Skin cell biomarkers and methods for identifying biomarkers using nucleic acid microarrays

• US 20030232356A1
• Filed: 02/10/2003
• Published: 12/18/2003
• Est. Priority Date: 02/08/2002
• Status: Abandoned Application

• Current Assignee: Mediquest Therapeutics, Inc.
• Original Assignee: Mediquest Therapeutics, Inc.
• Inventors: Davis, Richard L. Jr., Curto, Ernest V., Dooley, Thomas P.
• Application Number:
  US10/361,006
• Publication Number:
  US 20030232356A1
• Time in Patent Office: Days
• US Class Current: 435/6.12
• CPC Class Codes: C12Q 1/6886 for cancer immunoassay for cancer G01N33/574
• CPC Class Codes: C12Q 2600/158 Expression markers
• CPC Class Codes: G16B 25/00 ICT specially adapted for hybridisation; ICT specially adapted for gene or protein expression
• CPC Class Codes: G16B 25/10 Gene or protein expression profiling; Expression-ratio estimation or normalisation

Abstract

The present invention provides biomarker genes of mammalian skin-derived cells. A plurality of differentially-expressed up-regulated (signature) and down-regulated (anti-signature) biomarker genes for human keratinocytes, melanocytes, and fibroblasts are identified. Biomarker genes for cells at abnormal states such as melanoma cells are also provided. Further, there are provided analytical bioinformatic methods for identifying biomarker genes based on nucleic acid microarray data.

Claims

1. A method for identifying one or more biomarker genes for a first type of cells among a group of m different types of cells, from a multiplicity of genes whose expression levels in cells of said group are measured using one or more nucleic acid arrays, thereby generating a plurality of measurements of expression levels for said m types of cells, which method comprises:

(a) calculating, for each gene, a likelihood ratio in said first type of cells by dividing (i) the product of (m−

1) and said measurement for said first type of cells by (ii) the sum of said measurements for said m types of cells excluding the measurement for said first type of cells;

(b) repeating step (a) for (m−

1) times to calculate, for said each gene, a likelihood ratio in each of said m types of cells excluding said first type of cells, thereby obtaining (m−

1) likelihood ratios for said gene; and

(c) comparing said likelihood ratio of step (a) with said (m−

1) likelihood ratios of step (b) for each gene and thereby determining a rank order for said each gene among said multiplicity,

wherein said one or more biomarker genes are identified from said rank order.

2. The method of claim 1, wherein a natural logarithm is taken for each likelihood ratio calculated for each gene in each type of cells in the group and the natural logarithm is designated as the Gibbs likelihood for said each gene, wherein said rank order is determined according to said Gibbs likelihood for said each gene among said multiplicity.

3. The method of claim 2, wherein the comparing further comprises ordering said each gene by said Gibbs likelihoods, or sum of the Gibbs likelihoods for said each gene in the m types of cells, or average of the Gibbs likelihoods for said each gene in the m types of cells, thereby generating a Gibbs gene expression rank, wherein said rank order is determined based on said Gibbs gene expression rank.

4. The method of claim 3, wherein an arithmetic mean of the Gibbs likelihoods for said genes in the multiplicity is taken and a standard deviation of said Gibbs likelihoods in the m types of cells is assessed, wherein the Gibbs likelihoods for said each gene in the first type of cells is represented in the units of said standard deviation plus or minus the corresponding arithmetic mean thereby determining a rank for said each gene in said rank order.

5. The method of claim 4, wherein one or more genes with a Gibbs likelihood greater than u times said standard deviation are designated as up-regulated biomarker genes of said first type of cells.

6. The method of claim 5, wherein u is greater than 1.

7. The method of claim 5, wherein u equals 2.

8. The method of claim 4, wherein one or more genes with a Gibbs likelihood ratio smaller than v times said standard deviation are designated as down-regulated biomarker genes of said first type of cells.

9. The method of claim 8, wherein v is greater than 1.

10. The method of claim 8, wherein v equals 2.

11. The method of claim 1, wherein a median is taken for the likelihood ratios calculated for each gene in the m types of cells, said median being designated as median likelihood, wherein said rank order is determined according to said median likelihood for said each gene among said multiplicity.

