# US 2016/0259883 A1 · Sense-antisense gene pairs for patient stratification, prognosis, and therapeutic biomarkers identification

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- Number: US 2016/0259883 A1
- Document ID: US20160259883A1
- Status: Published application
- Kind: A1
- Application number: 15/030,370
- Filed: 2014-10-20
- Published: 2016-09-08
- Earliest claimed: 2013-10-18
- Applicants: Agency for Science, Technology and Research
- Inventors: Oleg GRINCHUK; Efthimios MOTAKIS; Surya Pavan YENAMANDRA; Vladimir Andreevich KUZNETSOV
- Web page: https://patentgrep.com/patent/US20160259883A1

## CPC

- G16B 25/10: Gene or protein expression profiling; Expression-ratio estimation or normalisation
- C12Q 1/6886: for cancer (immunoassay for cancer G01N33/575)
- G16B 20/00: ICT specially adapted for functional genomics or proteomics, e.g. genotype-phenotype associations
- G16B 20/20: Allele or variant detection, e.g. single nucleotide polymorphism [SNP] detection
- G16B 25/00: ICT specially adapted for hybridisation; ICT specially adapted for gene or protein expression
- G16B 35/00: ICT specially adapted for in silico combinatorial libraries of nucleic acids, proteins or peptides
- G16B 40/00: ICT specially adapted for biostatistics; ICT specially adapted for bioinformatics-related machine learning or data mining, e.g. knowledge discovery or pattern finding
- G16B 40/20: Supervised data analysis
- G16C 20/60: In silico combinatorial chemistry
- C12Q 2600/106: Pharmacogenomics, i.e. genetic variability in individual responses to drugs and drug metabolism
- C12Q 2600/118: Prognosis of disease development
- C12Q 2600/158: Expression markers
- G16B: BIOINFORMATICS, i.e. INFORMATION AND COMMUNICATION TECHNOLOGY [ICT] SPECIALLY ADAPTED FOR GENETIC OR PROTEIN-RELATED DATA PROCESSING IN COMPUTATIONAL MOLECULAR BIOLOGY
- C12Q: MEASURING OR TESTING PROCESSES INVOLVING ENZYMES, NUCLEIC ACIDS OR MICROORGANISMS (immunoassay G01N33/53); COMPOSITIONS OR TEST PAPERS THEREFOR; PROCESSES OF PREPARING SUCH COMPOSITIONS; CONDITION-RESPONSIVE CONTROL IN MICROBIOLOGICAL OR ENZYMOLOGICAL PROCESSES
- G16C: COMPUTATIONAL CHEMISTRY; CHEMOINFORMATICS; COMPUTATIONAL MATERIALS SCIENCE

## Abstract

The present invention relates to a method of identification of clinically and genetically distinct sub-groups of patients subject to a medical condition, particularly breast, lung, and colon cancer patients using a composition of respective gene expression values for certain gene pairs. Sense-antisense gene pairs (SAGPs) which are relevant for a medical condition and the disease prognosis are used by the method to generate statistical models based on the expression values of the SAGPs. SAGPs for which the statistical models are found to have high value in prognosis of the variation of medical condition and the diseases are selected and integrated in the prognostic signature including specified parameters (e.g. cut-off values) of the prognostic model. It further relates to using respective gene expression values for these genes to predict patient′ risk groups (in context of patient's survival or/and disease progression) and to using the predicted groups for identification of patient risk, and specific and robust prognostic biomarkers with mechanistic interpretations of biological changes (associated with the gene signatures) appropriating for an implementation of therapeutic targeting.

