Genome-Wide Analysis of Caffeoyl-CoA-O-methyltransferase (CCoAOMT) Family Genes and the Roles of <i>GhCCoAOMT7</i> in Lignin Synthesis in Cotton by Lina Ma, Jin Wang, Kaikai Qiao, Yuewei Quan, Shuli Fan, Liqiang Wu

“…A synteny analysis suggested that segmental duplications were the primary cause in the expansion of the <i>CCoAOMT</i> genes family. Transcriptomic data analysis of <i>GhCCoAOMTs</i> revealed that <i>GhCCoAOMT2</i>, <i>GhCCoAOMT7,</i> and <i>GhCCoAOMT14</i> were highly expressed in stems. …”
Get full text

Neural network prediction model based on Levy flight and natural biomimetic technology for its application in cancer prediction. by Ruiyu Zhan

“…-led initiative conducting in-depth molecular research to elucidate the causative mechanisms of cancer - this study focuses on three specific cancer types within the dataset: lung, breast, and esophageal cancers. TCGA provides a rich repository of genomic, transcriptomic, epigenomic, and patient-specific clinical data across 33 cancer types. …”
Get full text

Endophytic fungi enhance drought tolerance in Fagopyrum tataricum: Insights into flavonoid biosynthesis and photosynthetic pathways by Yujie Jia, Qiqi Xie, Jiwen Tao, Yixin Chen, Yixuan Qi, Hongying Zhu, Tongliang Bu, Xinyu Zhang, Yirong Xiao, Zhao Chen, Qingfeng Li, Zizhong Tang, Ming Yuan

“…Integrated metabolomic and transcriptomic analyses revealed distinct mechanisms of action for the two strains: B. dothidea J46 upregulated key genes in the flavonoid biosynthesis pathway, including Cinnamate-4-hydroxylase (C4H), Chalcone synthase (CHS), and Chalcone isomerase (CHI), whereas I. lacteus J79 enhanced the expression of genes associated with photosynthesis. …”
Get full text

MiR-7 inhibits progression of glioblastoma by impairing autophagy resolution, energy metabolism and ECM remodeling by Marta Torrecilla-Parra, Virginia Pardo-Marqués, Antonio C. Fuentes-Fayos, Miguel E. G-García, Mario Fernández-de Frutos, José L. López-Aceituno, Cristina Puigdueta, Carmen Zamora, Ana Pérez-García, Juan F. Aranda, Rebeca Busto, Manuel D. Gahete, Raúl M. Luque, Cristina M. Ramírez

“…Additional mechanistic approaches, including transcriptomics, bioinformatics, and histopathological analyses, indicate that miR-7 modifies the tumor phenotype by altering key genes involved in extracellular matrix (ECM) remodeling in vivo. …”
Get full text

Combining multi-omics analysis with machine learning to uncover novel molecular subtypes, prognostic markers, and insights into immunotherapy for melanoma by Songyun Zhao, Zihao Li, Kaibo Liu, Gaoyi Wang, Quanqiang Wang, Hua Yu, Wanying Chen, Hao Dai, Yijun Li, Jiaheng Xie, Yucang He, Liqun Li

“…Methods We obtained and processed transcriptomic data, including RNA expression profiles, methylation microarray data, gene mutation data, and clinical information, from the TCGA dataset using multi-omics analysis and machine learning techniques. …”
Get full text

PRMT5 deficiency in myeloid cells reprograms macrophages to enhance antitumor immunity and synergizes with anti-PD-L1 therapy by Jian Cao, Yongyu Chen, Bingqian Zhou, Shiyu Chen, Zheyi Chen, Yiren Huang, Lisong Shen, Yingxia Zheng

“…Bulk and single-cell transcriptomics were employed to explore the mechanistic roles of PRMT5 in regulating lipid metabolism and macrophage polarization. …”
Get full text

Multipronged SMAD pathway targeting by lipophilic poly(β-amino ester) miR-590-3p nanomiRs inhibits mesenchymal glioblastoma growth and prolongs survival by Jack Korleski, Sophie Sall, Kathryn M. Luly, Maya K. Johnson, Amanda L. Johnson, Harmon Khela, Bachchu Lal, TC Taylor, Jean Micheal Ashby, Hector Alonso, Alice Li, Weiqiang Zhou, Karen Smith-Connor, Russell Hughes, Stephany Y. Tzeng, John Laterra, Jordan J. Green, Hernando Lopez-Bertoni

