# US 11,309,059 B2 · Medical prognosis and prediction of treatment response using multiple cellular signalling pathway activities

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- Number: US 11,309,059 B2
- Document ID: US11309059B2
- Status: Granted
- Kind: B2
- Application number: 14/785,400
- Filed: 2014-04-24
- Published: 2016-04-21
- Granted: 2022-04-19
- Earliest claimed: 2013-04-26
- Assignees: Koninklijke Philips N.V.
- Applicants: Koninklijke Philips N.V.
- Inventors: Wilhelmus Franciscus Johannes Verhaegh; Hendrik Jan Van Ooijen; Anja Van De Stolpe; Marcia Alves De Inda
- Web page: https://patentgrep.com/patent/US11309059B2

## CPC

- G16B 5/20: Probabilistic models
- C12Q 1/6886: for cancer (immunoassay for cancer G01N33/575)
- G16B 5/00: ICT specially adapted for modelling or simulations in systems biology, e.g. gene-regulatory networks, protein interaction networks or metabolic networks
- 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 25/10: Gene or protein expression profiling; Expression-ratio estimation or normalisation
- G16H 50/30: for calculating health indices; for individual health risk assessment
- C12Q 2600/118: Prognosis of disease development
- C12Q 2600/158: Expression markers
- G16B 25/00: ICT specially adapted for hybridisation; ICT specially adapted for gene or protein expression
- 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
- G16H: HEALTHCARE INFORMATICS, i.e. INFORMATION AND COMMUNICATION TECHNOLOGY [ICT] SPECIALLY ADAPTED FOR THE HANDLING OR PROCESSING OF MEDICAL OR HEALTHCARE DATA

## Abstract

A method for determining a risk score that indicates a risk that a clinical event will occur within a certain period of time. The risk score is based at least in part on a combination of inferred activities of two or more cellular signaling pathways in a tissue and/or cells and/or a body fluid of a subject. The cellular signaling pathways comprise a Wnt pathway, an ER pathway, an HH pathway, and/or an AR pathway. The risk score is defined such that the indicated risk that the clinical event will occur within the certain period of time decreases with an increasing PER and increases with an increasing max(PWnt, PHH), wherein PER, PWnt, and PHH denote the inferred activity of the ER pathway, the Wnt pathway, and the HH pathway, respectively.

## Claims

### Claim 1

A method comprising:
obtaining a sample from a subject, comprising tissue and/or cells and/or a body fluid of the subject;
measuring, from the obtained sample, expression levels of one or more target gene(s) of each of at least three cellular signaling pathways;
inferring, by a processor, activities of the at least three cellular signaling pathways in the tissue and/or cells and/or a body fluid of the subject based at least on the measured expression levels of the one or more target gene(s) of each of the at least three cellular signaling pathways,
determining, by the processor, a risk score that indicates a risk that a clinical event will occur within a certain period of time, based at least in part on a combination of the inferred activities, wherein the clinical event is the occurrence or recurrence of cancer in the subject,
deciding, by the processor, a treatment recommended for the subject based at least in part on the indicated risk that the clinical event will occur within the certain period of time, wherein the recommended treatment comprises at least one or more of hormone treatment and chemotherapy configured to prevent or minimize the occurrence or recurrence of cancer in the subject when the indicated risk is a low risk that the clinical event will occur within the certain period of time, and wherein the recommended treatment comprises at least one or more of chemotherapy, radiation therapy, and immunotherapy configured to prevent or minimize the occurrence or recurrence of cancer in the subject when the indicated risk is an intermediate or high risk that the clinical event will occur within the certain period of time, and
administering the recommended treatment to the subject;
wherein the at least three cellular signaling pathways comprise a Wnt pathway, an ER pathway, and an HH pathway,
wherein the risk score is defined such that the indicated risk that the clinical event will occur within the certain period of time decreases with an increasing PER and increases with an increasing max (Pwnt, PHH), and
wherein PER, Pwnt, and PHH denote the inferred activities of the ER pathway, the Wnt pathway, and the HH pathway, respectively.

### Claim 2 (depends on 1)

The method of claim 1, wherein the combination of the inferred activities comprises the expression
−α·PER+β·max(Pwnt,PHH),
wherein α and β are positive constant scaling factors, and the indicated risk that the clinical event will take place within the certain period of time monotonically increases with an increasing value of the expression.

