Establishment and characterization of 24 breast cancer cell lines and 3 breast cancer organoids reveals molecular heterogeneity and drug response variability in malignant pleural e... by Soon-Chan Kim, Ga-Hye Kim, Jae-Hyeon Park, Kyung-Hun Lee, Jiwon Koh, Tae-Yong Kim, Dae-Won Lee, Yu-Jin Kim, Seongyeong Kim, Song-Yi Park, Ahrum Min, Young-Kyoung Shin, Seock-Ah Im, Ja-Lok Ku

“…By establishing 24 cell lines and 3 organoids from MPE samples of breast cancer patients, we performed extensive genomic, transcriptomic, and drug sensitivity analyses. Our findings reveal substantial genetic and transcriptomic diversity among MPE-derived cell lines, highlighting dynamic alterations in driver mutations and signaling pathways that correlate with variable drug responses. …”
Get full text

Spatiotemporal profiling reveals the impact of caloric restriction in the aging mammalian brain by Zehao Zhang, Alexander Epstein, Chloe Schaefer, Abdulraouf Abdulraouf, Weirong Jiang, Wei Zhou, Junyue Cao

“…In this study, we profiled >500,000 cells from 36 control and CR mouse brains across three age groups with EasySci single-nucleus transcriptomics and performed imaging-free IRISeq spatial transcriptomics on twelve brain sections from CR and control aged mice. …”
Get full text

Mapping striatal functional gradients and associated gene expression in Parkinson’s disease with continuous cognitive impairment by Xiaolu Li, Shuting Bu, Huize Pang, Hongmei Yu, Mengwan Zhao, Juzhou Wang, Yu Liu, Guoguang Fan

“…These findings provide valuable insights into striatal macro- and microstructural changes in PD and their role in cognitive impairment.…”
Get full text

Predicting antimicrobial resistance in Pseudomonas aeruginosa with machine learning‐enabled molecular diagnostics by Ariane Khaledi, Aaron Weimann, Monika Schniederjans, Ehsaneddin Asgari, Tzu‐Hao Kuo, Antonio Oliver, Gabriel Cabot, Axel Kola, Petra Gastmeier, Michael Hogardt, Daniel Jonas, Mohammad RK Mofrad, Andreas Bremges, Alice C McHardy, Susanne Häussler

“…Our results pave the way for the development of a molecular resistance profiling tool that reliably predicts antimicrobial susceptibility based on genomic and transcriptomic markers. The implementation of a molecular susceptibility test system in routine microbiology diagnostics holds promise to provide earlier and more detailed information on antibiotic resistance profiles of bacterial pathogens and thus could change how physicians treat bacterial infections.…”
Get full text

PCMR: a comprehensive precancerous molecular resource by Yichun Xiong, Jiaqi Li, Wang Jin, Xiaoran Sheng, Hui Peng, Zhiyi Wang, Caifeng Jia, Lili Zhuo, Yibo Zhang, Jingzhe Huang, Modi Zhai, Beibei Lyu, Jie Sun, Meng Zhou

“…Comprehensive analysis of genomic, transcriptomic, proteomic and epigenomic alterations can provide insights into the early stages of carcinogenesis. …”
Get full text

A multi-omic approach implicates novel protein dysregulation in post-traumatic stress disorder by Jiawei Wang, Yujing Liu, Hongyu Li, Tuan P. Nguyen, John Lee Soto-Vargas, Rashaun Wilson, Weiwei Wang, TuKiet T. Lam, Chi Zhang, Chen Lin, Traumatic Stress Brain Research Group, David A. Lewis, Jill Glausier, Paul E. Holtzheimer, Matthew J. Friedman, Kenneth R. Williams, Marina R. Picciotto, Angus C. Nairn, John H. Krystal, Ronald S. Duman, Keith A. Young, Hongyu Zhao, Matthew J. Girgenti

“…We substantially expand the number of differentially expressed genes and proteins in PTSD and identify downregulation of GABAergic processes in the PTSD proteome. This provides a novel framework for future studies integrating proteomic profiling with transcriptomics and non-coding RNAs in the human brain studies.…”
Get full text

The impact of dropouts in scRNAseq dense neighborhood analysis by Alisa Pavel, Manja Gersholm Grønberg, Line H. Clemmensen

“…Single cell RNA sequencing (scRNAseq) provides the possibility to investigate transcriptomic profiles on a single cell level. …”
Get full text

THE REORGANIZATION OF PLANT GENOMES DURING ALLOPOLYPLOIDISATION by A. B. Shcherban

“…The data on various genomic changes at early stages of allopolyploidization, including activation of mobile elements, chromosomal rearrangements, epigenetic and transcriptomic changes, etc., are summarized. We note that these changes provide evolutionary success of allopolyploids and their prevalence among higher plants due to formation of stable organization of the allopolyploid genome.…”
Get full text

Relationship between Abnormal Lipid Metabolism and Gallstone Formation by Xiang Li, Xiaodan Yin, Jun Xu, Lei Geng, Zhengtao Liu

“…This study aimed to determine the role of lipid metabolism in the pathogenesis of gallstones and provide insights for future studies using previous research in genomics, metabolomics, transcriptomics, and other fields.…”
Get full text

The salivary gland mRNA and protein datasets after diapause of the soybean hawkmoth, Clanis bilineata tsingtauica by Yehua Li, Feiyang Ji, Pengjun Zhang, Tingting Xiao