## Claims

### Claim 1

A computerized method of identifying candidate biomolecules relevant to a medical condition, the candidate biomolecules being putative clinical biomarkers for prognosis of, or putative therapeutic targets for treating, the medical condition, the method comprising:
for each subject k of a set of K subjects suffering from the medical condition, receiving subject data which indicates (i) for each gene pair i, j of a plurality of sense-antisense gene pairs (SAGPs), corresponding gene expression values yi,k, yj,k of subject k; and (ii) a survival time and survival event of subject k;
identifying, using said subject data, a prognostic subset of said SAGPs which optimally stratifies the subjects into low-risk and high-risk disease progression subgroups;
comparing gene expression values of each gene in the low-risk and high-risk subgroups which have been stratified by said prognostic subset of SAGPs, to identify a set of prognostic genes which are differentially expressed between the low-risk and high-risk subgroups; and
identifying one or more predefined biologically-related categories of genes which are over-represented in the set of differentially expressed prognostic genes, wherein the candidate biomolecules comprise genes or gene products belonging to said over-represented categories.

### Claim 2 (depends on 1)

A computerized method according to claim 1, wherein the set of K subjects comprises a plurality of independent cohorts of subjects.

### Claim 3 (depends on 2)

A computerized method according to claim 2, wherein said differentially expressed prognostic genes are identified by:
for each cohort, identifying a cohort-specific set of genes which is differentially expressed in said cohort, to thereby obtain a plurality of cohort-specific sets; and
finding the intersection of the cohort-specific sets to obtain the set of differentially expressed genes.

### Claim 4 (depends on 1, 2, 3)

A computerized method according to any one of claims 1 to 3, wherein genes in respective predefined categories of biologically-related genes are related by one or more of:
cellular localization, biological process, molecular function, or biological pathway.

### Claim 5

A computerized method according to any one of the preceding claims, wherein identifying the prognostic subset of SAGPs comprises:
generation of a statistical partition model (SPM) for each of each SAGPs using said subject data;
obtaining data characterizing the statistical significance of the SPMs; and
identifying of a subset of said SAGPs using the data characterizing the statistical significance.

### Claim 6 (depends on 5)

A computerized method according to claim 5,
the method comprising for each SAGP:
(i) defining a plurality of trial values for each of two cut-off values ci and cj;
(ii) for each of a plurality of angles α, for each subject, and for each of the trial cut-off values ci and cj:
(a) comparing the expression values to a respective pair of lines in a two-dimensional space spanned by the expression values to obtain comparison data indicating on which side of the pair of lines the expression values for the corresponding subject lie, the pair of lines being formed using the cut-off values ci and cj, each of the lines having angle α to a direction in the space indicating increasing values of a corresponding one of the expression values; and
(b) generating at least one SPM based on the comparison data; and
(iii) selecting the one of the SPMs (‘the maximally predictive SPM’) which has the maximal statistical value in predicting the survival times of the subjects.

### Claim 7 (depends on 6)

A computerized method according to claim 6 in which for each of the plurality of angles α, and for each subject, and for each of the trial cut-off values ci and cj, a plurality of statistical partition models of survival prognosis of the patients are constructed based on a plurality of respective designs, each design representing a respective combination of possibilities for realizations of the comparison data.

### Claim 8 (depends on 7)

A computerized method according to claim 7 in which the comparison data for a given subject, a given angle α, a given said subject, and a given pair of trial cut-off values ci and cj, takes one of four possibilities:
A: indicating that both the corresponding expression values lie on a first side of the lines;
B: indicating that a first of the expression values lies on the first side of a first of the lines, and the second value lies on a second side of the second of the lines;
C: indicating that the first of the expression values lies on a second side of the first of the lines, and the second value lies on the first side of the second of the lines; and
D: indicating that both expression values lie on the second side of the lines;
and the plurality of designs include:
a first design indicating whether the subjects' expression level values are within regions A or D, rather than B or C;
a second design indicating whether the subjects' expression level values are within regions A, B or C, rather than D;
a third design indicating whether the subjects' expression level values are within regions A, C or D, rather than B;
a fourth design indicating whether the subjects' expression level values are within regions B, C or D, rather than A;
a fifth design indicating whether the subjects' expression level values are within regions A, B or D, rather than C;
a sixth design indicating whether the subjects' expression level values are within regions A or C, rather than B or D;
a seventh design indicating whether the subjects' expression level values are within regions A or B, rather than C or D.