### Claim 3 (depends on 2)

The method of claim 2, wherein the inferring of the activities of the at least three cellular signaling pathways comprises:
inferring activity of the Wnt pathway in the tissue and/or the cells and/or the body fluid of the subject based at least on expression levels of one or more target gene(s) of the Wnt pathway measured in the extracted sample of the tissue and/or the cells and/or the body fluid of the subject selected from the group consisting of: KIAA1199, AXIN2, RNF43, TBX3, TDGF1, SOX9, ASCL2, IL8, SP5, ZNRF3, KLF6, CCND1, DEFA6, and FZD7, and
inferring activity of the ER pathway in the tissue and/or the cells and/or the body fluid of the subject based at least on expression levels of one or more target gene(s) of the ER pathway measured in the extracted sample of the tissue and/or the cells and/or the body fluid of the subject selected from the group consisting of: GREB1, PGR, XBP1, CA12, SOD1, CTSD, IGFBP4, TFF1, SGK3, NRIP1, CELSR2, WISP2, and AP1B1, and
inferring activity of the HH pathway in the tissue and/or the cells and/or the body fluid of the subject based at least on expression levels of one or more target gene(s) of the HH pathway measured in the extracted sample of the tissue and/or the cells and/or the body fluid of the subject selected from the group consisting of: GLI1, PTCH1, PTCH2, IGFBP6, SPP1, CCND2, FST, FOXL1, CFLAR, TSC22D1, RAB34, S100A9, S100A7, MYCN, FOXM1, GLI3, TCEA2, FYN, and CTSL1, and
inferring activity of an AR pathway in the tissue and/or the cells and/or the body fluid of the subject based at least on expression levels of one or more target gene(s) of the AR pathway measured in the extracted sample of the tissue and/or the cells and/or the body fluid of the subject selected from the group consisting of: KLK2, PMEPA1, TMPRSS2, NKX3 1, ABCC4, KLK3, FKBPS, ELL2, UGT2B15, DHCR24, PPAP2A, NDRG1, LRIG1, CREB3L4, LCP1, GUCY1A3, AR, and EAF2.

### Claim 4 (depends on 3)

The method of claim 3, wherein the inferring of the activities of the at least three cellular signaling pathways is further based on:
expression levels of at least one target gene of the Wnt pathway measured in the extracted sample of the tissue and/or the cells and/or the body fluid of the subject selected from the group consisting of: NKD1, OAT, FAT1, LEF1, GLUL, REG1B, TCF7L2, COL18A1, BIVIP7, SLC1A2, ADRA2C, PPARG, DKK1, HNF1A, and LECT2, and/or
expression levels of at least one target gene of the ER pathway measured in the extracted sample of the tissue and/or the cells and/or the body fluid of the subject selected from the group consisting of: RARA, MYC, DSCAM, EBAG9, COX7A2L, ERBB2, PISD, KRT19, HSPB1, TRIM25, PIMA, COL18A1, CDH26, NDUFV3, PRDM15, ATPSJ, and ESR1, and/or
expression levels of at least one target gene of the HH pathway measured in the extracted sample of the tissue and/or the cells and/or the body fluid of the subject selected from the group consisting of: BCL2, FOXA2, FOXF1, H19, HHIP, IL1R2, JAG2, JUP, MIF, MYLK, NKX2.2, NKX2.8, PITRM1, and TOM1, and/or
expression levels of at least one target gene of the AR pathway measured in the extracted sample of the tissue and/or the cells and/or the body fluid of the subject selected from the group consisting of: APP, NTS, PLAU, CDKN1A, DRG1, FGF8, IGF1, PRKACB, PTPN1, SGK1, and TACC2.

### Claim 5 (depends on 1)

The method of claim 1, further comprising:
assigning, by the processor, the subject to at least one of a plurality of risk groups associated with different indicated risks that the clinical event will occur within the certain period of time, the plurality of risk groups comprising at least a first risk group wherein the subject has a low risk that the clinical event will occur within the certain period of time, and at least a second risk group wherein the subject has an intermediate or high risk that the clinical event will occur within the certain period of time.

### Claim 6 (depends on 5)

The method of claim 5, comprising:
inferring, by the processor, activity of the Wnt pathway in the tissue and/or the cells and/or the body fluid of the subject based at least on expression levels of two, three or more target genes of a set of target genes of the Wnt pathway measured in the extracted sample of the tissue and/or the cells and/or the body fluid of the subject, and/or
inferring, by the processor, activity of the ER pathway in the tissue and/or the cells and/or the body fluid of the subject based at least on expression levels of two, three or more target genes of a set of target genes of the ER pathway measured in the extracted sample of the tissue and/or the cells and/or the body fluid of the subject, and/or
inferring, by the processor, activity of the HH pathway in the tissue and/or the cells and/or the body fluid of the subject based at least on expression levels of two, three or more target genes of a set of target genes of the HH pathway measured in the extracted sample of the tissue and/or the cells and/or the body fluid of the subject, and/or
inferring, by the processor, activity of an AR pathway in the tissue and/or the cells and/or the body fluid of the subject based at least on expression levels of two, three or more target genes of a set of target genes of the AR pathway measured in the extracted sample of the tissue and/or the cells and/pr the body fluid of the subject.

