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Li J, Yu T, Sun J, Ma M, Zheng Z, Kang W, Ye X. Comprehensive integration of single-cell RNA and transcriptome RNA sequencing to establish a pyroptosis-related signature for improving prognostic prediction of gastric cancer. Comput Struct Biotechnol J 2024; 23:990-1004. [PMID: 38404710 PMCID: PMC10884435 DOI: 10.1016/j.csbj.2024.02.002] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/09/2023] [Revised: 02/04/2024] [Accepted: 02/04/2024] [Indexed: 02/27/2024] Open
Abstract
Cell pyroptosis, a Gasdermin-dependent programmed cell death characterized by inflammasome, plays a complex and dynamic role in Gastric cancer (GC), a serious threat to human health. Therefore, the value of pyroptosis-related genes (PRGs) as prognostic biomarkers and therapeutic indicators for patients needs to be exploited in GC. This study integrates single-cell RNA sequencing (scRNA-seq) dataset GSE183904 with GC transcriptome data from the TCGA database, focusing on the expression and distribution of PRGs in GC at the single-cell level. The prognostic signature of PRGs was established by using Cox and LASSO analyses. The differences in long-term prognosis, immune infiltration, mutation profile, CD274 and response to chemotherapeutic drugs between the two groups were analyzed and evaluated. A tissue array was used to verify the expression of six PRGs, CD274, CD163 and FoxP3. C12orf75, VCAN, RGS2, MKNK2, SOCS3 and TNFAIP2 were successfully screened out to establish a signature to potently predict the survival time of GC patients. A webserver (https://pumc.shinyapps.io/GastricCancer/) for prognostic prediction in GC patients was developed based on this signature. High-risk score patients typically had worse prognoses, resistance to classical chemotherapy, and a more immunosuppressive tumor microenvironment. VCAN, TNFAIP2 and SOCS3 were greatly elevated in the GC while RGS2 and MKNK2 were decreased in the tumor samples. Further, VCAN was positively related to the infiltrations of Tregs and M2 TAMs in GC TME and the CD274 in tumor cells. In summary, a potent pyroptosis-related signature was established to accurately forecast the survival time and treatment responsiveness of GC patients.
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Affiliation(s)
| | | | - Juan Sun
- Department of General Surgery, Peking Union Medical College Hospital, Chinese Academy of Medical Sciences & Peking Union Medical College, No.1 Shuaifu Yuan, Dongcheng District, 100730 Beijing, People’s Republic of China
| | - Mingwei Ma
- Department of General Surgery, Peking Union Medical College Hospital, Chinese Academy of Medical Sciences & Peking Union Medical College, No.1 Shuaifu Yuan, Dongcheng District, 100730 Beijing, People’s Republic of China
| | - Zicheng Zheng
- Department of General Surgery, Peking Union Medical College Hospital, Chinese Academy of Medical Sciences & Peking Union Medical College, No.1 Shuaifu Yuan, Dongcheng District, 100730 Beijing, People’s Republic of China
| | - Weiming Kang
- Department of General Surgery, Peking Union Medical College Hospital, Chinese Academy of Medical Sciences & Peking Union Medical College, No.1 Shuaifu Yuan, Dongcheng District, 100730 Beijing, People’s Republic of China
| | - Xin Ye
- Department of General Surgery, Peking Union Medical College Hospital, Chinese Academy of Medical Sciences & Peking Union Medical College, No.1 Shuaifu Yuan, Dongcheng District, 100730 Beijing, People’s Republic of China
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Shen W, Wei W, Wang S, Yang X, Wang R, Tian H. RNA-binding protein AZGP1 inhibits epithelial cell proliferation by regulating the genes of alternative splicing in COPD. Gene 2024; 927:148736. [PMID: 38950687 DOI: 10.1016/j.gene.2024.148736] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/09/2024] [Revised: 05/22/2024] [Accepted: 06/26/2024] [Indexed: 07/03/2024]
Abstract
BACKGROUND Chronic Obstructive Pulmonary Disease (COPD) is characterized by high morbidity, disability, and mortality rates worldwide. RNA-binding proteins (RBPs) might regulate genes involved in oxidative stress and inflammation in COPD patients. Single-cell transcriptome sequencing (scRNA-seq) offers an accurate tool for identifying intercellular heterogeneity and the diversity of immune cells. However, the role of RBPs in the regulation of various cells, especially AT2 cells, remains elusive. MATERIALS AND METHODS A scRNA-seq dataset (GSE173896) and a bulk RNA-seq dataset acquired from airway tissues (GSE124180) were employed for data mining. Next, RNA-seq analysis was performed in both COPD and control patients. Differentially expressed genes (DEGs) were identified using criteria of fold change (FC ≥ 1.5 or ≤ 1.5) and P value ≤ 0.05. Lastly, Gene Ontology (GO), Kyoto Encyclopedia of Genes and Genomes (KEGG), and alternative splicing identification analyses were carried out. RESULTS RBP genes exhibited specific expression patterns across different cell groups and participated in cell proliferation and mitochondrial dysfunction in AT2 cells. As an RBP, AZGP1 expression was upregulated in both the scRNA-seq and RNA-seq datasets. It might potentially be a candidate immune biomarker that regulates COPD progression by modulating AT2 cell proliferation and adhesion by regulating the expression of SAMD5, DNER, DPYSL3, GBP5, GBP3, and KCNJ2. Moreover, AZGP1 regulated alternative splicing events in COPD, particularly DDAH1 and SFRP1, holding significant implications in COPD. CONCLUSION RBP gene AZGP1 inhibits epithelial cell proliferation by regulating genes participating in alternative splicing in COPD.
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Affiliation(s)
- Wen Shen
- General Medicine Department, The Second Affiliated Hospital of Kunming Medical University, China.
| | - Wei Wei
- General Medicine Department, The Second Affiliated Hospital of Kunming Medical University, China
| | - Shukun Wang
- General Medicine Department, The Second Affiliated Hospital of Kunming Medical University, China
| | - Xiaolei Yang
- General Medicine Department, The Second Affiliated Hospital of Kunming Medical University, China
| | - Ruili Wang
- General Medicine Department, The Second Affiliated Hospital of Kunming Medical University, China
| | - Hong Tian
- General Medicine Department, The Second Affiliated Hospital of Kunming Medical University, China
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Kumar V, Bermea KC, Kumar D, Singh A, Verma A, Kaileh M, Sen R, Lakatta EG, Adamo L. RelA-mediated signaling connects adaptation to chronic cardiomyocyte stress with myocardial and systemic inflammation in the ADCY8 model of accelerated aging. GeroScience 2024; 46:4243-4262. [PMID: 38499959 DOI: 10.1007/s11357-024-01121-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/08/2024] [Accepted: 03/01/2024] [Indexed: 03/20/2024] Open
Abstract
Mice with cardiac-specific overexpression of adenylyl cyclase (AC) type 8 (TGAC8) are under a constant state of severe myocardial stress. They have a remarkable ability to adapt to this stress, but they eventually develop accelerated cardiac aging and experience reduced longevity. We have previously demonstrated through bioinformatics that constitutive adenylyl cyclase activation in TGAC8 mice is associated with the activation of inflammation-related signaling pathways. However, the immune response associated with chronic myocardial stress in the TGAC8 mouse remains unexplored. Here we demonstrate that chronic activation of adenylyl cyclase in cardiomyocytes of TGAC8 mice results in activation of cell-autonomous RelA-mediated NF-κB signaling. This is associated with non-cell-autonomous activation of proinflammatory and age-associated signaling in myocardial endothelial cells and myocardial smooth muscle cells, expansion of myocardial immune cells, increase in serum levels of inflammatory cytokines, and changes in the size or composition of lymphoid organs. All these changes precede the appearance of cardiac fibrosis. We provide evidence indicating that RelA activation in cardiomyocytes with chronic activation of adenylyl cyclase is mediated by calcium-protein Kinase A (PKA) signaling. Using a model of chronic cardiomyocyte stress and accelerated aging, we highlight a novel, calcium/PKA/RelA-dependent connection between cardiomyocyte stress, myocardial inflammation, and systemic inflammation. These findings suggest that RelA-mediated signaling in cardiomyocytes might be an adaptive response to stress that, when chronically activated, ultimately contributes to both cardiac and systemic aging.
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Affiliation(s)
- Vikas Kumar
- Laboratory of Cardiovascular Science, Intramural Research Program, National Institute On Aging, National Institutes of Health, 251 Bayview Boulevard, Suite 100, Baltimore, MD, 21224, USA
- Department of Medicine, NYU Grossman School of Medicine, New York, NY, 10016, USA
| | - Kevin Christian Bermea
- Division of Cardiology, Department of Medicine, Johns Hopkins School of Medicine, Ross Research Building - Room 809, 720 Rutland Avenue, Baltimore, MD, 21205, USA
| | - Dhaneshwar Kumar
- Immunoregulation Section, Kidney Diseases Branch, National Institute of Diabetes and Digestive and Kidney Diseases (NIDDK), National Institutes of Health, Bethesda, MD, USA
| | - Amit Singh
- Laboratory of Molecular Biology & Immunology, Intramural Research Program, National Institute On Aging, National Institutes of Health, Baltimore, MD, 21224, USA
| | - Anjali Verma
- Laboratory of Clinical Investigation, Intramural Research Program, National Institute On Aging, National Institutes of Health, Baltimore, MD, 21224, USA
| | - Mary Kaileh
- Laboratory of Molecular Biology & Immunology, Intramural Research Program, National Institute On Aging, National Institutes of Health, Baltimore, MD, 21224, USA
| | - Ranjan Sen
- Laboratory of Molecular Biology & Immunology, Intramural Research Program, National Institute On Aging, National Institutes of Health, Baltimore, MD, 21224, USA
| | - Edward G Lakatta
- Laboratory of Cardiovascular Science, Intramural Research Program, National Institute On Aging, National Institutes of Health, 251 Bayview Boulevard, Suite 100, Baltimore, MD, 21224, USA.
| | - Luigi Adamo
- Division of Cardiology, Department of Medicine, Johns Hopkins School of Medicine, Ross Research Building - Room 809, 720 Rutland Avenue, Baltimore, MD, 21205, USA.
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Kang MW, Lee SK, Jang EJ, Park JG, Seo DH, Han JW, Yoo JS, Kwon JH, Nam SW, Jang JW, Choi JY, Yoon SK, Sung PS. Expansion of effector regulatory T cells in steroid responders of severe alcohol-associated hepatitis. Liver Transpl 2024; 30:877-886. [PMID: 38809243 DOI: 10.1097/lvt.0000000000000378] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 01/09/2024] [Accepted: 04/05/2024] [Indexed: 05/30/2024]
Abstract
While steroid therapy is the preferred treatment for severe alcohol-associated hepatitis, the role of effector regulatory T (eTreg) cells and their association with steroid response and clinical outcomes in these patients remains to be elucidated. We prospectively enrolled 47 consecutive patients with alcohol-associated hepatitis, consisting of severe alcohol-associated hepatitis treated with steroids (n=18; steroid-treated group) and mild alcohol-associated hepatitis (n=29; nontreated group). After isolating peripheral blood mononuclear cells from the patients at enrollment and again 7 days later, the frequency of eTreg cells was examined using flow cytometry. Single-cell RNA sequencing analysis was conducted using paired peripheral blood mononuclear cells. In vitro experiments were also performed to assess phenotype changes and the suppressive function of Treg cells following steroid treatment. The steroid-treated group exhibited significantly higher Model for End-Stage Liver Disease scores than the nontreated group ( p < 0.01). Within the steroid-treated group, the proportion of eTreg cells significantly expanded in the steroid responders (n=13; p = 0.01). Furthermore, a significant positive correlation was observed between the decrease in the Model for End-Stage Liver Disease score and the increase in eTreg cells ( p < 0.05). Single-cell RNA sequencing using paired peripheral blood mononuclear cells (pre-steroid and post-steroid therapy) from a steroid responder revealed gene expression changes in T cells and monocytes, suggesting enhancement of Treg cell function. In vitro results showed an elevation in the proportion of eTreg cells after steroid therapy. In conclusion, our findings suggest that the efficacy of steroid therapy in patients with severe alcohol-associated hepatitis is mediated by an increase in the number of eTreg cells.
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Affiliation(s)
- Min Woo Kang
- Department of Biomedicine & Health Sciences, The Catholic University Liver Research Center, College of Medicine, POSTECH-Catholic Biomedical Engineering Institute, Seoul, Republic of Korea
| | - Soon Kyu Lee
- The Catholic University Liver Research Center, College of Medicine, The Catholic University of Korea, Seoul, Republic of Korea
- Department of Internal Medicine, Division of Gastroenterology and Hepatology, Incheon St. Mary's Hospital, College of Medicine, The Catholic University of Korea, Seoul, Republic of Korea
| | - Eun Ji Jang
- Department of Biomedicine & Health Sciences, The Catholic University Liver Research Center, College of Medicine, POSTECH-Catholic Biomedical Engineering Institute, Seoul, Republic of Korea
| | - Jong Geun Park
- Department of Biomedicine & Health Sciences, The Catholic University Liver Research Center, College of Medicine, POSTECH-Catholic Biomedical Engineering Institute, Seoul, Republic of Korea
| | - Deok Hwa Seo
- Department of Biomedicine & Health Sciences, The Catholic University Liver Research Center, College of Medicine, POSTECH-Catholic Biomedical Engineering Institute, Seoul, Republic of Korea
| | - Ji Won Han
- The Catholic University Liver Research Center, College of Medicine, The Catholic University of Korea, Seoul, Republic of Korea
- Department of Internal Medicine, Division of Gastroenterology and Hepatology, Seoul St. Mary's Hospital, College of Medicine, The Catholic University of Korea, Seoul, Republic of Korea
| | - Jae Sung Yoo
- The Catholic University Liver Research Center, College of Medicine, The Catholic University of Korea, Seoul, Republic of Korea
- Department of Internal Medicine, Division of Gastroenterology and Hepatology, Seoul St. Mary's Hospital, College of Medicine, The Catholic University of Korea, Seoul, Republic of Korea
| | - Jung Hyun Kwon
- The Catholic University Liver Research Center, College of Medicine, The Catholic University of Korea, Seoul, Republic of Korea
- Department of Internal Medicine, Division of Gastroenterology and Hepatology, Incheon St. Mary's Hospital, College of Medicine, The Catholic University of Korea, Seoul, Republic of Korea
| | - Soon Woo Nam
- The Catholic University Liver Research Center, College of Medicine, The Catholic University of Korea, Seoul, Republic of Korea
- Department of Internal Medicine, Division of Gastroenterology and Hepatology, Incheon St. Mary's Hospital, College of Medicine, The Catholic University of Korea, Seoul, Republic of Korea
| | - Jeong Won Jang
- The Catholic University Liver Research Center, College of Medicine, The Catholic University of Korea, Seoul, Republic of Korea
- Department of Internal Medicine, Division of Gastroenterology and Hepatology, Seoul St. Mary's Hospital, College of Medicine, The Catholic University of Korea, Seoul, Republic of Korea
| | - Jong Young Choi
- The Catholic University Liver Research Center, College of Medicine, The Catholic University of Korea, Seoul, Republic of Korea
- Department of Internal Medicine, Division of Gastroenterology and Hepatology, Seoul St. Mary's Hospital, College of Medicine, The Catholic University of Korea, Seoul, Republic of Korea
| | - Seung Kew Yoon
- The Catholic University Liver Research Center, College of Medicine, The Catholic University of Korea, Seoul, Republic of Korea
- Department of Internal Medicine, Division of Gastroenterology and Hepatology, Seoul St. Mary's Hospital, College of Medicine, The Catholic University of Korea, Seoul, Republic of Korea
| | - Pil Soo Sung
- The Catholic University Liver Research Center, College of Medicine, The Catholic University of Korea, Seoul, Republic of Korea
- Department of Internal Medicine, Division of Gastroenterology and Hepatology, Seoul St. Mary's Hospital, College of Medicine, The Catholic University of Korea, Seoul, Republic of Korea
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Song P, Deng H, Liu Y, Zhang M. Integrated bioinformatics analysis and experimental validation reveal the relationship between ALOX5AP and the prognosis and immune microenvironment in glioma. BMC Med Genomics 2024; 17:218. [PMID: 39169376 DOI: 10.1186/s12920-024-01991-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/19/2024] [Accepted: 08/13/2024] [Indexed: 08/23/2024] Open
Abstract
BACKGROUND Treatment of gliomas, the most prevalent primary malignant neoplasm of the central nervous system, is challenging. Arachidonate 5-lipoxygenase activating protein (ALOX5AP) is crucial for converting arachidonic acid into leukotrienes and is associated with poor prognosis in multiple cancers. Nevertheless, its relationship with the prognosis and the immune microenvironment of gliomas remains incompletely understood. METHODS The differential expression of ALOX5AP was evaluated based on public Databases. Kaplan-Meier, multivariate Cox proportional hazards regression analysis, time-dependent receiver operating characteristic, and nomogram were used to estimate the prognostic value of ALOX5AP. The relationship between ALOX5AP and immune infiltration was calculated using ESTIMATE and CIBERSORT algorithms. Relationships between ALOX5AP and human leukocyte antigen molecules, immune checkpoints, tumor mutation burden, TIDE score, and immunophenoscore were calculated to evaluate glioma immunotherapy response. Single gene GSEA and co-expression network-based GO and KEGG enrichment analysis were performed to explore the potential function of ALOX5AP. ALOX5AP expression was verified using multiplex immunofluorescence staining and its prognostic effects were confirmed using a glioma tissue microarray. RESULT ALOX5AP was highly expressed in gliomas, and the expression level was related to World Health Organization (WHO) grade, age, sex, IDH mutation status, 1p19q co-deletion status, MGMTp methylation status, and poor prognosis. Single-cell RNA sequencing showed that ALOX5AP was expressed in macrophages, monocytes, and T cells but not in tumor cells. ALOX5AP expression positively correlated with M2 macrophage infiltration and poor immunotherapy response. Immunofluorescence staining demonstrated that ALOX5AP was upregulated in WHO higher-grade gliomas, localizing to M2 macrophages. Glioma tissue microarray confirmed the adverse effect of ALOX5AP in the prognosis of glioma. CONCLUSION ALOX5AP is highly expressed in M2 macrophages and may act as a potential biomarker for predicting prognosis and immunotherapy response in patients with glioma.
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Affiliation(s)
- Ping Song
- Department of Oncology, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Hubei, Wuhan, 430030, P.R. China
| | - Hui Deng
- Department of Oncology, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Hubei, Wuhan, 430030, P.R. China
| | - Yushu Liu
- Department of Oncology, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Hubei, Wuhan, 430030, P.R. China
| | - Mengxian Zhang
- Department of Oncology, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Hubei, Wuhan, 430030, P.R. China.
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6
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Gulati GS, D'Silva JP, Liu Y, Wang L, Newman AM. Profiling cell identity and tissue architecture with single-cell and spatial transcriptomics. Nat Rev Mol Cell Biol 2024:10.1038/s41580-024-00768-2. [PMID: 39169166 DOI: 10.1038/s41580-024-00768-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 07/16/2024] [Indexed: 08/23/2024]
Abstract
Single-cell transcriptomics has broadened our understanding of cellular diversity and gene expression dynamics in healthy and diseased tissues. Recently, spatial transcriptomics has emerged as a tool to contextualize single cells in multicellular neighbourhoods and to identify spatially recurrent phenotypes, or ecotypes. These technologies have generated vast datasets with targeted-transcriptome and whole-transcriptome profiles of hundreds to millions of cells. Such data have provided new insights into developmental hierarchies, cellular plasticity and diverse tissue microenvironments, and spurred a burst of innovation in computational methods for single-cell analysis. In this Review, we discuss recent advancements, ongoing challenges and prospects in identifying and characterizing cell states and multicellular neighbourhoods. We discuss recent progress in sample processing, data integration, identification of subtle cell states, trajectory modelling, deconvolution and spatial analysis. Furthermore, we discuss the increasing application of deep learning, including foundation models, in analysing single-cell and spatial transcriptomics data. Finally, we discuss recent applications of these tools in the fields of stem cell biology, immunology, and tumour biology, and the future of single-cell and spatial transcriptomics in biological research and its translation to the clinic.
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Affiliation(s)
- Gunsagar S Gulati
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA, USA
| | | | - Yunhe Liu
- Department of Genomic Medicine, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Linghua Wang
- Department of Genomic Medicine, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
- The University of Texas MD Anderson Cancer Center UTHealth Houston Graduate School of Biomedical Sciences, Houston, TX, USA
| | - Aaron M Newman
- Department of Biomedical Data Science, Stanford University, Stanford, CA, USA.
