Unraveling the mechanisms of irAEs in endometrial cancer immunotherapy: insights from FAERS and scRNA-seq data by Lu Zhang, Mengjie Yang, Yiqian Zhang, Jianfa Lan, Qionghua Chen

“…By integrating FAERS and scRNA-seq data, key receptor-ligand interactions were identified, providing preliminary insights that could inform future efforts to optimize immunotherapy efficacy and mitigate AEs. …”
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Precision targeting of β-catenin induces tumor reprogramming and immunity in hepatocellular cancers by Brandon M. Lehrich, Evan R. Delgado, Tyler M. Yasaka, Silvia Liu, Catherine Cao, Yuqing Liu, Mohammad N. Taheri, Xiangnan Guan, Hartmut Koeppen, Sucha Singh, Vik Meadows, Jia-Jun Liu, Anya Singh-Varma, Yekaterina Krutsenko, Minakshi Poddar, T. Kevin Hitchens, Lesley M. Foley, Binyong Liang, Alex Rialdi, Ravi P. Rai, Panari Patel, Madeline Riley, Aaron Bell, Reben Raeman, Tulin Dadali, Jason J. Luke, Ernesto Guccione, Mo R. Ebrahimkhani, Amaia Lujambio, Xin Chen, Martin Maier, Yulei Wang, Wendy Broom, Junyan Tao, Satdarshan P. Monga

“…In conclusion, LNP-CTNNB1 is efficacious as monotherapy and in combination with ICI in CTNNB1-mutated HCCs through impacting tumor cell-intrinsic signaling and remodeling global immune surveillance, providing rationale for clinical investigations.…”
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Deviations From Normative Functioning Underlying Emotional Episodic Memory Revealed Cross-Scale Neurodiverse Alterations Linked to Affective Symptoms in Distinct Psychiatric Disord... by Yang Xiao, Mingzhu Li, Xiao Zhang, Yuyanan Zhang, Yuqi Ge, Zhe Lu, Mengying Ma, Yuqing Song, Hao-Yang Tan, Dai Zhang, Weihua Yue, Hao Yan

“…The microscale cellular signatures underlying macroscale variations were identified using imaging transcriptomic analysis and associated with affective symptoms. …”
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Comprehensive analysis of exosome-related gene signature in multiple myeloma prognosis and immune microenvironment evaluation by Dong Zheng, Bingxin Zhang, Quanqiang Wang, Sisi Zheng, Yibo Xia, Ziwei Zheng, Zhili Lin, Shuxia Zhu, Xinyi Zhang, Luning Cui, Hansen Ying, Tianyu Zhang, Shujuan Zhou, Zixing Chen, Enqing Lan, Yu Zhang, Xuanru Lin, Jingjing Chen, Honglan Qian, Xudong Hu, Yan Zhuang, Zuoting Xie, Xiangjing Zhou, Zhouxiang Jin, Songfu Jiang, Yongyong Ma

“…To our knowledge, this represents the first ERG-based prognostic system for MM, providing a biologically insightful and clinically applicable tool for personalized treatment strategies.…”
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KAT6A chimeras form a self-reinforcing epigenetic module with NURF and MLL/COMPASS to sustain AML by Junhui Lv, Zhinang Yin, Conghui Li, Honglin Wen, Jian Ni, Peiyuan Yang, Zemin Song, Ying Xiang, Honghong Wang, Rui Lu, Li Huang, Ying Zhou, Hai-Bing Zhou, Ruijing Xiao, Pingping Fang, Kaiwei Liang

“…Conclusions Our study identifies a self-reinforcing epigenetic module of histone modifiers and readers in KAT6A-rearranged AML, providing mechanistic insights into the genomic targeting of KAT6A chimeras and highlighting promising combinatorial therapeutic strategies.…”
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Epoxy metabolites of linoleic acid promote the development of breast cancer via orchestrating PLEC/NFκB1/CXCL9-mediated tumor growth and metastasis by Kai-Di Ni, Xian Fu, Ying Luo, Xin He, Hou-Hua Yin, Dong-Ping Mo, Jing-Xian Wu, Ming-Jun Wu, Xiao Zheng, Ya-Nan Liu, Qing Jiang, Ling-Tong Zhang, Ai-Zhi Lin, Ling Huang, Qing-Jin Pan, Xue-Dong Yin, Huan-Yu Zhang, Yi-Wen Meng, Xue Zhou, Jianbo Pan, Zufeng Guo, Jun-Yan Liu

“…This study extends the understanding of the function of PUFAs metabolism in BC development, providing potential therapeutic targets and dietary guidelines for patients with TNBC and other BCs. …”
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Intratracheal instillation of RSV is superior to intranasal inoculation as a model method inducing critical immune cell infiltration by Yinglin Lin, Yao Xiao, Bin Peng, Mengyuan Xie, Zesen Mai, Mingzhen Lin, Shanshan Miao, Xinru Yang, Wei Li, Yi Wang, Zhaoyu Liu, Wenxia Yao

