclonality, , and so on.
Generally, a total number of copies of the nucleotide site to which the mutated allele maps can
mean the absolute copy number of the mutation, which can mean the absolute copy number of
the SNY, in particular when the mutation is a SNV. Generally, the absolute copy number of the
mutation can preferably be given by the absolute copy number of a segment to which the
mutation maps (wherein the absolute copy number is in the diseased, e.g., tumor genome).
Generally, a copy number of a mutated allele encoding a neoepitope can mean an absolute copy
number of a mutated allele of a on, which can mean an absolute copy number of the
alternate allele of a SNV (a zygosity of a SNV), wherein the alternate allele of the SNV is the
mutated allele, in particular when the mutation is a SNV.
Preferably, when the mutation is not a SNV, the absolute copy number of a mutated allele of a
mutation can be estimated in a similar manner to the method applied for SNVs.
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Generally, a copy number of a gene can mean the absolute copy number of a segment, wherein
the segment can be the gene, or can encompass the gene. A copy number of a gene can mean
an absolute copy number of a gene.
Preferably, the disease can be any disease in which an immune response against the diseased
cell/tissue is desired, such as a virally-infected cell. Preferably, the disease is cancer.
The methods of the invention may comprise the further step of determining the
usability/appropriateness of the suitable neoepitopes identified by the methods of the invention
as suitable disease-specific targets for use in a method to provide an immune response against
the suitable neoepitope, such as inclusion of the suitable neoepitope in a cancer vaccine. Thus,
further steps can involve one or more of the following: determining the nicity and/or
immunogenicity of the suitable neoepitope; assessing whether the suitable tope is
expressed on the surface of the diseased cell; y of a peptide comprising the suitable
neoepitope to be presented as a MHC presented epitope; determining the efficacy of sion
of the suitable neoepitope from an encoding nucleic acid; determining whether the envisaged
suitable neoepitopes, in particular when present in their natural sequence context, e.g. when
d by amino acid sequences also flanking said neoepitopes in the naturally ing
protein, and when expressed in antigen presenting cells are able to stimulate T cells such as T
cells of the patient having the d specificity.
Once it has been determined that the neoepitope is suitable/appropriate for use as a target in
view of its antigenicity/immunogenicity, ability to be expressed, ability to be presented as a
MHC presented epitope, etc., the identified suitable neoepitopes can be ranked, i.e., prioritized,
on their ial to not be down-regulated or deleted from the diseased cell, that is less likely
that the diseased tissue can escape the ing of the neoepitope. For e, one
prioritization starts with the “best” neoepitope, which is one that is encoded by an essential
gene, in which all copies of the ial gene have the mutation encoding the neoepitope,
followed by a pair of tic sick or lethal genes, in which each copy of each gene has the
mutation encoding the neoepitope, followed by a neoepitope encoded by a known driver gene
with a very high absolute copy number in which all copies of the gene have the mutation,
followed by a neoepitope encoded by a gene that is not known to be a driver gene with a very
high absolute copy number and a high zygosity, followed by a neoepitope encoded by a gene
with a high copy number (zygosity), and so on.
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In an embodiment, a neoepitope encoded by an essential gene with a fractional zygosity of 1 is
preferred to other neoepitopes that are not encoded by an essential gene. In an embodiment,
between two essential genes encoding neoepitopes with a fractional zygosity of 1, the
neoepitope encoded by the gene having a higher absolute copy number is red. In an
embodiment, between two essential genes ng neoepitopes, the neoepitope encoded by
the gene leading to a lower fitness when deleted is preferred. In an embodiment, between genes
encoding topes in which all the genes have a fractional zygosity of 1, the neoepitopes
encoded by the genes having a higher absolute copy number are preferred. In an embodiment
where the fractional zygosity is less than 1, then neoepitopes encoded by genes having a high
zygosity are preferred to genes having a high fractional zygosity, and if the zygosity is the same
or similar, then genes having a high absolute copy number are preferred to those with a high
fractional zygosity (10 copies of the mutated allele/20 total copies of the tide site is better
than 3/4 due to higher zygosity; 10/100 is better than 10/20 because the former may be a driver
gene; 9/100 is better than 10/20 because the zygosity is similar but the former may be a driver
gene). In an embodiment, a neoepitope encoded by a driver gene, in which the disease-specific
mutation is responsible for transforming the cell into a cancerous phenotype is preferred to
those in which the on does not have a role in transforming the cell into the cancerous
phenotype. Moreover, it is preferred that the topes have a higher rather than lower clonal
fraction.
r embodiments of the present ion relate to the use of the methods of determining
the suitability of a neoepitope as a disease-specific target for the manufacture of a medicament,
such as a e, e.g., a personalized cancer e. The vaccine can be d from one or
more suitable topes or from a combination of suitable neoepitopes identified by the
methods of the invention. In a preferred embodiment, the vaccine comprises a peptide or
polypeptide comprising one or more suitable neoepitopes or a combination of suitable
neoepitopes fied by the methods of the ion, or a nucleic acid encoding said peptide
or polypeptide.
In particular, a recombinant e can be provided which when administered to a patient
preferably provides a collection of MHC presented epitopes at least one of which is a suitable
neoepitope or at least two of which are a suitable combination of neoepitopes identified by the
methods of the present invention, such as 2 or more, 5 or more, 10 or more, 15 or more, 20 or
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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 MHC presented epitopes. 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 MHC and thus, the patient's tumor, preferably the primary tumor as well as tumor
metastases, expressing antigens from which the MHC presented epitopes are derived and
presenting the same epitopes on the surface of the tumor cells.
The methods of the present invention are also useful in the manufacture of recombinant immune
cells expressing an antigen or targeted to a suitable neoepitope or to one neoepitope in a
combination of suitable topes. Preferably, the immune cells are T cells and the antigen
or is a T cell or.
The present invention also relates to a method for providing a recombinant immune cell targeted
to a suitable neoepitope or to one e in a combination of suitable neoepitopes, said method
comprising transfecting an immune cell with a inant antigen receptor targeted to the
suitable neoepitope or to the one e in a combination of suitable epitopes identified by the
methods of the present invention for determining the suitability of a neoepitope as a diseasespecific
target, as well as to recombinant immune cells produced by such methods.
The present invention also provides methods for ing a cell tion or tissue expressing
one or more neoepitopes. For example, an antibody directed against one or more of the
neoepitopes can be used to target the cells or tissue expressing the one or more neoepitopes
identified by the methods described herein. In one embodiment, the present invention provides
methods for providing an immune response to a target cell tion or target tissue expressing
one or more neoepitopes in a mammal, said method comprising administering to the mammal
(a) one or more immune cells expressing one or more antigen receptors targeted to the one or
more topes; (b) administering a nucleic acid encoding one or more of the topes;
or (c) administering a peptide or polypeptide comprising one or more of the neoepitopes, in
which the neoepitopes are identified according to the methods of the invention for determining
the suitability of a neoepitope as a disease-specific target. In one embodiment, the method for
providing an immune response to a target cell population or target tissue expressing one or more
neoepitopes in a mammal comprises the steps of (i) determining, in a diseased cell or population
of diseased cells, the copy number of a d allele in a gene which encodes a neoepitope (a
disease-specific mutation); and (ii) administering (a) an immune cell expressing an antigen
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receptor ed to the neoepitope resulting from the disease-specific mutation; (b)
administering a nucleic acid encoding the neoepitope resulting from the disease-specific
mutation; or (c) administering a peptide or polypeptide comprising the neoepitope ing
from the disease-specific mutation.
In one embodiment, the method for providing an immune response to a target cell tion
or target tissue expressing one or more neoepitopes in a mammal comprises the steps of (i)
ining, in a diseased cell or population of diseased cells, the copy number of a gene in
which at least one copy of the gene has a e-specific mutation which results in a
neoepitope; and (ii) administering (a) an immune cell expressing an antigen receptor targeted
to the neoepitope resulting from the disease-specific mutation; (b) administering a nucleic acid
encoding the neoepitope resulting from the disease-specific mutation; or (c) administering a
peptide or polypeptide comprising the tope resulting from the disease-specific mutation.
In one embodiment, the method for providing an immune response to a target cell population
or target tissue expressing one or more topes in a mammal comprises the steps of (i)
determining, in a ed cell or population of diseased cells, whether a gene having a diseasespecific
mutation resulting in a neoepitope is an essential gene; and (ii) administering (a) an
immune cell expressing an antigen receptor ed to the neoepitope resulting from the
disease-specific mutation; (b) administering a nucleic acid encoding the neoepitope resulting
from the e-specific mutation; or (c) administering a e or polypeptide comprising
the neoepitope ing from the disease-specific mutation. Preferably, all copies of the
essential gene have the disease-specific mutation, i.e., the fractional zygosity is 1.
In one ment, the method for providing an immune response to a target cell population
or target tissue expressing one or more neoepitopes in a mammal comprises the steps of (i)
determining, in a diseased cell or population of diseased cells, whether a combination of at least
two genes, each having a disease-specific mutation resulting in a neoepitope, are synthetic lethal
or synthetic sick genes; and (ii) administering (a) one or more immune cells expressing one or
more antigen receptors targeted to the one or more neoepitopes resulting from the diseasespecific
mutations of the at least two genes; (b) administering a nucleic acid ng the one
or more neoepitopes resulting from the disease-specific mutations of the at least two genes; or
(c) administering a peptide or polypeptide comprising the one or more neoepitopes resulting
from the disease-specific mutations of the at least two genes. Preferably, all the neoepitopes
resulting from the disease-specific ons of the at least two genes are targeted by the
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administered immune cells, encoded by the administered c acid, or comprised within the
administered peptide or polypeptide.
Moreover, the immune response can be provided to a mammal having a disease, disorder or
condition associated with expression of the neoepitope resulting from the disease-specific
mutation, such that the e, disorder or condition is treated or prevented. Preferably, the
disease, disorder or condition is cancer.
Preferably, the immune cells are T cells and the n receptors are T cell receptors, and the
immune response is a T cell-mediated immune response. More preferably, the immune se
is an anti-tumor immune response and the target cell population or target tissue expressing the
one or more suitable neoepitopes is tumor cells or tumor .
Other es and advantages of the t ion will be apparent from the following
detailed description and .
DETAILED DESCRIPTION OF THE INVENTION
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 ise, all
technical and scientific terms used herein have the same meanings as commonly tood by
one of ordinary skill in the art.
In the ing, the elements of the present invention will be described. These elements are
listed with specific embodiments, r, it should be understood that they may be combined
in any manner and in any number to create additional embodiments. The variously described
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
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the description of the present application unless the context indicates otherwise. For example,
if in a preferred embodiment the neoepitope has a high zygosity rather than a high fractional
zygosity, and in one preferred embodiment the neoepitope results from a mutation in an
ial gene, then in a preferred embodiment, the suitable neoepitope has a high fractional
zygosity and results from a mutation in an essential gene, and in a more preferred embodiment
the fractional ty is equal to 1.
Preferably, the terms used herein are defined as described in "A multilingual glossary of
biotechnological terms: (IUPAC Recommendations)", H.G.W. erger, B. Nagel, and H.
Kolbl, Eds., (1995) ica Chimica Acta, CH-4010 Basel, Switzerland.
The practice of the present ion 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,
2nd n, J. ok 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,
rs or steps although in some embodiments such other member, integer or step or group of
s, integers or steps maybe excluded, i.e., the subject-matter consists in the inclusion of
a stated member, r 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 ued 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 ted herein, each individual value
is incorporated into the specification as if it were individually recited herein.
All methods described herein can be performed in any suitable order unless otherwise indicated
herein or otherwise clearly dicted by context. For example, the determination of r
the neoepitope is a suitable disease-specific target by determining the copy number of the
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encoding gene can be determined before, after or concurrently with the determination that the
gene is a driver gene or essential gene, or can be ined before, after or concurrently with
the determination that the tope is expressed on the e of the cell or induces a
satisfactory immune response such that it would be suitable in a vaccine.
The use of any and all examples, or exemplary ge (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 ial to the practice of the invention.
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 te such disclosure by virtue of prior invention.
The present invention envisions the therapy of diseases, including immunotherapy and
radiotherapy, in particular cancer, by targeting topes (“suitable neoepitopes”) that are
only expressed in or on the diseased cells and that have the characteristic of being expressed
from genes that are less likely to be silenced by the diseased cell, such that the diseased cell is
less likely to be able to escape immune surveillance via the targeted neoepitope. The
immunotherapy can be effected by active and/or passive immunotherapeutic methods. For
example, in one embodiment an antibody or other molecule targeting ically to a
neoepitope and conjugated to a toxic agent capable of killing the cell expressing the neoepitope
can be used according to the present invention to target and kill that cell.
The invention ically is directed to the identification of such suitable neoepitopes as
disease-specific targets in immunotherapy. Once suitable neoepitopes have been identified,
they can be used in vaccines in order to induce an immune response t the tope, in
particular, by inducing and/or activating appropriate effector cells such as T cells that recognize
the identified suitable neoepitope, in particular when presented in the context of MHC, via an
appropriate antigen receptor, such as a T cell receptor or artificial T cell receptor, which results
in the death of the ed cell expressing the suitable neoepitope. Alternatively, or
onally, immune cells that recognize the identified suitable neoepitope through an
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appropriate antigen receptor can be administered, which also will result in the death of the cells
expressing the suitable neoepitope.
