Oncolytic adenovirus decreases the proportion of TIM-3+ subset of tumor-infiltrating CD8+ T cells with correlation to improved survival in patients with cancer by Matti Kankainen, Timo Joensuu, Akseli Hemminki, Juuso Juhila, Siri Tähtinen, Otto Hemminki, Anna Kanerva, Kristian Taipale, Ilkka Liikanen, Minna Oksanen, Dafne C A Quixabeira, Saru Basnet

“…Following patient stratification with regard to TIM-3 (increase vs decrease in tumors), overall survival and imaging/marker responses were evaluated by log-rank and Fisher’s test, while coinhibitory receptors/ligands, transcriptomic changes and tumor-reactive and tumor-infltrating immune cells in biopsies and blood samples were studied by microarray rank-based statistics and immunoassays.Results Preclinically, TIM-3+ tumor-infiltrating lymphocytes (TILs) in B16 melanoma showed an exhausted phenotype, whereas oncolytic adenovirus treatment significantly reduced the proportion of TIM-3+ TIL subset through recruitment of less-exhausted CD8+ TIL. …”
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Effect of broccoli extract supplement on carcass traits and lipid metabolism in Holstein steers by Shuangshuang Chen, Xinyu Zhang, Tao Zhu, Die Tang, Mingxing Wen, Chuang Tang, Ling Hou, Zhiyao Zeng, Shanfeng Tong, Xuelong Li, Lu Lu, Keren Long, Quanhui Peng, Anan Jiang, Jideng Ma

“…Blood metabolomics showed elevated prostaglandin E2 levels and enrichment in pathways related to inflammation and lipid metabolism. Transcriptomic analysis revealed enrichment of pathways associated with immune responses and lipid regulation. …”
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Tumor microenvironment assessment-based signatures for predicting response to immunotherapy in non-small cell lung cancer by Jiani Wu, Yuanyuan Wang, Zhenhua Huang, Jingjing Wu, Huiying Sun, Rui Zhou, Wenjun Qiu, Zilan Ye, Yiran Fang, Xiatong Huang, Jianhua Wu, Jianping Bin, Yulin Liao, Min Shi, Jiguang Wang, Wangjun Liao, Dongqiang Zeng

“…We retrospectively collected tumor tissues from 65 patients with advanced NSCLC before treatment, and performed transcriptomic and genomic analysis. By performing single-sample gene set enrichment analysis, we constructed a predictor named IKCscore based on the tumor microenvironment characteristics. …”
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Single‐cell dissection reveals immunosuppressive F13A1+ macrophage as a hallmark for multiple primary lung cancers by Chenglin Yang, Jiahao Qu, Jingting Wu, Songhua Cai, Wenyi Liu, Youjun Deng, Yiran Meng, Liuqing Zheng, Lishen Zhang, Li Wang, Xiaotong Guo

“…Conclusions This study unveils shared molecular mechanismsbetween MPLCs and SPLCs, while identifying MPLC‐specific cellular and molecularfeatures, such as the role of F13A1+ macrophages. …”
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Balancing LncRNA H19 and miR‐675 Bioconversion as a Key Regulator of Embryonic Myogenesis Under Maternal Obesity by Yao Gao, Md Nazmul Hossain, Liang Zhao, Xiangdong Liu, Yanting Chen, Jeanene Marie Deavila, Mei‐Jun Zhu, Gordon K. Murdoch, Min Du

“…Results Transcriptomic analysis showed that MO embryos contained less differentiated myocytes (1.34%) than CT embryos (2.86%). …”
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Multi-omics dissection of tumor microenvironment-mediated drug resistance: mechanisms and therapeutic reprogramming by Fanghua Chen, Fanghua Chen, Yuandong Fu, Yuandong Fu, Gaigai Bai, Gaigai Bai, Junjun Qiu, Junjun Qiu, Keqin Hua, Keqin Hua

“…Advances in multi-omics technologies now enable a comprehensive, multi-dimensional analysis of these interactions, integrating genomic, epigenomic, transcriptomic, proteomic, and metabolomic data to uncover critical molecular networks and vulnerabilities. …”
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<i>ZmNLR</i><i>-7</i>-Mediated Synergistic Regulation of ROS, Hormonal Signaling, and Defense Gene Networks Drives Maize Immunity to Southern Corn Leaf Blight by Bo Su, Xiaolan Yang, Rui Zhang, Shijie Dong, Ying Liu, Hubiao Jiang, Guichun Wu, Ting Ding