- Institute for Stem Cell Biology and Regenerative Medicine, Stanford University, Stanford, CA, USA.
- Stanford Cancer Institute, Stanford University, Stanford, CA, USA.
- Chan Zuckerberg Biohub - San Francisco, San Francisco, CA, USA.
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7
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Holman DR, Rubin SJS, Ferenc M, Holman EA, Koron AN, Daniel R, Boland BS, Nolan GP, Chang JT, Rogalla S. Automated spatial omics landscape analysis approach reveals novel tissue architectures in ulcerative colitis. Sci Rep 2024; 14:18934. [PMID: 39147769 PMCID: PMC11327370 DOI: 10.1038/s41598-024-68397-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/18/2024] [Accepted: 07/23/2024] [Indexed: 08/17/2024] Open
Abstract
The utility of spatial omics in leveraging cellular interactions in normal and diseased states for precision medicine is hampered by a lack of strategies for matching disease states with spatial heterogeneity-guided cellular annotations. Here we use a spatial context-dependent approach that matches spatial pattern detection to cell annotation. Using this approach in existing datasets from ulcerative colitis patient colonic biopsies, we identified architectural complexities and associated difficult-to-detect rare cell types in ulcerative colitis germinal-center B cell follicles. Our approach deepens our understanding of health and disease pathogenesis, illustrates a strategy for automating nested architecture detection for highly multiplexed spatial biology data, and informs precision diagnosis and therapeutic strategies.
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Affiliation(s)
- Derek R Holman
- Division of Gastroenterology and Hepatology, Department of Medicine, Stanford University, Stanford, CA, USA.
| | - Samuel J S Rubin
- Division of Gastroenterology and Hepatology, Department of Medicine, Stanford University, Stanford, CA, USA
| | - Mariusz Ferenc
- Nalecz Institute of Biocybernetics and Biomedical Engineering, Polish Academy of Sciences, Warsaw, Poland
| | - Elizabeth A Holman
- Division of Gastroenterology and Hepatology, Department of Medicine, Stanford University, Stanford, CA, USA
| | - Alexander N Koron
- Division of Gastroenterology and Hepatology, Department of Medicine, Stanford University, Stanford, CA, USA
| | - Robel Daniel
- Division of Gastroenterology and Hepatology, Department of Medicine, Stanford University, Stanford, CA, USA
| | - Brigid S Boland
- Division of Gastroenterology, Department of Medicine, University of California San Diego, San Diego, CA, USA
| | - Garry P Nolan
- Department of Pathology, Stanford University, Stanford, CA, USA
| | - John T Chang
- Division of Gastroenterology, Department of Medicine, University of California San Diego, San Diego, CA, USA
| | - Stephan Rogalla
- Division of Gastroenterology and Hepatology, Department of Medicine, Stanford University, Stanford, CA, USA.
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8
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Le Bars S, Glaab E. Single-Cell Cortical Transcriptomics Reveals Common and Distinct Changes in Cell-Cell Communication in Alzheimer's and Parkinson's Disease. Mol Neurobiol 2024:10.1007/s12035-024-04419-7. [PMID: 39143450 DOI: 10.1007/s12035-024-04419-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/02/2024] [Accepted: 08/02/2024] [Indexed: 08/16/2024]
Abstract
Alzheimer's disease (AD) and Parkinson's disease (PD) cause significant neuronal loss and severely impair daily living. Despite different clinical manifestations, these disorders share common pathological molecular hallmarks, including mitochondrial dysfunction and synaptic degeneration. A detailed comparison of molecular changes at single-cell resolution in the cortex, as one of the main brain regions affected in both disorders, may reveal common susceptibility factors and disease mechanisms. We performed single-cell transcriptomic analyses of post-mortem cortical tissue from AD and PD subjects and controls to identify common and distinct disease-associated changes in individual genes, cellular pathways, molecular networks, and cell-cell communication events, and to investigate common mechanisms. The results revealed significant disease-specific, shared, and opposing gene expression changes, including cell type-specific signatures for both diseases. Hypoxia signaling and lipid metabolism emerged as significantly modulated cellular processes in both AD and PD, with contrasting expression alterations between the two diseases. Furthermore, both pathway and cell-cell communication analyses highlighted shared significant alterations involving the JAK-STAT signaling pathway, which has been implicated in the inflammatory response in several neurodegenerative disorders. Overall, the analyses revealed common and distinct alterations in gene signatures, pathway activities, and gene regulatory subnetworks in AD and PD. The results provide insights into coordinated changes in pathway activity and cell-cell communication that may guide future diagnostics and therapeutics.
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Affiliation(s)
- Sophie Le Bars
- Biomedical Data Science Group, Luxembourg Centre for Systems Biomedicine (LCSB), University of Luxembourg, Esch-sur-Alzette, Luxembourg
| | - Enrico Glaab
- Biomedical Data Science Group, Luxembourg Centre for Systems Biomedicine (LCSB), University of Luxembourg, Esch-sur-Alzette, Luxembourg.
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Wells AC, Lima-Junior DS, Link VM, Smelkinson M, Krishnamurthy SR, Chi L, Segrist E, Rivera CA, Teijeiro A, Bouladoux N, Belkaid Y. Adaptive immunity to retroelements promotes barrier integrity. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.08.09.606346. [PMID: 39149266 PMCID: PMC11326312 DOI: 10.1101/2024.08.09.606346] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Subscribe] [Scholar Register] [Indexed: 08/17/2024]
Abstract
Maintenance of tissue integrity is a requirement of host survival. This mandate is of prime importance at barrier sites that are constitutively exposed to the environment. Here, we show that exposure of the skin to non-inflammatory xenobiotics promotes tissue repair; more specifically, mild detergent exposure promotes the reactivation of defined retroelements leading to the induction of retroelement-specific CD8 + T cells. These T cell responses are Langerhans cell dependent and establish tissue residency within the skin. Upon injury, retroelement-specific CD8 + T cells significantly accelerate wound repair via IL-17A. Collectively, this work demonstrates that tonic environmental exposures and associated adaptive responses to retroelements can be coopted to preemptively set the tissue for maximal resilience to injury.
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Rodrigues-Amorim D, Bozzelli PL, Kim T, Liu L, Gibson O, Yang CY, Murdock MH, Galiana-Melendez F, Schatz B, Davison A, Islam MR, Shin Park D, Raju RM, Abdurrob F, Nelson AJ, Min Ren J, Yang V, Stokes MP, Tsai LH. Multisensory gamma stimulation mitigates the effects of demyelination induced by cuprizone in male mice. Nat Commun 2024; 15:6744. [PMID: 39112447 PMCID: PMC11306744 DOI: 10.1038/s41467-024-51003-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/02/2023] [Accepted: 07/08/2024] [Indexed: 08/10/2024] Open
Abstract
Demyelination is a common pathological feature in a wide range of diseases, characterized by the loss of myelin sheath and myelin-supporting oligodendrocytes. These losses lead to impaired axonal function, increased vulnerability of axons to damage, and result in significant brain atrophy and neuro-axonal degeneration. Multiple pathomolecular processes contribute to neuroinflammation, oligodendrocyte cell death, and progressive neuronal dysfunction. In this study, we use the cuprizone mouse model of demyelination to investigate long-term non-invasive gamma entrainment using sensory stimulation as a potential therapeutic intervention for promoting myelination and reducing neuroinflammation in male mice. Here, we show that multisensory gamma stimulation mitigates demyelination, promotes oligodendrogenesis, preserves functional integrity and synaptic plasticity, attenuates oligodendrocyte ferroptosis-induced cell death, and reduces brain inflammation. Thus, the protective effects of multisensory gamma stimulation on myelin and anti-neuroinflammatory properties support its potential as a therapeutic approach for demyelinating disorders.
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Grants
- R01 AG069232 NIA NIH HHS
- R01 AT011460 NCCIH NIH HHS
- R01 NS122742 NINDS NIH HHS
- R56 AG069232 NIA NIH HHS
- We would like to acknowledge the following individuals and organizations for their support: Fundacion Bancaria la Caixa, The JPB Foundation, Carol and Gene Ludwig Family Foundation, Lester A. Gimpelson, Eduardo Eurnekian, The Dolby Family, Kathy and Miguel Octavio, the Marc Haas Foundation, Ben Lenail and Laurie Yoler, and NIH RO1 grants AG069232, AT011460 and R01NS122742 to L.-H.T.
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Affiliation(s)
- Daniela Rodrigues-Amorim
- Department of Brain and Cognitive Sciences, Picower Institute for Learning and Memory, Massachusetts Institute of Technology, Cambridge, MA, USA
| | - P Lorenzo Bozzelli
- Department of Brain and Cognitive Sciences, Picower Institute for Learning and Memory, Massachusetts Institute of Technology, Cambridge, MA, USA
| | - TaeHyun Kim
- Department of Brain and Cognitive Sciences, Picower Institute for Learning and Memory, Massachusetts Institute of Technology, Cambridge, MA, USA
| | - Liwang Liu
- Department of Brain and Cognitive Sciences, Picower Institute for Learning and Memory, Massachusetts Institute of Technology, Cambridge, MA, USA
| | | | - Cheng-Yi Yang
- Department of Brain and Cognitive Sciences, Picower Institute for Learning and Memory, Massachusetts Institute of Technology, Cambridge, MA, USA
| | - Mitchell H Murdock
- Department of Brain and Cognitive Sciences, Picower Institute for Learning and Memory, Massachusetts Institute of Technology, Cambridge, MA, USA
| | - Fabiola Galiana-Melendez
- Department of Brain and Cognitive Sciences, Picower Institute for Learning and Memory, Massachusetts Institute of Technology, Cambridge, MA, USA
| | - Brooke Schatz
- Department of Brain and Cognitive Sciences, Picower Institute for Learning and Memory, Massachusetts Institute of Technology, Cambridge, MA, USA
| | - Alexis Davison
- Department of Brain and Cognitive Sciences, Picower Institute for Learning and Memory, Massachusetts Institute of Technology, Cambridge, MA, USA
| | - Md Rezaul Islam
- Department of Brain and Cognitive Sciences, Picower Institute for Learning and Memory, Massachusetts Institute of Technology, Cambridge, MA, USA
| | - Dong Shin Park
- Department of Brain and Cognitive Sciences, Picower Institute for Learning and Memory, Massachusetts Institute of Technology, Cambridge, MA, USA
| | - Ravikiran M Raju
- Department of Brain and Cognitive Sciences, Picower Institute for Learning and Memory, Massachusetts Institute of Technology, Cambridge, MA, USA
- Division of Newborn Medicine, Harvard Medical School, Boston Children's Hospital, Boston, MA, USA
| | - Fatema Abdurrob
- Department of Brain and Cognitive Sciences, Picower Institute for Learning and Memory, Massachusetts Institute of Technology, Cambridge, MA, USA
| | | | - Jian Min Ren
- Cell Signaling Technology, 3 Trask Lane, Danvers, MA, USA
| | - Vicky Yang
- Cell Signaling Technology, 3 Trask Lane, Danvers, MA, USA
| | | | - Li-Huei Tsai
- Department of Brain and Cognitive Sciences, Picower Institute for Learning and Memory, Massachusetts Institute of Technology, Cambridge, MA, USA.
- Broad Institute of Harvard and MIT, Cambridge, MA, USA.
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11
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Cao X, Huang YA, You ZH, Shang X, Hu L, Hu PW, Huang ZA. scPriorGraph: constructing biosemantic cell-cell graphs with prior gene set selection for cell type identification from scRNA-seq data. Genome Biol 2024; 25:207. [PMID: 39103856 DOI: 10.1186/s13059-024-03357-w] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/26/2023] [Accepted: 07/29/2024] [Indexed: 08/07/2024] Open
Abstract
Cell type identification is an indispensable analytical step in single-cell data analyses. To address the high noise stemming from gene expression data, existing computational methods often overlook the biologically meaningful relationships between genes, opting to reduce all genes to a unified data space. We assume that such relationships can aid in characterizing cell type features and improving cell type recognition accuracy. To this end, we introduce scPriorGraph, a dual-channel graph neural network that integrates multi-level gene biosemantics. Experimental results demonstrate that scPriorGraph effectively aggregates feature values of similar cells using high-quality graphs, achieving state-of-the-art performance in cell type identification.
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Affiliation(s)
- Xiyue Cao
- School of Computer Science, Northwestern Polytechnical University, Xi'an, China
| | - Yu-An Huang
- School of Computer Science, Northwestern Polytechnical University, Xi'an, China.
| | - Zhu-Hong You
- School of Computer Science, Northwestern Polytechnical University, Xi'an, China.
| | - Xuequn Shang
- School of Computer Science, Northwestern Polytechnical University, Xi'an, China
| | - Lun Hu
- Xinjiang Technical Institute of Physics and Chemistry, Chinese Academy of Sciences, Ürümqi, China
| | - Peng-Wei Hu
- Xinjiang Technical Institute of Physics and Chemistry, Chinese Academy of Sciences, Ürümqi, China
| | - Zhi-An Huang
- Research Office, City University of Hong Kong (Dongguan), Dongguan, 523000, China
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12
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Wang S, Li H, Liu Y, Pang S, Qiao S, Su J, Wang S, Zhang Y. Connectivity Network Feature Sharing in Single-Cell RNA Sequencing Data Identifies Rare Cells. J Chem Inf Model 2024. [PMID: 39096508 DOI: 10.1021/acs.jcim.4c00796] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 08/05/2024]
Abstract
Single-cell RNA sequencing is a valuable technique for identifying diverse cell subtypes. A key challenge in this process is that the detection of rare cells is often missed by conventional methods due to low abundance and subtle features of these cells. To overcome this, we developed SCLCNF (Local Connectivity Network Feature Sharing in Single-Cell RNA sequencing), a novel approach that identifies rare cells by analyzing features uniquely expressed in these cells. SCLCNF creates a cellular connectivity network, considering how each cell relates to its neighbors. This network helps to pinpoint coexpression patterns unique to rare cells, utilizing a rarity score to confirm their presence. Our method performs better in detecting rare cells than existing techniques, offering enhanced robustness. It has proven to be effective in human gastrula data sets for accurately pinpointing rare cells, and in sepsis data sets where it uncovers previously unidentified rare cell populations.
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Affiliation(s)
- Shudong Wang
- Qingdao Institute of Software, College of Computer Science and Technology, China University of Petroleum (East China), Qingdao 266580, China
| | - Hengxiao Li
- Qingdao Institute of Software, College of Computer Science and Technology, China University of Petroleum (East China), Qingdao 266580, China
| | - Yahui Liu
- College of Science, China University of Petroleum (East China), Qingdao 266580, China
| | - Shanchen Pang
- Qingdao Institute of Software, College of Computer Science and Technology, China University of Petroleum (East China), Qingdao 266580, China
| | - Sibo Qiao
- The College of Software, Tiangong University, Tianjin 300387, China
| | - Jionglong Su
- School of AI and Advanced Computing, XJTLU Entrepreneur College (Taicang), Xi'an Jiaotong-Liverpool University, Suzhou 215123, Jiangsu, China
| | - Shaoqiang Wang
- School of Information and Control Engineering, Qingdao University of Technology, Qingdao 266525, China
| | - Yulin Zhang
- College of Mathematics and Systems Science, Shandong University of Science and Technology, Qingdao 266590, China
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13
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Zhang J, He J, Chen W, Chen G, Wang L, Liu Y, Wang Z, Yang M, Huang G, Yang Y, Ma W, Li Y. Single-cell RNA-binding protein pattern-mediated molecular subtypes depict the hallmarks of the tumor microenvironment in bladder urothelial carcinoma. ONCOLOGIE 2024; 26:657-669. [DOI: 10.1515/oncologie-2024-0071] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 08/21/2024]
Abstract
Abstract
Objectives
Bladder carcinoma (BC) is a common malignancy of the urinary tract. As a new hallmark of cancer for drug therapy, RNA-binding proteins (RBPs) are key regulatory factors in alternative splicing events. This work is to uncover the relationship between BC and RBP in order to find drug targets in BC.
Methods
In this work, data from single-cell RNA-seq GSE1355337, PRJNA662018, and the TCGA-Bladder urothelial carcinoma (BLCA) cohorts are integrated to identify their relationships. A scoring system is constructed according to RBPs gene expression and patients’ survival. A network is constructed to analyze the alternative splicing events and RBP genes.
Results
A scoring system identified 321 RBPs significantly associated with the prognosis of patients. Subsequent typing of these RBP genes in two single-cell datasets demonstrated that most of the RBP genes had variable copy numbers. Three RBP clusters were identified. Using RBP genes as a signature in BC epithelial cells allows for differentiation between different grades of BC samples. The novel RBP genes-based subtype system reflects BC clinical staging. Notably, CellChat analysis revealed that the RBP genes-associated cell subtypes of T cells had extensive interactions with epithelial cells. Further analysis showed that the ligand-receptor pair MIF-CXCR4 mediated the communication between RBP-associated subtypes of BC epithelial cells and T cells.
Conclusions
Taken together, RBP genes are associated with BC progress and offer new indicators for precision medicine in BC.
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Affiliation(s)
- Jun Zhang
- Department of Urology Surgery , Affiliated Hospital of Qinghai University , Xining , Qinghai Province , China
| | - Jiejie He
- Department of Surgical Oncology , Affiliated Hospital of Qinghai University and Affiliated Cancer Hospital of Qinghai University , Xining , Qinghai Province , China
| | - Wen Chen
- Wuhan Ruixing Biotechnology Co. Ltd. , Wuhan , Hubei Province , China
| | - Guojun Chen
- Department of Urology Surgery , Affiliated Hospital of Qinghai University , Xining , Qinghai Province , China
| | - Liang Wang
- Department of Gastrointestinal Oncology , Affiliated Hospital of Qinghai University and Affiliated Cancer Hospital of Qinghai University , Xining , Qinghai Province , China
| | - Yuchan Liu
- Department of Gynecology and Obstetrics , Jingmen Central Hospital , Jingmen , Hubei Province , China
| | - Zhanjin Wang
- Medical College of Qinghai University , Xining , Qinghai Province , China
| | - Ming Yang
- Department of Medical Records and Statistic, Affiliated Hospital of Qinghai University , Xining , Qinghai Province , China
| | - Guoyi Huang
- Wuhan Ruixing Biotechnology Co. Ltd. , Wuhan , Hubei Province , China
| | - Yongli Yang
- Department of Gynecology , Affiliated Hospital of Qinghai University , Xining , Qinghai Province , China
| | - Wei Ma
- Department of Surgery , Affiliated Hospital of Qinghai University , Xining , Qinghai Province , China
| | - Yan Li
- Department of Gynecologic Oncology , Affiliated Hospital of Qinghai University and Affiliated Cancer Hospital of Qinghai University , Xining , Qinghai Province , China
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14
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Hou W, Ji Z. Assessing GPT-4 for cell type annotation in single-cell RNA-seq analysis. Nat Methods 2024; 21:1462-1465. [PMID: 38528186 PMCID: PMC11310073 DOI: 10.1038/s41592-024-02235-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/16/2023] [Accepted: 03/05/2024] [Indexed: 03/27/2024]
Abstract
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.
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Affiliation(s)
- Wenpin Hou
- Department of Biostatistics, Columbia University Mailman School of Public Health, New York City, NY, USA.
| | - Zhicheng Ji
- Department of Biostatistics and Bioinformatics, Duke University School of Medicine, Durham, NC, USA.
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15
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Xu X, Yang X, Tang J, Wu X, He X. Identification of Regulatory RNA-Binding Proteins Associated with Immune Infiltration in Laryngeal Squamous Cell Carcinoma. JOURNAL OF IMMUNOLOGY (BALTIMORE, MD. : 1950) 2024; 213:394-402. [PMID: 38912837 DOI: 10.4049/jimmunol.2300498] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/24/2023] [Accepted: 03/27/2024] [Indexed: 06/25/2024]
Abstract
We analyzed bulk RNA sequencing and single-cell RNA sequencing (scRNA-seq) data to identify alternative splicing (AS) events and regulatory RNA-binding proteins (RBPs) associated with immune infiltration in human laryngeal squamous cell carcinoma (LSCC). Whole-transcriptome sequencing data of 20 human laryngeal cancer and paracancerous tissues were downloaded from the Gene Expression Omnibus public database, using newly published splicing-site usage variation analysis software to obtain highly conserved regulated AS (RAS) events, and scientific reverse convolution algorithm analysis was used to identify significantly different immune cells and perform a correlation analysis between the two. The software package edgeR was used to identify differentially expressed RBPs and the immune infiltration-related LSCC-RAS they may regulate. Finally, we present the expression profiles and survival curves of 117 human laryngeal cancer samples from The Cancer Genome Atlas dataset for the identified RBPs and LSCC-RAS. We also downloaded the gene set enrichment 150321 scRNA-seq data for two human LSCC tissue samples. The RBP expression pattern and the expression of prophase RBP genes were analyzed in different LSCC cell populations. RNA-binding motif protein 47 (RBM47) and filamin A, as well as the RBP-RAS events that were screened in both the fibulin 2 and fibronectin 1 genes, were all significantly associated with the prognosis, and the RBM47 gene was upregulated in myeloid cells. Because the prognosis was significantly associated with two RBP regulators and two LSCC-RAS events, they may be critical regulators of immune cell survival during laryngeal cancer progression, and RBM47 may regulate macrophage-associated AS and affect immunity.
