keyword
https://read.qxmd.com/read/38531851/fast-and-flexible-profiling-of-chromatin-accessibility-and-total-rna-expression-in-single-nuclei-using-microwell-seq3
#21
JOURNAL ARTICLE
Fang Ye, Shuang Zhang, Yuting Fu, Lei Yang, Guodong Zhang, Yijun Wu, Jun Pan, Haide Chen, Xinru Wang, Lifeng Ma, Haofu Niu, Mengmeng Jiang, Tingyue Zhang, Danmei Jia, Jingjing Wang, Yongcheng Wang, Xiaoping Han, Guoji Guo
Single cell chromatin accessibility profiling and transcriptome sequencing are the most widely used technologies for single-cell genomics. Here, we present Microwell-seq3, a high-throughput and facile platform for high-sensitivity single-nucleus chromatin accessibility or full-length transcriptome profiling. The method combines a preindexing strategy and a penetrable chip-in-a-tube for single nucleus loading and DNA amplification and therefore does not require specialized equipment. We used Microwell-seq3 to profile chromatin accessibility in more than 200,000 single nuclei and the full-length transcriptome in ~50,000 nuclei from multiple adult mouse tissues...
March 26, 2024: Cell Discovery
https://read.qxmd.com/read/38531664/poor-clinical-outcomes-and-immunoevasive-contexture-in-cd161-cd8-t-cells-barren-human-pancreatic-cancer
#22
JOURNAL ARTICLE
Qiangda Chen, Hanlin Yin, Zhenlai Jiang, Taochen He, Yuqi Xie, Weilin Mao, Jiande Han, Siyao Liu, Wenhui Lou, Wenchuan Wu, Joseph R Habib, Jun Yu, Liang Liu, Ning Pu
BACKGROUND: The role of CD161 expression on CD8+ T cells in tumor immunology has been explored in a few studies, and the clinical significance of CD161+ CD8+ T cells in pancreatic ductal adenocarcinoma (PDAC) remains unclear. This study seeks to clarify the prognostic value and molecular characteristics linked to CD161+ CD8+ T cell infiltration in PDAC. METHODS: This study included 186 patients with confirmed PDAC histology after radical resection. CD161+ CD8+ T cell infiltration was assessed using immunofluorescence staining on tumor microarrays...
March 26, 2024: Journal for Immunotherapy of Cancer
https://read.qxmd.com/read/38531610/characterisation-of-choroid-plexus-infiltrating-t-cells-reveals-novel-therapeutic-targets-in-murine-neuropsychiatric-lupus
#23
JOURNAL ARTICLE
Erica Moore, Sushma Bharrhan, Deepak A Rao, Fernando Macian, Chaim Putterman
OBJECTIVE: Diffuse central nervous system manifestations, referred to as neuropsychiatric lupus (NPSLE), are observed in 20-40% of lupus patients and involve complex mechanisms that have not yet been adequately elucidated. In murine NPSLE models, choroid plexus (ChP)-infiltrating T cells have not been fully evaluated as drivers of neuropsychiatric disease. METHOD: Droplet-based single-cell transcriptomic analysis (single-cell RNA sequencing) and immune T-cell receptor profiling were performed on ChP tissue from MRL/lpr mice, an NPSLE mouse model, at an 'early' and 'late' disease state, to investigate the infiltrating immune cells that accumulate with NPSLE disease progression...
March 26, 2024: Annals of the Rheumatic Diseases
https://read.qxmd.com/read/38531607/a-roadmap-for-selecting-and-utilizing-optimal-features-in-scrna-sequencing-data-analysis-for-stem-cell-research-a-comprehensive-review
#24
REVIEW
Maath Alani, Hamza Altarturih, Selin Pars, Bahaa Al-Mhanawi, Ernst J Wolvetang, Mohammed R Shaker
Stem cells and the cells they produce are unique because they vary from one cell to another. Traditional methods of studying cells often overlook these differences. However, the development of new technologies for studying individual cells has greatly changed biological research in recent years. Among these innovations, single-cell RNA sequencing (scRNA-seq) stands out. This technique allows scientists to examine the activity of genes in each cell, across thousands or even millions of cells. This makes it possible to understand the diversity of cells, identify new types of cells, and see how cells differ across different tissues, individuals, species, times, and conditions...
