Multi-omics integration reveals functional signatures of gut microbiome in atherosclerosis by Hongbo Shi, Meitao Wu, Xiaoliang Wu, Zhuoxin Liu, Shuo Jiang, Gen Li, Yetong Yang, Yanghe Fu, Qiuping Wang, Guangde Zhang, Liang Cheng

“…Atherosclerosis (AS), a predominant contributor to global cardiovascular disease burden, exhibits complex interplay with gut microbiota dysbiosis. While the associations between microbial imbalance and AS pathogenesis are well-documented, the pathophysiological mechanisms governing microbe-host crosstalk remain incompletely characterized. …”
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A Hidden Mark of a Troubled Past: Neuroimaging and Transcriptomic Analyses Reveal Interactive Effects of Maternal Immune Activation and Adolescent THC Exposure Suggestive of Increa... by Mario Moreno-Fernández, Víctor Luján, Shishir Baliyan, Celia Poza, Roberto Capellán, Natalia de las Heras-Martínez, Miguel Ángel Morcillo, Marta Oteo, Emilio Ambrosio, Marcos Ucha, Alejandro Higuera-Matas

“…Additionally, the transcriptomic studies demonstrated that maternal immune activation affected dopaminergic, glutamatergic, and serotoninergic genes, with the combination of both exposures in most cases shifting the expression from downregulation to upregulation. …”
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Incorporating gene expression and environment for genomic prediction in wheat by Jia Liu, Jia Liu, Andrew Gock, Kerrie Ramm, Sandra Stops, Tanya Phongkham, Adam Norman, Russell Eastwood, Eric Stone, Shannon Dillon

“…These models explored the relative contributions of different combinations of additive genomic (G), transcriptomic (T) and environment (E), with and without considering non-additive epistasis, dominance and genotype by environment (G × E) random effects.ResultsIn controlled environments, where traits were measured under contrasting daylength regimes (long and short days), transcriptome abundance outperformed other random effects when considered independently, while the model combining SNP, environment and G × E marginally outperformed the transcriptome. …”
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Hazard assessment of airborne and foodborne biodegradable polyhydroxyalkanoates microplastics and non-biodegradable polypropylene microplastics by Hua Zha, Shengjie Li, Aoxiang Zhuge, Jian Shen, Yuanyuan Yao, Kevin Chang, Lanjuan Li

“…Both foodborne PHA and PP MP caused intestinal microbiome dysbiosis, while foodborne PHA MP caused slighter intestinal and serum metabolome disruption, hepatic transcriptome disturbances and hepatotoxicity (e.g., lower serum aspartate aminotransferase and alanine aminotransferase) compared to foodborne PP MP. …”
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Alternative mRNA splicing in anthracycline-induced cardiomyopathy – a COG-ALTE03N1 report by Purnima Singh, David K. Crossman, Changde Cheng, Patrick J. Trainor, Noha Sharafeldin, Xuexia Wang, Liting Zhou, Lindsey Hageman, Saro H. Armenian, Frank M. Balis, Douglas S. Hawkins, Frank G. Keller, Melissa M. Hudson, Joseph P. Neglia, Jill P. Ginsberg, Wendy Landier, Smita Bhatia

“…Our findings suggest that differential alternative splicing events can provide additional insight into the peripheral blood transcriptomic landscape of anthracycline-induced cardiomyopathy. …”
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Drought priming-induced low temperature stress tolerance in wheat: insight into stress memory dynamics by Yi Wang, Lihao Zheng, Jiamin Song, Jian Cai, Qin Zhou, Yingxin Zhong, Dong Jiang, Xiao Wang

“…Here, we integrated physiological, transcriptomic, and metabolomic analyses to identify key stress memory genes or metabolites associated with priming-induced low temperature tolerance in wheat. …”
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GTSE1-expressed osteoblastic cells facilitate formation of pro-metastatic tumor microenvironment in osteosarcoma by Linzhu Wang, Wenyue Li, Weihang Ji, Danyang Bing, Mingyue Liu, Kaidong Liu, Bo Chen, Zhangxiang Zhao, Yunyan Gu, Xuelian Li, Xiaoqiang E, Lei Yang

“…Augmentation of GTSE1 enhanced the abilities of cell migration and invasion, while silencing of GTSE1 impaired the abilities in human OB cell lines. …”
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Comparative transcriptomics in B73-teosinte near-isogenic maize lines reveals key defense signaling and phytoalexins in response to Cercospora zeina infection by Xiaomeng Sun, Xiaomeng Sun, Ruiyu Zhang, Ruiyu Zhang, Zongping Wang, Zongping Wang, Haotian Zhang, Haotian Zhang, Hairun Wen, Hairun Wen, Junli Zhang, Naibin Yu, Naibin Yu, Zhe Wang, Zhe Wang, Huanhuan Tai, Huanhuan Tai, Qin Yang, Qin Yang

“…The URGs in Qgls8-R were significantly enriched in metabolic processes, phytohormone signaling, and response to biotic stress, while the URGs in Qgls8-S were mostly involved in plant growth and developmental processes. …”
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Exploring the utility of snRNA-seq in profiling human bladder tissue: A comprehensive comparison with scRNA-seq by Briana Santo, Emily E. Fink, Alexandra E. Krylova, Yi-Chia Lin, Mohamed Eltemamy, Alvin Wee, Oliver Wessely, Byron H. Lee, Angela H. Ting

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Combined microbiomic and transcriptomic analysis revealed that dietary Clostridium autoethanogenum protein could improve the disease resistance of Litopenaeus vannamei by regulatin... by Lili Shi, Xiaobo Yan, Zhao Yan, Hongming Wang, Jian Chen, Shuang Zhang

