Putative function and prognostic molecular marker of mast cells in colorectal cancer by Jiani Guo, Jie Chen, Yiting Wang, Xiaoming Bai, Haimei Feng, Siqi Sheng, Hongyu Wang, Ke Xu, Mengxi Huang, Zengjie Lei, Xiaoyuan Chu

“…This study aims to dissect the mast cells in CRC, characterize the role of mast cells in CRC development, coordinate molecular communication between mast cells and malignant cells, and construct and validate a prognostic classification model based on mast cell markers. Methods Single-cell transcriptome data of CRC patients were extracted from GSE146771 for cell classification and annotation. …”
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COL6A2 in clear cell renal cell carcinoma: a multifaceted driver of tumor progression, immune evasion, and drug sensitivity by Yashuang Yang, Ruixin Fan, Boming Zhang, Kai Liu

“…Methods The mRNA and protein expression data for ccRCC were sourced from TCGA, GEO, CPTAC, and ICPC. Single-cell and spatial transcriptomic data were processed using Seurat with quality control measures. …”
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Canonical prolactin signaling and global mRNA expression in the skin of Holstein heifers carrying the SLICK1 allele of the prolactin receptor gene by Montana D. Altman, Alice T. Mathews, Maria B. Rabaglino, Russell C. Hovey, Anna C. Denicol

“…Next, we investigated pSTAT3 immunoreactivity and the transcriptome of slick and nonslick skin explants after exposure to a controlled level of prolactin in vitro. …”
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Resolvin D1-mediated cellular crosstalk protects against MASH by Amaia Navarro-Corcuera, Yiwei Zhu, Fanglin Ma, Neha Gupta, Haley Asplund, Bruno Cogliati, Jerry E. Chipuk, Oren Rom, Scott L. Friedman, Brian E. Sansbury, Xin Huang, Bishuang Cai

“…However, the mechanisms underlying these beneficial effects are not well understood. Based on a series of co-culture primary cell experiments and unbiased transcriptomic analyses, we show that RvD1-mediated cellular crosstalk among hepatocytes and nonparenchymal cells protects against MASH progression. …”
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Targeting Mesothelin Enhances Personalized Neoantigen Vaccine Induced Antitumor Immune Response in Orthotopic Pancreatic Cancer Mouse Models by Zhixiong Cai, Zhenli Li, Wenting Zhong, Fangzhou Lin, Xiuqing Dong, Honghao Ye, Yutong Guo, Geng Chen, Xiaoling Yu, Haijun Yu, Ruijing Tang, Xiaolong Liu

“…Meanwhile, the combination of αMSLN and neoantigen peptide vaccine identified from pancreatic cancer cell lines is demonstrated to be more effective in inducing neoantigen‐specific T cell generation and infiltration at subcutaneous and orthotopic pancreatic cancer models for enhancing antitumor efficacy. Single‐cell transcriptome analysis shows that the combined treatment significantly reduces the proportion of fibroblasts, improves the infiltration of IFN‐γ+CD4+ and GZMK+CD8+ T cells, as well as reduces the interaction of antigen presentation‐associated ligands and receptors between antigen‐presenting Cancer‐Associated Fibroblasts (apCAFs) and naive CD4+ T cells. …”
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Application of multi-omics technology in pathogen identification and resistance gene screening of sheep pneumonia by Kai Huang, Lvfeng Yuan, Jia Liu, Xiaolong Li, Dan Xu, Xiaoxue Zhang, Jie Peng, Huibin Tian, Fadi Li, Weimin Wang

“…Integration of genome-wide association study (GWAS) data from 266 lung pathological scores with transcriptome-based differentially expressed genes analysis enabled the identification of five single nucleotide polymorphisms (SNPs) and three potential candidate genes associated with Mycoplasma pneumonia. …”
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In the coevolution of cotton and pathogenic fungi, resistant cotton varieties lead to an escalation in the virulence of Verticillium dahliae by Yalin Zhang, Lifang Cui, Ruibing Liu, Zili Feng, Hongjie Feng, Jinglong Zhou, Lihong Zhao, Feng Wei, Heqin Zhu

“…Collectively, this study has significant implications for elucidating the evolution of virulence in V. dahliae induced by the host, as well as for advancing holistic strategies for preventing and managing Verticillium wilt disease.…”
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Clinical significance of plasma-free amino acids and tryptophan metabolites in patients with non-small cell lung cancer receiving PD-1 inhibitor: a pilot cohort study for developin... by Akihiko Kawahara, Tetsuro Sasada, Koichi Azuma, Hidenobu Ishii, Norikazu Matsuo, Takaaki Tokito, Tomoaki Hoshino, Yohei Miyagi, Huihui Xiang, Tomoyuki Tagami, Rika Kasajima, Yumiko Kato, Sachise Karakawa, Shinya Kikuchi, Akira Imaizumi, Kenta Murotani