The immunotherapeutic approaches according to the invention include immunization with a
peptide or polypeptide containing the suitable neoepitope, ii) c acid encoding the peptide
or polypeptide containing the suitable neoepitope, iii) inant cells encoding the peptide
or polypeptide containing the suitable neoepitope, iv) recombinant viruses encoding the peptide
or polypeptide containing the neoepitope and v) antigen presenting cells pulsed with the e
or polypeptide containing the tope or transfected with nucleic acids encoding the peptide
or polypeptide. Other immunotherapeutic approaches ing to the invention include
transfer of vi) T cell receptors that ize the neoepitope, and vii) effector cells encoding
receptors (such as T cells) that recognize the neoepitope, in particular when presented in the
context of MHC.
The term "disease-specific mutation" in the context of the present invention relates to a somatic
mutation that is present in the nucleic acid of a diseased cell but absent in the nucleic acid of a
corresponding , not diseased cell. The disease can be cancer, thus, the term "tumorspecific
mutation" or r-specific mutation" relate to a somatic mutation that is present in
the nucleic acid of a tumor or cancer cell but absent in the c acid of a corresponding
normal, i.e. morous or non-cancerous, cell. The terms -specific on" and
"tumor on" and the terms "cancer-specific mutation" and "cancer mutation" are used
interchangeably herein.
As used herein, a single nucleotide polymorphism (SNP) is a site in the normal genome at which
at least one of the two alleles (maternal or paternal) has a different identity from that in the
normal genome, or with respect to, for example, a reference genome.
As used herein, a heterozygous single nucleotide polymorphism (heterozygous SNP) is d
as a site in the normal genome at which the two alleles (the maternal and paternal alleles) have
a different identity.
As used herein the term "fractional zygosity" refers to the fraction of the copy number of a gene
having a disease-specific mutation in view of the total copy number of the gene, whether the
gene has the mutation or not. For example, if there are a total of 20 copies of the gene and 10
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of the copies have the disease-specific mutation, then the fractional zygosity is 0.5. If all copies
of the gene have the e-specific mutation, then the fractional zygosity is 1. The fractional
ty can be at least 0.1, 0.2, 0.3, 0.4, 0.5, 0.6, 0.7, 0.8, 0.9, or at least 0.95. In the t
of the present invention, a higher fractional ty rather than a lower fractional zygosity is
preferred. In an embodiment, the fractional zygosity of a mutated allele that encodes an epitope,
preferably a neoepitope, is the ratio of the copy number of the mutated allele over the total
number of copies of the nucleotide site to which the mutated allele maps, e.g., in a reference
genome.
As used herein the term "clonal on" refers to the fraction of the number of diseased cells
that contain the same disease-specific mutation in the same gene and its genetic characteristics
such as copy number and fractional ty in view of the total number of diseased cells,
whether the diseased cells have the same mutation in the same gene or not. This term can also
apply to the tumor tissue in that the clonal fraction is the fraction of diseased cells in the tumor
tissue that contain the same disease-specific mutation in the same gene and its genetic
characteristics such as copy number in view of the total number of cells in the tumor tissue. For
example, in a sample ed from a tumor, where only half of the total number of tumor cells
has the same mutation in the same gene, then the clonal fraction is 0.5. The clonal fraction can
be at least 0.1, 0.2, 0.3, 0.4, 0.5, 0.6, 0.7, 0.8, 0.9, or at least 0.95. In the context of the present
invention, a higher clonal fraction rather than a lower clonal fraction is preferred. Most
preferred is a clonal fraction of 1, in which all of the diseased cells have the same diseasespecific
mutation in the same gene. "Clonal fraction", "fractional clonality" and "fractional
subclonality" are used interchangeably herein.
The term "focal amplification" refers to an amplification, or increase in copy number, of a part
of a genome, e.g., amplification of one or more genes d together on the same
chromosome, which results in a copy number of greater than 2, preferably greater than 5, 10,
, 20, 25, 50, 75, 100 for this part of the genome, provided no on event for the same part
of the genome has occurred. Thus, for the purposes of the present invention, genes that are
focally amplified in diseased cells are those genes that can have an sed copy number
ed to the wild-type copy number of 2 or the wild-type copy number of 1 for those genes
on the X and Y chromosomes in males. Focal amplification is ct from whole genome
duplication and/or amplification events.
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The term "immune response" refers to an integrated bodily response to an antigen and
preferably refers to a cellular immune se or a cellular as well as a humoral immune
response. The immune response may be protective/preventive/prophylactic and/or therapeutic.
"Inducing an immune response" may mean that there was no immune se t a
particular antigen before induction, but it may also mean that there was a n level of
immune response against a particular antigen 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 e or in a t
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.
A "cellular immune response", a "cellular response", a "cellular response against an antigen" or
a similar term is meant to include a cellular response directed to cells characterized by
presentation of an antigen with class I or class II MHC. The cellular response relates to cells
called T cells or T-lymphocytes which act as either "helpers" or "killers". The helper T cells
(also termed CD4+ T cells) play a central role by regulating the immune response and the killer
cells (also termed cytotoxic T cells, cytolytic T cells, CD8+ T cells or CTLs) kill diseased cells
such as cancer cells, preventing the production of more diseased cells. Preferably, an anti-tumor
CTL response is ated t tumor cells expressing one or more tumor expressed
ns and preferably ting such tumor sed antigens with class I MHC.
An "antigen" ing to the invention covers any substance, preferably a peptide or protein,
which 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
ic for the antigen (including cells expressing the antigen). The n or a T cell epitope
thereof is preferably presented by a cell, preferably by an antigen presenting cell which includes
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a diseased cell, in particular a cancer cell, in the context of MHC molecules, which results in
an immune response against the n (including cells expressing the antigen).
ably, 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.
According to the present invention, any suitable antigen may be used, which is a candidate for
an immune reaction, wherein the immune reaction may be both a humoral as well as a cellular
immune reaction. In the context of the present invention, the antigen is preferably presented by
a cell, preferably by an antigen presenting cell, in the context of MHC molecules, which results
in an immune on against the n. An antigen is preferably a t which
corresponds to or is derived from a naturally occurring antigen. Such naturally occurring
antigens may include or may be derived from allergens, viruses, bacteria, fungi, parasites and
other infectious agents and pathogens or an antigen may also be a tumor antigen. According to
the present invention, an antigen may correspond to a naturally occurring product, for example,
a viral protein, or a part thereof. In preferred embodiments, the n is a surface polypeptide,
i. e., a polypeptide lly displayed on the e of a cell, a pathogen, a bacterium, a virus,
a fungus, a te, an allergen, or a tumor. The antigen may elicit an immune response t
a cell, a en, a bacterium, a virus, a fungus, a te, an allergen, or a tumor.
The term “disease-associated antigen” or “disease-specific antigen” is used in it broadest sense
to refer to any antigen associated with or specific to a e. Such an antigen is a molecule
which contains epitopes that will stimulate a host's immune system to make a cellular antigenspecific
immune response and/or a l antibody response against the disease. The diseaseassociated
antigen may therefore be used for therapeutic purposes. Disease-associated antigens
are preferably associated with infection by microbes, typically microbial antigens, or associated
with cancer, typically tumors.
The term "pathogen" refers to pathogenic ical material capable of causing disease in an
organism, preferably a vertebrate organism. Pathogens include microorganisms such as
bacteria, unicellular eukaryotic organisms (protozoa), fungi, as well as viruses.
In the context of the present invention, the term "tumor n" or "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 antigen
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may be under normal conditions specifically expressed in stomach , preferably in the
gastric mucosa, in reproductive organs, e.g., in testis, in trophoblastic , 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, /.<?.. 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
ically expressed in testis and sometimes in placenta, and germ line specific antigens. In
the context of the present invention, the tumor n is preferably associated with the cell
surface of a cancer cell and is preferably not or only rarely sed in normal tissues.
Preferably, the tumor antigen or the aberrant expression of the tumor antigen identifies cancer
cells. In the context of the present invention, the tumor n that is expressed by a cancer
cell in a subject, e.g., a patient suffering from a cancer disease, is preferably a rotein in
said subject. In preferred embodiments, the tumor antigen in the context of the present invention
is expressed under normal ions 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 ures of the body which are not or only hardly ible by the
immune system. Preferably, the amino acid sequence of the tumor antigen is identical between
the tumor n which is expressed in normal tissues and the tumor n which is expressed
in cancer tissues.
According to the invention, the terms "tumor antigen", "tumor-expressed antigen", "cancer
antigen" and "cancer-expressed antigen" are equivalents and are used interchangeably herein.
The terms "epitope", "antigen peptide", "antigen epitope", "immunogenic peptide" and "MHC
binding peptide" are used hangeably herein and refer to an nic determinant in a
molecule such as an n, i.e., to a part in or fragment of an immunologically active
compound 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
preferably comprises a continuous or discontinuous portion of said n 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. According
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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" or en e". The term "major
ompatibility complex" and the abbreviation "MHC" include MHC class I and MHC class
II molecules and relate to a complex of genes which is present in all vertebrates. MHC proteins
or molecules are important for ing 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 d 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.
Preferred such immunogenic ns bind to an MHC class I or class II molecule. As used
herein, an immunogenic portion is said to "bind to" an MHC class I or class II molecule if such
binding is able using any assay known in the art. The term "MHC binding peptide" s
to a peptide which binds to an MHC class I and/or an MHC class II molecule. In the case of
class I MHC/peptide complexes, the binding peptides are typically 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 10-25 amino acids long and are in particular IS
IS amino acids long, whereas longer and shorter peptides may be effective.
As used herein the term "neoepitope" refers to an epitope that is not t in a reference such
as a normal non-cancerous or germline cell but is found in diseased cells, such as cancer cells.
This es, 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 neoepitope. Moreover, a neoepitope
may not only be specific to the diseased cells but also can be specific to the patient having the
disease. Since neoepitopes and suitable neoepitopes which are fied by the methods of the
invention are subsets of epitopes, disclosure herein relating to epitopes in general as
immunological targets applies equally to topes and suitable neoepitopes.
In one ularly preferred embodiment of the invention, an epitope or tope is a T cell
epitope. As used herein, the term "T cell epitope" refers to a peptide which binds to a MHC
molecule in a uration recognized by a T cell receptor. Typically, T cell epitopes are
presented on the surface of an antigen-presenting cell.
As used , the term "predicting immunogenic amino acid modifications" refers to a
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prediction whether a peptide comprising such amino acid modification will be immunogenic
and thus useful as epitope, in particular T cell epitope, in vaccination.
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 e or T cell e is produced following suitable processing.
T cell epitopes may be modified at one or more residues that are not essential for TCR
recognition or for g to MHC. Such modified T cell epitopes may be considered
immunologically equivalent.
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 e/MHC-complex.
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 1 and/or class II presented peptide.
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 n or cells characterized by sion 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 ar response against a cell characterized by presentation
of an antigen with class I MHC and ably is capable of stimulating an antigen-responsive
cytotoxic hocyte (CTL).
In some embodiments the antigen is a self-antigen, particularly a tumor antigen. Tumor antigens
and their determination are known to the skilled person.
The term "immunogenicity" s to the relative effectivity to induce an immune response that
is ably associated with therapeutic treatments, such as treatments against cancers. As used
herein, the term "immunogenic" relates to the property of having genicity. For example,
the term "immunogenic modification" when used in the context of a peptide, polypeptide or
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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 nonmodified
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
According to the invention, the term "immunogenicity" or "immunogenic" preferably relates to
the relative ivity to induce a biologically relevant immune se, in particular an
immune se which is useful for vaccination. Thus, in one preferred embodiment, an amino
acid cation 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.
"Antigen processing" or "processing" refers to the degradation of a polypeptide or antigen into
procession products, which are fragments of said polypeptide or antigen (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.
"Antigen presenting cells" (APC) are cells which present e fragments of protein antigens
in association with MHC les on their cell surface. Some APCs may activate antigen
specific T cells.
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 izes and
interacts with the antigen-class II MHC le complex on the membrane of the npresenting
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 ng
feature of professional antigen-presenting cells.
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 n-presenting
cells, macrophages, B-cells, and certain activated epithelial cells.
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Dendritic cells (DCs) are leukocyte populations that t 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 rs of immune responses and the activation of these cells is
a critical step for the induction of anti-tumor 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 lature 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 Fey 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 sible 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 y caused by biomolecules
with microbial features ed by innate receptors (bacterial DNA, viral RNA, endotoxin,
etc.), pro-inflammatory cytokines (TNF, IL-1, IFNs), ligation of CD40 on the dendritic cell
e 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
colony-stimulating factor (GM-CSF) and tumor necrosis factor alpha.
granulocyte-macrophage
Non-professional antigen-presenting cells do not tutively s 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 IFNy.
"Antigen presenting cells" can be loaded with MHC class I presented peptides by ucing
the cells with nucleic acid, preferably RNA, ng a peptide or polypeptide comprising the
e to be presented, e.g. a nucleic acid encoding the n.
In some embodiments, a pharmaceutical composition of the ion sing a gene
delivery vehicle that targets a dendritic or other antigen presenting cell may be administered to
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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 ch bed by Mahvi et al. Immunology
and cell Biology 75:456-460, 1997.
The term "antigen presenting cell" also includes target cells.
"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 or an antigen epitope, 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.
The term "portion" refers to a on. 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. ably, 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 on 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 e, a discontinuous on of an amino acid ce 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 ses at least 5 continuous amino acids, at least 10
continuous amino acids, ably at least 20 continuous amino acids, preferably at least 30
continuous amino acids of the amino acid sequence.
