Neoantigens and uses thereof for treating cancer
Systems and methods for determining the likely responsiveness of a human cancer subject to a checkpoint blockade immunotherapy regimen are provided. Sequencing reads are obtained from samples from the subject representative of the cancer. A human leukocyte antigen type and a plurality of clones is determined from the sequencing reads. For each clone, an initial frequency X α in the one or more samples is determined and a corresponding clone fitness score of the clone is computed, thereby computing clone fitness scores. Each such fitness score is computed by identifying neoantigens in the respective clone, computing a recognition potential for each neoantigen, and determining the corresponding clone fitness score of the respective clone as an aggregate of these recognition potentials. A total fitness, quantifying the likely responsiveness of the subject to the regimen, is computed by summing the clone fitness scores across the plurality of clones.
1. A method for selecting a human subject afflicted with a cancer for treatment with a checkpoint blockade immunotherapy comprising:
(A) obtaining a plurality of sequencing reads from one or more samples from the human cancer subject that is representative of the cancer;
(B) determining a human leukocyte antigen (HLA) type of the human cancer subject;
(C) determining a plurality of clones, and for each respective clone α in the plurality of clones, an initial frequency X α of the respective clone α in the one or more samples;
(D) for each respective clone α in the plurality of clones, computing a corresponding clone fitness score of the respective clone, thereby computing a plurality of clone fitness scores, each corresponding clone fitness score computed for a respective clone α by a first procedure comprising:
(a) identifying a plurality of neoantigens in the respective clone α;
(b) computing a recognition potential of each respective neoantigen in the plurality of neoantigens in the respective clone α by a second procedure comprising:
(i) computing an amplitude A of the respective neoantigen as a function of the relative major histocompatibility complex (MHC) affinity of the respective neoantigen and the wildtype counterpart of the respective neoantigen given the HLA type of the subject,
(ii) computing a probability of T-cell receptor recognition R of the respective neoantigen as a probability that the respective neoantigen is bound by T-cells that are specific to one or more known epitopes in a plurality of epitopes after class I MHC presentation, wherein the plurality of epitopes comprises 1×10 6 epitopes,
wherein the probability of T-cell receptor recognition R is computed as:
R
=
Z
(
k
)
-
1
∑
e
∈
D
exp
[
-
k
(
a
-
|
s
,
e
|
)
]
,
wherein
a is a number that represents a horizontal displacement of a binding curve for the respective neoantigen,
k is a number that sets the steepness of the binding curve at a,
Z(k) is a partition function over the unbound state and all bound states of the respective neoantigen of the form
1
+
∑
e
∈
D
exp
[
-
k
(
a
-
|
s
,
e
|
)
]
wherein,
D is the plurality of epitopes,
each respective epitope e is an epitope from the plurality of epitopes that is positively recognized by T-cells after class I MHC presentation, and
|s, e| is a measure of sequence similarity between the respective neoantigen s and the respective epitope e, and
(iii) computing the recognition potential of the respective neoantigen as a function of the amplitude A of the respective neoantigen and the probability of T-cell receptor recognition R of the respective neoantigen; and
(c) determining the corresponding clone fitness score of the respective clone α as an aggregate of the neoantigen recognition potentials across the plurality of neoantigens in the respective clone α;
(E) computing a total fitness for the one or more samples as a sum of the clone fitness scores across the plurality of clones, wherein:
each clone fitness score is weighted by the initial frequency X α of the corresponding clone α, and
the total fitness quantifies the likelihood that the human subject afflicted with the cancer will be responsive to the treatment regimen; and
(F) administering ipilimumab or tremelimumab to the subject when the total fitness of the subject is lower than a predetermined threshold.
2. The method of claim 1 , wherein the cancer is a carcinoma, a melanoma, a lymphoma/leukemia, a sarcoma, or a neuro-glial tumor.
3. The method of claim 1 , wherein the cancer is lung cancer, pancreatic cancer, colon cancer, stomach or esophagus cancer, breast cancer, ovary cancer, prostate cancer, or liver cancer.
4. The method of claim 1 , wherein
each clone α in the plurality of clones is uniquely defined by a unique set of somatic mutations, and
the plurality of clones is determined by a variant allele frequency of each respective somatic mutation in a plurality of somatic mutations determined from the plurality of sequencing reads.
