NPJ – Precision Oncology: Benchmarking mouse contamination removing protocols in patient-derived xenografts genomic profiling (Zheng, Wang, Kurmasheva, Houghton, Lai, & Chen Labs)

April 17, 2025

 Mukund Bhandari, Funan He, Anna Rogojina, Fuyang Li, Yi Zou, Jing Jiang, Zhao Lai, Peter Houghton, Raushan T. Kurmasheva, Yidong Chen, Xiaojing Wang & Siyuan Zheng Abstract Patient-derived xenograft (PDX) models are widely used in cancer research. Genomic and transcriptomic profiling of PDXs are inevitably contaminated by sequencing reads originated from mouse cells. Here, we examine [...]

Clinical Cancer Research: Update on Cancer and Central Nervous System Tumor Surveillance in Pediatric NF2-, SMARCB1-, and LZTR1-Related Schwannomatosis (Tomlinson)

April 15, 2025

 Melissa R. Perrino Marjolijn C.J. Jongmans Gail E. Tomlinson Mary-Louise C. Greer Sarah R. Scollon Sarah G. Mitchell Jordan R. Hansford Kris Ann P. Schultz Wendy K. Kohlmann Jennifer M. Kalish Suzanne P. MacFarland Anirban Das Kara N. Maxwell Stefan M. Pfister Rosanna Weksberg Orli Michaeli Uri Tabori Gina M. Ney Philip J. Lupo Jack [...]

IScience: Dissection of tumoral niches using spatial transcriptomics and deep learning (Chen)

April 15, 2025

 Karla Paniagua1 ∙ Yu-Fang Jin1 ∙ Yidong Chen2,3 ∙ Shou-Jiang Gao4,5 ∙ Yufei Huang4,6,7 ∙ Mario Flores1,8 mario.flores@utsa.edu Highlights •TG-ME integrates transformer and GraphVAE for cancer niche analysis •Achieves superior clustering and profiling tumor microenvironments •Leverages multimodal data for comprehensive TME analysis •Enables precise identification of tumor microenvironment composition Summary This study introduces TG-ME, an innovative computational framework that integrates transformer with graph variational autoencoder (GraphVAE) models for dissection of tumoral niches [...]

Structure: Structural insights into the assembly and regulation of 2′-O RNA methylation by SARS-CoV-2 nsp16/nsp10 (Gupta Lab)

April 14, 2025

 Anurag Misra 1 2, R. Rahisuddin 1 2, Manish Parihar 1, Shailee Arya 1, Thiruselvam Viswanathan 1 2, Nathaniel Jackson 3, Shan Qi 1 2, Siu-Hong Chan 4, Reuben S. Harris 2 5, Luis Martinez-Sobrido 3, Yogesh K. Gupta 1 2 6 Highlights SARS-CoV-2 nsp16/nsp10 oligomerizes on capped mRNA for efficient 2′-O methylation An aromatic zipper in nsp16 modulate oligomerization and methylation N-terminus of nsp10 is required for efficient 2′-O methylation A nucleotide-binding pocket on the backside of nsp16 modulates the 2′-O methylation Summary 2′-O-ribose methylation of viral RNA's first transcribed base (adenine or A1 in SARS-CoV-2) [...]

Molecular Oncology: Hijacking the BAF complex: the mechanistic interplay of ARID1A and EWS::FLI1 in Ewing sarcoma (Libich Lab)

April 10, 2025

 Erich J. Sohn, David S. Libich Abstract Ewing sarcoma, an aggressive pediatric cancer, is driven by the EWS::FLI1 fusion protein, which disrupts gene expression by hijacking the BAF chromatin remodeling complex. Central to this mechanism is the formation of biomolecular condensates, mediated by the prion-like domains (PrLDs) of EWS and ARID1A, a core BAF subunit. ARID1A serves [...]

Biomolecular NMR Assignments: The 1H, 15N and 13C backbone resonance assignments of the N-terminal (1-149) domain of Serpine mRNA Binding Protein 1 (SERBP1) (Libich Lab)

March 31, 2025

 Antoine Baudin1, Hoang H Dinh1, Xiaoping Xu1, David S Libich2 Abstract Serpine mRNA-Binding Protein 1 (SERBP1) is an RNA-binding protein implicated in diverse cellular functions, including translational regulation, tumor progression, and stress response. It interacts with ribosomal subunits, RNA, and proteins involved in stress granules, contributing to processes such as phase separation and epigenetic regulation. Recent studies have [...]

Int’l Journal of Molecular Sciences: The Role of the Tumor Microenvironment (TME) in Advancing Cancer Therapies: Immune System Interactions, Tumor-Infiltrating Lymphocytes (TILs), and the Role of Exosomes and Inflammasomes (Aune Lab)

March 28, 2025

 by, Atef M. Erasha Hanem EL-Gendy  Ahmed S. Aly  Marisol Fernández-Ortiz Ramy K. A. Sayed Abstract Understanding how different contributors within the tumor microenvironment (TME) function and communicate is essential for effective cancer detection and treatment. The TME encompasses all the surroundings of a tumor, such as blood vessels, fibroblasts, immune cells, signaling molecules, exosomes, [...]

Progress in Neurobiology: Pathogenic Oligomeric Tau alters Neuronal RNA Processes through the Formation of Nuclear Heteromeric Amyloids with RNA-Binding Protein Musashi1 (Penalva)

March 11, 2025

 Nicha Puangmalai a b 1, Abbigael E. Aday a b 1, Madison Samples a b, Nemil Bhatt a b, Filippa Lo Cascio a b, Michela Marcatti a b, Suhyeorn J. Park a b, Leiana Fung a b, Cynthia Jerez a b, Luiz O. Penalva c d, Yingxin Zhao e, Haiping Hao f, Doreen Lugano g, Rakez Kayed a b, Mauro Montalbano a b Abstract Alzheimer’s disease (AD) is marked by cytoplasmic proteinopathies, primarily involving misfolded Tau protein. Pathogenic Tau species, such as soluble oligomers and fibrils, disrupt RNA metabolism, though the mechanisms are unclear. Recent research indicates that RNA has a crucial role in Tau aggregation. Our study builds on this by noting [...]

ELife: SERBP1 interacts with PARP1 and is present in PARylation-dependent protein complexes regulating splicing, cell division, and ribosome biogenesis (Libich, Penalva, et al)

February 13, 2025

 Kira Breunig#1, Xuifen Lei#1, Mauro Montalbano#23, Gabriela D A Guardia4, Shiva Ostadrahimi15, Victoria Alers156, Adam Kosti15, Jennifer Chiou7, Nicole Klein1, Corina Vinarov1, Lily Wang1, Mujia Li1, Weidan Song8, W Lee Kraus8, David S Libich16, Stefano Tiziani7910, Susan T Weintraub6, Pedro A F Galante4, Luiz O Penalva15 Abstract RNA binding proteins (RBPs) containing intrinsically disordered regions (IDRs) are present in diverse molecular complexes where they function as dynamic regulators. Their characteristics promote liquid-liquid phase [...]