PARP9-PARP13-PARP14 axis tunes colorectal cancer response to radiotherapy by Rimvile Prokarenkaite, Karolina Kuodyte, Greta Gudoityte, Elzbieta Budginaite, Daniel Naumovas, Egle Strainiene, Kristijonas Velickevicius, Audrius Dulskas, Ernestas Sileika, Jonas Venius, Virginijus Tunaitis, Augustas Pivoriunas, Vytaute Starkuviene, Vaidotas Stankevicius, Kestutis Suziedelis

“…Furthermore, PARP13 loss in HT29 cells markedly impaired the expression of immune response related genes following multifractionated ionizing irradiation. …”
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Pre-immunotherapy alters stereotactic ablative radiotherapy-induced systemic T cell responses in early-stage NSCLC by Chao Liu, Yanjuan Chen, Xiaohui Li, Zhijie Bai, Meilin Jiang, Dongsheng Sheng, Wenxue Zou, Rui Huang, Qingyu Huang, Fuhao Wang, Jingyang Zhu, Huiru Sun, Bing Liu, Zongcheng Li, Bing Sun

“…Results We uncovered distinct T cell response patterns induced by these treatments: while terminal effector CD8+ T cells showed increased cytotoxic and inhibitory scores, and upregulated immune-activated pathways post-SABR, the reverse responses occurred post-icSABR. …”
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Influence of secretome from porcine cardiosphere-derived cells on porcine macrophage polarization and their possible implications for cardiac remodeling post-myocardial infarction... by M. Pulido, M. A. de Pedro, M. A. de Pedro, A. M. Marchena, A. M. Marchena, V. Alvarez, J. G. Casado, J. G. Casado, J. G. Casado, F. M. Sanchez-Margallo, F. M. Sanchez-Margallo, F. M. Sanchez-Margallo, E. López, E. López, E. López

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Predicting gene expression changes upon epigenomic drug treatment [version 3; peer review: 4 approved, 2 not approved] by Monjura Afrin Rumi, Vishaka Gopalan, Sridhar Hannenhalli, Piyush Agrawal

“…Results We found that in two cell lines (HCT116 treated with Largazole at eight doses and RH4 treated with Entinostat at 1µM) where the appropriate data (pre-treatment transcriptome and epigenome as well as post-treatment transcriptome) is available, our model distinguished the post-treatment up versus downregulated genes with high accuracy (up to ROC of 0.89). …”
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A multi-omics approach for understanding blood digestion dynamics in Ixodes scapularis and identification of anti-tick vaccine targets by Jeremiah B. Reyes, Molly McVicar, Saransh Beniwal, Arvind Sharma, Richard Tillett, Juli Petereit, Andrew Nuss, Monika Gulia-Nuss

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Toxoplasma gondii-induced host’s high secretion of 25-hydroxycholesterol for immunoprotection by Zi-Han Yang, Wei-Ling Wu, Jia-Jia Zheng, Chi Zhang, Ying-Ying Lu, Hong-Juan Peng

“…Methods The metabolic alterations in brain tissues of sv129 mice infected by T. gondii at 9 days post-infection (DPI) were analyzed through untargeted metabolomic detection. …”
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Epitranscriptomic Analysis of the Ventral Hippocampus in a Mouse Model of Post-Traumatic Stress Disorder Following Deep Brain Stimulation Treatment of the Basolateral Amygdala by Mingxi Ma, Hao Fan, Hui Zhang, Yao Yin, Yizheng Wang, Yan Gao

“…The N6-methyladenosine (m⁶A) methylation of RNAs in the hippocampus is known to play a significant role in regulating the brain’s response to stress and emotional disorders. Methods: This study aimed to comprehensively analyze the roles of transcriptome-wide m⁶A modifications of the hippocampus in the BLA DBS treatment of a PTSD mouse model using m⁶A sequencing. …”
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Characterization of full-length long noncoding RNAs and identification of virus-responsive lncRNAs in Sogatella furcifera by Yawen Ban, Yawen Ban, Ting Cui, Ting Cui, Lifei Zhao, Lifei Zhao, Xue Li, Xue Li, Qing Bai, Qing Bai, Qingfa Wu, Qingfa Wu

“…Long non-coding RNAs (lncRNAs) are crucial regulators of development and stress responses in eukaryotes, but their roles in non-model insects, particularly rice planthoppers, remain poorly characterized. …”
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Longitudinal single cell profiling of epitope specific memory CD4+ T cell responses to recombinant zoster vaccine by Xiaomin Wen, Alex K. Hu, Scott R. Presnell, Emily S. Ford, David M. Koelle, William W. Kwok

“…Differential gene expression indicates that cells post-vaccination are distinct from cells at baseline, suggesting committed memory T cells display transcriptional changes upon vaccination that could alter their responses against cognate immunogens.…”
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Exploring the role of TIGIT in patients with Small Cell Lung Cancer as a novel predictor of prognosis and immunotherapy response by Li Liu, Peng Wu, Bingzhi Wang, Jiyan Dong, Chaoqi Zhang, Wenchao Liu, Jianming Ying

“…Immunohistochemistry (IHC) was used to verify TIGIT expression in post-surgical and advanced SCLC samples, focusing on expression characteristics, prognostic value, and treatment response. …”
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Analysis of the Differences Among <i>Camellia oleifera</i> Grafting Combinations in Its Healing Process by Zhilong He, Ying Zhang, Chengfeng Xun, Zhen Zhang, Yushen Ma, Xin Wei, Zhentao Wan, Rui Wang

