Diagnostic Capabilities Beyond the Tumor Cell Genome

Gregory J. Tsongalis, PhD, HCLD

Professor of Pathology

Director, Molecular PathologyGeisel School of Medicine at Dartmouth

Dartmouth Hitchcock Medical CenterNorris Cotton Cancer Center

Lebanon, NH

gregory.j.tsongalis@hitchcock.org

Outline

• Technology and Personalized Medicine

• miRNAs

• The liquid biopsy

• Beyond that…….

Technology and Therapeutics as Drivers of Medical Care

Basic Science

Clinical Medicine

Translational Research

Clinical Laboratory Medicine

The Genome Or The Human Karyotype

Massively Parallel or Next Generation Sequencing at DHMC

MiSeq PGM

Sequence by Synthesis

Personalized Medicine

Shaw A T and Engelman J A JCO 2013;31:1105-1111

(A) Before crizotinib; (B) after 7 weeks of crizotinib.

NucleusNucleus

CytoplasmCytoplasm

Pri-miRNAPri-miRNA Pre-miRNAPre-miRNA

miRNA:mimiRNA:miRNA* RNA*

duplexduplexUnwindingUnwinding

DroshaDroshaDGCR8DGCR8

Exportin 5Exportin 5

DicerDicer

RISCRISC

RibosomeRibosome

Translational RepressionTranslational Repression mRNA CleavagemRNA Cleavage

C. L. Bartels and G.J. Tsongalis, Clin Chem, 2009;55: 623-631

Specificity(miRNAs as Biomarkers)

miRNA Profiling from Pancreatic FNAs

Szafranska, Doleshal, Edmunds , Gordon , Luttges, Mundingv Barth Jr , Gutmann, Siriawinata , Pipas , Tannapfel , Korc, Hahn, Labourier , Tsongalis . Clin Chem 54(10):1716-1724, 2008.

5

16

4

5

*

** **

Hanoun, Delpu, Suriawinata, Bournet, Bureau, Selves, Tsongalis , Dufresne, Buscail, Cordelier, Torrisani. Clin Chem 56(7):1107-1118, 2010.

24 FFPE matched tumor and normal HNSCC (6 laryngeal, 6 oral tongue)

miRs: 21, 205, 12746 upregulatedmiRs:451, 125b downregulated

Issues With The Tissues

– Tumor tissue has inherent limitations– Tumor tissue is a single snapshot in time– Selection bias due to tumor heterogeneity– Invasive procedure

Resected Specimen Small Needle Core Biopsy

Exhausted Block

A Huge Problem

The Liquid Biopsy

• Cell Free DNA (cfDNA)–Cells undergoing apoptosis or necrosis–Amount of cfDNA correlates with tumor staging and prognosis

http://stm.sciencemag.org/content/6/224/224ra24/F1.large.jpg

Xenograft Model

Kerrington Smith, MD

Promega PlexorHY

J. E. Hill, PhDThayer School of Engineering at Dartmouth

Breath-based Diagnostics

Breath-based Diagnostics

Conclusions

• Circulating nucleic acids become future biomarkers of choice

• More advanced analysis of simpler specimens

Molecular Pathology Laboratory and Translational Research Program

Samantha AllenPaul Burchard

Francine de Abreu, Ph.D.Leanne CookBetty Dokus

Amber ErskineTorrey Gallagher

Arnold HawkJoel Lefferts, Ph.D.

Emmeline LiuRebecca O’MearaJason Peterson

Elizabeth ReaderBarbara Soares

Heather SteinmetzLaura Tafe, M.D.Scott Turner, PhDWendy Wells, M.D.

Terri WilsonEric York