Identification and analysis of major latex protein (MLP) family genes in Rosa chinensis responsive to Botrytis cinerea infection by RNA-seq approaches by Haoyuan Chen, Qingkui Li, Peilei Cheng, Taotao Yan, Chunlan Dong, Zhe Hou, Peihuang Zhu, Changbing Huang

“…Here we inoculated the resistant rose variety ‘Yellow Leisure Liness’ with B. cinerea to investigate its resistance mechanisms against gray mold disease. Through transcriptome sequencing, we identified 578 differentially expressed genes (DEGs) that were significantly upregulated at 24, 48, and 72 hours post-inoculation, with these genes significantly enriched for three defense response-related GO terms. …”
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CRISPR/Cas9-mediated knockout of SLC15A4 gene involved in the immune response in bovine rumen epithelial cells by Mao-cheng JIANG, Zi-xuan HU, Ke-xin WANG, Tian-yu YANG, Miao LIN, Kang ZHAN, Guo-qi ZHAO

“…Five down-regulated pro-inflammatory genes and 13 down-regulated chemokine genes related to the inflammatory response were identified. Meanwhile, the down-regulated genes were mostly enriched in the nuclear factor κB (NF-κB) and mitogen-activated protein kinase (MAPK) signaling pathways. …”
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Genome-wide Analysis of CONSTANS-like (CqCOL) Transcription Factors in Quinoa (Chenopodium quinoa): Structural Diversity, Phylogeny, and Stress-Responsive Expression by Huyen Thi Thanh Tran, Gioi Huy Dong, Ha Duc Chu, Phi Bang Cao

“…Transcriptomic analyses under different conditions supported these insights, highlighting the importance of CqCOL genes in quinoa's developmental processes and stress responses. …”
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Characterization of the heat shock factor RcHsfA6 in Rosa chinensis and function in the thermotolerance of Arabidopsis by Yanhui Kang, Yuan Yang, Pei Sun, Maofu Li, Hua Wang, Xiangyi Sun, Wanmei Jin

“…Results In the present study, the transcriptomes of rose petals at normal (25 °C) and high (35 °C) temperature were compared. …”
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Systematic identification and expression profiling of calmodulin-binding transcription activator genes reveal insights into their functional diversity against pathogens in sugarcan... by Talha Javed, Wenzhi Wang, Juan Li, Tingting Sun, Linbo Shen, San-Ji Gao, Shuzhen Zhang

“…The temporal expression of SsnpCAMTA4/5 was ranged between 1.7–3.5 folds in sugarcane cultivars triggered by Xa infection. Most of the SsnpCAMTAs exhibited irregular expression profile in sugarcane cultivars triggered by Aaa infection. …”
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Tumor gene expression signatures associated with outcome in large B−cell lymphoma treated with CD19-directed CAR T−cell therapy (axicabtagene ciloleucel) by Yuan Tian, Justin Budka, Frederick L. Locke, Jason R. Westin, Christina To, Gayatri Tiwari, Daqin Mao, Davide Bedognetti, Rhine R. Shen, Jorge Andrade, Simone Filosto

“…Herein, we leveraged the ZUMA-7 phase III randomized trial of relapsed/refractory large B-cell lymphoma (LBCL) patients treated with axicabtagene ciloleucel (axi-cel; CD19-targeting CAR T cells) to discover tumor gene expression signatures (GES) associated with outcome.MethodsWith tumor transcriptomics from 134 axi-cel patients, we employed multivariate penalized Cox models analyzing event-free survival (EFS), progression-free survival (PFS), and duration of response (DOR).Results and DiscussionWe identified two novel GES, a six-gene/transcript signature (6-GES; CD19, CD45RA, CCL22, KLRK1, SOX11, SIGLEC5) correlated with improved outcome after axi-cel (HR: 0.27, 95% CI: 0.16–0.44 for EFS), representing lymphomas with abundant target antigen (CD19) expression, adhesion molecules, and relatively low immune infiltration mostly composed of cytotoxic lymphocytes (T and NK cells) and DCs, and secondly, a 17-gene/transcript signature (17-GES; CD45RO, BCL2, IL-18R1, TNFSF4 [OX40L], KLRB1 [CD161], KIR3DL2, ITGB8, DUSP5, GPC4, PSMB5, RPS6KB1, SERPINA9, NBN,GLUD1, ESR1, ARID1A, and SLC16A1) correlated with disease progression after axi-cel (HR: 6.12, 95% CI: 3.57–10.50 for EFS), consistent with high immune inflammation and escape mechanisms, such as the upregulation of genes involved in repair of damaged DNA or chromatin remodeling, inhibition of apoptosis, and a metabolically restrictive environment. …”
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Reproduction and Wing Differentiation of Gynoparae Are Regulated by Juvenile Hormone Signaling in <i>Aphis gossypii</i> by Liuyu Wang, Jingli Lv, Xiangzhen Zhu, Kaixin Zhang, Qingyu Shi, Li Wang, Weihua Ma, Jichao Ji, Junyu Luo, Jinjie Cui