### Claim 9 (depends on 6, 7, 8)

A computerized method according to any of claims 6 to 8, comprising selecting the subset of the gene pairs for which the corresponding selected models are of maximal statistical significance of the survival prognosis model.

### Claim 10 (depends on 9)

A computerized method according to claim 9 further including i) a step of determining for each gene of the selected gene pairs the statistical significance of the expression level of the individual genes of the survival prognosis model, and ii) a step of selecting of the gene pairs for which the statistical significance of the maximally predictive SPM is higher than a threshold of the statistical significance of the individual genes of the gene pair.

### Claim 11

A computerized method of clinical outcome prognosis in a subject having a medical condition, the method comprising:
receiving data representing parameters of one or more statistical partition models (SPMs) said SPMs being configured to stratify a cohort of subjects having the medical condition into subgroups, said parameters representing, for each gene pair of one or more sense-antisense gene pairs (SAGPs), a pair of lines in a two-dimensional space spanned by respective expression level values of respective genes i, j in the gene pair, the pair of lines being formed using two cut-off values ci and cj, and each of the lines having a non-zero angle α to each of two axis directions in the space indicating increasing values of a corresponding one of the expression level values;
receiving expression level data representing expression levels in the subject of genes of one or more selected SAGPs; and
for each SAGP of the selected SAGPs, comparing the expression levels to the pair of lines for the SAGP to obtain comparison data indicating on which side of the pair of lines the expression values for the subject lie, thereby obtaining a prediction of a subgroup to which the subject belongs.

### Claim 12 (depends on 11)

A computerized method according to claim 11, wherein the SAGPs comprise one or more of the gene pairs listed in Table 1A.

### Claim 13 (depends on 11, 12)

A computerized method according to claim 11 or claim 12, wherein the medical condition is breast cancer, colon cancer or non-small cell lung cancer, and wherein the SAGPs comprise one or more of the gene pairs listed in Table 1B.

### Claim 14 (depends on 11, 12, 13)

A computerized method according to any one of claims 11 to 13, wherein there are two or more selected SAGPs, and wherein the method comprises combining the predictions of the subgroups from the two or more SAGPs to obtain a composite prediction.

### Claim 15 (depends on 14)

A computerized method according to claim 14, wherein each prediction is represented by a group index, and wherein the predictions are combined by computing a weighted sum of the group indices.

### Claim 16 (depends on 15)

A computerized method according to claim 15, wherein weights of the weighted sum are generated from p-values of respective SPMs corresponding to the selected SAGPs.

### Claim 17

A kit for predicting clinical outcome in a subject having a medical condition, the kit comprising: a plurality of polynucleotide sequences, ones of the plurality of polynucleotide sequences being capable of specifically hybridizing to and/or detecting a gene of a plurality of genes and/or an expression product of the gene to obtain respective gene expression values, wherein the plurality of genes comprises one or more of the sense-antisense gene pairs (SAGPs) listed in Table 1A, and written instructions for comparing, and/or a tangible computer-readable medium having stored thereon machine-readable instructions for causing a computer processor to compare, the respective gene expression values to optimal gene expression cut-off values, wherein the plurality of genes comprises no more than 100 genes; and wherein the optimal gene expression cut-off values are determined for each SAGP by:
(i) defining a plurality of trial values for each of two cut-off values ci and cj;
(ii) for each of a plurality of angles α, for each subject, and for each of the trial cut-off values ci and cj:
(a) comparing the expression values to a respective pair of lines in a two-dimensional space spanned by the expression values to obtain comparison data indicating on which side of the pair of lines the expression values for the corresponding subject lie, the pair of lines being formed using the cut-off values ci and cj, each of the lines having angle α to a direction in the space indicating increasing values of a corresponding one of the expression values; and
(b) generating at least one SPM based on the comparison data; and
(iii) selecting the one of the SPMs (‘the maximally predictive SPM’) which has the maximal statistical value in predicting the survival times of the subjects,
whereby the cut-off values ci and cj for the maximally predictive SPM are the optimal gene expression cut-off values.

