In-depth characterization of vaccine-induced neoantigen-specific T cells in patients with IDH1-mutant glioma undergoing personalized peptide vaccination by Martin Glas, Florian Battke, Dirk Hadaschik, Martin Schulze, Saskia Biskup, David Reardon, Christina Kyzirakos, Simone Kayser, Oliver Bartsch, Armin Rabsteyn, Henning Zelba, Borong Shao, Annekathrin Reinhardt, Carsten Greve, Lisa Oenning, Pauline Latzer, Tabea Riedlinger, Julian Wünsche, Johannes Harter, Magdalena Feldhahn, Yannick Bantel, Janina Johänning, Jiri Ködding, Olga Maksimovic, Veit Scheble, Alexandra M Miller, Michael Castro, Deborah T Blumenthal

“…Strikingly, we detected two mutIDH1-specific TCRβ candidate sequences in three different patients. These three patients had the same human leukocyte antigen (HLA) DQA-DQB alleles. …”
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Differential Infiltration of Key Immune T-Cell Populations Across Malignancies Varying by Immunogenic Potential and the Likelihood of Response to Immunotherapy by Islam Eljilany, Sam Coleman, Aik Choon Tan, Martin D. McCarter, John Carpten, Howard Colman, Abdul Rafeh Naqash, Igor Puzanov, Susanne M. Arnold, Michelle L. Churchman, Daniel Spakowicz, Bodour Salhia, Julian Marin, Shridar Ganesan, Aakrosh Ratan, Craig Shriver, Patrick Hwu, William S. Dalton, George J. Weiner, Jose R. Conejo-Garcia, Paulo Rodriguez, Ahmad A. Tarhini

“…This study investigated candidate T-cell populations and their differential infiltration within different tumor types as estimated from mRNA co-expression levels of the corresponding cellular markers. …”
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Development and validation of a prognostic staging system for primary plasma cell leukemia by Mengru Tian, Gang An, Weijun Fu, Wenqiang Yan, Lu Li, Chunyan Sun, Zhenyu Li, Lijuan Chen, Aijun Liao, Guangxun Gao, Xiaoqi Qin, Mengyao Li, Chunrui Li, Hua Xue, Li Gao, Yi Wang, Aili He, Fan Zhou, Dongmei Guo, Yujun Dong, Zhihong Fang, Xiaoxia Chu, Jianqing Mi, Chengcheng Fu, Hui Zeng, Shuling Hou, Xiaotao Wang, Hua Wang, Yongqiang Wei, Xinyue Liang, Xingcheng Yi, Yue Sun, Lugui Qiu, Yun Dai, Fengyan Jin

“…Moreover, patients with different stages had highly diverse genomic and transcriptomic aberrations. …”
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Deciphering the dynamic expression network of fiber elongation and the functional role of the GhTUB5 gene for fiber length in cotton based on an introgression population of upland... by Jianjiang Ma, Liupeng Yang, Yuanyue Dang, Kashif Shahzad, Jikun Song, Bing Jia, Li Wang, Juanjuan Feng, Nuohan Wang, Wenfeng Pei, Man Wu, Xuexian Zhang, Jinfa Zhang, Jianyong Wu, Jiwen Yu

“…Methods: Coexpression analyses of 277 developing fiber transcriptomes integrated with QTL mapping using 250 introgression lines of different FL phenotypes were conducted to identify genes related to fiber elongation. …”
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Long noncoding RNA LINC00339 promotes osteoporosis development via modulating of regulator CDC42 by binding PARP1 by Dong-Li Zhu, Yan Zhang, Xiao-Yu Zhang, Zi-Han Qiu, Ke Li, Xiao-Rong Zhou, Zhen-Zhen He, Xiao-Feng Chen, Shan-Shan Dong, Wen Tian, Ya-Kang Wang, Tie-Lin Yang, Bo Yang, Yan Guo

“…Notably, integrated transcriptomic and rescue experiments revealed that LINC00339 and PARP1 coregulate CDC42 expression through post-transcriptional regulatory mechanisms. …”
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Activation of AMP-activated Protein Kinase by Metformin Inhibits Dedifferentiation of Platelet-derived Growth Factor-BB-induced Vascular Smooth Muscle Cells to Improve Arterial Rem... by Guangbo Wu, Qiang Fan, Min Chen, Guqing Luo, Zhenghao Wu, Jinbo Zhao, Jiayun Lin, Chihao Zhang, Hongjie Li, Xiaoliang Qi, Haizhong Huo, Lei Zheng, Meng Luo

