Temporal GeneTerrain: advancing precision medicine through dynamic gene expression visualization by Ehsan Saghapour, Ehsan Saghapour, Rahul Sharma, Delower Hossain, Delower Hossain, Kevin Song, Kevin Song, Zhandos Sembay, Zhandos Sembay, Jake Y. Chen, Jake Y. Chen

“…Expression values were first Z-score normalized, and the 1,000 most variably expressed genes were selected. To ensure coordinated temporal dynamics, we calculated Pearson correlation coefficients among these genes and retained those with r ≥ 0.5, resulting in 999 strongly co-expressed candidates. …”
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Lethal clinical outcome and chemotherapy and immunotherapy resistance in patients with urothelial carcinoma with MDM2 amplification or overexpression by Weijuan Zhang, Jiejie Xu, Hailong Liu, Yu Zhu, Zewei Wang, Han Zeng, Zhaopei Liu, Yuan Chang, Le Xu, Kaifeng Jin, Jingtong Xu, Xiaohe Su, Yawei Ding, Lingkai Zhang, Jiaxing Sun, Yuzhen Wu

“…Additionally, 2264 UC samples from five independent external cohorts, with genomic, transcriptomic, and clinical data, were used for validation.Results MDM2 amplification (MDM2Amp) or protein overexpression (MDM2OE) was associated with inferior overall survival (ZSHS cohort, Log-rank p<0.001; FUSCC cohort, Log-rank p=0.030) and reduced response to platinum-based chemotherapy (ZSHS cohort, Log-rank p<0.001) as well as anti-PD-1/PD-L1 immunotherapy (FUSCC cohort, Log-rank p=0.016) in patients with UC, irrespective of TP53/p53 status. …”
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Harnessing multi-omics and artificial intelligence: revolutionizing prognosis and treatment in hepatocellular carcinoma by Zhen Wang, Zhen Wang, Zhen Wang, Gangchen Zhou, Gangchen Zhou, Rongchuan Cao, Rongchuan Cao, Guolin Zhang, Guolin Zhang, Yongxu Zhang, Yongxu Zhang, Mingyue Xiao, Longbi Liu, Longbi Liu, Xuesong Zhang

“…BackgroundHepatocellular carcinoma (HCC) is the most prevalent form of liver cancer, characterized by elevated mortality rates and heterogeneity. …”
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A coagulation-related long non-coding RNA signature to predict prognosis and immune features of breast cancer by Yetao Han, Mengsi Hu, Yanzhong Wang, Shoufang Xu, Feiyu Jiang, Yingjian Wang, Zhiwei Liu

“…Abstract Breast cancer (BC) remains one of the most common malignancies among women worldwide, with persistently poor prognosis despite advancements in diagnostics and therapies. …”
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Molecular analysis of precursor lesions in familial pancreatic cancer. by Tatjana Crnogorac-Jurcevic, Claude Chelala, Sayka Barry, Tomohiko Harada, Vipul Bhakta, Sam Lattimore, Stipo Jurcevic, Mary Bronner, Nicholas R Lemoine, Teresa A Brentnall

“…Bulk frozen sections displaying the most extensive but not microdissected PanIN-2/3 lesions were used in order to obtain the holistic view of both the precursor lesions and their microenvironment. …”
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Genome-Wide Identification of the GPAT Family in <i>Medicago sativa</i> L. and Expression Profiling Under Abiotic Stress by Jianzhi Ma, Mingyang Du, Huiyan Xiong, Ruijun Duan

“…Alfalfa (<i>Medicago sativa</i> L.) is one of the most significant leguminous forages globally; however, its growth process is frequently exposed to environmental stress, giving rise to issues such as impeded growth and decreased yield. …”
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Tumor-associated myeloid cells support murine T-ALL in the central nervous system via integrin signaling by Ryan S. Humphrey, Seohee Nam, Dennis C. Wylie, Lauren I. R. Ehrlich