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 n, 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 ce preferably comprises, preferably consists of at least
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%, 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.
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 n or a cell characterized by presentation of an antigen or an antigen
peptide derived from an antigen 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, l killer cells, neutrophils,
macrophages, and tic cells. Preferably, in the context of the present invention,
"immunoreactive cells" are T cells, preferably CD4+ and/or CD8+ T cells.
Preferably, an "immunoreactive cell" recognizes an antigen or an antigen e derived from
an antigen with some degree of specificity, in ular if presented in the context of MHC
molecules such as on the surface of antigen presenting cells or diseased cells such as cancer
cells. ably, said recognition enables the cell that recognizes an antigen or an antigen
e d from said antigen to be responsive or reactive. If the cell is a helper T cell (CD4+
T cell) bearing ors that recognize an antigen or an antigen peptide derived from an antigen
in the context of MHC class II molecules such responsiveness or vity may involve the
release of cytokines and/or the activation of CD8+ 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 in-mediated cell lysis. CTL
responsiveness may include sustained calcium flux, cell division, production of cytokines such
as IFN-y and TNF-a, up-regulation of activation markers such as CD44 and CD69, and ic
cytolytic killing of n expressing target cells. CTL responsiveness may also be determined
using an artificial reporter that accurately indicates CTL siveness. Such CTL that
recognizes an antigen or an antigen peptide derived from an antigen and are responsive or
reactive are also termed "antigen-responsive CTL" herein. If the cell is a B cell such
responsiveness may e the release of immunoglobulins.
The terms "T cell" and "T lymphocyte" are used interchangeably herein and include T helper
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cells (CD4+ T cells) and cytotoxic T cells (CTLs, CD8+ T cells) which comprise cytolytic T
cells.
T cells belong to a group of white blood cells known as lymphocytes, and play a l role in
cell-mediated ty. They can be distinguished from other lymphocyte types, such as B
cells and natural killer cells by the presence of a l 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 ct function.
T helper cells assist other white blood cells in immunologic processes, including tion 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 e 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.
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 CDS
glycoprotein at their surface. These cells recognize their targets by binding to n associated
with MHC class I, which is present on the surface of nearly every cell of the body.
A majority of T cells have a T cell receptor (TCR) ng 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 (TCRa and TCRP) genes and are called a- and
P-TCR chains. y8 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 y8 T cells, the TCR is made up
of one y-chain and one 8-chain. This group of T cells is much less common (2% of total T cells)
than the aP T cells.
According to the invention, the term "antigen receptor" includes naturally occurring receptors
such as T cell receptor as well as engineered receptors, which confer an arbitrary icity
such as the specificity of a monoclonal dy onto an immune or cell such as a T cell.
In this way, a large number of antigen-specific T cells can be generated for adoptive cell
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transfer. Thus, an n receptor according to the invention may be present on T cells, e.g.
instead of or in addition to the T cell's own T cell receptor. Such T cells do not necessarily
require sing and tation of an antigen for recognition of the target cell but rather
may recognize preferably with specificity any antigen t on a target cell. Preferably, said
antigen receptor is expressed on the surface of the cells. For the purpose of the present
invention, T cells comprising an antigen receptor are comprised by the term "T cell" as used
. Specifically, according to the invention, the term "antigen receptor" includes artificial
receptors comprising a single molecule or a complex of molecules which recognize, i.e. bind
to, a target structure (e.g. an antigen) on a target cell such as a cancer cell (e.g. by binding of an
antigen binding site or antigen binding domain to an n expressed on the surface of the
target cell) and may confer specificity onto an immune effector cell such as a T cell expressing
said antigen receptor on the cell surface. Preferably, recognition of the target structure by an
antigen receptor results in activation of an immune effector cell expressing said antigen
receptor. An antigen receptor may comprise one or more protein units said protein units
comprising one or more domains as described herein. According to the ion an "antigen
receptor" also may be a ric antigen receptor (CAR)", "chimeric T cell receptor" or
"artificial T cell receptor".
An n can be recognized by an antigen receptor through any antigen recognition domains
(herein also referred to simply as "domains") able to form an antigen binding site such as
through antigen-binding portions of dies and T cell receptors which may reside on the
same or different peptide . In one embodiment, the two domains forming an antigen
binding site are derived from an immunoglobulin. In one embodiment, the two domains forming
an antigen binding site are derived from a T cell receptor. Particularly preferred are antibody
variable domains, such as single-chain le fragments (scFv) derived from monoclonal
antibodies and T cell or variable domains, in particular TCR alpha and beta single chains.
In fact almost anything that binds a given target with high affinity can be used as an antigen
recognition domain.
The first signal in tion of T cells is provided by binding of the T cell or to a short
peptide presented by the major histocompatibility complex (MHC) on another cell. This ensures
that only a T cell with a TCR specific to that peptide is activated. The r cell is usually a
professional antigen presenting cell (APC), usually a dendritic cell in the case of naive
responses, gh B cells and macrophages can be important APCs. The peptides presented
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to CD8+ T cells by MHC class I molecules are typically 8-10 amino acids in length; the peptides
presented to CD4+ T cells by MHC class II molecules are typically longer, as the ends of the
binding cleft of the MHC class II molecule are open.
According to the present invention, a molecule is capable of binding to a target if it has a
icant affinity for said predetermined target and binds to said ermined target in
standard assays. "Affinity" or "binding affinity" is often measured by equilibrium dissociation
constant (Kd). 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.
xic T lymphocytes may be generated in vivo by incorporation of an antigen or an antigen
peptide into antigen-presenting cells in vivo. The antigen or antigen peptide may be represented
as protein, as DNA (e.g. within a ) 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 ular, 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 el 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.
ic activation of CD4+ or CD8+ T cells may be ed 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 ic T cell activation is the
detection of the generation of cytolytic activity.
By "cell characterized by presentation of an antigen" or "cell presenting an antigen" or r
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 les, in particular MHC Class I
molecules. Similarly, the terms "disease characterized by tation of an antigen" denotes a
e involving cells characterized by presentation of an n, in particular with class I
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MHC. Presentation of an antigen by a cell maybe effected by transfecting the cell with a nucleic
acid such as RNA encoding the n.
By "fragment of an n which is ted" 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.
The term "immunologically equivalent" means that the immunologically equivalent molecule
such as the immunologically equivalent amino acid sequence exhibits the same or ially
the same immunological properties and/or exerts the same or essentially the same
immunological s, e.g., with respect to the type of the immunological effect such as
ion of a humoral and/or cellular immune response, the strength and/or duration of the
induced immune on, 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 ties of a peptide used for immunization. For example, an
amino acid sequence is immunologically equivalent to a reference amino acid ce if said
amino acid sequence when exposed to the immune system of a subject induces an immune
reaction having a specificity of ng with the reference amino acid sequence.
The term "immune effector functions" in the context of the present ion 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 t invention are T cell mediated effector functions. Such
functions comprise in the case of a helper T cell (CD4+ T cell) the recognition of an antigen or
an antigen peptide derived from an antigen in the context of MHC class II molecules by T cell
receptors, the release of cytokines and/or the activation of CD8+ lymphocytes (CTLs) and/or
B-cells, and in the case of CTL the recognition of an n or an antigen peptide derived from
an antigen 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,
tion of cytokines such as IFN-y and TNF-a, and specific cytolytic killing of antigen
expressing target cells.
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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 ons, 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 ng microorganisms) to a T
cell.
The MHC region is divided into three subgroups, class I, class II, and class III. MHC class I
proteins n an a-chain and (32-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 n-presenting cells, MHC class II proteins contain a- and (3-chains
and they present n fragments to T-helper cells. MHC class III region encodes for other
immune components, such as complement components and some that encode nes.
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).
As used herein, the term "haplotype" refers to the HLA alleles found on one chromosome and
the proteins d thereby. Haplotype may also refer to the allele t 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-DQA1, HLADQB1
, HLA-DPA1, HLA-DPB1, HLA-DMA, B, A, and HLA-DOB for
class II. The terms "HLA allele" and "MHC allele" are used interchangeably herein.
The MHCs exhibit extreme rphism. Within the human population there are, at each
genetic locus, a great number of haplotypes comprising distinct s. Different polymorphic
MHC alleles, of both class I and class II, have different peptide icities in that each allele
encodes proteins that bind peptides exhibiting particular sequence patterns.
In the context of the present invention, a MHC molecule is preferably an HLA molecule.
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In the context of the present invention, the term "MHC binding peptide" includes MHC class I
and/or class II binding peptides or peptides that can be sed 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 gh longer or r 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 es may be effective.
An "antigen e" preferably relates to a portion or fragment of an antigen which is e
of ating an immune response, preferably a cellular response against the antigen or cells
characterized by expression of the n and preferably by presentation of the antigen such
as diseased cells, in particular cancer cells. Preferably, an antigen e is capable of
stimulating a cellular response against a cell characterized by tation of an antigen with
class I MHC and preferably is capable of stimulating an antigen-responsive cytotoxic T-
lymphocyte (CTL). Preferably, the antigen peptides are MHC class I and/or class II presented
peptides or can be processed to produce MHC class I and/or class II presented peptides.
Preferably, the antigen peptides comprise 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. ably, an antigen peptide comprises
an amino acid sequence substantially corresponding to the amino acid sequence of such
nt and is processed to produce such fragment, i.e., an MHC class I and/or class II
presented peptide derived from an antigen.
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 7-20 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.
If a peptide is part of a larger entity comprising additional ces, e.g. of a vaccine sequence
or polypeptide, and is to be presented following processing, in particular following cleavage,
the peptide ed by processing has a length which is suitable for binding to an MHC
molecule, in particular a class I MHC molecule, and ably is 7-20 amino acids in length,
more preferably 7-12 amino acids in length, more preferably 8-11 amino acids in length, in
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particular 9 or 10 amino acids in length. Preferably, the ce of the e which is to be
presented following processing is derived from the amino acid sequence of an antigen, i.e., its
sequence substantially corresponds and is preferably completely identical to a fragment of an
antigen. Thus, an MHC binding peptide comprises a sequence which substantially corresponds
and is preferably completely identical to a fragment of an antigen.
Peptides having amino acid sequences ntially corresponding to a sequence of a peptide
which is presented by the class I MHC may differ at one or more residues that are not essential
for TCR recognition of the peptide as presented by the class I MHC, or for peptide binding to
MHC. Such substantially corresponding peptides are also capable of stimulating an antigenresponsive
CTL and may be considered immunologically lent. Peptides having amino
acid sequences differing from a presented peptide at residues that do not affect TCR recognition
but improve the stability of binding to MHC may improve the immunogenicity of the antigen
peptide, and may be ed to herein as ized e". Using existing dge about
which of these residues may be more likely to affect binding either to the MHC or to the TCR,
a rational approach to the design of ntially corresponding peptides may be employed.
Resulting peptides that are functional are contemplated as antigen peptides.
An antigen peptide when presented by MHC should be recognizable by a T cell receptor.
Preferably, the antigen peptide if recognized by a T cell or is able to induce in the presence
of appropriate co-stimulatory signals, clonal expansion of the T cell carrying the T cell receptor
specifically izing the antigen peptide. Preferably, antigen peptides, in particular if
presented in the context of MHC molecules, are capable of stimulating an immune response,
preferably a cellular response against the antigen from which they are derived or cells
characterized by expression of the antigen and preferably characterized by presentation of the
antigen. ably, an antigen peptide is capable of ating a cellular response against a
cell characterized by presentation of the antigen with class I MHC and preferably is capable of
stimulating an antigen-responsive CTL. Such cell preferably is a target cell.
The term e" relates to the total amount of genetic information in the chromosomes of
an sm or a cell.
The term " 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
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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 et al,
2008, PLoS Gen., 4(8): 1-15).
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 or RNAseq means the set of all RNA molecules
produced in one cell, a population of cells, ably a tion of cancer cells, or all cells
of a given individual at a certain time point.
A "nucleic acid" is preferably deoxyribonucleic acid (DNA) or ribonucleic acid (RNA), more
preferably RNA, most preferably in vitro ribed RNA (IVT RNA) or synthetic RNA.
Nucleic acids include genomic DNA, cDNA, mRNA, recombinantly produced and chemically
synthesized molecules. A nucleic acid may be present as a single-stranded or double-stranded
and linear or covalently circularly closed molecule. A nucleic acid can be ed. The term
"isolated nucleic acid" means 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 e, 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.
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.
The term "mutation" refers to a change of or ence in the c acid sequence (nucleotide
substitution, addition or on) in the diseased genome compared to a reference, and
preferably a matched normal . 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 ) cause cancer or other diseases. ably a mutation is a
non-synonymous mutation. The term "non-synonymous mutation" refers to a mutation,
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preferably a nucleotide substitution, which s in an amino acid change such as an amino
acid substitution in the translation product, which preferably results in the formation of a
neoepitope.
The term “single tide variant/variation” (SNV) refers to a difference in the nucleic acid
sequence at a particular site (allele) when comparing a genome from a diseased cell, such as a
tumor cell, and a genome of a preferably matched (corresponding) normal, non-diseased cell or
a reference genome. As used herein, the tenn mutation preferably encompasses a SNV.
A copy number variation (CNV) event in the diseased (tumor) genome is a somatic copy
number variation event occurring only in diseased cells, and defined as a change in the number
of copies of the maternal and/or paternal s of a region of the diseased (tumor) genome
with respect to a matched nonnal , where the alternation preferably affects a region of
the genome ng approximately 1 kb or longer.
