Comprehensive Analysis of Programmed Cell Death-Related Genes in Diagnosis and Synovitis During Osteoarthritis Development: Based on Bulk and Single-Cell RNA Sequencing Data by Zhou J, Jiao S, Huang J, Dai T, Xu Y, Xia D, Feng Z, Chen J, Li Z, Hu L, Meng Q

“…The diagnostic model constructed based on these Hub PCD-DEGs demonstrated diagnostic efficiency in distinguishing OA tissues as well as progression of OA. Additionally, a correlation was observed between the expression levels of Hub PCD-DEGs, immune cell infiltration, and inflammatory cytokine levels. …”
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Regorafenib plus sintilimab as a salvage treatment for microsatellite stable metastatic colorectal cancer: a single-arm, open-label, phase II clinical trial by Rui Liu, Zhi Ji, Xia Wang, Lila Zhu, Jiaqi Xin, Lijun Ma, Jiayu Zhang, Shaohua Ge, Le Zhang, Yuchong Yang, Tao Ning, Ming Bai, Jingjing Duan, Feixue Wang, Yansha Sun, Hongli Li, Ting Deng, Yi Ba, Jihui Hao

“…The combination therapy is well tolerated and has limited toxicity. Biomarker analysis, including transcriptome sequencing and multiplex immunohistochemistry staining are performed. …”
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Integrated single-cell analysis reveals distinct epigenetic-regulated cancer cell states and a heterogeneity-guided core signature in tamoxifen-resistant breast cancer by Kun Fang, Aigbe G. Ohihoin, Tianxiang Liu, Lavanya Choppavarapu, Bakhtiyor Nosirov, Qianben Wang, Xue-Zhong Yu, Sailaja Kamaraju, Gustavo Leone, Victor X. Jin

“…However, such integrated single-cell analysis has not yet been demonstrated to characterize the transcriptome and chromatin accessibility in breast cancer endocrine resistance. …”
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Effect of fibroblast heterogeneity on prognosis and drug resistance in high-grade serous ovarian cancer by Tingjie Wang, Lingxi Tian, Bing Wei, Jun Li, Cuiyun Zhang, Ruitao Long, Xiaofei Zhu, Yougai Zhang, Bo Wang, Guangbo Tang, Jun Yang, Yongjun Guo

“…Here, we used tumor evolution analysis to determine the intra- and intertumoral heterogeneity of high-grade serous ovarian cancer (HGSOC) and analyze the correlation between tumor heterogeneity and prognosis, as well as chemotherapy response, through single-cell and spatial transcriptomic analysis. …”
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Effect of Heterologous Expression of Key Enzymes Involved in Astaxanthin and Lipid Synthesis on Lipid and Carotenoid Production in <i>Aurantiochytrium</i> sp. by Yaping Shao, Zhengquan Gao, Fengjie Sun, Yulin Cui, Xinyu Zou, Jinju Ma, Qiaolei Wang, Hao Zhang, Yuyong Wu, Chunxiao Meng

“…The results showed that the overexpression of LPAAT of <i>Phaeodactylum tricornutum</i> in <i>Aurantiochytrium</i> sp. caused an increase of 39.3% in astaxanthin, 424.7% in β-carotene, 901.8% in canthaxanthin, and 575.9% in lutein, as well as a down-regulation of 15.3% in the fatty acid content. …”
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Neuronal heterogeneity in the ventral tegmental area: Distinct contributions to reward circuitry and motivated behavior by N. Dalton Fitzgerald, Jeremy J. Day

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Integrated multi-omics identify key signalling pathways for notochord lumenogenesis in ascidian Ciona savignyi by Jin Zhang, Zicheng Tan, Qishu Qin, Hongzhe Peng, Wenjie Shi, Haiyan Yu, Bo Dong

