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 [...]

Journal of Clinical & Translational Science: Examining access to care in clinical genomic research and medicine: Experiences from the CSER Consortium (Tomlinson)

December 13, 2021

 Amanda M. Gutierrez Jill O. Robinson, Simon M. Outram, Hadley S. Smith, Stephanie A. Kraft, Katherine E. Donohue, Barbara B. Biesecker, Kyle B. Brothers, Flavia Chen, Benyam Hailu, Lucia A. Hindorff, Hannah Hoban, Rebecca L. Hsu, Sara J. Knight, Barbara A. Koenig, Katie L. Lewis, Kristen Hassmiller Lich, Julianne M. O’Daniel, Sonia Okuyama, Gail E. [...]

CANCER RESEARCH: SNAI2-Mediated Repression of BIM Protects Rhabdomyosarcoma from Ionizing Radiation (Houghton, Ignatius, Vaseva, and Zheng labs)

November 24, 2021

 Long Wang, Nicole R. Hensch, Kathryn Bondra, Prethish Sreenivas, Xiang R. Zhao, Jiangfei Chen, Rodrigo Moreno Campos, Kunal Baxi, Angelina V. Vaseva, Benjamin D. Sunkel, Berkley E. Gryder, Silvia Pomella, Benjamin Z. Stanton, Siyuan Zheng, Eleanor Y. Chen, Rossella Rota, Javed Khan, Peter J. Houghton and Myron S. Ignatius Abstract Ionizing radiation (IR) and chemotherapy [...]

Hepatology Communications: Dissecting the Balance Between Metabolic and Oncogenic Functions of Astrocyte-Elevated Gene-1/Metadherin (Lai Lab)

November 9, 2021

 Yetirajam Rajesh, Saranya Chidambaranathan Reghupaty, Rachel G. Mendoza, Debashri Manna, Indranil Banerjee, Mark A. Subler, Korri Weldon, Zhao Lai, Shah Giashuddin, Paul B. Fisher, Arun J. Sanyal, Rebecca K. Martin, Mikhail G. Dozmorov, Jolene J. Windle, Devanand Sarkar   Abstract Obesity is an enormous global health problem, and obesity-induced nonalcoholic steatohepatitis (NASH) is contributing to [...]

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 [...]

Cancer Letters: KDM1A inhibition augments the efficacy of rapamycin for the treatment of endometrial cancer (Lai & Chen Labs)

October 28, 2021

 Prabhakar PittaVenkataa1 YihongChenab1 SalvadorAlejoa YiHeab Bridgitte E.Palaciosa IlannaLoeffela JunhaoLiuacUday P.Pratapa GabrielleGraya Sureshkumar MulampurathAchuthan Pillaia YiZoud ZhaoLaideT akayoshiSuzukif SuryavathiViswanadhapallia SrinathPalakurthig Rajeshwar R.Tekmalah Ratna K.Vadlamudiahi EdwardKosta Gangadhara R.Sareddyah Highlights • From the drug screen, we found that KDM1A inhibition is highly synergistic with mTOR inhibitors. • KDM1A inhibition attenuated the mTOR signaling cascade and abolished rapamycin-induced feedback [...]

Molecular Cancer Research: GLI3 Is Stabilized by SPOP Mutations and Promotes Castration Resistance via Functional Cooperation with Androgen Receptor in Prostate Cancer (Chen)

October 27, 2021

 Marieke Burleson, Janice J. Deng, Tai Qin, Thu Minh Duong, Yuqian Yan, Xiang Gu, Debodipta Das, Acarizia Easley, Michael A. Liss, P. Renee Yew, Roble Bedolla, Addanki Pratap Kumar, Tim Hui-Ming Huang, Yi Zou, Yidong Chen, Chun-Liang Chen, Haojie Huang, Lu-Zhe Sun and Thomas G. Boyer Abstract Although the Sonic hedgehog (SHH) signaling pathway has been implicated in promoting malignant phenotypes of prostate cancer, details on how it is activated and exerts its oncogenic role during prostate cancer development and progression are less clear. Here, we show that GLI3, a key SHH pathway [...]

Free Radical Biology and Medicine: Thioredoxin reductase-1 levels are associated with NRF2 pathway activation and tumor recurrence in non-small cell lung cancer (Bishop Lab)

October 26, 2021

 MarinaDelgoboa  Rosângela MayerGonçalvesag  Marco AntônioDelazerib  MarceloFalchettia  AlessandroZandonáb  RaquelNascimento das Nevesa  KarolineAlmeidaa  Adriane CristinaFagundesa  Daniel PensGelainc  João IsidroFracassod  Guilherme Baroni deMacêdod  LeonardoPriorid  NicklasBassanie  Alexander James RoyBishopef  Cassiano MateusForcelinib  José Cláudio FonsecaMoreirac1  AlfeuZanotto-Filhoa1 Highlights • Amid 64 redox genes, TXNRD1 shows association with poor survival in NSCLC. • High TXNRD1 levels predict poor DFS and DMFS in [...]