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Cuevas-Diaz Duran R, Wei H, Wu J. Data normalization for addressing the challenges in the analysis of single-cell transcriptomic datasets. BMC Genomics 2024; 25:444. [PMID: 38711017 PMCID: PMC11073985 DOI: 10.1186/s12864-024-10364-5] [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: 09/02/2023] [Accepted: 04/29/2024] [Indexed: 05/08/2024] Open
Abstract
BACKGROUND Normalization is a critical step in the analysis of single-cell RNA-sequencing (scRNA-seq) datasets. Its main goal is to make gene counts comparable within and between cells. To do so, normalization methods must account for technical and biological variability. Numerous normalization methods have been developed addressing different sources of dispersion and making specific assumptions about the count data. MAIN BODY The selection of a normalization method has a direct impact on downstream analysis, for example differential gene expression and cluster identification. Thus, the objective of this review is to guide the reader in making an informed decision on the most appropriate normalization method to use. To this aim, we first give an overview of the different single cell sequencing platforms and methods commonly used including isolation and library preparation protocols. Next, we discuss the inherent sources of variability of scRNA-seq datasets. We describe the categories of normalization methods and include examples of each. We also delineate imputation and batch-effect correction methods. Furthermore, we describe data-driven metrics commonly used to evaluate the performance of normalization methods. We also discuss common scRNA-seq methods and toolkits used for integrated data analysis. CONCLUSIONS According to the correction performed, normalization methods can be broadly classified as within and between-sample algorithms. Moreover, with respect to the mathematical model used, normalization methods can further be classified into: global scaling methods, generalized linear models, mixed methods, and machine learning-based methods. Each of these methods depict pros and cons and make different statistical assumptions. However, there is no better performing normalization method. Instead, metrics such as silhouette width, K-nearest neighbor batch-effect test, or Highly Variable Genes are recommended to assess the performance of normalization methods.
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Affiliation(s)
- Raquel Cuevas-Diaz Duran
- Tecnologico de Monterrey, Escuela de Medicina y Ciencias de la Salud, Monterrey, Nuevo Leon, 64710, Mexico.
| | - Haichao Wei
- The Vivian L. Smith Department of Neurosurgery, McGovern Medical School, The University of Texas Health Science Center at Houston, Houston, TX, 77030, USA
- Center for Stem Cell and Regenerative Medicine, UT Brown Foundation Institute of Molecular Medicine, Houston, TX, 77030, USA
| | - Jiaqian Wu
- The Vivian L. Smith Department of Neurosurgery, McGovern Medical School, The University of Texas Health Science Center at Houston, Houston, TX, 77030, USA.
- Center for Stem Cell and Regenerative Medicine, UT Brown Foundation Institute of Molecular Medicine, Houston, TX, 77030, USA.
- MD Anderson Cancer Center UTHealth Graduate School of Biomedical Sciences, Houston, TX, 77030, USA.
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152
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Deng X, Mo Y, Zhu X. Deciphering Müller cell heterogeneity signatures in diabetic retinopathy across species: an integrative single-cell analysis. Eur J Med Res 2024; 29:265. [PMID: 38698486 PMCID: PMC11067085 DOI: 10.1186/s40001-024-01847-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: 01/13/2024] [Accepted: 04/17/2024] [Indexed: 05/05/2024] Open
Abstract
Diabetic retinopathy (DR), a leading cause of visual impairment, demands a profound comprehension of its cellular mechanisms to formulate effective therapeutic strategies. Our study presentes a comprehensive single-cell analysis elucidating the intricate landscape of Müller cells within DR, emphasizing their nuanced involvement. Utilizing scRNA-seq data from both Sprague-Dawley rat models and human patients, we delineated distinct Müller cell clusters and their corresponding gene expression profiles. These findings were further validated through differential gene expression analysis utilizing human transcriptomic data. Notably, certain Müller cell clusters displayed upregulation of the Rho gene, implying a phagocytic response to damaged photoreceptors within the DR microenvironment. This phenomenon was consistently observed across species. Additionally, the co-expression patterns of RHO and PDE6G within Müller cell clusters provided compelling evidence supporting their potential role in maintaining retinal integrity during DR. Our results offer novel insights into the cellular dynamics of DR and underscore Müller cells as promising therapeutic targets for preserving vision in retinal disorders induced by diabetes.
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Affiliation(s)
- Xiyuan Deng
- Chengdu University of Traditional Chinese Medicine, Chengdu, China
| | - Ya Mo
- Hospital of Chengdu University of Traditional Chinese Medicine, Chengdu, China.
| | - Xiuying Zhu
- Chengdu University of Traditional Chinese Medicine, Chengdu, China
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153
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Wang Z, Zhen C, Guo X, Qu M, Zhang C, Song J, Fan X, Huang H, Xu R, Zhang J, Yuan J, Hong W, Li J, Wang F, Jiao Y, Linghu E. Landscape of gut mucosal immune cells showed gap of follicular or memory B cells into plasma cells in immunological non-responders. Clin Transl Med 2024; 14:e1699. [PMID: 38783408 PMCID: PMC11116468 DOI: 10.1002/ctm2.1699] [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: 12/26/2023] [Revised: 04/24/2024] [Accepted: 04/29/2024] [Indexed: 05/25/2024] Open
Abstract
BACKGROUND The gut is an important site for human immunodeficiency virus (HIV) infection and immune responses. The role of gut mucosal immune cells in immune restoration in patients infected with HIV undergoing antiretroviral therapy remains unclear. METHODS Ileocytes, including 54 475 immune cells, were obtained from colonoscopic biopsies of five HIV-negative controls, nine immunological responders (IRs), and three immunological non-responders (INRs) and were analyzed using single-cell RNA sequencing. Immunohistochemical assays were performed for validation. The 16S rRNA gene was amplified using PCR in faecal samples to analyze faecal microbiota. Flow cytometry was used to analyze CD4+ T-cell counts and the activation of T cells. RESULTS This study presents a global transcriptomic profile of the gut mucosal immune cells in patients infected with HIV. Compared with the IRs, the INRs exhibited a lower proportion of gut plasma cells, especially the IGKC+IgA+ plasma cell subpopulation. IGKC+IgA+ plasma cells were negatively associated with enriched f. Prevotellaceae the INRs and negatively correlated with the overactivation of T cells, but they were positively correlated with CD4+ T-cell counts. The INRs exhibited a higher proportion of B cells than the IRs. Follicular and memory B cells were significantly higher in the INRs. Reduced potential was observed in the differentiation of follicular or memory B cells into gut plasma cells in INRs. In addition, the receptor-ligand pairs CD74_MIF and CD74_COPA of memory B/ follicular helper T cells were significantly reduced in the INRs, which may hinder the differentiation of memory and follicular B cells into plasma cells. CONCLUSIONS Our study shows that plasma cells are dysregulated in INRs and provides an extensive resource for deciphering the immune pathogenesis of HIV in INRs. KEY POINTS An investigation was carried out at the single-cell-level to analyze gut mucosal immune cells alterations in PLWH after ART. B cells were significantly increased and plasma cells were significantly decreased in the INRs compared to the IRs and NCs. There are gaps in the transition from gut follicular or memory B cellsinto plasma cells in INRs.
