Transcriptome combined single-cell sequencing explores molecular mechanisms of ANGPTL4 in sepsis-induced acute lung injury. by Ying Qi, Changqi Zhou, Bing Chen

“…Recent evidence indicates that ANGPTL4 may influence inflammatory responses and endothelial barrier integrity; however, its cell-specific regulatory mechanisms in sepsis-associated ALI are not well understood. This study utilizes transcriptome profiling combined with single-cell sequencing to systematically analyze the spatiotemporal expression patterns and functional networks of ANGPTL4 during the progression of ALI.…”
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Comparative single‐cell transcriptomic profiling of patient‐derived renal carcinoma cells in cellular and animal models of kidney cancer by Richard Huang, Lynn Kee, Alexander Gont, Jalna Meens, Fraser G. Ferens, Meredith S. Irwin, Laurie Ailles, Scott A. Yuzwa, Claire M. Robinson, Michael Ohh

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A morphological cell atlas of the freshwater sponge Ephydatia muelleri with key insights from targeted single-cell transcriptomes by Sally P. Leys, Lauren Grombacher, Daniel Field, Glen R. D. Elliott, Vanessa R. Ho, Amanda S. Kahn, Pamela J. Reid, Ana Riesgo, Emilio Lanna, Yuriy Bobkov, Joseph F. Ryan, April L. Horton

“…With a goal to help bridge this gap, we have studied the morphology, behaviour and transcriptomics of cells and tissue types of an easily accessible and well-studied species of freshwater sponge, Ephydatia muelleri. …”
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Vitamin D binding protein and receptor prevalence in a large population with periodontitis: single nucleotide polymorphism and transcriptomic profiling by Ziyan Nie, Xiaopan Hu, Peinan Hu, Peiqiang Li, Haijing Zhou, Xiaodong Xie

“…Abstract Background There is an ongoing controversy regarding the expression of vitamin D receptor (VDR) and binding protein (VDBP) genes, as well as their polymorphisms, in periodontitis. We examined eight single nucleotide polymorphisms (SNPs) and performed a transcriptome-level bioinformatics analysis to clarify their relationship with periodontitis. …”
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Exploring Core Genes Associated with Sepsis and Systemic Inflammatory Response Syndrome Using Single-Cell Sequencing Technology by Shen Y, Leng L, Hu Y

“…The frequency of occurrence is on the rise, but there is a lack of certain indicators for the timely detection and recognition of illnesses.Methods: By virtue of scRNA-seq, this research has analyzed single-cell transcriptome data from samples taken from groups with septic death and systemic inflammatory response syndrome so as to identify the unique markers and patterns in immune response.Results: By revealing the status of twelve cell clusters of four major cell types in blood samples through UMAP cell clustering and the differences of major cell populations between the dead and SIRS patients, the results have elucidated the components of different cells and their marker genes in two disease states, and the response mechanism beneficial to disease diagnosis in blood samples.Conclusion: By establishing a theoretical framework centered on cellular and molecular regulation, the study has introduced a novel approach for diagnosing and treating sepsis death group and SIRS patients early, as well as differentiating and preventing these conditions.Keywords: sepsis, SIRS, single cell sequencing, biomarkers, single cell transcriptome…”
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Combined genome and transcriptome analysis identifies molecular signatures of aortic disease in patients with Marfan syndrome by Katherine B. Stanley, Alexa V. Mederos, Ethan H. Barksdale, Joel S. Corvera, Joshua L. Davis, Fang Fang, Hongyu Gao, Courtney E. Vujakovich, Yunlong Liu, Stephanie M. Ware, Benjamin J. Landis

“…Introduction: Transcriptional dysregulation in patients with Marfan syndrome (MFS) is complex and not well-defined. There are likely patient-specific and general mechanisms in the aortic pathology. …”
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48-Hour and 24-Hour Time-lapse Single-nucleus Transcriptomics Reveal Cell-type specific Circadian Rhythms in Arabidopsis by Yuwei Qin, Zhijian Liu, Shiqi Gao, Carlos Martínez-Vasallo, Yanping Long, Xinlong Zhu, Bin Liu, Ya Gao, Xiaodong Xu, Maria A. Nohales, Qiguang Xie, Jixian Zhai

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Transcriptomic profiling of Schlemm’s canal cells reveals a lymphatic-biased identity and three major cell states by Revathi Balasubramanian, Krishnakumar Kizhatil, Taibo Li, Nicholas Tolman, Aakriti Bhandari, Graham Clark, Violet Bupp-Chickering, Ruth A Kelly, Sally Zhou, John Peregrin, Marina Simón, Christa Montgomery, W Daniel Stamer, Jiang Qian, Simon WM John

“…We also analyzed mouse limbal tissues by single-cell and single-nucleus RNA sequencing (C57BL/6 J and 129/Sj strains), successfully sequencing 903 individual SECs. …”
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Meta-analyses of mouse and human prostate single-cell transcriptomes reveal widespread epithelial plasticity in tissue regression, regeneration, and cancer by Luis Aparicio, Laura Crowley, John R. Christin, Caroline J. Laplaca, Hanina Hibshoosh, Raul Rabadan, Michael M. Shen

“…In addition, we have integrated analyses of single-cell transcriptomic states with copy number variants to elucidate transcriptional programs in epithelial cells during human prostate cancer progression. …”
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Spatial transcriptomic and morpho-functional information derived from single mouse FFPE slides allows in-depth fingerprinting of lung fibrosis by Erica Ferrini, Costanza Bonfini, Giovanna Marchese, Martina Buccardi, Matteo Zoboli, Primetta Faccioli, Nicola Sverzellati, Gino Villetti, Simone Ottonello, Maria Ravo, Franco F. Stellari