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Affiliation(s)
- Xin Xu
- Department of Otolaryngology, Kunming Medical University, Kunming, China
| | - Xi Yang
- Department of Otolaryngology, Kunming Medical University, Kunming, China
| | - Jv Tang
- The Second Department of Otolaryngology, Head and Neck Surgery, The First Affiliated Hospital of Kunming Medical University, Kunming, China
| | - Xiaoguang Wu
- The Second Department of Otolaryngology, Head and Neck Surgery, The First Affiliated Hospital of Kunming Medical University, Kunming, China
| | - Xiaoguang He
- The Second Department of Otolaryngology, Head and Neck Surgery, The First Affiliated Hospital of Kunming Medical University, Kunming, China
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16
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Choa R, Harris JC, Yang E, Yokoyama Y, Okumura M, Kim M, To J, Lou M, Nelson A, Kambayashi T. Thymic stromal lymphopoietin induces IL-4/IL-13 from T cells to promote sebum secretion and adipose loss. J Allergy Clin Immunol 2024; 154:480-491. [PMID: 38157943 PMCID: PMC11211244 DOI: 10.1016/j.jaci.2023.11.923] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/20/2023] [Revised: 11/03/2023] [Accepted: 11/09/2023] [Indexed: 01/03/2024]
Abstract
BACKGROUND The cytokine TSLP promotes type 2 immune responses and can induce adipose loss by stimulating lipid loss from the skin through sebum secretion by sebaceous glands, which enhances the skin barrier. However, the mechanism by which TSLP upregulates sebaceous gland function is unknown. OBJECTIVES This study investigated the mechanism by which TSLP stimulates sebum secretion and adipose loss. METHODS RNA-sequencing analysis was performed on sebaceous glands isolated by laser capture microdissection and single-cell RNA-sequencing analysis was performed on sorted skin T cells. Sebocyte function was analyzed by histological analysis and sebum secretion in vivo and by measuring lipogenesis and proliferation in vitro. RESULTS This study found that TSLP sequentially stimulated the expression of lipogenesis genes followed by cell death genes in sebaceous glands to induce holocrine secretion of sebum. TSLP did not affect sebaceous gland activity directly. Rather, single-cell RNA-sequencing revealed that TSLP recruited distinct T-cell clusters that produce IL-4 and IL-13, which were necessary for TSLP-induced adipose loss and sebum secretion. Moreover, IL-13 was sufficient to cause sebum secretion and adipose loss in vivo and to induce lipogenesis and proliferation of a human sebocyte cell line in vitro. CONCLUSIONS This study proposes that TSLP stimulates T cells to deliver IL-4 and IL-13 to sebaceous glands, which enhances sebaceous gland function, turnover, and subsequent adipose loss.
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Affiliation(s)
- Ruth Choa
- Department of Pathology and Laboratory Medicine, Perelman School of Medicine, University of Pennsylvania, Philadelphia, Pa
| | - Jordan C Harris
- Department of Pathology and Laboratory Medicine, Perelman School of Medicine, University of Pennsylvania, Philadelphia, Pa
| | - EnJun Yang
- Institute of Molecular and Cell Biology, Agency for Science, Technology, and Research (A∗STAR), Singapore
| | - Yuichi Yokoyama
- Department of Pathology and Laboratory Medicine, Perelman School of Medicine, University of Pennsylvania, Philadelphia, Pa
| | - Mariko Okumura
- Department of Pathology and Laboratory Medicine, Perelman School of Medicine, University of Pennsylvania, Philadelphia, Pa
| | - MinJu Kim
- Department of Pathology and Laboratory Medicine, Perelman School of Medicine, University of Pennsylvania, Philadelphia, Pa
| | - Jerrick To
- Department of Pathology and Laboratory Medicine, Perelman School of Medicine, University of Pennsylvania, Philadelphia, Pa
| | - Meng Lou
- Department of Pathology and Laboratory Medicine, Perelman School of Medicine, University of Pennsylvania, Philadelphia, Pa
| | - Amanda Nelson
- Department of Dermatology, Penn State Milton S. Hershey Medical Center, Hershey, Pa
| | - Taku Kambayashi
- Department of Pathology and Laboratory Medicine, Perelman School of Medicine, University of Pennsylvania, Philadelphia, Pa.
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17
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Kim GD, Lim C, Park J. A practical handbook on single-cell RNA sequencing data quality control and downstream analysis. Mol Cells 2024; 47:100103. [PMID: 39094968 DOI: 10.1016/j.mocell.2024.100103] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/01/2024] [Revised: 07/19/2024] [Accepted: 07/29/2024] [Indexed: 08/04/2024] Open
Abstract
Advancements in single-cell analysis have facilitated high-resolution observation of the transcriptome in individual cells. However, standards for obtaining high-quality cells and data analysis pipelines remain variable. Here, we provide the groundwork for improving the quality of single-cell analysis by delineating guidelines for selecting high-quality cells and considerations throughout the analysis. This review will streamline researchers' access to single-cell analysis and serve as a valuable guide for analysis.
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Affiliation(s)
- Gyeong Dae Kim
- School of Life Sciences, Gwangju Institute of Science and Technology (GIST), Gwangju 61005, Republic of Korea
| | - Chaemin Lim
- School of Life Sciences, Gwangju Institute of Science and Technology (GIST), Gwangju 61005, Republic of Korea
| | - Jihwan Park
- School of Life Sciences, Gwangju Institute of Science and Technology (GIST), Gwangju 61005, Republic of Korea.
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18
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Nath PR, Maclean M, Nagarajan V, Lee JW, Yakin M, Kumar A, Nadali H, Schmidt B, Kaya KD, Kodati S, Young A, Caspi RR, Kuiper JJW, Sen HN. Single-cell profiling identifies a CD8 bright CD244 bright Natural Killer cell subset that reflects disease activity in HLA-A29-positive birdshot chorioretinopathy. Nat Commun 2024; 15:6443. [PMID: 39085199 PMCID: PMC11291632 DOI: 10.1038/s41467-024-50472-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/14/2022] [Accepted: 07/12/2024] [Indexed: 08/02/2024] Open
Abstract
Birdshot chorioretinopathy is an inflammatory eye condition strongly associated with MHC-I allele HLA-A29. The striking association with MHC-I suggests involvement of T cells, whereas natural killer (NK) cell involvement remains largely unstudied. Here we show that HLA-A29-positive birdshot chorioretinopathy patients have a skewed NK cell pool containing expanded CD16 positive NK cells which produce more proinflammatory cytokines. These NK cells contain populations that express CD8A which is involved in MHC-I recognition on target cells, display gene signatures indicative of high cytotoxic activity (GZMB, PRF1 and ISG15), and signaling through NK cell receptor CD244 (SH2D1B). Long-term monitoring of a cohort of birdshot chorioretinopathy patients with active disease identifies a population of CD8bright CD244bright NK cells, which rapidly declines to normal levels upon clinical remission following successful treatment. Collectively, these studies implicate CD8bright CD244bright NK cells in birdshot chorioretinopathy.
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Affiliation(s)
- Pulak R Nath
- Clinical and Translational Immunology Unit, Laboratory of Immunology, NEI, NIH, Bethesda, USA.
- Lentigen Technology Inc., A Miltenyi Biotec Company, 910 Clopper Road, Gaithersburg, MD, 20878, USA.
| | - Mary Maclean
- Clinical and Translational Immunology Unit, Laboratory of Immunology, NEI, NIH, Bethesda, USA
- Translational Immunology Section, Office of Science and Technology, NIAMS, Bethesda, NIH, USA
| | - Vijay Nagarajan
- Clinical and Translational Immunology Unit, Laboratory of Immunology, NEI, NIH, Bethesda, USA
- Immunoregulation Section, Laboratory of Immunology, NEI, NIH, Bethesda, USA
| | - Jung Wha Lee
- Clinical and Translational Immunology Unit, Laboratory of Immunology, NEI, NIH, Bethesda, USA
| | - Mehmet Yakin
- Clinical and Translational Immunology Unit, Laboratory of Immunology, NEI, NIH, Bethesda, USA
| | - Aman Kumar
- Clinical and Translational Immunology Unit, Laboratory of Immunology, NEI, NIH, Bethesda, USA
| | - Hadi Nadali
- Clinical and Translational Immunology Unit, Laboratory of Immunology, NEI, NIH, Bethesda, USA
| | - Brian Schmidt
- NIH Intramural Sequencing Center, NIH, Rockville, USA
| | - Koray D Kaya
- Medical Genetics and Ophthalmic Genomics Unit, NEI, NIH, Bethesda, USA
| | - Shilpa Kodati
- Clinical and Translational Immunology Unit, Laboratory of Immunology, NEI, NIH, Bethesda, USA
| | - Alice Young
- NIH Intramural Sequencing Center, NIH, Rockville, USA
| | - Rachel R Caspi
- Immunoregulation Section, Laboratory of Immunology, NEI, NIH, Bethesda, USA
| | - Jonas J W Kuiper
- Department of Ophthalmology, University Medical Center Utrecht, University of Utrecht, Utrecht, Netherlands.
| | - H Nida Sen
- Clinical and Translational Immunology Unit, Laboratory of Immunology, NEI, NIH, Bethesda, USA
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19
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Roach SN, Shepherd FK, Mickelson CK, Fiege JK, Thielen BK, Pross LM, Sanders AE, Mitchell JS, Robertson M, Fife BT, Langlois RA. Tropism for ciliated cells is the dominant driver of influenza viral burst size in the human airway. Proc Natl Acad Sci U S A 2024; 121:e2320303121. [PMID: 39008691 PMCID: PMC11295045 DOI: 10.1073/pnas.2320303121] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/20/2023] [Accepted: 05/26/2024] [Indexed: 07/17/2024] Open
Abstract
Influenza viruses pose a significant burden on global human health. Influenza has a broad cellular tropism in the airway, but how infection of different epithelial cell types impacts replication kinetics and burden in the airways is not fully understood. Using primary human airway cultures, which recapitulate the diverse epithelial cell landscape of the human airways, we investigated the impact of cell type composition on virus tropism and replication kinetics. Cultures were highly diverse across multiple donors and 30 independent differentiation conditions and supported a range of influenza replication. Although many cell types were susceptible to influenza, ciliated and secretory cells were predominantly infected. Despite the strong tropism preference for secretory and ciliated cells, which consistently make up 75% or more of infected cells, only ciliated cells were associated with increased virus production. Surprisingly, infected secretory cells were associated with overall reduced virus output. The disparate response and contribution to influenza virus production could be due to different pro- and antiviral interferon-stimulated gene signatures between ciliated and secretory populations, which were interrogated with single-cell RNA sequencing. These data highlight the heterogeneous outcomes of influenza virus infections in the complex cellular environment of the human airway and the disparate impacts of infected cell identity on multiround burst size, even among preferentially infected cell types.
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Affiliation(s)
- Shanley N. Roach
- Department of Microbiology and Immunology, University of Minnesota, Minneapolis, MN55455
| | - Frances K. Shepherd
- Department of Microbiology and Immunology, University of Minnesota, Minneapolis, MN55455
| | - Clayton K. Mickelson
- Department of Microbiology and Immunology, University of Minnesota, Minneapolis, MN55455
| | - Jessica K. Fiege
- Department of Microbiology and Immunology, University of Minnesota, Minneapolis, MN55455
| | - Beth K. Thielen
- Division of Pediatric Infectious Diseases and Immunology, Department of Pediatrics, University of Minnesota, Minneapolis, MN55455
| | - Lauren M. Pross
- Department of Microbiology and Immunology, University of Minnesota, Minneapolis, MN55455
| | - Autumn E. Sanders
- Department of Microbiology and Immunology, University of Minnesota, Minneapolis, MN55455
| | - Jason S. Mitchell
- Center for Immunology, University of Minnesota, Minneapolis, MN55455
| | - Mason Robertson
- Department of Microbiology and Immunology, University of Minnesota, Minneapolis, MN55455
| | - Brian T. Fife
- Center for Immunology, University of Minnesota, Minneapolis, MN55455
- Department of Medicine, University of Minnesota, Minneapolis, MN55455
| | - Ryan A. Langlois
- Department of Microbiology and Immunology, University of Minnesota, Minneapolis, MN55455
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20
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Chen L, Wang N, Zhang T, Zhang F, Zhang W, Meng H, Chen J, Liao Z, Xu X, Ma Z, Xu T, Liu H. Directed differentiation of pancreatic δ cells from human pluripotent stem cells. Nat Commun 2024; 15:6344. [PMID: 39068220 PMCID: PMC11283558 DOI: 10.1038/s41467-024-50611-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/23/2022] [Accepted: 07/11/2024] [Indexed: 07/30/2024] Open
Abstract
Dysfunction of pancreatic δ cells contributes to the etiology of diabetes. Despite their important role, human δ cells are scarce, limiting physiological studies and drug discovery targeting δ cells. To date, no directed δ-cell differentiation method has been established. Here, we demonstrate that fibroblast growth factor (FGF) 7 promotes pancreatic endoderm/progenitor differentiation, whereas FGF2 biases cells towards the pancreatic δ-cell lineage via FGF receptor 1. We develop a differentiation method to generate δ cells from human stem cells by combining FGF2 with FGF7, which synergistically directs pancreatic lineage differentiation and modulates the expression of transcription factors and SST activators during endoderm/endocrine precursor induction. These δ cells display mature RNA profiles and fine secretory granules, secrete somatostatin in response to various stimuli, and suppress insulin secretion from in vitro co-cultured β cells and mouse β cells upon transplantation. The generation of human pancreatic δ cells from stem cells in vitro would provide an unprecedented cell source for drug discovery and cell transplantation studies in diabetes.
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Affiliation(s)
- Lihua Chen
- School of Biomedical Engineering, Guangzhou Medical University, Guangzhou, Guangdong, China
- Guangzhou National Laboratory, Guangzhou, Guangdong, China
| | - Nannan Wang
- Guangzhou National Laboratory, Guangzhou, Guangdong, China
- College of Life Science and Technology, Huazhong University of Science and Technology, Wuhan, Hubei, China
| | - Tongran Zhang
- Guangzhou National Laboratory, Guangzhou, Guangdong, China
- Department of Pathophysiology, School of Basic Medicine, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, Hubei, China
| | - Feng Zhang
- Guangzhou National Laboratory, Guangzhou, Guangdong, China
| | - Wei Zhang
- Guangzhou National Laboratory, Guangzhou, Guangdong, China
| | - Hao Meng
- School of Biomedical Engineering, Guangzhou Medical University, Guangzhou, Guangdong, China
- Guangzhou National Laboratory, Guangzhou, Guangdong, China
| | - Jingyi Chen
- Guangzhou National Laboratory, Guangzhou, Guangdong, China
- School of Biomedical Sciences and Engineering, South China University of Technology, Guangzhou International Campus, Guangzhou, Guangdong, China
| | - Zhiying Liao
- School of Biomedical Engineering, Guangzhou Medical University, Guangzhou, Guangdong, China
- Guangzhou National Laboratory, Guangzhou, Guangdong, China
| | - Xiaopeng Xu
- Guangzhou National Laboratory, Guangzhou, Guangdong, China
| | - Zhuo Ma
- National Laboratory of Biomacromolecules, CAS Center for Excellence in Biomacromolecules, Institute of Biophysics, Chinese Academy of Sciences, Beijing, China
| | - Tao Xu
- School of Biomedical Engineering, Guangzhou Medical University, Guangzhou, Guangdong, China.
- Guangzhou National Laboratory, Guangzhou, Guangdong, China.
| | - Huisheng Liu
- School of Biomedical Engineering, Guangzhou Medical University, Guangzhou, Guangdong, China.
- Guangzhou National Laboratory, Guangzhou, Guangdong, China.
- College of Life Science and Technology, Huazhong University of Science and Technology, Wuhan, Hubei, China.
- School of Biomedical Sciences and Engineering, South China University of Technology, Guangzhou International Campus, Guangzhou, Guangdong, China.
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21
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Gan WL, Ren X, Ng VHE, Ng L, Song Y, Tano V, Han J, An O, Xie J, Ng BYL, Tay DJT, Tang SJ, Shen H, Khare S, Chong KHC, Young DY, Wu B, DasGupta R, Chen L. Hepatocyte-macrophage crosstalk via the PGRN-EGFR axis modulates ADAR1-mediated immunity in the liver. Cell Rep 2024; 43:114400. [PMID: 38935501 DOI: 10.1016/j.celrep.2024.114400] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/05/2023] [Revised: 04/23/2024] [Accepted: 06/11/2024] [Indexed: 06/29/2024] Open
Abstract
ADAR1-mediated RNA editing establishes immune tolerance to endogenous double-stranded RNA (dsRNA) by preventing its sensing, primarily by MDA5. Although deleting Ifih1 (encoding MDA5) rescues embryonic lethality in ADAR1-deficient mice, they still experience early postnatal death, and removing other MDA5 signaling proteins does not yield the same rescue. Here, we show that ablation of MDA5 in a liver-specific Adar knockout (KO) murine model fails to rescue hepatic abnormalities caused by ADAR1 loss. Ifih1;Adar double KO (dKO) hepatocytes accumulate endogenous dsRNAs, leading to aberrant transition to a highly inflammatory state and recruitment of macrophages into dKO livers. Mechanistically, progranulin (PGRN) appears to mediate ADAR1 deficiency-induced liver pathology, promoting interferon signaling and attracting epidermal growth factor receptor (EGFR)+ macrophages into dKO liver, exacerbating hepatic inflammation. Notably, the PGRN-EGFR crosstalk communication and consequent immune responses are significantly repressed in ADAR1high tumors, revealing that pre-neoplastic or neoplastic cells can exploit ADAR1-dependent immune tolerance to facilitate immune evasion.
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Affiliation(s)
- Wei Liang Gan
- Cancer Science Institute of Singapore, National University of Singapore, Singapore, Singapore
| | - Xi Ren
- Cancer Science Institute of Singapore, National University of Singapore, Singapore, Singapore
| | - Vanessa Hui En Ng
- Cancer Science Institute of Singapore, National University of Singapore, Singapore, Singapore
| | - Larry Ng
- Cancer Science Institute of Singapore, National University of Singapore, Singapore, Singapore
| | - Yangyang Song
- Cancer Science Institute of Singapore, National University of Singapore, Singapore, Singapore
| | - Vincent Tano
- Cancer Science Institute of Singapore, National University of Singapore, Singapore, Singapore
| | - Jian Han
- Cancer Science Institute of Singapore, National University of Singapore, Singapore, Singapore
| | - Omer An
- Cancer Science Institute of Singapore, National University of Singapore, Singapore, Singapore
| | - Jinghe Xie
- Cancer Science Institute of Singapore, National University of Singapore, Singapore, Singapore; School of Biomedical Sciences and Engineering, Guangzhou International Campus, South China University of Technology, Guangzhou, P.R. China
| | - Bryan Y L Ng
- Cancer Science Institute of Singapore, National University of Singapore, Singapore, Singapore
| | - Daryl Jin Tai Tay
- Cancer Science Institute of Singapore, National University of Singapore, Singapore, Singapore
| | - Sze Jing Tang
- Cancer Science Institute of Singapore, National University of Singapore, Singapore, Singapore
| | - Haoqing Shen
- Cancer Science Institute of Singapore, National University of Singapore, Singapore, Singapore
| | - Shruti Khare
- Genome Institute of Singapore, Agency for Science Technology and Research, 60 Biopolis Street, Genome, #02-01, Singapore, Singapore
| | - Kelvin Han Chung Chong
- School of Biological Sciences, Nanyang Technological University, Singapore, Singapore; NTU Institute of Structural Biology, Nanyang Technological University, Singapore, Singapore
| | - Dan Yock Young
- Cancer Science Institute of Singapore, National University of Singapore, Singapore, Singapore; Division of Gastroenterology and Hepatology, National University Health System, Singapore, Singapore
| | - Bin Wu
- School of Biological Sciences, Nanyang Technological University, Singapore, Singapore; NTU Institute of Structural Biology, Nanyang Technological University, Singapore, Singapore
| | - Ramanuj DasGupta
- Genome Institute of Singapore, Agency for Science Technology and Research, 60 Biopolis Street, Genome, #02-01, Singapore, Singapore
| | - Leilei Chen
- Cancer Science Institute of Singapore, National University of Singapore, Singapore, Singapore; NUS Center for Cancer Research, Yong Loo Lin School of Medicine, National University Singapore, Singapore, Singapore; Department of Anatomy, Yong Loo Lin School of Medicine, National University of Singapore, Singapore, Singapore.
