Leveraging Single-Cell Multi-Omics to Decode Tumor Microenvironment Diversity and Therapeutic Resistance by Hussein Sabit, Borros Arneth, Timothy M. Pawlik, Shaimaa Abdel-Ghany, Aysha Ghazy, Rawan M. Abdelazeem, Amany Alqosaibi, Ibtesam S. Al-Dhuayan, Jawaher Almulhim, Noof A. Alrabiah, Ahmed Hashash

“…These technologies are able to integrate data from molecular genomic, transcriptomic, proteomics, and metabolomics studies of cells at a single-cell resolution scale that give rise to the full cellular and molecular complexity in the TME. …”
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Hypoxia-induced CTCF mediates alternative splicing via coupling chromatin looping and RNA Pol II pause to promote EMT in breast cancer by Parik Kakani, Shruti Ganesh Dhamdhere, Deepak Pant, Rushikesh Joshi, Sachin Mishra, Anchala Pandey, Dimple Notani, Sanjeev Shukla

“…This further regulates the CTCF-mediated RNA polymerase II pause at COL5A1exon64A, leading to its inclusion in promoting the EMT under hypoxia. Genome-wide study indicates the association of gained CTCF occupancy with the alternative splicing of many cancer-related genes, similar to the proposed model. …”
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Glutathione reductase plays a role in the metabolism of methylmercury degradation in Rhodotorula mucilaginosa by Yi Guo, Wenlong Deng, Qigui Mo, You Yu, Zhenwang Zhang, Mingjie Wei, Ruiling Tang, Surui Lu, Yanting Su

“…Unlike the traditional microbial methylmercury degradation pathways, R. mucilaginosa’s genome does not encode the organomercury lyase gene MerB. …”
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Deciphering the nature and statistical optimization of antimicrobial metabolites of two endophytic bacilli by Raghda S. Isleem, Ahmed M. Eid, Saad El-Din Hassan, Khaled M. Aboshanab, Ghadir S. El-Housseiny

“…Both bacterial isolates displayed antioxidant and antiviral activity and mild cytotoxic action. Genomic sequence and antiSMASH analysis showed that the biosynthetic gene clusters of bacillomycin, mycosubtilin, fengycin, and macrolactin H in B. velezensis CCASU-C6 and bacillibactin and Macrolactin H in B. subtilis CCASU-C11 showed 100% conservation.…”
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The technology landscape for detection of DNA methylation in cancer liquid biopsies by Isabelle Neefs, Joe Ibrahim, Marc Peeters, Guy Van Camp, Ken Op de Beeck

“…The first methods were established for DNA methylation detection in genomic DNA, while new methods have focused more on compatibility with the emerging interest of cell-free DNA (cfDNA) from liquid biopsies. …”
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ENO1 promotes PDAC progression by inhibiting CD8+ T cell infiltration through upregulating PD-L1 expression via HIF-1α signaling by Aziguli Tulamaiti, Shu-Yu Xiao, Yan Yang, Musitaba Mutailifu, Xia-Qing Li, Shi-Qi Yin, Hong-Tai Ma, Hong-Fei Yao, Lin-Li Yao, Li-Peng Hu, Jun Li, Shu-Heng Jiang, Zhi-Gang Zhang, Yan-Miao Huo, Dong-Xue Li, Xue-Li Zhang

“…Under hypoxic conditions, the “Warburg effect” occurs to meet the nutrient and energy demands of rapid genome replication, remodeling the tumor microenvironment (TME) and influencing tumor immunity. α-Enolase (ENO1) is a multifunctional protein, acting as a glycolytic enzyme that catalyzes the conversion of 2-phosphoglyceric acid to phosphoenolpyruvic acid. …”
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Novel functional eQTL-SNPs associated with susceptibility to occupational pulmonary fibrosis: A multi-stage study by Rui Zhao, Xiaobo Tao, Wendi Zhang, Siqi Li, Shenxuan Zhou, Anhui Ning, Zhenyu Li, Minjie Chu, Wei Wang, Junhong Jiang

“…Methods: We first integrated the genome-wide association studies (GWASs) of IPF and silicosis to obtain the shared SNPs. …”
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Spatial transcriptome reveals histology-correlated immune signature learnt by deep learning attention mechanism on H&E-stained images for ovarian cancer prognosis by Chun Wai Ng, Kwong-Kwok Wong, Barrett C. Lawson, Sammy Ferri-Borgogno, Samuel C. Mok

“…Methods In this study, 773 WSIs of H&E-stained tumor sections from 335 patients with treatment naïve high-grade serous ovarian cancer who were included in The Cancer Genome Atlas (TCGA) Pan-Cancer study were used to train, and validate, and to test a ResNet101 CNN model modified with attention mechanism. …”
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The Prognostic Significance of TRs in Hepatocellular Carcinoma: Insights from TCGA and GEO Databases by Hao Zhou, Weijie Wang, Ruopeng Liang, Rongtao Zhu, Jiahui Cao, Chenguang Sun, Yuling Sun

“…Methods: This study utilized Kaplan-Meier analysis of TR expression profiles from The Cancer Genome Atlas (TCGA). Expression levels of TRs in HCC and immune single cells were assessed using datasets from the Gene Expression Omnibus (GEO) and TCGA, analyzed with R software. …”
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Polymorphism of microsattelite loci within the grape germplasm collection maintained at the Dagestan Experiment Station of VIR by M. M. Agakhanov, V. A. Volkov, P. S. Ulianich, K. M. Abdullaev, E. N. Kislin