March 27, 2024: International Journal of Stem Cells
https://read.qxmd.com/read/38530049/regulatory-t-cells-subgroups-in-the-tumor-microenvironment-cannot-be-overlooked-their-involvement-in-prognosis-and-treatment-strategy-in-melanoma
#25
JOURNAL ARTICLE
Wenyi Huang, Byeong Seop Kim, Yichi Zhang, Li Lin, Gang Chai, Zhijie Zhao
BACKGROUND: Melanoma, the most lethal form of skin cancer, presents substantial challenges despite effective surgical interventions for in situ lesions. Regulatory T cells (Tregs) wield a pivotal immunomodulatory influence within the tumor microenvironment, yet their impact on melanoma prognosis and direct molecular interactions with melanoma cells remain elusive. This investigation employs single-cell analysis to unveil the intricate nature of Tregs in human melanoma. METHODS: Single-cell RNA and bulk sequencing data, alongside clinical information, were obtained from public repositories...
March 26, 2024: Environmental Toxicology
https://read.qxmd.com/read/38529510/hippo-deficient-cardiac-fibroblasts-differentiate-into-osteochondroprogenitors
#26
Chang-Ru Tsai, Jong Kim, Xiao Li, Paulo Czarnewski, Rich Li, Fansen Meng, Mingjie Zheng, Xiaolei Zhao, Jeffrey Steimle, Francisco Grisanti, Jun Wang, Md Abul Hassan Samee, James Martin
Cardiac fibrosis, a common pathophysiology associated with various heart diseases, occurs from the excess deposition of extracellular matrix (ECM) 1 . Cardiac fibroblasts (CFs) are the primary cells that produce, degrade, and remodel ECM during homeostasis and tissue repair 2 . Upon injury, CFs gain plasticity to differentiate into myofibroblasts 3 and adipocyte-like 4,5 and osteoblast-like 6 cells, promoting fibrosis and impairing heart function 7 . How CFs maintain their cell state during homeostasis and adapt plasticity upon injury are not well defined...
September 8, 2023: bioRxiv
https://read.qxmd.com/read/38529320/single-cell-analysis-of-lung-lymphatic-endothelial-cells-and-lymphatic-responses-during-influenza-infection
#27
JOURNAL ARTICLE
Jian Ge, Hongxia Shao, Hongxu Ding, Yuefeng Huang, Xuebing Wu, Jie Sun, Jianwen Que
Tissue lymphatic vessels network plays critical roles in immune surveillance and tissue homeostasis in response to pathogen invasion, but how lymphatic system per se is remolded during infection is less understood. Here, we observed that influenza infection induces a significant increase of lymphatic vessel numbers in the lung, accompanied with extensive proliferation of lymphatic endothelial cells (LECs). Single-cell RNA sequencing illustrated the heterogeneity of LECs, identifying a novel PD-L1+ subpopulation that is present during viral infection but not at steady state...
March 2024: J Respir Biol Transl Med
https://read.qxmd.com/read/38529286/novel-prognostic-biomarker-tbc1d1-is-associated-with-immunotherapy-resistance-in-gliomas
#28
JOURNAL ARTICLE
Daqiang Song, Qian Yang, Liuying Li, Yuxian Wei, Chong Zhang, Huimin Du, Guosheng Ren, Hongzhong Li
BACKGROUND: Glioma, an aggressive brain tumor, poses a challenge in understanding the mechanisms of treatment resistance, despite promising results from immunotherapy. METHODS: We identified genes associated with immunotherapy resistance through an analysis of The Cancer Genome Atlas (TCGA), Chinese Glioma Genome Atlas (CGGA), and Gene Expression Omnibus (GEO) databases. Subsequently, qRT-PCR and western blot analyses were conducted to measure the mRNA and protein levels of TBC1 Domain Family Member 1 (TBC1D1), respectively...