The term "mutation" includes point mutations, indels, fusions, chromothripsis and RNA edits.
The term "indel" describes a special mutation class, defined as a mutation ing in a
colocalized insertion and deletion and a net gain or loss in tides. 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.
Fusions can generate hybrid genes formed from two previously separate genes. It can occur as
the result of a translocation, titial deletion, or chromosomal inversion. Often, fusion genes
are nes. 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 y 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.
The term "chromothripsis" refers to a genetic enon by which specific regions of the
genome are shattered and then stitched together via a single devastating event.
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The term “RNA edit“ or “RNA editing” refers to lar processes in which the information
content in an RNA molecule is d through a chemical change in the base makeup. RNA
editing es 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 d protein so that it
differs from that predicted by the genomic DNA sequence.
The term "cancer mutation signature" refers to a set of mutations which are present in cancer
cells when compared to non-cancerous reference cells.
A "reference" in the context of the present invention may be used to correlate and compare the
results obtained from a tumor specimen. Typically the "reference" maybe obtained on the basis
of one or more normal specimens, in particular ens which are not affected by a cancer
disease, either obtained from a patient or one or more different individuals, preferably y
individuals, in particular individuals of the same species. A "reference" can be determined
empirically by testing a sufficiently large number of normal specimens.
The term “reference genome” refers to a genome providing a coordinate system for the normal
genome and the diseased genome. A reference genome is used for mapping reads and providing
a coordinate system for the nonnal genome and the tumor , n the coordinate
system allows for the ion of the chromosome number, a nucleotide position in the
chromosome, as well as directionality of the read. A reference genome can be based on the
genome of one or more members from the same species as the subject providing the diseased
sample, or can be based on the normal genome of the subject (a matched genome).
Any suitable cing method can be used in the context of the present invention to identify
disease-specific mutations, Next Generation Sequencing (NGS) technologies being preferred,
and optionally in ation with SNP arrays to obtain absolute copy number information.
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 ion 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 el
along the entire genome by breaking the entire genome into small pieces. Such NGS
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technologies (also known as massively parallel sequencing technologies) are able to deliver
nucleic acid sequence information of a whole genome, exome, transcriptome (all ribed
sequences of a genome) or methylome (all methylated sequences of a genome) in very short
time periods, e.g. within 1 -2 weeks, ably within 1 -7 days or most preferably within less
than 24 hours and allow, in principle, single cell sequencing approaches. Multiple NGS
rms which are cially available or which are mentioned in the literature can be
used in the context of the present ion e.g. those described in detail in Zhang et a/., 2011,
The impact of next-generation cing 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 suchNGS technologies/platforms are
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, Connecticut), first described in Ronaghi et al, 1998, A sequencing
method based on real-time pyrophosphate, Science 281:363-365. 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 ication. During the pyrosequencing process, light d from
phosphate molecules during nucleotide incorporation is recorded as the polymerase
synthesizes the DNA strand.
2) The sequencing-by-synthesis approaches developed by Solexa (now part of Illumina
Inc., San Diego, California) which is based on reversible dye-tenninators and
ented e.g. in the na/Solexa Genome Analyzer™ and in the na HiSeq
2000 Genome Analyzer™. In this technology, all four nucleotides are added
simultaneously into oligo-primed cluster nts in flow-cell channels along with
DNA polymerase. Bridge amplification extends r strands with all four
fluorescently labeled nucleotides for sequencing.
3) Sequencing-by-ligation approaches, e.g. implemented in the SOLid™ platform of
Applied Biosystems (now Life Technologies ation, Carlsbad, California). 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 on. 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™ G.007
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rm of Dover Systems (Salem, New Hampshire) also employs a sequencing-byligation
approach by using a randomly arrayed, bead-based, emulsion PCR to amplify
DNA fragments for parallel sequencing.
4) Single-molecule sequencing technologies such as e.g. implemented in the PacBio RS
system of Pacific ences (Menlo Park, California) or in the HeliScope™ platform
of Helicos Biosciences (Cambridge, Massachusetts). 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 ive fluorescence detection system to directly
detect each nucleotide as it is synthesized. A r ch based on fluorescence
resonance energy transfer (FRET) has been developed from Visigen Biotechnology
on, Texas). Other scence-based single-molecule techniques are from U.S.
Genomics (GeneEngine™) and Genovoxx ne™).
) 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
le on a single strand during replication. miting 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™) platforms developed by Nabsys (Providence, Rhode Island), and the
proprietary ligase-based DNA sequencing platform with DNA nanoball (DNB)
technology called combinatorial probe-anchor ligation (cPAL™).
6) Electron microscopy based technologies for single-molecule sequencing, e.g. those
developed by peed Genomics vale, California) and n Molecular
(Redwood City, California)
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, California) 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.
In one embodiment, r a e-specific mutation occurred can be determined by a
method relating to determining that a site in the normal genome is consistent with a
homozygous genotype as ted by a normal allele and three noise alleles, and an ideal noise
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distribution and declaring a mutation where the corresponding site in the tumor genome is
inconsistent with the homozygous genotype and an ideal noise distribution, wherein reads are
consistent with an ideal noise distribution if the reads map to each of the noise alleles with a
probability of one third of an error rate per base, as disclosed in the International PCX Patent
ation entitled “Highly Accurate on Detection, In Particular for Personalized
Therapeutics” filed on even date herewith, the disclosure of which is incorporated by reference
herein in its entirety.
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. Nonnal non-mutated genomic DNA
or RNA can be extracted from normal, somatic tissue, however ne cells are preferred in
the context of the present invention. Germline DNA or RNA is extracted from peripheral blood
clear 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.
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 ction with the present invention. Many of these s (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 etal, 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 e, Illumina Inc. (San Diego, California) offers the TruSeq TM DNA Sample
Preparation Kit and the Exome Enrichment Kit TruSeq™ Exome Enrichment Kit.
In order to reduce the number of false positive findings in detecting cancer specific somatic
mutations or ce differences when ing e.g. the sequence of a tumor sample to the
sequence of a reference sample such as the ce of a germ line sample it is preferred to
ine 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 onally, the sequence of a tumor sample is
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determined twice, three times or more. It may also be possible to determine the ce 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 s of a sample should generate identical
results and any detected mutation in this "same vs. same comparison" is a false positive. In
ular, to determine the false discovery rate for somatic mutation detection in a tumor
sample relative to a reference , a technical repeat of the reference sample can be used as
a reference to estimate the number of false positives. rmore, various quality related
metrics (e.g. coverage or SNP quality) may be combined into a single quality score using a
machine learning approach. Optionally, for a given somatic variation all other variations with
an exceeding y score may be counted, which enables a ranking of all variations in a
dataset.
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
ition of a (3-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, tic RNA, and recombinantly generated RNA such as modified RNA which
differs from naturally occurring RNA by addition, deletion, tution and/or alteration of one
or more nucleotides. Such alterations can include addition of non-nucleotide al, such as
to the end(s) of a RNA or internally, for example at one or more nucleotides of the RNA.
Nucleotides in RNA les can also comprise andard nucleotides, such as urally
occurring nucleotides or chemically synthesized nucleotides or deoxynucleotides.
These altered RNAs can be referred to as analogs or analogs of naturally-occurring RNA.
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 ptide. Typically, an mRNA comprises a S’-UTR, a protein
coding region, and a S’-UTR. mRNA only possesses d ife in cells and in vitro. In
the context of the present invention, mRNA may be generated by in vitro transcription from a
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DNA template. The in vitro transcription methodology is known to the skilled person. For
example, there is a y of in vitro transcription kits commercially available.
The ity and translation ency 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 incorporated herein by reference. In order to
increase expression of the RNA used in embodiments of 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.
The term "modification" in the context of the RNA used in the present invention includes any
modification of an RNA which is not naturally t in said RNA.
In one embodiment of the invention, the RNA used according to the invention does not have
ed 5'-triphosphates. Removal of such uncapped phosphates can be achieved by
ng RNA with a phosphatase.
The RNA according to the invention may have ed ribonucleotides in order to increase its
stability and/or se 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, ably
completely, for uridine.
In one embodiment, the term "modification" s 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 ine 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 " refers to a naturally occurring RNA 5’-cap, preferably
to the 7-methyl guanosine cap (m7G). 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
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ability to stabilize RNA and/or enhance translation of RNA if ed thereto, preferably in
vivo and/or in a cell.
Providing an RNA with a 5’-cap or 5’-cap analog may be achieved by in vitro ription of
a DNA template in presence of said 5’-cap or 5’-cap analog, wherein said 5’-cap is cotranscriptionally
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 posttranscriptionally
using capping s, for example, capping enzymes of vaccinia virus.
The RNA may comprise further cations. 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 s (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, alphal-globin, beta-globin, preferably beta-globin,
more preferably human beta-globin.
RNA having an unmasked poly-A sequence is ated more ently than RNA having a
masked poly-A sequence. The term "poly(A) tail" or "poly-A ce" relates to a sequence
of adenyl (A) residues which typically is d 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 d
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
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
ity and/or expression of the RNA used according to the invention, the poly-A sequence
can be unmasked.
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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 s may be autologous or heterologous to the RNA into which they are
uced. In one particular embodiment the 3’-non translated region is derived from the
human P-globin gene.
A combination of the above described modifications, i.e. incorporation of a poly-A sequence,
ing of a poly-A ce and incorporation of one or more 3’-non translated regions,
has a synergistic influence on the stability of RNA and increase in translation efficiency.
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 tive for the stability of said
RNA. The half-life of RNA may influence the "duration of sion" of the RNA. It can be
expected that RNA having a long half-life will be expressed for an ed time period.
Of course, if it is desired to decrease stability and/or translation efficiency of RNA, it is possible
to modify RNA so as to interfere with the on of elements as described above increasing
the stability and/or translation efficiency of RNA.
The term "expression" is used in its most general meaning and comprises the production of
RNA and/or peptides or polypeptides, e.g. by transcription and/or translation. With respect to
RNA, the term "expression" or "translation" relates in particular to the production of peptides
or polypeptides. It also comprises partial sion of nucleic acids. Moreover, expression can
be transient or stable.
The term expression also includes an "aberrant expression" or "abnormal expression".
"Aberrant expression" or "abnormal expression" means that expression is altered, preferably
increased, compared to a nce, 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, sion is only found in a diseased , while
expression in a healthy tissue is repressed.
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The term "specifically expressed" means that a protein is essentially only expressed in a specific
tissue or organ. For e, a tumor antigen specifically expressed in gastric mucosa means
that said protein is primarily sed 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 , 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 e, if a tumor antigen is expressed under normal conditions
preferably to an approximately equal extent in lung and stomach, said tumor antigen is
specifically sed in lung and stomach.
In the t of the t invention, the term "transcription" relates to a s, 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 ated as transcription vectors and are
encompassed by the term "vector". The RNA used in the present invention preferably is in vitro
transcribed RNA (IVT-RNA) and may be ed by in vitro transcription of an riate
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 ription is controlled by a T7 or SP6 promoter. A
DNA template for in vitro ription 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.
The term lation" 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 or
polypeptide.
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Expression control sequences or regulatory sequences, which in the t of the present
invention may be linked functionally with a nucleic acid, can be homologous or heterologous
with respect to the nucleic acid. A coding ce 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 ated 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.
The term ssion control sequence" or "regulatory sequence" comprises, in the context of
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, the regulatory sequences can be controlled. The precise ure of regulatory
sequences can vary depending on the species or depending on the cell type, but generally
comprises 5’-untranscribed and 5’- and ranslated sequences, which are involved in the
initiation of ription or ation, 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 riptional control of the functionally bound
gene. Regulatory sequences can also comprise enhancer sequences or upstream activator
sequences.
Preferably, the 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 ription of an appropriate DNA template.
Terms such as "RNA capable of expressing" and "RNA ng" are used interchangeably
herein and with respect to a ular peptide or polypeptide mean that the RNA, if present in
the appropriate environment, preferably within a cell, can be sed to produce said peptide
or polypeptide. Preferably, RNA is able to interact with the cellular translation machinery to
provide the e or polypeptide it is capable of expressing.
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Terms such as "transferring", "introducing" or fecting" are used interchangeably herein
and relate to the introduction of nucleic acids, in ular exogenous or logous 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 sion for extended time periods.
Cells can be transfected with any carriers with which RNA can be associated, e.g. by forming
xes 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. Useful carriers e,
for example, lipid-containing carriers such as ic lipids, liposomes, in particular cationic
liposomes, and micelles, and nanoparticles. Cationic lipids may form complexes with
vely charged nucleic acids. Any cationic lipid may be used.
Preferably, the introduction of RNA which s a peptide or polypeptide into a cell, in
particular into a cell present in vivo, results in expression of said peptide or ptide in the
cell. In ular 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 e 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.
The term "cell" or "host cell" ably 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 e of carrying out its
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normal metabolic functions. Preferably said term relates to any cell which can be ormed
or transfected with an exogenous nucleic acid. The term "cell" includes prokaryotic cells (e.g.,
E. coli) or eukaryotic cells (e.g., tic 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 sed 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 nocytes, 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.
A cell which comprises a nucleic acid le preferably expresses the peptide or polypeptide
encoded by the nucleic acid.
The term "clonal ion" 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. ably, clonal expansion leads to
differentiation of the lymphocytes.
Tenns such as "reducing" or iting" relate to the ability to cause an overall decrease,
preferably of 5% or greater, 10% or r, 20% or greater, more preferably of 50% or greater,
and most preferably of 75% or greater, in the level. The tenn "inhibit" or similar phrases
includes a complete or essentially te tion, i.e. a reduction to zero or essentially to
zero.