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22
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Sun F, Li H, Sun D, Fu S, Gu L, Shao X, Wang Q, Dong X, Duan B, Xing F, Wu J, Xiao M, Zhao F, Han JDJ, Liu Q, Fan X, Li C, Wang C, Shi T. Single-cell omics: experimental workflow, data analyses and applications. SCIENCE CHINA. LIFE SCIENCES 2024:10.1007/s11427-023-2561-0. [PMID: 39060615 DOI: 10.1007/s11427-023-2561-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/07/2023] [Accepted: 04/18/2024] [Indexed: 07/28/2024]
Abstract
Cells are the fundamental units of biological systems and exhibit unique development trajectories and molecular features. Our exploration of how the genomes orchestrate the formation and maintenance of each cell, and control the cellular phenotypes of various organismsis, is both captivating and intricate. Since the inception of the first single-cell RNA technology, technologies related to single-cell sequencing have experienced rapid advancements in recent years. These technologies have expanded horizontally to include single-cell genome, epigenome, proteome, and metabolome, while vertically, they have progressed to integrate multiple omics data and incorporate additional information such as spatial scRNA-seq and CRISPR screening. Single-cell omics represent a groundbreaking advancement in the biomedical field, offering profound insights into the understanding of complex diseases, including cancers. Here, we comprehensively summarize recent advances in single-cell omics technologies, with a specific focus on the methodology section. This overview aims to guide researchers in selecting appropriate methods for single-cell sequencing and related data analysis.
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Affiliation(s)
- Fengying Sun
- Department of Clinical Laboratory, the Affiliated Wuhu Hospital of East China Normal University (The Second People's Hospital of Wuhu City), Wuhu, 241000, China
| | - Haoyan Li
- Pharmaceutical Informatics Institute, College of Pharmaceutical Sciences, Zhejiang University, Hangzhou, 310058, China
| | - Dongqing Sun
- Key Laboratory of Spine and Spinal Cord Injury Repair and Regeneration (Tongji University), Ministry of Education, Orthopaedic Department, Tongji Hospital, Bioinformatics Department, School of Life Sciences and Technology, Tongji University, Shanghai, 200082, China
- Frontier Science Center for Stem Cells, School of Life Sciences and Technology, Tongji University, Shanghai, 200092, China
| | - Shaliu Fu
- Key Laboratory of Spine and Spinal Cord Injury Repair and Regeneration (Tongji University), Ministry of Education, Orthopaedic Department, Tongji Hospital, Bioinformatics Department, School of Life Sciences and Technology, Tongji University, Shanghai, 200082, China
- Translational Medical Center for Stem Cell Therapy and Institute for Regenerative Medicine, Shanghai East Hospital, Bioinformatics Department, School of Life Sciences and Technology, Tongji University, Shanghai, 200082, China
- Research Institute of Intelligent Computing, Zhejiang Lab, Hangzhou, 311121, China
- Shanghai Research Institute for Intelligent Autonomous Systems, Shanghai, 201210, China
| | - Lei Gu
- Center for Single-cell Omics, School of Public Health, Shanghai Jiao Tong University School of Medicine, Shanghai, 200025, China
| | - Xin Shao
- Pharmaceutical Informatics Institute, College of Pharmaceutical Sciences, Zhejiang University, Hangzhou, 310058, China
- National Key Laboratory of Chinese Medicine Modernization, Innovation Center of Yangtze River Delta, Zhejiang University, Jiaxing, 314103, China
| | - Qinqin Wang
- Center for Single-cell Omics, School of Public Health, Shanghai Jiao Tong University School of Medicine, Shanghai, 200025, China
| | - Xin Dong
- Key Laboratory of Spine and Spinal Cord Injury Repair and Regeneration (Tongji University), Ministry of Education, Orthopaedic Department, Tongji Hospital, Bioinformatics Department, School of Life Sciences and Technology, Tongji University, Shanghai, 200082, China
- Frontier Science Center for Stem Cells, School of Life Sciences and Technology, Tongji University, Shanghai, 200092, China
| | - Bin Duan
- Key Laboratory of Spine and Spinal Cord Injury Repair and Regeneration (Tongji University), Ministry of Education, Orthopaedic Department, Tongji Hospital, Bioinformatics Department, School of Life Sciences and Technology, Tongji University, Shanghai, 200082, China
- Translational Medical Center for Stem Cell Therapy and Institute for Regenerative Medicine, Shanghai East Hospital, Bioinformatics Department, School of Life Sciences and Technology, Tongji University, Shanghai, 200082, China
- Research Institute of Intelligent Computing, Zhejiang Lab, Hangzhou, 311121, China
- Shanghai Research Institute for Intelligent Autonomous Systems, Shanghai, 201210, China
| | - Feiyang Xing
- Key Laboratory of Spine and Spinal Cord Injury Repair and Regeneration (Tongji University), Ministry of Education, Orthopaedic Department, Tongji Hospital, Bioinformatics Department, School of Life Sciences and Technology, Tongji University, Shanghai, 200082, China
- Frontier Science Center for Stem Cells, School of Life Sciences and Technology, Tongji University, Shanghai, 200092, China
| | - Jun Wu
- Center for Bioinformatics and Computational Biology, Shanghai Key Laboratory of Regulatory Biology, the Institute of Biomedical Sciences and School of Life Sciences, East China Normal University, Shanghai, 200241, China
| | - Minmin Xiao
- Department of Clinical Laboratory, the Affiliated Wuhu Hospital of East China Normal University (The Second People's Hospital of Wuhu City), Wuhu, 241000, China.
| | - Fangqing Zhao
- Beijing Institutes of Life Science, Chinese Academy of Sciences, Beijing, 100101, China.
| | - Jing-Dong J Han
- Peking-Tsinghua Center for Life Sciences, Academy for Advanced Interdisciplinary Studies, Center for Quantitative Biology (CQB), Peking University, Beijing, 100871, China.
| | - Qi Liu
- Key Laboratory of Spine and Spinal Cord Injury Repair and Regeneration (Tongji University), Ministry of Education, Orthopaedic Department, Tongji Hospital, Bioinformatics Department, School of Life Sciences and Technology, Tongji University, Shanghai, 200082, China.
- Translational Medical Center for Stem Cell Therapy and Institute for Regenerative Medicine, Shanghai East Hospital, Bioinformatics Department, School of Life Sciences and Technology, Tongji University, Shanghai, 200082, China.
- Research Institute of Intelligent Computing, Zhejiang Lab, Hangzhou, 311121, China.
- Shanghai Research Institute for Intelligent Autonomous Systems, Shanghai, 201210, China.
| | - Xiaohui Fan
- Pharmaceutical Informatics Institute, College of Pharmaceutical Sciences, Zhejiang University, Hangzhou, 310058, China.
- National Key Laboratory of Chinese Medicine Modernization, Innovation Center of Yangtze River Delta, Zhejiang University, Jiaxing, 314103, China.
- Zhejiang Key Laboratory of Precision Diagnosis and Therapy for Major Gynecological Diseases, Women's Hospital, Zhejiang University School of Medicine, Hangzhou, 310006, China.
| | - Chen Li
- Center for Single-cell Omics, School of Public Health, Shanghai Jiao Tong University School of Medicine, Shanghai, 200025, China.
| | - Chenfei Wang
- Key Laboratory of Spine and Spinal Cord Injury Repair and Regeneration (Tongji University), Ministry of Education, Orthopaedic Department, Tongji Hospital, Bioinformatics Department, School of Life Sciences and Technology, Tongji University, Shanghai, 200082, China.
- Frontier Science Center for Stem Cells, School of Life Sciences and Technology, Tongji University, Shanghai, 200092, China.
| | - Tieliu Shi
- Department of Clinical Laboratory, the Affiliated Wuhu Hospital of East China Normal University (The Second People's Hospital of Wuhu City), Wuhu, 241000, China.
- Center for Bioinformatics and Computational Biology, Shanghai Key Laboratory of Regulatory Biology, the Institute of Biomedical Sciences and School of Life Sciences, East China Normal University, Shanghai, 200241, China.
- Key Laboratory of Advanced Theory and Application in Statistics and Data Science-MOE, School of Statistics, East China Normal University, Shanghai, 200062, China.
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23
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Cavazzoni A, Salamon I, Fumarola C, Gallerani G, Laprovitera N, Gelsomino F, Riefolo M, Rihawi K, Porcellini E, Rossi T, Mazzeschi M, Naddeo M, Serravalle S, Broseghini E, Agostinis F, Deas O, Roncarati R, Durante G, Pace I, Lauriola M, Garajova I, Calin GA, Bonafè M, D'Errico A, Petronini PG, Cairo S, Ardizzoni A, Sales G, Ferracin M. Synergic activity of FGFR2 and MEK inhibitors in the treatment of FGFR2-amplified cancers of unknown primary. Mol Ther 2024:S1525-0016(24)00466-0. [PMID: 39033323 DOI: 10.1016/j.ymthe.2024.07.011] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/05/2023] [Revised: 04/30/2024] [Accepted: 07/17/2024] [Indexed: 07/23/2024] Open
Abstract
Patients with cancer of unknown primary (CUP) carry the double burden of an aggressive disease and reduced access to therapies. Experimental models are pivotal for CUP biology investigation and drug testing. We derived two CUP cell lines (CUP#55 and #96) and corresponding patient-derived xenografts (PDXs), from ascites tumor cells. CUP cell lines and PDXs underwent histological, immune-phenotypical, molecular, and genomic characterization confirming the features of the original tumor. The tissue-of-origin prediction was obtained from the tumor microRNA expression profile and confirmed by single-cell transcriptomics. Genomic testing and fluorescence in situ hybridization analysis identified FGFR2 gene amplification in both models, in the form of homogeneously staining region (HSR) in CUP#55 and double minutes in CUP#96. FGFR2 was recognized as the main oncogenic driver and therapeutic target. FGFR2-targeting drug BGJ398 (infigratinib) in combination with the MEK inhibitor trametinib proved to be synergic and exceptionally active, both in vitro and in vivo. The effects of the combined treatment by single-cell gene expression analysis revealed a remarkable plasticity of tumor cells and the greater sensitivity of cells with epithelial phenotype. This study brings personalized therapy closer to CUP patients and provides the rationale for FGFR2 and MEK targeting in metastatic tumors with FGFR2 pathway activation.
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Affiliation(s)
- Andrea Cavazzoni
- Department of Medicine and Surgery, University of Parma, 43126 Parma, Italy
| | - Irene Salamon
- IRCCS, Azienda Ospedaliero-Universitaria di Bologna, 40126 Bologna, Italy
| | - Claudia Fumarola
- Department of Medicine and Surgery, University of Parma, 43126 Parma, Italy
| | - Giulia Gallerani
- Department of Medical and Surgical Sciences (DIMEC), University of Bologna, 40126 Bologna, Italy
| | - Noemi Laprovitera
- IRCCS, Azienda Ospedaliero-Universitaria di Bologna, 40126 Bologna, Italy
| | | | - Mattia Riefolo
- IRCCS, Azienda Ospedaliero-Universitaria di Bologna, 40126 Bologna, Italy; Department of Medical and Surgical Sciences (DIMEC), University of Bologna, 40126 Bologna, Italy
| | - Karim Rihawi
- IRCCS, Azienda Ospedaliero-Universitaria di Bologna, 40126 Bologna, Italy
| | - Elisa Porcellini
- Department of Medical and Surgical Sciences (DIMEC), University of Bologna, 40126 Bologna, Italy
| | - Tania Rossi
- Biosciences Laboratory, IRCCS Istituto Romagnolo per lo Studio dei Tumori (IRST) "Dino Amadori", Meldola 47014, Italy
| | - Martina Mazzeschi
- Department of Medical and Surgical Sciences (DIMEC), University of Bologna, 40126 Bologna, Italy
| | - Maria Naddeo
- IRCCS, Azienda Ospedaliero-Universitaria di Bologna, 40126 Bologna, Italy
| | | | | | | | | | - Roberta Roncarati
- Department of Medical and Surgical Sciences (DIMEC), University of Bologna, 40126 Bologna, Italy; Istituto di Genetica Molecolare "Luigi Luca Cavalli-Sforza" (IGM)- Consiglio Nazionale delle Ricerche (CNR), 40136 Bologna, Italy
| | - Giorgio Durante
- Department of Medical and Surgical Sciences (DIMEC), University of Bologna, 40126 Bologna, Italy
| | - Ilaria Pace
- Department of Medical and Surgical Sciences (DIMEC), University of Bologna, 40126 Bologna, Italy
| | - Mattia Lauriola
- Department of Medical and Surgical Sciences (DIMEC), University of Bologna, 40126 Bologna, Italy
| | - Ingrid Garajova
- Medical Oncology Unit, University Hospital of Parma, 43126 Parma, Italy
| | - George A Calin
- Department of Experimental Therapeutics, The University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA
| | - Massimiliano Bonafè
- IRCCS, Azienda Ospedaliero-Universitaria di Bologna, 40126 Bologna, Italy; Department of Medical and Surgical Sciences (DIMEC), University of Bologna, 40126 Bologna, Italy
| | - Antonia D'Errico
- IRCCS, Azienda Ospedaliero-Universitaria di Bologna, 40126 Bologna, Italy; Department of Medical and Surgical Sciences (DIMEC), University of Bologna, 40126 Bologna, Italy
| | | | | | - Andrea Ardizzoni
- IRCCS, Azienda Ospedaliero-Universitaria di Bologna, 40126 Bologna, Italy; Department of Medical and Surgical Sciences (DIMEC), University of Bologna, 40126 Bologna, Italy
| | - Gabriele Sales
- Department of Biology, University of Padova, 35031 Padua, Italy
| | - Manuela Ferracin
- IRCCS, Azienda Ospedaliero-Universitaria di Bologna, 40126 Bologna, Italy; Department of Medical and Surgical Sciences (DIMEC), University of Bologna, 40126 Bologna, Italy.
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24
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Alsaggaf I, Buchan D, Wan C. Improving cell type identification with Gaussian noise-augmented single-cell RNA-seq contrastive learning. Brief Funct Genomics 2024; 23:441-451. [PMID: 38242863 DOI: 10.1093/bfgp/elad059] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/01/2023] [Revised: 12/14/2023] [Accepted: 12/18/2023] [Indexed: 01/21/2024] Open
Abstract
Cell type identification is an important task for single-cell RNA-sequencing (scRNA-seq) data analysis. Many prediction methods have recently been proposed, but the predictive accuracy of difficult cell type identification tasks is still low. In this work, we proposed a novel Gaussian noise augmentation-based scRNA-seq contrastive learning method (GsRCL) to learn a type of discriminative feature representations for cell type identification tasks. A large-scale computational evaluation suggests that GsRCL successfully outperformed other state-of-the-art predictive methods on difficult cell type identification tasks, while the conventional random genes masking augmentation-based contrastive learning method also improved the accuracy of easy cell type identification tasks in general.
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Affiliation(s)
- Ibrahim Alsaggaf
- School of Computing and Mathematical Sciences, Birkbeck, University of London, Malet Street, WC1E 7HX, London, United Kingdom
| | - Daniel Buchan
- Department of Computer Science, University College London, Gower Street, WC1E 6BT, London, United Kingdom
| | - Cen Wan
- School of Computing and Mathematical Sciences, Birkbeck, University of London, Malet Street, WC1E 7HX, London, United Kingdom
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25
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Burdett NL, Willis MO, Pandey A, Twomey L, Alaei S, Bowtell DDL, Christie EL. Timing of whole genome duplication is associated with tumor-specific MHC-II depletion in serous ovarian cancer. Nat Commun 2024; 15:6069. [PMID: 39025846 PMCID: PMC11258338 DOI: 10.1038/s41467-024-50137-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/08/2023] [Accepted: 07/02/2024] [Indexed: 07/20/2024] Open
Abstract
Whole genome duplication is frequently observed in cancer, and its prevalence in our prior analysis of end-stage, homologous recombination deficient high grade serous ovarian cancer (almost 80% of samples) supports the notion that whole genome duplication provides a fitness advantage under the selection pressure of therapy. Here, we therefore aim to identify potential therapeutic vulnerabilities in primary high grade serous ovarian cancer with whole genome duplication by assessing differentially expressed genes and pathways in 79 samples. We observe that MHC-II expression is lowest in tumors which have acquired whole genome duplication early in tumor evolution, and further demonstrate that reduced MHC-II expression occurs in subsets of tumor cells rather than in canonical antigen-presenting cells. Early whole genome duplication is also associated with worse patient survival outcomes. Our results suggest an association between the timing of whole genome duplication, MHC-II expression and clinical outcome in high grade serous ovarian cancer that warrants further investigation for therapeutic targeting.
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Affiliation(s)
- Nikki L Burdett
- Peter MacCallum Cancer Centre, Melbourne, VIC, 3000, Australia
- Sir Peter MacCallum Department of Oncology, The University of Melbourne, Melbourne, VIC, 3010, Australia
- Box Hill Hospital, Eastern Health, Box Hill, VIC, 3128, Australia
| | | | - Ahwan Pandey
- Peter MacCallum Cancer Centre, Melbourne, VIC, 3000, Australia
| | - Laura Twomey
- Peter MacCallum Cancer Centre, Melbourne, VIC, 3000, Australia
| | - Sara Alaei
- Peter MacCallum Cancer Centre, Melbourne, VIC, 3000, Australia
- Australian Regenerative Medicine Institute, Monash University, Clayton, VIC, 3168, Australia
| | - David D L Bowtell
- Peter MacCallum Cancer Centre, Melbourne, VIC, 3000, Australia
- Sir Peter MacCallum Department of Oncology, The University of Melbourne, Melbourne, VIC, 3010, Australia
| | - Elizabeth L Christie
- Peter MacCallum Cancer Centre, Melbourne, VIC, 3000, Australia.
- Sir Peter MacCallum Department of Oncology, The University of Melbourne, Melbourne, VIC, 3010, Australia.
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26
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Casey-Clyde T, Liu SJ, Serrano JAC, Teng C, Jang YG, Vasudevan HN, Bush JO, Raleigh DR. Eed controls craniofacial osteoblast differentiation and mesenchymal proliferation from the neural crest. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.03.13.584903. [PMID: 38558995 PMCID: PMC10979956 DOI: 10.1101/2024.03.13.584903] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 04/04/2024]
Abstract
The histone methyltransferase Polycomb repressive complex 2 (PRC2) is required for specification of the neural crest, and mis-regulation of neural crest development can cause severe congenital malformations. PRC2 is necessary for neural crest induction, but the embryonic, cellular, and molecular consequences of PRC2 activity after neural crest induction are incompletely understood. Here we show that Eed, a core subunit of PRC2, is required for craniofacial osteoblast differentiation and mesenchymal proliferation after induction of the neural crest. Integrating mouse genetics with single-cell RNA sequencing, our results reveal that conditional knockout of Eed after neural crest cell induction causes severe craniofacial hypoplasia, impaired craniofacial osteogenesis, and attenuated craniofacial mesenchymal cell proliferation that is first evident in post-migratory neural crest cell populations. We show that Eed drives mesenchymal differentiation and proliferation in vivo and in primary craniofacial cell cultures by regulating diverse transcription factor programs that are required for specification of post-migratory neural crest cells. These data enhance understanding of epigenetic mechanisms that underlie craniofacial development, and shed light on the embryonic, cellular, and molecular drivers of rare congenital syndromes in humans.
