Genome, transcriptome and proteome features of malignant cells as a source of combinatorial

biomarkers for clinical translation

Ancha Baranova

George Mason University, Fairfax, VA

Key word to understanding of cancer phenomenon

PROGRESSION

From bad to worse

then to full catastrophe

LUNG CARCINOMA PROGRESSION

e.g. Smoke

e.g. carcinogen from the smoke

How long it usually takes: DECADES

17 years10.1073/pnas.0712345105; Jones et al., 2008

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.

Major implication for translational research:

1) need for early biomarkers;2) need for evaluation of how far away the tumor was from sprouting metastasis basis for post-

surgical treatment and care

TRUTH: Majority of human tumors sit in our bodies undiagnosed for decades

Problem: in biomarker research all low-hanging fruits already collected

PSA, CEA, AFP….

Single biomarkers have problems with differentiating “grey area” diseases, i.e.

inflammatory conditions

Barak et al., 1989

Controls Prostate cancer

BPH Other cancers

Benign genitourinary diseases

Solution: Biomarker panels

PSA LeveL

Now: from where these biomarker for biomarker panels are usually coming ?

Image courtesy of Purdue University, Dr. W. Andy Tao

A fishing expedition:

Differences often reflect Inflammation,

fibrosis and other

common properties

Two-pronged approach proposed:

Most GENERAL approach:

Most TARGETED approach:

DISTANCE ANALYSIS: Use entire pattern of gene expression to evaluate of how far away the excised tumor was from sprouting metastasis

TUMOR vs. a MIX of various normal cellsPerform transcriptome (in silico) and proteome (using antigen screening) subtractions

Two-pronged approach proposed:

TUMOR vs. a MIX of various normal cellsPerform transcriptome (in silico) and proteome (using antigen screening) subtractions

Most TARGETED approach:

Will uncover tumor biomarkers

that cannot be masked by antigen production

in normal tissue

Based on previous works of collaborative consortium:

Most Targeted Approach: Consortium

Most TARGETED approach:

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)

Two-pronged approach proposed:

Most GENERAL approach:

DISTANCE ANALYSIS: Use entire pattern of gene expression to evaluate of how far away the excised tumor was from sprouting metastasis

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

Two-pronged approach proposed:

Most GENERAL approach:

DISTANCE ANALYSIS: Use entire pattern of gene expression to evaluate of 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)

VISION for the FUTURE

New generation of tumor markers specific to the malignancy but not to the any normal cell type will allow:

1)True early diagnostics of dormant tumors

2) More specific antibody-guided delivery of therapeutic agents to the tumors

Comparison of prognoses for This tumor and That tumor

VISION for the FUTURE

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

VISION for the FUTUREREFERENCE LAB

Profiles 100s normal samples for prostate;

Establishes its own, equipment-specificNORMAL SPACE

For every single tumor sample, the distance from normal tissue space is measured

How bad is my tumor?

Answer: exact distance

from “Ideal” norm

Your tumor