“…However, the key signalling pathways for lumenogenesis regulation were not well identified. Here, we performed tissue-specific transcriptomic sequencing for the isolated Ciona notochord tissue, in which 10 551 genes in total were identified. …”
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FB5P-seq-mAbs: monoclonal antibody production from FB5P-seq libraries for integrative single-cell analysis of B cells by Sakina Ado, Chuang Dong, Noudjoud Attaf, Myriam Moussa, Agathe Carrier, Agathe Carrier, Pierre Milpied, Jean-Marc Navarro

“…Parallel analysis of phenotype, transcriptome and antigen receptor sequence in single B cells is a useful method for tracking B cell activation and maturation during immune responses. …”
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Differential Response to Cisplatin between Co-cultured Cells and Pure Cultured Cells Based on Single-cell RNA Sequencing of Three-dimensional-cultured Breast Cancer Cells by Shuqing Yang, Peixian Chen, Xiaofan Mao, KaiRong Lin, Wei Li, Tiancheng He, Huiqi Huang, AiGuo Wu, Wei Luo, Guolin Ye, Guangyu Yao, Dan Zhou

“…Objective: The current study aimed to develop an experimental approach for the direct co-culture of three-dimensional breast cancer cells using single-cell RNA sequencing (scRNA-seq). …”
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Revealing the core suppression effects of various Di (2-ethylhexyl) phthalate exposure on early meiosis progression in postnatal male mice via single-cell RNA sequencing by Baoquan Han, Lei Hua, Shuai Yu, Wei Ge, Cong Huang, Yu Tian, Chunxiao Li, Jiamao Yan, Tian Qiao, Jiachen Guo, Dongliang Lu, Bin Wang, Diya Cai, Yunqi Zhang, Shaolin Liang, Jianjuan Zhao, Qi Hou, Wei Shen, Zhongyi Sun

“…Although previous research has suggested that DEHP exposure hinders the early meiotic progression of male germ cells, the underlying mechanisms are still not well understood. The transcriptomic changes in testicular cells of postnatal male rodents following DEHP exposure were meticulously analyzed using 10X Genomics single-cell RNA sequencing in this study. …”
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Cut&tag: a powerful epigenetic tool for chromatin profiling by Zhijun Fu, Sanjie Jiang, Yiwen Sun, Shanqiao Zheng, Liang Zong, Peipei Li

“…In addition, CUT&Tag has been developed as a strategy for joint profiling of the epigenome, transcriptome or proteome on the same sample. In this review, we will mainly consolidate the applications of CUT&Tag and its derivatives on different platforms, give a detailed explanation of the pros and cons of this technique as well as the potential development trends and applications in the future.…”
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Comprehensive multi-omics integration uncovers mitochondrial gene signatures for prognosis and personalized therapy in lung adenocarcinoma by Wenjia Zhang, Lei Zhao, Tiansheng Zheng, Lihong Fan, Kai Wang, Guoshu Li

“…This study sought to elucidate the prognostic significance of mitochondrial-related genes in LUAD through an integrative multi-omics approach, aimed at developing personalized therapeutic strategies. Utilizing transcriptomic and single-cell RNA sequencing (scRNA-seq) data, alongside clinical information from publicly available databases, we first applied dimensionality reduction and clustering techniques to the LUAD single-cell dataset, focusing on the subclassification of fibroblasts, epithelial cells, and T cells. …”
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Exploring the Causal Association Between 91 Circulating Inflammatory Proteins and Neurodegenerative Diseases: A Bidirectional Two‐Sample Mendelian Randomization and Bioinformatics... by Ziwei Gong, Rong Cao, Hong Zhu

“…Conversely, C2 exhibited higher levels of Tregs, resting NK cells, and activated dendritic cells, as well as upregulation in processes such as cholesterol homeostasis, glucose metabolism, and CD4/CD8 downregulation. …”
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Overexpression of Lol-miR11467 negatively affects osmotic resistance in Larix kaempferi 3 × L. gmelinii 9 by Sufang Zhang, Shanshan Yan, Li Zhang, Pingyu Yan, Hanguo Zhang, Lei Zhang