Terms such as "increasing", "enhancing", "promoting" or "prolonging" preferably relate to an
increase, enhancement, ion or prolongation by about at least 10%, preferably at least
%, 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, ement, 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.
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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, ably 16 more, preferably 21 or more and
up to preferably 8, 10, 20, 30, 40 or 50, in particular 100 amino acids joined ntly by
peptide bonds. The term "polypeptide" or "protein" refers to large peptides, ably to
peptides with more than 100 amino acid residues, but in general the terms "peptide",
eptide" and "protein" are synonyms and are used interchangeably herein. According to
the invention, the tenn ication" or "sequence change" 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, ptide or
protein. The term includes amino acid insertion variants, amino acid addition variants, amino
acid deletion variants and amino acid substitution ts, preferably amino acid substitution
variants. All these sequence changes according to the invention may potentially create new
epitopes.
Amino acid ion variants comprise insertions of single or two or more amino acids in a
ular amino acid ce.
Amino acid addition variants comprise amino- and/or carboxy-tenninal fusions of one or more
amino acids, such as 1, 2, 3, 4 or 5, or more amino acids.
Amino acid deletion variants are characterized by the l of one or more amino acids from
the sequence, such as by removal of 1, 2, 3, 4 or 5, or more amino acids.
Amino acid substitution variants are characterized by at least one residue in the ce being
removed and another residue being inserted in its place.
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.
The term "derived" means according to the invention that a particular entity, in particular a
ular peptide sequence, is present in the object from which it is derived. In the case of
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amino acid sequences, especially particular sequence s, "derived" in ular means that
the nt amino acid ce is derived from an amino acid sequence in which it is present.
The 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 n and
presenting an antigen peptide. Particularly preferred es are cancer diseases. The agents,
compositions and methods described herein may also be used for immunization or vaccination
to prevent a e described herein.
One such agent is a vaccine such as a cancer vaccine ed on the basis of suitable
neoepitopes that resist immune escape identified by the methods of the present ion.
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 dual cancer patient.
The cancer vaccines provided according to the invention when administered to a patent provide
one or more T cell es 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 ar response, preferably cytotoxic T cell activity, against a cancer
disease characterized by presentation of one or more tumor-associated neoantigens with class I
MHC. Since a vaccine provided herein will target cancer specific mutations it will be specific
for the patient's tumor.
In the context of the present invention, a vaccine s to a vaccine which when administered
to a patient preferably provides one or more T cell es (neoepitopes, suitable neoepitopes,
combination of suitable neoepitopes identified herein), 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
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modifications or modified peptides predicted as being suitable epitopes. 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 MHC and thus, the patient's tumor, preferably the primary
tumor as well as tumor metastases, expressing antigens from which the T cell epitopes are
d and ting the same epitopes on the surface of the tumor cells.
The methods of the invention may comprise the further step of determining the usability of the
identified amino acid modifications or modified es containing a suitable neoepitope
identified herein for cancer vaccination. Thus further steps can involve one or more of the
following: (i) assessing whether the cations are located in known or ted 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 ted epitopes, and (iii) in vitro testing
whether the envisaged ed epitopes, in particular when present in their natural ce
context, e.g. when flanked by amino acid sequences also flanking said es in the naturally
occurring protein, and when sed in n presenting cells are able to stimulate T cells
such as T cells of the patient having the desired specificity. Such ng 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 e ce N-
terminally and/or C-terminally.
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 ed for their usability in the respective vaccine to be provided. In a red
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.
The epitopes identified according to the invention and provided in a vaccine are preferably
present in the form of a polypeptide comprising said epitopes (neoepitopes, suitable
neoepitopes, neoepitopes found in a combination of suitable topes identified herein) such
as a polyepitopic polypeptide or a nucleic acid, in particular RNA, encoding said polypeptide.
Furthermore, the epitopes may be present in the polypeptide in the form of a vaccine sequence,
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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
or up to 30 amino acids and may flank the epitope sequence N-terminally and/or C-
tenninally. 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 ment, the epitopes and/or vaccine sequences are lined up in the polypeptide headto-tail.
In one embodiment, the epitopes/suitable neoepitopes identified herein and/or vaccine
sequences are spaced by linkers, in particular neutral s. The term "linker" used in the
context of the present invention relates to a peptide added n two e 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
s steric nce between the two peptide domains, is well ated, 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
epitopes like those generated from the on suture between adjacent 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. rmore, glycine was
observed to inhibit a strong binding in MHC binding groove positions ado et al., 1993,
J. Immunol. 151(7):3569-75). Schlessinger et al., 2005, Proteins 115-26 had found that
amino acids glycine and serine included in an amino acid sequence result in a more flexible
n that is more efficiently translated and processed by the proteasome, enabling better
access to the encoded epitopes. The linker each may comprise 3 or more, 6 or more, 9 or more,
or more, 15 or more, 20 or more and ably 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 e and serine. In one embodiment, the linker
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ses the amino acid sequence (GGS)a(GSS)b(GGG)c(SSG)d(GSG)e wherein a, b, c, d and
e is independently a number ed from 0, 1,2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16,
17,18,19, or 20 and n a + b + c + d + eare different from 0 and preferably are 2 or more,
3 or more, 4 or more or 5 or more. In one ment, the linker comprises a sequence as
described herein including the linker sequences described in the examples such as the sequence
GGSGGGGSG.
In one particularly preferred embodiment, a polypeptide incorporating one or more suitable
neoepitopes identified by the methods herein, such as a polyepitopic polypeptide, 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
ting 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 ribed or synthetic RNA, which may be
expressed in cells of a patient such as n ting cells to produce the one or more
polypeptides. In the case of an administration of more than one multiepitopic polypeptide the
suitable neoepitopes provided by the different pitopic polypeptides may be different or
partially overlapping. Once present in cells of a patient such as n presenting cells the
ptide according to the invention is processed to produce the suitable neoepitopes
identified according to the invention. Administration of a e provided according to the
invention may provide MHC class II-presented epitopes that are capable of eliciting a CD4+
helper T cell response against cells expressing ns from which the MHC presented
epitopes are derived. Alternatively or additionally, administration of a vaccine provided
according to the invention may provide MHC class I-presented neoepitopes that are capable of
eliciting a CD 8+ T cell response against cells expressing antigens from which the MHC
presented neoepitopes are derived. Furthermore, administration of a vaccine provided
according to the invention may provide one or more neoepitopes (including known neoepitopes
and suitable neoepitopes identified ing 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 ic
immune response. In one embodiment, administration of a vaccine provided ing to the
invention provides neoepitopes that are MHC class II-presented epitopes and/or are e of
eliciting a CD4+ helper T cell response against cells expressing antigens from which the MHC
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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 ted epitopes are derived.
In one embodiment, the epitopes not containing cancer-specific somatic mutations are derived
from a tumor antigen. In one embodiment, the neoepitopes and epitopes not containing cancerspecific
somatic mutations have a istic 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.
The vaccine provided according to the invention may be a inant e.
Another type of agent is an immune cell, such as a T cell expressing a T cell receptor, or a T
cell recombinantly expressing a T cell receptor, or expressing an artificial or chimeric T cell
receptor (CAR), which receptor is ed to an antigen, e.g., a le neoepitope identified
by the methods of the t invention as a suitable disease-specific target, preferably where
such neoepitope is expressed on the surface of a cell in a complex with MHC molecules.
Preferably, once the immune cell recognizes the antigen by receptor-antigen g, the
immune cell (immunoreactive cell) is stimulated, primed and/or expanded or exerts effector
functions of immunoreactive cells as described above.
The term "antigen-specific T cell" or similar terms relate to a T cell which izes an
antigen, e.g., a suitable neoepitope xed within MHC class I molecules, and upon binding
to said antigen preferably exerts or functions of T cells as described above. T cells and
other lymphoid cells are considered to be specific for antigen if the cells kill target cells
expressing the antigen. T cell specificity may be evaluated using any of a variety of standard
techniques, for example, within a chromium release assay or proliferation assay. Alternatively,
synthesis of lymphokines (such as interferon-y) can be measured.
T cell receptors and other antigen receptors are described supra. The term "CAR" (or "chimeric
antigen or") relates to an cial receptor sing a single molecule or a complex of
molecules which recognizes, i. e., binds to, a target structure (e.g. an antigen) on a target cell
such as a cancer cell (e.g., by binding of an antigen binding domain to an antigen expressed on
the surface of the target cell) and may confer specificity onto an immune effector cell such as a
T cell expressing said CAR on the cell surface. Preferably, recognition of the target structure
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by a CAR results in activation of an immune effector cell expressing said CAR. A CAR may
comprise one or more protein units said protein units sing one or more domains as
described herein. The term "CAR" does not include T cell receptors.
In one embodiment, a single-chain variable nt (scFv) derived from a monoclonal
antibody is fused to CD3-zeta transmembrane and endodomain. Such molecules result in the
transmission of a zeta signal in response to recognition by the scFv of its antigen target on a
target cell and g of the target cell that expresses the target antigen. Antigen recognition
domains which also may be used include among others T cell receptor (TCR) alpha and beta
single chains. In fact almost anything that binds a given target with high affinity can be used as
an antigen ition domain.
Following antigen recognition, receptors cluster and a signal is transmitted to the cell. In this
t, a "T cell signaling domain" is a domain, preferably an endodomain, which transmits
an activation signal to the T cell after n is bound. The most commonly used endodomain
ent is CD3-zeta.
Adoptive cell transfer therapy with CAR-engineered T cells sing chimeric antigen
receptors is a promising mode of therapy since CAR-modified T cells can be engineered to
target virtually any antigen expressed on diseased cells, for example tumor antigens. Preferably,
the tumor antigen is a neoepitope resulting from a tumor-specific mutation identified by the
methods of the present invention as a suitable tumor-specific target. For example, patient's T
cells may be genetically engineered (genetically modified) to express a CAR specifically
directed towards a specific neoepitope complexed with MHC molecules on the surface
of the patient's tumor cells, then infused back into the patient.
A CAR may replace the function of a T cell receptor and, in particular, may confer reactivity
such as cytolytic ty to a cell such as a T cell. However, in contrast to the binding of the T
cell receptor to an antigen peptide-MHC complex as described above, a CAR also may bind to
an antigen, in particular when expressed on the cell surface.
According to the invention, CARs may generally comprise three domains. The first domain is
the binding domain which recognizes and binds n. The second domain is the costimulation
domain. The co-stimulation domain serves to e the proliferation and survival
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of the cytotoxic lymphocytes upon binding of the CAR to a targeted moiety. The identity of the
co-stimulation domain is limited only in that it has the ability to enhance cellular proliferation
and survival upon binding of the targeted moiety by the CAR. Suitable co-stimulation domains
include CD28, CD137 (4-1BB), a member of the tumor necrosis factor (TNF) receptor family,
CD 134 (0X40), a member of the TNFR-superfamily of receptors, and CD278 (ICOS), a CD28-
superfamily co-stimulatory le expressed on activated T cells. The third domain is the
tion signaling domain (or T cell signaling domain). The activation signaling domain
serves to activate cytotoxic lymphocytes upon binding of the CAR to antigen. The identity of
the activation signaling domain is limited only in that it has the ability to induce activation of
the ed cytotoxic lymphocyte upon binding of the antigen by the CAR. Suitable activation
signaling domains include the T cell CD3 [zeta] chain and Fc receptor ].
The CARs may comprise the three domains, together in the form of a fusion protein. Such
fusion proteins will generally comprise a binding domain, one or more co-stimulation domains,
and an activation signaling domain, linked in an N-terminal to C-terminal direction. However,
the CARs are not limited to this arrangement and other arrangements are acceptable and include
a binding domain, an activation ing domain, and one or more co-stimulation domains. It
will be understood that because the binding domain must be free to bind antigen, the placement
of the binding domain in the fusion protein will generally be such that display of the region on
the exterior of the cell is achieved. In the same manner, because the co-stimulation and
activation signaling domains serve to induce activity and proliferation of the cytotoxic
cytes, the fusion protein will generally y these two domains in the interior of the
cell. The CARs may include additional ts, such as a signal e to ensure proper
export of the fusion protein to the cells surface, a transmembrane domain to ensure the fusion
protein is maintained as an integral membrane protein, and a hinge domain (or spacer region)
that imparts flexibility to the binding domain and allows strong binding to n.
The cells used in tion with CARs and other artificial antigen ors are preferably T
cells, in particular cytotoxic lymphocytes, preferably selected from cytotoxic T cells, l
killer (NK) cells, and lymphokine-activated killer (LAK) cells. Upon activation, each of these
cytotoxic lymphocytes triggers the destruction of target cells. For e, cytotoxic T cells
trigger the ction of target cells by either or both of the following means. First, upon
activation T cells release cytotoxins such as perforin, granzymes, and granulysin. Perforin and
granulysin create pores in the target cell, and granzymes enter the cell and trigger a caspase
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cascade in the cytoplasm that induces apoptosis (programmed cell death) of the cell. Second,
apoptosis can be induced via Fas-Fas ligand interaction between the T cells and target cells.
The xic lymphocytes will preferably be autologous cells, although heterologous cells or
allogenic cells can be used.
A binding domain for an antigen which may be present within a CAR has the ability to bind to
(target) an n, i.e. the ability to bind to (target) an epitope present in an antigen, preferably
the ability to bind to (target) a neoepitope fied by the methods of the t invention as
a suitable disease-specific target where the neoepitope is presented in the context of MHC on
the surface of the cell. Preferably, a binding domain for an antigen is specific for the antigen.
