Cell-type specific epigenetic and transcriptional mechanisms in substance use disorder by Bin Wang, Bin Wang, Jiale Wang, Jiale Wang, Nicholas J. Beacher, Da-Ting Lin, Da-Ting Lin, Yan Zhang

“…Recent advancements in single-cell transcriptomics, epigenetics, and neural circuit research have unveiled molecular and cellular alterations associated with SUD. …”
Get full text

Analysis of Gene Regulatory Network and Transcription Factors in Different Tissues of the <i>Stropharia rugosoannulata</i> Fruiting Body by Jia Lu, Jing Yan, Na Lu, Jiling Song, Jiayao Lin, Xiaohua Zhou, Xuebing Ying, Zhen Li, Zufa Zhou, Fangjie Yao

“…In summary, the present findings offer a molecular mechanism for the development of the fruiting body and provide directions for the enhancement of cultivation techniques of <i>S. rugosoannulata</i>.…”
Get full text

Subcutaneous adipose tissue-secreted proteins as endocrine regulators of physical and cognitive function in older adults by Cheehoon Ahn, Ian Tamburini, James A. Sanford, Mingqi Zhou, Farah Gamie, Reichelle X. Yeo, Carlos H. Viesi, Maria Pino, Katie L. Whytock, Lauren E. Oberlin, Theresa Mau, Joshua N. Adkins, Jamie N. Justice, Ashlee N. Wood, Zana M. Ross, Paul.D. Piehowski, Chelsea M. Hutchinson Bunch, Kirk I. Erickson, Frederico G.S. Toledo, Nancy E. Lane, Peggy M. Cawthon, Anne B. Newman, Stephen B. Kritchevsky, Steven R. Cummings, Bret H. Goodpaster, Erin E. Kershaw, Marcus M. Seldin, Lauren M. Sparks

“…Here, leveraging ASAT transcriptomics and explant-conditioned media proteomics from participants in the Study of Muscle, Mobility and Aging (SOMMA; age ≥70 years, n = 229), we identified ASAT gene clusters and secreted proteins strongly associated with comprehensive assessments of physical and cognitive function in older adults. …”
Get full text

Heterologous prime-boost vaccination drives stromal activation and adaptive immunity against SARS-CoV-2 variants by Ji Hyang Jeon, Ji Hyang Jeon, Seongryong Kim, Seo-Yeon Kim, Kwang-Soo Shin, Bongju Park, Soojeong Chang, Chang-Yuil Kang, You-Jin Kim, Jong-Eun Park, Sungsu Youk, Sungsu Youk, Dokeun Kim, Jinah Yeo

“…These findings suggest that adenoviral priming enhances local immune activation upon boosting, contributing to the heightened adaptive immune response observed in heterologous vaccination. This study provides mechanistic insights into the immunological effects of heterologous prime-boost strategies against SARS-CoV-2 variants.…”
Get full text

Matrix mechano-sensing at the invasive front induces a cytoskeletal and transcriptional memory supporting metastasis by Oscar Maiques, Marta C. Sallan, Roman Laddach, Pahini Pandya, Adrian Varela, Eva Crosas-Molist, Jaume Barcelo, Olivia Courbot, Yanbo Liu, Vittoria Graziani, Youssef Arafat, Joanne Sewell, Irene Rodriguez-Hernandez, Bruce Fanshawe, Yaiza Jung-Garcia, Paul RC Imbert, Eloise M. Grasset, Jean Albrengues, Maria Santacana, Anna Macià, Jordi Tarragona, Xavier Matias-Guiu, Rosa M. Marti, Sophia Tsoka, Cedric Gaggioli, Jose L. Orgaz, Gilbert O. Fruhwirth, Fredrik Wallberg, Kai Betteridge, Constantino Carlos Reyes-Aldasoro, Syed Haider, Andrejs Braun, Sophia N. Karagiannis, Alberto Elosegui-Artola, Victoria Sanz-Moreno

“…These findings provide mechanistic insights into how ECM organization shapes local invasion and distant metastasis.…”
Get full text

Effects of mode of reproduction on genetic polymorphism and divergence in wild yams (Dioscoreaceae: Dioscorea) by Xin Wang, Qing-Hong Feng, Zhi-Hua Zeng, Zhi-Qiang Zhang, Jie Cai, Gao Chen, De-Zhu Li, Hong Wang, Wei Zhou

“…We investigated evidence for differences among the transcriptomes of 19 Dioscorea species (wild yams) with diverse reproductive systems. …”
Get full text

