Ancha Baranova George Mason University, Fairfax, VA

1. Genome, transcriptome and proteome features of malignant cells as a source of combinatorial biomarkers for clinical translation Ancha Baranova George Mason University, Fairfax, VA

2. Key word to understanding of cancer phenomenon PROGRESSION From bad to worse then to full catastrophe

3. LUNG CARCINOMA PROGRESSION e.g. carcinogen from the smoke e.g. Smoke

4. How long it usually takes: DECADES It takes ≈17 years for a large benign tumor to evolve into an advanced cancer but <2 years for cells within that cancer to acquire the ability to metastasize Sequencing studies show that virtually all of the mutations necessary for metastasis are already present in all of the cells of the antecedent carcinoma. 10.1073/pnas.0712345105; Jones et al., 2008 17 years

5. TRUTH: Majority of human tumors sit in our bodies undiagnosed for decades Major implication for translational research: 1) need for early biomarkers;2) need for evaluationof how far away the tumor was from sprouting metastasis  basis for post-surgical treatment and care

6. Problem: in biomarker research all low-hanging fruits already collected PSA, CEA, AFP….

7. Single biomarkers have problems with differentiating “grey area” diseases, i.e. inflammatory conditions Solution: Biomarker panels PSA LeveL Controls Prostate cancer Other cancers Benign genitourinary diseases BPH Barak et al., 1989

8. Now: from where these biomarker for biomarker panels are usually coming ? A fishing expedition: Differences often reflect Inflammation, fibrosis and other common properties Image courtesy of Purdue University, Dr. W. Andy Tao

9. Two-pronged approach proposed: TUMOR vs. a MIX of various normal cells Performtranscriptome (in silico) and proteome (using antigen screening) subtractions DISTANCE ANALYSIS: Use entire pattern of gene expression to evaluateof how far away the excised tumor was from sprouting metastasis Most TARGETED approach: Most GENERAL approach:

10. Two-pronged approach proposed: Will uncover tumor biomarkers that cannot be masked by antigen production in normal tissue Based on previous works of collaborative consortium: TUMOR vs. a MIX of various normal cells Performtranscriptome (in silico) and proteome (using antigen screening) subtractions Most TARGETED approach:

11. Most Targeted Approach: Consortium Blokhin Russian Oncological Scientific Center, Moscow (sample collection and processing) Caerus Discovery LLC, Manassas, VA (capture of protein biomarker as differentially expressed antigens) Institute of Chemical Biology and Fundamental Medicine SB RAS, Novosibirsk (development of tumor protein biomarkers as targets for antibody-guided drug delivery) Biomedical Center, StPeterburg (differential display of tumor RNAs) Research Center for Medical Genetics RAMS (non-coding Tumor RNAs) George Mason University, Fairfax, USA (biomarker validation, bioinformatics support and general coordination) Most TARGETED approach:

12. Two-pronged approach proposed: DISTANCE ANALYSIS: Use entire pattern of gene expression to evaluateof how far away the excised tumor was from sprouting metastasis Most GENERAL approach:

13. Simple words explanation forusing entire transcriptome as biomarker • Who is that? -- Instant answer (same person, Darwin) Biomarker approach: X: Distance from the end of nose to the upper lip Y: Diameter of the eye orbit Z: Number of hairs in the beard

14. Two-pronged approach proposed: DISTANCE ANALYSIS: Use entire pattern of gene expression to evaluateof how far away the excised tumor was from sprouting metastasis Blokhin Russian Oncological Scientific Center, Moscow (sample collection and processing) Institute of Chemical Biology and Fundamental Medicine SB RAS, Novosibirsk (next gene sequencing and microarray) Vavilov Institute of General Genetics (next gene sequencing and microarray) Research Center for Medical Genetics RAMS (distance analysis of samples based on summed evaluation of non-coding RNAs) University of Arkansas for Medical Sciences (Little Rock, AK) (distance analysis of whole genome patterns) George Mason University, Fairfax, USA (development of attractor descriptors, bioinformatics support and general coordination) Most GENERAL approach:

15. VISION for the FUTURE New generation of tumor markers specific to the malignancy but not to the any normal cell type will allow: • True early diagnostics of dormant tumors 2) More specific antibody-guided delivery of therapeutic agents to the tumors

16. VISION for the FUTURE Comparison of prognoses for This tumor and That tumor

17. Same strategy can be realized using NextGen Seq Very possible; low sequence coverage of transcripts will be enough; cost-efficient cut-off needs to be determined

18. VISION for the FUTURE REFERENCE LAB Profiles 100s normal samples for prostate; Establishes its own, equipment-specific NORMAL SPACE For every single tumor sample, the distance from normal tissue space is measured

19. How bad is my tumor? Answer: exact distance from “Ideal” norm Your tumor