Targeting glycolysis in esophageal squamous cell carcinoma: single-cell and multi-omics insights for risk stratification and personalized therapy by Yan Wang, Yan Wang, Yunjie Shi, Yunjie Shi, Xiao Hu, Xiao Hu, Chenfang Wang, Chenfang Wang

“…BackgroundEsophageal squamous cell carcinoma (ESCC) is closely linked to aberrant glycolytic metabolism, a hallmark of cancer progression, immune evasion, and therapy resistance. This study employs single-cell transcriptomics and multi-omics approaches to unravel glycolysis-mediated mechanisms in ESCC, with a focus on risk stratification and therapeutic opportunities.MethodsData from TCGA and GEO databases were integrated with single-cell RNA sequencing, bulk RNA sequencing, as well as clinical datasets to investigate glycolysis-associated cell subtypes and their clinical implications in ESCC. …”
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Comprehensive analysis of anoikis-related genes in diagnosis osteoarthritis: based on machine learning and single-cell RNA sequencing data by Jun-Song Zhang, Run-Sang Pan, Guo-Lu Li, Jian-Xiang Teng, Hong-Bo Zhao, Chang-Hua Zhou, Ji-Sheng Zhu, Hao Zheng, Xiao-Bin Tian

“…The XGB, SVM, RF, and GLM models identified five hub genes (CDH2, SHCBP1, SCG2, C10orf10, P FKFB3), and the diagnostic model built using these five genes performed well in the training and validation cohorts. analysing single-cell RNA sequencing data from GSE152805, including 25,852 cells of 6 OA cartilage.…”
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Filtering cells with high mitochondrial content depletes viable metabolically altered malignant cell populations in cancer single-cell studies by Josephine Yates, Agnieszka Kraft, Valentina Boeva

“…Abstract Background Single-cell transcriptomics has transformed our understanding of cellular diversity, yet noise from technical artifacts and low-quality cells can obscure key biological signals. …”
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Protocol update to: High-throughput scNMT protocol for multiomics profiling of single cells from mouse brain and pancreatic organoids by Santiago Cerrizuela, Oguzhan Kaya, Lukas P.M. Kremer, Andrea Sarvari, Tobias Ellinger, Jannes Straub, Jan Brunken, Andrés Sanz-Morejón, Aylin Korkmaz, Ana Martín-Villalba

“…Summary: Single-cell nucleosome, methylome, and transcriptome (scNMT) sequencing is a recently developed method that allows multiomics profiling of single cells. …”
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Single-cell RNA sequencing using split-pool barcoding reveals transcriptional heterogeneity in Porphyromonas gingivalis with implications for periodontal pathogenesis by Eun-Young Jang, Seok Bin Yang, Jeewan Chun, Kyu Hwan Kwack, Sang-Wook Kang, Jae-Hyung Lee, Ji-Hoi Moon

“…While its virulence mechanisms are well characterized, its transcriptional heterogeneity at the single-cell level remains unexplored.Materials and Methods We applied split-pool barcoding-based single-cell RNA sequencing to profile gene expression in 1,942 individual P. gingivalis W83 cells cultured under anaerobic conditions. …”
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Single-cell RNA sequencing provides new insights into the interaction between astrocytes and neurons after spinal cord injury in mice by Zhi Tang, Hengyang Lu, Xiao Yang, Mao Wu, Junfeng Yang, Shaoshuo Li, Heng Liu, Junkang Zhou, Bin Tang, Xinyao Du, Fei Xu, Yang Shao, Jianwei Wang

“…Methods and results: In this study, single-cell RNA sequencing (scRNA-seq) was used to analyze the transcriptome data of acute, subacute and intermediate stages of SCI in mice as well as normal tissues. …”
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A Novel 14-Gene Panel Associated With Efferocytosis for Predicting Pancreatic Cancer Prognosis Through Bulk and Single-Cell Databases by Yaheng Wu, Lin Zhao, Dingyan Yi, Zhihua Tian, Bin Dong, Chunxiang Ye, Jingtao Liu, Huachong Ma, Wei Zhao

