Contrasting transcriptional responses of a virulent and an attenuated strain of Mycobacterium tuberculosis infecting macrophages. by Alice H Li, Simon J Waddell, Jason Hinds, Chad A Malloff, Manjeet Bains, Robert E Hancock, Wan L Lam, Philip D Butcher, Richard W Stokes

“…<h4>Background</h4>H37Rv and H37Ra are well-described laboratory strains of Mycobacterium tuberculosis derived from the same parental strain, H37, that show dramatically different pathogenic phenotypes.…”
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Multi-omics analysis untangles the crosstalk between intratumor microbiome, lactic acid metabolism and immune status in lung squamous cell carcinoma by Xun Qiu, Dan Li

“…However, its specific implications in lung squamous cell carcinoma (LUSC) remain unclear.MethodsWe used numerous datasets encompassing bulk and single-cell transcriptome, genome, intratumor microbiome, and digital pathome to systematically investigate the LM patterns in LUSC. …”
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Multinucleated giant cells are hallmarks of ovarian aging with unique immune and degradation-associated molecular signatures. by Aubrey Converse, Madeline J Perry, Shweta S Dipali, Jose V V Isola, Emmett B Kelly, Joseph M Varberg, Mary B Zelinski, Michael B Stout, Michele T Pritchard, Francesca E Duncan

“…The function and consequence of ovarian MNGCs remain unknown as their biological activity is highly context-dependent, and their large size has limited their isolation and analysis through technologies such as single-cell RNA sequencing. In this study, we define ovarian MNGCs through a deep analysis of their presence across age and species using advanced imaging technologies as well as their unique transcriptome using laser capture microdissection. …”
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Characterization of subcutaneous and visceral de-differentiated fat cells by Yan Li, Houyu Zhang, Carlos F. Ibáñez, Meng Xie

“…Finally, combining genetic lineage tracing and single cell/nucleus RNA sequencing, we demonstrate the existence of DFAT cells in inguinal and epididymal adipose depots in vivo, with transcriptomes resembling late-stage ASPCs. …”
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GLN2 as a key biomarker and therapeutic target: evidence from a comprehensive pan-cancer study using molecular, functional, and bioinformatic analyses by Shuang Gao, Lei Zhang, Guoping Sun

“…Multiple immune infiltration algorithms from the TIMER2.0 database were utilized to examine the correlation between GNL2 expression and the tumor immune microenvironment. The transcriptome-wide immune infiltration results were validated using 72 single-cell datasets from the Tumor Immune Single-cell Hub (TISCH) database. …”
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Genetic associations of plasma metabolites with immune cells in hyperthyroidism revealed by Mendelian randomization and GWAS-sc-eQTLs xQTLbiolinks analysis by Yutong Li, Xingyu Song, Yuyang Huang, Sifan Zhou, Linkun Zhong

“…In addition, sensitivity analyses were used to evaluate robustness, heterogeneity, and horizontal pleiotropy of results. Single-cell transcriptome-based exploration of potential key molecule and mechanism by which plasma metabolites regulated the immune cell differentiation in HD pathogenesis. …”
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Predicting prognosis and immunotherapy response of ferroptosis-related genes in colorectal cancer by Hongyun Wei, Keyu Ren, Yanchun Jin, Yao Wen, Bin Cao, Yu Gan, Ying Shi, Zhihong Wu, Linlin Chen

“…Abstract To identify ferroptosis markers, which were associated with prognosis and immune response in colorectal cancer (CRC), we integrated spatial transcriptome, single-cell transcriptome, and bulk transcriptome data for analysis, and this multi-omics integration approach is an innovation that distinguishes this study from previous ones. …”
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GPX4 deficiency-induced ferroptosis drives endometrial epithelial fibrosis in polycystic ovary syndrome by Zhenhong Ye, Ming Cheng, Weisi Lian, Yueqi Leng, Xunsi Qin, Yue Wang, Ping Zhou, Xiyao Liu, Tianliu Peng, Ruiqi Wang, Yilei He, Heng Pan, Yue Zhao, Rong Li

“…However, the underlying mechanisms remain incompletely understood. Though integrating single-cell RNA-sequencing, transcriptomics, and metabolomics analysis, we found that glutathione (GSH) metabolism disorder and the overactivation of ferroptosis, triggered by glutathione peroxidase 4 (GPX4) deficiency in endometrial epithelial cells, were the consequences of the prolonged endometrial proliferative phase in PCOS. …”
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FGF7 secreted from dermal papillae cell regulates the proliferation and differentiation of hair follicle stem cell by Niu Wang, Weidong Zhang, Zhenyu Zhong, Xiongbo Zhou, Xinran Shi, Xin Wang

“…FGF7 functions as a paracrine protein regulating epithelial proliferation, differentiation and migration. The single-cell transcriptome profiling and immunofluorescence analysis demonstrated that FGF7 localizes at DPC, while FGF7 receptor (FGFR2) expresses in both DPC and HFSC. …”
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Unveiling the role of TGF-β signaling pathway in breast cancer prognosis and immunotherapy by Yifan Zheng, Yifan Zheng, Li Li, Wenqian Cai, Lin Li, Rongxin Zhang, Wenbin Huang, Wenbin Huang, Yulun Cao

“…Nonetheless, the connection between genes associated with the TSP and the clinical outcomes of breast cancer, as well as their impact on the tumor microenvironment and immunotherapeutic responses, remains elusive.MethodsBreast cancer transcriptomic and single-cell sequencing data were obtained from the The Cancer Genome Atlas (TCGA) and the Gene Expression Omnibus (GEO) databases. …”
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Identification of GBN5 as a molecular biomarker of pan-cancer species by integrated multi-omics analysis by Qian Guo, Xinxin Zhong, Zihan Dang, Baiquan Zhang, Zixin Yang