12. The method of claim 11, wherein the comparing further comprises generating a median rank distribution by sorting the genes in said multiplicity according to the corresponding median likelihoods, wherein said rank order is determined based on said median gene expression rank.

13. The method of claim 12, wherein an arithmetic mean of the median likelihoods for said genes in the multiplicity is taken and a standard deviation of said median likelihoods in the m types of cells is assessed, wherein the median likelihoods for said each gene in the first type of cells is represented in the units of said standard deviation plus or minus the corresponding arithmetic mean thereby determining a rank for said each gene in said rank order.

14. The method of claim 13, wherein one or more genes with a median likelihood greater than u times said standard deviation are designated as down-regulated biomarker genes of said first type of cells.

15. The method of claim 14, wherein u is greater than 1.

16. The method of claim 14, wherein u equals 2.

17. The method of claim 14, wherein one or more genes with a median likelihood ratio smaller than v times said standard deviation are designated as up-regulated biomarker genes of said first type of cells.

18. The method of claim 17, wherein v is greater than 1.

19. The method of claim 17, wherein v equals 2.

20. The method of claim 1, wherein m is greater than or equals 3.

21. The method of claim 1, wherein the different types of cells are cells or tissues that are normal or abnormal.

22. The method of claim 1, wherein the different types of cells may be exposed to one or more of the treatments selected from the group consisting of treatments with a chemical, a drug, a toxin, a biological agent, an environmental stimulus, and combinations thereof.

23. The method of claim 22, wherein the environmental stimulus comprises electromagnetic radiation, heat, mechanical force, or a combination thereof.

24. The method of claim 1, wherein the different types of cells are skin cells.

25. The method of claim 24, wherein said skin cells comprise keratinocyte cells, melanocyte cells, fibroblast cells or combinations thereof.

26. The method of claim 24, wherein said skin cells comprise melanocyte cells, cutaneous primary melanoma cells, metastatic melanoma cells, or combinations thereof.

27. A gene selected from the group consisting of transducer of ERBB2 member 2, Finkel-Biskis-Reilly murine sarcoma virus, RAB6, homeobox A10, Tax1 binding protein 1, SET binding factor 1, maternally expressed 3, ubiquitination factor E4A, solute carrier family 1 member 3, solute carrier family 2 member 4, heterogeneous nuclear ribonucleoprotein A3, hemogen, apolipoprotein D, cartilage linking protein 1, RNA helicase-related protein, hippocalcin, dystrobrevin alpha, coagulation factor C homolog, putative receptor protein, mitochondrial ornithine transporter, cyclin G2, EST cDNA ID 471826, EST cDNA ID 427657, EST cDNA ID 298104, EST cDNA ID 1571632, EST cDNA ID 591143, and EST cDNA ID 208082 as set forth in Table 10, which gene is an up-regulated biomarker of metastatic melanoma cells.

28. A gene selected from the group consisting of histidyl-tRNA synthetase homolog and an EST cDNA ID 209841 as set forth in Table 9, which gene is an up-regulated biomarker of primary cutaneous melanoma cells.

29. A gene selected from the group consisting of hypothetical protein expressed in osteoblasts, nidogen 2, erythroid alpha-spectrin 1, afx1 transcription factor, and sarcoma-amplified sequence, visinin-like 1, checkpoint suppressor 1, putative nuclear protein, ephrin-B1, biglycan, protein tyrosine phosphatase IVA member 2, prostaglandin E synthase, mitogen-activated protein kinase 10, methylenetetrahydrofolate dehydrogenase, mitochondrial F1 alpha 1 ATP synthase, peroxisomal biogenesis factor 12, pleiomorphic adenoma gene 1, HLA class II region expressed gene K4, coagulation factor VIII-associated, and cardiac muscle slow twitch 2 ATPase, which gene is an up-regulated biomarker of melanocytes.

30. A gene selected from the group consisting of keratin 1, fibroblast growth factor 12, intercellular adhesion molecule 2, hematopoietic protein 1, nuclear domain 10, interleukin-1 receptor-associated kinase, and macrophage associated antigen, which gene is a down-regulated biomarker gene for metastatic melanoma cells.