“…Transcriptomic analysis revealed a significant inhibition of the expression of the key genes <i>NPR1</i> and <i>ACS6</i> in the SA/ET signaling pathway and a decrease in the expression of disease-related genes <i>ERF1</i> and <i>PR1</i>. …”
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Mechanistic insights into 5-aminolevulinic acid photodynamic therapy for acne vulgaris: targeting lipogenesis via the OLR1-Wnt/β-catenin pathway by Jia Yan, Linglin Zhang, Qingyu Zeng, Yitao Qian, Ke Li, Xiaojing Liu, Yun Wu, Yu Yan, Haiyan Zhang, Szeman Cheung, Jia Liu, Ronald Sroka, Xiuli Wang, Lei Shi

“…In this study, we investigated the impact of ALA-PDT on lipid metabolism in an acne-like mouse model and in immortalized human sebocytes (XL-i-20), focusing on the role of the OLR1-Wnt/β-catenin pathway. We employed transcriptomic analysis, lipid staining, and gene silencing techniques to dissect the molecular interactions induced by ALA-PDT. …”
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Cadmium induced ferroptosis and inflammation in sheep via targeting ACSL4/NF-κB axis by Zimeng Ma, Zimeng Ma, Shuo Yan, Shuo Yan, Huimin Zhang, Huimin Zhang, Ruilin Du, Ruilin Du, Xinyue Cheng, Xinyue Cheng, Siqin Bao, Siqin Bao, Xihe Li, Xihe Li, Xihe Li, Yongli Song, Yongli Song

“…Elucidating its pathogenic mechanisms is crucial for developing therapeutic interventions.MethodsThis study employed multi-omics approaches to systematically investigated cadmium-induced ileal dysfunction in Hu sheep and the intervention mechanisms of sodium octanoate.ResultsPhenotypic assessment revealed cadmium exposure caused intestinal barrier impairment and histopathological changes. Integrated transcriptomic-proteomic analysis revealed cadmium disrupted mitochondrial dysfunction via oxidative phosphorylation pathway inhibition. …”
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Chidamide and cytarabine synergistically treat acute myeloid leukemia: inhibiting ribosome biogenesis via the MYC-RRP9 pathway by Qing Li, Fangfang Wang, Xinrong Xiang, Lei Zhao, Xuefeng Li, Ying Qu, Jingcao Huang, Yunfan Yang, Yang Dai, Xiao Shuai, Jiazhuo Liu, Jie Huang, Yu Liu, Yu Wu

“…In both in vitro and in vivo models, the drug combination demonstrated significant synergism in combating acute myeloid leukemia. Transcriptomic analysis revealed that the combination treatment notably downregulates the MYC signaling pathway. …”
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snCED-seq: high-fidelity cryogenic enzymatic dissociation of nuclei for single-nucleus RNA-seq of FFPE tissues by Yunxia Guo, Junjie Ma, Ruicheng Qi, Rongrong Ma, Xiaoying Ma, Jitao Xu, Kaiqiang Ye, Yan Huang, Xi Yang, Jianyou Zhang, Guangzhong Wang, Xiangwei Zhao

“…Abstract Recent advances have shown that single-nucleus RNA sequencing (snRNA-seq) can be applied to formalin-fixed, paraffin-embedded (FFPE) tissues, opening avenues for transcriptomic analysis of archived specimens. Yet, isolating intact nuclei remains difficult due to RNA cross-linking. …”
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Loss of <i>Myostatin</i> Alters Gut Microbiota and Carbohydrate Metabolism to Influence the Gut–Muscle Axis in Cattle by Chao Hai, Hongyu Gong, Yanan Xu, Xuefei Liu, Chunling Bai, Guanghua Su, Lei Yang, Guangpeng Li

“…These changes correlated with reduced serum glucose and insulin levels while increasing muscle gene expression related to glucose-to-lactose conversion. …”
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The Mkx- TGF-β pathway induced the development of the myodural bridge complex in SD rats by Ji-Hang Li, Ji-Hang Li, Wen-Bin Jiang, Lu Zhang, Yun-Feng Liu, Yi-Tong Sun, Hua-Xun Lai, M. Adeel Alam Shah, Wei Ma, Chan Li, Campbell Gilmore, Jian-Fei Zhang, Hong-Jin Sui