### Claim 18 (depends on 17)

A kit according to claim 17, wherein the plurality of genes comprises the sense-antisense gene pairs listed in Table 1A.

### Claim 19 (depends on 17)

A kit according to claim 17, wherein the plurality of genes comprises the sense-antisense gene pairs listed in Table 1B.

### Claim 20 (depends on 17, 18, 19)

A kit according to any one of claims 17 to 19, wherein the polynucleotide sequences are immobilized on a solid support.

### Claim 21 (depends on 17, 18, 19, 20)

A kit according to any one of claims 17 to 20, comprising at least one primer for amplification of one or more of the plurality of genes, or at least part thereof.

### Claim 22 (depends on 21)

A kit according to claim 21, wherein the primers are selected from the primers listed in Table 9.

### Claim 23

A computerized method of composite survival prediction combining the output values from a plurality of SPMs associated with prognosis of a potentially fatal medical condition in each subject k of a set of K subjects suffering from the medical condition, each SPM being a model of the statistical significance of the expression level values of a corresponding set of one or more genes or gene pairs, the method employing test data which for each gene i of the pair of genes indicates a corresponding gene expression value yi,k of subject k;
the method including:
for each subject obtaining for each of the SPMs a respective risk level value indicative of a risk level for the subject;
forming a weighted average of the risk level values using a set of respective weights, the weights being indicative of the relative quality of patient separation according to the given SPM versus others of the respective models in context of statistical significance of the relative risk statistics of the medical condition;
comparing the weighted average with a cut-off value to obtain a prognosis value.

### Claim 26 (depends on 23, 24, 25)

A computerized method according to any one of claims 23 to 25 in which each of said models is a SPM of an individual gene or a gene pair.

### Claim 27 (depends on 6, 23, 24, 25, 26)

A computerized method according to any of claims 23 to 26 in which each of said models is a SPM of a pair of genes obtained by a method according to claim 6 or any claim dependent therefrom.

### Claim 28 (depends on 11, 12, 13, 14, 15, 16)

A computerized method according to any one of claims 11 to 16, wherein the medical condition is Estrogen Receptor positive (ER“+”), Lymph Node negative (LN“−”) breast cancer, and wherein the subject has received adjuvant systemic tamoxifen treatment upon or after curative surgery.

### Claim 29 (depends on 28)

A computerized method according to claim 28 in which the selected gene pair is or the selected gene pairs include the RNF139/TATDN1 SAGP.

### Claim 30 (depends on 11, 12, 13, 14, 15)

A computerized method according to any one of claims 11 to 15, wherein the medical condition is a grade 3 breast tumor.

### Claim 31 (depends on 30)

A computerized method according to claim 30 in which the selected gene pair is or the selected gene pairs include the VPRBP/RBM15B SAGP.

### Claim 32 (depends on 11, 12, 13, 14, 15, 16)

A computerized method according to any one of claims 11 to 16, wherein the medical condition is a grade 3 or grade 3-like breast tumor.

### Claim 33 (depends on 32)

A computerized method according to claim 32 in which the selected gene pair is or the selected gene pairs include the C18orf8/NPC1 and/or the EME1/LRRC59 SAGP.

### Claim 34 (depends on 11, 12, 13, 14, 15)

A computerized method according to any one of claims 11 to 15, wherein the medical condition is a grade 1 or grade 1-like breast tumor.

### Claim 35 (depends on 34)

A computerized method according to claim 34 in which the selected gene pair is or the selected gene pairs include the SHMT1/SMCR8 SAGP.

### Claim 36 (depends on 11, 12, 13, 14, 15, 16)

A computerized method according to any one of claims 11 to 16, wherein the medical condition is a grade 1 breast tumor.

