Frontiers in Physics: Predicting Sites of Epitranscriptome Modifications Using Unsupervised Representation Learning Based on Generative Adversarial Networks

June 19, 2020

Sirajul Salekin1, Milad Mostavi1, Yu-Chiao Chiu2, Yidong Chen2,3, Jianqiu Zhang1* and Yufei Huang1,3*   Abstract Epitranscriptome is an exciting area that studies different types of modifications in transcripts, and the prediction of such modification sites from the transcript sequence is of significant interest. However, the scarcity of positive sites for most modifications imposes critical challenges for […]

BMC: Age-associated genes in human mammary gland drive human breast cancer progression

June 15, 2020

Xiang Gu, Bingzhi Wang, Haiyan Zhu, You Zhou, Aaron M. Horning, Tim H-M Huang, Yidong Chen, Peter Houghton, Zhao Lai, Joel E. Michalek & Lu-Zhe Sun Abstract Background Aging is a comorbidity of breast cancer suggesting that aging-associated transcriptome changes may promote breast cancer progression. However, the mechanism underlying the age effect on breast cancer remains poorly understood. Method We analyzed transcriptomics of the matched normal […]

Oncogene: Knock-out of Hopx disrupts stemness and quiescence of hematopoietic stem cells in mice (Chen Lab)

June 12, 2020

Chien-Chin Lin, Chi-Yuan Yao, Yueh-Chwen Hsu, Hsin-An Hou, Chang-Tsu Yuan, Yi-Hung Li, Chein-Jun Kao, Po-Han Chuang, Yu-Chiao Chiu, Yidong Chen, Wen-Chien Chou & Hwei-Fang Tien Abstract HOPX is a stem cell marker in hair follicles and intestines. It was shown critical for primitive hematopoiesis. We previously showed an association between higher HOPX expression and clinical characteristics related to stemness and quiescence of leukemic cells in acute myeloid […]

Jove: Mass Spectrometry Analysis to Identify Ubiquitylation of EYFP-tagged CENP-A (EYFP-CENP-A)

June 10, 2020

Yohei Niikura*1, Lei Fang*2, Risa Kitagawa*3, Peizhao Li1, Yao Xi1, Ju You1, Yan Guo2, Katsumi Kitagawa3 Summary CENP-A ubiquitylation is an important requirement for CENP-A deposition at the centromere, inherited through dimerization between cell division, and indispensable to cell viability. Here we describe mass spectrometry analysis to identify ubiquitylation of EYFP-tagged CENP-A (EYFP-CENP-A) protein. Abstract Studying the structure and the dynamics of […]

Clinical Cancer Research: Evaluation of Eribulin Combined with Irinotecan for Treatment of Pediatric Cancer Xenografts

June 1, 2020

Andrew J. Robles, Raushan T. Kurmasheva, Abhik Bandyopadhyay, Doris A. Phelps, Stephen W. Erickson, Zhao Lai, Dias Kurmashev, Yidong Chen, Malcom A. Smith, and Peter J. Houghton Abstract Purpose: Vincristine combined with camptothecin derivatives showed synergy in preclinical pediatric cancer models, and the combinations are effective in the treatment of childhood solid tumors. We determined whether the synergy between vincristine and irinotecan extends to eribulin, another microtubule inhibitor. Experimental Design: Vincristine or eribulin, alone or […]

Springer Link: Genetic markers for treatment-related pancreatitis in a cohort of Hispanic children with acute lymphoblastic leukemia

May 24, 2020

Allison C. Grimes, Yidong Chen, Hima Bansal, Christine Aguilar, Luz Perez Prado, Gerardo Quezada, Jaime Estrada & Gail E. Tomlinson Abstract Purpose Treatment-related pancreatitis (TRP) is a serious complication occurring in children with acute lymphoblastic leukemia (ALL). Those affected are at high risk for severe organ toxicity and treatment delays that can impact outcomes. TRP is associated with asparaginase, a standard therapeutic agent […]

Kunal Baxi, PhD to receive Translational Science Training (TST) TL1 award. (Ignatius Lab)

May 18, 2020

The Greehey Children’s Cancer Research Institute, UT Health San Antonio wishes to congratulate Kunal Baxi, PhD, from the lab of Principal Investigator, Myron Ignatius, PhD. on receiving the UT Health San Antonio, Translational Science Training (TST) TL1 award.  ABOUT THE PROGRAM This program is meant to enhance the quality and scope of the doctoral/postdoctoral research experience […]

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 […]