“…Methods: Liver cirrhosis with PHT was induced in the rats by common bile duct ligation (BDL). Based on the transcriptomic sequencing of the mesenteric arteries, we investigated the effects and mechanisms of metformin on the arterial remodeling at different stages of cirrhosis. …”
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Integration of co-culture conditions and 3D gelatin methacryloyl hydrogels to improve human-induced pluripotent stem cells-derived cardiomyocytes maturation by Ilaria Gisone, Monica Boffito, Elisa Persiani, Roberta Pappalardo, Elisa Ceccherini, Andrea Alliaud, Manuela Cabiati, Rossella Laurano, Letizia Guiducci, Chiara Caselli, Rosetta Ragusa, Claudio Cassino, Chiara Ippolito, Silvia Del Ry, Susanna Sartori, Antonella Cecchettini, Antonella Cecchettini, Salvador Fernández-Arroyo, Gianluca Ciardelli, Federico Vozzi

“…Omics analyses were carried out to compare terms of biological processes, cellular components, and molecular functions between the 3D model here presented and a classical 2D monoculture of hiPSC-CMs.ResultsGelMA was successfully synthesized with two different DoMs (i.e., 30%–40% and 96%–97%) and used to prepare hydrogels at 5%, 7.5% and 10% w/v concentrations. …”
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GPX4 deficiency-induced ferroptosis drives endometrial epithelial fibrosis in polycystic ovary syndrome by Zhenhong Ye, Ming Cheng, Weisi Lian, Yueqi Leng, Xunsi Qin, Yue Wang, Ping Zhou, Xiyao Liu, Tianliu Peng, Ruiqi Wang, Yilei He, Heng Pan, Yue Zhao, Rong Li

“…GSH intervention to the EEOs of PCOS could alleviate their fibrotic phenotypes at different stages. These findings may serve as a promising therapeutic target for PCOS-related endometrial dysfunction, as well as valuable strategies for improving PCOS-related adverse pregnancy outcomes.…”
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Interleukin‐11 promotes lung adenocarcinoma tumourigenesis and immune evasion by Cristina Cirauqui, Laura Ojeda, Itziar Otano, Irene Pazos, Alba Santos, Eva M. Garrido‐Martín, Patricia Yagüe, Javier Ramos‐Paradas, Sonia Molina‐Pinelo, Giovanna Roncador, José Luis Solórzano, M. Teresa Muñoz, Patricia Cozar, Patricia Plaza, Rocío Suárez, Marta Jiménez, Roberto Moreno, Arantxa Rosado, Pablo Gámez, Ricardo García‐Luján, Jon Zugazagoitia, E. Alejandro Sweet‐Cordero, Mariano Barbacid, Amancio Carnero, Irene Ferrer, Luis Paz‐Ares

“…Methods Here, we used transcriptomic and digital spatial profiling analyses together with clinic data from two retrospective LUAD patient cohorts. …”
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Blood-based detection of MMP11 as a marker of prostate cancer progression regulated by the ALDH1A1-TGF-β1 signaling mechanism by Ielizaveta Gorodetska, Vasyl Lukiyanchuk, Marta Gawin, Myroslava Sliusar, Annett Linge, Fabian Lohaus, Tobias Hölscher, Kati Erdmann, Susanne Fuessel, Angelika Borkowetz, Anna Wojakowska, Daniel Fochtman, Mark Reardon, Ananya Choudhury, Yasmin Antonelli, Aldo Leal-Egaña, Ayse Sedef Köseer, Uğur Kahya, Jakob Püschel, Andrea Petzold, Daria Klusa, Claudia Peitzsch, Romy Kronstein-Wiedemann, Torsten Tonn, Lukasz Marczak, Christian Thomas, Piotr Widłak, Monika Pietrowska, Mechthild Krause, Anna Dubrovska

“…Results We could show that ALDH1A1 and ALDH1A3 genes differently regulate TGFB1 expression in a RAR- and AR-dependent manner. …”
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Artificial intelligence-driven genotype–epigenotype–phenotype approaches to resolve challenges in syndrome diagnosticsResearch in context by Christopher C.Y. Mak, Hannah Klinkhammer, Sanaa Choufani, Nikola Reko, Angela K. Christman, Elise Pisan, Martin M.C. Chui, Mianne Lee, Fiona Leduc, Jennifer C. Dempsey, Pedro A. Sanchez-Lara, Hannah M. Bombei, John A. Bernat, Laurence Faivre, Frederic Tran Mau-Them, Irene Valenzuela Palafoll, Natalie Canham, Ajoy Sarkar, Yuri A. Zarate, Bert Callewaert, Ewelina Bukowska-Olech, Aleksander Jamsheer, Andreas Zankl, Marjolaine Willems, Laura Duncan, Bertrand Isidor, Benjamin Cogne, Odile Boute, Clémence Vanlerberghe, Alice Goldenberg, Elliot Stolerman, Karen J. Low, Vianney Gilard, Jeanne Amiel, Angela E. Lin, Christopher T. Gordon, Dan Doherty, Peter M. Krawitz, Rosanna Weksberg, Tzung-Chien Hsieh, Brian H.Y. Chung