“…T-ALL cells in the CNS that rebounded after chemotherapy retained myeloid dependence in vitro, and myeloid depletion improved responsiveness to chemotherapy, prolonging mouse survival. …”
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Inhibiting the RNA helicase DDX3X in Burkitt lymphoma induces oxydative stress and impedes tumor progression in xenografts by Hugues Beauchemin, Zeinab Dalloul, Eva-Maria Piskor, Eva-Maria Piskor, Virginie Calderon, Andrew Chatr-aryamontri, Thierry Bertomeu, Tarik Möröy, Tarik Möröy, Tarik Möröy

“…We found that the 3 cell lines exhibited differential sensitivities to the drugs in vitro, with Daudi being the most susceptible and Raji the most resistant. In vivo, RK-33 treatment in a xenograft BL model reduced tumor progression in all cell lines, albeit with variable efficacy compared to the clinical drug Pevonedistat, and again with the Daudi cells being the most responsive to the treatment. …”
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PRMT1-mediated methylation of UBE2m promoting calcium oxalate crystal-induced kidney injury by inhibiting fatty acid metabolism by Tianhui Yuan, Zehua Ye, Shuqin Mei, Miao Zhang, Ming Wu, Fangyou Lin, Weimin Yu, Wei Li, Xiangjun Zhou, Fan Cheng

“…Abstract Calcium oxalate (CaOx) is the most common type of kidney stone, and its crystal deposition can induce oxidative stress, inflammatory responses, and cell death. …”
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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

“…Abstract The therapeutic efficacy of lung adenocarcinoma (LUAD), the most prevalent histological subtype of primary lung cancer, remains inadequate, with accurate prognostic assessment posing significant challenges. …”
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Comparative miRNome analysis of colostrum- and mature milk–derived extracellular vesicles from Holstein and Jersey cows by Daye Mun, Sangdon Ryu, Dong-Hyun Lim, Sangnam Oh, Younghoon Kim

“…Gene Ontology and Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway enrichment analyses revealed that miRNAs from colostrum EVs predominantly regulated immune-related pathways. Transcriptomic analysis of human colon cell line HT-29 treated with Holstein colostrum EVs confirmed the modulation of genes associated with immune responses. …”
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Biomarker-driven drug repurposing for NAFLD-associated hepatocellular carcinoma using machine learning integrated ensemble feature selection by Subhajit Ghosh, Sukhen Das Mandal, Subarna Thakur

“…These include genes ABAT, ABCB11, MBTPS1, and ZFP1 mostly involved in alanine and glutamate metabolism, butanoate metabolism, and ER protein processing. …”
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hiPSC-neurons recapitulate the subtype-specific cell intrinsic nature of susceptibility to neurodegenerative disease-relevant aggregation by Ian Weidling, Christina N. Preiss, Sarah E. Chancellor, Gyan Srivastava, Lauren Gibilisco, Gen Lin, Melanie Shackett Brennan, Janice Lee, Lindsay M. Roth, Olga Morozova, Kyong Nyon Nam, Nehal R. Patel, Qing Liu, J. K. Thomas, Peter Reinhardt, Ruven Wilkens, Dagmar E. Ehrnhoefer, Andreas Striebinger, Stefan Barghorn, Christina Xanthopoulos, Marie-Theres Weil, Sandra Biesinger, Miroslav Cik, Nandini Romanul, Kiran Yanamandra, Alessandra M. Welker, Jessica Wu, Laura Gasparini, Jan Stöhr, Xavier Langlois, Justine D. Manos

