Single-cell transcriptomics link gene expression signatures to clinicopathological features of gonadotroph and lactotroph PitNET by T. Elise Potthoff, Carolin Walter, Daniela Jeising, Daniel Münter, Archana Verma, Eric Suero Molina, Walter Stummer, Martin Dugas, Wolfgang Hartmann, Matthias Dottermusch, Lea Altendorf, Ulrich Schüller, Sophia Scheuermann, Christian Seitz, Thomas K. Albert, Kornelius Kerl

“…Methods We performed differential expression analysis as well as gene expression program identification based on single-cell RNA sequencing to comparatively characterize the transcriptome of seven gonadotroph and three lactotroph PitNET and correlate it with clinical features using bulk RNA-seq data from an independent cohort of 134 PitNET. …”
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Integrated Single-Cell and Spatial Transcriptomic Analysis Identifies ISR-Related Genes Driving Immune Regulation in Parkinson’s Disease by Jiang H, Zhang X, Feng S, Feng W

“…The Integrated Stress Response (ISR) helps cells cope with stress and is linked to neurodegenerative diseases, but its role in PD is not well known. In this study, we used advanced transcriptomic techniques, including single-cell RNA sequencing and spatial transcriptomics, to analyze gene expression patterns in PD. …”
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Differences in transcriptome characteristics and drug repositioning of Alzheimer's disease according to sex by Jingqi Shi, Minghua Zhang, Yazhuo Hu, Jing Liu, Ke Li, Xuan Sun, Siyu Chen, Jianwei Liu, Ling Ye, Jiao Fan, Jianjun Jia

“…Conclusion: The characteristics of the transcriptome in peripheral blood and single-cell transcriptome in the prefrontal cortex exhibit significant differences between male and female patients with AD, which providing a basis for future sex stratified treatment of AD.…”
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CCR7 in esophageal squamous cell carcinoma: an identification from single-cell and bulk transcriptome sequencing by Yang Yu, Qian Zhao, Hongguang Cui, Liang Song

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Single-cell transcriptomic landscape reveals complex cellular heterogeneity and dysregulated signaling pathways in nasopharyngeal carcinoma by Xiaoyan Zhang, Zuojia Guan, Zhan Xu

“…This study aimed to systematically analyze the transcriptional characteristics of different cell types in NPC and their roles in tumor development using single-cell transcriptomics. Methods The research team collected NPC and normal tissue samples, and performed in-depth single-cell sequencing analysis of the transcriptomes. …”
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Orthologous marker groups reveal broad cell identity conservation across plant single-cell transcriptomes by Tran N. Chau, Prakash Raj Timilsena, Sai Pavan Bathala, Sanchari Kundu, Bastiaan O. R. Bargmann, Song Li

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Deciphering the regulatory programs of RNA binding proteins in rheumatoid arthritis through single-cell transcriptome analysis by Hongbin Luo, Qunya Zheng, Youzheng Zhou, Weipeng Lai, Nanwen Zhang, Peng Chen

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Single-cell transcriptomic analysis of the human vascular atlas provides new insights into vasorelaxation redundancy and heterogeneity by Elisa Avolio, Sarah F. Pearce, David Wambeke, Paolo Madeddu

“…Recent whole-genomic, single-cell transcriptomic analysis of human vascular cells has revealed angiotypic heterogeneity. …”
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Single-cell transcriptomic analysis reveals gut microbiota-immunotherapy synergy through modulating tumor microenvironment by Minyuan Cao, Yun Deng, Qing Hao, Huayun Yan, Quan-Lin Wang, Chunyan Dong, Jing Wu, Yajiao He, Li-Bin Huang, Xuyang Xia, Yongchao Gao, Hai-Ning Chen, Wei-Han Zhang, Yan-Jing Zhang, Xiaozhen Zhuo, Lunzhi Dai, Hongbo Hu, Yong Peng, Feng Zhang, Zhaoqian Liu, Weihua Huang, Huiyuan Zhang, Li Yang, Yang Shu, Wei Zhang, Yan Zhang, Heng Xu

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Unveiling the cell-type-specific landscape of cellular senescence through single-cell transcriptomics using SenePy by Mark A. Sanborn, Xinge Wang, Shang Gao, Yang Dai, Jalees Rehman

“…We utilize 72 mouse and 64 human weighted single-cell transcriptomic signatures of cellular senescence to create the SenePy scoring platform. …”
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Integrated transcriptomic and single-cell analysis reveals key immune-related genes and cellular crosstalk in the myocarditis microenvironment by Yuanqing Li, Shangfei He, Jun Wu, Shenrong Liu, Ruiming Liu, Yipeng Du, Dunzheng Han, Wenjie Luo, Zheng Huang, Pingzhen Yang