Another type of agent is an immune cell, such as a lymphoid cell, loaded with a peptide
ning a suitable neoepitope identified by the methods of the present invention. In a
preferred embodiment, the lymphoid cell is a dendritic cell. In the context of the t
invention, lymphoid cells preferably isolated from the patient to be treated are incubated with
an antigen to be ed and the incubated cells are then administered to the patient where an
immune response to cells expressing the antigen is induced. Thus, a peptide comprising a
suitable epitope can be incubated with dendritic cells and the incubated cells can be
administered in order to induce an immune response against cells expressing the suitable
neoepitope.
The term "recombinant" in the t of the present invention means "made through genetic
engineering". Preferably, a "recombinant entity" such as a recombinant polypeptide in the
t of the present invention is not ing 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 t 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.
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 t in an organism (including viruses)
and can be isolated from a source in nature and which has not been ionally modified by
man in the laboratory is naturally occurring.
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According to the invention, the term "disease" refers to any pathological state, including cancer
diseases, in particular those forms of cancer diseases described herein.
The term l" refers to the healthy state or the ions in a healthy subject or tissue, i.e.,
non-pathological conditions, wherein "healthy" preferably means non-cancerous.
"Disease involving cells expressing an antigen" means 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 ment, 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.
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 asis (spread to other locations in the body
via lymph or . These three malignant properties of cancers differentiate them from benign
tumors, which are imited, and do not invade or metastasize. Most s form a tumor
but some, like leukemia, do not.
Malignant tumor is essentially synonymous with cancer. Malignancy, malignant neoplasm, and
malignant tumor are essentially synonymous with cancer.
According to the invention, the term "tumor" or "tumor disease" refers to an abnormal growth
of cells (called neoplastic cells, genous cells or tumor cells) preferably forming a
swelling or lesion. By "tumor cell" is meant an abnormal cell that grows by a rapid, uncontrolled
ar proliferation and continues to grow after the stimuli that initiated the new growth cease.
Tumors show partial or complete lack of ural organization and functional coordination
with the normal tissue, and y form a distinct mass of tissue, which may be either benign,
pre-malignant or malignant.
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A benign tumor is a tumor that lacks all three of the malignant properties of a cancer. Thus, by
definition, a benign tumor does not grow in an unlimited, aggressive manner, does not invade
surrounding tissues, and does not spread to non-adjacent tissues (metastasize).
Neoplasm is an abnormal mass of tissue as a result of neoplasia. Neoplasia (new growth in
Greek) is the abnormal eration 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.
"Growth of a tumor" or "tumor growth" in the context of the present invention relates to the
tendency of a tumor to increase its size and/or to the tendency of tumor cells to proliferate.
For purposes of the present invention, the terms r" and "cancer disease" are used
interchangeably with the terms "tumor" and "tumor disease".
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 ogy and the location, respectively.
The term "cancer" according to the invention comprises leukemias, seminomas, melanomas,
teratomas, mas, neuroblastomas, gliomas, rectal cancer, endometrial , kidney
cancer, l cancer, thyroid , blood cancer, skin cancer, cancer of the brain, al
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) , breast cancer, prostate cancer, cancer of
the , n cancer and lung cancer and the metastases thereof. Examples thereof are
lung carcinomas, mamma carcinomas, prostate carcinomas, colon carcinomas, renal cell
omas, 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.
By "metastasis" is meant the spread of cancer cells from its original site to another part of the
body. The formation of asis is a very complex process and depends on detachment of
malignant cells from the primary tumor, invasion of the extracellular matrix, penetration of the
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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 l of the primary tumor because tumor cells or
ents 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.
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 n cells, not of abnormal liver cells. The tumor in the liver is then called
metastatic ovarian cancer, not liver cancer.
The term "circulating tumor cells" or "CTCs" s 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 onal 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 ped 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 s 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 ic 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 a/., 2004, Clin Cancer Res 10:6897-6904). A second method for isolating CTCs
uses a microfluidic-based CTC capture device which involves g whole blood through a
chamber embedded with 80,000 microposts that have been ed 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 nates. 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%
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(Nagrath et al, 2007, Nature 450:1235-1239). Another possibility for isolating CTCs is using
the CellSearch™ ating Tumor Cell (CTC) Test from Veridex, LLC (Raritan, NJ) which
captures, identifies, and counts CTCs in a tube of blood. The CellSearch™ system is a U.S.
Food and Drug Administration (FDA) ed 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 ture all of which
can be used in conjunction with the present invention.
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 ence of an ovarian tumor or the
occurrence of a tumor at a site different to ovary. A relapse or recurrence of a tumor also
es situations wherein a tumor occurs at a site ent to the site of the original tumor as
well as at the site of the original tumor. ably, the original tumor for which the patient has
received a treatment is a primary tumor and the tumor at a site ent to the site of the original
tumor is a secondary or metastatic tumor.
The term “immune response” relates to a reaction of the immune system such as to
immunogenic organisms, such as bacteria or viruses, cells or substances. The term “immune
response” includes the innate immune response and the adaptive immune response. Preferably,
the immune response is d to an activation of immune cells, an induction of cytokine
biosynthesis and/or antibody production.
It is preferred that the immune se induced by the compositions of the present invention
comprises the steps of activation of antigen presenting cells, such as dendritic cells and/or
macrophages, presentation of an antigen or fragment f by said antigen ting cells
and activation of xic T cells due to this presentation.
The term “immune cells” refers to cells of the immune system involved in defending the body
of an individual. The term e cells” encompasses specific types of immune cells and
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their precursors including leucocytes comprising macrophages, monocytes (precursors of
macrophages), granulocytes such as neutrophils, eosinophils and basophils, dendritic cells,
mast cells, and lymphocytes such as B cells, T cells and natural killer (NK) cells. Macrophages,
monocytes (precursors of macrophages), neutrophils, dendritic cells, and mast cells are
phagocytic cells.
The term “immunotherapy” relates to the treatment of a disease or condition by inducing,
ing, or suppressing an immune response. Immunotherapies designed to elicit or amplify
an immune response are fied as activation immunotherapies, while immunotherapies that
reduce or suppress an immune response are classified as ssion immunotherapies. The
term “immunotherapy” includes n immunization or antigen vaccination, or tumor
immunization or tumor vaccination. The term otherapy” also relates to the
manipulation of immune responses such that opriate immune responses are ted
into more appropriate ones in the t of autoimmune es such as rheumatic arthritis,
allergies, diabetes or multiple sclerosis.
The terms “immunization” or “vaccination” describe the process of administering an antigen to
an individual with the purpose of inducing an immune response, for example, for therapeutic
or prophylactic reasons.
By "treat" is meant to administer a compound or composition as described herein to a subject
in order to prevent or ate 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 t; decrease the frequency or ty 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 ular, the term "treatment of a disease" includes curing,
shortening the duration, ameliorating, preventing, slowing down or inhibiting progression or
worsening, or preventing or ng the onset of a disease or the symptoms thereof.
By "being at risk" is meant a subject, i.e. a patient, that is fied as having a higher than
normal chance of developing a disease, in particular cancer, compared to the general population.
In on, 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
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develop a disease. Subjects who currently have, or who have had, a cancer also have an
increased risk for cancer metastases.
A prophylactic administration of an immunotherapy, for example, a prophylactic administration
of the composition of the invention, preferably protects the recipient from the development of
a disease. A therapeutic stration of an immunotherapy, for example, a therapeutic
administration of the composition 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
e, in particular a tion of the progression of the disease, which ably leads to
elimination of the disease.
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 ic for an antigen or
a cell expressing an antigen.
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 se-modifying agents (such as
polypeptides and c acids as provided herein).
The agents and compositions provided herein may be used alone or in combination with
conventional therapeutic regimens such as y, irradiation, chemotherapy and/or bone
marrow transplantation (autologous, syngeneic, allogeneic or ted).
The term "in vivo" relates to the situation in a subject.
The terms "subject", "individual", “organism” or "patient" relate to vertebrates, particularly
mammals. For example, mammals in the context of the present invention are humans, nonhuman
primates, domesticated mammals such as dogs, cats, sheep, cattle, goats, pigs, horses
etc., laboratory animals such as mice, rats, s, guinea pigs, etc. as well as animals in
captivity such as animals of zoos. The terms also relate to non-mammalian vertebrates such as
birds (particularly domesticated birds such as chicken, ducks, geese, turkeys) and to fish
(particularly farmed fish, e.g. salmon or catfish). The term "animal" as used herein also includes
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humans.
The term "autologous" is used to describe ng 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 logical barrier
which otherwise s in rejection.
The term "heterologous" is used to describe something consisting of le different
elements. As an example, the transfer of one individual’s bone marrow into a different
individual tutes a heterologous transplant. A heterologous gene is a gene derived from a
source other than the subject.
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 gs 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 n any known adjuvant. Adjuvants comprise
a heterogeneous group of compounds such as oil emulsions (e.g., ’s adjuvants), mineral
compounds (such as alum), bacterial products (such as Bordetella sis toxin), liposomes,
and -stimulating complexes. Examples for adjuvants are osphoryl-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 ah, 1997, Mol.
Cells 7: 178-186), incomplete Freund’s adjuvants, complete ’s adjuvants, vitamin E,
montanid, alum, CpG oligonucleotides (Krieg et ah, 1995, Nature 374: 546-549), and various
water-in-oil emulsions which are ed from biologically degradable oils such as squalene
and/or tocopherol.
Other nces 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 cytes. Such cytokines comprise, for example, interleukin-12 (IL-12) which was
shown to increase the protective actions of vaccines (see, Hall, 1995, IL-12 at the crossroads,
Science 268:1432-1434), GM-CSF and IL-18.
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There are a number of compounds which enhance an immune response and which therefore
may be used in a vaccination. Said nds comprise co-stimulating molecules provided in
the form of proteins or nucleic acids such as B7-1 and B7-2 (CD80 and CD86, respectively).
ing to the invention, a "tumor specimen" is a sample such as a bodily sample containing
tumor or cancer cells such as circulating tumor cells (CTC), in particular a tissue sample,
including body fluids, and/or a cellular sample. According to the invention, a "non-tumorous
specimen" is a sample such as a bodily sample not containing tumor or cancer cells such as
circulating tumor cells (CTC), in particular a tissue sample, ing 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 ion, the term "sample" also includes
processed samples such as fractions or isolates of biological samples, e.g. nucleic acid or cell
isolates.
The eutically active agents, vaccines and compositions described herein may be
stered via any conventional route, ing by injection or infusion. The administration
may be carried out, for e, orally, intravenously, intraperitoneally, intramuscularly,
subcutaneously or transdermally. In one embodiment, administration is carried out intranodally
such as by ion into a lymph node. Other forms of administration envision the in vitro
transfection of antigen ting cells such as dendritic cells with nucleic acids described
herein followed by administration of the antigen presenting cells.
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 ular condition, the desired
reaction preferably relates to inhibition of the course of the e. This comprises slowing
down the progress of the disease and, in particular, interrupting or reversing the progress of the
disease. The d 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.
An effective amount of an agent described herein will depend on the ion to be treated,
the severity of the disease, the individual parameters of the t, including age, physiological
condition, size and weight, the duration of treatment, the type of an accompanying therapy (if
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present), the specific route of administration and similar factors. Accordingly, the doses
administered of the agents bed herein may variously depend on 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.
The term “pharmaceutically acceptable” refers to the non-toxicity of a material which does not
interact with the action of the active component of the pharmaceutical composition.
The pharmaceutical compositions of the present invention may contain salts, buffers, ving
, carriers and optionally other therapeutic agents. Preferably, the pharmaceutical
compositions of the present invention comprise one or more pharmaceutically acceptable
carriers, diluents and/or excipients.
The term ient” is intended to indicate all substances in a pharmaceutical composition
which are not active ingredients such as binders, lubricants, thickeners, surface active agents,
preservatives, emulsifiers, buffers, flavoring agents, or colorants.
The term “diluent” relates a diluting and/or thinning agent. Moreover, the term “diluent”
includes any one or more of fluid, liquid or solid suspension and/or mixing media.
The term er” relates to one or more compatible solid or liquid s or diluents, which
are suitable for an administration to a human. The term “carrier” relates to a natural or synthetic
organic or inorganic component which is combined with an active component in order to
facilitate the application of the active component. Preferably, carrier components are sterile
liquids such as water or oils, including those which are derived from mineral oil, s, or
, such as peanut oil, soybean oil, sesame oil, sunflower oil, etc. Salt solutions and aqueous
dextrose and glycerin ons may also be used as aqueous carrier compounds.
Pharmaceutically acceptable carriers or ts for therapeutic use are well known in the
pharmaceutical art, and are described, for example, in Remington's Pharmaceutical Sciences,
Mack Publishing Co. (A. R Gennaro edit. 1985). Examples of suitable rs include, for
example, magnesium carbonate, magnesium stearate, talc, sugar, lactose, pectin, dextrin, ,
gelatin, tragacanth, methylcellulose, sodium ymethylcellulose, a low melting wax, cocoa
butter, and the like. Examples of suitable diluents include ethanol, glycerol and water.