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Affiliation(s)
- Tim Casey-Clyde
- Department of Radiation Oncology, University of California San Francisco, San Francisco, CA, USA
- Department of Neurosurgery, University of California San Francisco, San Francisco, CA, USA
- Department of Pathology, University of California San Francisco, San Francisco, CA, USA
| | - S John Liu
- Department of Radiation Oncology, University of California San Francisco, San Francisco, CA, USA
- Department of Neurosurgery, University of California San Francisco, San Francisco, CA, USA
- Department of Pathology, University of California San Francisco, San Francisco, CA, USA
| | - Juan Antonio Camara Serrano
- Helen Diller Family Comprehensive Cancer Center, University of California San Francisco, San Francisco, CA, USA
| | - Camilla Teng
- Department of Cell and Tissue Biology, University of California San Francisco, San Francisco, CA, USA
| | - Yoon-Gu Jang
- Department of Cell and Tissue Biology, University of California San Francisco, San Francisco, CA, USA
| | - Harish N Vasudevan
- Department of Radiation Oncology, University of California San Francisco, San Francisco, CA, USA
- Department of Neurosurgery, University of California San Francisco, San Francisco, CA, USA
| | - Jeffrey O Bush
- Department of Cell and Tissue Biology, University of California San Francisco, San Francisco, CA, USA
| | - David R Raleigh
- Department of Radiation Oncology, University of California San Francisco, San Francisco, CA, USA
- Department of Neurosurgery, University of California San Francisco, San Francisco, CA, USA
- Department of Pathology, University of California San Francisco, San Francisco, CA, USA
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27
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Zhang Z, Melzer ME, Arun KM, Sun H, Eriksson CJ, Fabian I, Shaashua S, Kiani K, Oren Y, Goyal Y. Synthetic DNA barcodes identify singlets in scRNA-seq datasets and evaluate doublet algorithms. CELL GENOMICS 2024; 4:100592. [PMID: 38925122 PMCID: PMC11293576 DOI: 10.1016/j.xgen.2024.100592] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/08/2023] [Revised: 03/26/2024] [Accepted: 06/05/2024] [Indexed: 06/28/2024]
Abstract
Single-cell RNA sequencing (scRNA-seq) datasets contain true single cells, or singlets, in addition to cells that coalesce during the protocol, or doublets. Identifying singlets with high fidelity in scRNA-seq is necessary to avoid false negative and false positive discoveries. Although several methodologies have been proposed, they are typically tested on highly heterogeneous datasets and lack a priori knowledge of true singlets. Here, we leveraged datasets with synthetically introduced DNA barcodes for a hitherto unexplored application: to extract ground-truth singlets. We demonstrated the feasibility of our framework, "singletCode," to evaluate existing doublet detection methods across a range of contexts. We also leveraged our ground-truth singlets to train a proof-of-concept machine learning classifier, which outperformed other doublet detection algorithms. Our integrative framework can identify ground-truth singlets and enable robust doublet detection in non-barcoded datasets.
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Affiliation(s)
- Ziyang Zhang
- Department of Cell and Developmental Biology, Feinberg School of Medicine, Northwestern University, Chicago, IL, USA; Center for Synthetic Biology, Northwestern University, Chicago, IL, USA; Robert H. Lurie Comprehensive Cancer Center, Feinberg School of Medicine, Northwestern University, Chicago, IL, USA
| | - Madeline E Melzer
- Department of Cell and Developmental Biology, Feinberg School of Medicine, Northwestern University, Chicago, IL, USA; Center for Synthetic Biology, Northwestern University, Chicago, IL, USA; Robert H. Lurie Comprehensive Cancer Center, Feinberg School of Medicine, Northwestern University, Chicago, IL, USA.
| | - Keerthana M Arun
- Department of Cell and Developmental Biology, Feinberg School of Medicine, Northwestern University, Chicago, IL, USA; Center for Synthetic Biology, Northwestern University, Chicago, IL, USA; Robert H. Lurie Comprehensive Cancer Center, Feinberg School of Medicine, Northwestern University, Chicago, IL, USA
| | - Hanxiao Sun
- Department of Cell and Developmental Biology, Feinberg School of Medicine, Northwestern University, Chicago, IL, USA; Center for Synthetic Biology, Northwestern University, Chicago, IL, USA; Robert H. Lurie Comprehensive Cancer Center, Feinberg School of Medicine, Northwestern University, Chicago, IL, USA
| | - Carl-Johan Eriksson
- Department of Cell and Molecular Biology, Karolinska Institute, Stockholm, Sweden
| | - Itai Fabian
- Department of Human Molecular Genetics & Biochemistry, Faculty of Medicine, Tel Aviv University, Tel Aviv, Israel
| | - Sagi Shaashua
- Department of Human Molecular Genetics & Biochemistry, Faculty of Medicine, Tel Aviv University, Tel Aviv, Israel
| | - Karun Kiani
- Medical Scientist Training Program, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA
| | - Yaara Oren
- Department of Human Molecular Genetics & Biochemistry, Faculty of Medicine, Tel Aviv University, Tel Aviv, Israel
| | - Yogesh Goyal
- Department of Cell and Developmental Biology, Feinberg School of Medicine, Northwestern University, Chicago, IL, USA; Center for Synthetic Biology, Northwestern University, Chicago, IL, USA; Robert H. Lurie Comprehensive Cancer Center, Feinberg School of Medicine, Northwestern University, Chicago, IL, USA; CZ Biohub Chicago, Chicago, IL, USA.
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28
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Verhey TB, Seo H, Gillmor A, Thoppey-Manoharan V, Schriemer D, Morrissy S. mosaicMPI: a framework for modular data integration across cohorts and -omics modalities. Nucleic Acids Res 2024; 52:e53. [PMID: 38813827 PMCID: PMC11229337 DOI: 10.1093/nar/gkae442] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/02/2023] [Revised: 04/26/2024] [Accepted: 05/10/2024] [Indexed: 05/31/2024] Open
Abstract
Advances in molecular profiling have facilitated generation of large multi-modal datasets that can potentially reveal critical axes of biological variation underlying complex diseases. Distilling biological meaning, however, requires computational strategies that can perform mosaic integration across diverse cohorts and datatypes. Here, we present mosaicMPI, a framework for discovery of low to high-resolution molecular programs representing both cell types and states, and integration within and across datasets into a network representing biological themes. Using existing datasets in glioblastoma, we demonstrate that this approach robustly integrates single cell and bulk programs across multiple platforms. Clinical and molecular annotations from cohorts are statistically propagated onto this network of programs, yielding a richly characterized landscape of biological themes. This enables deep understanding of individual tumor samples, systematic exploration of relationships between modalities, and generation of a reference map onto which new datasets can rapidly be mapped. mosaicMPI is available at https://github.com/MorrissyLab/mosaicMPI.
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Affiliation(s)
- Theodore B Verhey
- Department of Biochemistry and Molecular Biology, University of Calgary, Calgary, Alberta, Canada
- Charbonneau Cancer institute, University of Calgary, Calgary, Alberta, Canada
- Alberta Children's Hospital Research Institute, University of Calgary, Calgary, Alberta, Canada
| | - Heewon Seo
- Department of Biochemistry and Molecular Biology, University of Calgary, Calgary, Alberta, Canada
- Charbonneau Cancer institute, University of Calgary, Calgary, Alberta, Canada
| | - Aaron Gillmor
- Department of Biochemistry and Molecular Biology, University of Calgary, Calgary, Alberta, Canada
- Charbonneau Cancer institute, University of Calgary, Calgary, Alberta, Canada
| | - Varsha Thoppey-Manoharan
- Department of Biochemistry and Molecular Biology, University of Calgary, Calgary, Alberta, Canada
- Charbonneau Cancer institute, University of Calgary, Calgary, Alberta, Canada
| | - David Schriemer
- Department of Biochemistry and Molecular Biology, University of Calgary, Calgary, Alberta, Canada
- Charbonneau Cancer institute, University of Calgary, Calgary, Alberta, Canada
| | - Sorana Morrissy
- Department of Biochemistry and Molecular Biology, University of Calgary, Calgary, Alberta, Canada
- Charbonneau Cancer institute, University of Calgary, Calgary, Alberta, Canada
- Alberta Children's Hospital Research Institute, University of Calgary, Calgary, Alberta, Canada
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29
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Deguchi S, Kosugi K, Takeishi N, Watanabe Y, Morimoto S, Negoro R, Yokoi F, Futatsusako H, Nakajima-Koyama M, Iwasaki M, Yamamoto T, Kawaguchi Y, Torisawa YS, Takayama K. Construction of multilayered small intestine-like tissue by reproducing interstitial flow. Cell Stem Cell 2024:S1934-5909(24)00220-0. [PMID: 38996472 DOI: 10.1016/j.stem.2024.06.012] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/30/2023] [Revised: 04/18/2024] [Accepted: 06/18/2024] [Indexed: 07/14/2024]
Abstract
Recent advances have made modeling human small intestines in vitro possible, but it remains a challenge to recapitulate fully their structural and functional characteristics. We suspected interstitial flow within the intestine, powered by circulating blood plasma during embryonic organogenesis, to be a vital factor. We aimed to construct an in vivo-like multilayered small intestinal tissue by incorporating interstitial flow into the system and, in turn, developed the micro-small intestine system by differentiating definitive endoderm and mesoderm cells from human pluripotent stem cells simultaneously on a microfluidic device capable of replicating interstitial flow. This approach enhanced cell maturation and led to the development of a three-dimensional small intestine-like tissue with villi-like epithelium and an aligned mesenchymal layer. Our micro-small intestine system not only overcomes the limitations of conventional intestine models but also offers a unique opportunity to gain insights into the detailed mechanisms underlying intestinal tissue development.
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Affiliation(s)
- Sayaka Deguchi
- Center for iPS Cell Research and Application (CiRA), Kyoto University, Kyoto 606-8507, Japan.
| | - Kaori Kosugi
- Center for iPS Cell Research and Application (CiRA), Kyoto University, Kyoto 606-8507, Japan
| | - Naoki Takeishi
- Faculty of Mechanical Engineering, Kyoto Institute of Technology, Kyoto 606-8585, Japan
| | - Yukio Watanabe
- Center for iPS Cell Research and Application (CiRA), Kyoto University, Kyoto 606-8507, Japan
| | - Shiho Morimoto
- Center for iPS Cell Research and Application (CiRA), Kyoto University, Kyoto 606-8507, Japan
| | - Ryosuke Negoro
- Laboratory of Molecular Pharmacokinetics, College of Pharmaceutical Sciences, Ritsumeikan University, Kusatsu 525-8577, Japan
| | - Fuki Yokoi
- Center for iPS Cell Research and Application (CiRA), Kyoto University, Kyoto 606-8507, Japan; Department of Human Health Sciences, Graduate School of Medicine, Kyoto University, Kyoto 606-8501, Japan
| | - Hiroki Futatsusako
- Center for iPS Cell Research and Application (CiRA), Kyoto University, Kyoto 606-8507, Japan; Department of Human Health Sciences, Graduate School of Medicine, Kyoto University, Kyoto 606-8501, Japan
| | - May Nakajima-Koyama
- Center for iPS Cell Research and Application (CiRA), Kyoto University, Kyoto 606-8507, Japan
| | - Mio Iwasaki
- Center for iPS Cell Research and Application (CiRA), Kyoto University, Kyoto 606-8507, Japan
| | - Takuya Yamamoto
- Center for iPS Cell Research and Application (CiRA), Kyoto University, Kyoto 606-8507, Japan; Institute for the Advanced Study of Human Biology (WPI-ASHBi), Kyoto University, Kyoto 606-8501, Japan; Medical-risk Avoidance based on iPS Cells Team, RIKEN Center for Advanced Intelligence Project (AIP), Kyoto 606-8507, Japan
| | - Yoshiya Kawaguchi
- Center for iPS Cell Research and Application (CiRA), Kyoto University, Kyoto 606-8507, Japan
| | - Yu-Suke Torisawa
- Department of Micro Engineering, Kyoto University, Kyoto 615-8540, Japan
| | - Kazuo Takayama
- Center for iPS Cell Research and Application (CiRA), Kyoto University, Kyoto 606-8507, Japan; AMED-CREST, Japan Agency for Medical Research and Development (AMED), Tokyo 100-0004, Japan.
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30
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Nader K, Tasci M, Ianevski A, Erickson A, Verschuren EW, Aittokallio T, Miihkinen M. ScType enables fast and accurate cell type identification from spatial transcriptomics data. Bioinformatics 2024; 40:btae426. [PMID: 38936341 PMCID: PMC11236089 DOI: 10.1093/bioinformatics/btae426] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/20/2024] [Revised: 06/02/2024] [Accepted: 06/26/2024] [Indexed: 06/29/2024] Open
Abstract
SUMMARY The limited resolution of spatial transcriptomics (ST) assays in the past has led to the development of cell type annotation methods that separate the convolved signal based on available external atlas data. In light of the rapidly increasing resolution of the ST assay technologies, we made available and investigated the performance of a deconvolution-free marker-based cell annotation method called scType. In contrast to existing methods, the spatial application of scType does not require computationally strenuous deconvolution, nor large single-cell reference atlases. We show that scType enables ultra-fast and accurate identification of abundant cell types from ST data, especially when a large enough panel of genes is detected. Examples of such assays are Visium and Slide-seq, which currently offer the best trade-off between high resolution and number of genes detected by the assay for cell type annotation. AVAILABILITY AND IMPLEMENTATION scType source R and python codes for spatial data are openly available in GitHub (https://github.com/kris-nader/sp-type or https://github.com/kris-nader/sc-type-py). Step-by-step tutorials for R and python spatial data analysis can be found in https://github.com/kris-nader/sp-type and https://github.com/kris-nader/sc-type-py/blob/main/spatial_tutorial.md, respectively.
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Affiliation(s)
- Kristen Nader
- Institute for Molecular Medicine Finland (FIMM), HiLIFE, University of Helsinki, Helsinki 00290, Finland
- iCAN Digital Precision Cancer Medicine Flagship, University of Helsinki and Helsinki University Hospital, Helsinki 00290, Finland
| | - Misra Tasci
- School of Medicine, Koç University, Istanbul 34450, Turkey
| | - Aleksandr Ianevski
- Institute for Molecular Medicine Finland (FIMM), HiLIFE, University of Helsinki, Helsinki 00290, Finland
- iCAN Digital Precision Cancer Medicine Flagship, University of Helsinki and Helsinki University Hospital, Helsinki 00290, Finland
| | - Andrew Erickson
- iCAN Digital Precision Cancer Medicine Flagship, University of Helsinki and Helsinki University Hospital, Helsinki 00290, Finland
- Research Program in Systems Oncology, University of Helsinki, Helsinki 00290, Finland
| | - Emmy W Verschuren
- Institute for Molecular Medicine Finland (FIMM), HiLIFE, University of Helsinki, Helsinki 00290, Finland
| | - Tero Aittokallio
- Institute for Molecular Medicine Finland (FIMM), HiLIFE, University of Helsinki, Helsinki 00290, Finland
- iCAN Digital Precision Cancer Medicine Flagship, University of Helsinki and Helsinki University Hospital, Helsinki 00290, Finland
- Institute for Cancer Research, Department of Cancer Genetics, Oslo University Hospital, Oslo 0310, Norway
- Oslo Centre for Biostatistics and Epidemiology (OCBE), Faculty of Medicine, University of Oslo, Oslo 0372, Norway
| | - Mitro Miihkinen
- Institute for Molecular Medicine Finland (FIMM), HiLIFE, University of Helsinki, Helsinki 00290, Finland
- iCAN Digital Precision Cancer Medicine Flagship, University of Helsinki and Helsinki University Hospital, Helsinki 00290, Finland
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31
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Sun H, Han X, Du Z, Chen G, Guo T, Xie F, Gu W, Shi Z. Machine learning for the identification of neoantigen-reactive CD8 + T cells in gastrointestinal cancer using single-cell sequencing. Br J Cancer 2024; 131:387-402. [PMID: 38849478 PMCID: PMC11263575 DOI: 10.1038/s41416-024-02737-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/13/2023] [Revised: 05/18/2024] [Accepted: 05/23/2024] [Indexed: 06/09/2024] Open
Abstract
BACKGROUND It appears that tumour-infiltrating neoantigen-reactive CD8 + T (Neo T) cells are the primary driver of immune responses to gastrointestinal cancer in patients. However, the conventional method is very time-consuming and complex for identifying Neo T cells and their corresponding T cell receptors (TCRs). METHODS By mapping neoantigen-reactive T cells from the single-cell transcriptomes of thousands of tumour-infiltrating lymphocytes, we developed a 26-gene machine learning model for the identification of neoantigen-reactive T cells. RESULTS In both training and validation sets, the model performed admirably. We discovered that the majority of Neo T cells exhibited notable differences in the biological processes of amide-related signal pathways. The analysis of potential cell-to-cell interactions, in conjunction with spatial transcriptomic and multiplex immunohistochemistry data, has revealed that Neo T cells possess potent signalling molecules, including LTA, which can potentially engage with tumour cells within the tumour microenvironment, thereby exerting anti-tumour effects. By sequencing CD8 + T cells in tumour samples of patients undergoing neoadjuvant immunotherapy, we determined that the fraction of Neo T cells was significantly and positively linked with the clinical benefit and overall survival rate of patients. CONCLUSION This method expedites the identification of neoantigen-reactive TCRs and the engineering of neoantigen-reactive T cells for therapy.
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Affiliation(s)
- Hongwei Sun
- Key Laboratory of Laboratory Medicine, Ministry of Education, School of Laboratory Medicine and Life Sciences, Wenzhou Medical University, The First Affiliated Hospital of Wenzhou Medical University, Wenzhou, China
| | - Xiao Han
- KangChen Bio-tech., Ltd, ShangHai, China
| | - Zhengliang Du
- Key Laboratory of Laboratory Medicine, Ministry of Education, School of Laboratory Medicine and Life Sciences, Wenzhou Medical University, The First Affiliated Hospital of Wenzhou Medical University, Wenzhou, China
| | - Geer Chen
- Key Laboratory of Laboratory Medicine, Ministry of Education, School of Laboratory Medicine and Life Sciences, Wenzhou Medical University, The First Affiliated Hospital of Wenzhou Medical University, Wenzhou, China
| | - Tonglei Guo
- Data and Analysis Center for Genetic Diseases, Beijing Chigene Translational Medicine Research Center Co, Ltd, Tongzhou District, Beijing, China
| | - Fei Xie
- Data and Analysis Center for Genetic Diseases, Beijing Chigene Translational Medicine Research Center Co, Ltd, Tongzhou District, Beijing, China
| | - Weiyue Gu
- Data and Analysis Center for Genetic Diseases, Beijing Chigene Translational Medicine Research Center Co, Ltd, Tongzhou District, Beijing, China
- Chineo Medical Technology Co., Ltd, Beijing, 100101, China
| | - Zhiwen Shi
- Key Laboratory of Laboratory Medicine, Ministry of Education, School of Laboratory Medicine and Life Sciences, Wenzhou Medical University, The First Affiliated Hospital of Wenzhou Medical University, Wenzhou, China.
- Data and Analysis Center for Genetic Diseases, Beijing Chigene Translational Medicine Research Center Co, Ltd, Tongzhou District, Beijing, China.
- Chineo Medical Technology Co., Ltd, Beijing, 100101, China.
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32
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Zhang J, Hu G, Lu Y, Ren H, Huang Y, Wen Y, Ji B, Wang D, Wang H, Liu H, Ma N, Zhang L, Pan G, Qu Y, Wang H, Zhang W, Miao Z, Yao H. CTCF mutation at R567 causes developmental disorders via 3D genome rearrangement and abnormal neurodevelopment. Nat Commun 2024; 15:5524. [PMID: 38951485 PMCID: PMC11217373 DOI: 10.1038/s41467-024-49684-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/12/2023] [Accepted: 06/14/2024] [Indexed: 07/03/2024] Open
Abstract
The three-dimensional genome structure organized by CTCF is required for development. Clinically identified mutations in CTCF have been linked to adverse developmental outcomes. Nevertheless, the underlying mechanism remains elusive. In this investigation, we explore the regulatory roles of a clinically relevant R567W point mutation, located within the 11th zinc finger of CTCF, by introducing this mutation into both murine models and human embryonic stem cell-derived cortical organoid models. Mice with homozygous CTCFR567W mutation exhibit growth impediments, resulting in postnatal mortality, and deviations in brain, heart, and lung development at the pathological and single-cell transcriptome levels. This mutation induces premature stem-like cell exhaustion, accelerates the maturation of GABAergic neurons, and disrupts neurodevelopmental and synaptic pathways. Additionally, it specifically hinders CTCF binding to peripheral motifs upstream to the core consensus site, causing alterations in local chromatin structure and gene expression, particularly at the clustered protocadherin locus. Comparative analysis using human cortical organoids mirrors the consequences induced by this mutation. In summary, this study elucidates the influence of the CTCFR567W mutation on human neurodevelopmental disorders, paving the way for potential therapeutic interventions.