“…Methods: We utilized an expanded cohort of 56 patients (22 previously unpublished individuals) with truncating variants in the MN1 gene and attempted different methods to assess plausible strategies to objectively delineate phenotypic differences between the C-Terminal Truncation (CTT) and N-Terminal Truncation (NTT) groups. …”
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Microglial Nrf2-mediated lipid and iron metabolism reprogramming promotes remyelination during white matter ischemia by Hang Zhang, Sheng Yang, Yi-Lin Lu, Luo-Qi Zhou, Ming-Hao Dong, Yun-Hui Chu, Xiao-Wei Pang, Lian Chen, Lu-Lu Xu, Lu-Yang Zhang, Li-Fang Zhu, Ting Xu, Wei Wang, Ke Shang, Dai-Shi Tian, Chuan Qin

“…Flow cytometric sorting and transcriptomic sequencing were combined to explore the underlying mechanisms regulating microglial oxidative stress and functional phenotypes. …”
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Research advances in the molecular regulatory mechanisms of fruit coloration in fruit trees by MA Shurui, CHI Fumei, SONG Yang

“…Therefore, new gene editing techniques and multi-omics combined analysis (metabolomics, transcriptomics, and proteomics) are being widely used. …”
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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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Microarray Evidences the Role of Pathologic Adipose Tissue in Insulin Resistance and Their Clinical Implications by Sandeep Kumar Mathur, Priyanka Jain, Prashant Mathur

“…This technique has several potential applications in understanding pathologic adipose tissue. They are: (1) transcriptomic differences between various depots of adipose tissue, adipose tissue from obese versus lean individuals, high insulin resistant versus low insulin resistance, brown versus white adipose tissue, (2) transcriptomic profiles of various stages of adipogenesis, (3) effect of diet, cytokines, adipokines, hormones, environmental toxins and drugs on transcriptomic profiles, (4) influence of adipokines on transcriptomic profiles in skeletal muscle, hepatocyte, adipose tissue etc., and (5) genetics of gene expression. …”
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Neurotransmission Sex Dichotomy in the Rat Hypothalamic Paraventricular Nucleus in Healthy and Infantile Spasm Model by Dumitru Andrei Iacobas, Jana Veliskova, Tamar Chachua, Chian-Ru Chern, Kayla Vieira, Sanda Iacobas, Libor Velíšek

“…The transcriptomic differences assist in providing a molecular explanation of the behavioral differences and development of infantile epilepsy spasm syndrome in the two sexes.…”
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Integrating Proteomics and GWAS to Identify Key Tissues and Genes Underlying Human Complex Diseases by Chao Xue, Miao Zhou

“…Compared to GWAS-based gene association estimates alone, incorporating proteomic data significantly improved gene association detection (AUC difference test, <i>p</i> = 0.0028). Furthermore, proteomic data revealed unique disease-associated genes that were not identified using transcriptomic data, such as the association between bipolar disorder and <i>CREB1</i>. …”
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Liver cancer multiomics reveals diverse protein kinase A disruptions convergently produce fibrolamellar hepatocellular carcinoma by David Requena, Jack A. Medico, Luis F. Soto-Ugaldi, Mahsa Shirani, James A. Saltsman, Michael S. Torbenson, Philip Coffino, Sanford M. Simon

“…Additionally, we study FLC metastases, finding small differences from the primary tumors.…”
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Regulation of RNA splicing in endometrial tissue and its association with endometriosis by Fei Yang, Ting Qi, Allan F. McRae, Peter A.W. Rogers, Grant W. Montgomery, Sally Mortlock

“…Transcriptomic differences were most pronounced in the mid-secretory (receptive) phase in endometriosis samples. …”
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Assessment of the new Next Generation Sequencing (NGS) tools to identify genes associated with tolerance to water deficit in sugarcane by John Jaime Riascos Arcos, Héctor Fabio Espitia Navarro, Jershon López Gerena

“…Also, it was possible to detect differences in expression levels of highly similar transcripts. …”
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