Human Pituitary Organoids: Transcriptional Landscape Deciphered by scRNA‐Seq and Stereo‐Seq, with Insights into SOX3's Role in Pituitary Development by Shengjie Wang, Deyue Jiang, Yan Xiao, Qiaozhen Qin, Heyang Zhang, Lingtong Ye, Jide Jin, Xiaoxia Jiang, Qinghua Guo

“…Altogether, the research provides an optimized protocol for the human pituitary organoid culture and a valuable transcriptomic dataset for future explorations, laying the foundation for subsequent research in the field of pituitary organoids or pituitary diseases.…”
Get full text

Extracellular vesicles from adipose-derived stromal/stem cells reprogram dendritic cells to alleviate rat TMJOA by transferring mitochondria by Ziyi Mei, Hanyue Li, Chuling Huang, Shiyong Ma, Yuejia Li, Pingmeng Deng, Sha Zhou, Aizhuo Qian, Bin Yang, Jie Li

“…Subsequently, we conducted transcriptomic and metabolomic analyses to elucidate the specific mechanisms by which EVs affect DCs. …”
Get full text

Aflatoxin B1 and Eimeria ovinoidalis impair meat quality of sheep by regulating the HIF-1ɑ/HK2/glycolysis axis by Yan-feng He, Xi-shuai Tong, Ke Yue, Bo-wen Xu, Wen-li Ding, Ya-nan Lu, Tao-jing Yue, Pan Chen, Kai-li Liu, Aftab Shaukat, Sen-yang Li, Fu-chun Jian, Shu-cheng Huang

“…Metabolomics and transcriptomics further revealed that the alteration in mutton quality is closely associated with glycolysis mediated by the hypoxia inducible factor-1α (HIF-1α) pathway. …”
Get full text

Uncovering minimal pathways in melanoma initiation by Hui Xiao, Jessica Shiu, Chi-Fen Chen, Jie Wu, Peijie Zhou, Sahil S. Telang, Rolando Ruiz-Vega, Robert A. Edwards, Qing Nie, Arthur D. Lander, Anand K. Ganesan

“…This state may serve as an intermediate on a slow path to malignancy that may provide a diagnostically and therapeutically important source of cellular heterogeneity.…”
Get full text

An experimentally supported model of the Bacillus subtilis global transcriptional regulatory network by Mario L Arrieta‐Ortiz, Christoph Hafemeister, Ashley Rose Bate, Timothy Chu, Alex Greenfield, Bentley Shuster, Samantha N Barry, Matthew Gallitto, Brian Liu, Thadeous Kacmarczyk, Francis Santoriello, Jie Chen, Christopher DA Rodrigues, Tsutomu Sato, David Z Rudner, Adam Driks, Richard Bonneau, Patrick Eichenberger

“…Although accurate global regulatory models would provide critical evolutionary and functional insights, they remain incomplete, even for the best studied organisms. …”
Get full text

Electrolyte and metabolite composition of cystic fluid from a rat model of ARPKD by Christine A. Klemens, Mykhailo Fedoriuk, Marharyta Semenikhina, Mariia Stefanenko, Adrian Zietara, Vladislav Levchenko, Lashodya V. Dissanayake, Oleg Palygin, Alexander Staruschenko

“…Untargeted metabolomics combined with transcriptomic data identified tryptophan metabolism, enzyme metabolism, steroid hormone biosynthesis, and fatty acid metabolism as pathways differing between male and female PCK rats. …”
Get full text

Multiomics analysis reveals signatures of selection and loci associated with complex traits in pigs by Lei Liu, Guoqiang Yi, Yilong Yao, Yuwen Liu, Jiang Li, Yalan Yang, Mei Liu, Lingzhao Fang, Delin Mo, Longchao Zhang, Yonggang Liu, Yongchao Niu, Liyuan Wang, Xiaolu Qu, Zhangyuan Pan, Lei Wang, Muya Chen, Xinhao Fan, Yun Chen, Yongsheng Zhang, Xingzheng Li, Zhen Wang, Yijie Tang, Hetian Huang, Pengxiang Yuan, Yuying Liao, Xinjian Li, Zongjun Yin, Di Liu, Dongjie Zhang, Quanyong Zhou, Wangjun Wu, Jicai Jiang, Yahui Gao, George E. Liu, Lixian Wang, Yaosheng Chen, Kui Li, Martien A. M. Groenen, Zhonglin Tang

“…Altogether, our work provides valuable resources for understanding molecular mechanisms behind phenotypic variations and enhancing the genetic improvement programs in pigs.…”
Get full text

