Li, Xing

Almudena Martinez Fernandez, 2012 Finalist and Presenting Author

Abstract Chronic lymphocytic leukemia (CLL) is the most common adult leukemia in western countries that has a strong genetic basis. Using data from both chromatin immunoprecipitation and sequencing (ChIP-seq) and assay for transposase-accessible chromatin using sequencing (ATAC-seq), recent studies have uncovered alterations of chromatin landscape in CLL. However, the spectrum of epigenetic changes and the mechanisms of casualtyare only partially understood. In this study, we used ATAC-seq to profile chromatin accessibility across the two major CLL subtypes, IGHV-mutated (n=19) and IGHV-unmutated (n=22). DNA library of accessible chromatin regions was generated from purified CD5+/CD19+ leukemiacells. All libraries were assessed to have high data quality based on the ENCODE quality metrics. Additionally, publicly available ATAC-seq data (GSE118189 and GSE111015) from total (n=5), memory (n=6) and naïve B cells (n=6) were analyzed in parallel and used as normal reference. ATAC-seq peaks from CLL and normal B cells were merged to generate a consensus list of 107,928 high-confidence peaks that did not overlap ENCODE blacklisted regions, were present in at least two CLL or two normal B-cell samples, and had ≥1 counts-per-million in at least 10% of the samples. Raw read counts were Trimmed Mean of M-values normalized and log2 transformed. K-means clustering of differential peaks revealed an extensive reprogramming of chromatin accessibility landscape in CLL, with over 11,000 lost and nearly 9,000 gained open chromatin regions relative to normal B-cells. In particular, we identified two clusters comprising 1,401 regions that were largely open either in IGHV-mutated(571 peaks) or in IGHV-unmutated CLL (830 peaks). Open chromatin regions gained in IGHV-mutatedwere preferentially linked to genes in the B cell receptor signaling pathway and those in IGHV-mutatedto genes enriched in the interferon type I signaling pathway. These discriminatory regions are highly enriched with DNA binding motifs for transcription factors (TFs) with key roles in B cell development, such as PU.1, AP-1, c-Jun, BATF, and TCF family. In addition, 94% of the 1,401 peaks were located in distal regulatory regions, being ≥2.5 kb away from transcription start sites of genes; two-third of these distal regulatory regions overlapped H3K27ac peaks from CLL patients or immune cell types in the Roadmap reference epigenomes,indicating that enhancers are the prime sites of epigenetic differentiation between the two subtypes. Together, our analyses provide new insights into the global alterations of regulatory regions in CLL. Given the noticeable heterogeneity of chromatin landscape, further integration with histone modifications, TF binding, chromatin interaction, gene expression and genetic variation data are needed to understand the roles of epigenetic dysregulation and its interaction with genetic lesions in CLL pathogenesis. Citation Format: Huihuang Yan, Zhiquan Wang, Shulan Tian, Geffen Kleinstern, Nicholas Boddicker, Xing Li, Susan Slager, Esteban Braggio. Widespread alterations of chromatin accessibility in chronic lymphocytic leukemia (CLL) [abstract]. In: Proceedings of the Annual Meeting of the American Association for Cancer Research 2020; 2020 Apr 27-28 and Jun 22-24. Philadelphia (PA): AACR; Cancer Res 2020;80(16 Suppl):Abstract nr 1256.

Background— Cardiac development is a complex process resulting in an integrated, multilineage tissue with developmental corruption in early embryogenesis leading to congenital heart disease. Interrogation of individual genes has provided the backbone for cardiac developmental biology, yet a comprehensive transcriptome derived from natural cardiogenesis is required to gauge innate developmental milestones. Methods and Results— Stage-specific cardiac structures were dissected from 8 distinctive mouse embryonic time points to produce genome-wide expressome analysis across cardiogenesis. With reference to this native cardiogenic expression roadmap, divergent induced pluripotent stem cell–derived cardiac expression profiles were mapped from procardiogenic 3-factor (SOX2, OCT4, KLF4) and less-cardiogenic 4-factor (plus c-MYC) reprogrammed cells. Expression of cardiac-related genes from 3-factor–induced pluripotent stem cell differentiated in vitro at days 5 and 11 and recapitulated expression profiles of natural embryos at days E7.5-E8.5 and E14.5-E18.5, respectively. By contrast, 4-factor–induced pluripotent stem cells demonstrated incomplete cardiogenic gene expression profiles beginning at day 5 of differentiation. Differential gene expression within the pluripotent state revealed 23 distinguishing candidate genes among pluripotent cell lines with divergent cardiogenic potentials. A confirmed panel of 12 genes, differentially expressed between high and low cardiogenic lines, was transformed into a predictive score sufficient to discriminate individual induced pluripotent stem cell lines according to relative cardiogenic potential. Conclusions— Transcriptome analysis attuned to natural embryonic cardiogenesis provides a robust platform to probe coordinated cardiac specification and maturation from bioengineered stem cell–based model systems. A panel of developmental-related genes allowed differential prognosis of cardiogenic competency, thus prioritizing cell lines according to natural blueprint to streamline functional applications.