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JOURNAL ARTICLE
Joseph B Lin, Kathryn L Pepple, Christian Concepcion, Yulia Korshunova, Michael A Paley, Grace L Paley, Jennifer Laurent, Rajendra S Apte, Lynn M Hassman
PURPOSE: Uveitis is a heterogenous group of inflammatory eye disease for which current cytokine-targeted immune therapies are effective for only a subset of patients. We hypothesized that despite pathophysiologic nuances that differentiate individual disease states, all forms of eye inflammation might share common mechanisms for immune cell recruitment. Identifying these mechanisms is critical for developing novel, broadly acting therapeutic strategies. DESIGN: Experimental study...
2024: Ophthalmol Sci
#22
JOURNAL ARTICLE
Reinhard Grausenburger, Paula Herek, Shahrokh F Shariat, Bernhard Englinger
PURPOSE OF REVIEW: Current risk stratification and treatment decision-making for bladder cancer informed by histopathology as well as molecular diagnostics face limitations. This review summarizes recent advancements in single-cell and spatial omics methodologies for understanding bladder cancer biology and their potential impact on development of novel therapeutic strategies. RECENT FINDINGS: Single-cell RNA sequencing and spatial omics techniques offer unprecedented insights into various aspects of tumor microenvironment (TME), bladder cancer heterogeneity, cancer stemness, and cellular plasticity...
April 23, 2024: Current Opinion in Urology
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JOURNAL ARTICLE
Nicholas Chapman, Joshua Greenwald, Jolee Suddock, Dong Xu, Alexander Markowitz, Maeve Humphrey, Jennifer A Cotter, Mark D Krieger, Debra Hawes, Jianling Ji
Integration of molecular data with histologic, radiologic, and clinical features is imperative for accurate diagnosis of pediatric central nervous system (CNS) tumors. Whole transcriptome RNA sequencing (RNAseq), a genome-wide and non-targeted approach, allows for the detection of novel or rare oncogenic fusion events that contribute to the tumorigenesis of a substantial portion of pediatric low- and high-grade glial and glioneuronal tumors. We present two cases of pediatric glioneuronal tumors occurring in the occipital region with a CLIP2::MET fusion detected by RNAseq...
April 22, 2024: Acta Neuropathologica Communications
#24
JOURNAL ARTICLE
Fang Fu, Xin Yang, Ru Li, Yingsi Li, Hang Zhou, Ken Cheng, Ruibin Huang, You Wang, Fei Guo, Lina Zhang, Min Pan, Jin Han, Li Zhen, Lushan Li, Tingying Lei, Dongzhi Li, Can Liao
BACKGROUND: The molecular mechanism of fetal cystic hygroma (CH) is still unclear, and no study has previously reported the transcriptome changes of single cells in CH. In this study, single-cell transcriptome sequencing (scRNA-seq) was used to investigate the characteristics of cell subsets in the lesion tissues of CH patients. METHODS: Lymphoid tissue collected from CH patients and control donors for scRNA-seq analysis. Differentially expressed gene enrichment in major cell subpopulations as well as cell-cell communication were analyzed...
April 22, 2024: BMC Medical Genomics
#25
JOURNAL ARTICLE
S Y Wang, S J Zhang, H F Meng, H Q Xu, Z X Guo, J F Yan, J L Gao, L N Niu, S L Wang, K Jiao
BACKGROUND: Oral submucous fibrosis (OSF) is a precancerous lesion characterized by fibrous tissue deposition, the incidence of which correlates positively with the frequency of betel nut chewing. Prolonged betel nut chewing can damage the integrity of the oral mucosal epithelium, leading to chronic inflammation and local immunological derangement. However, currently, the underlying cellular events driving fibrogenesis and dysfunction are incompletely understood, such that OSF has few treatment options with limited therapeutic effectiveness...
April 23, 2024: Stem Cell Research & Therapy
#26
JOURNAL ARTICLE
Mengyi Liu, Zhicheng Ji, Vaibhav Jain, Vanessa L Smith, Emily Hocke, Anoop P Patel, Roger E McLendon, David M Ashley, Simon G Gregory, Giselle Y López
Glioblastoma (GBM) remains an untreatable malignant tumor with poor patient outcomes, characterized by palisading necrosis and microvascular proliferation. While single-cell technology made it possible to characterize different lineage of glioma cells into neural progenitor-like (NPC-like), oligodendrocyte-progenitor-like (OPC-like), astrocyte-like (AC-like) and mesenchymal like (MES-like) states, it does not capture the spatial localization of these tumor cell states. Spatial transcriptomics empowers the study of the spatial organization of different cell types and tumor cell states and allows for the selection of regions of interest to investigate region-specific and cell-type-specific pathways...