“…Methodology and Results: In this study, we comprehensively analyzed the Cancer Genome Atlas (TCGA) and Gene Expression Omnibus (GEO) database, as well as additional databases from multiple bioinformatics websites, utilizing 167 ER features derived from the integration of single-cell RNA sequencing (scRNA-seq) and bulk transcriptomic data. …”
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The Helicobacter pylori orphan ATTAAT-specific methyltransferase M.Hpy99XIX plays a central role in the coordinated regulation of genes involved in iron metabolism by Wilhelm Gottschall, Florent Ailloud, Christine Josenhans, Sebastian Suerbaum

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Incorporating gene expression and environment for genomic prediction in wheat by Jia Liu, Jia Liu, Andrew Gock, Kerrie Ramm, Sandra Stops, Tanya Phongkham, Adam Norman, Russell Eastwood, Eric Stone, Shannon Dillon

“…Here we explored the role transcriptome data could play in enhancing GS in wheat.MethodsAcross 286 wheat lines, we integrated phenotype and multi-omic data from controlled environment and field experiments including ca. 40K single nucleotide polymorphisms (SNP), abundance data for ca. 50K transcripts as well as meta-data (e.g. categorical environments) to predict individual genetic merit for two agronomic traits, flowering time and height. …”
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The modulatory effect of oolong tea polyphenols on intestinal flora and hypothalamus gene expression in a circadian rhythm disturbance mouse model by Ruonan Yan, Chi-Tang Ho, Yanan Liu, Shengnan Zhan, Zufang Wu, Xin Zhang

“…After fecal microbiota transplantation from the OTP group, the single-cell transcriptomic analysis revealed that OTP significantly increased the number of hypothalamus cell clusters, up-regulated the number of astrocytes and fibroblasts, and enhanced the expression of circadian rhythm genes Cry2, Per3, Bhlhe41, Nr1d1, Nr1d2, Dbp and Rorb in hypothalamic cells. …”
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Topologically associating domains of chromatin on single-cell Hi-C data: a survey of bioinformatic tools and applications in the light of artificial intelligence by Hongqiang Lyu, Yao Li, Xinran Chen, Yuan Liu, Erhu Liu, Xiaoliang Cheng

“…The computational analysis of TADs on single-cell Hi-C (scHi-C) data in the era of single-cell transcriptomics has received continuous attention since it may provide information beyond that on bulk Hi-C data. …”
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BCMA: An integrative and versatile database for multi-scale and multi-omics molecular atlas of breast cancer by Wenbo Guo, Zikang Yin, Qinglin Mei, Lianshuo Li, Yonghui Gong, Xinqi Li, Wei Zhang, Wenjie Lei, Bingqiang Liu, Lin Hou, Mei Yang, Jin Gu

“…Here, we present BCMA (Breast Cancer Molecular Atlas, http://lifeome.net/database/bcma/), a multi-scale, multi-omics BC database that encompasses 6 bulk multi-omics datasets and 9 single-cell transcriptomics datasets, collectively covering 5424 cases and 236,363 cells. …”
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Single-cell RNA sequencing analysis of human Alzheimer's disease brain samples reveals neuronal and glial specific cells differential expression. by Lilach Soreq, Hannah Bird, Wael Mohamed, John Hardy

“…Astrocytes and microglia displayed the greatest transcriptomic impacts, with the induction of both shared and distinct gene programs.…”
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Identification of osteoarthritis-associated chondrocyte subpopulations and key gene-regulating drugs based on multi-omics analysis by Ting Hao, Zhiwei Pei, Sile Hu, Zhenqun Zhao, Wanxiong He, Jing Wang, Liuchang Jiang, jirigala Ariben, Lina Wu, Xiaolong Yang, Leipeng Wang, Yonggang Wu, Xiaofeng Chen, Qiang Li, Haobo Yang, Siqin Li, Xing Wang, Mingqi Sun, Baoxin Zhang

