BMC: SETDB1 interactions with PELP1 contributes to breast cancer endocrine therapy resistance (Lai, Chen, Rao)

April 11, 2022

Zexuan Liu, Junhao Liu, Behnam Ebrahimi, Uday P. Pratap, Yi He, Kristin A. Altwegg, Weiwei Tang, Xiaonan Li, Zhao Lai, Yidong Chen, Liangfang Shen, Gangadhara R. Sareddy, Suryavathi Viswanadhapalli, Rajeshwar R. Tekmal, Manjeet K. Rao & Ratna K. Vadlamudi Abstract Background Methyltransferase SETDB1 is highly expressed in breast cancer (BC), however, the mechanisms by which SETDB1 [...]

Cancer Research: M6A RNA Methylation Regulates Histone Ubiquitination to Support Cancer Growth and Progression (Gupta, Zheng, Houghton, Chen, and Rao Labs)

March 21, 2022

Pooja Yadav; Panneerdoss Subbarayalu; Daisy Medina, Saif Nirzhor;  Santosh Timilsina; Subapriya Rajamanickam; Vijay K. Eedunuri; Yogesh Gupta Siyuan Zheng Nourhan Abdelfattah Yufei Huang Ratna Vadlamudi Robert Hromas; Paul Meltzer Peter Houghton; Yidong Chen Manjeet K. Rao Abstract Osteosarcoma is the most common malignancy of the bone, yet the survival for osteosarcoma patients is virtually unchanged [...]

Cell Death & Disease: Global profiling reveals common and distinct N6-methyladenosine (m6A) regulation of innate immune responses during bacterial and viral infections (Lai & Chen Labs)

March 15, 2022

Jian Feng, Teng Zhang, Océane Sorel, Wen Meng, Xinquan Zhang, Zhao Lai, Weiming Yuan, Yidong Chen, Yufei Huang & Shou-Jiang Gao Abstract N6-methyladenosine (m6A) is a dynamic post-transcriptional RNA modification influencing all aspects of mRNA biology. While m6A modifications during numerous viral infections have been described, the role of m6A in innate immune response remains unclear. [...]

eLife: Signature-scoring methods developed for bulk samples are not adequate for cancer single-cell RNA sequencing data (Zheng, Chen, & Wang Labs)

March 7, 2022

Nighat Noureen,  Zhenqing Ye,  Yidong Chen,  Xiaojing Wang,  Siyuan Zheng  Abstract Quantifying the activity of gene expression signatures is common in analyses of single-cell RNA sequencing data. Methods originally developed for bulk samples are often used for this purpose without accounting for contextual differences between bulk and single-cell data. More broadly, these methods have not [...]

Cancers: Global Genomic and Proteomic Analysis Identified Critical Pathways Modulated by Proto-Oncogene PELP1 in TNBC (Chen & Lai)

February 25, 2022

by Zexuan Liu 1,2,†,Kristin A. Altwegg 1,3,†ORCID,Junhao Liu 1,2,Susan T. Weintraub 4,Yidong Chen 5,6,Zhao Lai 5,7,Gangadhara R. Sareddy 1,3,Suryavathi Viswanadhapalli 1,3,*ORCID and Ratna K. Vadlamudi 1,3,8,* Simple Summary The proto-oncogene PELP1 is commonly overexpressed in many cancers including triple-negative breast cancer (TNBC). In this study, we utilized global proteomic and RNA-seq approaches to elucidate the [...]

Cellular Oncology: Single-cell RNA profiling identifies diverse cellular responses to EWSR1/FLI1 down regulation in Ewing sarcoma cells (Houghton, Chen, Kitagawa, Ignatius)

January 12, 2022

Roxane Khoogar, Fuyang Li, Yidong Chen, Myron Ignatius, Elizabeth R. Lawlor, Katsumi Kitagawa, Tim H.-M. Huang, Doris A. Phelps & Peter J. Houghton Background The EWSR1/FLI1 gene fusion is the most common rearrangement leading to cell transformation in Ewing sarcoma (ES). Previous studies have indicated that expression at the cellular level is heterogeneous and that levels [...]

Briefings in Bioinformatics: Deep learning tackles single-cell analysis—a survey of deep learning for scRNA-seq analysis (Chen Lab)

January 4, 2022

        Mario Flores, Zhentao Liu, Tinghe Zhang, Md Musaddaqui Hasib, Yu-Chiao Chiu, Zhenqing Ye, Karla Paniagua, Sumin Jo, Jianqiu Zhang, Shou-Jiang Gao, Yu-Fang Jin, Yidong Chen, Yufei Huang Abstract Since its selection as the method of the year in 2013, single-cell technologies have become mature enough to provide answers to complex research questions. With the growth of single-cell profiling technologies, there has also [...]

MSN: Using Next Generation Sequencing, the Greehey CCRI bioinformatics team is helping determine COVID19 strains (Chen, Lai, Zheng, Wang Labs)

December 17, 2021

"Since the coronavirus pandemic began almost two years ago there have been over a dozen strains of the virus. Here at UT Health San Antonio, they have a lab which differentiates between each of the strains in an effort to save lives. UT Health San Antonio uses a technology called next-generation sequencing to differentiate the [...]

Molecular Cancer Therapeutics: Vertical Inhibition of the RAF-MEK-ERK Cascade Induces Myogenic Differentiation, Apoptosis and Tumor Regression in H/NRAS Q61X-mutant Rhabdomyosarcoma (Houghton, Chen, Ignatius, Vaseva)

November 8, 2021

Natalia Garcia, Vanessa Del Pozo, Marielle E. Yohe, Craig M. Goodwin, Terry J Shackleford, Long Wang, Kunal Baxi, Yidong Chen, Anna T Rogojina, Sara M. Zimmerman, Cody J. Peer, William D. Figg, Myron S. Ignatius, Kris C Wood, Peter J. Houghton, and Angelina V Vaseva Abstract Oncogenic RAS signaling is an attractive target for fusion-negative rhabdomyosarcoma (FN-RMS). Our study validates the role of the ERK MAPK effector pathway in mediating RAS dependency in a panel of H/NRASQ61X-mutant RMS cells and correlates in vivo efficacy of the MEK [...]

Communications Biology: LIFR inhibition enhances the therapeutic efficacy of HDAC inhibitors in triple negative breast cancer (Chen)

November 1, 2021

Mengxing Li, Suryavathi Viswanadhapalli, Bindu Santhamma, Uday P. Pratap, Yiliao Luo, Junhao Liu, Kristin A. Altwegg, Weiwei Tang, Zexuan Liu, Xiaonan Li, Behnam Ebrahimi, Hui Yan, Yi Zou, Swapna Konda, Gangadhara R. Sareddy, Zhenming Xu, Yidong Chen, Manjeet K. Rao, Andrew J. Brenner, Virginia G. Kaklamani, Rajeshwar R. Tekmal, Gulzar Ahmed, Ganesh V. Raj, Klaus [...]