### Claim 37 (depends on 11, 12, 13, 14, 15, 16)

A computerized method according to any one of claims 11 to 16, wherein the medical condition is Estrogen Receptor negative (ER“−”) breast cancer.

### Claim 38 (depends on 37)

A computerized method according to claim 37 in which the selected gene pair is or the selected gene pairs include the CTNS/TAX1BP3 SAGP.

### Claim 39 (depends on 11, 12, 13, 14, 15, 16)

A computerized method according to any one of claims 11 to 16, wherein the medical condition is a basal-like grade 3 (G3) breast tumor.

### Claim 40 (depends on 39)

A computerized method according to claim 39 in which the selected gene pair is or the selected gene pairs include the CTNS/TAX1BP3 and/or the RNF139/TATDN1 SAGP.

### Claim 41 (depends on 11, 12, 13, 14, 15, 16)

A computerized method according to any one of claims 11 to 16, wherein the medical condition is a Luminal A breast tumor.

### Claim 42 (depends on 41)

A computerized method according to claim 41 in which the selected gene pair is or the selected gene pairs include the BIVM/KDELC1 SAGPs.

### Claim 43 (depends on 11, 12, 13, 14, 15, 16)

A computerized method according to any one of claims 11 to 16, wherein the medical condition is ER“+”, LN“−”, Progesterone Receptor positive (PgR“+”) breast cancer and the subject has a breast tumor <=2 cm.

### Claim 44 (depends on 1, 2, 3, 4)

A method of prognosis of survival or treatment response in a subject suffering from breast cancer, comprising:
obtaining a test sample from the subject;
measuring a gene expression level in the test sample for one or more of the prognostic genes obtained according to claims 1 to 4 and listed in Table 11; and
comparing the measured gene expression level to a predefined threshold;
wherein a measured gene expression level which is above the predefined threshold is indicative of a poor prognosis.

### Claim 45 (depends on 44)

A method according to claim 44, wherein the one or more genes comprises one or more of the genes listed in Table 10.

### Claim 46 (depends on 44, 45)

A method according to claim 44 or claim 45, wherein said measuring comprises contacting with the sample at least one nucleic acid probe capable of specifically hybridizing to the one or more genes or part thereof.

### Claim 47

A kit for prognosis of survival or treatment response in a subject having breast cancer, the kit comprising: at least one nucleic acid probe capable of specifically hybridizing to and/or detecting a gene of a plurality of genes and/or an expression product of the gene, wherein the plurality of genes comprises one or more of the genes listed in Table 11, and wherein the plurality of genes comprises no more than 200 genes.

### Claim 48 (depends on 47)

A kit according to claim 47, wherein the plurality of genes comprises the genes listed in Table 11.

### Claim 49 (depends on 47)

A kit according to claim 47, wherein the plurality of genes comprises the genes listed in Table 10.

### Claim 50 (depends on 47, 48, 49)

A kit according to any one of claims 47 to 49, wherein the nucleic acid probe or probes is or are immobilized on a solid support.

### Claim 51 (depends on 47, 48, 49, 50)

A kit according to any one of claims 47 to 50, comprising at least one primer for amplification of one or more of the plurality of genes, or part thereof.

### Claim 52 (depends on 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46)

A system for identifying candidate biomolecules relevant to a medical condition, the candidate biomolecules being putative clinical biomarkers for prognosis of, or putative therapeutic targets for treating, the medical condition; or for clinical outcome prognosis in a subject having a medical condition; or for composite survival prediction combining the output values from a plurality of SPMs associated with prognosis of a potentially fatal medical condition; or for prognosis of survival or treatment response in a subject suffering from breast cancer; the system comprising: at least one processor; and a tangible computer-readable storage medium having stored thereon machine-readable instructions for causing the at least one processor to perform the method according to any one of claims 1 to 16 or 23 to 46.