Nucleic Acids Research: TLK1-Mediated RAD54 Phosphorylation Spatio-Temporally Regulates Homologous Recombination Repair (Chen, Sung)

July 13, 2023

Ishita Ghosh, Youngho Kwon, Aida Badamchi Shabestari, Rupesh Chikhale, Jing Chen, Claudia Wiese, Patrick Sung, Arrigo De Benedetti Abstract Environmental agents like ionizing radiation (IR) and chemotherapeutic drugs can cause severe damage to the DNA, often in the form of double-strand breaks (DSBs). Remaining unrepaired, DSBs can lead to chromosomal rearrangements and cell death. One major error-free pathway to repair DSBs is homologous [...]

Bioinformatics Advances: DepLink: an R Shiny app to systematically link genetic and pharmacologic dependencies of cancer (Zheng, Houghton, & Chen Labs)

June 27, 2023

Tapsya Nayak, Li-Ju Wang, Michael Ning, Gabriela Rubannelsonkumar, Eric Jin, Siyuan Zheng, Peter J Houghton, Yufei Huang, Yu-Chiao Chiu, Yidong Chen Abstract Motivation Large-scale genetic and pharmacologic dependency maps are generated to reveal genetic vulnerabilities and drug sensitivities of cancer. However, user-friendly software is needed to link such maps systematically. Results Here, we present DepLink, a web server to identify genetic and pharmacologic perturbations [...]

Nature: Structural Insights into BCDX2 Complex Function in Homologous Recombination (Sung Lab)

June 22, 2023

Yashpal Rawal, Lijia Jia, Aviv Meir, Shuo Zhou, Hardeep Kaur, Eliza A. Ruben, Youngho Kwon, Kara A. Bernstein, Maria Jasin, Alexander B. Taylor, Sandeep Burma, Robert Hromas, Alexander V. Mazin, Weixing Zhao, Daohong Zhou, Elizabeth V. Wasmuth, Eric C. Greene, Patrick Sung & Shaun K. Olsen Abstract Homologous recombination (HR) fulfils a pivotal role in the [...]

RNA Biology: The Paralogues MAGOH and MAGOHB are Oncogenic Factors in High-Grade Gliomas and Safeguard the Splicing of Cell Division and Cell Cycle Genes (Penalva Lab)

June 9, 2023

Rodrigo A. S. Barreiro, Gabriela D. A. Guardia, Fabiana M. Meliso, Xiufen Lei, Wei-Qing Li, Andre Savio, Martin Fellermeyer, Helena B. Conceição, Rafael L. V. Mercuri, Tesha Landry, Mei Qiao, Lorea Blazquez, Jernej Ule, Luiz O.F. Penalva & Pedro A. F. Galante ABSTRACT The exon junction complex (EJC) plays key roles throughout the lifespan of [...]

Journal of Clinical Oncology: The Childhood Cancer Data Initiative: Using the Power of Data to Learn From and Improve Outcomes for Every Child and Young Adult With Pediatric Cancer (Aune Co-author)

June 5, 2023

Joseph A. Flores-Toro  , PhD1; Subhashini Jagu  , PhD1; Gregory T. Armstrong, MD, MSCE2; David F. Arons, JD3; Gregory J. Aune, MD, PhD4; Stephen J. Chanock  , MD1; Douglas S. Hawkins  , MD5; Allison Heath  , PhD6; Lee J. Helman  , MD7; Katherine A. Janeway  , MD, MMSc8; Jason E. Levine  , MD1; Ellyn Miller, [...]

ELife: Defining function of wild-type and three patient specific TP53 mutations in a zebrafish model of embryonal rhabdomyosarcoma (Ignatius Lab, Houghton Lab, Libich Lab, Chen, Tomlinson)

June 2, 2023

Jiangfei Chen Kunal Baxi Amanda E Lipsitt Nicole Rae Hensch Long Wang Prethish Sreenivas Paulomi Modi Xiang Ru Zhao Antoine Baudin Daniel G Robledo Abhik Bandyopadhyay Aaron Sugalski Anil K Challa Dias Kurmashev Andrea R Gilbert Gail E Tomlinson Peter Houghton Yidong Chen Madeline N Hayes Eleanor Y Chen David S Libich Myron S Ignatius [...]

Cell Reports: EWSR1 Maintains Centromere Identity (Kitagawa & Houghton labs)

May 30, 2023

Risa Kitagawa 1, Yohei Niikura 1 2, Argentina Becker 1 3, Peter J. Houghton 1, Katsumi Kitagawa 1 4 Highlights EWSR1 is required to maintain CENP-A at the centromere in interphase cells EWSR1 binds to CENP-A through the SYGQ2 region, important for phase separation EWSR1 binds to R loops in vitro through its RNA-recognition motif (RRM) EWSR1 protects CENP-A in the centromeric chromatin by binding to centromeric RNAs Summary The centromere is essential [...]

Clinical Cancer Research: Phase II Investigation of TVB-2640 (Denifanstat)with Bevacizumabin Patients with First Relapse High-Grade Astrocytoma (Chen)

May 24, 2023

William Kelly 1, Adolfo Enrique Diaz Duque 1,Joel Michalek 2, Brandon Konkel 3,L aura Caflisch 3, Yidong Chen 2,Sarath Chand Pathuri 1,Vinu Madhusudanannair-Kunnuparampil 4, John Floyd II 5,and Andrew Brenner 1 ABSTRACT Purpose: Glioblastoma represents the most common primary brain tumor. Although antiangiogenics are used in the recurrent setting, they do not prolong survival. Glioblastoma [...]

Biomolecules: Enhancing the Conformational Stability of the cl-Par-4 Tumor Suppressor via Site-Directed Mutagenesis (Libich Lab)

May 17, 2023

Samjhana Pandey Krishna K. Raut Andrea M. Clark  Antoine Baudin  Lamya Djemri  David S. Libich  Komala Ponniah Steven M. Pascal Abstract Intrinsically disordered proteins play important roles in cell signaling, and dysregulation of these proteins is associated with several diseases. Prostate apoptosis response-4 (Par-4), an approximately 40-kilodalton proapoptotic tumor suppressor, is a predominantly intrinsically disordered [...]

Cells: The RNA Demethylase ALKBH5 Maintains Endoplasmic Reticulum Homeostasis by Regulating UPR, Autophagy, and Mitochondrial Function (Chen, Sung, & Rao Labs)

May 17, 2023

Panneerdoss Subbarayalu Pooja Yadav Santosh Timilsina Daisy Medina Kunal Baxi Robert Hromas Ratna K. Vadlamudi Yidong Chen Patrick Sung Manjeet K. Rao Abstract Eukaryotic cells maintain cellular fitness by employing well-coordinated and evolutionarily conserved processes that negotiate stress induced by internal or external environments. These processes include the unfolded protein response, autophagy, endoplasmic reticulum-associated degradation [...]