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Pharmaceutical carriers, excipients or diluents can be selected with regard to the intended route
of administration and standard pharmaceutical ce. The pharmaceutical compositions of
the present invention may comprise as, or in addition to, the carrier(s), excipient(s) or diluent(s)
any suitable binder(s), lubricant(s), suspending agent(s), coating agent(s), and/or solubilising
agent(s). Examples of suitable binders include starch, gelatin, natural sugars such as glucose,
anhydrous lactose, free-flow lactose, beta-lactose, com sweeteners, natural and synthetic gums,
such as acacia, tragacanth or sodium alginate, carboxymethyl cellulose and polyethylene .
Examples of suitable lubricants include sodium oleate, sodium te, magnesium stearate,
sodium benzoate, sodium acetate, sodium chloride and the like. Preservatives, stabilizers, dyes
and even flavoring agents may be provided in the pharmaceutical ition. Examples of
preservatives include sodium benzoate, sorbic acid and esters of oxybenzoic acid.
idants and suspending agents may be also used.
In one embodiment, the composition is an aqueous composition. The aqueous composition may
optionally comprise s, e.g. salts. In one embodiment, the ition is in the form of a
freeze-dried composition. A freeze-dried composition is obtainable by freeze-drying a
tive aqueous composition.
The agents and compositions provided herein may be used alone or in combination with other
therapeutic regimens such as surgery, irradiation, chemotherapy and/or bone marrow
transplantation ogous, syngeneic, allogeneic or unrelated).
The present invention is described in detail and is illustrated by the s and examples, 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 ion are
accessible to the skilled worker.
FIGURES
Figures la and lb Glioblastoma sample with high focal amplification of the epidermal growth
factor receptor gene (EGER). Fig. la: A cal entation of local genes surrounding
EGER on chromosome 7. Fig. lb: Listing of the 12 single nucleotide variations with the highest
absolute copy numbers.
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Figure 2 A listing of a number of genes having a disease-specific mutation of a melanoma
sample sorted by zygosity (Cx).
Figure 3 A listing of a number of genes of a melanoma sample in which all copies have the
disease-specific mutation (fractional zygosity is equal to 1), of which three of the genes are
essential genes in humans or ed to be essential genes in humans.
Abbreviations for the figures: chr_pos chromosomal position; CN te copy number; Cx
zygosity; EC error correction of the absolute copy number; VAF t allele frequency; rho
estimated percent of tumor cells ning the mutated allele (SNV); FLRT+u ence
score in the mutation; Site fication is the confidence class of the mutation; essential gene,
Y if the gene is found to be essential..
EXAMPLE 1 Targeting disease-specific ons in genes with high copy number
Genomic information for glioblastoma sample (Chin et al, 2008, Comprehensive genomic
characterization defines human glioblastoma genes and core ys, Nature 455:1061-1068)
was analyzed by looking for genes having a high copy number and in which at least one copy
of the gene contained a disease-specific mutation. The y analysis indicated that there was
a high fidelity of copy number assignment for the 11,574 individual genes analyzed, and the
ploidy of the genome of the sample was determined to be 1.95. Figure la shows a graphical
representation of the local genes surrounding epidermal growth factor receptor (EGFR) on
chromosome 7, which is a known driver gene and have been a target for treatment. It was shown
that EGFR in this genome had an error corrected absolute copy number of 76, of which 13
copies contained the disease-specific single nucleotide variation. Figure lb provides a list of
the genes in this genomic sample with the highest absolute copy number. There are four
additional genes having an absolute copy number greater than 2. , EGFR amplification
is a known genetic rk of primary glioblastomas (Benito et al, 2009, Neuropathology 30
(4):392-400) and this gene has been ered as a target for treatment (Taylor, 2012, Cun-
Cancer Drug Targets. Mar; 12(3): 197-209).
EXAMPLE 2 Targeting disease-specific mutations with a high zygosity
An exome obtained from a sample of melanoma cells from a tumor in a human was analyzed
by looking for genes in which at least one copy of the gene has a disease-specific mutation and
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looking at the number of copies of the gene having the disease-specific mutation as well as the
total number of copies of the gene, r the gene has the mutation or not. Figure 2 provides
a list of genes sorted by zygosity in which the disease-specific mutation is found on multiple
copies of the gene. For example, the disease-specific mutation in the OXGR1 gene has the
highest zygosity (4), and in particular also has the highest fractional zygosity of 4/5 or 0.8 since
there are a total of 5 copies of the OXGR1 gene and 4 of which copies contain the diseasespecific
mutation. The list provides 10 additional genes in which 3 copies of the gene out of a
total of 4 copies have the mutation, ting that the disease-specific mutation in these genes
has a fractional zygosity of 3/4 or 0.75. The ing listed genes have mutations that have a
fractional zygosity of 2/3 or 0.66 since 2 copies out of a total of 3 copies have the mutation.
EXAMPLE 3 Targeting disease-specific mutations present in all conies of an essential gene
An exome obtained from a sample of melanoma cells from a tumor in a human was analyzed
by looking for genes in which all copies of the gene have the same disease-specific mutation
and ining which of these genes is an essential gene. The genes were determined to be
essential by ing their essentiality in humans from the knowledge that they are essential in
mice (Georgi et ai, 2013, From mouse to human: evolutionary genomics analysis of human
orthologs of essential genes, PLoS Genetics 9 (5):el003484; Liao et al, 2007, Mouse duplicate
genes areas essential as singletons, Trends Genet. 23:378-381). Figure 3 lists a number of genes
in which all copies of the gene have the same disease-specific mutation. Moreover, the three
highlighted genes were determined to be ial by inferring their essentiality from mouse
data.
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We claim
1. A method for determining the suitability of a neoepitope resulting from a disease-specific
mutation at an allele in a gene (mutated allele) as a disease-specific target comprising
determining, in a diseased cell or population of diseased cells, the copy number of the mutated
allele encoding the neoepitope.
2. The method according to claim 1, n a high copy number of the mutated allele indicates
the suitability of the neoepitope as a disease-specific target.
3. The method according to claim 2, wherein the higher the copy number of the mutated ,
the higher the suitability of the neoepitope as a disease-specific target.
4. The method according to claim 1, wherein when the copy number of the mutated allele is
greater than 2 indicates the ility of the neoepitope as a disease-specific target.
. The method according to claim 4, wherein when the copy number of the mutated allele is
greater than 3, 4, 5, 6, 7, 8, 9, 10, 20, 30, 40, 50, 60, 70, 80, 90, or is r than 100 indicates
the suitability of the neoepitope as a disease-specific target.
6. The method according to any one of claims 1 to 5, wherein the mutated allele is found in a
high on of copies of the gene of which at least one copy has the mutated allele (fractional
zygosity), which onal zygosity is the ratio of the copy number of the mutated allele over
the total number of copies of the nucleotide site to which the mutation maps.
7. The method according to claim 6, wherein the higher the fractional zygosity, the higher the
suitability of the neoepitope as a disease-specific target.
8. The method according to claim 6 or 7, n the fractional zygosity is greater than 0.5,
preferably the fractional zygosity is 1.
9. The method according to any one of claims 1 to 8, n the copy number of the mutated
allele and/or the fractional zygosity and/or the total number of copies of the nucleotide site to
which the mutated allele maps is found in a high fraction of diseased cells.
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. The method according to claim 9, n the higher the fraction of diseased cells having
the copy number of the mutated allele and/or the fractional zygosity and/or the total number of
copies of the nucleotide site to which the mutated allele maps, the higher the suitability of the
neoepitope as a disease-specific target.
11. The method according to claim 9 or 10, wherein the fraction of diseased cells is 1.
12. The method according to any one of claims 1 to 11, wherein the gene is a driver gene whose
expression results in transformation of the cell into a cancerous phenotype or whose lack of
expression results in a cancerous cell losing its cancerous phenotype.
13. The method according to any one of claims 1 to 11, wherein the gene is an essential gene.
14. The method according to claim 13, wherein the ial gene is a gene, which when
silenced or its expression is reduced, at least results in impaired growth or d fitness of a
cell in which the essential gene is expressed, preferably the ed cell.
. The method according to claim 13, wherein the essential gene is expressed in a wide variety
of ent tissues and is sed with a minimal RPKM threshold r than 0.
16. A method for determining the suitability of a tope resulting from a disease-specific
mutation in a gene as a disease-specific target comprising determining, in a diseased cell or
population of diseased cells, the copy number of the gene, of which at least one copy has the
disease-specific mutation.
17. The method according to claim 16, wherein a high copy number of the gene indicates the
suitability of the neoepitope as a disease-specific target.
18. The method according to claim 16 or 17, wherein the higher the copy number of the gene,
the higher the suitability of the neoepitope as a disease-specific target.
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[Annotation] mpg
MigrationNone set by mpg
[Annotation] mpg
Unmarked set by mpg
[Annotation] mpg
None set by mpg
[Annotation] mpg
MigrationNone set by mpg
[Annotation] mpg
Unmarked set by mpg
19. The method according to any one of claims 16 to 18, wherein the gene is a driver gene
whose expression results in transformation of the cell into a cancerous phenotype or whose lack
of expression results in a cancerous cell losing its ous phenotype.
. The method according to any one of claims 16 to 19, wherein the copy number of the gene
is found in a high fraction of ed cells.
21. The method according to claim 20, wherein the higher the on of diseased cells having
the copy number, the higher the suitability of the neoepitope as a disease-specific target.
22. The method according to claim 20 or 21, n the fraction of diseased cells is 1.
23. The method according to any one of claims 1 to 22, wherein the copy number is the absolute
copy number.
24. The method according to claim 23, wherein the absolute copy number is an error corrected
absolute copy number.
. The method according to claim 23 or 24, wherein the absolute copy number or the error
ted absolute copy number is normalized against a , preferably the ploidy of the
genome of the diseased cell, or the ploidy of the chromosome or a portion of the chromosome
on which the mutation or mutated gene is located in the ed cell.
26. A method for determining the suitability of a neoepitope ing from a disease-specific
mutation in a gene as a disease-specific target comprising determining, in a diseased cell or
population of diseased cells, whether the gene having the disease-specific mutation is an
essential gene.
27. The method ing to claim 26, wherein the essential gene is a gene which when
silenced or its expression is reduced, at least results in impaired growth or reduced fitness of a
cell in which the essential gene is expressed, preferably the diseased cell.
28. The method according to claim 26, wherein the essential gene is expressed in a wide variety
of different tissues and is expressed with a minimal RPKM threshold greater than 0.
ation] mpg
None set by mpg
[Annotation] mpg
MigrationNone set by mpg
[Annotation] mpg
Unmarked set by mpg
[Annotation] mpg
None set by mpg
[Annotation] mpg
MigrationNone set by mpg
ation] mpg
Unmarked set by mpg
29. The method according to any one of claims 26 to 28, wherein where the gene is an essential
gene and all copies of the essential gene have the disease-specific mutation indicates the
suitability of the neoepitope as a disease-specific .
. The method according to any one of claims 26 or 29, wherein a high fraction of diseased
cells contain copies of the essential gene in which all copies of the essential gene have the
disease-specific mutation.
31. The method according to claim 30, wherein the higher the fraction of diseased cells
containing copies of the essential gene in which all copies of the essential gene have the diseasespecific
mutation, the higher the suitability of the neoepitope as a disease-specific target.
32. The method according to claim 30 or 31, n the fraction of diseased cells is 1.
33. A method for determining the suitability of a combination of at least two neoepitopes
resulting from disease-specific mutations in at least two genes as a combination of diseasespecific
targets comprising determining whether a combination of the at least two genes each
having a disease-specific mutation are synthetic lethal or tic sick genes.
34. The method according to claim 33, wherein when the combination of the at least two genes
are synthetic lethal or tic sick indicates the ility of the combination of neoepitopes
as a combination of disease-specific targets.
. The method according to claim 33 or 34, wherein all copies of the at least two genes have
the disease-specific mutations.
36. The method according to claim 35, wherein a high fraction of diseased cells contain the at
least two genes having the e-specific mutations.
37. The method according to claim 36, wherein the fraction of diseased cells is 1.
38. The method according to any one of claims 1 to 37, wherein the e-specific mutation
is a single nucleotide variation.
[Annotation] mpg
None set by mpg
[Annotation] mpg
MigrationNone set by mpg
[Annotation] mpg
Unmarked set by mpg
[Annotation] mpg
None set by mpg
[Annotation] mpg
MigrationNone set by mpg
[Annotation] mpg
Unmarked set by mpg
39. The method according to any one of claims 1 to 38, wherein the disease is cancer.
40. The method according to any one of claims 1 to 39, wherein the neoepitope is identified by
a method comprising sequencing the genome or a portion f of a diseased cell.
41. The method according to any one of claims 1 to 40 for use in the manufacture of a
medicament.
42. The method according to any one of claims 1 to 40 for use in the manufacture of a vaccine.
43. The method according to claim 42, n the vaccine is derived from one or more suitable
neoepitopes or from a combination of suitable neoepitopes.
44. The method according to claim 42 or 43, wherein the vaccine comprises a peptide or
polypeptide comprising one or more suitable neoepitopes or a combination of suitable
neoepitopes, or a c acid encoding said peptide or polypeptide.
45. A method for providing a vaccine comprising identifying a suitable neoepitope or a
ation of suitable topes ing to the method of any one of claims 1 to 40.
46. The method according to claim 45, wherein the vaccine comprises a peptide or ptide
comprising one or more suitable neoepitopes or a combination of suitable neoepitopes, or a
nucleic acid encoding said peptide or polypeptide.
47. A vaccine produced by the method of any one of claims 42 to 46.
48. The method according to any one of claims 1 to 40 for use in the manufacture of
recombinant immune cells sing an antigen or targeted to a suitable neoepitope or
to one neoepitope in a combination of suitable neoepitopes.