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Affiliation(s)
- Zerui Wang
- Senior Department of Gastroenterologythe First Medical Center of Chinese PLA General HospitalBeijingChina
| | - Cheng Zhen
- Senior Department of Infectious Diseasesthe Fifth Medical Centre of Chinese PLA General HospitalNational Clinical Research Center for Infectious DiseasesBeijingChina
| | - Xiaoyan Guo
- Senior Department of Infectious Diseasesthe Fifth Medical Centre of Chinese PLA General HospitalNational Clinical Research Center for Infectious DiseasesBeijingChina
| | - Mengmeng Qu
- Senior Department of Infectious Diseasesthe Fifth Medical Centre of Chinese PLA General HospitalNational Clinical Research Center for Infectious DiseasesBeijingChina
| | - Chao Zhang
- Senior Department of Infectious Diseasesthe Fifth Medical Centre of Chinese PLA General HospitalNational Clinical Research Center for Infectious DiseasesBeijingChina
| | - Jinwen Song
- Senior Department of Infectious Diseasesthe Fifth Medical Centre of Chinese PLA General HospitalNational Clinical Research Center for Infectious DiseasesBeijingChina
| | - Xing Fan
- Senior Department of Infectious Diseasesthe Fifth Medical Centre of Chinese PLA General HospitalNational Clinical Research Center for Infectious DiseasesBeijingChina
| | - Huihuang Huang
- Senior Department of Infectious Diseasesthe Fifth Medical Centre of Chinese PLA General HospitalNational Clinical Research Center for Infectious DiseasesBeijingChina
| | - Ruonan Xu
- Senior Department of Infectious Diseasesthe Fifth Medical Centre of Chinese PLA General HospitalNational Clinical Research Center for Infectious DiseasesBeijingChina
| | - Jiyuan Zhang
- Senior Department of Infectious Diseasesthe Fifth Medical Centre of Chinese PLA General HospitalNational Clinical Research Center for Infectious DiseasesBeijingChina
| | - Jinhong Yuan
- Senior Department of Infectious Diseasesthe Fifth Medical Centre of Chinese PLA General HospitalNational Clinical Research Center for Infectious DiseasesBeijingChina
| | - Weiguo Hong
- Senior Department of Infectious Diseasesthe Fifth Medical Centre of Chinese PLA General HospitalNational Clinical Research Center for Infectious DiseasesBeijingChina
| | - Jiaying Li
- Senior Department of Infectious Diseasesthe Fifth Medical Centre of Chinese PLA General HospitalNational Clinical Research Center for Infectious DiseasesBeijingChina
| | - Fu‐Sheng Wang
- Senior Department of Infectious Diseasesthe Fifth Medical Centre of Chinese PLA General HospitalNational Clinical Research Center for Infectious DiseasesBeijingChina
| | - Yan‐Mei Jiao
- Senior Department of Infectious Diseasesthe Fifth Medical Centre of Chinese PLA General HospitalNational Clinical Research Center for Infectious DiseasesBeijingChina
| | - Enqiang Linghu
- Senior Department of Gastroenterologythe First Medical Center of Chinese PLA General HospitalBeijingChina
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154
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Jiang TT, Cao S, Kruglov O, Virmani A, Geskin LJ, Falo LD, Akilov OE. Deciphering Tumor Cell Evolution in Cutaneous T-Cell Lymphomas: Distinct Differentiation Trajectories in Mycosis Fungoides and Sézary Syndrome. J Invest Dermatol 2024; 144:1088-1098. [PMID: 38036289 PMCID: PMC11034798 DOI: 10.1016/j.jid.2023.10.018] [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: 09/04/2023] [Revised: 10/08/2023] [Accepted: 10/25/2023] [Indexed: 12/02/2023]
Abstract
Cutaneous T-cell lymphomas are a heterogeneous group of neoplasms originating in the skin, with mycosis fungoides (MF) and Sézary syndrome (SS) representing the most common variants. The cellular origin of cutaneous lymphomas has remained controversial owing to their immense phenotypic heterogeneity that obfuscates lineage reconstruction on the basis of classical surface biomarkers. To overcome this heterogeneity and reconstruct the differentiation trajectory of malignant cells in MF and SS, TCR sequencing was performed in parallel with targeted transcriptomics at the single-cell resolution among cutaneous samples in MF and SS. Unsupervised lineage reconstruction showed that Sézary cells exist as a population of CD4+ T cells distinct from those in patch, plaque, and tumor MF. Further investigation of malignant cell heterogeneity in SS showed that Sézary cells phenotypically comprised at least 3 subsets on the basis of differential proliferation potentials and expression of exhaustion markers. A T helper 1-polarized cell type, intermediate cell type, and exhausted T helper 2-polarized cell type were identified, with T helper 1- and T helper 2-polarized cells displaying divergent proliferation potentials. Collectively, these findings provide evidence to clarify the relationship between MF and SS and reveal cell subsets in SS that suggest a possible mechanism for therapeutic resistance.