2024: Frontiers in Immunology
https://read.qxmd.com/read/38528587/single-cell-rna-sequencing-reveals-recruitment-of-the-m2-like-ccl8-high-macrophages-in-lewis-lung-carcinoma-bearing-mice-following-hypofractionated-radiotherapy
#29
JOURNAL ARTICLE
Haonan Yang, Zheng Lei, Jiang He, Lu Zhang, Tangmin Lai, Liu Zhou, Nuohan Wang, Zheng Tang, Jiangdong Sui, Yongzhong Wu
BACKGROUND: Tumor-associated macrophages (TAMs) play a pivotal role in reshaping the tumor microenvironment following radiotherapy. The mechanisms underlying this reprogramming process remain to be elucidated. METHODS: Subcutaneous Lewis lung carcinoma (LLC) murine model was treated with hypofrationated radiotherapy (8 Gy × 3F). Single-cell RNA sequencing was utilized to identify subclusters and functions of TAMs. Multiplex assay and enzyme-linked immunosorbent assay (ELISA) were employed to measure serum chemokine levels...
March 25, 2024: Journal of Translational Medicine
https://read.qxmd.com/read/38528532/integrated-analysis-of-disulfidptosis-related-immune-genes-signature-to-boost-the-efficacy-of-prognostic-prediction-in-gastric-cancer
#30
JOURNAL ARTICLE
Jie Li, Tian Yu, Juan Sun, Mingwei Ma, Zicheng Zheng, Yixuan He, Weiming Kang, Xin Ye
BACKGROUND: Gastric cancer (GC) remains a malignant tumor with high morbidity and mortality, accounting for approximately 1,080,000 diagnosed cases and 770,000 deaths worldwide annually. Disulfidptosis, characterized by the stress-induced abnormal accumulation of disulfide, is a recently identified form of programmed cell death. Substantial studies have demonstrated the significant influence of immune clearance on tumor progression. Therefore, we aimed to explore the intrinsic correlations between disulfidptosis and immune-related genes (IRGs) in GC, as well as the potential value of disulfidptosis-related immune genes (DRIGs) as biomarkers...
March 25, 2024: Cancer Cell International
https://read.qxmd.com/read/38528462/single-cell-transcriptional-signature-based-drug-repurposing-and-in-vitro-evaluation-in-colorectal-cancer
#31
JOURNAL ARTICLE
Roohallah Mahdi-Esferizi, Zahra Shiasi, Razieh Heidari, Ali Najafi, Issa Mahmoudi, Fatemeh Elahian, Shahram Tahmasebian
BACKGROUND: The need for intelligent and effective treatment of diseases and the increase in drug design costs have raised drug repurposing as one of the effective strategies in biomedicine. There are various computational methods for drug repurposing, one of which is using transcription signatures, especially single-cell RNA sequencing (scRNA-seq) data, which show us a clear and comprehensive view of the inside of the cell to compare the state of disease and health. METHODS: In this study, we used 91,103 scRNA-seq samples from 29 patients with colorectal cancer (GSE144735 and GSE132465)...
March 25, 2024: BMC Cancer
https://read.qxmd.com/read/38528186/assessing-gpt-4-for-cell-type-annotation-in-single-cell-rna-seq-analysis
#32
JOURNAL ARTICLE
Wenpin Hou, Zhicheng Ji
Here we demonstrate that the large language model GPT-4 can accurately annotate cell types using marker gene information in single-cell RNA sequencing analysis. When evaluated across hundreds of tissue and cell types, GPT-4 generates cell type annotations exhibiting strong concordance with manual annotations. This capability can considerably reduce the effort and expertise required for cell type annotation. Additionally, we have developed an R software package GPTCelltype for GPT-4's automated cell type annotation...
March 25, 2024: Nature Methods
https://read.qxmd.com/read/38528180/pericyte-signaling-via-soluble-guanylate-cyclase-shapes-the-vascular-niche-and-microenvironment-of-tumors
#33
JOURNAL ARTICLE
Jing Zhu, Wu Yang, Jianyun Ma, Hao He, Zhen Liu, Xiaolan Zhu, Xueyang He, Jing He, Zhan Chen, Xiaoliang Jin, Xiaohong Wang, Kaiwen He, Wu Wei, Junhao Hu
Pericytes and endothelial cells (ECs) constitute the fundamental components of blood vessels. While the role of ECs in tumor angiogenesis and the tumor microenvironment is well appreciated, pericyte function in tumors remains underexplored. In this study, we used pericyte-specific deletion of the nitric oxide (NO) receptor, soluble guanylate cyclase (sGC), to investigate via single-cell RNA sequencing how pericytes influence the vascular niche and the tumor microenvironment. Our findings demonstrate that pericyte sGC deletion disrupts EC-pericyte interactions, impairing Notch-mediated intercellular communication and triggering extensive transcriptomic reprogramming in both pericytes and ECs...
