# US 2014/0193419 A1 · Methods and compositions for treating and diagnosing diseases

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- Number: US 2014/0193419 A1
- Document ID: US20140193419A1
- Status: Published application
- Kind: A1
- Application number: 14/098,888
- Filed: 2013-12-06
- Published: 2014-07-10
- Earliest claimed: 2006-12-07
- Assignees: Celera Corporation
- Applicants: Celera Corporation
- Inventors: Steve RUBEN; Karen VAN ORDEN; Bruno DOMON; Candy LEE; Tao HE; Mehdi MESRI; Elizabeth JOSELOFF; Katherine MCKINNON; Paul MOORE; Charles BIRSE
- Web page: https://patentgrep.com/patent/US20140193419A1

## CPC

- A61K 47/6843: {the antibody targeting a material from animals or humans}
- A61P 35/00: Antineoplastic agents
- C07K 14/47: from mammals
- C07K 16/18: against material from animals or humans
- C12N 15/113: Non-coding nucleic acids modulating the expression of genes, e.g. antisense oligonucleotides; {Antisense DNA or RNA; Triplex- forming oligonucleotides; Catalytic nucleic acids, e.g. ribozymes; Nucleic acids used in co-suppression or gene silencing (when used in plants C12N15/8218)}
- C12Q 1/6886: for cancer (immunoassay for cancer G01N33/575)
- G01N 33/575: for cancer
- G01N 33/5752: of the lungs
- G01N 33/5758: {involving compounds serving as markers for tumours, cancers or neoplasias, e.g. cellular determinants, receptors, heat shock/stress proteins, A-protein, oligosaccharides or metabolites}
- G01N 33/6893: {related to diseases not provided for elsewhere}
- A61K 38/00: Medicinal preparations containing peptides (peptides containing beta-lactam rings A61K31/00; cyclic dipeptides not having in their molecule any other peptide link than those which form their ring, e.g. piperazine-2,5-diones, A61K31/00; ergot alkaloids of the cyclic peptide type A61K31/48; containing macromolecular compounds having statistically distributed amino acid units A61K31/74; medicinal preparations containing antigens or antibodies A61K39/00; medicinal preparations characterised by the non-active ingredients, e.g. peptides as drug carriers, A61K47/00)
- A61K 2039/505: {comprising antibodies}
- C07K 2317/24: containing regions, domains or residues from different species, e.g. chimeric, humanized or veneered
- C07K 2317/54: F(ab')2
- C07K 2317/55: Fab or Fab'
- C07K 2317/56: variable (Fv) region, i.e. VH and/or VL
- C07K 2317/622: Single chain antibody (scFv)
- C12N 2310/11: Antisense
- C12N 2310/14: interfering nucleic acids [NA]
- C12N 2330/30: chemically synthesised
- C12Q 2600/106: Pharmacogenomics, i.e. genetic variability in individual responses to drugs and drug metabolism
- C12Q 2600/118: Prognosis of disease development
- C12Q 2600/136: Screening for pharmacological compounds
- G01N 2500/10: involving cells
- Y10T 436/143333: Saccharide [e.g., DNA, etc.]
- 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
- C07K: PEPTIDES (peptides in foodstuffs A23; obtaining protein compositions for foodstuffs, working-up proteins for foodstuffs A23J; preparations for medicinal purposes A61K; peptides containing beta-lactam rings C07D; cyclic dipeptides not having in their molecule any other peptide link than those which form their ring, e.g. piperazine-2,5-diones, C07D; ergot alkaloids of the cyclic peptide type C07D519/02; macromolecular compounds having statistically distributed amino acid units in their molecules, i.e. when the preparation does not provide for a specific; but for a random sequence of the amino acid units, homopolyamides and block copolyamides derived from amino acids C08G69/00; macromolecular products derived from proteins C08H1/00; preparation of glue or gelatine C09H; single cell proteins, enzymes C12N; genetic engineering processes for obtaining peptides C12N15/00; compositions for measuring or testing processes involving enzymes C12Q; investigation or analysis of biological material G01N33/00)
- C12N: MICROORGANISMS OR ENZYMES; COMPOSITIONS THEREOF; PROPAGATING, PRESERVING, OR MAINTAINING MICROORGANISMS; MUTATION OR GENETIC ENGINEERING; CULTURE MEDIA (microbiological testing media C12Q1/00)
- 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
- G01N: INVESTIGATING OR ANALYSING MATERIALS BY DETERMINING THEIR CHEMICAL OR PHYSICAL PROPERTIES (measuring or testing apparatus or processes other than immunoassay, involving enzymes or microorganisms C12M, C12Q)
- Y10T: TECHNICAL SUBJECTS COVERED BY FORMER US CLASSIFICATION

## Abstract

Methods and compositions for diagnosing and treating diseases, particularly cancer, associated with differential expression of cancer-associated targets (CAT) in disease cells compared to healthy cells are provided. Also provided are antagonists and agonists of CAT, and methods for screening agents that modulate CAT level or activity in vivo or in vitro.

