Integrated Transcriptomic and Proteomic Analysis Reveals Differential Gene and Protein Expression and Signaling Pathways During a 20 Km Endurance Exercise and Recovery in Mongolian... by Xinzhuang Zhang, Yuanyi Liu, Wei Ma, Lianhao Li, Dongyi Bai, Manglai Dugarjaviin

“…By integrating the transcriptomic and proteomic data, we were able to pinpoint overlapping DEGs/DEPs and implicate crucial signaling pathways, including the HIF-1 signaling pathway and glycolysis, in the molecular response of Mongolian horses to exercise. …”
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Berberine Reveals Anticoccidial Activity by Influencing Immune Responses in <i>Eimeria acervulina</i>-Infected Chickens by Binh T. Nguyen, Bujinlkham Altanzul, Rochelle A. Flores, Honghee Chang, Woo H. Kim, Suk Kim, Wongi Min

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Comparative transcriptome analysis reveals various host responses to sacbrood virus infection in Apis cerana and Apis mellifera by Zih-Ting Chang, Yu-Feng Huang, Tzu-Han Chen, Li-Hung Chen, Chung-Yu Ko, Yu-Shin Nai, Yue-Wen Chen

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The host response to influenza infections in human lung and macrophages cell lines by Carmen Aguilar, Ruth Lydia Olga Lambertz, Mark Heise, Ana Eulalio, Klaus Schughart

“…Data We infected human lung adenocarcinoma (A549) and human monocytic (THP-1) cells with H3N2 influenza virus A virus and performed transcriptome analysis using next generation RNA sequencing at various times post infection. …”
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Epigenomic preconditioning of peripheral monocytes determines their transcriptional response to the tumor microenvironment by Máté Kiss, Laszlo Halasz, Eva Hadadi, Wilhelm K. Berger, Petros Tzerpos, Szilard Poliska, Daliya Kancheva, Aurélie Gabriel, Romina Mora Barthelmess, Ayla Debraekeleer, Jan Brughmans, Yvon Elkrim, Liesbet Martens, Yvan Saeys, Bence Daniel, Zsolt Czimmerer, Damya Laoui, Laszlo Nagy, Jo A. Van Ginderachter

“…Epigenomic features, such as post-translational modification of histones and chromatin accessibility, are key determinants of transcription factor binding and thereby play an important role in controlling transcriptional responses to the tissue environment. …”
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Comparative Analysis of Digital Transcriptomics Between Pre- and Post-Treatment Samples of Patients with Locally Advanced Cervical Cancer: A Preliminary Study by Sunhwa Baek, Fabian Dominik Mairinger, Sabrina Borchert, Yue Zhao, Dominik Ratiu, Peter Konrad Mallmann, Henryk Pilch, Ka-Won Noh

“…Pathway enrichment analysis highlighted that the immune response and apoptosis pathways are crucial to post-treatment changes. …”
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Patients with post-COVID-19 condition show minor blood transcriptomic changes, with altered erythrocyte gene expression in a male subgroup by Piia Karisola, Mari Kanerva, Mari Kanerva, Aki Vuokko, Helena Liira, Shuyuan Wang, Kirsi Kvarnström, Mikko Varonen, Hille Suojalehto, Harri Alenius, Harri Alenius

“…This study aimed to investigate transcriptomic changes in peripheral blood cells of patients with post-COVID-19 condition (PCC) and assess if distinct clinical subtypes with specific gene signatures could be identified.MethodsThe cohort included 111 PCC patients from the SARS-CoV-2 Omicron variant era, with 57 recovered (Recov) and 54 having prolonged symptoms indicative of PCC. …”
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Genomic, transcriptomic, and T cell receptor profiling in stratifying response to first-line chemoradiotherapy or radiotherapy for esophageal squamous cell carcinoma by Xiaqin Zhang, Jianhong Lian, Fukun Chen, Kai Wang, Haoyuan Xue, Sufang Jia, Weili Wang, Zhongkang Li, Hua Liang, Hongwei Li

“…Richness was significantly decreased from pre-treat to post-treat.DiscussionMultiomics analysis provided the basic TCRs dynamics and their genomic and transcriptome association during the radio-chemotherapy of 23 locally advanced ESCC in China, and provided a valuable insights into the heterogeneity and the tumor microenvironment and treatment responses. …”
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Transcriptomic analysis reveals long non-coding RNA involved in the key metabolic pathway in response to Botrytis cinerea in kiwifruit by Yijia Ma, Tianjing Zeng, Zhexin Li, Dengwei Jue, Yuan Sui, Xu Wang, Hongpan Zhong, Jiaqi Yang

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Unravelling NK cell subset dynamics and specific gene signatures post-ibrutinib therapy in chronic lymphocytic leukaemia via single-cell transcriptomics by Chunlan Liu, Tianjian Ding, Rong Zou, Aili Zhang, Zhengzhuo Zhi, Sili Wang

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Transcriptome analyses reveal differences in the response to temperature in Florida and Northern largemouth bass (Micropterus spp.) during early life stages. by Moisés A Bernal, Gavin L Aguilar, Josh Sakmar, Sebastian N Politis, Savannah L Oglesby, Allen Nicholls, Anita M Kelly, Luke A Roy, Ian A E Butts