March 25, 2024: EMBO Journal
https://read.qxmd.com/read/38528071/transcriptomic-dysregulation-and-autistic-like-behaviors-in-kmt2c-haploinsufficient-mice-rescued-by-an-lsd1-inhibitor
#34
JOURNAL ARTICLE
Takumi Nakamura, Toru Yoshihara, Chiharu Tanegashima, Mitsutaka Kadota, Yuki Kobayashi, Kurara Honda, Mizuho Ishiwata, Junko Ueda, Tomonori Hara, Moe Nakanishi, Toru Takumi, Shigeyoshi Itohara, Shigehiro Kuraku, Masahide Asano, Takaoki Kasahara, Kazuo Nakajima, Takashi Tsuboi, Atsushi Takata, Tadafumi Kato
Recent studies have consistently demonstrated that the regulation of chromatin and gene transcription plays a pivotal role in the pathogenesis of neurodevelopmental disorders. Among many genes involved in these pathways, KMT2C, encoding one of the six known histone H3 lysine 4 (H3K4) methyltransferases in humans and rodents, was identified as a gene whose heterozygous loss-of-function variants are causally associated with autism spectrum disorder (ASD) and the Kleefstra syndrome phenotypic spectrum. However, little is known about how KMT2C haploinsufficiency causes neurodevelopmental deficits and how these conditions can be treated...
March 26, 2024: Molecular Psychiatry
https://read.qxmd.com/read/38528036/single-cell-rna-sequencing-unveils-tumor-heterogeneity-and-immune-microenvironment-between-subungual-and-plantar-melanoma
#35
JOURNAL ARTICLE
Panpan Wang, Yangyang Ma, Yige Zhao, Yong Li, Chenyu Tang, Shiwen Wang, Sha Jin, Jiaqi Wang, Mengyan Zhu, Bo Xie, Ping Wang
Acral melanoma (AM) is a subtype of melanoma with high prevalence in East Asians. AM is characterized by greater aggressiveness and lower survival rates. However, there are still fewer studies on immune mechanisms of AM especially subungual melanoma (SM) versus non-subungual melanoma (NSM). In order to explore tumor heterogeneity and immune microenvironment in different subtypes of AM, we applied single-cell RNA sequencing to 24,789 single cells isolated from the SM and plantar melanoma (PM) patients. Aspects of tumor heterogeneity, melanocytes from PM and SM had significant differences in gene expression, CNV and pathways in which tumor-associated such as NF-kb and Wnt were involved...
March 25, 2024: Scientific Reports
https://read.qxmd.com/read/38527764/inhibition-of-jak-stat-pathway-corrects-salivary-gland-inflammation-and-interferon-driven-immune-activation-in-sj%C3%A3-gren-s-disease
#36
JOURNAL ARTICLE
Sarthak Gupta, Eiko Yamada, Hiroyuki Nakamura, Paola Perez, Thomas Jf Pranzatelli, Kalie Dominick, Shyh-Ing Jang, Mehdi Abed, Daniel Martin, Peter Burbelo, ChangYu Zheng, Ben French, Ilias Alevizos, Zohreh Khavandgar, Margaret Beach, Eileen Pelayo, Brian Walitt, Sarfaraz Hasni, Mariana J Kaplan, Mayank Tandon, Maria Teresa Magone, David E Kleiner, John A Chiorini, Alan Baer, Blake M Warner
OBJECTIVES: Inflammatory cytokines that signal through the Janus kinases-signal transducer and activator of transcription (JAK-STAT) pathway, especially interferons (IFNs), are implicated in Sjögren's disease (SjD). Although inhibition of JAKs is effective in other autoimmune diseases, a systematic investigation of IFN-JAK-STAT signalling and the effect of JAK inhibitor (JAKi) therapy in SjD-affected human tissues has not been fully investigated. METHODS: Human minor salivary glands (MSGs) and peripheral blood mononuclear cells (PBMCs) were investigated using bulk or single-cell (sc) RNA sequencing (RNAseq), immunofluorescence (IF) microscopy and flow cytometry...