## Claims

### Claim 1

An isolated CAT protein comprising an amino acid sequence selected from the group consisting of SEQ ID NOS:1-4, 9, 11-12, 16-19, 24-36, 51-59, 69-74, 81-85, 91-102, 115-116, 119-121, 127-134, 144-145, 148-149, 152-159, 168-174, and 182-183.

### Claim 2 (depends on 1)

A composition comprising the CAT protein of claim 1 and a pharmaceutically acceptable carrier.

### Claim 3

An isolated nucleic acid molecule comprising a nucleotide sequence selected from the group consisting of:
a) SEQ ID NOS:5-8, 10, 13-15, 20-23, 37-50, 60-68, 75-80, 86-90, 103-114, 117-118, 122-126, 135-143, 146-147, 150-151, 160-167, 175-181, 184-185;
b) nucleotide sequences that encode a CAT protein comprising an amino acid sequence selected from the group consisting of SEQ ID NOS:1-4, 9, 11-12, 16-19, 24-36, 51-59, 69-74, 81-85, 91-102, 115-116, 119-121, 127-134, 144-145, 148-149, 152-159, 168-174, and 182-183; and
c) nucleotide sequences that are completely complementary to the nucleotide sequences of a) or b).

### Claim 4 (depends on 3)

An isolated RNAi or antisense nucleic acid molecule that selectively binds to the nucleic acid molecule of claim 3.

### Claim 5 (depends on 1)

An isolated antibody that selectively binds to the CAT protein of claim 1.

### Claim 6 (depends on 5)

The antibody of claim 5, wherein the antibody is at least one of a monoclonal, polyclonal, fully human, humanized, chimeric, single-chain, or anti-idiotypic antibody.

### Claim 7 (depends on 5)

A cell line, hybridoma, phage, or transgenic organism that produces the antibody of claim 5.

### Claim 8 (depends on 5)

The antibody of claim 5, wherein the antibody is coupled to a composition selected from the group consisting of detectable substances and therapeutic agents.

### Claim 9 (depends on 5)

A composition comprising the antibody of claim 5 and a pharmaceutically acceptable carrier.

### Claim 10 (depends on 5)

An isolated antibody fragment of the antibody of claim 5, wherein the antibody fragment comprises a fragment selected from the group consisting of:
a) an Fab fragment;
b) an F(ab′)2 fragment; and
c) an Fv fragment.

### Claim 11 (depends on 5)

A method of modulating cell proliferation or apoptosis, the method comprising contacting a cell with the antibody of claim 5.

### Claim 12 (depends on 11)

The method of claim 11, wherein the method comprises either inhibiting proliferation of cancer cells or stimulating apoptosis of cancer cells.

### Claim 13 (depends on 4)

A method of modulating cell proliferation or apoptosis, the method comprising contacting a cell with the RNAi or antisense nucleic acid molecule of claim 4.

### Claim 14 (depends on 1)

A method of detecting the CAT protein of claim 1 in a sample, the method comprising contacting the sample with an isolated antibody that selectively binds to the CAT protein and determining whether the antibody binds to the CAT protein.

### Claim 15 (depends on 3)

A method of detecting the nucleic acid molecule of claim 3 in a sample, the method comprising contacting the sample with an oligonucleotide that specifically hybridizes to the nucleic acid molecule and determining whether the oligonucleotide binds to the nucleic acid molecule.

### Claim 16

A method of diagnosing, prognosing, or determining risk of cancer in a subject, the method comprising detecting at least one molecule in a sample, wherein the presence or abundance of the molecule is indicative of cancer, and wherein the molecule is selected from the group consisting of:
a) CAT proteins comprising an amino acid sequence selected from the group consisting of SEQ ID NOS:1-4, 9, 11-12, 16-19, 24-36, 51-59, 69-74, 81-85, 91-102, 115-116, 119-121, 127-134, 144-145, 148-149, 152-159, 168-174, and 182-183;
b) antibodies that selectively bind to the CAT protein of a);
c) nucleic acid molecules comprising a nucleotide sequence selected from the group consisting of SEQ ID NOS:5-8, 10, 13-15, 20-23, 37-50, 60-68, 75-80, 86-90, 103-114, 117-118, 122-126, 135-143, 146-147, 150-151, 160-167, 175-181, 184-185 and nucleotide sequences that encode the CAT protein of a); and
d) nucleic acid molecules comprising a nucleotide sequence that is completely complementary to the nucleic acid molecule of c).

### Claim 17 (depends on 5)

A method of treating cancer, the method comprising administering a therapeutically effective amount of the antibody of claim 5 to a subject.

### Claim 18 (depends on 1)

A method of screening agents, the method comprising contacting the CAT protein of claim 1 or a cell that expresses the CAT protein with an agent, and assaying for whether the agent binds to the CAT protein or modulates the function, activity, or expression of the CAT protein.

### Claim 19 (depends on 18)

A composition comprising the agent identified by the method of claim 18 and a pharmaceutically acceptable carrier.

### Claim 20 (depends on 1)

A method of determining or predicting the effectiveness of a treatment or selecting a treatment for administration to a subject having cancer, the method comprising detecting the presence, abundance, or activity of the CAT protein of claim 1 in a sample and determining or predicting the effectiveness of the treatment or selecting the treatment for administration based on the presence, abundance, or activity of the CAT protein.