BMC Systems Biology: GSAE: an autoencoder with embedded gene-set nodes for genomics functional characterization

December 21, 2018

Hung-I Harry Chen, Yu-Chiao Chiu, Tinghe Zhang, Songyao Zhang, Yufei Huang & Yidong Chen Abstract Background Bioinformatics tools have been developed to interpret gene expression data at the gene set level, and these gene set-based analyses improve the biologists’ capability to discover the functional relevance of their experiment design. While elucidating gene set individually, inter-gene sets association is rarely taken into […]

BMC Systems Biology: scdNet: a computational tool for single-cell differential network analysis

December 21, 2018

Yu-Chiao Chiu, Tzu-Hung Hsiao, Li-Ju Wang, Yidong Chen & Yu-Hsuan Joni Shao Abstract Background Single-cell RNA sequencing (scRNA-Seq) is an emerging technology that has revolutionized the research of tumor heterogeneity. However, the highly sparse data matrices generated by the technology have posed an obstacle to the analysis of differential gene regulatory networks. Results Addressing the challenges, this study presents, as […]

PLoS One: microRNA-2110 functions as an onco-suppressor in neuroblastoma by directly targeting Tsukushi

December 14, 2018

Zhenze Zhao, Veronica Partridge, Michaela Sousares, Spencer D. Shelton, Cory L. Holland, Alexander Pertsemlidis, Liqin Du  Abstract microRNA-2110 (miR-2110) was previously identified as inducing neurite outgrowth in neuroblastoma cell lines BE(2)-C, suggesting its differentiation-inducing and oncosuppressive function in neuroblastoma. In this study, we demonstrated that synthetic miR-2110 mimic had a generic effect on reducing cell […]

Frontiers in Genetics: Estrogen-Dependent Upregulation of Adcyap1r1 Expression in Nucleus Accumbens Is Associated With Genetic Predisposition of Sex-Specific QTL for Alcohol Consumption on Rat Chromosome 4

December 4, 2018

John Paul Spence 1, Jill L Reiter 1, Bin Qiu 2, Hao Gu 2, Dawn K Garcia 3, Lingling Zhang 2, Tamara Graves 1, Kent E Williams 1, Paula J Bice 4, Yi Zou 3, Zhao Lai 4, Weidong Yong 2, Tiebing Liang 1 Abstract Humans show sex differences related to alcohol use disorders (AUD). Animal model research has the potential to provide important insight into how sex differences affect alcohol consumption, particularly because female animals frequently drink more than […]

Clinical Cancer Research: Abemaciclib Is Active in Preclinical Models of Ewing Sarcoma via Multipronged Regulation of Cell Cycle, DNA Methylation, and Interferon Pathway Signaling

December 1, 2018

Michele Dowless, Caitlin D. Lowery, Terry Shackleford, Matthew Renschler, Jennifer Stephens, Robert Flack, Wayne Blosser, Simone Gupta, Julie Stewart, Yue Webster, Jack Dempsey, Alle B. VanWye, Philip Ebert, Philip Iversen, Jonathan B. Olsen, Xueqian Gong, Sean Buchanan, Peter Houghton, and Louis Stancato Abstract Purpose: Ewing sarcoma (ES) is a rare and highly malignant cancer that occurs in the bone and surrounding tissue of children and adolescents. The EWS/ETS fusion transcription factor that drives ES pathobiology was previously demonstrated to modulate cyclin D1 expression. In this study, we evaluated abemaciclib, a small-molecule CDK4, and CDK6 (CDK4 […]

Genome Biology: The proBAM and proBed standard formats: enabling a seamless integration of genomics and proteomics data

December 1, 2018

Gerben Menschaert, Xiaojing Wang, Andrew R Jones, Fawaz Ghali, David Fenyö, Volodimir Olexiouk, Bing Zhang, Eric W Deutsch, Tobias Ternent, Juan Antonio Vizcaíno On behalf of The Human Proteome Organization (HUPO) Proteomics Standards Initiative, we introduce here two novel standard data formats, proBAM and proBed, that have been developed to address the current challenges of […]

International Journal of Cancer: Profiles of brain metastases: Prioritization of therapeutic targets

December 1, 2018

Sherise D Ferguson 1, Siyuan Zheng 2, Joanne Xiu 3, Shouhao Zhou 4, Mustafa Khasraw 5, Priscilla K Brastianos 6, Santosh Kesari 7, Jethro Hu 8, Jeremy Rudnick 8, Michael E Salacz 9, David Piccioni 10, Suyun Huang 1, Michael A Davies 11, Isabella C Glitza 11, John V Heymach 12, Jianjun Zhang 12, Nuhad K Ibrahim 13, John F DeGroot 14, Joseph McCarty 1, Barbara J O’Brien 14, Raymond Sawaya 1, Roeland G W Verhaak 2, Sandeep K Reddy 3, Waldemar Priebe 15, Zoran Gatalica 3, David Spetzler 3, Amy B Heimberger 1 Abstract We sought to compare the tumor profiles of brain metastases from common cancers […]

RNA Biology: Luteolin inhibits Musashi1 binding to RNA and disrupts cancer phenotypes in glioblastoma cells

November 18, 2018

Caihong Yi,Guiming Li,Dmitri N. Ivanov,Zhonghua Wang,Mitzli X. Velasco,Greco Hernández,Soni Kaundal,Johanna Villarreal,Yogesh K. Gupta  ,Mei Qiao,Christopher G. Hubert,Matthew J. Hart &Luiz O.F. Penalva ABSTRACT RNA binding proteins have emerged as critical oncogenic factors and potential targets in cancer therapy. In this study, we evaluated Musashi1 (Msi1) targeting as a strategy to treat glioblastoma (GBM); the most […]

Cancer Research: Astrocyte Elevated Gene-1 Regulates Macrophage Activation in Hepatocellular Carcinogenesis

November 15, 2018

Chadia L Robertson 1, Rachel G Mendoza 1, Nidhi Jariwala 1, Mikhail Dozmorov 2 3, Nitai D Mukhopadhyay 2 3, Mark A Subler 1, Jolene J Windle 1 3, Zhao Lai 4, Paul B Fisher 1 3 5, Shobha Ghosh 6, Devanand Sarkar 7 3 5 Abstract Chronic inflammation is a known hallmark of cancer and is central to the onset and progression of hepatocellular carcinoma (HCC). Hepatic macrophages play a critical role in the inflammatory process leading to HCC. The oncogene Astrocyte […]

Science Daily: Tiny molecule has big effect in childhood brain tumor studies

November 7, 2018

Sometimes small things make the biggest difference. A new study by UT Health San Antonio researchers found that a molecule thousands of times smaller than a gene are able to kill medulloblastoma, the most common childhood brain cancer. This tiny molecule, named MiR-584-5p, is quite efficient in its action. MiR-584-5p sensitizes cancer to chemotherapy and […]