Repurposed clindamycin suppresses pyroptosis in tumor-associated macrophages through Inhibition of caspase-1 by Adrian Weich, Johannes Berges, Cindy Flamann, Katrin Bitterer, Krishna Pal Singh, David Chambers, Christopher Lischer, Xin Lai, Olaf Wolkenhauer, Carola Berking, Gerhard Krönke, Shailendra Gupta, Heiko Bruns, Julio Vera, Research Group Macrophages

“…Methods In our work, we designed a novel computational pipeline that combines single-cell transcriptomics data, network analysis, multicriteria decision techniques, and pharmacophore-based docking simulations to select molecular targets and matching repurposable drugs for TAM immunomodulation. …”
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Machine learning based identification of an amino acid metabolism related signature for predicting prognosis and immune microenvironment in pancreatic cancer by Xiaohong Liu, Xing Wang, Jie Ren, Yuan Fang, Minzhi Gu, Feihan Zhou, Ruiling Xiao, Xiyuan Luo, Jialu Bai, Decheng Jiang, Yuemeng Tang, Bo Ren, Lei You, Yupei Zhao

“…CIBERSORT and ssGSEA were harnessed to delve into the immune landscape disparities. Single-cell transcriptomics, qPCR, and Immunohistochemistry were performed to corroborate the expression levels and prognostic significance of this signature. …”
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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

“…A novel cancer stem cell index (CSCI) was developed and validated using multiple advanced algorithms and large-scale datasets, as well as corresponding clinical features, including 14 OV transcriptomic datasets, 7 pan-cancer ICI transcriptomic cohorts and one melanoma scRNA dataset derived from PD-1 treated patients.ResultsChromosomal 20q gain, 8q gain, and 5q loss have been identified as ovarian cancer-specific driving variations. …”
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Regulation of cortical neurogenesis by MED13L via transcriptional priming and its implications for MED13L syndrome by Jia Li, Yu-zhu Hao, Jia Cui, Xiao-xiao Cao, Nan Wu, Ji Ma, Shuang-yi Xie, Yi-Hsuan Pan, Xue-lian He, Yu-lan Zhao, Xiao-Bing Yuan

“…Additionally, heterozygous mice show microcephaly with simplified neuronal morphology in the motor cortex. Single-cell transcriptomics and immunofluorescence reveal severe cortical neurogenesis deficits in Med13l knockout embryos, driven by impaired neural progenitor differentiation. …”
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Redefining the role of IL-18 in post-surgical recovery and sepsis: a key mediator of inflammation resolution by Ioanna Papatheodorou, Gabriela Blažková, Veronika Bosáková, Zuzana Tomášiková, Erin Spearing, Robin Klieber, Pavel Ostašov, Julie Štíchová, Martina Dvončová, Alexandra Mýtniková, Jan Emmer, Kamila Bendíčková, Tomáš Tomáš, Vladimír Šrámek, Petros Kolovos, Monika Holubová, Martin Helán, Marcela Vlková, Jan Frič, Marcela Hortová-Kohoutková

“…These results were further validated in vitro by comparing IL-18 and TNF-α effects on monocytes, and in 3D human intestine organoids together with single cell (sc)-RNAseq analysis. Results Transcriptomics of ORT monocytes revealed upregulation of ITG family integrins, namely ITGB3 and ITGB5, CXCL family chemokines, notably CXCL1-3, CXCL5, and SCL/TAL1 factor controlling differentiation and migration, but not pro-inflammatory genes. …”
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Integrated multi-omics profiling characterizes the crucial role of human dental epithelium during tooth development by Ran Zhang, Zongshan Shen, Zhenni Zhao, Xiuge Gu, Tianxing Yan, Wei Wei, Chuan Wu, Jinxuan Xia, Yuanyuan Zhang, Suwen Chen, Linsha Ma, Dong Zhang, Xiaoshan Wu, Paul T. Sharpe, Songlin Wang