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Affiliation(s)
- Jie Zhang
- State Key Laboratory of Respiratory Disease, Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences, Guangzhou, China
- The First Affiliated Hospital of Guangzhou Medical University, Guangzhou, China
| | - Gongcheng Hu
- Department of Basic Research, Guangzhou National Laboratory, Guangzhou, China
| | - Yuli Lu
- State Key Laboratory of Respiratory Disease, Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences, Guangzhou, China
- University of Chinese Academy of Sciences, Beijing, China
| | - Huawei Ren
- College of Veterinary Medicine, Shanxi Agricultural University, Jinzhong, China
| | - Yin Huang
- Department of Basic Research, Guangzhou National Laboratory, Guangzhou, China
| | - Yulin Wen
- State Key Laboratory of Respiratory Disease, Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences, Guangzhou, China
- University of Chinese Academy of Sciences, Beijing, China
| | - Binrui Ji
- State Key Laboratory of Respiratory Disease, Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences, Guangzhou, China
- Division of Life Sciences and Medicine, University of Science and Technology of China, Hefei, China
| | - Diyang Wang
- Key Laboratory of CNS Regeneration (Ministry of Education), Guangdong-Hong Kong-Macau Institute of CNS Regeneration, Jinan University, Guangzhou, China
| | - Haidong Wang
- College of Veterinary Medicine, Shanxi Agricultural University, Jinzhong, China
| | - Huisheng Liu
- Department of Basic Research, Guangzhou National Laboratory, Guangzhou, China
| | - Ning Ma
- Department of Basic Research, Guangzhou National Laboratory, Guangzhou, China
| | - Lingling Zhang
- Institute of Clinical Pharmacology, Key Laboratory of Anti-Inflammatory and Immune Medicine (Ministry of Education), Anhui Medical University, Hefei, China
| | - Guangjin Pan
- State Key Laboratory of Respiratory Disease, Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences, Guangzhou, China
- University of Chinese Academy of Sciences, Beijing, China
| | - Yibo Qu
- Key Laboratory of CNS Regeneration (Ministry of Education), Guangdong-Hong Kong-Macau Institute of CNS Regeneration, Jinan University, Guangzhou, China
| | - Hua Wang
- Institute of Clinical Pharmacology, Key Laboratory of Anti-Inflammatory and Immune Medicine (Ministry of Education), Anhui Medical University, Hefei, China
| | - Wei Zhang
- Department of Basic Research, Guangzhou National Laboratory, Guangzhou, China
| | - Zhichao Miao
- Department of Basic Research, Guangzhou National Laboratory, Guangzhou, China
| | - Hongjie Yao
- State Key Laboratory of Respiratory Disease, Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences, Guangzhou, China.
- The First Affiliated Hospital of Guangzhou Medical University, Guangzhou, China.
- Department of Basic Research, Guangzhou National Laboratory, Guangzhou, China.
- University of Chinese Academy of Sciences, Beijing, China.
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33
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Lovell JP, Duque C, Rousseau S, Bhalodia A, Bermea K, Cohen CD, Adamo L. B cell-mediated antigen presentation promotes adverse cardiac remodeling in chronic heart failure. RESEARCH SQUARE 2024:rs.3.rs-4536350. [PMID: 38978561 PMCID: PMC11230502 DOI: 10.21203/rs.3.rs-4536350/v1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 07/10/2024]
Abstract
Cardiovascular disease remains the leading cause of death worldwide. A primary driver of cardiovascular mortality is ischemic heart failure, a form of cardiac dysfunction that can develop in patients who survive myocardial infarction. Acute cardiac damage triggers robust changes in the spleen with rapid migration of immune cells from the spleen to the heart. Activating this "cardio-splenic" axis contributes to progressive cardiac dysfunction. The cardio-splenic axis has, therefore, been identified as a promising therapeutic target to prevent or treat heart failure. However, our understanding of the precise mechanisms by which specific immune cells contribute to adverse cardiac remodeling within the cardio-splenic axis remains limited. Here, we show that splenic B cells contribute to the development of heart failure via MHC II-mediated antigen presentation. We found that the adoptive transfer of splenic B cells from mice with ischemic heart failure promoted adverse cardiac remodeling and splenic inflammatory changes in naïve recipient mice. Based on single-cell RNA sequencing analysis of splenic B cells from mice with ischemic heart failure, we hypothesized that B cells contributed to adverse cardiac remodeling through antigen presentation by MHC II molecules. This mechanism was confirmed using transgenic mice with B cell-specific MHC II deletion, and by analyzing circulating B cells from humans who experienced myocardial infarction. Our results broaden our understanding of B lymphocyte biology, reshape current models of immune activation in response to myocardial injury, and point towards MHC II-mediated signaling in B cells as a novel and specific therapeutic target in chronic heart failure.
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Affiliation(s)
- Jana P Lovell
- Division of Cardiology, Department of Medicine, Johns Hopkins University School of Medicine, Baltimore, Maryland
| | - Carolina Duque
- Division of Cardiology, Department of Medicine, Johns Hopkins University School of Medicine, Baltimore, Maryland
| | - Sylvie Rousseau
- Division of Cardiology, Department of Medicine, Johns Hopkins University School of Medicine, Baltimore, Maryland
| | - Aashik Bhalodia
- Division of Cardiology, Department of Medicine, Johns Hopkins University School of Medicine, Baltimore, Maryland
| | - Kevin Bermea
- Division of Cardiology, Department of Medicine, Johns Hopkins University School of Medicine, Baltimore, Maryland
| | - Charles D Cohen
- Division of Cardiology, Department of Medicine, Johns Hopkins University School of Medicine, Baltimore, Maryland
| | - Luigi Adamo
- Division of Cardiology, Department of Medicine, Johns Hopkins University School of Medicine, Baltimore, Maryland
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34
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Fei L, Zhang K, Hautaniemi S, Sahu B. Protocol to identify defined reprogramming factor expression using a factor-indexing single-nuclei multiome sequencing approach. STAR Protoc 2024; 5:103148. [PMID: 38909361 PMCID: PMC11250849 DOI: 10.1016/j.xpro.2024.103148] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/04/2024] [Revised: 05/04/2024] [Accepted: 06/03/2024] [Indexed: 06/25/2024] Open
Abstract
Ectopic expression of lineage-specific transcription factors (TFs) of another cell type can induce cell fate reprogramming. However, the heterogeneity of reprogramming cells has been a challenge for data interpretation and model evaluation. Here, we present a protocol to characterize cells expressing defined factors during direct cell reprogramming using a factor-indexing approach based on single-nuclei multiome sequencing (FI-snMultiome-seq). We describe the steps for barcoding TFs, converting human fibroblasts to pancreatic ductal-like cells using defined TFs, and preparing library for FI-snMultiome-seq analysis. For complete details on the use and execution of this protocol, please refer to Fei et al.1.
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Affiliation(s)
- Liangru Fei
- Centre for Molecular Medicine Norway, Faculty of Medicine, University of Oslo, Gaustadelléen 21, 0349 Oslo, Norway
| | - Kaiyang Zhang
- Research Program in Systems Oncology, Research Programs Unit, Faculty of Medicine, University of Helsinki, Haartmaninkatu 8, 00014 Helsinki, Finland
| | - Sampsa Hautaniemi
- Research Program in Systems Oncology, Research Programs Unit, Faculty of Medicine, University of Helsinki, Haartmaninkatu 8, 00014 Helsinki, Finland
| | - Biswajyoti Sahu
- Centre for Molecular Medicine Norway, Faculty of Medicine, University of Oslo, Gaustadelléen 21, 0349 Oslo, Norway; Applied Tumor Genomics Program, Research Programs Unit, Faculty of Medicine, University of Helsinki, Haartmaninkatu 8, 00014 Helsinki, Finland; iCAN Digital Precision Cancer Medicine Flagship, University of Helsinki, Haartmaninkatu 8, 00014 Helsinki, Finland; Department of Cancer Genetics, Institute for Cancer Research, Oslo University Hospital, Oslo, Norway.
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35
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Wang Y, Thistlethwaite W, Tadych A, Ruf-Zamojski F, Bernard DJ, Cappuccio A, Zaslavsky E, Chen X, Sealfon SC, Troyanskaya OG. Automated single-cell omics end-to-end framework with data-driven batch inference. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2023.11.01.564815. [PMID: 37961197 PMCID: PMC10635042 DOI: 10.1101/2023.11.01.564815] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/15/2023]
Abstract
To facilitate single-cell multi-omics analysis and improve reproducibility, we present SPEEDI (Single-cell Pipeline for End to End Data Integration), a fully automated end-to-end framework for batch inference, data integration, and cell type labeling. SPEEDI introduces data-driven batch inference and transforms the often heterogeneous data matrices obtained from different samples into a uniformly annotated and integrated dataset. Without requiring user input, it automatically selects parameters and executes pre-processing, sample integration, and cell type mapping. It can also perform downstream analyses of differential signals between treatment conditions and gene functional modules. SPEEDI's data-driven batch inference method works with widely used integration and cell-typing tools. By developing data-driven batch inference, providing full end-to-end automation, and eliminating parameter selection, SPEEDI improves reproducibility and lowers the barrier to obtaining biological insight from these valuable single-cell datasets. The SPEEDI interactive web application can be accessed at https://speedi.princeton.edu/.
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Affiliation(s)
- Yuan Wang
- Department of Computer Science, Princeton University, Princeton, NJ, USA
- Lewis-Sigler Institute of Integrative Genomics, Princeton University, Princeton, NJ, USA
- These authors contributed equally
| | - William Thistlethwaite
- Lewis-Sigler Institute of Integrative Genomics, Princeton University, Princeton, NJ, USA
- These authors contributed equally
| | - Alicja Tadych
- Lewis-Sigler Institute of Integrative Genomics, Princeton University, Princeton, NJ, USA
| | | | - Daniel J Bernard
- Department of Pharmacology and Therapeutics, McGill University, Montreal, QC, H3G 1Y6, Canada
| | - Antonio Cappuccio
- Department of Neurology, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Elena Zaslavsky
- Department of Neurology, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Xi Chen
- Lewis-Sigler Institute of Integrative Genomics, Princeton University, Princeton, NJ, USA
- Center for Computational Biology, Flatiron Institute, New York, NY, USA
| | - Stuart C. Sealfon
- Department of Neurology, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Olga G. Troyanskaya
- Department of Computer Science, Princeton University, Princeton, NJ, USA
- Lewis-Sigler Institute of Integrative Genomics, Princeton University, Princeton, NJ, USA
- Center for Computational Biology, Flatiron Institute, New York, NY, USA
- Lead contact
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36
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İş Ö, Wang X, Reddy JS, Min Y, Yilmaz E, Bhattarai P, Patel T, Bergman J, Quicksall Z, Heckman MG, Tutor-New FQ, Can Demirdogen B, White L, Koga S, Krause V, Inoue Y, Kanekiyo T, Cosacak MI, Nelson N, Lee AJ, Vardarajan B, Mayeux R, Kouri N, Deniz K, Carnwath T, Oatman SR, Lewis-Tuffin LJ, Nguyen T, Carrasquillo MM, Graff-Radford J, Petersen RC, Jr Jack CR, Kantarci K, Murray ME, Nho K, Saykin AJ, Dickson DW, Kizil C, Allen M, Ertekin-Taner N. Gliovascular transcriptional perturbations in Alzheimer's disease reveal molecular mechanisms of blood brain barrier dysfunction. Nat Commun 2024; 15:4758. [PMID: 38902234 PMCID: PMC11190273 DOI: 10.1038/s41467-024-48926-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/09/2023] [Accepted: 05/17/2024] [Indexed: 06/22/2024] Open
Abstract
To uncover molecular changes underlying blood-brain-barrier dysfunction in Alzheimer's disease, we performed single nucleus RNA sequencing in 24 Alzheimer's disease and control brains and focused on vascular and astrocyte clusters as main cell types of blood-brain-barrier gliovascular-unit. The majority of the vascular transcriptional changes were in pericytes. Of the vascular molecular targets predicted to interact with astrocytic ligands, SMAD3, upregulated in Alzheimer's disease pericytes, has the highest number of ligands including VEGFA, downregulated in Alzheimer's disease astrocytes. We validated these findings with external datasets comprising 4,730 pericyte and 150,664 astrocyte nuclei. Blood SMAD3 levels are associated with Alzheimer's disease-related neuroimaging outcomes. We determined inverse relationships between pericytic SMAD3 and astrocytic VEGFA in human iPSC and zebrafish models. Here, we detect vast transcriptome changes in Alzheimer's disease at the gliovascular-unit, prioritize perturbed pericytic SMAD3-astrocytic VEGFA interactions, and validate these in cross-species models to provide a molecular mechanism of blood-brain-barrier disintegrity in Alzheimer's disease.
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Affiliation(s)
- Özkan İş
- Department of Neuroscience, Mayo Clinic, Jacksonville, FL, USA
| | - Xue Wang
- Department of Quantitative Health Sciences, Mayo Clinic, Jacksonville, FL, USA
| | - Joseph S Reddy
- Department of Quantitative Health Sciences, Mayo Clinic, Jacksonville, FL, USA
| | - Yuhao Min
- Department of Neuroscience, Mayo Clinic, Jacksonville, FL, USA
| | - Elanur Yilmaz
- Department of Neurology, Columbia University Irving Medical Center, New York, NY, USA
- Taub Institute for Research on Alzheimer's Disease and the Aging Brain, Columbia University Irving Medical Center, New York, NY, USA
| | - Prabesh Bhattarai
- Department of Neurology, Columbia University Irving Medical Center, New York, NY, USA
- Taub Institute for Research on Alzheimer's Disease and the Aging Brain, Columbia University Irving Medical Center, New York, NY, USA
| | - Tulsi Patel
- Department of Neuroscience, Mayo Clinic, Jacksonville, FL, USA
| | | | - Zachary Quicksall
- Department of Quantitative Health Sciences, Mayo Clinic, Jacksonville, FL, USA
| | - Michael G Heckman
- Department of Quantitative Health Sciences, Mayo Clinic, Jacksonville, FL, USA
| | | | - Birsen Can Demirdogen
- Department of Neuroscience, Mayo Clinic, Jacksonville, FL, USA
- Department of Biomedical Engineering, TOBB University of Economics and Technology, Ankara, Turkey
| | - Launia White
- Department of Quantitative Health Sciences, Mayo Clinic, Jacksonville, FL, USA
| | - Shunsuke Koga
- Department of Neuroscience, Mayo Clinic, Jacksonville, FL, USA
| | - Vincent Krause
- Department of Neuroscience, Mayo Clinic, Jacksonville, FL, USA
| | - Yasuteru Inoue
- Department of Neuroscience, Mayo Clinic, Jacksonville, FL, USA
| | | | - Mehmet Ilyas Cosacak
- German Center for Neurodegenerative Diseases (DZNE) within Helmholtz Association, Dresden, Germany
| | - Nastasia Nelson
- Department of Neurology, Columbia University Irving Medical Center, New York, NY, USA
- Taub Institute for Research on Alzheimer's Disease and the Aging Brain, Columbia University Irving Medical Center, New York, NY, USA
| | - Annie J Lee
- Department of Neurology, Columbia University Irving Medical Center, New York, NY, USA
- Taub Institute for Research on Alzheimer's Disease and the Aging Brain, Columbia University Irving Medical Center, New York, NY, USA
- The Gertrude H. Sergievsky Center, College of Physicians and Surgeons, Columbia University, New York, NY, USA
| | - Badri Vardarajan
- Department of Neurology, Columbia University Irving Medical Center, New York, NY, USA
- Taub Institute for Research on Alzheimer's Disease and the Aging Brain, Columbia University Irving Medical Center, New York, NY, USA
- The Gertrude H. Sergievsky Center, College of Physicians and Surgeons, Columbia University, New York, NY, USA
| | - Richard Mayeux
- Department of Neurology, Columbia University Irving Medical Center, New York, NY, USA
- Taub Institute for Research on Alzheimer's Disease and the Aging Brain, Columbia University Irving Medical Center, New York, NY, USA
- The Gertrude H. Sergievsky Center, College of Physicians and Surgeons, Columbia University, New York, NY, USA
- Department of Psychiatry, Columbia University Irving Medical Center, New York, NY, USA
- Department of Epidemiology, Mailman School of Public Health, Columbia University, New York, NY, USA
| | - Naomi Kouri
- Department of Neuroscience, Mayo Clinic, Jacksonville, FL, USA
| | - Kaancan Deniz
- Department of Neuroscience, Mayo Clinic, Jacksonville, FL, USA
| | - Troy Carnwath
- Department of Neuroscience, Mayo Clinic, Jacksonville, FL, USA
| | | | - Laura J Lewis-Tuffin
- Mayo Clinic Florida Cytometry and Cell Imaging Laboratory, Mayo Clinic, Jacksonville, FL, USA
| | - Thuy Nguyen
- Department of Neuroscience, Mayo Clinic, Jacksonville, FL, USA
| | | | | | - Ronald C Petersen
- Department of Neurology, Mayo Clinic, Rochester, MN, USA
- Mayo Clinic Alzheimer's Disease Research Center, Rochester, MN, USA
| | | | - Kejal Kantarci
- Mayo Clinic Alzheimer's Disease Research Center, Rochester, MN, USA
| | | | - Kwangsik Nho
- Center for Computational Biology and Bioinformatics, Indiana University School of Medicine, Indianapolis, IN, USA
- Department of Radiology and Imaging Sciences, Indiana University School of Medicine, Indianapolis, IN, USA
- Indiana Alzheimer's Disease Research Center, Indiana University School of Medicine, Indianapolis, IN, USA
| | - Andrew J Saykin
- Department of Radiology and Imaging Sciences, Indiana University School of Medicine, Indianapolis, IN, USA
- Indiana Alzheimer's Disease Research Center, Indiana University School of Medicine, Indianapolis, IN, USA
- Department of Medical and Molecular Genetics, Indiana University School of Medicine, Indianapolis, IN, USA
| | | | - Caghan Kizil
- Department of Neurology, Columbia University Irving Medical Center, New York, NY, USA
- Taub Institute for Research on Alzheimer's Disease and the Aging Brain, Columbia University Irving Medical Center, New York, NY, USA
- The Gertrude H. Sergievsky Center, College of Physicians and Surgeons, Columbia University, New York, NY, USA
| | - Mariet Allen
- Department of Neuroscience, Mayo Clinic, Jacksonville, FL, USA
| | - Nilüfer Ertekin-Taner
- Department of Neuroscience, Mayo Clinic, Jacksonville, FL, USA.
- Department of Neurology, Mayo Clinic, Jacksonville, FL, USA.
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Wei HT, Xie LY, Liu YG, Deng Y, Chen F, Lv F, Tang LP, Hu BL. Elucidating the role of angiogenesis-related genes in colorectal cancer: a multi-omics analysis. Front Oncol 2024; 14:1413273. [PMID: 38962272 PMCID: PMC11220232 DOI: 10.3389/fonc.2024.1413273] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/18/2024] [Accepted: 05/31/2024] [Indexed: 07/05/2024] Open
Abstract
Background Angiogenesis plays a pivotal role in colorectal cancer (CRC), yet its underlying mechanisms demand further exploration. This study aimed to elucidate the significance of angiogenesis-related genes (ARGs) in CRC through comprehensive multi-omics analysis. Methods CRC patients were categorized according to ARGs expression to form angiogenesis-related clusters (ARCs). We investigated the correlation between ARCs and patient survival, clinical features, consensus molecular subtypes (CMS), cancer stem cell (CSC) index, tumor microenvironment (TME), gene mutations, and response to immunotherapy. Utilizing three machine learning algorithms (LASSO, Xgboost, and Decision Tree), we screen key ARGs associated with ARCs, further validated in independent cohorts. A prognostic signature based on key ARGs was developed and analyzed at the scRNA-seq level. Validation of gene expression in external cohorts, clinical tissues, and blood samples was conducted via RT-PCR assay. Results Two distinct ARC subtypes were identified and were significantly associated with patient survival, clinical features, CMS, CSC index, and TME, but not with gene mutations. Four genes (S100A4, COL3A1, TIMP1, and APP) were identified as key ARCs, capable of distinguishing ARC subtypes. The prognostic signature based on these genes effectively stratified patients into high- or low-risk categories. scRNA-seq analysis showed that these genes were predominantly expressed in immune cells rather than in cancer cells. Validation in two external cohorts and through clinical samples confirmed significant expression differences between CRC and controls. Conclusion This study identified two ARG subtypes in CRC and highlighted four key genes associated with these subtypes, offering new insights into personalized CRC treatment strategies.
