Research Paper

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 [...]

BMC Med Informatics & Decision Making: On the Role of Deep Learning Model Complexity in Adversarial Robustness for Medical Images (Chen Lab)

June 21, 2022

David Rodriguez, Tapsya Nayak, Yidong Chen, Ram Krishnan & Yufei Huang Abstract Deep learning (DL) models are highly vulnerable to adversarial attacks for medical image classification. An adversary could modify the input data in imperceptible ways such that a model could be tricked to predict, say, an image that actually exhibits a malignant tumor to a [...]

American Journal of Heart & Circulatory Physiology: Development and Characterization of a Mass Cytometry Panel for Detecting the Effect of Acute Doxorubicin Exposure on Murine Cardiac Non-myocytes (Bishop, Chen, & Aune Labs)

June 8, 2022

Brian S. Iskra, Logan R. Davis, Henry E. Miller, Yu-Chiao Chiu, Alexander J.R. Bishop, Yidong Chen, and Gregory J. Aune Abstract Childhood cancer survivors (CCSs) face lifelong side effects related to their treatment with chemotherapy. Anthracycline agents, such as doxorubicin (DOX), are important in the treatment of childhood cancers but are associated with cardiotoxicity. Cardiac toxicities represent a significant source [...]

Molecular Cancer Therapeutics: Comprehensive Surfaceome Profiling to Identify and Validate Novel Cell-Surface Targets in Osteosarcoma (Houghton, Kurmasheva)

June 1, 2022

Yifei Wang; Xiangjun Tian; Wendong Zhang; Zhongting Zhang; Rossana Lazcano; Pooja Hingorani; Michael E. Roth; Jonathan D. Gill; Douglas J. Harrison; Zhaohui Xu; Sylvester Jusu; Sankaranarayanan Kannan; Jing Wang; Alexander J. Lazar; Eric J. Earley; Stephen W. Erickson; Tara Gelb; Philip Huxley; Johanna Lahdenranta; Gemma Mudd; Raushan T. Kurmasheva; Peter J. Houghton; Malcolm A. Smith; [...]

Cancer Letters: The antidepressant imipramine inhibits breast cancer growth by targeting estrogen receptor signaling and DNA repair events (Rao & Chen Labs)

May 18, 2022

Santosh Timilsinaab1 Subapriya Rajamanickambc1 Arhan Raoh Panneerdoss Subbarayaluab Saif Nirzhorab Nourhan Abdelfattahi Suryavathi Viswanadhapallie Yidong Chenbd IsmailJatoif Andrew Brennerg Manjeet K.Raoab Ratna Vadlamudie Virginia Kaklamanig Highlights • Anti-depressant imipramine blocks the growth and progression of breast cancers. • Imipramine induces cell cycle arrest and blocks heightened DNA repair activities in breast cancer cells. • Imipramine [...]

JCO Oncology Practice: Disparities in Cancer Genetic Testing and Variants of Uncertain Significance in the Hispanic Population of South Texas (Tomlinson Lab, Ignatius Lab)

May 12, 2022

Stephanie Soewito, BS, MS1; Rachel Wyatt, MS2; Emily Berenson, MS2; Natalie Poullard, MS, MA3; Shawn Gessay, MS2,3,4; Lindsey Mette, MS, MPH2,3,5; Elena Marin, CHW6; Kristin Shelby, BA6; Elise Alvarez, BA3; Byeong Yeob Choi, PhD7; Clarissa Aviles, MSHS6; Anna Maria Pulido-Saldivar, MPH6,8; Pamela M. Otto, MD9; Ismail Jatoi, MD3,10; Chethan Ramamurthy, MD3; Myron Ignatius, PhD6; Virginia G. Kaklamani, MD, DSc3; and Gail E. Tomlinson, MD, PhD2,3,6 PURPOSE: Racial and ethnic disparities have included [...]

Molecular Carcinogenesis: SIRT1 inhibition-induced senescence as a strategy to prevent prostate cancer progression (Chen, Lai)

April 25, 2022

Abstract Emerging evidence suggests an important role for SIRT1, a nicotinamide adenine dinucleotide (NAD)-dependent deacetylase in cancer development, progression, and therapeutic resistance; making it a viable therapeutic target. Here, we examined the impact of resveratrol-mediated pharmacological activation of SIRT1 on the progression of HGPIN lesions (using the Pten−/− mouse model) and on prostate tumor development (using [...]

Oncogene: Targeting farnesylation as a novel therapeutic approach in HRAS-mutant rhabdomyosarcoma (Vaseva)

April 25, 2022

Patience Odeniyide, Marielle E. Yohe, Kai Pollard, Angelina V. Vaseva,  Ana Calizo, Lindy Zhang, Fausto J. Rodriguez, John M. Gross, Amy N. Allen, Xiaolin Wan, Romel Somwar, Karisa C. Schreck, Linda Kessler, Jiawan Wang & Christine A. Pratilas Abstract Activating RAS mutations are found in a subset of fusion-negative rhabdomyosarcoma (RMS), and therapeutic strategies to directly [...]

Clinical Cancer Research: The B7-H3-Targeting Antibody-Drug Conjugate m276-SL-PBD Is Potently Effective Against Pediatric Cancer Preclinical Solid Tumor Models (Kurmasheva & Houghton)

April 22, 2022

Nathan M Kendsersky # 1 2, Jarrett Lindsay # 1 2, E Anders Kolb 3, Malcolm A Smith 4, Beverly A Teicher 4, Stephen W Erickson 5, Eric J Earley 5, Yael P Mosse 1, Daniel Martinez 6, Jennifer Pogoriler 2 6, Kateryna Krytska 1, Khushbu Patel 1 7, David Groff 1, Matthew Tsang 1, Samson Ghilu 8, Yifei Wang 9, Steven Seaman 10, Yang Feng 10, Brad St Croix 10, Richard Gorlick 9, Raushan Kurmasheva 8, Peter J Houghton 11, John M Maris 12 2 Abstract Purpose: Patients with relapsed pediatric solid malignancies have few therapeutic options, and many of these patients die of their disease. B7-H3 [...]

Non-Coding RNA: Current Status of Epitranscriptomic Marks Affecting lncRNA Structures and Functions (Bishop Lab)

April 22, 2022

by Henry E. Miller 1,2,3ORCID, Mirolyuba Ilieva 4, Alexander J. R. Bishop 1,2,5ORCID and Shizuka Uchida 4, Non-Coding RNA 2022, 8(2), 23; Received: 1 March 2022 / Revised: 21 March 2022 / Accepted: 25 March 2022 / Published: 28 March 2022 Abstract Long non-coding RNAs (lncRNAs) belong to a class of non-protein-coding RNAs with [...]