“…Summary: The development of early human tooth primordia is not well understood. Here, we linked single-cell RNA sequencing, spatial transcriptomics, and secretome analysis to characterize human fetal tooth development over time. …”
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Integrative multi-omics analysis to gain new insights into COVID-19 by Setegn Eshetie, Karmel W. Choi, Elina Hyppönen, Beben Benyamin, S. Hong Lee

“…The dataset included COVID-19 phenotypic data as well as genome, imputed-transcriptome, metabolome and exposome data. …”
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Genome assembly and annotation of the parasitoid jewel wasp Nasonia oneida by Anjali Rana, Paras Verma, Shashi Bhushan Pandit, John H. Werren, Xu Wang, Rhitoban Raychoudhury

“…Here, we present the genome of N. oneida, a species lacking prior genomic characterization, using 10× Genomics linked-read (400× coverage), Illumina short-read (120× coverage), and transcriptome data (30× coverage). The assembled genome size is 267 Mb, comprising 4,675 scaffolds, with a scaffold N50 of 1 Mb and 98.40% Benchmarking Universal Single-Copy Orthologues (BUSCOs) completeness score. …”
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Identification of gene signatures associated with lactation for predicting prognosis and treatment response in breast cancer patients through machine learning by Jinfeng Zhao, Longpeng Li, Yaxin Wang, Jiayu Huo, Jirui Wang, Huiwen Xue, Yue Cai

“…Lactylation-related gene signature (LRS) was constructed by 15 machine learning algorithms, and the relationship between LRS and tumor microenvironment (TME) as well as drug sensitivity was analyzed. In addition, the expression of genes in the LRS in different cells was explored by single-cell analysis and spatial transcriptome. …”
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Functional loss of rffG and rfbB, encoding dTDP-glucose 4,6-dehydratase, alters colony morphology, cell shape, motility and virulence in Salmonella Typhimurium by Subhashish Chakraborty, Pip Banerjee, Joel P. Joseph, Sanmoy Pathak, Taru Verma, Aagosh Kishor Karhale, Deepti Chandra, Mrinmoy Das, Pritam Saha, Dipankar Nandi

“…Furthermore, transcriptomic analysis identified flagellar and SPI-1 pathways to be highly downregulated in ΔrfbBΔrffG which led to impaired swimming as well as swarming motility, lower adhesion and invasion of HeLa cells. …”
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CNTools: A computational toolbox for cellular neighborhood analysis from multiplexed images. by Yicheng Tao, Fan Feng, Xin Luo, Conrad V Reihsmann, Alexander L Hopkirk, Jean-Philippe Cartailler, Marcela Brissova, Stephen C J Parker, Diane C Saunders, Jie Liu

“…Therefore, it is critical to accurately and efficiently identify cellular neighborhoods from spatially-resolved single-cell transcriptomic data or single-cell resolution tissue imaging data. …”
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Lactylation Modification as a Promoter of Bladder Cancer: Insights from Multi-Omics Analysis by Yipeng He, Lingyan Xiang, Jingping Yuan, Honglin Yan

“…This model has significant biological implications at the single-cell level as well as at the spatial level.…”
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<strong>Gene expression changes in response to combination stresses in <em>Phaseolus vulgaris</em> L. (Fabaceae)</strong> by Samaneh Sabzi, Zahra Tahmasebi, Mehrshad Barary

“…The obtained results addressed for the impact of combined stresses at the transcriptome level, with some gene expression (PAL in Naz, Akhtar, LOX in Naz and Akhtar, PR4 in Akhtar and Ks41128, PR3 in Ks41128 and OS in Ks41128 and G11867) increasing after multiple stresses but not after single stress. …”
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Integrated multiomics of pressure overload in the human heart prioritizes targets relevant to heart failure by Brian R. Lindman, Andrew S. Perry, Michelle L. Lance, Kaushik Amancherla, Namju Kim, Quanhu Sheng, Phillip Lin, Ryan D. Pfeiffer, Eric Farber-Eger, William F. Fearon, Samir Kapadia, Dharam J. Kumbhani, Linda Gillam, Ravinder R. Mallugari, Deepak K. Gupta, Francis J. Miller, Anna Vatterott, Natalie Jackson, Yan Ru Su, Kelsey Tomasek, Tarek Absi, Jane E. Freedman, Matthew Nayor, Saumya Das, Quinn S. Wells, Marc R. Dweck, Robert E. Gerszten, Eric R. Gamazon, Nathan R. Tucker, Ravi Shah, Sammy Elmariah

