Single-cell dissection of prognostic architecture and immunotherap response in Helicobacter pylori infection-associated gastric cancer by Xin Zhang, Guangyu Zhang, Shuli Sang, Yang Fei, Xiaopeng Cao, Wenge Song, Feide Liu, Jinze Che, Haoxia Tao, Hongwei Wang, Lihua Zhang, Yiyan Guan, Shipeng Rong, Lijuan Pei, Sheng Yao, Yanchun Wang, Min Zhang, Chunjie Liu

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Human alveolar macrophage response to Mycobacterium tuberculosis: immune characteristics underlying large inter-individual variability by Wolfgang Sadee, Ian H. Cheeseman, Audrey Papp, Maciej Pietrzak, Michal Seweryn, Xiaofei Zhou, Shili Lin, Amanda M. Williams, Mark D. Wewers, Heather M. Curry, Hao Zhang, Hong Cai, Carine Kunsevi-Kilola, Happy Tshivhula, Gerhard Walzl, Blanca I. Restrepo, Léanie Kleynhans, Katharina Ronacher, Yufeng Wang, Eusondia Arnett, Abul K. Azad, Larry S. Schlesinger

“…Systems analysis of VE RNAs identified a top-scoring network anchored by IL1B, involved in TB immune response. Independent M.tb-HAM transcriptome results from a TB-endemic region show significant overlap in DE genes, including VE genes identified in the main study. …”
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Response mechanism of water status and photosynthetic characteristics of Cotoneaster multiflorus under drought stress and rehydrated conditions by Qiu-liang Huang, Miao-miao Zhang, Chang-shun Li, Chang-shun Li, Bo-yang Li, Sheng-lan Zhuo, Yu-shan Yang, Yu-da Chen, An-na Zhong, Hao-yang Liu, Wen-feng Lai, Zhen-bei Huang, Ming-hui Cao, Zong-sheng Yuan, Guo-fang Zhang

“…In addition, we studied the stress response of C. multiflorus transcriptome factors, and we also discussed drought adaptation strategies of C. multiflorus.ResultsC. multiflorus adapted to drought stress by a series of structural and physiological mechanisms, such as promoting closing stomata, increasing nocturnal sap flow. …”
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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

“…However, understanding of transcriptomic changes and fates of antigen-specific T cells upon vaccination remains limited. …”
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Harnessing the diversity of a lettuce wild relative to identify anthocyanin-related genes transcriptionally responsive to drought stress by Inés Medina-Lozano, Inés Medina-Lozano, Jérôme Grimplet, Jérôme Grimplet, Aurora Díaz, Aurora Díaz

“…RNA-seq revealed more differentially expressed genes (DEGs), especially upregulated, in the wild species, in which the most abundant and significant GO terms were involved in regulatory processes (including response to water). …”
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Genome-wide identification, expression analysis, and stress response analysis of the RdbZIP gene family in Rhododendron delavayi by Mengxian Cai, Chunxing Sun, Junxing Yu, Jing Ou, Bin Zhu

“…Additionally, cis-acting element analysis indicated that RdbZIP family members may be involved in various biological processes, including transcription, development, hormone regulation, and responses to biotic and abiotic stresses. Transcriptomic analysis revealed that RdbZIP family genes were highly expressed in reproductive tissues. …”
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NSD2 and miRNAs as Key Regulators of Melanoma Response to Romidepsin and Interferon‐α2b Treatment by Alessandro De Santis, Lucrezia De Santis, Francesca Rossi, Silvia Gasparini, Valerio Licursi, Vito Antonio Amico, Imerio Capone, Alessandra Fragale, Stefania D'atri, Lucia Gabriele, Carlo Presutti

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Dose-response assessment of dipentyl phthalate effects on testosterone production and morphogenesis of late-gestation fetal rat testis by Maansi V. Gupta, Justin M. Conley, Christy Lambright, Logan F. Chin, Susan J. Hall, L. Earl Gray, Daniel J. Spade

“…We aimed to test whether testosterone production, MNG density, or gene expression would be most sensitive to DPeP exposure and to determine which transcriptomic processes are initiated at the lowest DPeP dose. …”
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ATF3 Within the Interferon Signaling Pathway: A Potential Biomarker for Predicting Pathological Response to Neoadjuvant Chemoimmunotherapy by Chao He, Rui Han, Taiming Zhang, Peng Zhong, Daijuan Huang, Conghua Lu, Yimin Zhang, Jianghua Li, Yuwen Deng, Yong He

“…Methods This study analyzed baseline transcriptomic data from 24 NSCLC patients (9 major pathological response [MPR], 15 nonmajor pathological response [NMPR]) treated with neoadjuvant chemoimmunotherapy, sourced from the GEO database. …”
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Genome-wide identification and bioinformatics analysis of PRX gene family in Brassica rapa by CHEN Guohu, WANG Hao, LI Guang, TANG Xiaoyan, WANG Chenggang, ZHANG Lei, HOU Jinfeng, YUAN Lingyun