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A rare IDH-Mutant glioma case: insights from single-cell transcriptomic analysis of tumor recurrences by Wen Li, Yuanshuai Zhou, Shaheryar Shafi, Jun Dong, Minxuan Sun

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Single-cell and transcriptomic analyses reveal the role of PCDH17 in the non-inflammatory tumor microenvironment of pancreatic cancer by Yong Sun, Hong Wan, Jie Xiong, Kun Cao, Dashuai Yang, Jun Huang

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Integrated single-cell transcriptome and TCR profiles of hepatocellular carcinoma highlight the convergence on interferon signaling during immunotherapy by Xiaobo Li, Chang Xu, Mingjie Zhang, Shengnan Guo, Dapeng Hao, Changqing Liu, Jing Ren, Guangyu Wang, Cheng Lyu, Tianhao Li, Huanhuan Xu, Zepeng Hou, Mingshuo Zhang, Dan Kong

“…The development of reliable, predictive markers is important for accurate patient stratification and further mechanistic understanding of therapy response.Methods We comprehensively analyzed paired single-cell RNA transcriptome and T-cell repertoire profiles from 14 HCC ascites samples, collected from 7 patients before and after treatment with the combination of sintilimab (anti-PD-1) and bevacizumab (anti-VEGF).Results We identify a widespread convergence on interferon (IFN) signaling across various immune cell lineages in treatment-responsive patients with HCC, indicating a common transcriptional state transition in the immune microenvironment linked to immunotherapy response in HCC. …”
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A single-cell transcriptomic map of the murine and human multiple myeloma immune microenvironment across disease stages by Emma Verheye, Daliya Kancheva, Hatice Satilmis, Niels Vandewalle, Rong Fan, Pauline M. R. Bardet, Emile J. Clappaert, Kevin Verstaen, Ann De Becker, Karin Vanderkerken, Kim De Veirman, Damya Laoui

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A Single-Cell Transcriptome Atlas of Epithelial Subpopulations in HPV-Positive and HPV-Negative Head and Neck Cancers by Mary C. Bedard, Cosette M. Rivera-Cruz, Tafadzwa Chihanga, Andrew VonHandorf, Alice L. Tang, Chad Zender, Matthew T. Weirauch, Robert Ferris, Trisha M. Wise-Draper, Mike Adam, Susanne I. Wells

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Single‐cell polyadenylation site mapping reveals 3′ isoform choice variability by Lars Velten, Simon Anders, Aleksandra Pekowska, Aino I Järvelin, Wolfgang Huber, Vicent Pelechano, Lars M Steinmetz

“…Here, we perform genome‐wide quantification of polyadenylation site usage in single mouse embryonic and neural stem cells using a novel single‐cell transcriptomic method, BATSeq. …”
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Transcriptome sequencing and SSR prediction of Clematis calyx based on SMRT sequencing platform by Song Liu, Wei Song, Wei Pan, Gangshan Wu

“…Abstract Clematis is an excellent vertical greening plant for garden viewing vines, with great ornamental and high medicinal value. To obtain transcriptome information and functional gene data for the Clematis calyx, this study utilized three biological replicates of the calyx from each of the three Clematis varieties: ‘Henryi’, ‘Polish spirit’, and ‘Mme Julia Correvon’ Single-molecule real-time sequencing technology was employed for full-length transcriptome sequencing. …”
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Immunogenic cell death genes in single-cell and transcriptome analyses perspectives from a prognostic model of cervical cancer by Li Ning, Li Ning, Xiu Li, Xiu Li, Yating Xu, Yating Xu, Yu Si, Yu Si, Hongting Zhao, Qinling Ren, Qinling Ren

“…BackgroundThe role of immunogenic cell death (ICD) in cervical cancer (CESC) is not well understood. This study sought to investigate the significance of ICD in CESC and to establish an ICDRs prognostic model to improve immunotherapy efficacy for patients with cervical cancer.MethodsICD-associated genes were screened at the single-cell and transcriptome levels based on AddModuleScore, single-sample gene set enrichment analysis (ssGSEA) and weighted gene co-expression network (WGCNA) analysis. …”
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A novel necroptosis related prognostic signature for skin cutaneous melanoma based on transcriptome and single cell sequencing analysis by Xin Fan, Lingyi Lu, Sihan Wang, Qiongyan Zhou, Bingjiang Lin

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