“…Combined analysis of transcriptomic and microbiomic revealed that oxidative phosphorylation pathway-related gene expression was positively correlated with Rubritaleaceae while negatively correlated with Rubinisphaeraceae. …”
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Leveraging expression from multiple tissues using sparse canonical correlation analysis and aggregate tests improves the power of transcriptome-wide association studies. by Helian Feng, Nicholas Mancuso, Alexander Gusev, Arunabha Majumdar, Megan Major, Bogdan Pasaniuc, Peter Kraft

“…Transcriptome-wide association studies (TWAS) test the association between traits and genetically predicted gene expression levels. …”
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Clinical and prognostic significance of m6A hypomethylation and IGF2BP3 overexpression in gastric cancer: an integrated epigenomic-transcriptomic analysis by Xiangchen Hu, Zhe Wang, Youwei Kou, Yujing Huang

“…Gene Ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway analyses were conducted on 253 hypomethylated mRNAs to delineate the biological pathways associated with m6A dysregulation. The transcriptomic profiles were analyzed using RNA-seq, while a retrospective cohort analysis (n = 58) evaluated the correlations between IGF2BP3 expression and the clinicopathological characteristics of patients with GC. …”
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stGRL: spatial domain identification, denoising, and imputation algorithm for spatial transcriptome data based on multi-task graph contrastive representation learning by Xin Lu, Murong Zhou, Bo Gao, Fang Wang, Shuilin Jin, Qiaoming Liu, Guohua Wang

“…Abstract Background Spatial transcriptomics now enables sequencing while preserving the spatial location of cells. …”
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MEK inhibition prevents human skin graft rejection by promoting CD8+TCF1+ over CD8 effector T cells by Christine Chauveau, Veronique Nerriere-Daguin, Maeva Fourny, Cynthia Fourgeux, Thibaut Larcher, Laurence Delbos, Martin Braud, Lucas Brusselle, Olivia Rousseau, Jeremie Poschmann, Julien Verdier, Fabienne Haspot, Gilles Blancho, Simon Ville

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Transcriptome sequencing revealed that lymph node metastasis of papillary thyroid microcarcinoma is associated with high THBS4 expression and PDGFRA+ cancer-associated fibroblasts by LeYin Hu, Yi Lin, JingYu Zheng, Li Wan, Rui Zhao, Yi Ma, JianMin Li

“…LNM PTMCs were also associated with a higher presence of PDGFRA+ inflammatory CAFs (P < 0.05), while no significant difference in the quantity of SMA+ myofibroblastic CAFs was observed between the two groups(P>0.05). …”
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Epizootic shell disease induces systemic transcriptomic shifts in Homarus americanus, characterized by increased shell degradation and impaired energy metabolism across tissues by Minseo Kim, Dianjun Cao, Vincent Cavaleri, Kyudong Han, Kyudong Han, Kyudong Han, Seyoung Mun, Seyoung Mun, Seyoung Mun, Soo Jin Jeon

“…Notably, chitinase genes involved in chitin degradation were upregulated, while the acetyl-coenzyme A transporter 1-like gene related to energy metabolism was significantly downregulated in the testis. …”
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Preliminary Analysis of the Formation Mechanism of Floret Color in Broccoli (<i>Brassica oleracea L var. italica</i>) Based on Transcriptomics and Targeted Metabolomics by Qingqing Shao, Mindong Chen, Saichuan Cheng, Huangfang Lin, Biying Lin, Honghui Lin, Jianting Liu, Haisheng Zhu

“…The color difference and pigment content of florets were measured, and a combined analysis of anthocyanin-targeted metabolome and transcriptome was conducted. Our findings revealed that chlorophyll a primarily influences green, yellow-green, and light green coloration, while the wax content may contribute to gray-green coloration. …”
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Genome-wide and transcriptome analysis of PdWRKY transcription factors in date palm (Phoenix dactylifera) revealing insights into heat and drought stress tolerance by Ibrahim Khan, Lubna, Saqib Bilal, Ashraf M. M. Abdelbacki, Sang-Mo Kang, Ahmed AL-Harrasi, Sajjad Asaf, In-Jung Lee

“…Our findings show that 52% of PdWRKYs have strong homology with OsWRKYs, while only 9 PdWRKYs have orthologous relationships with AtWRKYs. …”
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Potential effect of Wolbachia on virus restriction in the spider mite T. truncatus by Lucas Yago Melo Ferreira, João Pedro Nunes Santos, David Gabriel do Nascimento Souza, Lixsy Celeste Bernardez Orellana, Sabrina Ferreira de Santana, Anderson Gonçalves Sousa, Paula Luize Camargos Fonseca, Amanda Gabrielly Santana Silva, Vinicius Castro Santos, Isaque João da Silva de Faria, Roenick Proveti Olmo, Luis Gustavo Carvalho Pacheco, Marcio Gilberto Cardoso Costa, Carlos Priminho Pirovani, Anibal Ramadan Oliveira, Eric Roberto Guimarães Rocha Aguiar

“…However, the viral restriction phenotype vanishes in co-infected mites. Transcriptomics analysis of singly-infected mites revealed upregulation of piRNA and autophagy-related genes, while lipid metabolism processes-related genes were downregulated, indicating an endosymbiont-sharing mechanisms of viral interference. …”
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Transcriptomics and non-targeted metabolomics provide mechanistic insights into the improvement of the growth performance and meat quality of lambs supplemented with fermented Lyci... by Jiale Liao, Wencan Ke, Bing Wang, Min Du, Qiang Lu, Yajun Zhang, Guijie Zhang

“…Serum total protein (P = 0.007) and glucose (P = 0.002) levels were higher in the FLBR-fed lambs, while urea nitrogen level was lower (P = 0.001). …”
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