Research Paper

Cancers MDPI: Transformer for Gene Expression Modeling (T-GEM): An Interpretable Deep Learning Model for Gene Expression-Based Phenotype Predictions (Chen Lab)

October 14, 2022

Ting-He Zhang, Md Musaddaqul Hasib, Yu-Chiao Chiu, Zhi-Feng Han,  Yu-Fang Jin, Mario Flores, Yidong Chen and Yufei Huang Simple Summary Cancer is the second leading cause of death worldwide. Predicting phenotype and understanding makers that define the phenotype are important tasks. We propose an interpretable deep learning model called T-GEM that can predict cancer-related phenotype [...]

Hepatology: Melanoma Differentiation Associated Gene-9/Syndecan Binding Protein (MDA-9/SDCBP) Promotes Hepatocellular Carcinoma (HCC) [Lai]

September 22, 2022

Debashri Manna,Saranya Chidambaranathan Reghupaty,Maria Del Carmen Camarena,Rachel G. Mendoza,Mark A. Subler,Jennifer E. Koblinski,Rebecca Martin,Mikhail G. Dozmorov,Nitai D. Mukhopadhyay,Jinze Liu,Xufeng Qu,Swadesh K. Das,Zhao Lai,Jolene J. Windle,Paul B. Fisher,Devanand Sarkar Abstract The oncogene Melanoma differentiation-associated gene-9/syndecan binding protein (MDA-9/SDCBP) is overexpressed in many cancers promoting aggressive, metastatic disease. However, the role of MDA-9 in regulating hepatocellular carcinoma [...]

NPJ | Precision Oncology: An international working group consensus report for the prioritization of molecular biomarkers for Ewing sarcoma (Bishop)

September 21, 2022

David S. Shulman, Sarah B. Whittle, Didier Surdez, Kelly M. Bailey, Enrique de Álava, Jason T. Yustein, Adam Shlien, Masanori Hayashi, Alexander J. R. Bishop, Brian D. Crompton, Steven G. DuBois, Neerav Shukla, Patrick J. Leavey, Stephen L. Lessnick, Heinrich Kovar, Olivier Delattre, Thomas G. P. Grünewald, Cristina R. Antonescu, Ryan D. Roberts, Jeffrey A. [...]

Nucleic Acids Research: Exploration and analysis of R-loop mapping data with RLBase (Bishop Lab)

August 30, 2022

Henry E Miller, Daniel Montemayor, Janet Li, Simon A Levy, Roshan Pawar, Stella Hartono, Kumar Sharma, Bess Frost, Frédéric Chedin, Alexander J R Bishop Abstract R-loops are three-stranded nucleic acid structures formed from the hybridization of RNA and DNA. In 2012, Ginno et al. introduced the first R-loop mapping method. Since that time, dozens of R-loop mapping studies have been conducted, yielding hundreds of publicly available [...]

Molecular Cancer Theraputics: Trastuzumab Deruxtecan, Antibody–Drug Conjugate Targeting HER2, Is Effective in Pediatric Malignancies: A Report by the Pediatric Preclinical Testing Consortium (Houghton, Kurmasheva)

August 3, 2022

Pooja Hingorani Wendong Zhang; Zhongting Zhang; Zhaohui Xu; Wei-Lien Wang; Michael E. Roth Yifei Wang; Jonathan B. Gill Douglas J. Harrison; Beverly A. Teicher; Stephen W. Erickson Gregory Gatto; Edward A. Kolb Malcolm A. Smith Raushan T. Kurmasheva Peter J. Houghton Richard Gorlick Abstract HER2 is expressed in many pediatric solid tumors and is a [...]

Clinical Cancer Research: Regulation of TORC1 by MAPK Signaling Determines Sensitivity and Acquired Resistance to Trametinib in Pediatric BRAFV600E Brain Tumor Models (Houghton & Kurmasheva)

August 1, 2022

Fuyang Li; Kathryn M. Bondra; Samson Ghilu; Adam Studebaker; Qianqian Liu Joel E. Michalek Mari Kogiso; Xiao-Nan Li John A. Kalapurakal; C. David James; Sandeep Burma; Raushan T. Kurmasheva Peter J. Houghton Abstract Purpose: We investigated why three patient-derived xenografts (PDX) childhood BRAFV600E-mutant brain tumor models are highly sensitive to trametinib. Mechanisms of acquired resistance [...]

Non-Coding RNA: Systematic Analysis of Long Non-Coding RNA Genes in Nonalcoholic Fatty Liver Disease (Bishop Lab)

July 27, 2022

Mirolyuba Ilieva James Dao Henry E. Miller Jens Hedelund Madsen Alexander J. R. Bishop Sakari Kauppinen Shizuka Uchida   Abstract The largest solid organ in humans, the liver, performs a variety of functions to sustain life. When damaged, cells in the liver can regenerate themselves to maintain normal liver physiology. However, some damage is beyond [...]

Neuro – Oncology: ELF4 is a critical component of a miRNA-transcription factor network and is a bridge regulator of glioblastoma receptor signaling and lipid dynamics (Penalva Lab)

July 22, 2022

Adam Kosti, Jennifer Chiou, Gabriela D A Guardia, Xiufen Lei, Henriette Balinda, Tesha Landry, Xiyuan Lu, Mei Qiao, Andrea Gilbert, Andrew Brenner ... Show more Abstract Background The loss of neurogenic tumor suppressor microRNAs miR-124, miR-128, and miR-137 is associated with glioblastoma’s undifferentiated state. Most of their impact comes via the repression of a network of oncogenic transcription factors. We conducted a high-throughput functional siRNA screen [...]

Cell Reports Medicine: A RET::GRB2 fusion in pheochromocytoma defies the classic paradigm of RET oncogenic fusions (Wang)

July 21, 2022

Cynthia M.Estrada-Zuniga18  Zi-MingCheng18  PurushothEthiraj18  QianjinGuo1  HectorGonzalez-Cantú1  ElainaAdderley2  HectorLopez1  Bethany N.Landry1  AbirZainal2  NeilAronin2  YanliDing3  XiaojingWang45  Ricardo C.T.Aguiar167  Patricia L.M.Dahia169 Highlights • A RET::GRB2 fusion was found in a pheochromocytoma • RET retains its kinase domain, swaps the C tail with GRB2, a normal RET binding partner • RET::GRB2 relies on RET kinase function for transformation • RET::GRB2 renders cells sensitive [...]

Nucleic Acids Research: Quality-controlled R-loop meta-analysis reveals the characteristics of R-loop consensus regions (Bishop Lab)

June 27, 2022

Henry E Miller, Daniel Montemayor, Jebriel Abdul, Anna Vines, Simon A Levy, Stella R Hartono, Kumar Sharma, Bess Frost, Frédéric Chédin, Alexander J R Bishop Abstract R-loops are three-stranded nucleic acid structures formed from the hybridization of RNA and DNA. While the pathological consequences of R-loops have been well-studied to date, the locations, classes, and [...]