Dissertation/Thesis Abstract

Flow-sorting of Hodgkin Reed-Sternberg cells, low-input sequencing, and bioinformatic profiling: Methodological development and characterization of cancer exomes and transcriptomes
by Reichel, Jonathan B., Ph.D., Weill Medical College of Cornell University, 2015, 153; 3726441
Abstract (Summary)

Here we created, adapted, and applied technological methodologies to ascertain and analyze next-generation sequence data from a range of cancer-related samples. Hodgkin and Reed Sternberg (HRS) cell genomics had not previously been cataloged, due to difficulties acquiring and processing insufficient genomic material from the tumors of classical Hodgkin Lymphoma (cHL) patients. We applied flow cytometric cell sorting and low-input DNA sequencing, generating and analyzing high quality exome and transcriptome data from isolated HRS cells from ten primary cases of cHL. We discovered that nearly all cHL cases belonging to the Nodular Sclerosis subtype harbor inactivating mutations in Beta-2-microglobulin, which leads to lack of protein expression. We showed that ectopic expression of B2M is sufficient to restore MHC-Class1, and that B2M staining is a biomarker for a molecular type of cHL correlated with younger age at presentation and better prognosis.

RNA sequencing can be used to detect additional somatic alterations—such as alternative splicing, highly expressed mutations, and gene fusions—that can serve as cancer driver events as well as evolved mechanisms of drug resistance. We wrote and applied a gene fusion detection algorithm that was used in the discovery of FGFR3-TACC3 from glioblastoma multiforme (GBM) and BATF-TTLL5 in cHL. FGFR3-TACC3 has constitutive kinase activity, induces mitotic and chromosomal segregation defects, triggers aneuploidy, and responds to FGFR kinase inhibition. BATF-TTLL5 is theorized to alter transcriptional control. In addition, we detected and identified previously unreported differentially expressed genes and activated pathways in cHL.

We also investigated cultured and xenografted primary effusion lymphoma (PEL) cells that underwent robust response to treatment with 6-ethylthioinosine (6-ETI), a novel nucleoside analog that is a highly effective and selective inhibitor of primary effusion lymphoma and myeloma after subsequent evolution of drug resistance. Using RNA “resistome” analysis, we identified somatic polymorphisms, exon loss, and differential expression of adenosine kinase (ADK) from among the full transcriptome. Thereafter, ADK was determined to be the mechanism of specificity (and mode of acquired resistance) for this new and preclinically effective drug treatment.

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Indexing (document details)
Advisor: Cesarman, Ethel, Rabadan, Raul
Commitee: Elemento, Olivier, Leslie, Christina, Myers, Chris, Rubin, Mark
School: Weill Medical College of Cornell University
Department: Physiology, Biophysics and Systems Biology
School Location: United States -- New York
Source: DAI-B 77/02(E), Dissertation Abstracts International
Subjects: Genetics, Bioinformatics
Keywords: Cancer, Gene fusion, Hodgkin lymphoma, Illumina, Reed-Sternberg, Sequencing
Publication Number: 3726441
ISBN: 9781339111520
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