March 25, 2024: Annals of the Rheumatic Diseases
https://read.qxmd.com/read/38527061/atf4-slc7a11-gsh-axis-mediates-the-acquisition-of-immunosuppressive-properties-by-activated-cd4-t%C3%A2-cells-in-low-arginine-condition
#37
JOURNAL ARTICLE
Ziqi Zou, Qian Cheng, Jiajie Zhou, Chenyao Guo, Andreas V Hadjinicolaou, Mariolina Salio, Xinghua Liang, Cuiyu Yang, Yue Du, Weiran Yao, Dongrui Wang, Vincenzo Cerundolo, Qingqing Wang, Meng Xia
The tumor microenvironment (TME) is restricted in metabolic nutrients including the semi-essential amino acid arginine. While complete arginine deprivation causes T cell dysfunction, it remains unclear how arginine levels fluctuate in the TME to shape T cell fates. Here, we find that the 20-μM low arginine condition, representing the levels found in the plasma of patients with cancers, confers Treg-like immunosuppressive capacities upon activated T cells. In vivo mouse tumor models and human single-cell RNA-sequencing datasets reveal positive correlations between low arginine condition and intratumoral Treg accumulation...
March 23, 2024: Cell Reports
https://read.qxmd.com/read/38526745/the-crucial-prognostic-signaling-pathways-of-pancreatic-ductal-adenocarcinoma-were-identified-by-single-cell-and-bulk-rna-sequencing-data
#38
JOURNAL ARTICLE
Wenwen Wang, Guo Chen, Wenli Zhang, Xihua Zhang, Manli Huang, Chen Li, Ling Wang, Zifan Lu, Jielai Xia
Pancreatic ductal adenocarcinoma (PDAC) is a malignant tumor with poor prognosis and high mortality. Although a large number of studies have explored its potential prognostic markers using traditional RNA sequencing (RNA-Seq) data, they have not achieved good prediction effect. In order to explore the possible prognostic signaling pathways leading to the difference in prognosis, we identified differentially expressed genes from one scRNA-seq cohort and four GEO cohorts, respectively. Then Cox and Lasso regression analysis showed that 12 genes were independent prognostic factors for PDAC...
March 25, 2024: Human Genetics
https://read.qxmd.com/read/38526709/constructing-a-novel-amino-acid-metabolism-signature-a-new-perspective-on-pheochromocytoma-diagnosis-immune-landscape-and-immunotherapy
#39
JOURNAL ARTICLE
Zechen Yan, Yongkun Luan, Yu Wang, Yilin Ren, Zhiyuan Li, Luyang Zhao, Linnuo Shen, Xiaojie Yang, Tonghu Liu, Yukui Gao, Weibo Sun
Pheochromocytoma/paraganglioma (PGPG) is a rare neuroendocrine tumor. Amino acid metabolism is crucial for energy production, redox balance, and metabolic pathways in tumor cell proliferation. This study aimed to build a risk model using amino acid metabolism-related genes, enhancing PGPG diagnosis and treatment decisions. We analyzed RNA-sequencing data from the PCPG cohort in the GEO dataset as our training set and validated our findings using the TCGA dataset and an additional clinical cohort. WGCNA and LASSO were utilized to identify hub genes and develop risk prediction models...
March 25, 2024: Biochemical Genetics
https://read.qxmd.com/read/38526643/investigation-of-cellular-communication-and-signaling-pathways-in-tumor-microenvironment-for-high-tp53-expressing-osteosarcoma-cells-through-single-cell-rna-sequencing
#40
JOURNAL ARTICLE
Kai Xiong, Yuqi Fang, Boyuan Qiu, Chaotao Chen, Nanchang Huang, Feiyuan Liang, Chuangming Huang, Tiantian Lu, Li Zheng, Jinmin Zhao, Bo Zhu
Osteosarcoma (OS) stands as the most prevalent primary bone cancer in children and adolescents, and its limited treatment options often result in unsatisfactory outcomes, particularly for metastatic cases. The tumor microenvironment (TME) has been recognized as a crucial determinant in OS progression. However, the intercellular dynamics between high TP53-expressing OS cells and neighboring cell types within the TME are yet to be thoroughly understood. In our study, we harnessed the single-cell RNA sequencing (scRNA-seq) technology in combination with the computational tool-Cellchat, aiming to elucidate the intercellular communication networks present within OS...
March 25, 2024: Medical Oncology
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