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Affiliation(s)
- Tony T Jiang
- Department of Dermatology, University of Pittsburgh, Pittsburgh, Pennsylvania, USA
| | - Simon Cao
- Department of Dermatology, University of Pittsburgh, Pittsburgh, Pennsylvania, USA
| | - Oleg Kruglov
- Department of Dermatology, University of Pittsburgh, Pittsburgh, Pennsylvania, USA
| | - Aman Virmani
- School of Art and Science, University of Pittsburgh, Pittsburgh, Pennsylvania, USA
| | - Larisa J Geskin
- Department of Dermatology, Columbia University, New York, New York, USA
| | - Louis D Falo
- Department of Dermatology, University of Pittsburgh, Pittsburgh, Pennsylvania, USA
| | - Oleg E Akilov
- Department of Dermatology, University of Pittsburgh, Pittsburgh, Pennsylvania, USA.
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155
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Oh S, Yeo E, Shim J, Noh H, Park J, Lee KT, Kim SH, Lee D, Lee JH. Revealing the pathogenesis of keloids based on the status: Active vs inactive. Exp Dermatol 2024; 33:e15088. [PMID: 38685820 DOI: 10.1111/exd.15088] [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: 10/10/2023] [Revised: 04/05/2024] [Accepted: 04/14/2024] [Indexed: 05/02/2024]
Abstract
Recently, the pathomechanisms of keloids have been extensively researched using transcriptomic analysis, but most studies did not consider the activity of keloids. We aimed to profile the transcriptomics of keloids according to their clinical activity and location within the keloid lesion, compared with normal and mature scars. Tissue samples were collected (keloid based on its activity (active and inactive), mature scar from keloid patients and normal scar (NS) from non-keloid patients). To reduce possible bias, all keloids assessed in this study had no treatment history and their location was limited to the upper chest or back. Multiomics assessment was performed by using single-cell RNA sequencing and multiplex immunofluorescence. Increased mesenchymal fibroblasts (FBs) was the main feature in keloid patients. Noticeably, the proportion of pro-inflammatory FBs was significantly increased in active keloids compared to inactive ones. To explore the nature of proinflammatory FBs, trajectory analysis was conducted and CCN family associated with mechanical stretch exhibited higher expression in active keloids. For vascular endothelial cells (VECs), the proportion of tip and immature cells increased in keloids compared to NS, especially at the periphery of active keloids. Also, keloid VECs highly expressed genes with characteristics of mesenchymal activation compared to NS, especially those from the active keloid center. Multiomics analysis demonstrated the distinct expression profile of active keloids. Clinically, these findings may provide the future appropriate directions for development of treatment modalities of keloids. Prevention of keloids could be possible by the suppression of mesenchymal activation between FBs and VECs and modulation of proinflammatory FBs may be the key to the control of active keloids.
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Affiliation(s)
- Sejin Oh
- Department of Dermatology, Samsung Medical Center, Sungkyunkwan University School of Medicine, Seoul, Republic of Korea
| | - Eunhye Yeo
- Department of Dermatology, Samsung Medical Center, Sungkyunkwan University School of Medicine, Seoul, Republic of Korea
- Department of Medical Device Management and Research, Samsung Advanced Institute for Health Sciences and Technology, Sungkyunkwan University, Seoul, Republic of Korea
| | - Joonho Shim
- Department of Dermatology, Samsung Medical Center, Sungkyunkwan University School of Medicine, Seoul, Republic of Korea
| | - Hyungrye Noh
- Department of Dermatology, Samsung Medical Center, Sungkyunkwan University School of Medicine, Seoul, Republic of Korea
| | - Jihye Park
- Department of Dermatology, Samsung Medical Center, Sungkyunkwan University School of Medicine, Seoul, Republic of Korea
| | - Kyeong-Tae Lee
- Department of Plastic Surgery, Samsung Medical Center, Sungkyunkwan University School of Medicine, Seoul, Republic of Korea
| | - Seok-Hyung Kim
- Department of Pathology, Samsung Medical Center, Sungkyunkwan University School of Medicine, Seoul, Republic of Korea
| | - Dongyoun Lee
- Department of Dermatology, Samsung Medical Center, Sungkyunkwan University School of Medicine, Seoul, Republic of Korea
| | - Jong Hee Lee
- Department of Dermatology, Samsung Medical Center, Sungkyunkwan University School of Medicine, Seoul, Republic of Korea
- Department of Medical Device Management and Research, Samsung Advanced Institute for Health Sciences and Technology, Sungkyunkwan University, Seoul, Republic of Korea
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156
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Woodall MNJ, Cujba AM, Worlock KB, Case KM, Masonou T, Yoshida M, Polanski K, Huang N, Lindeboom RGH, Mamanova L, Bolt L, Richardson L, Cakir B, Ellis S, Palor M, Burgoyne T, Pinto A, Moulding D, McHugh TD, Saleh A, Kilich E, Mehta P, O'Callaghan C, Zhou J, Barclay W, De Coppi P, Butler CR, Cortina-Borja M, Vinette H, Roy S, Breuer J, Chambers RC, Heywood WE, Mills K, Hynds RE, Teichmann SA, Meyer KB, Nikolić MZ, Smith CM. Age-specific nasal epithelial responses to SARS-CoV-2 infection. Nat Microbiol 2024; 9:1293-1311. [PMID: 38622380 PMCID: PMC11087271 DOI: 10.1038/s41564-024-01658-1] [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: 03/24/2023] [Accepted: 03/04/2024] [Indexed: 04/17/2024]
Abstract
Children infected with SARS-CoV-2 rarely progress to respiratory failure. However, the risk of mortality in infected people over 85 years of age remains high. Here we investigate differences in the cellular landscape and function of paediatric (<12 years), adult (30-50 years) and older adult (>70 years) ex vivo cultured nasal epithelial cells in response to infection with SARS-CoV-2. We show that cell tropism of SARS-CoV-2, and expression of ACE2 and TMPRSS2 in nasal epithelial cell subtypes, differ between age groups. While ciliated cells are viral replication centres across all age groups, a distinct goblet inflammatory subtype emerges in infected paediatric cultures and shows high expression of interferon-stimulated genes and incomplete viral replication. In contrast, older adult cultures infected with SARS-CoV-2 show a proportional increase in basaloid-like cells, which facilitate viral spread and are associated with altered epithelial repair pathways. We confirm age-specific induction of these cell types by integrating data from in vivo COVID-19 studies and validate that our in vitro model recapitulates early epithelial responses to SARS-CoV-2 infection.