### Claim 7 (depends on 6)

The method of claim 6, wherein
the set of target genes of the Wnt pathway includes at least nine target genes selected from the group consisting of: KIAA1199, AXIN2, RNF43, TBX3, TDGF1, SOX9, ASCL2, IL8, SP5, ZNRF3, KLF6, CCND1, DEFA6, and FZD7, and/or
the set of target genes of the ER pathway includes at least nine target genes selected from the group consisting of: GREB1, PGR, XBPI, CA12, SOD1, CTSD, IGFBP4, TFF1, SGK3, NRIP1, CELSR2, WISP2, and AP1B1, and/or
the set of target genes of the HH pathway includes at least nine target genes selected from the group consisting of: GLI1, PTCH1, PTCH2, IGFBP6, SPP1, CCND2, FST, FOXL1, CFLAR, TSC22D1, RAB34, S100A9, S100A7, MYCN, FOXM1, GLI3, TCEA2, FYN, and CTSL1, and/or
the set of target genes of the AR pathway includes at least nine target genes selected from the group consisting of: KLK2, PMEPA1, TMPRSS2, NKX3_1, ABCC4, KLK3, FKBPS, ELL2, UGT2B15, DHCR24, PPAP2A, NDRG1, LRIG1, CREB3L4, LCP1, GUCY1A3, AR, and EAF2.

### Claim 8 (depends on 7)

The method of claim 7, wherein
the set of target genes of the Wnt pathway further includes at least one target gene selected from the group consisting of: NKD1, OAT, FAT1, LEF1, GLUL, REG1B, TCF7L2, COL18A1, BMP7, SLC1A2, ADRA2C, PPARG, DKK1, HNF1A, and LECT2, and/or
the set of target genes of the ER pathway further includes at least one target gene selected from the group consisting of: RARA, MYC, DSCAM, EBAG9, COX7A2L, ERBB2, PISD, KRT19, HSPB1, TRIM25, PTMA, COL18A1, CDH26, NDUFV3, PRDIVI15, ATPSJ, and ESR1, and/or
the set of target genes of the HH pathway further includes at least one target gene selected from the group consisting of: BCL2, FOXA2, FOXF1, H19, HHIP, IL1R2, JAG2, JUP, MIF, MYLK, NKX2.2, NKX2.8, PITRM1 and TOM1, and/or
the set of target genes of the AR pathway further includes at least one target gene selected from the group consisting of: APP, NTS, PLAU, CDKN1A, DRG1, FGF8, IGF1, PRKACB, PTPN1, SGK1, and TACC2.

### Claim 9 (depends on 8)

The method of claim 8, further comprising combining, by the processor, the risk score and/or at least one of the inferred activities with one or more additional risk scores obtained from one or more additional prognostic tests to obtain a combined risk score, wherein the combined risk score indicates a risk that the clinical event will occur within the certain period of time.

### Claim 10 (depends on 9)

The method of claim 9, further comprising the step of providing, to medical personnel via a display device in communication with the processor, the obtained combined risk score.

### Claim 11 (depends on 1)

The method of claim 1, wherein the at least three cellular signaling pathways further comprise an AR pathway.

### Claim 12 (depends on 1)

The method of claim 1, further comprising the step of extracting mRNA from the obtained sample, wherein the step of measuring expression levels of one or more target gene(s) of each of the at least three cellular signaling pathways comprises analysis of the extracted mRNA.

### Claim 13 (depends on 1)

The method of claim 1, further comprising the step of providing, to medical personnel via a display device in communication with the processor, the determined risk score.

### Claim 14 (depends on 1)

The method of claim 1, further comprising the step of providing, to medical personnel via a display device in communication with the processor, the decided treatment recommended for the subject.

### Claim 15

A method for treating a subject determined to comprise a risk that cancer will occur within a certain period of time, comprising:
receiving a risk score for the subject indicating a risk that cancer will occur within the certain period of time, wherein the risk score is generated by the steps:
(i) receiving measured expression levels of one or more target genes of each of at least three cellular signaling pathways, wherein the expression levels are measured from a sample from a subject, the sample comprising tissue and/or cells and/or a body fluid of the subject;
(ii) inferring activities of the at least three cellular signaling pathways in the tissue and/or cells and/or body fluid of the subject based at least on the expression levels of the one or more target genes of each of the at least three cellular signaling pathways;
(iii) determining a risk score that indicates a risk that cancer will occur within a certain period of time, based at least in part on a combination of the inferred activities, wherein the at least three cellular signaling pathways comprise a Wnt pathway, an ER pathway, and an HH pathway, wherein the risk score is defined such that the indicated risk that the cancer will occur within the certain period of time decreases with an increasing PER and increases with an increasing max (Pwnt, PHH), and wherein PER, Pwnt, and PHH denote the inferred activities of the ER pathway, the Wnt pathway, and the HH pathway, respectively;
identifying a treatment recommended for the subject based at least in part on the received risk for the subject that the cancer will occur within the certain period of time, and
administering the identified treatment to the subject,
wherein the recommended treatment comprises at least one or more of hormone treatment and chemotherapy configured to prevent or minimize occurrence or recurrence of cancer in the subject when the received risk is a low risk that the clinical event will occur within the certain period of time, and wherein the recommended treatment comprises at least one or more of chemotherapy, radiation therapy, and immunotherapy configured to prevent or minimize occurrence or recurrence of cancer in the subject when the received risk is an intermediate or high risk that the clinical event will occur within the certain period of time.

### Claim 16 (depends on 15)

The apparatus of claim 15, wherein the at least three cellular signaling pathways further comprise an AR pathway.