“…As for any other large germplasm collections, the problem of genetic identification of the accessions and their originality is critical for the ampelographical collection. Genome of Vitis vinifera L. contains many polymorphic microsatellite loci, their allele diversity could be used to reveal the genetic structure of the ex situ collection as well as for the identification of duplicates. …”
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DHX37 Impacts Prognosis of Hepatocellular Carcinoma and Lung Adenocarcinoma through Immune Infiltration by Yanni Xu, Qiongchao Jiang, Hejun Liu, Xiaoyun Xiao, Dinghong Yang, Phei Er Saw, Baoming Luo

“…Coexpression genes, Gene Ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG), and fundamental regulators were performed via LinkedOmics. …”
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A functional approach to analyze the genetic basis for differences in virulence of monkeypox virus clades by Patricia L. Earl, Jeffrey L. Americo, Sara Reynolds, Wei Xiao, Catherine Cotter, Bernard Moss

“…The present study was intended to evaluate the CAST mouse as a model for investigating genomic differences by replacing genes of Zaire-1979 005 (Z-79) clade Ia MPXV with homologous gene sequences of the less virulent and less transmissible USA-2003 clade IIa MPXV. …”
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Development, optimization and application of a universal fluorescence multiplex PCR-based assay to detect BCOR genetic alterations in pediatric tumors by Meng Zhang, Xingfeng Yao, Nan Zhang, Yongbo Yu, Chao Jia, Xiaoxing Guan, Wenjian Xu, Xin Ni, Yongli Guo, Lejian He

“…Results The assay achieved a detection threshold of 10 copies for fusion genes and 0.32 ng genomic DNA for BCOR ITDs. The performance of this assay was also tested in a cohort of 43 pediatric tumors (17 undifferentiated small round cell sarcomas, and 26 tumors with a histological diagnosis of CCSK). …”
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SLC25A38 is required for mitochondrial pyridoxal 5’-phosphate (PLP) accumulation by Izabella A. Pena, Jeffrey S. Shi, Sarah M. Chang, Jason Yang, Samuel Block, Charles H. Adelmann, Heather R. Keys, Preston Ge, Shveta Bathla, Isabella H. Witham, Grzegorz Sienski, Angus C. Nairn, David M. Sabatini, Caroline A. Lewis, Nora Kory, Matthew G. Vander Heiden, Myriam Heiman

“…In this study, we used a genome-wide CRISPR interference screen in erythroleukemia cells and organellar metabolomics to identify the mitochondrial inner membrane protein SLC25A38 as a regulator of mitochondrial pyridoxal 5’-phosphate. …”
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Using spectrometric analysis for indirect estimation of 146S component concentration while measuring FMDV RNA amount by M. I. Doronin, D. V. Mikhalishin, N. Ye. Kamalova, A. V. Borisov

“…As expected, no FMDV genome or 146S particles were detected in the negative control sample.…”
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Pediatric pancreatic acinar cell carcinoma with a non-canonical BRAF-KMT2C fusion and a classic SND1-BRAF fusion: a case report and literature review by Yaqin Wang, Jiasi Zhang, Dimin Nie, Ai Zhang, Qun Hu, Aiguo Liu

“…Pathological and imaging evidence confirmed the diagnosis of PACC, with no lymph node infiltration or distant metastasis. Comprehensive genomic profiling by next-generation sequencing identified a non-canonical BRAF fusion with KMT2C at the DNA level and a classic SND1-BRAF fusion at the RNA level. …”
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Revealing systematic changes in the transcriptome during the transition from exponential growth to stationary phase by Hyun Gyu Lim, Ye Gao, Kevin Rychel, Cameron Lamoureux, Xuwen A. Lou, Bernhard O. Palsson

“…This study demonstrates how the combination of genome-scale datasets and new data analytics reveals the fundamental characteristics of a key transition in the life cycle of bacteria.IMPORTANCENutrient limitations are critical environmental perturbations in bacterial physiology. …”
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Associations between sleep traits and colorectal cancer: a mendelian randomization analysis by Xiangyue Meng, Enshuo Fan, Dan Lv, Yongjing Yang, Shixin Liu

“…Publicly accessible GWAS (Genome-Wide Association Study) data were used to identify these variants to investigate the putative causal relationships between sleep traits and CRC. …”
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Intersection of rare pathogenic variants from TCGA in the All of Us Research Program v6 by Blaine A. Bates, Kylee E. Bates, Spencer A. Boris, Colin Wessman, David Stone, Justin Bryan, Mary F. Davis, Matthew H. Bailey

“…Summary: Using rare cancer predisposition alleles derived from The Cancer Genome Atlas (TCGA) and high cancer prevalence (14% of participants) in All of Us (version 6), we assessed the impact of these rare alleles on cancer occurrence in six broad groups of genetic similarity provided by All of Us: African/African American (AFR), Admixed American/Latino (AMR), East Asian (EAS), European (EUR), Middle Eastern (MID), or South Asian (SAS). …”
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Chromatin environment-dependent effects of DOT1L on gene expression in male germ cells by Manon Coulée, Alberto de la Iglesia, Mélina Blanco, Clara Gobé, Clémentine Lapoujade, Côme Ialy-Radio, Lucia Alvarez-Gonzalez, Guillaume Meurice, Aurora Ruiz-Herrera, Pierre Fouchet, Julie Cocquet, Laïla El Khattabi

“…This coincides with a significant increase in DOT1L expression at this stage and a genome-wide acquisition of H3K79me2, particularly on the sex chromosomes. …”
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