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Affiliation(s)
| | | | - Kaylee B Worlock
- UCL Respiratory, Division of Medicine, University College London, London, UK
| | | | - Tereza Masonou
- Great Ormond Street UCL Institute of Child Health, London, UK
| | - Masahiro Yoshida
- UCL Respiratory, Division of Medicine, University College London, London, UK
| | | | - Ni Huang
- Wellcome Sanger Institute, Cambridge, UK
| | | | | | - Liam Bolt
- Wellcome Sanger Institute, Cambridge, UK
| | | | | | - Samuel Ellis
- Great Ormond Street UCL Institute of Child Health, London, UK
| | - Machaela Palor
- Great Ormond Street UCL Institute of Child Health, London, UK
| | - Thomas Burgoyne
- UCL Institute of Ophthalmology, University College London, London, UK
- Royal Brompton Hospital, Guy's and St Thomas' NHS Foundation Trust, London, UK
| | - Andreia Pinto
- Royal Brompton Hospital, Guy's and St Thomas' NHS Foundation Trust, London, UK
| | - Dale Moulding
- Great Ormond Street UCL Institute of Child Health, London, UK
| | - Timothy D McHugh
- UCL Centre for Clinical Microbiology, Division of Infection and Immunity, University College London, London, UK
| | - Aarash Saleh
- Royal Free Hospital NHS Foundation Trust, London, UK
| | - Eliz Kilich
- UCL Respiratory, Division of Medicine, University College London, London, UK
- University College London Hospitals NHS Foundation Trust, London, UK
| | - Puja Mehta
- UCL Respiratory, Division of Medicine, University College London, London, UK
- University College London Hospitals NHS Foundation Trust, London, UK
| | | | - Jie Zhou
- Department of Infectious Disease, Imperial College London, London, UK
| | - Wendy Barclay
- Department of Infectious Disease, Imperial College London, London, UK
| | - Paolo De Coppi
- Great Ormond Street UCL Institute of Child Health, London, UK
- Great Ormond Street Hospital NHS Foundation Trust, London, UK
| | - Colin R Butler
- Great Ormond Street Hospital NHS Foundation Trust, London, UK
- Epithelial Cell Biology in ENT Research (EpiCENTR) Group, Developmental Biology and Cancer Department, Great Ormond Street UCL Institute of Child Health, University College London, London, UK
| | | | - Heloise Vinette
- Great Ormond Street UCL Institute of Child Health, London, UK
| | - Sunando Roy
- Great Ormond Street UCL Institute of Child Health, London, UK
| | - Judith Breuer
- Great Ormond Street UCL Institute of Child Health, London, UK
| | - Rachel C Chambers
- UCL Respiratory, Division of Medicine, University College London, London, UK
| | - Wendy E Heywood
- Great Ormond Street UCL Institute of Child Health, London, UK
| | - Kevin Mills
- Great Ormond Street UCL Institute of Child Health, London, UK
| | - Robert E Hynds
- Epithelial Cell Biology in ENT Research (EpiCENTR) Group, Developmental Biology and Cancer Department, Great Ormond Street UCL Institute of Child Health, University College London, London, UK
- UCL Cancer Institute, University College London, London, UK
| | - Sarah A Teichmann
- Wellcome Sanger Institute, Cambridge, UK.
- Theory of Condensed Matter, Cavendish Laboratory/Dept Physics, University of Cambridge, Cambridge, UK.
| | | | - Marko Z Nikolić
- UCL Respiratory, Division of Medicine, University College London, London, UK.
- University College London Hospitals NHS Foundation Trust, London, UK.
| | - Claire M Smith
- Great Ormond Street UCL Institute of Child Health, London, UK.
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157
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Duhan L, Kumari D, Naime M, Parmar VS, Chhillar AK, Dangi M, Pasrija R. Single-cell transcriptomics: background, technologies, applications, and challenges. Mol Biol Rep 2024; 51:600. [PMID: 38689046 DOI: 10.1007/s11033-024-09553-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: 02/09/2024] [Accepted: 04/15/2024] [Indexed: 05/02/2024]
Abstract
Single-cell sequencing was developed as a high-throughput tool to elucidate unusual and transient cell states that are barely visible in the bulk. This technology reveals the evolutionary status of cells and differences between populations, helps to identify unique cell subtypes and states, reveals regulatory relationships between genes, targets and molecular mechanisms in disease processes, tumor heterogeneity, the state of the immune environment, etc. However, the high cost and technical limitations of single-cell sequencing initially prevented its widespread application, but with advances in research, numerous new single-cell sequencing techniques have been discovered, lowering the cost barrier. Many single-cell sequencing platforms and bioinformatics methods have recently become commercially available, allowing researchers to make fascinating observations. They are now increasingly being used in various industries. Several protocols have been discovered in this context and each technique has unique characteristics, capabilities and challenges. This review presents the latest advancements in single-cell transcriptomics technologies. This includes single-cell transcriptomics approaches, workflows and statistical approaches to data processing, as well as the potential advances, applications, opportunities and challenges of single-cell transcriptomics technology. You will also get an overview of the entry points for spatial transcriptomics and multi-omics.