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Red Blood Cell Transcriptome Reflects Physiological Responses to Alternative Nutrient Sources in Gilthead Seabream (<i>Sparus aurata</i>) by Rafael Angelakopoulos, Andreas Tsipourlianos, Alexia E. Fytsili, Leonidas Papaharisis, Arkadios Dimitroglou, Dimitrios Barkas, Zissis Mamuris, Themistoklis Giannoulis, Katerina A. Moutou

“…Blood samples were collected at multiple time points (15, 20, and 30 days post-diet initiation) from genetically diverse full-sib families reared under commercial conditions, integrating transcriptomic analysis with long-term growth assessments. …”
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Goblet cell breakdown: transcriptomics reveals Acinetobacter baumannii early and robust inflammatory response in differentiated human bronchial epithelial cells by Daniela Scribano, Claudia Tito, Astri D. Tagueha, Martina Pasqua, Luciana De Angelis, Francesco Fazi, Dolores Limongi, Marta De Angelis, Lucia Nencioni, Anna Teresa Palamara, Cecilia Ambrosi

“…Transcriptomic data at 4 hpi revealed 668 differentially expressed genes (441 upregulated, 227 downregulated), mainly involved in a strong pro-inflammatory response and characterized by IL-8/CCL20-driven neutrophil recruitment and type 2 cytokine activation (IL-4, IL-13). …”
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Dynamic changes and transcriptome analyses reveal the microfilament skeleton response to water stress in thalli of Neopyropia yezoensis inhabiting the intertidal zone by Jiqiang Yin, Ying Sun, Xinping Miao, Jiaxin Qu, Kunjie Zhang, Xue qing Han, Yichi Li, Jiahui Sun, Fanna Kong

“…This indicate that phosphorylation modification was involved in MFs response to desiccation and rehydration stress. Transcriptome analysis revealed that Latrunculin A, an MF polymerization inhibitor, significantly suppressed the expression of actin and ABPs genes. …”
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Host cellular transcriptional response to respiratory syncytial virus infection in HEp-2 cells: insights from cDNA microarray and quantitative PCR analyses by Manoj K. Pastey, Christopher Lupfer

“…The proinflammatory cytokine interleukin-6 was elevated ~7-fold, underscoring the inflammatory response to RSV. These findings provide a global snapshot of the host transcriptomic response to RSV infection and yield insights into how RSV modulates host cellular machinery to favor viral replication and spread. …”
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Differential Gene and Protein Expressions Responsible for Vasomotor Signaling Provide Mechanistic Bases for the Opposite Flow-Induced Responses of Pre- and Post-Circle of Willis Ar... by Zoltan Nemeth, Krisztian Eros, Gyongyi Munkacsy, Akos Koller

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Multimodal sequencing of neoadjuvant nivolumab treatment in hepatocellular carcinoma reveals cellular and molecular immune landscape for drug response by Fanhong Zeng, Qingyang Zhang, Yu-Man Tsui, Huanhuan Ma, Lu Tian, Abdullah Husain, Jingyi Lu, Joyce Man-Fong Lee, Vanilla Xin Zhang, Po-Man Li, Gary Cheuk-Hang Cheung, Tan-To Cheung, Daniel Wai-Hung Ho, Irene Oi-Lin Ng

“…Notably, we identified a UBASH3B/NR1I2/CEACAM1/HAVCR2 signaling axis, highlighting the intense communication among TAMs, tumor cells, and T-cells that leads to pro-tumorigenic outcomes resulting in poorer nivolumab response. In summary, using integrative multimodal sequencing investigations, combined with the multi-faceted exploration of pre- and post-treatment samples of neoadjuvant nivolumab-treated HCC patients, we identified useful mechanistic determinants of therapeutic response. …”
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Morphotype-Specific Antifungal Defense in <i>Cacopsylla chinensis</i> Arises from Metabolic and Immune Network Restructuring by Jiayue Ji, Xin Gao, Zengli Hu, Ruiyan Ma, Longlong Zhao

“…Using PacBio SMRT sequencing and Illumina RNA-seq, we analyzed transcriptomic changes post-infection, revealing form-specific immune responses, with 18,232 and 5027 differentially expressed genes identified in summer- and winter-form pear psylla, respectively, and a total of 3715 DEGs shared between the two seasonal phenotypes. …”
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Endurance training promotes chromatin closure and timely repression of the post-exercise immediate early stress response by Laura M. de Smalen, Volkan Adak, Aurel B. Leuchtmann, Konstantin Schneider-Heieck, Stefan A. Steurer, Christoph Handschin

“…Methods: A multi-omics analysis was performed: ATAC-sequencing was used to map chromatin accessibility in myonuclei isolated from endurance-trained and untrained mice at multiple time points (0 h, 6 h, and 72 h) post-exercise. Gene expression was assessed via RNA-sequencing, and motif activity analysis identified regulatory factors involved in exercise-induced chromatin remodeling and transcriptomic response. …”
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Resiquimod induces a mixed Th1 and Th2 response via STAT1 and STAT3 signalling in chickens by Deepthi Kappala, Saravanan Ramakrishnan, Patel Nikunjkumar Prakashbhai, Abinaya Kaliappan, Prasad Thomas, Jörg Linde, Mithilesh Singh, Sohini Dey, Madhan Mohan Chellappa

“…These results align with transcriptomic findings and highlight the upregulation of STAT1 and STAT3 as potential contributors to the induction of Th1 and Th2 immune responses by R-848 in chickens. …”
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