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Affiliation(s)
- Hao-tang Wei
- Department of Gastrointestinal Surgery, Third Affiliated Hospital of Guangxi Medical University, Nanning, China
| | - Li-ye Xie
- Department of Research, Guangxi Medical University Cancer Hospital, Nanning, China
| | - Yong-gang Liu
- Department of Gastrointestinal Surgery, Third Affiliated Hospital of Guangxi Medical University, Nanning, China
| | - Ya Deng
- Department of Gastrointestinal Surgery, Third Affiliated Hospital of Guangxi Medical University, Nanning, China
| | - Feng Chen
- Department of Gastrointestinal Surgery, Third Affiliated Hospital of Guangxi Medical University, Nanning, China
| | - Feng Lv
- Department of Research, Guangxi Medical University Cancer Hospital, Nanning, China
| | - Li-ping Tang
- Department of Information, Library of Guangxi Medical University, Nanning, China
| | - Bang-li Hu
- Department of Research, Guangxi Medical University Cancer Hospital, Nanning, China
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38
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Nirgude S, Tichy ED, Liu Z, Pradieu RD, Byrne M, Gil De Gomez L, Mamou B, Bernt KM, Yang W, MacFarland S, Xie M, Kalish JM. Single-nucleus multiomic analysis of Beckwith-Wiedemann syndrome liver reveals PPARA signaling enrichment and metabolic dysfunction. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.06.14.599077. [PMID: 38948745 PMCID: PMC11212859 DOI: 10.1101/2024.06.14.599077] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 07/02/2024]
Abstract
Beckwith-Wiedemann Syndrome (BWS) is an epigenetic overgrowth syndrome caused by methylation changes in the human 11p15 chromosomal locus. Patients with BWS exhibit tissue overgrowth, as well as an increased risk of childhood neoplasms in the liver and kidney. To understand the impact of these 11p15 changes, specifically in the liver, we performed single-nucleus RNA sequencing (snRNA-seq) and single-nucleus assay for transposase-accessible chromatin with sequencing (snATAC-seq) to generate paired, cell-type-specific transcriptional and chromatin accessibility profiles of both BWS-liver and nonBWS-liver nontumorous tissue. Our integrated RNA+ATACseq multiomic approach uncovered hepatocyte-specific enrichment and activation of the peroxisome proliferator-activated receptor α (PPARA) - a liver metabolic regulator. To confirm our findings, we utilized a BWS-induced pluripotent stem cell (iPSC) model, where cells were differentiated into hepatocytes. Our data demonstrates the dysregulation of lipid metabolism in BWS-liver, which coincided with observed upregulation of PPARA during hepatocyte differentiation. BWS liver cells exhibited decreased neutral lipids and increased fatty acid β-oxidation, relative to controls. We also observed increased reactive oxygen species (ROS) byproducts in the form of peroxidated lipids in BWS hepatocytes, which coincided with increased oxidative DNA damage. This study proposes a putative mechanism for overgrowth and cancer predisposition in BWS liver due to perturbed metabolism.
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39
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Wang X, Menezes CJ, Jia Y, Xiao Y, Venigalla SSK, Cai F, Hsieh MH, Gu W, Du L, Sudderth J, Kim D, Shelton SD, Llamas CB, Lin YH, Zhu M, Merchant S, Bezwada D, Kelekar S, Zacharias LG, Mathews TP, Hoxhaj G, Wynn RM, Tambar UK, DeBerardinis RJ, Zhu H, Mishra P. Metabolic inflexibility promotes mitochondrial health during liver regeneration. Science 2024; 384:eadj4301. [PMID: 38870309 PMCID: PMC11232486 DOI: 10.1126/science.adj4301] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/28/2023] [Accepted: 04/17/2024] [Indexed: 06/15/2024]
Abstract
Mitochondria are critical for proper organ function and mechanisms to promote mitochondrial health during regeneration would benefit tissue homeostasis. We report that during liver regeneration, proliferation is suppressed in electron transport chain (ETC)-dysfunctional hepatocytes due to an inability to generate acetyl-CoA from peripheral fatty acids through mitochondrial β-oxidation. Alternative modes for acetyl-CoA production from pyruvate or acetate are suppressed in the setting of ETC dysfunction. This metabolic inflexibility forces a dependence on ETC-functional mitochondria and restoring acetyl-CoA production from pyruvate is sufficient to allow ETC-dysfunctional hepatocytes to proliferate. We propose that metabolic inflexibility within hepatocytes can be advantageous by limiting the expansion of ETC-dysfunctional cells.
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Affiliation(s)
- Xun Wang
- Children's Research Institute, University of Texas Southwestern Medical Center, Dallas, TX 75390, USA
| | - Cameron J Menezes
- Children's Research Institute, University of Texas Southwestern Medical Center, Dallas, TX 75390, USA
| | - Yuemeng Jia
- Children's Research Institute, University of Texas Southwestern Medical Center, Dallas, TX 75390, USA
| | - Yi Xiao
- Children's Research Institute, University of Texas Southwestern Medical Center, Dallas, TX 75390, USA
| | | | - Feng Cai
- Children's Research Institute, University of Texas Southwestern Medical Center, Dallas, TX 75390, USA
| | - Meng-Hsiung Hsieh
- Children's Research Institute, University of Texas Southwestern Medical Center, Dallas, TX 75390, USA
| | - Wen Gu
- Children's Research Institute, University of Texas Southwestern Medical Center, Dallas, TX 75390, USA
| | - Liming Du
- Children's Research Institute, University of Texas Southwestern Medical Center, Dallas, TX 75390, USA
| | - Jessica Sudderth
- Children's Research Institute, University of Texas Southwestern Medical Center, Dallas, TX 75390, USA
| | - Dohun Kim
- Children's Research Institute, University of Texas Southwestern Medical Center, Dallas, TX 75390, USA
| | - Spencer D Shelton
- Children's Research Institute, University of Texas Southwestern Medical Center, Dallas, TX 75390, USA
| | - Claire B Llamas
- Children's Research Institute, University of Texas Southwestern Medical Center, Dallas, TX 75390, USA
| | - Yu-Hsuan Lin
- Children's Research Institute, University of Texas Southwestern Medical Center, Dallas, TX 75390, USA
| | - Min Zhu
- Children's Research Institute, University of Texas Southwestern Medical Center, Dallas, TX 75390, USA
| | - Salma Merchant
- Children's Research Institute, University of Texas Southwestern Medical Center, Dallas, TX 75390, USA
| | - Divya Bezwada
- Children's Research Institute, University of Texas Southwestern Medical Center, Dallas, TX 75390, USA
| | - Sherwin Kelekar
- Children's Research Institute, University of Texas Southwestern Medical Center, Dallas, TX 75390, USA
| | - Lauren G Zacharias
- Children's Research Institute, University of Texas Southwestern Medical Center, Dallas, TX 75390, USA
| | - Thomas P Mathews
- Children's Research Institute, University of Texas Southwestern Medical Center, Dallas, TX 75390, USA
| | - Gerta Hoxhaj
- Children's Research Institute, University of Texas Southwestern Medical Center, Dallas, TX 75390, USA
- Department of Pediatrics, University of Texas Southwestern Medical Center, Dallas, TX 75390, USA
| | - R Max Wynn
- Department of Biochemistry, University of Texas Southwestern Medical Center, Dallas, TX 75390, USA
| | - Uttam K Tambar
- Department of Biochemistry, University of Texas Southwestern Medical Center, Dallas, TX 75390, USA
| | - Ralph J DeBerardinis
- Children's Research Institute, University of Texas Southwestern Medical Center, Dallas, TX 75390, USA
- Department of Pediatrics, University of Texas Southwestern Medical Center, Dallas, TX 75390, USA
- Harold C. Simmons Comprehensive Cancer Center, University of Texas Southwestern Medical Center, Dallas, TX 75390, USA
- Howard Hughes Medical Institute, University of Texas Southwestern Medical Center, Dallas, TX 75390, USA
| | - Hao Zhu
- Children's Research Institute, University of Texas Southwestern Medical Center, Dallas, TX 75390, USA
- Department of Pediatrics, University of Texas Southwestern Medical Center, Dallas, TX 75390, USA
- Harold C. Simmons Comprehensive Cancer Center, University of Texas Southwestern Medical Center, Dallas, TX 75390, USA
- Departments of Internal Medicine, University of Texas Southwestern Medical Center, Dallas, TX 75390, USA
- Center for Regenerative Science and Medicine, University of Texas Southwestern Medical Center, Dallas, TX 75390, USA
| | - Prashant Mishra
- Children's Research Institute, University of Texas Southwestern Medical Center, Dallas, TX 75390, USA
- Department of Pediatrics, University of Texas Southwestern Medical Center, Dallas, TX 75390, USA
- Harold C. Simmons Comprehensive Cancer Center, University of Texas Southwestern Medical Center, Dallas, TX 75390, USA
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Singh A, Del-Valle-Anton L, de Juan Romero C, Zhang Z, Ortuño EF, Mahesh A, Espinós A, Soler R, Cárdenas A, Fernández V, Lusby R, Tiwari VK, Borrell V. Gene regulatory landscape of cerebral cortex folding. SCIENCE ADVANCES 2024; 10:eadn1640. [PMID: 38838158 DOI: 10.1126/sciadv.adn1640] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/27/2023] [Accepted: 05/02/2024] [Indexed: 06/07/2024]
Abstract
Folding of the cerebral cortex is a key aspect of mammalian brain development and evolution, and defects are linked to severe neurological disorders. Primary folding occurs in highly stereotyped patterns that are predefined in the cortical germinal zones by a transcriptomic protomap. The gene regulatory landscape governing the emergence of this folding protomap remains unknown. We characterized the spatiotemporal dynamics of gene expression and active epigenetic landscape (H3K27ac) across prospective folds and fissures in ferret. Our results show that the transcriptomic protomap begins to emerge at early embryonic stages, and it involves cell-fate signaling pathways. The H3K27ac landscape reveals developmental cell-fate restriction and engages known developmental regulators, including the transcription factor Cux2. Manipulating Cux2 expression in cortical progenitors changed their proliferation and the folding pattern in ferret, caused by selective transcriptional changes as revealed by single-cell RNA sequencing analyses. Our findings highlight the key relevance of epigenetic mechanisms in defining the patterns of cerebral cortex folding.
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Affiliation(s)
- Aditi Singh
- Wellcome-Wolfson Institute for Experimental Medicine, School of Medicine, Dentistry, and Biomedical Science, Queens University Belfast, Belfast BT9 7BL, UK
| | - Lucia Del-Valle-Anton
- Instituto de Neurociencias, Consejo Superior de Investigaciones Científicas and Universidad Miguel Hernández, Sant Joan d'Alacant 03550, Spain
| | - Camino de Juan Romero
- Instituto de Neurociencias, Consejo Superior de Investigaciones Científicas and Universidad Miguel Hernández, Sant Joan d'Alacant 03550, Spain
| | - Ziyi Zhang
- Wellcome-Wolfson Institute for Experimental Medicine, School of Medicine, Dentistry, and Biomedical Science, Queens University Belfast, Belfast BT9 7BL, UK
| | - Eduardo Fernández Ortuño
- Instituto de Neurociencias, Consejo Superior de Investigaciones Científicas and Universidad Miguel Hernández, Sant Joan d'Alacant 03550, Spain
| | - Arun Mahesh
- Wellcome-Wolfson Institute for Experimental Medicine, School of Medicine, Dentistry, and Biomedical Science, Queens University Belfast, Belfast BT9 7BL, UK
- Institute for Molecular Medicine, University of Southern Denmark, Odense M, Denmark
| | - Alexandre Espinós
- Instituto de Neurociencias, Consejo Superior de Investigaciones Científicas and Universidad Miguel Hernández, Sant Joan d'Alacant 03550, Spain
| | - Rafael Soler
- Instituto de Neurociencias, Consejo Superior de Investigaciones Científicas and Universidad Miguel Hernández, Sant Joan d'Alacant 03550, Spain
| | - Adrián Cárdenas
- Instituto de Neurociencias, Consejo Superior de Investigaciones Científicas and Universidad Miguel Hernández, Sant Joan d'Alacant 03550, Spain
| | - Virginia Fernández
- Instituto de Neurociencias, Consejo Superior de Investigaciones Científicas and Universidad Miguel Hernández, Sant Joan d'Alacant 03550, Spain
| | - Ryan Lusby
- Wellcome-Wolfson Institute for Experimental Medicine, School of Medicine, Dentistry, and Biomedical Science, Queens University Belfast, Belfast BT9 7BL, UK
| | - Vijay K Tiwari
- Wellcome-Wolfson Institute for Experimental Medicine, School of Medicine, Dentistry, and Biomedical Science, Queens University Belfast, Belfast BT9 7BL, UK
- Institute for Molecular Medicine, University of Southern Denmark, Odense M, Denmark
- Danish Institute for Advanced Study (DIAS), Odense M, Denmark
- Department of Clinical Genetics, Odense University Hospital, Odense C, Denmark
| | - Víctor Borrell
- Instituto de Neurociencias, Consejo Superior de Investigaciones Científicas and Universidad Miguel Hernández, Sant Joan d'Alacant 03550, Spain
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Bansal P, Banda EC, Glatt-Deeley HR, Stoddard CE, Linsley JW, Arora N, Deleschaux C, Ahern DT, Kondaveeti Y, Massey RE, Nicouleau M, Wang S, Sabariego-Navarro M, Dierssen M, Finkbeiner S, Pinter SF. A dynamic in vitro model of Down syndrome neurogenesis with trisomy 21 gene dosage correction. SCIENCE ADVANCES 2024; 10:eadj0385. [PMID: 38848354 PMCID: PMC11160455 DOI: 10.1126/sciadv.adj0385] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/23/2023] [Accepted: 05/03/2024] [Indexed: 06/09/2024]
Abstract
Excess gene dosage from chromosome 21 (chr21) causes Down syndrome (DS), spanning developmental and acute phenotypes in terminal cell types. Which phenotypes remain amenable to intervention after development is unknown. To address this question in a model of DS neurogenesis, we derived trisomy 21 (T21) human induced pluripotent stem cells (iPSCs) alongside, otherwise, isogenic euploid controls from mosaic DS fibroblasts and equipped one chr21 copy with an inducible XIST transgene. Monoallelic chr21 silencing by XIST is near-complete and irreversible in iPSCs. Differential expression reveals that T21 neural lineages and iPSCs share suppressed translation and mitochondrial pathways and activate cellular stress responses. When XIST is induced before the neural progenitor stage, T21 dosage correction suppresses a pronounced skew toward astrogenesis in neural differentiation. Because our transgene remains inducible in postmitotic T21 neurons and astrocytes, we demonstrate that XIST efficiently represses genes even after terminal differentiation, which will empower exploration of cell type-specific T21 phenotypes that remain responsive to chr21 dosage.
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Affiliation(s)
- Prakhar Bansal
- Graduate Program in Genetics and Developmental Biology, UCONN Health, University of Connecticut, Farmington, CT, USA
- Department of Genetics and Genome Sciences, UCONN Health, University of Connecticut, Farmington, CT, USA
| | - Erin C. Banda
- Department of Genetics and Genome Sciences, UCONN Health, University of Connecticut, Farmington, CT, USA
| | - Heather R. Glatt-Deeley
- Department of Genetics and Genome Sciences, UCONN Health, University of Connecticut, Farmington, CT, USA
| | - Christopher E. Stoddard
- Cell and Genome Engineering Core, UCONN Health, University of Connecticut, Farmington, CT, USA
| | - Jeremy W. Linsley
- Center for Systems and Therapeutics, Gladstone Institutes, San Francisco, CA, USA
- Taube/Koret Center for Neurodegenerative Disease, Gladstone Institutes, San Francisco, CA, USA
| | - Neha Arora
- Center for Systems and Therapeutics, Gladstone Institutes, San Francisco, CA, USA
| | - Cécile Deleschaux
- Department of Genetics and Genome Sciences, UCONN Health, University of Connecticut, Farmington, CT, USA
| | - Darcy T. Ahern
- Graduate Program in Genetics and Developmental Biology, UCONN Health, University of Connecticut, Farmington, CT, USA
- Department of Genetics and Genome Sciences, UCONN Health, University of Connecticut, Farmington, CT, USA
| | - Yuvabharath Kondaveeti
- Department of Genetics and Genome Sciences, UCONN Health, University of Connecticut, Farmington, CT, USA
| | - Rachael E. Massey
- Graduate Program in Genetics and Developmental Biology, UCONN Health, University of Connecticut, Farmington, CT, USA
- Department of Genetics and Genome Sciences, UCONN Health, University of Connecticut, Farmington, CT, USA
- Institute for Systems Genomics, University of Connecticut, Farmington, CT, USA
| | - Michael Nicouleau
- Department of Genetics and Genome Sciences, UCONN Health, University of Connecticut, Farmington, CT, USA
| | - Shijie Wang
- Center for Systems and Therapeutics, Gladstone Institutes, San Francisco, CA, USA
| | - Miguel Sabariego-Navarro
- Centre for Genomic Regulation (CRG), The Barcelona Institute of Science and Technology, Barcelona, Spain
| | - Mara Dierssen
- Centre for Genomic Regulation (CRG), The Barcelona Institute of Science and Technology, Barcelona, Spain
- Universitat Pompeu Fabra (UPF), Barcelona, Spain
- Human Pharmacology and Clinical Neurosciences Research Group, Neurosciences Research Program, Hospital Del Mar Medical Research Institute (IMIM), Barcelona, Spain
- Centro de Investigación Biomédica en Red de Enfermedades Raras (CIBERER), Madrid, Spain
| | - Steven Finkbeiner
- Center for Systems and Therapeutics, Gladstone Institutes, San Francisco, CA, USA
- Taube/Koret Center for Neurodegenerative Disease, Gladstone Institutes, San Francisco, CA, USA
- Departments of Neurology and Physiology, University of California San Francisco, San Francisco, CA, USA
- Neuroscience and Biomedical Sciences Graduate Programs, University of California San Francisco, San Francisco, CA, USA
| | - Stefan F. Pinter
- Graduate Program in Genetics and Developmental Biology, UCONN Health, University of Connecticut, Farmington, CT, USA
- Department of Genetics and Genome Sciences, UCONN Health, University of Connecticut, Farmington, CT, USA
- Institute for Systems Genomics, University of Connecticut, Farmington, CT, USA
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42
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Jia Y, Ma P, Yao Q. CellMarkerPipe: cell marker identification and evaluation pipeline in single cell transcriptomes. Sci Rep 2024; 14:13151. [PMID: 38849445 PMCID: PMC11161599 DOI: 10.1038/s41598-024-63492-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/13/2024] [Accepted: 05/29/2024] [Indexed: 06/09/2024] Open
Abstract
Assessing marker genes from all cell clusters can be time-consuming and lack systematic strategy. Streamlining this process through a unified computational platform that automates identification and benchmarking will greatly enhance efficiency and ensure a fair evaluation. We therefore developed a novel computational platform, cellMarkerPipe ( https://github.com/yao-laboratory/cellMarkerPipe ), for automated cell-type specific marker gene identification from scRNA-seq data, coupled with comprehensive evaluation schema. CellMarkerPipe adaptively wraps around a collection of commonly used and state-of-the-art tools, including Seurat, COSG, SC3, SCMarker, COMET, and scGeneFit. From rigorously testing across diverse samples, we ascertain SCMarker's overall reliable performance in single marker gene selection, with COSG showing commendable speed and comparable efficacy. Furthermore, we demonstrate the pivotal role of our approach in real-world medical datasets. This general and opensource pipeline stands as a significant advancement in streamlining cell marker gene identification and evaluation, fitting broad applications in the field of cellular biology and medical research.
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Affiliation(s)
- Yinglu Jia
- School of Computing, University of Nebraska Lincoln, 256 Avery Hall, Lincoln, NE, 68588, USA
- Department of Chemistry, University of Nebraska Lincoln, Hamilton Hall, Lincoln, NE, 68588, USA
| | - Pengchong Ma
- School of Computing, University of Nebraska Lincoln, 256 Avery Hall, Lincoln, NE, 68588, USA
| | - Qiuming Yao
- School of Computing, University of Nebraska Lincoln, 256 Avery Hall, Lincoln, NE, 68588, USA.
- Nebraska Center for the Prevention of Obesity Diseases, 316C Leverton Hall, Lincoln, NE, 68583, USA.
- Nebraska Center for Virology, University of Nebraska, 4240 Fair St., Lincoln, NE, 68583, USA.