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Affiliation(s)
- Lucky Duhan
- Department of Biochemistry, Maharshi Dayanand University, Rohtak, Haryana, 124001, India
| | - Deepika Kumari
- Department of Biochemistry, Maharshi Dayanand University, Rohtak, Haryana, 124001, India
| | - Mohammad Naime
- Central Research Institute of Unani Medicine (Under Central Council for Research in Unani Medicine, Ministry of Ayush, Govt of India), Uttar Pradesh, Lucknow, India
| | - Virinder S Parmar
- CUNY-Graduate Center and Departments of Chemistry, Nanoscience Program, City College & Medgar Evers College, The City University of New York, 1638 Bedford Avenue, Brooklyn, NY, 11225, USA
- Institute of Click Chemistry Research and Studies, Amity University, Noida, Uttar Pradesh, 201303, India
| | - Anil K Chhillar
- Centre for Biotechnology, Maharshi Dayanand University, Rohtak, Haryana, 124001, India
| | - Mehak Dangi
- Centre for Bioinformatics, Maharshi Dayanand University, Rohtak, Haryana, 124001, India
| | - Ritu Pasrija
- Department of Biochemistry, Maharshi Dayanand University, Rohtak, Haryana, 124001, India.
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158
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Lee MK, Azizgolshani N, Shapiro JA, Nguyen LN, Kolling FW, Zanazzi GJ, Frost HR, Christensen BC. Identifying tumor type and cell type-specific gene expression alterations in pediatric central nervous system tumors. Nat Commun 2024; 15:3634. [PMID: 38688897 PMCID: PMC11061189 DOI: 10.1038/s41467-024-47712-8] [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: 02/18/2023] [Accepted: 04/09/2024] [Indexed: 05/02/2024] Open
Abstract
Central nervous system (CNS) tumors are the leading cause of pediatric cancer death, and these patients have an increased risk for developing secondary neoplasms. Due to the low prevalence of pediatric CNS tumors, major advances in targeted therapies have been lagging compared to other adult tumors. We collect single nuclei RNA-seq data from 84,700 nuclei of 35 pediatric CNS tumors and three non-tumoral pediatric brain tissues and characterize tumor heterogeneity and transcriptomic alterations. We distinguish cell subpopulations associated with specific tumor types including radial glial cells in ependymomas and oligodendrocyte precursor cells in astrocytomas. In tumors, we observe pathways important in neural stem cell-like populations, a cell type previously associated with therapy resistance. Lastly, we identify transcriptomic alterations among pediatric CNS tumor types compared to non-tumor tissues, while accounting for cell type effects on gene expression. Our results suggest potential tumor type and cell type-specific targets for pediatric CNS tumor treatment. Here we address current gaps in understanding single nuclei gene expression profiles of previously under-investigated tumor types and enhance current knowledge of gene expression profiles of single cells of various pediatric CNS tumors.
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Affiliation(s)
- Min Kyung Lee
- Department of Epidemiology, Geisel School of Medicine at Dartmouth, Lebanon, NH, USA
| | - Nasim Azizgolshani
- Department of Epidemiology, Geisel School of Medicine at Dartmouth, Lebanon, NH, USA
- Department of Surgery, Columbia University Irving Medical Center, New York, NY, USA
| | - Joshua A Shapiro
- Childhood Cancer Data Lab, Alex's Lemonade Stand Foundation, Bala Cynwyd, PA, USA
| | - Lananh N Nguyen
- Department of Laboratory Medicine and Pathobiology, University of Toronto, Toronto, ON, Canada
| | | | - George J Zanazzi
- Dartmouth Cancer Center, Lebanon, NH, USA
- Department of Pathology and Laboratory Medicine, Geisel School of Medicine at Dartmouth, Lebanon, NH, USA
| | - Hildreth Robert Frost
- Department of Biomedical Data Science, Geisel School of Medicine at Dartmouth, Lebanon, NH, USA
| | - Brock C Christensen
- Department of Epidemiology, Geisel School of Medicine at Dartmouth, Lebanon, NH, USA.
- Department of Molecular and Systems Biology, Geisel School of Medicine at Dartmouth, Lebanon, NH, USA.
- Department of Community and Family Medicine, Geisel School of Medicine at Dartmouth, Lebanon, NH, USA.
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159
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Yoshimura S, Shimada R, Kikuchi K, Kawagoe S, Abe H, Iisaka S, Fujimura S, Yasunaga KI, Usuki S, Tani N, Ohba T, Kondoh E, Saio T, Araki K, Ishiguro KI. Atypical heat shock transcription factor HSF5 is critical for male meiotic prophase under non-stress conditions. Nat Commun 2024; 15:3330. [PMID: 38684656 PMCID: PMC11059408 DOI: 10.1038/s41467-024-47601-0] [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: 09/15/2023] [Accepted: 04/04/2024] [Indexed: 05/02/2024] Open
Abstract
Meiotic prophase progression is differently regulated in males and females. In males, pachytene transition during meiotic prophase is accompanied by robust alteration in gene expression. However, how gene expression is regulated differently to ensure meiotic prophase completion in males remains elusive. Herein, we identify HSF5 as a male germ cell-specific heat shock transcription factor (HSF) for meiotic prophase progression. Genetic analyzes and single-cell RNA-sequencing demonstrate that HSF5 is essential for progression beyond the pachytene stage under non-stress conditions rather than heat stress. Chromatin binding analysis in vivo and DNA-binding assays in vitro suggest that HSF5 binds to promoters in a subset of genes associated with chromatin organization. HSF5 recognizes a DNA motif different from typical heat shock elements recognized by other canonical HSFs. This study suggests that HSF5 is an atypical HSF that is required for the gene expression program for pachytene transition during meiotic prophase in males.