Characterization of wheat oligo‐tiller mutant ot2 and fine mapping of the mutant gene Taot2 by Chenxi Wang, Jiaxing Bai, Hongchun Xiong, Yongdun Xie, Jiayu Gu, Linshu Zhao, Huiyuan Li, Yuping Ding, Xinmei Guo, Huijun Guo, Luxiang Liu

“…Our findings provide the foundation for map‐based cloning of Taot2, a novel wheat tiller gene, and offer valuable insights into wheat tiller bud initiation.…”
Get full text

A 3D tumor spheroid model with robust T cell infiltration for evaluating immune cell engagers by Hin Ching Lo, Hana Choi, Kevin Kolahi, Samantha Rodriguez, Leiru Gonzalez, Felix Chu, Aditee Shrotre, Xi Zhao, Aloma L. D’Souza, Ron Ferrando, Somdutta Roy

“…We developed and validated a 3D tumor spheroid model from non-small cell lung cancer (NSCLC) PDXs to enable T cell infiltration. Histologic and transcriptomic analysis suggested that tumor spheroids closely recapitulate the source PDX tumor tissues. …”
Get full text

Decoding yeast transcriptional regulation via a data-and mechanism-driven distributed large-scale network model by Xingcun Fan, Guangming Xiang, Wenbin Liao, Luchi Xiao, Siwei He, Na Luo, Hongzhong Lu, Xuefeng Yan

“…Subsequently, DLTRNM is pre-trained on pan-transcriptomic data and fine-tuned with time-series data, enabling it to accurately predict regulatory correlations. …”
Get full text

Deciphering the Complexity of the Immune Cell Landscape in Kidney Allograft Rejection by George Terinte-Balcan, George Terinte-Balcan, George Terinte-Balcan, Emilie Lebraud, Julien Zuber, Dany Anglicheau, Dany Anglicheau, Gener Ismail, Gener Ismail, Marion Rabant, Marion Rabant

“…In the last few years, multiplex IF techniques and automatic counting systems as well as transcriptomics studies (bulk, single-cell and spatial techniques) have provided invaluable clues to further decipher the complex puzzle of rejection. …”
Get full text

Temporal single-cell sequencing analysis reveals that GPNMB-expressing macrophages potentiate muscle regeneration by Yu-Fan Chen, Chien-Wei Lee, Yi-Shuan J. Li, Wei-Ting Lin, Hsiao-Yun Chen, Yu-Chuan Chen, Chia-Hao Lin, Jennifer Hui-Chun Ho, Li-Fan Lu, Shu Chien, Oscar Kuang-Sheng Lee

“…Functional studies demonstrated that GPNMB acts directly on muscle cells in vitro and improves muscle regeneration in vivo. These findings provide a comprehensive transcriptomic atlas of macrophages during muscle injury, highlighting the key role of the GPNMB macrophage subset in regenerative processes. …”
Get full text

Identification of reactive CpGs and RNA expression in early COVID-19 through cis-eQTM analysis reflecting disease severity and recovery by Hyojung Ryu, Kyungwhan An, Yoonsung Kwon, Yeonsu Jeon, Sungwon Jeon, Hansol Choi, Yeo Jin Kim, Sunhwa Kim, Ok Joo Sul, SangJoon Lee, Asaph Young Chun, Eun-Seok Shin, Seung Won Ra, Jong Bhak

“…Interestingly, during the recovery phase, methylation and gene expression levels returned to baseline, underscoring the rapid and reversible nature of these molecular changes. These findings provide insight into the dynamics of epigenetic and transcriptomic shifts according to the infectious stage, supporting potential prognostic and therapeutic approaches for severe COVID-19.…”
Get full text

Intestinal tuft cell subtypes represent successive stages of maturation driven by crypt-villus signaling gradients by Julian R. Buissant des Amorie, Max A. Betjes, Jochem H. Bernink, Joris H. Hageman, Veerle E. Geurts, Harry Begthel, Dimitrios Laskaris, Maria C. Heinz, Ingrid Jordens, Tiba Vinck, Ronja M. Houtekamer, Ingrid Verlaan-Klink, Sascha R. Brunner, Jacco van Rheenen, Martijn Gloerich, Hans Clevers, Sander J. Tans, Jeroen S. van Zon, Hugo J. G. Snippert

“…Here, we reveal common intermediary transcriptomes among the previously described tuft-1 and tuft-2 subtypes in mouse and human. …”
Get full text