“…Abstract Alzheimer’s disease (AD) is characterized by the accumulation and spread of Tau intraneuronal inclusions throughout most of the telencephalon, leaving hindbrain regions like the cerebellum and spinal cord largely spared. …”
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HERV-derived epitopes represent new targets for T-cell-based immunotherapies in ovarian cancer by Qing Wang, Maha Ayyoub, Olivia Le Saux, Paola Bonaventura, Isabelle Treilleux, Nicolas Chopin, Clarisse Dubois, Virginie Mutez, Nicolas Chuvin, Yann Estornes, Jenny Valladeau-Guilemond, Stephane Depil, Nicolas Gadot, Marie Michelas, Audrey Page, Olivier Tabone, Marie Delles, Sarah Moran, Thibault Richard, Marjorie Lacourrège, Dina M Tawfik, Ema Etchegaray, Adrian Valente, Rasha E Boulos, Gabriel Jimenez Dominguez

“…Background Ovarian cancer represents the most lethal gynecological cancer with poor response to checkpoint inhibitors. …”
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Harnessing cell size to separate genetically and functionally distinct dental pulp-derived mesenchymal stromal cell subpopulations by Yiyue Jiang, Zheng Zhang, Kangkang Ren, Shujuan Zhou, Yang Qiao, Weilu Huang, Nanyang Zhang, Hanyan Xu, Xinping Xu, Bing Wen, Wei Zhang, Lu Yin

“…Therefore, identifying and selecting the most potent subpopulation of DPMSCs following expansion is key to improving therapeutic efficacy and consistency. …”
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Acute blood loss in mice forces differentiation of both CD45-positive and CD45-negative erythroid cells and leads to a decreased CCL3 chemokine production by bone marrow erythroid... by Kirill Nazarov, Roman Perik-Zavodskii, Olga Perik-Zavodskaia, Saleh Alrhmoun, Marina Volynets, Julia Shevchenko, Sergey Sennikov

“…In this study, we studied the immunological response of murine erythroid cells to acute blood loss using flow cytometry, NanoString immune transcriptome profiling, and BioPlex cytokine secretome profiling. …”
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In ovo delivery of carvacrol triggers expression of chemotactic factors, antimicrobial peptides and pro-inflammatory pathways in the yolk sac of broiler chicken embryos by Mila M. Y. Meijer, Henry van den Brand, Shahram Niknafs, Eugeni Roura

“…Abstract Background Broiler chickens are most vulnerable immediately after hatching due to their immature immune systems, making them susceptible to infectious diseases. …”
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Genome-Wide Identification of the <i>Eceriferum</i> Gene Family and Analysis of Gene Expression Patterns Under Different Treatments in Pepper (<i>Capsicum annuum</i> L.) by Fan Yang, Kai Wei, Ying Zhang, Xiaoke Chang, Wenrui Yang, Qiuju Yao, Huaijuan Xiao

“…Promoter <i>cis</i>-element analysis revealed enrichment of light-responsive elements, abscisic acid (ABA), jasmonic acid (JA), and stress-responsive regulatory motifs, indicating multi-pathway regulation. …”
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Identification and characterization of Eco-miR 169-EcNF-YA13 gene regulatory network reveal their role in conferring tolerance to dehydration and salinity stress in finger millet by Varsha Rani, Sumi Rana, Mehanathan Muthamilarasan, D. C. Joshi, Ramwant Gupta, Rajesh Singh, Dinesh Yadav

“…The miR169 is one of the most conserved miRNA families, while Eco_N1 is a species-specific miRNA prevalent in finger millet. …”
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High fat diet-induced loss of pituitary plasticity in aging female mice with ablated leptin signaling in somatotropes by Tiffany K. Miles, Tiffany K. Miles, Angela K. Odle, Stephanie D. Byrum, Stephanie D. Byrum, Stephanie D. Byrum, Alex N. Lagasse, Anessa C. Haney, Victoria G. Ortega, Ashley K. Herdman, Melanie C. MacNicol, Melanie C. MacNicol, Angus M. MacNicol, Gwen V. Childs

“…IntroductionSomatotropes lacking leptin receptors (LEPR) produce less growth hormone and are poorly responsive to growth hormone releasing hormone (GHRH). …”
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