“…The analysis of cis-acting regulatory elements of BrPRX family genes showed that they played important roles in hormone response regulation, light response and resistance to adversity. …”
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The 3D genome of plasma cells in multiple myeloma by Kaiji Zhang, Mengsi Chen, Ming Chen, Yue Wang, Haibo Liu, Yanju Li, Xiaohong Guan, Lihua Lei, Li Tao, Xiaoxiao Liu, Dong He, Xiaoli Fei

“…It is an incurable disease, accounting for about 10% of blood malignancies and the second most common hematologic malignancy. Therefore, in-depth research into the molecular mechanisms and therapeutic targets of the disease is crucial. …”
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Comparison and Analysis of Resistance Differences in <i>Alternaria alternata</i> from Fungicides with Three Different Mechanisms by Qian Bai, Xinbo Ma, Mansoor Hayat, Yuxin Tang, Zhanbin Wang

“…Collinear trend analysis indicates that MZ exhibits a unique pattern, with FLU treatment causing the most significant overexpression of genes, followed by PCZ. …”
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How “Omics” Studies Contribute to a Better Understanding of Fuchs’ Endothelial Corneal Dystrophy by Erika Prašnikar, Spela Stunf Pukl

“…In addition, highlighted loci from each omics layer were combined according to a comparison with similar study groups from original studies for downstream gene-set enrichment analysis, which provided the most significant biological pathways related to extracellular-matrix organization. …”
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Investigating the Role of Osteopontin (OPN) in the Progression of Breast, Prostate, Renal and Skin Cancers by Gautam Kundu, Selvakumar Elangovan

“…These effects are primarily caused by the upregulation of oncogenes, of which SPP1 (secreted phosphoprotein 1), a non-collagenous bone matrix protein, is one of the most well-known. <b>Methods</b>: In this study, we conducted a further examination of the transcriptomic expression profile of SPP1 (Osteopontin) during the progression of cancer in four human tissues, breast, prostate, renal and skin, in order to understand the circumstances conducive to its activation and dysregulation, the biological pathways and other mechanisms involved as well as differences in its splicing patterns influencing its expression and functionality. …”
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Current state and future prospects of spatial biology in colorectal cancer by Francisco G. Carranza, Fernando C. Diaz, Maria Ninova, Enrique Velazquez-Villarreal, Enrique Velazquez-Villarreal

“…To gain a deeper understanding of the molecular mechanisms driving this solid tumor, researchers have increasingly turned their attention to the tumor microenvironment (TME). Spatial transcriptomics and proteomics have emerged as a particularly powerful technology for deciphering the complexity of CRC tumors, given that the TME and its spatial organization are critical determinants of disease progression and treatment response. …”
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RNA-Seq analysis revealed genes associated with drought stress response in kabuli chickpea (Cicer arietinum L.). by Keyvan Mahdavi Mashaki, Vanika Garg, Ali Asghar Nasrollahnezhad Ghomi, Himabindu Kudapa, Annapurna Chitikineni, Khalil Zaynali Nezhad, Ahad Yamchi, Hasan Soltanloo, Rajeev Kumar Varshney, Mahendar Thudi

“…Drought is the most important constraint that effects chickpea production globally. …”
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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

“…Transcriptome analysis and qRT-PCR validation showed that most ACBPs genes in H. rhamnoides were significantly downregulated at 1000 mg·kg-1 lead, with up-regulation occurring at 5000 mg·kg-1. …”
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Early transcriptional and cellular abnormalities in choroid plexus of a mouse model of Alzheimer’s disease by Zhong-Jiang Yan, Maosen Ye, Jiexi Li, Deng-Feng Zhang, Yong-Gang Yao

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The Role of EZH2 in Initiating Epigenetic Regulation of CRSwNP by Zeng R, Wang Y, Song X, Wang J

“…Gene set enrichment analysis and immune infiltration analysis revealed the most critical gene was EZH2, with its expression exhibiting a positive relationship with HMGA2. …”
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ATP Synthase Members of Chloroplasts and Mitochondria in Rubber Trees (<i>Hevea brasiliensis</i>) Response to Plant Hormones by Bingbing Guo, Songle Fan, Mingyang Liu, Hong Yang, Longjun Dai, Lifeng Wang

“…A large number of cis elements related to light, phytohormones and stress resistance were present in the promoters of ATP synthase genes in rubber trees, of which the light signal accounts for the most. Transcriptome and qRT-PCR analysis showed that HbATP synthases responded to cold stress and hormone stimulation, and the response to ethylene was most significant. …”
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