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Affiliation(s)
- Saori Yoshimura
- Department of Chromosome Biology, Institute of Molecular Embryology and Genetics (IMEG), Kumamoto University, Honjo 2-2-1, Chuo-ku, Kumamoto, 860-0811, Japan
- Department of Obstetrics and Gynecology, Faculty of Life Sciences, Kumamoto University, Kumamoto, 860-8556, Japan
| | - Ryuki Shimada
- Department of Chromosome Biology, Institute of Molecular Embryology and Genetics (IMEG), Kumamoto University, Honjo 2-2-1, Chuo-ku, Kumamoto, 860-0811, Japan
| | - Koji Kikuchi
- Department of Chromosome Biology, Institute of Molecular Embryology and Genetics (IMEG), Kumamoto University, Honjo 2-2-1, Chuo-ku, Kumamoto, 860-0811, Japan
| | - Soichiro Kawagoe
- Division of Molecular Life Science, Institute of Advanced Medical Sciences, Tokushima University, Tokushima, 770-8503, Japan
| | - Hironori Abe
- Department of Chromosome Biology, Institute of Molecular Embryology and Genetics (IMEG), Kumamoto University, Honjo 2-2-1, Chuo-ku, Kumamoto, 860-0811, Japan
| | - Sakie Iisaka
- Department of Chromosome Biology, Institute of Molecular Embryology and Genetics (IMEG), Kumamoto University, Honjo 2-2-1, Chuo-ku, Kumamoto, 860-0811, Japan
| | - Sayoko Fujimura
- Liaison Laboratory Research Promotion Center, IMEG, Kumamoto University, Kumamoto, 860-0811, Japan
| | - Kei-Ichiro Yasunaga
- Liaison Laboratory Research Promotion Center, IMEG, Kumamoto University, Kumamoto, 860-0811, Japan
| | - Shingo Usuki
- Liaison Laboratory Research Promotion Center, IMEG, Kumamoto University, Kumamoto, 860-0811, Japan
| | - Naoki Tani
- Liaison Laboratory Research Promotion Center, IMEG, Kumamoto University, Kumamoto, 860-0811, Japan
| | - Takashi Ohba
- Department of Obstetrics and Gynecology, Faculty of Life Sciences, Kumamoto University, Kumamoto, 860-8556, Japan
| | - Eiji Kondoh
- Department of Obstetrics and Gynecology, Faculty of Life Sciences, Kumamoto University, Kumamoto, 860-8556, Japan
| | - Tomohide Saio
- Division of Molecular Life Science, Institute of Advanced Medical Sciences, Tokushima University, Tokushima, 770-8503, Japan
| | - Kimi Araki
- Institute of Resource Development and Analysis, Kumamoto University, Kumamoto, 860-0811, Japan
- Center for Metabolic Regulation of Healthy Aging, Kumamoto University, Kumamoto, 860-8556, Japan
| | - Kei-Ichiro Ishiguro
- Department of Chromosome Biology, Institute of Molecular Embryology and Genetics (IMEG), Kumamoto University, Honjo 2-2-1, Chuo-ku, Kumamoto, 860-0811, Japan.
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Brinkmeier ML, Wang SQ, Pittman H, Cheung LY, Prasov L. Myelin regulatory factor ( Myrf ) is a critical early regulator of retinal pigment epithelial development. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.04.26.591281. [PMID: 38746430 PMCID: PMC11092522 DOI: 10.1101/2024.04.26.591281] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/16/2024]
Abstract
Myelin regulatory factor (Myrf) is a critical transcription factor in early retinal and retinal pigment epithelial development, and human variants in MYRF are a cause for nanophthalmos. Single cell RNA sequencing (scRNAseq) was performed on Myrf conditional knockout mice ( Rx>Cre Myrf fl/fl ) at 3 developmental timepoints. Myrf was expressed specifically in the RPE, and expression was abrogated in Rx>Cre Myrf fl/fl eyes. scRNAseq analysis revealed a loss of RPE cells at all timepoints resulting from cell death. GO-term analysis in the RPE revealed downregulation of melanogenesis and anatomic structure morphogenesis pathways, which were supported by electron microscopy and histologic analysis. Novel structural target genes including Ermn and Upk3b , along with macular degeneration and inherited retinal disease genes were identified as downregulated, and a strong upregulation of TGFß/BMP signaling and effectors was observed. Regulon analysis placed Myrf downstream of Pax6 and Mitf and upstream of Sox10 in RPE differentiation. Together, these results suggest a strong role for Myrf in the RPE maturation by regulating melanogenesis, cell survival, and cell structure, in part acting through suppression of TGFß signaling and activation of Sox10 . SUMMARY STATEMENT Myrf regulates RPE development, melanogenesis, and is important for cell structure and survival, in part through regulation of Ermn , Upk3b and Sox10, and BMP/TGFb signaling.
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Xu DM, Chen LX, Zhuang XY, Han H, Mo M. The Role of JAK-STAT-SOCS1 Axis in Tumorigenesis, Malignant Progression and Lymphatic Metastasis of Penile Cancer. Int J Med Sci 2024; 21:1176-1186. [PMID: 38774752 PMCID: PMC11103387 DOI: 10.7150/ijms.95490] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 02/19/2024] [Accepted: 04/24/2024] [Indexed: 05/24/2024] Open
Abstract
Background: To uncover the potential significance of JAK-STAT-SOCS1 axis in penile cancer, our study was the pioneer in exploring the altered expression processes of JAK-STAT-SOCS1 axis in tumorigenesis, malignant progression and lymphatic metastasis of penile cancer. Methods: In current study, the comprehensive analysis of JAK-STAT-SOCS1 axis in penile cancer was analyzed via multiple analysis approaches based on GSE196978 data, single-cell data (6 cancer samples) and bulk RNA data (7 cancer samples and 7 metastasis lymph nodes). Results: Our study observed an altered molecular expression of JAK-STAT-SOCS1 axis during three different stages of penile cancer, from tumorigenesis to malignant progression to lymphatic metastasis. STAT4 was an important dominant molecule in penile cancer, which mediated the immunosuppressive tumor microenvironment by driving the apoptosis of cytotoxic T cell and was also a valuable biomarker of immune checkpoint inhibitor treatment response. Conclusions: Our findings revealed that the complexity of JAK-STAT-SOCS1 axis and the predominant role of STAT4 in penile cancer, which can mediate tumorigenesis, malignant progression, and lymphatic metastasis. This insight provided valuable information for developing precise treatment strategies for patients with penile cancer.
