Evaluation of Three Atlantic Salmon Strains for Resistance to Copepodid Sea Lice Attachment by Michael R. Pietrak, Thomas A. Delomas, Demitri Lifgren, Mark P. Polinski

“…Attached lice did have different transcriptomic profiles on GLS relative to CAS or SJR. …”
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A diagnostic host-specific transcriptome response for Mycoplasma pneumoniae pneumonia to guide pediatric patient treatment by Sandra Viz-Lasheras, Alberto Gómez-Carballa, Xabier Bello, Irene Rivero-Calle, Ana Isabel Dacosta, Myrsini Kaforou, Dominic Habgood-Coote, Aubrey J. Cunnington, Marieke Emonts, Jethro A. Herberg, Victoria J. Wright, Enitan D. Carrol, Stephane C. Paulus, Werner Zenz, Daniela S. Kohlfürst, Nina Schweintzger, Michiel Van der Flier, Ronald de Groot, Luregn J. Schlapbach, Philipp Agyeman, Andrew J. Pollard, Colin Fink, Taco T. Kuijpers, Suzanne Anderson, Ulrich Von Both, Marko Pokorn, Dace Zavadska, María Tsolia, Henriëtte A. Moll, Clementien Vermont, Michael Levin, Federico Martinón-Torres, Antonio Salas, On behalf of EUCLIDS, PERFORM, and DIAMONDS consortia

“…Using a LASSO regression simulation approach and blood microarray data from 107 children with pneumonia (including 30 M. pneumoniae) we identify eight different transcriptomic signatures, ranging from 3-10 transcripts, that differentiate mycoplasma pneumonia from other bacterial/viral pneumonias with high accuracy (AUC: 0.84–0.95). …”
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A patient-based iPSC-derived hepatocyte model of alcohol-associated cirrhosis reveals bioenergetic insights into disease pathogenesis by Bani Mukhopadhyay, Cheryl Marietta, Pei-Hong Shen, Abdul Oiseni, Faridoddin Mirshahi, Maria Mazzu, Colin Hodgkinson, Eli Winkler, Qiaoping Yuan, Daniel Miranda, George Kunos, Arun J. Sanyal, David Goldman

“…Induced pluripotent stem cell-derived hepatocytes (iHLCs) from patients with AC and healthy controls differ transcriptomically, bioenergetically and histologically. …”
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Priming grapevines with oregano essential oil vapour results in a metabolomic shift eliciting resistance against downy mildew by Ana Cecilia Aliaga Fandino, Nicolas Vigneron, Esteban Alfonso, Jean-Philippe Burdet, Eric Remolif, Amanda Malvessi Cattani, Tara Smit-Sadki, Stéphanie Cluzet, Josep Valls-Fonayet, Pierre Pétriacq, Markus Rienth

“…Chasselas), activating different transcriptomic regulated defence mechanisms. Results In the present study, we complement transcriptomic data with metabolomic insights, confirming some previous regulating patterns and highlighting new mechanisms underlying OEOV-induced resistance. …”
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SUV39H1-dependent methyl-degron is a critical regulator of skeletal homeostasis by Qian Li, Hongguang An, Rushui Bai, Qiannan Sun, Ruili Yang, Tianyi Xin, Zimeng Zhuang, Yuntao Lu, Yunyi Tang, Gengyao Chen, Weifang Zhang, Yu Zhang, Bing Han

“…Both experiments in primary samples and Suv39h1-deficient mice show enhanced osteogenesis upon SUV39H1 ablation with gender differences. Transcriptomic analysis reveals the aberrant NF-κB activation and inflammation signatures independent of H3K9me3 underlying SUV39H1-inhibited osteogenesis. …”
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A sort and sequence approach to dissect heterogeneity of response to a self-amplifying RNA vector in a novel human muscle cell line by Rachel D. Barton, John S. Tregoning, Ziyin Wang, Daniel Gonçalves-Carneiro, Radhika Patel, Paul F. McKay, Robin J. Shattock

“…We used a sort and sequence approach to identify host cell factors associated with transgene expression from saRNA; the hypothesis was that cells with different expression levels would have different transcriptomes. We tested this in CDK4/hTERT immortalized human muscle cells transfected with Venezuelan equine encephalitis virus (VEEV)-derived saRNA encoding GFP. …”
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Characteristics of immune-active and immune-silent phenotypes of early-stage cervical carcinoma as revealed by transcriptome sequencing by O. V. Kurmyshkina, P. I. Kovchur, T. O. Volkova

“…Overall, the existence and detectability of different transcriptomic immune-based phenotypes of invasive CeCa at its initial stages of progression is shown, which may provide new options to broaden the knowledge and applicability of target and immune anti-cancer therapy.…”
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Transcriptional time-course analysis during ash dieback infection revealed different responses in tolerant and susceptible Fraxinus excelsior genotypes by Víctor Chano, Renata Callegari Ferrari, Tania Domínguez-Flores, Karuna Shrestha, Barbara Fussi, Hannes Seidel, Oliver Gailing, Katharina B. Budde

“…Overall, these results revealed different transcriptomic expression patterns not only between ADB-tolerant and ADB-susceptible genotypes, but also within these two groups. …”
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Implication of fibroblast growth factor 7 in ovarian cancer metastases and patient survival by Laura F. Mortan, Laura F. Mortan, Brooke A. Meelheim, Justin Garland, Justin Garland, Jacqueline A. Bohn, Zitha Redempta Isingizwe, Doris M. Benbrook, Doris M. Benbrook