“…These findings provide a multi-omics resource for identifying key regulators of diapause and elucidating its molecular basis in CBT. …”
Get full text

Flavonoid biomarkers and co-expression gene networks characterized in ten Hemerocallis citrina accessions via multi-omics by Tao Ma, Hui Wang, Xinli Yue, Lu Meng, Yuchao Wang, Jiongyu Hao, Yue Zhao, Siyu Hou, Zhaoxia Sun

“…Integrated transcriptomic and metabolic analyses identified 14 differential flavonoid metabolites (DFMs) and 47 differentially expressed genes (DEGs) associated with flavonoid biosynthesis through Pearson’s correlation analysis and WGCNA analyses. qRT-PCR validation of 13 DEGs confirmed the consistency of transcriptomic data. …”
Get full text

Interactions between starvation, cold stress and water velocities on immunological and metabolic responses of large yellow croaker by Chengzhang Huang, Huirong Lv, Xuming Huang, Xiaolong Yin, Zhangjie Chu, Jungyeol Park, Junwook Hur, Yang Gao, Weiye Li

“…Transcriptomic analyses revealed a significant shift towards fatty acid oxidation and down-regulation of steroid biosynthesis pathways, particularly under combined stress conditions. …”
Get full text

Key processes required for the different stages of fungal carnivory by a nematode-trapping fungus. by Hung-Che Lin, Guillermo Vidal-Diez de Ulzurrun, Sheng-An Chen, Ching-Ting Yang, Rebecca J Tay, Tomoyo Iizuka, Tsung-Yu Huang, Chih-Yen Kuo, A Pedro Gonçalves, Siou-Ying Lin, Yu-Chu Chang, Jason E Stajich, Erich M Schwarz, Yen-Ping Hsueh

“…A. oligospora enacts a dynamic transcriptomic response, especially of protein secretion-related genes, in the presence of prey. …”
Get full text

Epimedium-Derived Exosome-Loaded GelMA Hydrogel Enhances MC3T3-E1 Osteogenesis via PI3K/Akt Pathway by Weijian Hu, Xin Xie, Jiabin Xu

“…Underlying mechanisms were examined at transcriptomic and protein levels to elucidate GelMA@Exo’s therapeutic osteogenesis actions. …”
Get full text

Single-cell immune profiling and validation of PBMCs in the onset of and recovery from herpes zoster by Shang Zheng, Shuyao Zhang, Xiangyao Li, Yong Fei, Lei Yang, Beibei Liu, Kangli Shen, Qinli Feng, Qinghe Zhou, Ming Yao, Longsheng Xu

“…The integrative analysis of the transcriptomes and epigenomes provided a comprehensive description and validation of the key changes in peripheral blood. …”
Get full text

Lactiplantibacillus plantarum 299v supplementation modulates β-cell ER stress and antioxidative defense pathways and prevents type 1 diabetes in gluten-free BioBreeding rats by Pinar Sargin, Mark F. Roethle, Shuang Jia, Tarun Pant, Ashley E. Ciecko, Samantha N. Atkinson, Nita H. Salzman, Ru-Jeng Teng, Yi-Guang Chen, Susanne M. Cabrera, Martin J. Hessner

“…HCD+Lp299v pups exhibited increased plasma propionate and butyrate levels, which correlated with enriched fecal Bifidobacteriaceae and Clostridiales taxa. Islet transcriptomic and histologic analyses at 40-days of age revealed that rats fed HCD expressed an autophagy profile, while those provided HCD+Lp299v expressed ER-associated protein degradation (ERAD) and antioxidative defense pathways, including Nrf2. …”
Get full text

Multi-omics analysis and experiments uncover the link between cancer intrinsic drivers, stemness, and immunotherapy in ovarian cancer with validation in a pan-cancer census by Yilin Li, Cen Chen, Xiaoyu Ji, Ningxiao Jiang, Fei Wang, Xiangqian Gao, Weiwei Chen, Qiang Tang, Yan Li, Shinan Zhang, Gaofeng Qin, Yingjiang Xu, Yanlin Wang, Lingwen Kong, Lei Han, Jie Mei

“…When applied to PD1/PD-L1 ICI transcriptomic cohorts, CSCI consistently and accurately predicts tumor progression and immunotherapy benefits, with a mean AUC greater than 0.8. …”
Get full text

Phenotypic plasticity evolves at multiple biological levels in response to environmental predictability in a long-term experiment with a halotolerant microalga. by Christelle Leung, Daphné Grulois, Leandro Quadrana, Luis-Miguel Chevin

“…These transcriptomic effects were independent of DNA methylation changes in cis. …”
Get full text

Detecting global and local hierarchical structures in cell-cell communication using CrossChat by Xinyi Wang, Axel A. Almet, Qing Nie

“…Current existing methods infer CCC from single-cell RNA-seq or Spatial Transcriptomics only between predefined cell groups, neglecting the existing hierarchical structure within CCC that are determined by signaling molecules, in particular, ligands and receptors. …”
Get full text

NiCo identifies extrinsic drivers of cell state modulation by niche covariation analysis by Ankit Agrawal, Stefan Thomann, Sukanya Basu, Dominic Grün

“…The rapidly growing availability of single-cell resolution spatial transcriptomics makes it possible to meet this challenge. …”
Get full text