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Affiliation(s)
- Da-Ming Xu
- State Key Laboratory of Oncology in South China, Guangdong Provincial Clinical Research Center for Cancer, Sun Yat-sen University Cancer Center, Guangzhou 510060, P. R. China
- Department of Urology, Sun Yat-sen University Cancer Center, Guangzhou 510060, P.R. China
| | - Ling-Xiao Chen
- Department of Urology, Xiangya Hospital, Central South University, Changsha 410008, P.R. China
| | - Xiao-Yu Zhuang
- Department of Anesthesiology, Second Affiliated Hospital of Shantou University Medical College, Shantou 515041, P. R. China
| | - Hui Han
- State Key Laboratory of Oncology in South China, Guangdong Provincial Clinical Research Center for Cancer, Sun Yat-sen University Cancer Center, Guangzhou 510060, P. R. China
- Department of Urology, Sun Yat-sen University Cancer Center, Guangzhou 510060, P.R. China
| | - Miao Mo
- Department of Urology, Xiangya Hospital, Central South University, Changsha 410008, P.R. China
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Chen Q, Deng Y, Li Y, Chen J, Zhang R, Yang L, Guo R, Xing B, Ding P, Cai J, Zhao H. Association of preoperative aspartate aminotransferase to platelet ratio index with outcomes and tumour microenvironment among colorectal cancer with liver metastases. Cancer Lett 2024; 588:216778. [PMID: 38458593 DOI: 10.1016/j.canlet.2024.216778] [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: 11/20/2023] [Revised: 02/24/2024] [Accepted: 02/29/2024] [Indexed: 03/10/2024]
Abstract
This study aims to investigate applicable robust biomarkers that can improve prognostic predictions for colorectal liver metastasis (CRLM) patients receiving simultaneous resection. A total of 1323 CRLM patients from multiple centres were included. The preoperative aspartate aminotransferase to platelet ratio index (APRI) level from blood of patients were obtained. Patients were stratified into a high APRI group and a low APRI group, and comparisons were conducted by analyzing progression-free survival (PFS), overall survival (OS) and postoperative early recurrence. Tumour samples of CRLM were collected to perform single-cell RNA sequencing and multiplex immunohistochemistry/immunofluorescence (mIHC/IF) to investigate the association of APRI levels and the tumour microenvironment of CRLM. Compared with APRI <0.33, PFS disadvantage (IPTW-adjusted HR = 1.240, P = 0.015) and OS disadvantage (IPTW- adjusted HR = 1.507, P = 0.002) of APRI ≥0.33 were preserved in the IPTW-adjusted Cox hazards regression analyses. An APRI ≥0.25 was associated with a significantly increased risk of postoperative early recurrence after adjustment (IPTW-adjusted OR = 1.486, P = 0.001). The external validation showed consistent results with the training cohort. In the high APRI group, the single-cell RNA sequencing results revealed a heightened malignancy of epithelial cells, the enrichment of inflammatory-like cancer-associated fibroblasts and SPP1+ macrophages associated with activation of malignant cells and fibrotic microenvironment, and a more suppressed-function T cells; mIHC/IF showed that PD1+ CD4+ T cells, FOXP3+ CD4+ T cells, PD1+ CD8+ T cells, FOXP3+ CD8+ T cells, SPP1+ macrophages and iCAFs were significantly increased in the intratumoral region and peritumoral region. This study contributed valuable evidence regarding preoperative APRI for predicting prognoses among CRLM patients receiving simultaneous resection and provided underlying clues supporting the association between APRI and clinical outcomes by single-cell sequencing bioinformatics analysis and mIHC/IF.
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Affiliation(s)
- Qichen Chen
- Department of Colorectal Surgery, State Key Laboratory of Oncology in South China, Guangdong Provincial Clinical Research Center for Cancer, Sun Yat-sen University Cancer Center, Guangzhou, 510060, China; Department of Hepatobiliary Surgery, National Cancer Center/National Clinical Research Center for Cancer/Cancer Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, 100021, Beijing, China
| | - Yiqiao Deng
- Department of Hepatobiliary Surgery, National Cancer Center/National Clinical Research Center for Cancer/Cancer Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, 100021, Beijing, China
| | - Yuan Li
- Department of Colorectal Surgery, State Key Laboratory of Oncology in South China, Guangdong Provincial Clinical Research Center for Cancer, Sun Yat-sen University Cancer Center, Guangzhou, 510060, China
| | - Jinghua Chen
- Department of Hepatobiliary Surgery, National Cancer Center/National Clinical Research Center for Cancer/Cancer Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, 100021, Beijing, China
| | - Rui Zhang
- Department of Colorectal Surgery, Cancer Hospital of China Medical University, Liaoning Cancer Hospital & Insititute, China
| | - Lang Yang
- Department of Hepatobiliary Surgery, National Cancer Center/National Clinical Research Center for Cancer/Cancer Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, 100021, Beijing, China
| | - Rui Guo
- Key Laboratory of Carcinogenesis and Translational Research, Hepatopancreatobiliary Surgery Department I, School of Oncology, Beijing Cancer Hospital and Institute, Peking University, Ministry of Education, Beijing, China
| | - Baocai Xing
- Key Laboratory of Carcinogenesis and Translational Research, Hepatopancreatobiliary Surgery Department I, School of Oncology, Beijing Cancer Hospital and Institute, Peking University, Ministry of Education, Beijing, China.
| | - Peirong Ding
- Department of Colorectal Surgery, State Key Laboratory of Oncology in South China, Guangdong Provincial Clinical Research Center for Cancer, Sun Yat-sen University Cancer Center, Guangzhou, 510060, China.
| | - Jianqiang Cai
- Department of Hepatobiliary Surgery, National Cancer Center/National Clinical Research Center for Cancer/Cancer Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, 100021, Beijing, China.
| | - Hong Zhao
- Department of Hepatobiliary Surgery, National Cancer Center/National Clinical Research Center for Cancer/Cancer Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, 100021, Beijing, China.