5. The method of claim 4 , wherein the somatic mutation is a single nucleotide variant or an indel.
6. The method of claim 1 , wherein
each clone α in the plurality of clones is uniquely defined by a unique set of somatic mutations, and
the plurality of clones is determined by a combination of (i) a variant allele frequency of each respective somatic mutation in the plurality of somatic mutations determined from the plurality of sequencing reads and (ii) an identification of a plurality of inferred copy number variations using the whole-genome sequencing data.
7. The method of claim 1 , wherein each neoantigen in the plurality of neoantigens of a clone in the plurality of clones is a peptide that is eight, nine, ten, or eleven residues in length.
8. The method of claim 1 , the method further comprising identifying a population of neoantigens present in the one or more samples by a third procedure comprising:
determining a plurality of somatic single nucleotide polymorphisms (SNPs) in the plurality of sequencing reads by comparison of the plurality of sequencing reads to a reference human genome; and
evaluating each respective somatic SNP in the plurality of SNPs as a neoantigen candidate by evaluation of a peptide encoded by a portion of one or more sequencing reads in the plurality of sequencing reads that includes the respective somatic SNP against a classifier that has been trained to predict peptide binding to class 1 MHC of the HLA type of the cancer subject, wherein a neoantigen candidate having a binding score below a threshold value is deemed to be a neoantigen in the population of neoantigens, and
wherein the identifying the plurality of neoantigens in the respective clone α comprises matching the SNPs in the respective clone α to respective neoantigens in the population of neoantigens.
9. The method of claim 1 , wherein the function of the relative class I MHC affinity of the respective neoantigen and the wildtype counterpart of the respective neoantigen given the HLA type of the subject is a ratio of:
(1) a dissociation constant between the respective neoantigen and the class I MHC presented by the cancer subject given the HLA type of the cancer subject, and
(2) a dissociation constant between the wildtype counterpart of the respective neoantigen and the class I MHC presented by the cancer subject given the HLA type of the cancer subject.
10. The method of claim 9 , wherein:
the dissociation constant between the respective neoantigen and the class I MHC presented by the cancer subject is obtained as output from a first classifier upon inputting into the first classifier the amino acid sequence of the neoantigen,
the dissociation constant between the wildtype counterpart of the respective neoantigen and the class I MHC presented by the cancer subject of the HLA type of the subject is obtained as output from the first classifier upon inputting into the first classifier the amino acid sequence of the respective wildtype counterpart of the neoantigen, and
the first classifier is specific to the HLA type of the cancer subject and has been trained with the respective class I MHC binding coefficient and sequence data of each peptide epitope in a plurality of epitopes presented by class I MHC in a training population having the HLA type of the subject.
11. The method of claim 1 , wherein the measure of sequence similarity |s, e| is computed as a sequence alignment between the sequence of the respective neoantigen s and the sequence of the respective epitope e using an amino-acid similarity matrix.
12. The method of claim 1 , wherein the aggregate of the neoantigen recognition potentials across the plurality of neoantigens in the respective clone α is computed as:
F
α
=
-
max
i
∈
Clone
α
(
A
i
×
R
i
)
wherein i is an index iterating over each neoantigen in the plurality of neoantigens in the respective clone α.
13. The method of claim 12 , wherein the computing a total fitness for the one or more samples as a sum of the clone fitness scores across the plurality of clones is computed as:
n (τ)= Z α X α exp( F α τ),
wherein τ is a characteristic evolutionary time scale.
14. The method of claim 1 , wherein the aggregate of the neoantigen recognition potentials across the plurality of neoantigens in the respective clone α is computed as a summation of the recognition potential of all or a subset of the neoantigens in the plurality of neoantigens.
15. The method of claim 1 , wherein the aggregate of the neoantigen recognition potentials across the plurality of neoantigens in the respective clone α is computed as a nonlinear combination of the recognition potential of all or a subset of the neoantigens in the plurality of neoantigens.
16. The method of claim 1 , wherein the total fitness is inversely proportional to (a) a likelihood that the cancer subject will be responsive to immunotherapy and (b) an indication of survival of the cancer subject.
17. The method of claim 1 , wherein the plurality of epitopes consists of epitopes that have been recognized by human T-cells from the human subject.