49. The method according to claim 48, wherein the immune cells are T cells and the antigen
receptor is a T cell receptor.
ation] mpg
None set by mpg
[Annotation] mpg
MigrationNone set by mpg
ation] mpg
Unmarked set by mpg
[Annotation] mpg
None set by mpg
[Annotation] mpg
MigrationNone set by mpg
[Annotation] mpg
Unmarked set by mpg
50. A method for providing a recombinant immune cell targeted to a suitable neoepitope or to
one epitope in a combination of suitable neoepitopes, said method comprising ecting an
immune cell with a recombinant antigen or targeted to the suitable neoepitope or to the
one epitope in a combination of suitable epitopes identified by the method according to any one
of claims 1 to 40.
51. The method according to claim 50, wherein the immune cell is a T cell and the antigen
receptor is a T cell receptor.
52. A inant immune cell produced by the method of any one of claims 48 to 51.
53. A method for providing an immune response to a target cell tion or target tissue
expressing one or more topes in a mammal, said method comprising administering to the
mammal:
(a) one or more immune cells expressing one or more antigen receptors targeted to the one or
more neoepitopes identified according to the method of any one of claims 1 to 40;
(b) administering a c acid encoding one or more of the neoepitopes identified according
to the method of any one of claims 1 to 40; or
(c) administering a peptide or polypeptide comprising one or more of the neoepitopes identified
according to the method of any one of claims 1 to 40.
54. The method according to claim 53, wherein the immune cells are T cells and the antigen
receptors are T cell receptors.
55. The method according to claim 53 or 54, n the immune response is aT cell-mediated
immune response.
56. The method according to any one of claims 53 to 55, wherein the immune response is an
anti-tumor immune response and the target cell population or target tissue expressing the one
or more suitable neoepitopes is tumor cells or tumor tissue.
57. A method for treating a mammal having a disease, disorder or condition associated with
expression of a neoepitope, the method comprising administering to the mammal:
[Annotation] mpg
None set by mpg
[Annotation] mpg
MigrationNone set by mpg
[Annotation] mpg
Unmarked set by mpg
[Annotation] mpg
None set by mpg
[Annotation] mpg
ionNone set by mpg
[Annotation] mpg
Unmarked set by mpg
(a) one or more immune cells sing one or more antigen ors targeted to the one or
more neoepitopes identified according to the method of any one of claims 1 to 40;
(b) administering a nucleic acid encoding one or more of the neoepitopes identified according
to the method of any one of claims 1 to 40; or
(c) administering a peptide or polypeptide comprising one or more of the neoepitopes identified
according to the method of any one of claims 1 to 40.
58. The method according to claim 57, n the immune cells are T cells and the antigen
receptors are T cell receptors.
59. The method according to claim 57 or 58, wherein the disease, disorder or condition is
cancer.
[Annotation] mpg
None set by mpg
[Annotation] mpg
MigrationNone set by mpg
[Annotation] mpg
Unmarked set by mpg
[Annotation] mpg
None set by mpg
[Annotation] mpg
MigrationNone set by mpg
[Annotation] mpg
Unmarked set by mpg
4- GBAS 7 x 10 84 ZNF713 MRPS17 i H 5.6 C09 /^EPT14 I DQ575984 FKBP9L.\ I I 77 V0PP1LANCL2 5.55 chr7 GU228584 (bp)
EGFR 111111111111111111111111 lllllllllllllllllllllllll imiiimimmimiii Jr /+ 7^ position SNV i 5.5 C
undetermined CN
SEC61G
CN=2 CN=3 I BC036261 oocara CN=4 b.'v^w- CN=53 qn=76 \ ■ ■ i 1a ■ i ■ AB074160 LOC285878 VSTM2A-~^4/ i 5.45 Figure CN legend
[Annotation] mpg
None set by mpg
[Annotation] mpg
MigrationNone set by mpg
[Annotation] mpg
Unmarked set by mpg
[Annotation] mpg
None set by mpg
[Annotation] mpg
MigrationNone set by mpg
ation] mpg
Unmarked set by mpg
kj 4- nt A A T T A A T A A C T T wt mut nt G G C C C G C G G T C C std) std) Clone type ? FIXED FIXED ? FIXED (>4 (>4 FIXED FIXED FIXED FIXED FIXED not fixed not fixed Site classification SOMATIC_HI SOMATIC_HI SOMATIC_HI SOMATIC_HI SOMATIC_HI SOMATIC_HI SOMATIC_HI SOMATIC_HI SOMATIC_HI SOMATIC_HI SOMATIC_HI C_HI FLRT+u 284,984 -80,215 -216, 9 64,0632 20,1572 34,0489 21,4224 63,2453 54,2955 -14,37 26,0748 114,485 rho 0,968 1,126 0, 858 0, 9 0, 943 0,568 0,515 1,005 0, 9 0, 83 0, 756 0, 984 (Nx_ VAF=Nx_Q3 0/ Q30+Nz_Q30) 0, 165 0,262 0,26 0,545 0,286 0, 247 0, 224 0, 437 0,392 0,361 0,329 0, 428 Cx 13 1 1 2 1 1 1 1 1 1 1 1 EC 4 3 3 3 2 2 2 2 2 2 2 CN w/ 76EGER NPRL2 GNPTG HOXB1 TPMS NR1I3,TOMM40L PLCL1 gene MUG 17 SLC11A1 OBSL1 CLEC3B D ZIP1L
72 0 6 432
chr3_50 38 based) 412528 77082 9
chr_pos (0 chr7_55233108 00677038 chr1 6_1 chrl7_46607714 chr1_154148651 chr1_161206280 chr2_198950755 19255986 chr2_2 20422919 chr3_45 0 chr3_137 7 Figure 1b
ation] mpg
None set by mpg
[Annotation] mpg
MigrationNone set by mpg
[Annotation] mpg
Unmarked set by mpg
[Annotation] mpg
None set by mpg
[Annotation] mpg
MigrationNone set by mpg
[Annotation] mpg
Unmarked set by mpg
4- mut nt A A T A T C C T A T A T T A T T T A A T wt nt G G C G C A A C G C C C C G A C C G G C Clone type ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? Site classificatio n SOMATIC_HI SOMATIC_HI SOMATIC_HI SOMATIC_HI SOMATIC_HI SOMATIC_HI SOMATIC_HI SOMATIC_HI C_HI SOMATIC_HI SOMATIC_HI SOMATIC_HI SOMATIC_HI SOMATIC_HI SOMATIC_HI C_HI C_HI SOMATIC_HI SOMATIC_HI SOMATIC_HI FLRT+u -915,97 -328,977 -795,252 -290,407 -165,72 -206,449 -1035,86 -314,949 -1559,58 -187,055 -845,185 -522,497 -418,868 49 -419,633 -172,683 -173,545 -456,673 -465,294 -290,253 rho 0, 948 0, 923 1, 025 0, 943 0, 929 1, 008 0, 929 1, 079 0, 966 0, 903 0, 977 1, 084 1, 091 1, 015 0, 988 0, 973 0, 984 1, 014 1, 043 1, 032 VAF= Nx_Q30/(Nx_Q 30+Nz_Q30) 0, 743 0, 675 0, 749 0, 689 0, 679 0, 736 0, 679 0, 789 0, 706 0, 66 0,714 0, 698 0, 703 0, 654 0, 636 0, 627 0, 634 0, 653 0, 672 0, 664 Cx 4 3 3 3 3 3 3 3 3 3 3 2 2 2 2 2 2 2 2 2
CN w/ EC 5 4 4 4 4 4 4 4 4 4 4 3 3 3 3 3 3 3 3 3
gene OXGR1 GJB6 LM07 SLC28A2 UNC13C MAP2K1 EDC3 ANKRD34C FAH SYNM C15orf59 KIAA0353, C14orf105 ZSCAN2 SCN4A KCNJ2 SLC38A10 SLC38A10 THOC4 1 ACOT8
chrl3_96437970 chrl3_19694928 6 7 chrl5_43349693 0 6 8 4 0 7 37 504 3587 97 94 414 chr15_52 64 chr15_64 514 5 6958 8 997 934 3 9455 chrl5_71819607 chr15_7 2 7 51030 7 7 37 chr15_7 82 97 4 chrl4_57 007 (0 based) 4 341837
chr_pos chr13_7 52 chr15_82 964 chr17_5 937 chr17_65 683550 chrl7_76839795 chrl7_76839796 chrl7_7 7 chr2 0_42 chr20_43919430 Figure 2
[Annotation] mpg
None set by mpg
[Annotation] mpg
MigrationNone set by mpg
[Annotation] mpg
Unmarked set by mpg
[Annotation] mpg
None set by mpg
[Annotation] mpg
MigrationNone set by mpg
[Annotation] mpg
Unmarked set by mpg
4- Essential Y Y Y mut nt A T A A T A A T T T T T T A A T C A T C A T wt nt G C G G A G G C C C C C C G G C T G C T C C Clone type 9 9 9 9 9 9 9 9 9 9 9 9 9 9 9 9 9 9 9 9 9 9 Site classification SOMAIIC_HI SOMAIIC_HI SOMAIIC_HI SOMAIIC_HI SOMAIIC_HI SOMAIIC_HI SOMAIIC_HI SOMAIIC_HI SOMAIIC_HI SOMAIIC_HI SOMAIIC_HI SOMAIIC_HI SOMAIIC_HI SOMAIIC_HI SOMAIIC_HI SOMAIIC_HI SOMAIIC_HI SOMAIIC_HI SOMAIIC_HI SOMAIIC_HI SOMAIIC_HI SOMAIIC_HI FLRT+u 22,8242 633,922 936, 399 -149,83 97,1867 5 339, 266 70,1344 346, 631 141,696 3 32,7025 135,186 69,8589 35,6228 322,993 9 235,171 214,582 150,986 7 94,7646 rho 1, 004 1, 049 0, 991 1,01 1, 043 1, 005 1, 024 0, 997 0, 97 0, 874 0, 923 1, 052 0, 975 1, 082 0, 947 1, 081 0, 972 0, 983 1, 032 1, 025 0, 989 0, 991 VAF=Nx_Q3 0/( Nx_Q30+Nz_Q3 0) 0, 929 0, 97 0, 917 0, 934 0, 964 0, 929 0,881 0,857 0,834 0,752 0,794 0, 905 0,838 0, 93 0,815 0, 93 0,836 0,845 0,887 0,881 0,851 0,852 Cx 4 4 4 4 4 4 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 EC 4 4 4 4 4 4 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2
CN w/ .14 ,PCDHA4 _ _ _ _ _ _ _
gene 1 7 618 ,PCDHA3
AK 02 SAMD9L CALD1, OK/SW-cl BRAF GIMAP1,GIMAP2 ClOorf71 IBC1D12 CYP2C18,CYP2C19 CYP2C19 TACC2 PWWP2B KCTD14 DNAH5 CDH9 PRLR PCDHB7 GPR116 ZDHHC2 SLC39A14 PCDHAl, PCDHA2 _ _ _ _ _ _ _ CDKN2A,MTAP
6 (0 6
3 6 9
04 0 72 4 7 5 6
98 70 9 9 5381 9 6
75 9 64 02 082 2 2 0 9 6 05 63 32 chr7_9 2 5 chr7_134 2 chr_pos based) chr7_12 3 chr7_140 0 chr7_15 0 0 9 53 929663 chr1 0_5 chrl0_96272140 chrl0_96474217 chrl0_96530337 chr2_l7 chr10_12 3 chrl0_134068510 chrll_77405330 chr5_13 8 chr5_2 702413 chr5_351012 chr5_140167962 405337 61 chr6_4 6 chr8_l7107 chr8_22323567 chr9_21961095 Figure 3
SEQUENCE LISTING
<110> BioNTech RNA Pharmaceuticals GmbH
<120> Selecting Neoepitopes as Disease‐Specific Targets for Therapy
with Enhanced Efficacy
<130> 755‐2 PCT2
<140> 2017/068226
<141> 2017‐07‐19
<150>
<151> 2016‐07‐20
<160> 2
<170> PatentIn version 3.5
<210> 1
<211> 15
<212> PRT
<213> Artificial ce
<220>
<223> Linker sequence
<220>
<221> REPEAT
<222> (1)..(3)
<223> Portion of ce 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 20
<220>
<221> MISC_FEATURE
<222> (1)..(15)
<223> 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
<220>
<221> REPEAT
<222> 6)
<223> 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 20
<220>
<221> REPEAT
<222> (7)..(9)
<223> 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,
Page 1
13, 14, 15, 16, 17, 18, 19, or 20
<220>
<221> REPEAT
<222> (10)..(12)
<223> 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 20
<220>
<221> REPEAT
<222> (13)..(15)
<223> 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 20
<400> 1
Gly Gly Ser Gly Ser Ser Gly Gly Gly Ser Ser Gly Gly Ser Gly
1 5 10 15
<210> 2
<211> 9
<212> PRT
<213> cial Sequence
<220>
<223> linker sequence
<400> 2
Gly Gly Ser Gly Gly Gly Gly Ser Gly
1 5
Page 2
Applications Claiming Priority (1)
Application Number | Priority Date | Filing Date | Title |
---|---|---|---|
EPPCT/EP2016/067348 | 2016-07-20 |
Publications (1)
Publication Number | Publication Date |
---|---|
NZ790046A true NZ790046A (en) | 2022-07-29 |
Family
ID=
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