“…Collectively, our study offers novel insights into the rational design of future in vivo infection methods with RSV, as well as providing a foundation for the investigation of the immune pathogenesis of RSV.…”
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The African Initiative for Bioinformatics Online Training in Neurodegenerative Diseases (AI‐BOND): Investing in the next generation of African neuroscientists by Bernard Fongang, Biniyam A. Ayele, Yannick N. Wadop, Emmanuel Epenge, Cyrille D. Nkouonlack, Wepnyu Y. Njamnshi, Xueqiu Jian, Murali Sargurupremraj, Alice B. S. Nono Djotsa, Paul F. Seke Etet, Rebecca Bernal, Abdon Atangana, Jose E. Cavazos, Jayandra Jung Himali, Alfred N. Fonteh, Gladys Maestre, Alfred K. Njamnshi, Sudha Seshadri

“…This innovative online training program will last 6 months and provide training in skill sets R, SAS, and Python programing, genome‐wide association studies, genomics, transcriptomics, proteomics, metabolomics, microbiome analysis, and advanced statistical methods. …”
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Dual RNA-seq study of the dynamics of coding and non-coding RNA expression during Clostridioides difficile infection in a mouse model by Victor Kreis, Claire Toffano-Nioche, Cécile Denève-Larrazet, Jean-Christophe Marvaud, Julian R. Garneau, Florent Dumont, Erwin L. van Dijk, Yan Jaszczyszyn, Anaïs Boutserin, Francesca D'Angelo, Daniel Gautheret, Imad Kansau, Claire Janoir, Olga Soutourina

“…From the pathogen side, this transcriptomic analysis revealed the upregulation of virulence factors, metabolism, and sporulation genes, as well as the identification of 61 ncRNAs differentially expressed during infection that correlated with the analysis of available raw RNA-seq data sets from two independent studies. …”
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Oxidative stress-related biomarkers in thyroid eye disease: evidence from bioinformatics analysis and experimental validation by Yuanping Hai, Yuanping Hai, Qintao Ma, Zhitao Liu, Dongxiao Li, Anqi Huang, Yan Zhu, Duan Yongbo, Cheng Song, Genfeng Yu, Sijie Fang, Lan Liu, Yi Wang, Yi Wang, Thomas Efferth, Jie Shen

“…Bioinformatics enables the identification of differentially expressed genes through transcriptomic analysis. However, distinguishing truly relevant findings from false discoveries remains challenging. …”
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Multi-omics derivation of a core gene signature for predicting therapeutic response and characterizing immune dysregulation in inflammatory bowel disease by Mingming Wang, Liping Liang, Zibo Tang, Jimin Han, Lele Wu, Le Liu, Le Liu, Ye Chen, Ye Chen

“…Current precision medicine approaches lack robust molecular tools integrating transcriptomic signatures with immune dynamics for personalized treatment guidance.MethodsWe performed multi-omics analyses of GEO datasets using machine learning algorithms (LASSO/Random Forest) to derive a four-gene signature. …”
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Multi-omics analysis unveils the predictive value of IGF2BP3/SPHK1 signaling in cancer stem cells for prognosis and immunotherapeutic response in muscle-invasive bladder cancer by Yaobang Wang, Wuyue Song, Chao Feng, Shulin Wu, Zezu Qin, Tao Liu, Yu Ye, Rong Huang, Yuanliang Xie, Zhong Tang, Qiuyan Wang, Tianyu Li

“…Further snRNA-seq, scRNA-seq, ST, and CODEX analysis revealed a closer topographical distance between IGF2BP3 + SPHK1 + bladder cancer cells and exhausted CD8 + T cells, providing one explanation for the superior response to immunotherapy in IGF2BP3 + SPHK1 + bladder cancer cells-enriched patients. …”
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USP19 deficiency enhances T-cell-mediated antitumor immunity by promoting PD-L1 degradation in colorectal cancer by Feng Shi, Guang-Jing Li, Yi Liu, Hai-Meng Zhou, Yue Zhang, Si-Yi Wei, Bo-Jun Zan, Meng Gao, Fei-Shan Chen, Bo-Xin Li, Bai-Qi Wang, Ming-You Dong, Run-Lei Du, Xiao-Dong Zhang

“…These findings establish USP19 as a key driver of immune evasion in CRC and suggest that targeting USP19 could enhance the efficacy of immunotherapy, providing a promising new avenue for CRC treatment.…”
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Decoding disease–specific ageing mechanisms through pathway-level epigenetic clock: insights from multi-cohort validationResearch in context by Pan Li, Jijun Zhu, Shenghan Wang, Haowen Zhuang, Shunjie Zhang, Zhongting Huang, Fuqiang Cai, Zhijian Song, Yuxin Liu, Weixin Liu, Sebastian Freidel, Sijia Wang, Emanuel Schwarz, Junfang Chen