April 22, 2024: Acta Neuropathologica Communications
#27
JOURNAL ARTICLE
Qingyu Xu, Zhenyu Yang, Yupeng Jia, Rui Wang, Qiyu Zhang, Ruonan Gai, Yiding Wu, Qingyong Yang, Guoren He, Ju Hua Wu, Feng Ming
The molecular basis of orchid flower development involves a specific regulatory program in which MADS-box transcription factors play a central role. The recent 'perianth code' model hypothesizes that two types of higher-order heterotetrameric complexes, namely SP complex and L complex, play pivotal roles in the orchid perianth organ formation. Therefore, we explored their roles and searched for other components of the regulatory network.Through the combined analysis for transposase-accessible chromatin with high-throughput sequencing and RNA sequencing of the lip-like petal and lip from Phalaenopsis equestris var...
April 23, 2024: Mol Hortic
#28
REVIEW
Qilian Du, Qi An, Jiajun Zhang, Chao Liu, Qinyong Hu
The relationship between the immune cell and tumor occurrence and progression remains unclear. Profiling alterations in the tumor immune microenvironment (TIME) at high resolution is crucial to identify factors influencing cancer progression and enhance the effectiveness of immunotherapy. However, traditional sequencing methods, including bulk RNA sequencing, exhibit varying degrees of masking the cellular heterogeneity and immunophenotypic changes observed in early and late-stage tumors. Single-cell RNA sequencing (scRNA-seq) has provided significant and precise TIME landscapes...
April 22, 2024: Cancer Cell International
#29
JOURNAL ARTICLE
Sara Lamei Javan, Arman Beyraghdar Kashkooli, AbdolAli Shojaeiyan, Sina Majidian
Medicinal plants are rich sources for treating various diseases due their bioactive secondary metabolites. Fenugreek (Trigonella foenum-graecum) is one of the medicinal plants traditionally used in human nutrition and medicine which contains an active substance, called diosgenin, with anticancer properties. Biosynthesis of this important anticancer compound in fenugreek can be enhanced using eliciting agents which involves in manipulation of metabolite and biochemical pathways stimulating defense responses...
April 22, 2024: BMC Genomics
#30
JOURNAL ARTICLE
Rashidul Islam, Jannis Heyer, Miriam Figura, Xiaoyan Wang, Xichen Nie, Benedict Nathaniel, Sivanjah Indumathy, Katja Hartmann, Christiane Pleuger, Monika Fijak, Sabine Kliesch, Florian Dittmar, Adrian Pilatz, Florian Wagenlehner, Mark Hedger, Bruce Loveland, James H Hotaling, Jingtao Guo, Kate L Loveland, Hans-Christian Schuppe, Daniela Fietz
BACKGROUND: Immune cell infiltration is heterogeneous but common in testicular germ cell tumors (TGCT) and pre-invasive germ cell neoplasia in situ (GCNIS). Tumor-infiltrating T cells including regulatory T (Treg) and follicular helper T (Tfh) cells are found in other cancer entities, but their contributions to TGCT are unknown. METHODS: Human testis specimens from independent patient cohorts were analyzed using immunohistochemistry, flow cytometry and single-cell RNA sequencing (scRNA-seq) with special emphasis on delineating T cell subtypes...
April 22, 2024: British Journal of Cancer
#31
JOURNAL ARTICLE
Joe W Chiles, Ava C Wilson, Rachel Tindal, Kaleen Lavin, Samuel Windham, Harry B Rossiter, Richard Casaburi, Anna Thalacker-Mercer, Thomas W Buford, Rakesh Patel, J Michael Wells, Marcas M Bamman, Beatriz Y Hanaoka, Mark Dransfield, Merry-Lynn N McDonald
BACKGROUND: Skeletal muscle dysfunction is a common extrapulmonary manifestation of chronic obstructive pulmonary disease (COPD). Alterations in skeletal muscle myosin heavy chain expression, with reduced type I and increased type II myosin heavy chain expression, are associated with COPD severity when studied in largely male cohorts. The objectives of this study were (1) to define an abnormal myofibre proportion phenotype in both males and females with COPD and (2) to identify transcripts and transcriptional networks associated with abnormal myofibre proportion in COPD...
