# US 2023/0056481 A1 · Methods of diagnosis and therapeutic targeting of clinically intractable malignant tumors

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- Number: US 2023/0056481 A1
- Document ID: US20230056481A1
- Status: Published application
- Kind: A1
- Application number: 17/851,462
- Filed: 2022-06-28
- Published: 2023-02-23
- Earliest claimed: 2016-05-19
- Assignees: OncoScar LLC
- Applicants: OncoScar LLC
- Inventors: Llew Keltner; Guennadi V. Glinskii
- Web page: https://patentgrep.com/patent/US20230056481A1

## CPC

- C12Q 1/6886: for cancer (immunoassay for cancer G01N33/575)
- A61K 31/513: having oxo groups directly attached to the heterocyclic ring, e.g. cytosine
- A61K 31/7088: Compounds having three or more nucleosides or nucleotides
- A61P 35/00: Antineoplastic agents
- A61P 43/00: Drugs for specific purposes, not provided for in groups A61P1/00-A61P41/00
- C12Q 1/702: {for retroviruses}
- G16B 25/00: ICT specially adapted for hybridisation; ICT specially adapted for gene or protein expression
- G16B 25/10: Gene or protein expression profiling; Expression-ratio estimation or normalisation
- 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
- C12Q 2600/106: Pharmacogenomics, i.e. genetic variability in individual responses to drugs and drug metabolism
- C12Q 2600/118: Prognosis of disease development
- C12Q 2600/156: Polymorphic or mutational markers
- C12Q 2600/158: Expression markers
- 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
- A61K: PREPARATIONS FOR MEDICAL, DENTAL OR TOILETRY PURPOSES (devices or methods specially adapted for bringing pharmaceutical products into particular physical or administering forms A61J3/00; chemical aspects of, or use of materials for deodorisation of air, for disinfection or sterilisation, or for bandages, dressings, absorbent pads or surgical articles A61L; soap compositions C11D)
- A61P: SPECIFIC THERAPEUTIC ACTIVITY OF CHEMICAL COMPOUNDS OR MEDICINAL PREPARATIONS
- G16B: BIOINFORMATICS, i.e. INFORMATION AND COMMUNICATION TECHNOLOGY [ICT] SPECIALLY ADAPTED FOR GENETIC OR PROTEIN-RELATED DATA PROCESSING IN COMPUTATIONAL MOLECULAR BIOLOGY

## Abstract

The present disclosure is directed to methodologies or technologies for generating a predictor of a disease state (e.g. cancer-therapy efficacy status, cancer therapy progress, cancer prognosis, cancer diagnosis, therapy failure, relapse, recurrence, and the like) based on genomic and proteomic signatures, gene expression, and pathways & networks activation of endogenous human stem cell-associated retroviruses (SCAR). This disclosure is also directed to methods of targeting, designing, and using treatments for clinically intractable malignant tumors.

## Claims

### Claim at position 1

1-18. (canceled)

### Claim 19

A system for diagnosing cancer or predicting cancer-therapy outcome in a subject, comprising:
circuitry configured to generate target marker information responsive to one or more inputs indicative of a genomic signature pathway and one or more inputs indicative of a proteomic signature pathway of endogenous human Stem Cell-Associated Retroviruses (SCAR); and
circuitry configured to generate aberrant object information responsive to comparing at least one input indicative of an expression levels and at least one input indicative of a sequence of a biological sample with target marker information.

### Claim at position 3

20-23. (canceled)

### Claim 24

A method for diagnosing cancer or predicting cancer-therapy outcome in a subject, comprising:
concurrently screening a biological sample for a presence of an aberrant sequences and an aberrant expression level of one or more target markers associated with a pathway involving genomic and proteomic signatures of endogenous human Stem Cell-Associated Retroviruses (SCAR);
scoring a sequence associated with the biological sample as aberrant when the quality of the sequence is distinct compared with a reference sequence; and
scoring an expression level associated with the biological sample as being aberrant when a detected expression level is above a target threshold coefficient.

### Claim at position 5

25-60. (canceled)

### Claim 61

A method for treating cancer in a subject in need thereof, the method comprising detecting SCARS pathway activation caused by a transcriptionally active Stem Cell-Associated Retroviruses (SCARs) locus or a plurality of transcriptionally active SCARS loci in cancer cells obtained from the subject, wherein the method comprises
detecting the expression of each of the genes in a set of human genes selected from (i) the set of 74 genes listed in FIG. 19A, and (ii) the set of 55 genes listed in FIG. 19B, or both;
determining SCARs pathway activation in the cancer by a method comprising comparing the expression of each gene in the set of genes in (i) and/or (ii) to a reference gene expression value, which is the expression of each gene in nonmalignant somatic tissues, and determining a correlation coefficient for expression of the genes in the cancer and the nonmalignant somatic tissues,
wherein a positive correlation coefficient indicates no SCARS pathway activation and a negative correlation coefficient indicates SCARS pathway activation; and
administering to the subject with SCARs pathway activation in the cancer a therapeutic treatment effective to suppress LTR7/HERVH loci in the cancer cells of the subject.

### Claim 62 (depends on 61)

The method of claim 61, wherein the cancer is prostate cancer.

### Claim 63 (depends on 62)

The method of claim 62, wherein the prostate cancer is a clinically intractable malignant cancer.