“…Moreover, exogenous addition of kinoprene also significantly altered the expression levels of four key genes responsible for the synthesis and degradation of JH. …”
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The Root Development Genes (RDGs) Network in <i>Brassica napus</i> and the Role of <i>BnaSHR-6</i> in Response to Low Nitrogen by Xingying Chen, Sining Zhou, Shuang Ye, Zhuo Chen, Zexuan Wu, Shiying Liu, Liping Hu, Xiwen Yang, Xiaoya Yang, Peiji He, Xingzhi Qian, Huafang Wan, Ti Zhang, Nengwen Ying, Huiyan Zhao, Jiana Li, Cunmin Qu, Hai Du

“…Transcriptome analysis under multiple stresses revealed that low nitrogen (LN) induced the most pronounced changes, with >50% (109/218) of RDGs differentially expressed in roots. …”
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The Expression and Sequence Analysis of MdMATE52 in Apple Roots During Activation of Defense Against <i>Pythium ultimum</i> Infection by Yanmin Zhu, Bianca Ortiz-Uriarte, Jordan Rainbow, Zhe Zhou

“…To understand the molecular regulation of host defense responses in the pathosystem between apple roots and a necrotrophic oomycete pathogen <i>Pythium ultimum</i>, a series of transcriptome analyses have revealed a multi-phase and multi-layer defense tactic in apple root tissues. …”
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Early posttranscriptional response to tetracycline exposure in a gram-negative soil bacterium reveals unexpected attenuation mechanism of a DUF1127 gene by Jennifer A. F. Kothe, Till Sauerwein, Theresa Dietz, Robina Scheuer, Muhammad Elhossary, Susanne Barth-Weber, Jan Wähling, Konrad U. Förstner, Elena Evguenieva-Hackenberg

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Ferroptosis Transcriptional Regulation and Prognostic Impact in Medulloblastoma Subtypes Revealed by RNA-Seq by Christophe Desterke, Yuanji Fu, Jenny Bonifacio-Mundaca, Claudia Monge, Pascal Pineau, Jorge Mata-Garrido, Raquel Francés

“…Medulloblastoma (MB) is the most common malignant brain tumor in children, typically arising during infancy and childhood. …”
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TCF1-positive and TCF1-negative TRM CD8 T cell subsets and cDC1s orchestrate melanoma protection and immunotherapy response by Saraí G De León-Rodríguez, Cristina Aguilar-Flores, Julián A Gajón, Ángel Juárez-Flores, Alejandra Mantilla, Raquel Gerson-Cwilich, José Fabián Martínez-Herrera, Diana Alejandra Villegas-Osorno, Claudia T Gutiérrez-Quiroz, Sergio Buenaventura-Cisneros, Mario Alberto Sánchez-Prieto, Edmundo Castelán-Maldonado, Samuel Rivera Rivera, Ezequiel M Fuentes-Pananá, Laura C Bonifaz

“…There is evidence underscoring the significance of tissue-resident memory (TRM) CD8 T cells and classic dendritic cell type 1 (cDC1) in cancer protection. Transcriptomic studies also support the existence of a TCF7+ (encoding TCF1) T cell as the most important for immunotherapy response, although uncertainty exists about whether there is a TCF1+TRM T cell due to evidence indicating TCF1 downregulation for tissue residency activation.Methods We used multiplexed immunofluorescence and spectral flow cytometry to evaluate TRM CD8 T cells and cDC1 in two melanoma patient cohorts: one immunotherapy-naive and the other receiving immunotherapy. …”
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Knockout of the inhibitory receptor TIGIT enhances the antitumor response of ex vivo expanded NK cells and prevents fratricide with therapeutic Fc-active TIGIT antibodies by Dean A Lee, Jeremiah L Oyer, Md Faqrul Hasan, Tayler J Croom-Perez, Liza D Robles-Carrillo, Sanjana Kumar, Brendan W Andersen, Brian P Tullius, Alicja J Copik, Amanda R Campbell, Thomas A Dieffenthaller, Catherine A Cash, Jonathan E Eloriaga, Meisam Naeimi Kararoudi

