Cell Press: A Modular Master Regulator Landscape Controls Cancer Transcriptional Identity (Zheng Lab)

January 21, 2021

Evan O.Paull114,  Alvaro Aytes121314,  Sunny J.Jones114,  Prem S.Subramaniam1,  Federico M.Giorgi3,  Eugene F.Douglass1,  Somnath Tagore1,  Brennan Chu1,  Alessandro Vasciaveo1,  Siyuan Zheng4,  Roel Verhaak5,  Cory Abate-Shen1678,  Mariano J.Alvarez19,  Andrea Califano16910111215 Summary Despite considerable efforts, the mechanisms linking genomic alterations to the transcriptional identity of cancer cells remain elusive. Integrative genomic analysis, using a network-based approach, identified 407 […]

Methods: Prediction and interpretation of cancer survival using graph convolution neural networks (Chen)

January 21, 2021

RicardoRamireza, Yu-ChiaoChiub, SongYaoZhangc, JoshuaRamireza, YidongChenbd, YufeiHuangad, Yu-FangJina Highlights •  Predicting cancer survival outcomes using Graph Convolutional Neural Networks with TCGA dataset. •  Combining clinical data and the GCNN improves cancer prognostic prediction. •  Interpreting the GCNN model and identifying significant genes with network modules identified by HotNet2. Abstract The survival rate of cancer has increased […]

MDPI: Synergism of Proneurogenic miRNAs Provides a More Effective Strategy to Target Glioma Stem Cells (Penalva & Pertsemlidis Labs)

January 14, 2021

Adam Kosti, Rodrigo Barreiro, Gabriela D. A. Guardia, Shiva Ostadrahimi, Erzsebet Kokovay, Alexander Pertsemlidis, Pedro A. F. Galante, Luiz O. F. Penalva Simple Summary miRNAs function as critical regulators of gene expression and have been defined as contributors to cancer phenotypes by acting as oncogenes or tumor suppressors. Based on these findings, miRNA-based therapies have been explored in the treatment of many […]

BMC Microbiology: Comparison of rectal swab, glove tip, and participant-collected stool techniques for gut microbiome sampling

January 14, 2021

Meghan I. Short, Robert Hudson, Benjamin D. Besasie, Kelly R. Reveles, Dimpy P. Shah, Susannah Nicholson, Teresa L. Johnson-Pais, Korri Weldon, Zhao Lai, Robin J. Leach, Bernard Fongang & Michael A. Liss Abstract Background Studies of the gut microbiome are becoming increasingly important. Such studies require stool collections that can be processed or frozen in a […]

Nature Communications: Interaction between SNAI2 and MYOD enhances oncogenesis and suppresses differentiation in Fusion Negative Rhabdomyosarcoma (Ignatius, Houghton, Chen)

January 14, 2021

Silvia Pomella, Prethish Sreenivas, Berkley E. Gryder, Long Wang, David Milewski, Matteo Cassandri, Kunal Baxi, Nicole R. Hensch, Elena Carcarino, Young Song, Hsien-Chao Chou, Marielle E. Yohe, Benjamin Z. Stanton, Bruno Amadio, Ignazio Caruana, Cristiano De Stefanis, Rita De Vito, Franco Locatelli, Yidong Chen, Eleanor Y. Chen, Peter Houghton, Javed Khan, Rossella Rota & Myron S. […]

Nature Communications: Integrated analysis of telomerase enzymatic activity unravels an association with cancer stemness and proliferation (Zheng Lab)

January 12, 2021

        Nighat Noureen, Shaofang Wu, Yingli Lv, Juechen Yang, W. K. Alfred Yung, Jonathan Gelfond, Xiaojing Wang, Dimpy Koul, Andrew Ludlow & Siyuan Zheng Abstract Active telomerase is essential for stem cells and most cancers to maintain telomeres. The enzymatic activity of telomerase is related but not equivalent to the expression of TERT, the catalytic subunit of the complex. Here we […]

Cancer Letters: COX-2 promotes mammary adipose tissue inflammation, local estrogen biosynthesis, and carcinogenesis in high-sugar/fat diet treated mice

January 9, 2021

Author links open overlay panelRosângela MayerGonçalvesa,  MarinaDelgoboa, Jonathan PauloAgnesa, Raquel Nascimentodas Nevesa, MarceloFalchettia, TuanyCasagrandea, Ana Paula VargasGarciab, Thaynan CunhaVieirab, NauanaSomensic, Maciel AlencarBruxeld, Daniel Augusto Gasparin BuenoMendese, AlexRafachod, AndréBáficae, Daniel PensGelainc, José Cláudio FonsecaMoreirac, Geovanni DantasCassalib, Alexander James RoyBishopf, AlfeuZanotto-Filhoa Highlights •   HSF diet accelerates mammary tumor formation in mice exposed to a carcinogen. •  COX-2 […]

MDPI: MSI1 Promotes the Expression of the GBM Stem Cell Marker CD44 by Impairing miRNA-Dependent Degradation

December 5, 2020

Rebecca Pötschke  1,2,† Jacob Haase 1,†,  Markus Glaß 1  Sebastian Simmermacher  3,Claudia Misiak 1,Luiz O. F. Penalva 4,5  Caspar D. Kühnöl, 2 and Stefan Hüttelmaier  1, Simple Summary Glioblastoma (GBM) is the most lethal brain tumor with a median survival rate of approximately 14 months. GBM patients commonly suffer from tumor recurrence, indicating that populations of chemo/radio-resistant stem cell-like tumor cells […]

Molecular Oncology: Interaction of transcription factor AP‐2 gamma with proto‐oncogene PELP1 promotes tumorigenesis by enhancing RET signaling

December 2, 2020

Junhao Liu, Zexuan Liu, Mengxing Li, , Weiwei Tang, Uday P. Pratap, Yiliao Luo, Kristin A. Altwegg, Xiaonan Li, Yi Zou, Hong Zhu, Gangadhara R. Sareddy,  Suryavathi Viswanadhapalli, Ratna K. Vadlamudi Abstract A significant proportion of estrogen receptor‐positive (ER+) breast cancer (BC) initially responds to endocrine therapy but eventually evolves into therapy‐resistant BC. Transcription factor AP‐2 gamma (TFAP2C) is a known regulator of ER […]

PNAS: Oncogenic allelic interaction in Xiphophorus highlights hybrid incompatibility

November 24, 2020

Yuan Lu,  View ORCID ProfileAngel Sandoval,  View ORCID ProfileSarah Voss, Zhao Lai, Susanne Kneitz, Will Boswell, Mikki Boswell, Markita Savage,  View ORCID ProfileChristi Walter, Wes Warren,  View ORCID ProfileManfred Schartl, and Ronald Walter Abstract Mixing genomes of different species by hybridization can disrupt species-specific genetic interactions that were adapted and fixed within each species population. Such disruption can predispose the hybrids to abnormalities and disease that […]