“…MicroRNAs (miRNAs) are non-coding, single-stranded small RNAs that primarily affect plant growth and stress resistance, including drought stress. …”
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Single-Cell Sequence and Machine Learning Identify a CD79A+B Cells-Related Transcriptional Signature for Predicting Clinical Outcomes and Immune Microenvironment in Breast Cancer by Haihong Hu, Wendi Zhan, Hongxia Zhu, Bo Hao, Ting Yan, Jingdi Zhang, Siyu Wang, Taolan Zhang

“…Conclusion: This study comprehensively explored the heterogeneity of CD79A + B cells through transcriptome analysis and chromatin analysis, which contributes to an in-depth understanding of the function of CD79A + B cells in biological processes as well as the molecular mechanism of breast carcinogenesis, providing a theoretical basis for treatment and prevention.…”
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The impact of carbon-ion beam irradiation on the phenotypic and molecular variation of wheat by Huihui Fan, Qianwen Xue, Hongchun Xiong, Huijun Guo, Yongdun Xie, Linshu Zhao, Jiayu Gu, Shirong Zhao, Yuping Ding, Huiyuan Li, Libin Zhou, Luxiang Liu

“…We examined a total of 1840 M2 plants for phenotypic mutations and found a mean mutation frequency of 2.68%. Transcriptome sequencing revealed that irradiation induced single nucleotide polymorphisms (SNPs) and small insertions and deletions (indels), with transition/transversion ratios ranging from 1.96 to 2.03. …”
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Divergent B-cell and cytotoxic TNK cell activation signatures in HLA-B27-associated ankylosing spondylitis and acute anterior uveitis by Eisa Mahyari, Sean Davin, Kimberly Ogle, Emma Fale-Olsen, Carley Shaut, Tammy M. Martin, Jasvinder S. Ahuja, Eric Suhler, Atul Deodhar, James T. Rosenbaum, James T. Rosenbaum, Tejpal Gill, Tejpal Gill

“…Using cellular indexing of transcriptomes and epitopes (CITE-Seq) in a well-characterized cohort of 25 subjects—including AS (HLA-B27pos), AS+AAU (HLA-B27pos), AAU (HLA-B27pos), HCs (HLA-B27pos), and HCs (HLA-B27neg); N = 5/group—we identified transcriptomic differences at the single-cell level, along with differentially expressed cell surface markers. …”
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CYLD as a key regulator of myocardial infarction-to-heart failure transition revealed by multi-omics integration by Jingya Xu, Jingya Xu, Zhonghua Dong, Zhaodong Li, Xuan Wang, Xuan Wang

“…These hubs were significantly associated with immune-related processes, suggesting their potential role in the pathogenesis of HF after MI. Single-cell transcriptomic analysis demonstrated that CYLD exhibited the strongest correlation with the transition from MI to HF; using random forest modelling, we validated its predictive value in this context.DiscussionIn conclusion, our study identified CYLD as a critical regulator of the transition from MI to HF. …”
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Multi-omics identify ribosome related causal genes methylation, splicing, and expression in prostate cancer by Chengcheng Wei, Jingke He, Yunfan Li, Yu Luo, Liangdong Song, Kun Han, Jindong Zhang, Shuai Su, Delin Wang

“…We used summary-data-based Mendelian randomization (SMR) and colocalization analysis, as well as single-cell analysis, to investigate the association between ribosome-related genes and prostate cancer by integrating multi-omics. …”
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Comprehensive analysis of plasma cell heterogeneity and immune interactions in multiple myeloma by Shuang Qu, Zhihai Zheng, Xiaoling Guo, Jiaqi Mei, Sicong Jiang, Biyun Chen

“…Through single-cell sequencing, 10 major cell types were identified and annotated. …”
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