18. The method of claim 1 , wherein the probability that the respective neoantigen is bound by T-cells that are specific to one or more known epitopes in the plurality of epitopes after class I MHC presentation is computed as:
R
=
Z
(
k
)
-
1
∑
t
∈
F
exp
[
-
k
(
a
-
|
s
,
t
|
)
]
,
wherein
a is a number that represents a horizontal displacement of a binding curve for the respective neoantigen,
k is a number that sets the steepness of the binding curve at a,
Z(k) is a partition function over the unbound state and all bound states of the respective neoantigen of the form
1
+
∑
t
∈
F
exp
[
-
k
(
a
-
|
s
,
t
|
)
]
wherein,
F is a plurality of T-cell receptor sequences,
each respective T-cell receptor t is a T-cell receptor from the plurality of T-cell receptor sequences F, and
|s, t| is a measure of affinity between the respective neoantigen s and the respective T-cell receptor t.
19. The method of claim 18 , wherein the plurality of T-cell receptors is drawn exclusively from the subject.
20. The method of claim 1 , wherein the plurality of clones is determined by identifying a plurality of inferred copy number variations using the plurality of sequencing reads.
21. A method for selecting an immunotherapy for treating a cancer in a subject in need thereof, the method comprising:
(A) obtaining a plurality of sequencing reads from one or more samples from a human cancer subject that is representative of the cancer;
(B) determining a human leukocyte antigen (HLA) type of the human cancer subject from the plurality of sequencing reads;
(C) determining a plurality of clones, and for each respective clone α in the plurality of clones, an initial frequency X α of the respective clone α in the one or more samples from the plurality of sequencing reads;
(D) for each respective clone α in the plurality of clones, computing a corresponding clone fitness score of the respective clone, thereby computing a plurality of clone fitness scores, each corresponding clone fitness score computed for a respective clone α by a first procedure comprising:
(a) identifying a plurality of neoantigens in the respective clone α;
(b) computing a recognition potential of each respective neoantigen in the plurality of neoantigens in the respective clone α by a second procedure comprising:
(i) computing an amplitude A of the respective neoantigen as a function of the relative major histocompatibility complex (MHC) affinity of the respective neoantigen and the wildtype counterpart of the respective neoantigen given the HLA type of the subject,
(ii) computing a probability of T-cell receptor recognition R of the respective neoantigen as a probability that the respective neoantigen is bound by T-cells that are specific to one or more known epitopes in a plurality of epitopes after class I MHC presentation, wherein the plurality of epitopes comprises 1×10 6 epitopes,
wherein the probability of T-cell receptor recognition R is computed as:
R
=
Z
(
k
)
-
1
∑
e
∈
D
exp
[
-
k
(
a
-
❘
"\[LeftBracketingBar]"
s
,
e
❘
"\[RightBracketingBar]"
)
]
,
wherein
a is a number that represents a horizontal displacement of a binding curve for the respective neoantigen,
k is a number that sets the steepness of the binding curve at a,
Z(k) is a partition function over the unbound state and all bound states of the respective neoantigen of the form
1
+
∑
e
∈
D
exp
[
-
k
(
a
-
❘
"\[LeftBracketingBar]"
s
,
e
❘
"\[RightBracketingBar]"
)
]
wherein,
D is the plurality of epitopes,
each respective epitope e is an epitope from the plurality of epitopes that is positively recognized by T-cells after class I MHC presentation, and
|s, e| is a measure of sequence similarity between the respective neoantigen s and the respective epitope e, and
(iii) computing the recognition potential of the respective neoantigen as a function of the amplitude A of the respective neoantigen and the probability of T-cell receptor recognition R of the respective neoantigen; and
(c) determining the corresponding clone fitness score of the respective clone α as an aggregate of the neoantigen recognition potentials across the plurality of neoantigens in the respective clone α; and
(E) selecting at least a first neoantigen from a plurality of neoantigens for a respective clone α in the plurality of respective clones based upon the recognition potential of the at least first neoantigen as the immunotherapy for the cancer,
(F) administering to the human cancer subject a vaccine comprising the at least first neoantigen, a vaccine comprising a polynucleotide encoding the at least first neoantigen, or a T cell population that targets the at least first neoantigen.