Get full text

Limosilactobacillus reuteri SXDT-32-derived shikimic acid protects against colonic inflammation in piglets by inhibiting the PI3K-Akt pathway by Ying Chen, Chengzeng Luo, Zhaohan Zhan, Shuo Liu, Chunran Teng, Ruixiao Mao, Shunfen Zhang, Xunbozan Zhang, Qingshi Meng, Ruqing Zhong, Liang Chen, Hongfu Zhang

“…Conclusions L. reuteri SXDT-32 alleviated intestinal inflammation in piglets by producing SA that inhibits the PI3K-Akt pathway. This study provides an innovative approach for the treatment and prevention of colitis caused by bacterial infection.…”
Get full text

Genetic transcriptional regulation profiling of cartilage reveals pathogenesis of osteoarthritisResearch in context by Wen Tian, Shan-Shan Dong, Feng Jiang, Jun-Qi Zhang, Chen Wang, Chang-Yi He, Shou-Ye Hu, Ruo-Han Hao, Hui-Miao Song, Hui-Wu Gao, Ke An, Dong-Li Zhu, Zhi Yang, Yan Guo, Tie-Lin Yang

“…Methods: We performed cis-eQTL analysis using genomics and cartilage transcriptomics data from 204 patients with OA (largest sample size to date). …”
Get full text

Induced pluripotent stem cell-derived mesenchymal stem cells (iMSCs) inhibit M1 macrophage polarization and reduce alveolar bone loss associated with periodontitis by Liang Chen, Yuanqing Liu, Chenhao Yu, Pei Cao, Yiming Ma, Yiran Geng, Yu Cai, Yong Zhang, Jia Liu, Yang Li, Qingxian Luan

“…Co-culture assays, cytokine analysis, reactive oxygen species (ROS) detection, transcriptomic analysis, flow cytometry, reverse transcription-quantitative polymerase chain reaction (RT-qPCR), and western blot analysis were performed to elucidate the underlying mechanisms. …”
Get full text

Glutathione S-transferase in mediating adaptive responses of oats (Avena sativa) to osmotic and cadmium stress: genome-wide analysis by Chenbiao Xu, Lyu Jiang, Aixue Li, Jie Meng, Ping Yun, Jianfang Li, Changbin Liu, Yang Chen, Han Zhang, Hassan Ahmed Ibraheem Ahmed, Quan Gao, Lana Shabala, Sergey Shabala, Bin Luo, Peichen Hou

“…The findings enhance our understanding of the mechanisms underlying stress tolerance and offer valuable genetic resources for breeding stress-tolerant A. sativa. The work also provides a theoretical framework and identifies gene targets for the development of stress-resistant A. sativa varieties.…”
Get full text

HERV-derived epitopes represent new targets for T-cell-based immunotherapies in ovarian cancer by Qing Wang, Maha Ayyoub, Olivia Le Saux, Paola Bonaventura, Isabelle Treilleux, Nicolas Chopin, Clarisse Dubois, Virginie Mutez, Nicolas Chuvin, Yann Estornes, Jenny Valladeau-Guilemond, Stephane Depil, Nicolas Gadot, Marie Michelas, Audrey Page, Olivier Tabone, Marie Delles, Sarah Moran, Thibault Richard, Marjorie Lacourrège, Dina M Tawfik, Ema Etchegaray, Adrian Valente, Rasha E Boulos, Gabriel Jimenez Dominguez

“…Human endogenous retroviruses (HERVs) are aberrantly expressed by tumor cells and may represent a source of shared T-cell epitopes for cancer immunotherapy regardless of the tumor mutational burden.Methods A transcriptomic analysis based on RNA sequencing was developed to quantify the expression of HERV-K sequences containing the selected epitopes. …”
Get full text

Dissecting the tumor microenvironment in primary breast angiosarcoma: insights from single-cell RNA sequencing by Peikai Ding, Shengbin Pei, Yi Zhai, Zheng Qu, Yazhe Yang, Xiaolong Feng, Qiang Liu, Xiangyu Wang, Wenxiang Zhang, Zhongzhao Wang, Xiangyi Kong, Jing Wang, Yi Fang

“…Single-cell RNA sequencing (scRNA-seq) was conducted to capture the transcriptomic profiles of individual cells within the tumor samples. …”
Get full text