“…Mkx knockdown exhibited diminished collagen fiber development accompanied by compensatory hyperplasia of occipital periosteum-derived fibrous tissues. Transcriptomic analysis revealed that Mkx overexpression upregulated tendon-related genes (Scx, Egr1) and downregulated myogenic regulators (Myod), with inverse expression patterns observed in knockdown models. …”
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Physiological and molecular responses of tomato and citrus to chromium (III) stress at early growth stage by Min Wang, Hangfei Li, Kai Xu, Jiaying Fang, Chao Yu, Weiwei Zheng, Haijie Ma

“…Additionally, low Cr (III) concentrations could result in the death of various microorganisms, including Escherichia coli, Agrobacterium rhizogenes, and Agrobacterium tumefaciens. Transcriptomic analysis identified differentially expressed genes related to “MAPK signaling pathway” and “Plant hormone signal transduction pathway”. …”
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Chaperone-mediated autophagy directs a dual mechanism to balance premature senescence and senolysis to prevent intervertebral disc degeneration by Zhangrong Cheng, Haiyang Gao, Pengzhi Shi, Anran Zhang, Xianglong Chen, Yuhang Chen, Weikang Gan, Kangcheng Zhao, Shuai Li, Cao Yang, Yukun Zhang

“…Abstract Intervertebral disc degeneration (IDD) is a progressive and dynamic process in which the senescence-associated secretory phenotype (SASP) of nucleus pulposus cells (NPC) plays a significant role. While impaired chaperone-mediated autophagy (CMA) has been associated with inflammation and cellular senescence, its specific involvement in the self-perpetuating feedback loop of NPC senescence remains poorly understood. …”
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FGFR4 p.Gly388Arg polymorphism in PBMCs of LAM patients: findings of a pilot study by Sinem Koc-Gunel, Sinem Koc-Gunel, Amy L. Ryan, Melanie Winter, Thomas O. F. Wagner, Thomas O. F. Wagner

“…Patients with the variant exhibited significantly faster rates of lung function decline, as measured by FEV₁%, compared to those without the variant. Spatial transcriptomic analysis of LAM lung tissue revealed FGFR4 expression predominantly in alveolar fibroblasts and AT2 epithelial cells, key compartments in lung remodeling, while detection in PBMCs supports a potential systemic role. …”
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BTLA agonist attenuates Th17-driven inflammation in a mouse model of steroid-resistant asthma by Christine Quach, Xin Li, Pedram Shafiei-Jahani, Meng Li, Stephen Shen, Doumet Georges Helou, Benjamin P. Hurrell, Pejman Soroosh, Omid Akbari

“…The effects of BTLA agonist treatment were assessed on airway hyperreactivity and lung inflammation.ResultsTranscriptomic analysis revealed increased HVEM expression and decreased BTLA expression, both critical immune regulators associated with stimulatory and inhibitory signaling, respectively. …”
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PROS1‐MERTK Axis Drives Tumor Microenvironment Crosstalk and Progression in Papillary Thyroid Microcarcinoma by Wenqian Zhang, Ye Zhang, Zhu Liu, Zhiyuan Wang, Huaqin Wang, Xiaoyu Ji, Hongyue Su, Fan Yang, Lirong Yan, Ying Xu, Hao Zhang, Wei Sun

“…Abstract The incidence of papillary thyroid carcinoma (PTC) has been rising annually, with papillary thyroid microcarcinoma (PTMC) accounting for more than half of the cases. While most PTMCs exhibit indolent growth and a favorable prognosis, some undergo clinical progression with poor outcomes. …”
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Effects of cold environment exposure on female reproductive health and its regulatory mechanisms by Hongyi Sun, Qianqian Zhao, Xiaolan Liang, Yalun He, Yangshuo Li, Jin Yu, Jie Ding, Chaoqin Yu

“…Immunohistochemical analysis showed that the expression levels of IL-1, IL-6, and IL-18 were markedly increased in ovarian tissue, while IL-6 and IL-18 expression levels were significantly elevated in uterine tissue. …”
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Impact of c-di-AMP Accumulation, L-cysteine, and Oxygen on Catalase Activity and Oxidative Stress Resistance of <i>Listeria monocytogenes</i> 10403S by Mahide Muge Yilmaz Topcam, Dimitrios P. Balagiannis, Kimon Andreas G. Karatzas

“…These findings indicate that <i>pdeA</i> contributes to catalase activity in <i>L. monocytogenes</i>. Transcriptomic analysis revealed differential expression of pathways mainly including pentose phosphate pathway, carbon metabolism, O-antigen nucleotide sugar biosynthesis and ABC transporters in Δ<i>pdeA</i> compared to WT. …”
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