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43
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Lovell JP, Duque C, Rousseau S, Bhalodia A, Bermea K, Cohen CD, Adamo L. B cell-mediated antigen presentation promotes adverse cardiac remodeling in chronic heart failure. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.05.08.593153. [PMID: 38766182 PMCID: PMC11100706 DOI: 10.1101/2024.05.08.593153] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/22/2024]
Abstract
Cardiovascular disease remains the leading cause of death worldwide. A primary driver of cardiovascular mortality is ischemic heart failure, a form of cardiac dysfunction that can develop in patients who survive myocardial infarction. Acute cardiac damage triggers robust changes in the spleen with rapid migration of immune cells from the spleen to the heart. Activating this "cardio-splenic" axis contributes to progressive cardiac dysfunction. The cardio-splenic axis has, therefore, been identified as a promising therapeutic target to prevent or treat heart failure. However, our understanding of the precise mechanisms by which specific immune cells contribute to adverse cardiac remodeling within the cardio-splenic axis remains limited. Here, we show that splenic B cells contribute to the development of heart failure via MHC II-mediated antigen presentation. We found that the adoptive transfer of splenic B cells from mice with ischemic heart failure promoted adverse cardiac remodeling and splenic inflammatory changes in naïve recipient mice. Based on single-cell RNA sequencing analysis of splenic B cells from mice with ischemic heart failure, we hypothesized that B cells contributed to adverse cardiac remodeling through antigen presentation by MHC II molecules. This mechanism was confirmed using transgenic mice with B cell-specific MHC II deletion, and by analyzing circulating B cells from humans who experienced myocardial infarction. Our results broaden our understanding of B lymphocyte biology, reshape current models of immune activation in response to myocardial injury, and point towards MHC II-mediated signaling in B cells as a novel and specific therapeutic target in chronic heart failure.
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44
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Kim A, Martinez S, Edwards N, Horvath A. ScSNViz: a user-friendly toolset for visualization and analysis of Cell-Specific Expressed SNVs. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.05.31.596816. [PMID: 38895293 PMCID: PMC11185531 DOI: 10.1101/2024.05.31.596816] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/21/2024]
Abstract
Motivation Understanding genetic variation at the single-cell level is crucial for insights into cellular heterogeneity, clonal evolution, and gene expression regulation, but there is a scarcity of tools for visualizing and analyzing cell-level genetic variants. Results We introduce scSNViz, a comprehensive R-based toolset for visualization and analysis of cell-specific expressed Single Nucleotide Variants (sceSNVs) within cell-barcoded single-cell RNA-sequencing (scRNA-seq) data. ScSNViz offers 3D sceSNV visualization capabilities for dimensionally reduced scRNA-seq gene expression data, compatibility with popular scRNA-seq processing tools like Seurat, cell-type classification tools such as SingleR and scType, and trajectory inference computation using Slingshot. Furthermore, scSNViz conducts estimation, summary, and graphical representation of statistical metrics pertaining to sceSNVs distribution and expression across individual cells. It also provides support for the analysis of individual sceSNVs as well as sets comprising multiple expressed sceSNVs of interest. Availability ScSNViz is implemented as user-friendly R-scripts, freely available on https://horvathlab.github.io/NGS/scSNViz , supported by help utilities, and requiring no specialized bioinformatics skills for use.
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45
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Yalçın B, Pomrenze MB, Malacon K, Drexler R, Rogers AE, Shamardani K, Chau IJ, Taylor KR, Ni L, Contreras-Esquivel D, Malenka RC, Monje M. Myelin plasticity in the ventral tegmental area is required for opioid reward. Nature 2024; 630:677-685. [PMID: 38839962 PMCID: PMC11186775 DOI: 10.1038/s41586-024-07525-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/27/2023] [Accepted: 05/07/2024] [Indexed: 06/07/2024]
Abstract
All drugs of abuse induce long-lasting changes in synaptic transmission and neural circuit function that underlie substance-use disorders1,2. Another recently appreciated mechanism of neural circuit plasticity is mediated through activity-regulated changes in myelin that can tune circuit function and influence cognitive behaviour3-7. Here we explore the role of myelin plasticity in dopaminergic circuitry and reward learning. We demonstrate that dopaminergic neuronal activity-regulated myelin plasticity is a key modulator of dopaminergic circuit function and opioid reward. Oligodendroglial lineage cells respond to dopaminergic neuronal activity evoked by optogenetic stimulation of dopaminergic neurons, optogenetic inhibition of GABAergic neurons, or administration of morphine. These oligodendroglial changes are evident selectively within the ventral tegmental area but not along the axonal projections in the medial forebrain bundle nor within the target nucleus accumbens. Genetic blockade of oligodendrogenesis dampens dopamine release dynamics in nucleus accumbens and impairs behavioural conditioning to morphine. Taken together, these findings underscore a critical role for oligodendrogenesis in reward learning and identify dopaminergic neuronal activity-regulated myelin plasticity as an important circuit modification that is required for opioid reward.
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Affiliation(s)
- Belgin Yalçın
- Department of Neurology and Neurological Sciences, Stanford University, Stanford, CA, USA
| | - Matthew B Pomrenze
- Nancy Pritzker Laboratory, Department of Psychiatry and Behavioral Sciences, Stanford University, Stanford, CA, USA
| | - Karen Malacon
- Department of Neurology and Neurological Sciences, Stanford University, Stanford, CA, USA
| | - Richard Drexler
- Department of Neurology and Neurological Sciences, Stanford University, Stanford, CA, USA
| | - Abigail E Rogers
- Department of Neurology and Neurological Sciences, Stanford University, Stanford, CA, USA
| | - Kiarash Shamardani
- Department of Neurology and Neurological Sciences, Stanford University, Stanford, CA, USA
| | - Isabelle J Chau
- Department of Neurology and Neurological Sciences, Stanford University, Stanford, CA, USA
| | - Kathryn R Taylor
- Department of Neurology and Neurological Sciences, Stanford University, Stanford, CA, USA
| | - Lijun Ni
- Department of Neurology and Neurological Sciences, Stanford University, Stanford, CA, USA
| | | | - Robert C Malenka
- Nancy Pritzker Laboratory, Department of Psychiatry and Behavioral Sciences, Stanford University, Stanford, CA, USA
| | - Michelle Monje
- Department of Neurology and Neurological Sciences, Stanford University, Stanford, CA, USA.
- Howard Hughes Medical Institute, Stanford, CA, USA.
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46
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Yarlagadda S, Giorgio TD. A guide to single-cell RNA sequencing analysis using web-based tools for non-bioinformatician. FEBS J 2024; 291:2545-2561. [PMID: 38148322 DOI: 10.1111/febs.17036] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/12/2023] [Accepted: 12/14/2023] [Indexed: 12/28/2023]
Abstract
Single-cell RNA sequencing (scRNA-seq) is a technique that has proven to be a powerful tool for a wide range of fields and research studies. However, scRNA-seq data analysis has been dominated by scientists highly trained in bioinformatics or those with extensive computational experience and understanding. Recently, this trend has begun to shift as more user-friendly web-based scRNA-seq analysis tools have been developed that require little computational experience to use. However, barriers persist for nonbioinformaticians in using this technique. Complex, unfamiliar language and scarce comprehensive literature guidance to provide a framework for understanding scRNA-seq analysis outputs are among the obstacles. This work introduces many popular web-based tools for scRNA-seq and provides a general overview of their user interfaces and features. Then, a comprehensive start-to-finish introductory scRNA-seq analysis pipeline is described in detail, which aims to enable researchers to carry out scRNA-seq analysis, regardless of computational experience. Companion video tutorials can be found at "EasyScRNAseqTutorials" on YouTube (https://www.youtube.com/@scrnaseqtutorials). However, as scRNA-seq continues to penetrate new fields and expand in importance, there remains a need for more literature to help overcome barriers to its use by explaining further the highly complex and advanced analyses that are introduced within this paper.
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Affiliation(s)
| | - Todd D Giorgio
- Biomedical Engineering, Vanderbilt University, Nashville, TN, USA
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47
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Sampson MM, Morgan RK, Sloan SA, Bakulski KM. Single-cell investigation of lead toxicity from neurodevelopment to neurodegeneration: Current review and future opportunities. CURRENT OPINION IN TOXICOLOGY 2024; 38:100464. [PMID: 39086983 PMCID: PMC11290315 DOI: 10.1016/j.cotox.2024.100464] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 08/02/2024]
Abstract
Human exposure to the metal lead (Pb) is prevalent and associated with adverse neurodevelopmental and neurodegenerative outcomes. Pb disrupts normal brain function by inducing oxidative stress and neuroinflammation, altering cellular metabolism, and displacing essential metals. Prior studies on the molecular impacts of Pb have examined bulk tissues, which collapse information across all cell types, or in targeted cells, which are limited to cell autonomous effects. These approaches are unable to represent the complete biological implications of Pb exposure because the brain is a cooperative network of highly heterogeneous cells, with cellular diversity and proportions shifting throughout development, by brain region, and with disease. New technologies are necessary to investigate whether Pb and other environmental exposures alter cell composition in the brain and whether they cause molecular changes in a cell-type-specific manner. Cutting-edge, single-cell approaches now enable research resolving cell-type-specific effects from bulk tissues. This article reviews existing Pb neurotoxicology studies with genome-wide molecular signatures and provides a path forward for the field to implement single-cell approaches with practical recommendations.
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Affiliation(s)
- Maureen M Sampson
- Department of Human Genetics, School of Medicine, Emory University, Atlanta, GA, USA
| | - Rachel K Morgan
- Department of Environmental Health Sciences, School of Public Health, University of Michigan, Ann Arbor, MI, USA
| | - Steven A Sloan
- Department of Human Genetics, School of Medicine, Emory University, Atlanta, GA, USA
| | - Kelly M Bakulski
- Department of Epidemiology, School of Public Health, University of Michigan, Ann Arbor, MI, USA
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48
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Kessler S, Burke B, Andrieux G, Schinköthe J, Hamberger L, Kacza J, Zhan S, Reasoner C, Dutt TS, Kaukab Osman M, Henao-Tamayo M, Staniek J, Villena Ossa JF, Frank DT, Ma W, Ulrich R, Cathomen T, Boerries M, Rizzi M, Beer M, Schwemmle M, Reuther P, Schountz T, Ciminski K. Deciphering bat influenza H18N11 infection dynamics in male Jamaican fruit bats on a single-cell level. Nat Commun 2024; 15:4500. [PMID: 38802391 PMCID: PMC11130286 DOI: 10.1038/s41467-024-48934-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/12/2024] [Accepted: 05/17/2024] [Indexed: 05/29/2024] Open
Abstract
Jamaican fruit bats (Artibeus jamaicensis) naturally harbor a wide range of viruses of human relevance. These infections are typically mild in bats, suggesting unique features of their immune system. To better understand the immune response to viral infections in bats, we infected male Jamaican fruit bats with the bat-derived influenza A virus (IAV) H18N11. Using comparative single-cell RNA sequencing, we generated single-cell atlases of the Jamaican fruit bat intestine and mesentery. Gene expression profiling showed that H18N11 infection resulted in a moderate induction of interferon-stimulated genes and transcriptional activation of immune cells. H18N11 infection was predominant in various leukocytes, including macrophages, B cells, and NK/T cells. Confirming these findings, human leukocytes, particularly macrophages, were also susceptible to H18N11, highlighting the zoonotic potential of this bat-derived IAV. Our study provides insight into a natural virus-host relationship and thus serves as a fundamental resource for future in-depth characterization of bat immunology.
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Affiliation(s)
- Susanne Kessler
- Institute of Virology, Medical Center University of Freiburg, Freiburg, Germany
- Faculty of Medicine, University of Freiburg, Freiburg, Germany
| | - Bradly Burke
- Center for Vector-borne Infectious Diseases, Department of Microbiology, Immunology and Pathology, College of Veterinary Medicine and Biomedical Sciences, Colorado State University, Fort Collins, CO, USA
| | - Geoffroy Andrieux
- Faculty of Medicine, University of Freiburg, Freiburg, Germany
- Institute of Medical Bioinformatics and Systems Medicine, Medical Center - University of Freiburg, Freiburg, Germany
| | - Jan Schinköthe
- Institute of Veterinary Pathology, Faculty of Veterinary Medicine, Leipzig University, Leipzig, Germany
| | - Lea Hamberger
- Institute of Virology, Medical Center University of Freiburg, Freiburg, Germany
- Faculty of Medicine, University of Freiburg, Freiburg, Germany
| | - Johannes Kacza
- BioImaging Core Facility, Faculty of Veterinary Medicine, University of Leipzig, Leipzig, Germany
| | - Shijun Zhan
- Center for Vector-borne Infectious Diseases, Department of Microbiology, Immunology and Pathology, College of Veterinary Medicine and Biomedical Sciences, Colorado State University, Fort Collins, CO, USA
| | - Clara Reasoner
- Center for Vector-borne Infectious Diseases, Department of Microbiology, Immunology and Pathology, College of Veterinary Medicine and Biomedical Sciences, Colorado State University, Fort Collins, CO, USA
| | - Taru S Dutt
- Department of Microbiology, Immunology and Pathology, Colorado State University, Fort Collins, CO, USA
| | - Maria Kaukab Osman
- Institute of Virology, Medical Center University of Freiburg, Freiburg, Germany
- Faculty of Medicine, University of Freiburg, Freiburg, Germany
- Spemann Graduate School of Biology and Medicine, University of Freiburg, Freiburg, Germany
- Faculty of Biology, University of Freiburg, Freiburg, Germany
| | - Marcela Henao-Tamayo
- Department of Microbiology, Immunology and Pathology, Colorado State University, Fort Collins, CO, USA
| | - Julian Staniek
- Faculty of Biology, University of Freiburg, Freiburg, Germany
- Department of Rheumatology and Clinical Immunology, Medical Center - University of Freiburg, Faculty of Medicine, University of Freiburg, Freiburg, Germany
- Center for Chronic Immunodeficiency (CCI), Medical Center - University of Freiburg, Freiburg, Germany
| | - Jose Francisco Villena Ossa
- Center for Chronic Immunodeficiency (CCI), Medical Center - University of Freiburg, Freiburg, Germany
- Institute for Transfusion Medicine and Gene Therapy, Medical Center-University of Freiburg, Freiburg, Germany
| | - Dalit T Frank
- Center for Vector-borne Infectious Diseases, Department of Microbiology, Immunology and Pathology, College of Veterinary Medicine and Biomedical Sciences, Colorado State University, Fort Collins, CO, USA
| | - Wenjun Ma
- Department of Veterinary Pathobiology and Department of Molecular Microbiology and Immunology, University of Missouri, Columbia, MO, USA
| | - Reiner Ulrich
- Institute of Veterinary Pathology, Faculty of Veterinary Medicine, Leipzig University, Leipzig, Germany
| | - Toni Cathomen
- Faculty of Medicine, University of Freiburg, Freiburg, Germany
- Center for Chronic Immunodeficiency (CCI), Medical Center - University of Freiburg, Freiburg, Germany
- Institute for Transfusion Medicine and Gene Therapy, Medical Center-University of Freiburg, Freiburg, Germany
| | - Melanie Boerries
- Faculty of Medicine, University of Freiburg, Freiburg, Germany
- Institute of Medical Bioinformatics and Systems Medicine, Medical Center - University of Freiburg, Freiburg, Germany
- German Cancer Consortium (DKTK), Partner site Freiburg, a partnership between DKFZ and Medical Center - University of Freiburg, Freiburg, Germany
| | - Marta Rizzi
- Department of Rheumatology and Clinical Immunology, Medical Center - University of Freiburg, Faculty of Medicine, University of Freiburg, Freiburg, Germany
- Center for Chronic Immunodeficiency (CCI), Medical Center - University of Freiburg, Freiburg, Germany
- CIBSS - Centre for Integrative Biological Signalling Studies, University of Freiburg, Freiburg, Germany
- Division of Clinical and Experimental Immunology, Institute of Immunology, Center for Pathophysiology, Infectiology and Immunology, Medical University of Vienna, Vienna, Austria
| | - Martin Beer
- Institute of Diagnostic Virology, Friedrich-Loeffler-Institut, Greifswald, Insel Riems, Germany
| | - Martin Schwemmle
- Institute of Virology, Medical Center University of Freiburg, Freiburg, Germany
- Faculty of Medicine, University of Freiburg, Freiburg, Germany
| | - Peter Reuther
- Institute of Virology, Medical Center University of Freiburg, Freiburg, Germany
- Faculty of Medicine, University of Freiburg, Freiburg, Germany
| | - Tony Schountz
- Center for Vector-borne Infectious Diseases, Department of Microbiology, Immunology and Pathology, College of Veterinary Medicine and Biomedical Sciences, Colorado State University, Fort Collins, CO, USA.
| | - Kevin Ciminski
- Institute of Virology, Medical Center University of Freiburg, Freiburg, Germany.
- Faculty of Medicine, University of Freiburg, Freiburg, Germany.
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49
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Lyons A, Brown J, Davenport KM. Single-Cell Sequencing Technology in Ruminant Livestock: Challenges and Opportunities. Curr Issues Mol Biol 2024; 46:5291-5306. [PMID: 38920988 PMCID: PMC11202421 DOI: 10.3390/cimb46060316] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/30/2024] [Revised: 05/20/2024] [Accepted: 05/25/2024] [Indexed: 06/27/2024] Open
Abstract
Advancements in single-cell sequencing have transformed the genomics field by allowing researchers to delve into the intricate cellular heterogeneity within tissues at greater resolution. While single-cell omics are more widely applied in model organisms and humans, their use in livestock species is just beginning. Studies in cattle, sheep, and goats have already leveraged single-cell and single-nuclei RNA-seq as well as single-cell and single-nuclei ATAC-seq to delineate cellular diversity in tissues, track changes in cell populations and gene expression over developmental stages, and characterize immune cell populations important for disease resistance and resilience. Although challenges exist for the use of this technology in ruminant livestock, such as the precise annotation of unique cell populations and spatial resolution of cells within a tissue, there is vast potential to enhance our understanding of the cellular and molecular mechanisms underpinning traits essential for healthy and productive livestock. This review intends to highlight the insights gained from published single-cell omics studies in cattle, sheep, and goats, particularly those with publicly accessible data. Further, this manuscript will discuss the challenges and opportunities of this technology in ruminant livestock and how it may contribute to enhanced profitability and sustainability of animal agriculture in the future.
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50
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Celik C, Lee STT, Tanoto FR, Veleba M, Kline K, Thibault G. Decoding the complexity of delayed wound healing following Enterococcus faecalis infection. eLife 2024; 13:RP95113. [PMID: 38767331 PMCID: PMC11105157 DOI: 10.7554/elife.95113] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/22/2024] Open
Abstract
Wound infections are highly prevalent and can lead to delayed or failed healing, causing significant morbidity and adverse economic impacts. These infections occur in various contexts, including diabetic foot ulcers, burns, and surgical sites. Enterococcus faecalis is often found in persistent non-healing wounds, but its contribution to chronic wounds remains understudied. To address this, we employed single-cell RNA sequencing (scRNA-seq) on infected wounds in comparison to uninfected wounds in a mouse model. Examining over 23,000 cells, we created a comprehensive single-cell atlas that captures the cellular and transcriptomic landscape of these wounds. Our analysis revealed unique transcriptional and metabolic alterations in infected wounds, elucidating the distinct molecular changes associated with bacterial infection compared to the normal wound healing process. We identified dysregulated keratinocyte and fibroblast transcriptomes in response to infection, jointly contributing to an anti-inflammatory environment. Notably, E. faecalis infection prompted a premature, incomplete epithelial-mesenchymal transition in keratinocytes. Additionally, E. faecalis infection modulated M2-like macrophage polarization by inhibiting pro-inflammatory resolution in vitro, in vivo, and in our scRNA-seq atlas. Furthermore, we discovered macrophage crosstalk with neutrophils, which regulates chemokine signaling pathways, while promoting anti-inflammatory interactions with endothelial cells. Overall, our findings offer new insights into the immunosuppressive role of E. faecalis in wound infections.
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Affiliation(s)
- Cenk Celik
- School of Biological Sciences, Nanyang Technological UniversitySingaporeSingapore
| | - Stella Tue Ting Lee
- School of Biological Sciences, Nanyang Technological UniversitySingaporeSingapore
| | - Frederick Reinhart Tanoto
- Singapore Centre for Environmental Life Science Engineering, Nanyang Technological UniversitySingaporeSingapore
| | - Mark Veleba
- Singapore Centre for Environmental Life Science Engineering, Nanyang Technological UniversitySingaporeSingapore
| | - Kimberly Kline
- School of Biological Sciences, Nanyang Technological UniversitySingaporeSingapore
- Singapore Centre for Environmental Life Science Engineering, Nanyang Technological UniversitySingaporeSingapore
- Department of Microbiology and Molecular Medicine, Faculty of Medicine, University of GenevaGenevaSwitzerland
| | - Guillaume Thibault
- School of Biological Sciences, Nanyang Technological UniversitySingaporeSingapore
- Mechanobiology Institute, National University of SingaporeSingaporeSingapore
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