Integration and functionality of human iPSC-derived microglia in a chimeric mouse retinal model by Chun Tang, Qi-Qi Zhou, Xiu-Feng Huang, Ya-Yi Ju, Bi-Lin Rao, Zhi-Cong Liu, Yi-An Jia, Zhan-Pei Bai, Qing-Yang Lin, Lin Liu, Jia Qu, Jun Zhang, Mei-Ling Gao

“…Conclusion This model provides a powerful platform for studying human microglia in the retinal context, offering significant insights for advancing research into retinal degenerative diseases and developing potential therapeutic strategies. …”
Get full text

Cellular and Molecular Atlas of Peripheral Blood Mononuclear Cells from a Pregnant Woman After Recovery from COVID-19 by Lili Du, Yingyu Liang, Xiaoyi Wang, Lijun Huang, Xingfei Pan, Jingsi Chen, Dunjin Chen, Dandan Shi

“…Conclusion. Our study provides a single-cell resolution atlas of the immune gene expression patterns in PBMCs from a COVID_RS patient. …”
Get full text

Deciphering the dynamic expression network of fiber elongation and the functional role of the GhTUB5 gene for fiber length in cotton based on an introgression population of upland... by Jianjiang Ma, Liupeng Yang, Yuanyue Dang, Kashif Shahzad, Jikun Song, Bing Jia, Li Wang, Juanjuan Feng, Nuohan Wang, Wenfeng Pei, Man Wu, Xuexian Zhang, Jinfa Zhang, Jianyong Wu, Jiwen Yu

“…Methods: Coexpression analyses of 277 developing fiber transcriptomes integrated with QTL mapping using 250 introgression lines of different FL phenotypes were conducted to identify genes related to fiber elongation. …”
Get full text

Integrated lipidomics and RNA-seq reveal prognostic biomarkers in well-differentiated and dedifferentiated retroperitoneal liposarcoma by Xiaopeng Wang, Jingjing Ye, Yan Wu, Hongtao Zhang, Chengpeng Li, Bonan Liu, Xiaoya Guan, Xiuyun Tian, Weiwei Jia, Qiao Liu, Shuquan Li, Rongze Sun, Daoning Liu, Guoqiang Xue, Zhen Wang, Liang Yan, Ang Lv, Jianhui Wu, Hui Qiu, Chunyi Hao

“…Integrated lipidomic and transcriptomic analysis identified 29 genes as potential biomarkers between WDLPS and DDLPS. …”
Get full text

Harnessing multi-omics and artificial intelligence: revolutionizing prognosis and treatment in hepatocellular carcinoma by Zhen Wang, Zhen Wang, Zhen Wang, Gangchen Zhou, Gangchen Zhou, Rongchuan Cao, Rongchuan Cao, Guolin Zhang, Guolin Zhang, Yongxu Zhang, Yongxu Zhang, Mingyue Xiao, Longbi Liu, Longbi Liu, Xuesong Zhang

“…A multi-omics approach has the potential to offer more profound insights into HCC subtypes and enhance patient stratification for personalized treatments.MethodsA comprehensive data set comprising clinical, transcriptomic, genomic and epigenomic information from HCC patients was retrieved from the TCGA, ICGC, GEO and CPTAC databases. …”
Get full text

Breast tumors from ATM pathogenic variant carriers display a specific genome-wide DNA methylation profile by Nicolas M. Viart, Anne-Laure Renault, Séverine Eon-Marchais, Yue Jiao, Laetitia Fuhrmann, Sophia Murat El Houdigui, Dorothée Le Gal, Eve Cavaciuti, Marie-Gabrielle Dondon, Juana Beauvallet, Virginie Raynal, Dominique Stoppa-Lyonnet, Anne Vincent-Salomon, Nadine Andrieu, Melissa C. Southey, Fabienne Lesueur

“…Correlation between promoter methylation and gene expression was assessed for 10 tumors for which transcriptomic data were available. Results We found that the ATM promoter was hypermethylated in 62% of tumors of heterozygous PV carriers compared to the mean methylation level of ATM promoter in tumors of noncarriers. …”
Get full text

Machine learning-based diagnostic and prognostic models for breast cancer: a new frontier on the clinical application of natural killer cell-related gene signatures in precision me... by Yutong Fang, Rongji Zheng, Yefeng Xiao, Qunchen Zhang, Junpeng Liu, Jundong Wu

“…With the advent of machine learning (ML) techniques, predictive modeling based on NRGs may offer a new avenue for precision oncology.MethodsWe collected transcriptomic and clinical data from The Cancer Genome Atlas (TCGA) and Gene Expression Omnibus (GEO) databases. …”
Get full text