31. A gene selected from the group consisting of small proline-rich protein 2C, type VIII alpha 1 collagen, type IV alpha 4 collagen, trophinin, chondroitin sulfate proteoglycan 3, activin A receptor type II-like 1, paired box gene 6, homeobox D4, homeobox B5, zinc finger protein 131, special AT-rich sequence binding 1, ubiquitin specific protease 16, pyrolin-5-carboxylate synthetase, neural expressed developmentally down-regulated 5, ribonuclease P (30 kD), protein tyrosine phosphatase (rec F), endothelial lipase, ras homolog gene, valyl-tRNA synthetase 2, arylsulfatase A, aldo-keto reductase 1C1, protein phosphatase 1 regulatory 3C, developmentally regulated GTP-binding 1, 3-hydroxybutyrate dehydrogenase, adipose most abundant transcript, pancreatic polypeptide 2, solute carrier 11A2, solute carrier 22A11, cardiac ankyrin repeat protein, heparin-binding growth factor binding protein, Ewing sarcoma break point region 1, and EST cDNA ID 415281, EST cDNA ID 460258, EST cDNA ID 415235, EST cDNA ID 67330, EST cDNA ID 460247, EST cDNA ID 1522679, EST cDNA ID 378420, EST cDNA ID 341317, EST cDNA ID 461287, EST cDNA ID 415613 as set forth in Table 3, which gene is an up-regulated biomarker for keratinocytes.

32. A gene selected from the group consisting of fibulin 5, interleukin 2 receptor gamma, eukaryotic translation elongation factor 2, mitochondrial ribosomal protein L23, ribosomal protein L7a, SEC23-like protein B, solute carrier family 16A3, metallothionein 1F, metallothionein 1H, interferon induced transmembrane 2, Dickkopf homolog 3, episialin, high mobility group protein I-C, and growth factor receptor-bound protein 14, EST cDNA ID 1049033, and EST cDNA ID 378458 as set forth in Table 2, which gene is an up-regulated biomarker for fibroblasts.

33. A gene selected from the group consisting of galectin 3, syndecan binding protein (syntenin), dystroglycan 1, prostate differentiation factor, glutaminyl cyclotransferase, Na+/K+ transporting ATPase alpha 1, cAMP-dependent protein kinase I alpha 1, protein tyrosine phosphatase IVA 2, fyn oncogene, 6-pyruvoyl-tetrahydropterin synthase, dihydopyrimidinase, pirin, major histocompatibility complex I-C, 4F2 antigen heavy chain (solute carrier 3), abl-interactor 2b, coxsackie virus and adenovirus receptor, prostatic binding protein, proteolipid protein 1, v-abl oncogene 1, ets2 repressor factor, proline-rich Gla 1, axin 1 up-regulated, voltage-gated K+ channel beta subunit, vaccinia-related kinase 3, EST cDNA ID 712604, EST cDNA ID 267859, EST cDNA ID 320588, EST cDNA ID 305843, as set forth in Table 3, which gene is an up-regulated biomarker of melanocytes.

34. A gene selected from the group consisting of MIC2 (antigen to antibodies 12E7, F21, and O13), microtubule-associated protein 1B, monocytic leukemia zinc finger protein, Clathrin heavy chain 1, non-metastatic cells 4, TC10-like Rho GTPase, Myclin gene expression factor 2, and CAAX box 1, EST cDNA ID 53371, and EST cDNA ID 1467936 as set forth in Table 4, which gene is a down-regulated biomarker for keratinocytes.

35. A gene selected from the group consisting of long chain 2 of Fatty-acid coenzyme A ligase, calcium modulating ligand, and nuclear receptor coactivator 3 (amplified breast cancer—

AIBI), which gene is a down-regulated biomarker for fibroblasts.

36. A gene selected from the group consisting of ribosomal protein L30 and orosomucoid 1, which gene is a down-regulated biomarker for melanocytes.

37. A sequence selected from the group consisting of the genes and sequences identified in Tables 1-11, and combinations thereof, which is a diagnostic biomarker for a mammal.

38. The sequence of claim 37, wherein the mammal is a human.

39. The sequence selected from the group consisting of the genes and sequences identified on Tables 1-11, and combinations thereof, which is a molecular target for therapeutics of a mammalian disorder or for the discovery of therapeutics of a mammalian disorder.

40. The sequence of claim 39, wherein the mammalian disorder is a human disorder.