Date of Award
7-27-2020
Degree Name
Doctor of Philosophy (PhD)
Degree Type
Dissertation
Abstract
Dynamic changes to the epigenome are essential regulators of cell differentiation and, when disrupted, can be oncogenic. Pervasive epigenetic alternations are a hallmark of many Non-Hodgkin Lymphomas (NHLs), a heterogeneous group of B and T cell cancers with an incidence of 80,000 new cases and 20,000 deaths in the U.S. per year. My thesis studies have defined the epigenetic landscapes of primary human B and T cell lymphomas and linked them to dynamic changes in the transcriptomes of these cancers. The first of these projects focused on mature B cell lymphoma/leukemia (BCL). To identify common and distinct epigenetic perturbations that promote oncogenesis, we compared three subtypes of BCL with normal B lymphocytes. Purified malignant B cells from 52 patients with follicular or diffuse large B cell lymphoma or chronic lymphocytic leukemia and normal B cell subsets from 28 donor tonsils were subjected to chromatin immunoprecipitation and sequencing (ChIP-seq) for H3K4me1, H3K9/14ac, and H3K27ac; FAIRE-seq for open chromatin; RNA-seq; and genome copy number arrays. We identified 113 novel B cell super enhancers (SE). Functional studies showed that one of these novel SEs is connected to the deregulated expression of two immunoglobulin receptors, which may promote uncontrolled B-cell receptor signaling. Our studies also revealed pervasive downregulation across BCL subtypes of crucial B cell identity transcription factors (TF) and tumor suppressors including PU.1 (SPI1), OCT2 (POU2F2), E2A (TCF3), and RUNX3 in concordance with loss of active chromatin marks in adjacent SEs. Motif analysis and TF ChIP-seq indicate that these TFs and SEs form self-regulatory transcriptional feedback loops whose loss inhibits B cell maturation and promotes proliferation. In sum, this study defined common regulome alterations in the 3 major types of mature BCL and implicates SEs as important hubs of tumor-suppressing transcriptional feedback loops whose disruption is a common mechanism driving mature B cell cancers. T cell lymphomas make up less than 8% of NHL cases, Cutaneous T Cell Lymphoma (CTCL) accounting for nearly half of these. CTCL are often treated with histone deacetylase inhibitors (HDACi), which broadly affect the chromatin landscape and protein acetylation, but only 30% of patients respond to drug treatment. We defined differences in histone acetylation of regulatory elements and target gene expression in HDACi-sensitive versus -resistant CTCL. These include genes in apoptotic (BCL2, BIRC5), cell cycle (CDK1, RRM2), and cell adhesion/migration (CCR6, CXCR4, LAIR2) pathways, many of which were not previously associated with CTCL or HDACi- resistance. Expression of some genes, including LAIR2, was elevated in HDACi-resistant samples before and after therapy, suggesting it may be predictive of resistance. Our findings identified new mechanisms of HDACi-resistance in CTCL and define novel predictive markers as potential targets for therapeutic development. Disease progression of CTCL has not been mapped at the genomic or transcriptomic level and thus factors that contribute to progression or therapy resistance are unknown. To address this, we subjected longitudinal samples from 10 CTCL patients to single-cell RNA-seq (scRNA-seq) and exome + low coverage whole genome sequencing (eWGS). We selected 2-4 specimens per patient, consisting of peripheral blood (PB) samples, skin and lymph node biopsies from distinct clinical timepoints separated by 3 months. scRNA- and T-cell receptor (TCR)-seq were performed on 16 PBMC or CD4+ cells from PB samples from six MF/SS patients, sequencing an average of 7413 cells per sample. For eWGS, DNA was isolated from CD4+ cells (PB), unsorted PBMCs, frozen or FFPE biopsies (skin or lymph node) from 25 samples from the same six patients plus an additional four patients, along with patient-matched benign cells as controls. These data will define clonal evolution of the transcriptome and genome during progression of CTCL. The two complementary T cell lymphoma studies defined mechanisms of HDACi resistance, map the clonal evolution of CTCL, and reveal high-resolution intra and inter-sample differences in malignant cell populations that contribute to the pathogenesis and progression of this challenging disease. Taken together, my dissertation work is a focused ‘omics evaluation of the dynamic changes in gene regulation and epigenome landscape in B and T cell cancers in which I collected, processed, and analyzed hundreds of primary cancer samples. Beyond informatics, I performed molecular and cellular experiments to elucidate the functional impact of a prioritized set of epigenetic perturbations that I identified. In sum, my studies defined novel epigenetic alterations that comprise the malignant underpinnings of these diseases.
Language
English (en)
Chair and Committee
Jacqueline Payton
Recommended Citation
Andrews, Jared, "Elucidating Novel Mechanisms and Pathways of Pathogenesis, HDACi Resistance, and Disease Progression in B and T Cell Lymphomas through Integrated ‘omics Analyses" (2020). Arts & Sciences Electronic Theses and Dissertations. 3248.
https://openscholarship.wustl.edu/art_sci_etds/3248