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Natural ligand 3,3’-diindolylmethane functions as an AHR agonist to modulate angiogenesis and organ development in chicken embryos by Gee-yea Lim, Hao Chen, Woo-seon Song, Dong-hee Koh, Dong-ha Kim, Hisato Iwata, Eun-Young Kim

“…Notably, 3,3′-diindolylmethane (DIM), previously reported to have anti-cancer and anti-inflammatory effects in rodents, was identified as the most responsive natural ligand to chicken AHR, as it induced the highest fold change in luciferase activity in both COS-7 and LMH cells, suggesting strong agonistic activity in vitro. …”
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Single cell analysis of host response to helminth infection reveals the clonal breadth, heterogeneity, and tissue-specific programming of the responding CD4+ T cell repertoire. by Ivy K Brown, Nathan Dyjack, Mindy M Miller, Harsha Krovi, Cydney Rios, Rachel Woolaver, Laura Harmacek, Ting-Hui Tu, Brian P O'Connor, Thomas Danhorn, Brian Vestal, Laurent Gapin, Clemencia Pinilla, Max A Seibold, James Scott-Browne, Radleigh G Santos, R Lee Reinhardt

“…Using IL-4-reporter mice to identify responding CD4+ T cells to Nippostrongylus brasiliensis infection, T cell receptor sequencing paired with novel clustering algorithms revealed a broadly reactive and clonally diverse CD4+ T cell response. While the most prevalent clones and clonotypes exhibited some tissue selectivity, most were observed to reside in both the lung and lung-draining lymph nodes. …”
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Histone ZmH2B regulates resistance to the Southern corn leaf blight pathogen Bipolaris maydis in maize by Ying Ding, Hongliang Wu, Na Ning, Haiyue Yu, Chaotian Liu, Ruoya Lv, Shu Li, Junjie Hao, Xintao Wang, Xuecai Zhang, Xin Xie, Xinfeng Li, Wende Liu, Zhiqiang Li

“…Abstract Background H2B histones play crucial roles in plant responses to biotic stress. However, to date, most research on H2B histones has focused on their roles in post-translational modification, and studies specifically investigating the intrinsic properties of these histones remain relatively limited. …”
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The imprint of viral oncoproteins on the variable clinical behavior among human papilloma virus-related oropharyngeal squamous cell carcinomas by Malay K. Sannigrahi, Lovely Raghav, Ahmed Diab, Devraj Basu

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Human-augmented large language model-driven selection of glutathione peroxidase 4 as a candidate blood transcriptional biomarker for circulating erythroid cells by Bishesh Subba, Mohammed Toufiq, Fuadur Omi, Marina Yurieva, Taushif Khan, Darawan Rinchai, Karolina Palucka, Damien Chaussabel

“…Abstract The identification of optimal candidate genes from large-scale blood transcriptomic data is crucial for developing targeted assays to monitor immune responses. …”
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Identification and Characterization of SQUAMOSA Promoter Binding Protein-like Transcription Factor Family Members in <i>Zanthoxylum bungeanum</i> and Their Expression Profiles in R... by Shengshu Wang, Weiming Hu, Xueli Zhang, Yulin Liu, Fen Liu

“…Ka/Ks ratio analysis indicates that most <i>ZbSPL</i> genes have undergone purifying selection. …”
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Human cytomegalovirus UL23 inhibits immune cell migration and blocks antiviral immune cell responses by reducing the expression of chemokines CCL2 and CCL5 by Hankun Wang, Chunling Zhang, Moran Li, Wangchun Zhao, Jialin Wang, Yanhong Ran, Xiaoping Yang, Zemin Deng, Jun Chen, Hongjian Li

“…Human cytomegalovirus (HCMV) is a typical opportunistic human pathogen, which can endanger the lives of individuals with immune insufficiency or low immune function. One of the most effective immune mechanisms against HCMV in host cells is the production of antiviral cytokines. …”
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