“…Serum FGF7 protein levels above the median of 25 patients with ovarian cancer were associated with worse progression-free and overall survival (p = 0.005 and 0.019, respectively) independent of patient and tumor characteristics.ConclusionsIn comparison to ascites, tumors exhibit different transcriptomic profiles that identify candidate biomarkers and drug targets for predicting and preventing recurrence. …”
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Transcriptomic and metabolomic insights into flavor variations in wild and cultivated Agaricus bisporus by Zhi-Xin Cai, Zhi-Heng Zeng, Wen-Zhi Chen, Zhong-Jie Guo, Yuan-Ping Lu, Jian-Hua Liao, Hui Zeng, Mei-Yuan Chen

“…Results showed that although total protein and amino acid contents exhibited no significant differences, transcriptomic analysis identified significant upregulation of AGABI2DRAFT_188981 and AGABI2DRAFT_191000 (genes associated with high-affinity methionine permease MUP1) in cultivated strains, suggesting their indirect regulation of flavor formation via methionine metabolism. …”
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Profiling type I and II interferon responses reveals distinct subgroups of pediatric patients with autoinflammatory disorders by Anaïs Nombel, PharmD, Magali Perret, MSc, Sophie Trouillet-Assant, PhD, Marine Villard, PhD, Christine Lombard, PharmD, Lorna Garnier, PharmD, Anne-Perrine Foray, MD, PhD, Sarah Benezech, MD, Remi Pescarmona, PharmD, Samira Khaldi-Plassart, PhD, Thierry Walzer, PhD, Alexandre Belot, MD, PhD, Sébastien Viel, PharmD, PhD

“…Type I and II interferons induce different transcriptomic signatures in vitro and in vivo, and our results highlight the value of monitoring both IFN-I and IFN-II in interferon-related diseases.…”
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Transcriptome and Metabolome Insights into Key Genes Regulating Fat Deposition and Meat Quality in Pig Breeds by Suthar Teerath Kumar, Yunlong Zheng, Jing Xu, Ziyi Zhao, Qi Zhang, Yunpeng Zhang, Min Li, Hong Zou, Riaz Muhammad Azeem, Wu-Sheng Sun, Yuan Zhao, Shu-Min Zhang

“…Fatty acid (FA) analysis identified 15 significant FAs in the LWLDP, with docosahexaenoic acid (DHA) in the SBP, while amino acid (AA) analysis revealed no breed-based differences. Transcriptome analysis identified 134 upregulated and 362 downregulated genes in the SBP. …”
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Experiences of discrimination are associated with microbiome and transcriptome alterations in the gut by Tien S. Dong, Tien S. Dong, Tien S. Dong, Tien S. Dong, Tien S. Dong, Simer Shera, Kirstin Peters, Gilbert C. Gee, Gilbert C. Gee, Hiram Beltrán-Sánchez, Hiram Beltrán-Sánchez, May C. Wang, Lisa A. Kilpatrick, Lisa A. Kilpatrick, Lisa A. Kilpatrick, Lisa A. Kilpatrick, Xiaobei Zhang, Xiaobei Zhang, Xiaobei Zhang, Xiaobei Zhang, Xiaobei Zhang, Jennifer S. Labus, Jennifer S. Labus, Jennifer S. Labus, Jennifer S. Labus, Jennifer S. Labus, Allison Vaughan, Allison Vaughan, Allison Vaughan, Allison Vaughan, Arpana Church, Arpana Church, Arpana Church, Arpana Church, Arpana Church

“…This study explored the impact of discrimination on gut health, specifically focusing on microbiome changes, predicted metagenomic differences, transcriptomic profiles, and the potential for using a multi-omic approach to predict discrimination to identify discrimination status for an individual. …”
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M1hot tumor-associated macrophages boost tissue-resident memory T cells infiltration and survival in human lung cancer by Eva M Garrido-Martin, Toby W P Mellows, James Clarke, Anusha-Preethi Ganesan, Oliver Wood, Angelica Cazaly, Gregory Seumois, Serena J Chee, Aiman Alzetani, Emma V King, Gareth Thomas, Peter S Friedmann, Pandurangan Vijayanand, Tilman Sanchez-Elsner

“…Immunohistochemistry related the distribution of TAM transcriptomic signatures to density of CD8+ tissue-resident memory T cells (TRM) in tumors and survival data from an independent cohort of 393 patients with lung cancer.Results TAMs have significantly different transcriptomic profiles from NTAMs with >1000 differentially expressed genes. …”
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Identification and expression analysis of ACBPs family members of Hippophae rhamnoides subsp. sinensis Rousi in response to lead stress by CHEN Ke, LI Xinjuan, ZHANG Tian, REN Qiandan, SUN Jing, ZHOU Wu

“…Protein 3D structure predictions revealed that Group 3 proteins were the most complex with high model similarity; Group 1 proteins were simpler but also similar; Group 4 proteins showed low similarity and large differences. Transcriptome analysis and qRT-PCR validation indicated that, except for HrLACBPs1, the other genes had lower expression levels at 2000 mg·kg-1 lead compared to controls, while their expression increased at 5000 mg·kg-1 lead. …”
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