“…Gene expression in peripheral blood mononuclear cells (PBMCs) was compared between the high-risk and low-risk patients by this multivariate model.Results On Cox proportional hazard analysis, higher concentrations of seven PFAAs (glycine, histidine, threonine, alanine, citrulline, arginine, and tryptophan) as well as lower concentrations of three metabolites (3h-kynurenine, anthranilic acid, and quinolinic acid) and neopterin in plasma were significantly correlated with better OS (p<0.05). …”
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Multi-omics analyses of the heterogenous immune microenvironment in triple-negative breast cancer implicate UQCRFS1 potentiates tumor progression by Yuhui Tang, Aiqi Xu, Zhongbiao Xu, Jindong Xie, Wei Huang, Liulu Zhang, Yitian Chen, Lu Yang, Shasha Du, Kun Wang

“…The public spatial transcriptome, proteome data and qRT-PCR, western blotting experiments were exploited to corroborate UQCRFS1 expression in RNA and protein levels. …”
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METAB‐HTX: prospective, longitudinal cohort study evaluating cardiac and systemic metabolism after heart transplantation by Amin Polzin, Daniel Scheiber, Fabian Voss, Jean Haurand, Elric Zweck, Daniel Oehler, Oliver Maier, Mareike Cramer, Maximilian Spieker, Constanze Moos, Ursala Tokhi, David Naguib, Philipp Mourikis, Marcel Benkhoff, Robert Wagner, Michael Roden, Heinz‐Peter Schultheiss, Sascha Dietrich, Hug Aubin, Udo Boeken, Artur Lichtenberg, Malte Kelm

“…Complex analyses will be conducted to evaluate (i) myocardial substrate utilization and energy metabolism by cardiac and circulating cell respirometry, (ii) impact of genetic (including immunogenetic) and transcriptomic factors by third‐ and fourth generation sequencing (short‐ and long‐read sequencing), (iii) circulating signatures of future neoplasia by single‐cell sequencing of circulating leucocytes, and (iv) evaluation of thromboinflammation in association with heart transplant events. …”
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Effects of β-catenin deficiency on adipose tissue physiology by Romina M. Uranga, Akira Nishii, Jessica N. Maung, Hiroyuki Mori, Brian Desrosiers, Jannis Jacobs, Keegan S. Hoose, Rebecca L. Schill, Devika P. Bagchi, Hannah Guak, Clair Crewe, Ivo D. Dinov, Erin D. Giles, Carey N. Lumeng, Ormond A. MacDougald

“…Methods: To investigate mechanisms through which adipose tissue attempts to maintain homeostasis in the absence of β-catenin in adipocytes, we employed standard methods of metabolic phenotyping as well as bulk RNA sequencing, flow cytometry, single-cell RNA sequencing, and isolation of secreted extracellular vesicles. …”
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Systems biology approaches investigating mitochondrial dysfunction in cyanotic heart disease: a systematic reviewResearch in context by Malak Elbatarny, Yu Tong Lu, Mostin Hu, John Coles, Seema Mital, Amanda Ross-White, Osami Honjo, David J. Barron, Anthony O. Gramolini

“…Findings: From 31 included studies (genomic: n = 5, epigenomic: n = 3, transcriptomic: n = 23, proteomic: n = 2, metabolomic: n = 3, lipidomic: n = 1), we identified 8 pathogenic/likely pathogenic single nucleotide polymorphisms, 73 differentially methylated genes, 4170 differentially expressed genes, 173 differentially expressed proteins between CCHD versus unaffected controls. …”
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The impact of aztreonam–clavulanic acid exposure on gene expression and mutant selection using a multidrug-resistant E. coli by Tongtong Lin, Jiayuan Zhang, Shuo Diao, Jinke Yan, Kexin Zhang, Jichao Cao, Junyi Huang, Yaohai Wang, Zhihua Lv, Xiaopeng Shen, Sherwin K. B. Sy, Michael Lynch, Hongan Long, Mingming Yu