“…Transcriptome sequencing and WGCNA analysis identified 3781 differentially expressed genes, with notable enrichment in stress response pathways (Hsp70, DnaJ) and auxin biosynthesis (YUCCA), while also revealing key hub genes (FKBP19) associated with graft-healing efficiency. …”
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Biochemical Defense Arsenal, Genes/QTLs and Transcripts for Imparting Anthracnose Resistance in Common bean (Phaseolus vulgaris L.) by Safoora Shafi, Mohd Tahir, Vanya Bawa, Farkhandah Jan, Neeraj Choudhary, Mohd Anwar Khan, Yogita Singh, Upendra Kumar, Bilal Ahmad Bhat, Waseem Ahmad Dar, Parvaze Ahmad Sofi, Mohd. Ashraf Bhat, Bilal Ahmad Padder, Asif Bashir Shikari, Rajneesh Paliwal, Rajeev Kumar Varshney, Reyazul Rouf Mir

“…Notably, 03 MTAs (BMr205, BMr269 and BMr244) present on chromosome Pv07 were validated for ANT, and the remaining MTAs were novel MTAs for ANT. Transcriptome sequencing of resistant (PBG-3) and susceptible (PBG-26) genotypes under mock and 120-hour post inoculation conditions revealed key differentially expressed genes, such as leucine-rich repeat domain-containing protein (PHAVU_007G087700g), NB-ARC domain-containing protein (PHAVU_003G002500g) and transcription factors pivotal for disease resistance. …”
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Genome-wide identification and characterization of the bZIP family in the Mangrove Plant Kandelia obovata and its role in response to stress by Yuchong Yi, Yuting Qiu, Hongyao Hu, Dandan Qin, Hechen Huang, Taiping Chen, Wenqi Zha, Yingjia Shen

“…The expression profiles of KobZIP genes during root development and post-embryonic stages, along with their responses to ABA, low temperature, and salt stress, underscore their potential significance in the adaptation of mangrove plants to the intertidal environment.…”
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Distinct immune responses to proton and photon radiotherapy: implications for anti-PD-L1 combination therapy in colorectal cancer by Hélène Burckel, Anaïs Nicol, Carole Mura, Marc Rousseau, Jolie Bou-Gharios, Lisa Froidurot, Corentin Richard, Véronique Morgand, Pierre-Antoine Laurent, Emeric Limagne, Romain Boidot, Georges Noël, Céline Mirjolet

“…Methods Balb/c mice bearing subcutaneous CT26 colon tumors were treated with RT or PT, delivered with 3 × 8 Gy. Seven days post-treatment, transcriptomic analysis and immune response assessments to characterize lymphoid cells, myeloid cells, and PD-L1 expression were performed. …”
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A double-edged sword role of IFN-γ-producing iNKT cells in sepsis: Persistent suppression of Treg cell formation in an Nr4a1-dependent manner by Yingyu Qin, Yilin Qian, Shengqiu Liu, Rong Chen

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Sequencing illustrates the transcriptional response of Legionella pneumophila during infection and identifies seventy novel small non-coding RNAs. by Barbara A Weissenmayer, James G D Prendergast, Amanda J Lohan, Brendan J Loftus

“…Here we present analysis of strand specific sequencing of the transcriptional response of L. pneumophila during exponential and post-exponential broth growth and during the replicative and transmissive phase of infection inside A. castellanii. …”
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Matrix Metalloproteinase‐Responsive Controlled Release of Self‐Assembly Nanoparticles Accelerates Heart Valve Regeneration In Situ by Orchestrating Immunomodulation by Xing Chen, Yunlong Wu, Peng Song, Liandong Feng, Ying Zhou, Jiawei Shi, Nianguo Dong, Weihua Qiao

“…Matrix metalloproteinase (MMP)‐responsive hydrogel is used to encapsulate the nanoparticles, enabling targeted and sustained release. …”
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Spleen-based proteogenomics reveals that Escherichia coli infection induces activation of phagosome maturation pathway in chicken by Jiahui Shi, Songhao Jiang, Qiang Wang, Jilin Dong, Huiming Zhu, Peijia Wang, Shuhong Meng, Zhenpeng Zhang, Lei Chang, Guibin Wang, Xiaoqin Xu, Ping Xu, Yao Zhang

“…Transcriptomic method was further used to assess the changes of dysregulated proteins at 72 h post infection at the mRNA level. …”
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Multi-omics characterization of a lytic phage targeting Listeria monocytogenes by Stevan Cucić, Leena Putzeys, Maarten Boon, Dion Lepp, Rob Lavigne, Cezar M. Khursigara, Hany Anany

“…Profound changes in the host transcriptome became evident 5 min post-infection. GO enrichment and KEGG pathway analysis indicate a downregulation of host transcription factor expression and an upregulation of translation, cobalamin biosynthesis, and propanediol metabolism. …”
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Mitigating Response of <i>SlCSE06</i> Induced by 2-Ethylfuran to <i>Botrytis cinerea</i> Infection by Huilan Ye, Hongdou Gao, Jinnian Li, Linye Lu, Shilan Zheng, Chengxin Wu, Youliang Jin, Chengjuan Cao, Haisheng Zhu, Shuang Liu, Fenglin Zhong

“…In this study, 11 <i>SlCSE</i> family members were identified from the tomato genome using bioinformatics analyses. Public transcriptome databases and RT-qPCR experiments were used to analyze gene expression in tomato tissues, responses to <i>Botrytis cinerea</i> infection, and the temporal characteristics of the response to 2-ethylfuran treatment during infection. …”
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