April 22, 2024: Journal of Cachexia, Sarcopenia and Muscle
#32
JOURNAL ARTICLE
Jonathan Z Pan, Zhanqiang Wang, Wei Sun, Peipei Pan, Wei Li, Yongtao Sun, Shoulin Chen, Amity Lin, Wulin Tan, Liangliang He, Jacob Greene, Virginia Yao, Lijun An, Rich Liang, Qifeng Li, Jessica Yu, Lingyi Zhang, Nikolaos Kyritsis, Xuan Duong Fernandez, Sara Moncivais, Esmeralda Mendoza, Pamela Fung, Gongming Wang, Xinhuan Niu, Qihang Du, Zhaoyang Xiao, Yuwen Chang, Peiyuan Lv, J Russell Huie, Abel Torres-Espin, Adam R Ferguson, Debra D Hemmerle, Jason F Talbott, Philip R Weinstein, Lisa U Pascual, Vineeta Singh, Anthony M DiGiorgio, Rajiv Saigal, William D Whetstone, Geoffrey T Manley, Sanjay S Dhall, Jacqueline C Bresnahan, Mervyn Maze, Xiangning Jiang, Neel S Singhal, Michael S Beattie, Hua Su, Zhonghui Guan
BACKGROUND: Although many molecules have been investigated as biomarkers for spinal cord injury (SCI) or ischemic stroke, none of them are specifically induced in central nervous system (CNS) neurons following injuries with low baseline expression. However, neuronal injury constitutes a major pathology associated with SCI or stroke and strongly correlates with neurological outcomes. Biomarkers characterized by low baseline expression and specific induction in neurons post-injury are likely to better correlate with injury severity and recovery, demonstrating higher sensitivity and specificity for CNS injuries compared to non-neuronal markers or pan-neuronal markers with constitutive expressions...
April 2024: Clinical and Translational Medicine
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JOURNAL ARTICLE
Timothy Barry, Kathryn Roeder, Eugene Katsevich
CRISPR genome engineering and single-cell RNA sequencing have accelerated biological discovery. Single-cell CRISPR screens unite these two technologies, linking genetic perturbations in individual cells to changes in gene expression and illuminating regulatory networks underlying diseases. Despite their promise, single-cell CRISPR screens present considerable statistical challenges. We demonstrate through theoretical and real data analyses that a standard method for estimation and inference in single-cell CRISPR screens-"thresholded regression"-exhibits attenuation bias and a bias-variance tradeoff as a function of an intrinsic, challenging-to-select tuning parameter...
April 22, 2024: Biostatistics
#34
JOURNAL ARTICLE
Ruth E Drury, Susana Camara, Irina Chelysheva, Sagida Bibi, Katherine Sanders, Salle Felle, Katherine Emary, Daniel Phillips, Merryn Voysey, Daniela M Ferreira, Paul Klenerman, Sarah C Gilbert, Teresa Lambe, Andrew J Pollard, Daniel O'Connor
The immune mechanisms mediating COVID-19 vaccine attenuation of COVID-19 remain undescribed. We conducted comprehensive analyses detailing immune responses to SARS-CoV-2 virus in blood post-vaccination with ChAdOx1 nCoV-19 or a placebo. Samples from randomised placebo-controlled trials (NCT04324606 and NCT04400838) were taken at baseline, onset of COVID-19-like symptoms, and 7 days later, confirming COVID-19 using nucleic amplification test (NAAT test) via real-time PCR (RT-PCR). Serum cytokines were measured with multiplexed immunoassays...
April 22, 2024: Nature Communications
#35
JOURNAL ARTICLE
Shuai Cheng, Hui Guo, Mingyu Bai, Yang Cui, He Tian, Xifan Mei
Spinal-cord injury (SCI) is a severe condition that can lead to limb paralysis and motor dysfunction, and its pathogenesis is not fully understood. The objective of this study was to characterize the differential gene expression and molecular mechanisms in the spinal cord of mice three days after spinal cord injury. By analyzing RNA sequencing data, we identified differentially expressed genes and discovered that the immune system and various metabolic processes play crucial roles in SCI. Additionally, we identified UHRF1 as a key gene that plays a significant role in SCI and found that SCI can be improved by suppressing UHRF1...
April 22, 2024: Cellular and Molecular Neurobiology
#36
JOURNAL ARTICLE
Targeting dysregulated phago-/auto-lysosomes in Sertoli cells to ameliorate late-onset hypogonadism.