“…Cross-omics validation using transcriptomic data further supported the model's biological relevance (Rho = 0.70, MAE = 7.21). …”
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Anti-galectin-9 therapy synergizes with EGFR inhibition to reprogram the tumor microenvironment and overcome immune evasion by Mien-Chie Hung, Jun Yao, Chia-Hung Chen, Chih-Yen Tu, Zhiguo Liu, Qihui Chen, Liyan Gu, Dongli Linghu, Jiaming Song, Chengjie Liu, Boning Liu, Riyao Yang, Swathi Priya Manickam, Navaneethan Sundhar, Delong Liu, Hsiao-Fan Chen, Shasha Shi, Shunjie Xiong, Linlin Sun

“…Blocking the IFN-I pathway attenuated Gal-9 expression and enhanced the antitumor immunity of afatinib in the LLC tumor model.Conclusions These findings identify Gal-9 upregulation as a key mechanism mediating immune evasion and limiting EGFR-TKI efficacy, providing a promising combinational therapeutic strategy of EGFR-TKI and Gal-9 blockade for the treatment of EGFR-driven cancers.…”
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Identification of the crucial circ-mi-mRNA interaction networks regulating testicular development and spermatogenesis in ganders by Xiaopeng Li, Xiaoyong He, Guibi Li, Zhujun Wang, Fuli Huang, Jiasen Chen, Yang Song, Tanze Liu, Zhaoyan Chen, Xiangfeng Wang, Jiwei Hu, Hua He, Hehe Liu, Liang Li, Jiwen Wang, Shenqiang Hu

“…In the present study, we firstly compared the morphological and histological differences in the testes of ganders from normozoospermic group (NG) and azoospermic group (AG), and then analyzed the testicular expression patterns of circRNAs, miRNAs, and mRNAs between the two groups by using whole-transcriptome sequencing technology. Results from histomorphological analysis demonstrated that the body weight alone was not accountable for the occurrence of gander azoospermia, and the possible cause might be the observed testicular abnormalities. …”
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Response‐adapted zanubrutinib and tislelizumab as a potential strategy to enhance CD19 CAR T‐cell therapy in relapsed/refractory large B‐cell lymphoma: A retrospective observationa... by Rong Shen, Wei‐Guo Cao, Li Wang, Ling‐Shuang Sheng, Yi‐Lun Zhang, Wen Wu, Peng‐Peng Xu, Shu Cheng, Meng‐Ke Liu, Yan Dong, Yue Wang, Xiang‐Qin Weng, Xu‐Feng Jiang, Qi Song, Hong‐Mei Yi, Lei Li, Sheng Chen, Zi‐Xun Yan, Wei‐Li Zhao

“…This regimen effectively abrogates T‐cell exhaustion, but fails to overcome the immunosuppressive effects of M2 macrophages, providing a rationale for remodelling TME to optimise CAR T‐cell therapy.…”
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Molecular heterogeneity of CD30+ peripheral T-cell lymphoma with prognostic significance and therapeutic implications: a retrospective multi-centre studyResearch in context by Yu-Jia Huo, Shu Cheng, Hong-Mei Yi, Ting Niu, Lei Fan, Guo-Hui Cui, Fu-Ling Zhou, Xian-Min Song, Fei Li, Ou Bai, Xiao-Jing Yan, Jun Shi, Ming-Ci Cai, Yao-Hui Huang, Lei Dong, Jie Xiong, Song Hu, Yu-Ran Qiu, Yan Zhao, Peng-Peng Xu, Li Wang, Min Lu, Hong-Mei Jing, Wei-Li Zhao

“…Our findings further elucidated molecular regulatory networks of CD30+ PTCL, providing potential co-targeted approaches for genotype-guided precision medicine in PTCL. …”
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Normal tissue transcriptional signatures for tumor-type-agnostic phenotype prediction by Corey Weistuch, Kevin A. Murgas, Jiening Zhu, Larry Norton, Ken A. Dill, Allen R. Tannenbaum, Joseph O. Deasy

“…Starting with normal tissue transcriptomic profiles, we use non-negative matrix factorization to derive six distinct transcriptomic phenotypes, called archetypes, which combine to describe both normal tissue patterns and variations across a broad spectrum of malignancies. …”
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G2S3: A gene graph-based imputation method for single-cell RNA sequencing data. by Weimiao Wu, Yunqing Liu, Qile Dai, Xiting Yan, Zuoheng Wang

“…Single-cell RNA sequencing technology provides an opportunity to study gene expression at single-cell resolution. …”
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