“…Cell communication and pseudo-temporal analysis, as well as High-dimensional Weighted Gene Co-expression Network Analysis (hdWGCNA), were conducted on the single-cell data to identify key chondrocyte subtypes and module genes. …”
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Synovial macrophage diversity and activation of M-CSF signaling in post-traumatic osteoarthritis by Alexander J Knights, Easton C Farrell, Olivia M Ellis, Michelle J Song, C Thomas Appleton, Tristan Maerz

“…Characterization of synovial macrophage polarization states was performed, alongside computational modeling of macrophage differentiation, as well as implicated transcriptional regulators and stromal-immune communication axes. …”
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Mutual suppression between mutations in the Dictyostelium Greenbeard pathway restores wild-type development by Mariko Katoh-Kurasawa, Lena Trnovec, Peter Lehmann, Blaž Zupan, Gad Shaulsky

“…Using RNA-sequencing analyses, we compared the transcriptomes of the wild type to those of several mutant strains and found that the single-gene mutations attenuated transcriptome progression over developmental time, whereas the double-gene mutation strain rapgapB – tgrB1 – and the activated tgrB1 mutation exhibited near wild-type transcriptomes. …”
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A single cysteine residue in vimentin regulates long non-coding RNA XIST to suppress epithelial–mesenchymal transition and stemness in breast cancer by Saima Usman, William Andrew Yeudall, Muy-Teck Teh, Fatemah Ghloum, Hemanth Tummala, Ahmad Waseem

“…The expression of C328-VIM impacted vimentin–actin interactions and induced EMT-like features that include enhanced cell proliferation, migration, and invasion accompanied by reduced cell adhesion when compared to the wildtype cells. Functional transcriptomic studies confirmed the upregulation of EMT and mesenchymal markers, downregulation of epithelial markers, as well as acquisition of signatures associated with cancer stemness (CD56, POU5F1, PROCR, and CD49f), thus transforming MCF-7 cells from oestrogen-positive to triple-reduced (ESR1, PGR, and HER2) status. …”
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CXCL12/CXCR4 axis mediates CD8 + T cell overactivation in the progression of viral myocarditis by Li Zhang, Keyu Liu, Xiuyun Duan, Shan Zhou, Hailin Jia, Yingnan You, Bo Han

“…Deletion and adoptive transfer of CD8+T cells, as well as blockade of CXCR4, were conducted in vivo. …”
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Multi-omics analysis reveals glutathione metabolism-related immune suppression and constructs a prognostic model in lung adenocarcinoma by Yuxiang Chi, Yuxiang Chi, Guoyuan Ma, Qiang Liu, Qiang Liu, Yunzhi Xiang, Yunzhi Xiang, Defeng Liu, Jiajun Du, Jiajun Du

“…Whole-transcriptome data from the TCGA database were analyzed for functional enrichment, immune infiltration, and immune functionality. …”
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Combining single-cell analysis and molecular docking techniques to construct a prognostic model for colon adenocarcinoma and uncovering inhibin subunit βb as a novel therapeutic ta... by Qinqing Wu, Qinqing Wu, Lu Ye, Yuwei Wu, Mengyu Zhao, Mengyu Zhao, Jiaxin Lu, Yanping Yu, Yanping Yu, Yixiao Niu, Yixiao Niu, Luxiao Zhang, Peijun Zuo, Peijun Zuo

“…However, the specific biological link between anoikis and COAD, as well as its mechanisms in tumor progression, remains unclear, making it a potential new direction for therapeutic strategy research.MethodsWe employed transcriptomic data and clinical information from The Cancer Genome Atlas (TCGA) and Gene Expression Omnibus (GEO) to pinpoint differentially expressed anoikis-related genes (ARGs) in COAD. …”
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