Nature Cell Biology: Enhancer reprogramming driven by high-order assemblies of transcription factors promotes phenotypic plasticity and breast cancer endocrine resistance

May 18, 2020

Mingjun Bi 1, Zhao Zhang 1, Yi-Zhou Jiang 2, Pengya Xue 1, Hu Wang 1, Zhao Lai 1, Xiaoyong Fu 3, Carmine De Angelis 3, Yue Gong 2, Zhen Gao 4, Jianhua Ruan 1 4, Victor X Jin 1, Elisabetta Marangoni 5, Elodie Montaudon 5, Christopher K Glass 6, Wei Li 7, Tim Hui-Ming Huang 1, Zhi-Ming Shao 2, Rachel Schiff 3, Lizhen Chen 8 9, Zhijie Liu 10 Abstract Acquired therapy resistance is a major problem for anticancer treatment, yet the underlying molecular mechanisms remain unclear. Using an established breast cancer cellular model, we show that endocrine […]

Cell Chemical Biology: MYC Regulation of D2HGDH and L2HGDH Influences the Epigenome and Epitranscriptome

May 1, 2020

ZhiJun Qiu 1, An-Ping Lin 1, Shoulei Jiang 1, Sara M Elkashef 1, Jamie Myers 1, Subramanya Srikantan 2, Binu Sasi 1, John Z Cao 3, Lucy A Godley 3, Dinesh Rakheja 4, Yingli Lyu 5, Siyuan Zheng 6, Muniswamy Madesh 2, Yuzuru Shiio 7, Patricia L M Dahia 1, Ricardo C T Aguiar 8 Abstract Mitochondrial D2HGDH and L2HGDH catalyze the oxidation of D-2-HG and L-2-HG, respectively, into αKG. This contributes to cellular homeostasis in part by modulating the activity of αKG-dependent dioxygenases. Signals that […]

Nucleic Acids Research: Cohesin SA1 and SA2 are RNA binding proteins that localize to RNA containing regions on DNA (Bishop)

April 30, 2020

Hai Pan, Miao Jin, Ashwin Ghadiyaram, Parminder Kaur, Henry E Miller, Hai Minh Ta, Ming Liu, Yanlin Fan, Chelsea Mahn, Aparna Gorthi … Show more   Abstract Cohesin SA1 (STAG1) and SA2 (STAG2) are key components of the cohesin complex. Previous studies have highlighted the unique contributions of SA1 and SA2 to 3D chromatin organization, DNA replication fork progression, and DNA double-strand break (DSB) repair. Recently, […]

MDPI Cancers Magazine – Reconstruction of Ewing Sarcoma Developmental Context from Mass-Scale Transcriptomics Reveals Characteristics of EWSR1-FLI1 Permissibility (Bishop Lab)

April 16, 2020

by  Henry E. Miller 1,2, Aparna Gorthi 1,2, Nicklas Bassani 2, Liesl A. Lawrence 1,2, Brian S. Iskra 1,2 and Alexander J. R. Bishop 1,2,* This study aims at defining the features of the cell of origin for Ewing sarcoma through comparative bioinformatics analysis of normal tissues with Ewing sarcoma. Key findings are that the […]

Familial Cancer: Highly aggressive thoracic desmoid tumors in adolescent siblings with fatal outcomes in an FAP kindred: a need for increased vigilance and intervention in at-risk AYAs

April 13, 2020

Mohamed M. Gad, Anne-Marie Langevin, Aaron J. Sugalski & Gail E. Tomlinson Abstract Desmoid tumors are a manifestation of familial adenomatous polyposis (FAP), associated with mutation of the APC gene. Although considered benign tumors, desmoids can be aggressive and cause considerable morbidity. Known risk factors for desmoid tumor growth include the location of mutations within the APC gene, family […]

BMG Medical Genomics: Convolutional neural network models for cancer type prediction based on gene expression

April 3, 2020

Milad Mostavi, Yu-Chiao Chiu, Yufei Huang & Yidong Chen Abstract Background Precise prediction of cancer types is vital for cancer diagnosis and therapy. Through a predictive model, important cancer marker genes can be inferred. Several studies have attempted to build machine learning models for this task however none has taken into consideration the effects of tissue of origin that can […]

Pain Reports: Reliable approaches to extract high-integrity RNA from skin and other pertinent tissues used in pain research

March 27, 2020

Peter M LoCoco 1, Jacob T Boyd 1, Claudia M Espitia Olaya 2, Ashley R Furr 1, Dawn K Garcia 3, Korri S Weldon 3, Yi Zou 3, Erin Locke 1, Alejandro Tobon 4, Zhao Lai 3 5, Shivani B Ruparel 1, Nikita B Ruparel 1, Kenneth M Hargreaves 1 Abstract Introduction: Comprehensive mRNA sequencing is a powerful tool for conducting unbiased, quantitative differential gene expression analysis. However, the reliability of these data is contingent on the extraction of high-quality RNA from […]

Katsumi Kitagawa, Pharm.D., PhD Awarded $1M NSF Grant

March 16, 2020

Overview: Centromeres are essential for chromosome segregation during mitosis. The kinetochore is the protein complex associated with the centromere. Dysfunction in centromeres causes chromosome instability and can result in aneuploidy. The overall goal of our research is to understand the mechanisms that help maintain centromere function. Centromere identity does not rely on specific DNA sequences, […]

bioRxiv : Assessing the Heterogeneity of Cardiac Non-myocytes and the Effect of Cell Culture with Integrative Single Cell Analysis

March 4, 2020

Abstract Cardiac non-myocytes comprise a diverse and crucial cell population in the heart that plays dynamic roles in cardiac wound healing and growth. Non-myocytes broadly fall into four cell types: endothelium, fibroblasts, leukocytes, and pericytes. Here we characterize the diversity of the non-myocytes in vivo and in vitro using mass cytometry. By leveraging single-cell RNA […]