“…Materials and methods We employed a multi-omics approach, including transcriptomic, genomic, proteomic, single-cell cytomic, spatial transcriptomic, and genomic data, to explore the prognostic value and potential oncogenic mechanisms of GBN5 across pan-cancers from multiple perspectives. …”
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Sjögren’s syndrome is associated with a reduction in the surface area of the right caudal anterior cingulate gyrus by Ping Wang, Yunpeng Tai, Xiaofang Zhu, Xinyi Wan, An Sun, Jiajia Wang, Hui Cheng, Jingwei Hong, Yi Zhang, Xiaobing Wang

“…The relationship between cerebral cortex structure and neurological pathologies is well-documented, yet the impact of SS on cerebral cortex structure remains unclear. …”
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Oreocharis scutifolia (Gesneriaceae), a Peltate‐Leaved New Species From the Dry–Hot Valley of the Jinsha River Basin, Yunnan, China by Zhi Xie, Na‐Na Peng, Miao Zhang, Guo‐En Ding, Fang Wen, Hang‐Hui Kong

“…(LPP = 1), and well apart from the remaining members of the genus. …”
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Analysis of the molecular nature associated with microsatellite status in colon cancer identifies clinical implications for immunotherapy by Wei Wu, Qihan Fu, Lulu Liu, Yi Zheng, Hangyu Zhang, Peng Zhao, Weijia Fang, Xuanwen Bao, Shaobing Cheng, Xiaomeng Dai, Xudong Zhu, Zhou Tong, Fanglong Liu

“…However, the molecular nature of microsatellite instability is not well elucidated.Methods We examined the immune microenvironment of colon cancer using assessments of the bulk transcriptome and the single-cell transcriptome focusing on molecular nature of microsatellite stability (MSS) and microsatellite instability (MSI) in colorectal cancer from a public database. …”
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ANKRD22 participates in the proinflammatory activities of macrophages in the colon cancer tumor microenvironment by Xiaoying Wang, Keqing Yang, Bin Yang, Rui Wang, Yongliang Zhu, Tianhui Pan

“…Single-cell RNA sequencing, spatial transcriptomic studies, and subcutaneous xenograft experiments in mice revealed that Ankrd22 silencing altered the subtype distribution of macrophages, attenuated their proinflammatory activity, and enhanced their protumor activity. …”
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<i>AtAUEs</i>, a Small Family of ABA Up-Regulated EAR Motif-Containing Proteins Regulate ABA Responses in Arabidopsis by Wei Wang, Xutong Wang, Xiaoyu Liu, Yating Wang, Yingying Li, Saddam Hussain, Xiaoxiao Jing, Siyu Chen, Shucai Wang

“…We generated CRISPR/Cas9 gene-edited <i>ataue1</i>, <i>ataue2</i> and <i>ataue3</i> single, <i>ataue1 ataue2</i> (<i>ataue12</i>) double, and <i>ataue1 ataue2 ataue3</i> (<i>ataue123</i>) triple mutants, as well as transgenic plants overexpressing <i>AtAUE1</i>, and examined their ABA sensitivity. …”
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Isolation, Expression, and Promoter Analysis of GbWRKY2: A Novel Transcription Factor Gene from Ginkgo biloba by Yong-Ling Liao, Yong-Bao Shen, Jie Chang, Wei-Wei Zhang, Shui-Yuan Cheng, Feng Xu

“…WRKY transcription factor is involved in multiple life activities including plant growth and development as well as biotic and abiotic responses. We identified 28 WRKY genes from transcriptome data of Ginkgo biloba according to conserved WRKY domains and zinc finger structure and selected three WRKY genes, which are GbWRKY2, GbWRKY16, and GbWRKY21, for expression pattern analysis. …”
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Abscisic acid pathway involved in the regulation of watermelon fruit ripening and quality trait evolution. by Yanping Wang, Shaogui Guo, Shouwei Tian, Jie Zhang, Yi Ren, Honghe Sun, Guoyi Gong, Haiying Zhang, Yong Xu

“…To date, the mechanisms of watermelon fruit ripening, and the role of abscisic acid (ABA) in this process, has not been well understood. We quantified levels of free and conjugated ABA contents in the fruits of cultivated watermelon (97103; C. lanatus subsp. vulgaris), semi-wild germplasm (PI179878; C. lanatus subsp. mucosospermus), and wild germplasm (PI296341-FR; C. lanatus subsp. lanatus). …”
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The TOR kinase pathway is relevant for nitrogen signaling and antagonism of the mycoparasite Trichoderma atroviride. by Rossana Segreto, Hoda Bazafkan, Julia Millinger, Martina Schenk, Lea Atanasova, Maria Doppler, Christoph Büschl, Mélanie Boeckstaens, Silvia Soto Diaz, Ulrike Schreiner, Fabiano Sillo, Raffaella Balestrini, Rainer Schuhmacher, Susanne Zeilinger

“…Trichoderma atroviride (Ascomycota, Sordariomycetes) is a well-known mycoparasite applied for protecting plants against fungal pathogens. …”
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Microglial polarization pathways and therapeutic drugs targeting activated microglia in traumatic brain injury by Liping Shi, Shuyi Liu, Jialing Chen, Hong Wang, Zhengbo Wang

“…In the future, new technologies, such as single-cell RNA sequencing and transcriptome analysis, can facilitate further experimental studies. …”
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