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Spatial heterogeneity reveals an evolutionary signature predicting therapeutic response and clinical outcomes in hepatocellular carcinoma by Shangyi Luo, Li Liu, Yang Sun, Jian Shi, Yajing Zhang, Yajing Zhang, Yajing Zhang

“…The HCC evolutionary signature (HCCEvoSig) was developed and assessed across six cross-platform HCC cohorts.ResultsGenes exhibiting high intra- and inter-tumor expression variation were significantly enriched in a gene set associated with HCC prognosis, from which we developed and validated a reproducible and robust transcriptomic signature, HCCEvoSig. Multiregional single-cell data confirmed the high intra- and inter-tumoral heterogeneity of HCCEvoSig genes across different cell types, and importantly, demonstrated that the dysregulation of HCCEvoSig genes exhibited a geospatially gradual transition from the non-tumor region to the tumor border and tumor core, as well as from non-malignant to malignant epithelial cells. …”
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Alternative splicing in stem cells and development: research progress and emerging technologies by Yan Jin, XiaoLin Liang, Xiangting Wang

“…Abstract Alternative splicing is a key regulatory mechanism that generates transcriptomic diversity by selectively splicing pre-RNA molecules in different ways, leading to the production of multiple RNA isoforms from a single gene. …”
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Placozoan secretory cell types implicated in feeding, innate immunity and regulation of behavior. by Tatiana D Mayorova, Thomas Lund Koch, Bechara Kachar, Jae Hoon Jung, Thomas S Reese, Carolyn L Smith

“…They lack organs, body cavities, muscles and a nervous system and have only seven broadly defined morphological cell types, each with a unique distribution. Analyses of single cell transcriptomes of four species of placozoans revealed greater diversity of secretory cell types than evident from morphological studies, but the locations of many of these new cell types were unknown and it was unclear which morphological cell types they represent. …”
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Activation of Adenosine Phosphate Signaling Promotes Antitumor Immunity in Tumor Microenvironment and Facilitate Immunotherapy by Yantao Xu, Ying Wang, Zixi Jiang, Yi He, Guowei Zhou, Benliang Wei, Jiachen Liu, Xiang Chen

“…Additionally, through single‐cell and spatial transcriptomic analysis, we explored how APsig promotes antitumor immunity by activating myeloid lineage cells for antigen presentation. …”
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High-throughput SHAPE analysis reveals structures in HIV-1 genomic RNA strongly conserved across distinct biological states. by Kevin A Wilkinson, Robert J Gorelick, Suzy M Vasa, Nicolas Guex, Alan Rein, David H Mathews, Morgan C Giddings, Kevin M Weeks

“…Seven structurally homologous binding sites occur in a well-defined domain in the genome, consistent with a role in directing specific packaging of genomic RNA into nascent virions. …”
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Investigating ferroptosis-related genes NFE2L2 in neutrophils for ankylosing spondylitis: therapeutic potential of cassia twigs by Tianyou Chen, Jichong Zhu, Xinli Zhan, Chenxing Zhou, Chengqian Huang, Shaofeng Wu, Bin Zhang, Sitan Feng, Jiarui Chen, Jiang Xue, Zhenwei Yang, Chong Liu

“…We analyzed clinical data on ankylosing spondylitis, transcriptome data, single-cell sequencing data, and genes related to ferroptosis and Cassia twigs. …”
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