“…Abstract Background Transcriptome profiling by RNA sequencing (RNAseq) can provide insightful information on the molecular processes underlying disease development and progression. …”
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A single‐cell RNA labeling strategy for measuring stress response upon tissue dissociation by Anika Neuschulz, Olga Bakina, Victor Badillo‐Lisakowski, Pedro Olivares‐Chauvet, Thomas Conrad, Michael Gotthardt, Helmut Kettenmann, Jan Philipp Junker

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A single-cell atlas of the murine limb skeleton integrating the developmental and adult stages by Tim Herpelinck, Liesbeth Ory, Tom Verbraeken, Gabriele Nasello, Mojtaba Barzegari, Johanna Bolander, Frank P. Luyten, Przemko Tylzanowski, Liesbet Geris

“…Abstract The recent growth of single-cell transcriptomics has made single-cell RNA sequencing (scRNA-seq) into a near-routine technique. …”
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Refining the resolution of the yeast genotype–phenotype map using single-cell RNA-sequencing by Arnaud N'Guessan, Wen Yuan Tong, Hamed Heydari, Alex N Nguyen Ba

“…More precisely, we performed expression quantitative trait loci (eQTL) mapping with the scRNA-seq data to identify single-cell eQTL and transcriptome variation patterns associated with fitness variation inferred from the segregant bulk fitness assay. …”
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Integrated analysis of single-cell, spatial and bulk RNA-sequencing identifies a cell-death signature for predicting the outcomes of head and neck cancer by Yue Pan, Lei Fei, Shihua Wang, Hua Chen, Changqing Jiang, Hong Li, Changsong Wang, Yao Yang, Qinggao Zhang, Yongwen Chen

“…BackgroundCell death plays an essential role in carcinogenesis, but its function in the recurrence and postoperative prognosis of head and neck cancer (HNC), which ranks as the 7th most common malignancy globally, remains unclear.MethodsData from five main subtypes of HNC related single-cell RNA sequencing (scRNA-seq) were recruited to establish a single-cell atlas, and the distribution of cell death models (CDMs) across different tissues as well as cell subtypes were analyzed. …”
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Single-cell transcriptome analysis identifies a novel tumor-associated macrophage subtype predicting better prognosis in pancreatic ductal adenocarcinoma by Xiaonan Wang, Dongyi Li, Bo Zhu, Zichun Hua, Zichun Hua, Zichun Hua, Zichun Hua

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Single-cell transcriptome analysis reveals the malignant characteristics of tumour cells and the immunosuppressive landscape in HER2-positive inflammatory breast cancer by Juan Huang, Yongwei Zhu, Wenjing Zeng, Yulong Zhang, Weizhi Xia, Fan Xia, Liyu Liu, Kuansong Wang, Yidi Guan, Taohong Shen, Bingjian Jiang, Lunquan Sun, Ayong Cao, Shouman Wang, Zhi Li

“…Methods In this study, we used single-cell transcriptome technology (scRNA-seq) to investigate the molecular features of the TME of HER2 + IBC patients and performed a comprehensive and detailed comparison of the cellular components and molecular phenotypes of the TME between IBC patients and noninflammatory breast cancer (nIBC) patients to elucidate the cell types that are specifically enriched in the TME of IBC patients, as well as the molecular features that are responsible for the preferential remodelling of the cellular functional state in the TME. …”
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High-resolution transcriptome atlas of bladder cancer highlights the functional myeloid subsets in modulating immune microenvironmentResearch in context by Jiachen Liu, Zhen Shi, Yajian Li, Jie Ma, Jiaying Yao, Zan Yuan, Yuanhao Wang, Chunyuan Yang, Xiao Li, Nianzeng Xing, Yunping Zhu, Jianhong Zhang, Li Wu

“…Methods: We employed density gradient centrifugation to enrich the population of immune cells and collected paired tumour and normal bladder tissues from 11 patients with bladder cancer for single-cell transcriptome analysis. Additionally, in vitro cultures and mouse tumour models were further used to validate our findings. …”
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Single-cell transcriptomics and time-series metabolite profiling reveal the spatiotemporal regulation of flavonoid biosynthesis genes and phytohormone homeostasis by PAP1 in Arabid... by Bingxu Zhang, Thomas Ka Yam Lam, Linheng Chen, Chen Zhang, Liping Zhu, Hailei Zhang, Pengxi Wang, Jianing Wang, Zongwei Cai, Yiji Xia

“…By comparing single-cell transcriptomes of the pap1-D mutant and wild-type plant leaves, we constructed a cell-type-specific atlas of gene expression and high-resolution dynamics of metabolites across developmental stages. …”
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Pathway-based cancer transcriptome deciphers a high-resolution intrinsic heterogeneity within bladder cancer classification by Zhan Wang, Zhaokai Zhou, Shuai Yang, Zhengrui Li, Run Shi, Ruizhi Wang, Kui Liu, Xiaojuan Tang, Qi Li

“…Materials and methods In this study, BLCA single-cell transcriptome data from GSE135337 were used to identify pure tumor cells in BLCA and explore the different intrinsic heterogeneous cell subgroups of BLCA through pathway-based cancer transcriptome classification. …”
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Deciphering the role of SEMA4A/MAPK signaling in sepsis: insights from Mendelian randomization, transcriptomic, single-cell sequencing analyses, and vitro experiments by Meng-Qin Pei, Yan-Ling Lin, Li-Ming Xu, Yu-Shen Yang, Zhen-Dong Sun, Ya-Fen Zeng, Gui-Dan Wang, He-Fan He, Li-Ying Yu, Li-Ying Yu

“…This study aims to uncover new therapeutic targets for sepsisMethodsThree independent transcriptomic datasets from sepsis patients in the GEO database were utilized. …”
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