Zhiwen Deng, Liangyu Zhao, Sha Li, Xiaoyang Chen, Xiaohan Ling, Jiajun Zheng, Kunkun Yu, Jing Xu, Chencheng Yao, Sha Han, Jiayi Liang, Huimin Feng, Lanlan Wu, Peng Li, Ruhui Tian, Tao Jing, Yuxin Tang, Yingbo Dai, Minbo Yan, Chenchen Wang, Zheng Li, Zhi Zhou
Age-related changes in testicular function can impact health and well-being. The mechanisms underlying age-related testicular dysfunction, such as late-onset hypogonadism (LOH), remain incompletely understood. Using single-cell RNA sequencing on human testes with LOH, we delineated Sertoli cells (SCs) as pivotal metabolic coordinators within the testicular microenvironment. In particular, lysosomal acidity probing revealed compromised degradative capacity in aged SCs, hindering autophagy and phagocytic flux...
April 22, 2024: Nature aging
#37
JOURNAL ARTICLE
Lu Wang, Huijuan Liu, Qinglu Wu, Yiqian Liu, Zhenpeng Yan, Guohui Chen, Yao Shang, Songrui Xu, Qichao Zhou, Ting Yan, Xiaolong Cheng
Exosomes are emerging mediators of cell-cell communication, which are secreted from cells and may be delivered into recipient cells in cell biological processes. Here, we examined microRNA (miRNA) expression in esophageal squamous cell carcinoma (ESCC) cells. We performed miRNA sequencing in exosomes and cells of KYSE150 and KYSE450 cell lines. Among these differentially expressed miRNAs, 20 of the miRNAs were detected in cells and exosomes. A heat map indicated that the level of miR-451a was higher in exosomes than in ESCC cells...
April 22, 2024: Cancer Gene Therapy
#38
JOURNAL ARTICLE
Yinggui Yang, Tengteng Ding, Ying Cong, Xiaomin Luo, Changlin Liu, Ting Gong, Min Zhao, Xichun Zheng, Chenglin Li, Yuanbin Zhang, Jiayi Zhou, Chuping Ni, Xueyu Zhang, Ziliang Ji, Tao Wu, Shaodong Yang, Qingchun Zhou, Dinglan Wu, Xinqi Gong, Qingyou Zheng, Xin Li
Epstein-Barr virus (EBV) can infect both B cells and epithelial cells (ECs), causing diseases such as mononucleosis and cancer. It enters ECs via Ephrin receptor A2 (EphA2). The function of interferon-induced transmembrane protein-1 (IFITM1) in EBV infection of ECs remains elusive. Here we report that IFITM1 inhibits EphA2-mediated EBV entry into ECs. RNA-sequencing and clinical sample analysis show reduced IFITM1 in EBV-positive ECs and a negative correlation between IFITM1 level and EBV copy number. IFITM1 depletion increases EBV infection and vice versa...
April 22, 2024: Nature Microbiology
#39
JOURNAL ARTICLE
Wen Pan, Chao Liu, Tao Ren, Xiaohong Chen, Cuiting Liang, Jin Wang, Jinlin Yang
A higher incidence of chronic atrophic gastritis (CAG) is generally considered as a precancerous lesion in gastric cancer (GC). The aim of this study was to identify potential molecules involved in the pathogenesis of CAG in the Tibetan plateau, hoping to help the diagnosis and management of the disease. Atrophic and non-atrophic gastric mucosal tissue samples were collected from seven patients with chronic gastritis (CG). Differentially expressed lncRNAs, circRNAs, miRNAs, and mRNAs between CAG and chronic non-atrophic gastritis (CNAG) groups were identified based on DNBSEQ-G99 RNA sequencing...
April 22, 2024: Scientific Reports
#40
JOURNAL ARTICLE
Andreas Roller, Iakov I Davydov, Petra C Schwalie, Martha L Serrano-Serrano, Astrid Heller, Nicolas Staedler, Cláudia S Ferreira, Gabriele Dietmann, Irina Klaman, Alberto Valdeolivas, Konstanty Korski, Michael A Cannarile
BACKGROUND: The immune status of a patient's tumor microenvironment (TME) may guide therapeutic interventions with cancer immunotherapy and help identify potential resistance mechanisms. Currently, patients' immune status is mostly classified based on CD8+tumor-infiltrating lymphocytes. An unmet need exists for comparable and reliable precision immunophenotyping tools that would facilitate clinical treatment-relevant decision-making and the understanding of how to overcome resistance mechanisms...
April 22, 2024: Journal for Immunotherapy of Cancer
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