“…In this investigation, we conducted a transcriptomic analysis to reveal the downstream differential gene expression in E. coli ymmD45 (a strain newly isolated and found to carry the New Delhi metallo-β-lactamase gene) following exposure to aztreonam and clavulanate separately, as well as their combination. …”
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Exploring new drug treatment targets for immune related bone diseases using a multi omics joint analysis strategy by Wei Yang, Chenglin Liu, Zhenhua Li, Miao Cui

“…Using the combination of MR and Bayesian colocalization analysis, as well as LDSC analysis, it was concluded that RA was related to CCL19 and TNFRSF14. …”
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NAD+ metabolism enzyme NNMT in cancer-associated fibroblasts drives tumor progression and resistance to immunotherapy by modulating macrophages in urothelial bladder cancer by Jian Huang, Bo Wang, Dong Yan, Tianxin Lin, Lu Pei, Hao Yu, Wang He, Kaiwen Li, Meihua Yang, Weibin Hou, Honghui Zeng, Xin-Ke Zhang, Long Huang, Haide Qin

“…Background This study comprehensively investigates the association between the expression of nicotinamide N-methyltransferase (NNMT) and clinical outcomes of urothelial bladder cancer (UBC), as well as the molecular mechanisms by which NNMT in cancer-associated fibroblast (CAF) modulates tumor progression and immunotherapy resistance in UBC.Methods Single-cell transcriptomic analyses, immunohistochemical and immunofluorescence assays were performed on bladder cancer samples to validate the relationship between NNMT expression and clinical outcomes. …”
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Assessing and enhancing migration of human myogenic progenitors using directed iPS cell differentiation and advanced tissue modelling by SungWoo Choi, Giulia Ferrari, Louise A Moyle, Kirsty Mackinlay, Naira Naouar, Salma Jalal, Sara Benedetti, Christine Wells, Francesco Muntoni, Francesco Saverio Tedesco

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Role of Maternal Obesity in Offspring Cardiovascular Development and Congenital Heart Defects by Ashleigh McMullan, James B. Zwierzynski, Nina Jain, Laura S. Haneline, Weinian Shou, Kok Lim Kua, Swetansu K. Hota, Matthew D. Durbin

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Maternal obesity impairs fetal brown adipogenesis by attenuating fetal FGF21 signaling by Lun Hua, Wenxue Shen, Dengfeng Gao, Yi Yang, Xiaohan Yang, Haoqi Zhang, Siyuan Liu, Luting Liu, Yaxue Cao, Xuemei Jiang, Xingfa Han, Chao Jin, Bin Feng, Lianqiang Che, Shengyu Xu, Yan Lin, Jian Li, Zhengfeng Fang, Ting Luo, Mingzhou Li, De Wu, Yong Zhuo

“…However, the mechanisms behind this phenomenon are not well understood. Our single-nucleus transcriptomic analysis revealed dynamic changes in cell heterogeneity within the fetal interscapular BAT (iBAT) from obese dams, leading to compromised thermogenesis in their offspring. …”
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EIF4A3 Promotes Muscle Atrophy and Aging by Inhibiting the FAK Pathway Through NEDD9 mRNA Destabilization by Qian Li, Xiaohang Yin, Wensi Wan, Yi Zhou, Siqi Wang, Yuwei Yan, Jingying Chen, Xinyi Ren, Junli Gao, Yuying Chen, Yanan Zhang, Caiyue Cui, Emeli Chatterjee, Guoping Li, Ming Wu, Yan Zhang, Dongchao Lu, Tingting Yang, Yongjun Zheng, Jin Li

“…This study aims to investigate the role of the EJC in muscle atrophy. Methods Single‐cell transcriptome analysis and western blot were employed to analyse EJC expression in muscle atrophy. …”
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Stress resilience in Coffea arabica and Coffea canephora under harsh drought and/or heat conditions: selected genes, proteins, and lipid integrated responses by José C. Ramalho, José C. Ramalho, Isabel Marques, Isabel P. Pais, Isabel P. Pais, Jean Armengaud, Duarte Gouveia, Ana P. Rodrigues, Danielly Dubberstein, Danielly Dubberstein, Danielly Dubberstein, António E. Leitão, António E. Leitão, Miroslava Rakočević, Paula Scotti-Campos, Paula Scotti-Campos, Sónia Martins, Sónia Martins, Magda C. Semedo, Magda C. Semedo, Fábio L. Partelli, Fernando C. Lidon, Fábio M. DaMatta, Ana I. Ribeiro-Barros, Ana I. Ribeiro-Barros

“…Conilon Clone 153 (CL153—subjected to single and combined exposure to severe water deficit (SWD) and heat (up to 42°C/30°C, day/night). …”
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