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Cao T, Zhang W, Wang Q, Wang C, Ma W, Zhang C, Ge M, Tian M, Yu J, Jiao A, Wang L, Liu M, Wang P, Guo Z, Zhou Y, Chen S, Yin W, Yi J, Guo H, Han H, Zhang B, Wu K, Fan D, Wang X, Nie Y, Lu Y, Zhao X. Cancer SLC6A6-mediated taurine uptake transactivates immune checkpoint genes and induces exhaustion in CD8 + T cells. Cell 2024; 187:2288-2304.e27. [PMID: 38565142 DOI: 10.1016/j.cell.2024.03.011] [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: 05/19/2023] [Revised: 12/12/2023] [Accepted: 03/08/2024] [Indexed: 04/04/2024]
Abstract
Taurine is used to bolster immunity, but its effects on antitumor immunity are unclear. Here, we report that cancer-related taurine consumption causes T cell exhaustion and tumor progression. The taurine transporter SLC6A6 is correlated with aggressiveness and poor outcomes in multiple cancers. SLC6A6-mediated taurine uptake promotes the malignant behaviors of tumor cells but also increases the survival and effector function of CD8+ T cells. Tumor cells outcompete CD8+ T cells for taurine by overexpressing SLC6A6, which induces T cell death and malfunction, thereby fueling tumor progression. Mechanistically, taurine deficiency in CD8+ T cells increases ER stress, promoting ATF4 transcription in a PERK-JAK1-STAT3 signaling-dependent manner. Increased ATF4 transactivates multiple immune checkpoint genes and induces T cell exhaustion. In gastric cancer, we identify a chemotherapy-induced SP1-SLC6A6 regulatory axis. Our findings suggest that tumoral-SLC6A6-mediated taurine deficiency promotes immune evasion and that taurine supplementation reinvigorates exhausted CD8+ T cells and increases the efficacy of cancer therapies.
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Affiliation(s)
- Tianyu Cao
- State Key Laboratory of Holistic Integrative Management of Gastrointestinal Cancers, National Clinical Research Center for Digestive Diseases, Xijing Hospital, Fourth Military Medical University, Xi'an, Shaanxi 710032, China
| | - Wenyao Zhang
- State Key Laboratory of Holistic Integrative Management of Gastrointestinal Cancers, National Clinical Research Center for Digestive Diseases, Xijing Hospital, Fourth Military Medical University, Xi'an, Shaanxi 710032, China
| | - Qi Wang
- State Key Laboratory of Holistic Integrative Management of Gastrointestinal Cancers, National Clinical Research Center for Digestive Diseases, Xijing Hospital, Fourth Military Medical University, Xi'an, Shaanxi 710032, China; Department of Gastroenterology, Tangdu Hospital, Fourth Military Medical University, Xi'an, Shaanxi 710038, China; College of Life Sciences, Northwest University, Xi'an, Shaanxi 710069, China
| | - Chen Wang
- State Key Laboratory of Holistic Integrative Management of Gastrointestinal Cancers, National Clinical Research Center for Digestive Diseases, Xijing Hospital, Fourth Military Medical University, Xi'an, Shaanxi 710032, China; Department of Gastroenterology, Tangdu Hospital, Fourth Military Medical University, Xi'an, Shaanxi 710038, China; College of Life Sciences, Northwest University, Xi'an, Shaanxi 710069, China
| | - Wanqi Ma
- State Key Laboratory of Holistic Integrative Management of Gastrointestinal Cancers, National Clinical Research Center for Digestive Diseases, Xijing Hospital, Fourth Military Medical University, Xi'an, Shaanxi 710032, China
| | - Cangang Zhang
- Department of Pathogenic Microbiology and Immunology, Xi'an Jiaotong University, Xi'an, Shaanxi 710049, China
| | - Minghui Ge
- Simcere Diagnostics Co., Ltd., Nanjing, Jiangsu 210042, China
| | - Miaomiao Tian
- State Key Laboratory of Holistic Integrative Management of Gastrointestinal Cancers, National Clinical Research Center for Digestive Diseases, Xijing Hospital, Fourth Military Medical University, Xi'an, Shaanxi 710032, China
| | - Jia Yu
- Department of Gastroenterology, Tangdu Hospital, Fourth Military Medical University, Xi'an, Shaanxi 710038, China
| | - Anjun Jiao
- Department of Pathogenic Microbiology and Immunology, Xi'an Jiaotong University, Xi'an, Shaanxi 710049, China
| | - Liang Wang
- Department of Medical Genetics and Developmental Biology, Fourth Military Medical University, Xi'an, Shaanxi 710032, China
| | - Manjiao Liu
- Simcere Diagnostics Co., Ltd., Nanjing, Jiangsu 210042, China
| | - Pei Wang
- State Key Laboratory of Holistic Integrative Management of Gastrointestinal Cancers, National Clinical Research Center for Digestive Diseases, Xijing Hospital, Fourth Military Medical University, Xi'an, Shaanxi 710032, China
| | - Zhiyu Guo
- State Key Laboratory of Holistic Integrative Management of Gastrointestinal Cancers, National Clinical Research Center for Digestive Diseases, Xijing Hospital, Fourth Military Medical University, Xi'an, Shaanxi 710032, China
| | - Yun Zhou
- Department of Gastroenterology, Tangdu Hospital, Fourth Military Medical University, Xi'an, Shaanxi 710038, China
| | - Shuyi Chen
- State Key Laboratory of Holistic Integrative Management of Gastrointestinal Cancers, National Clinical Research Center for Digestive Diseases, Xijing Hospital, Fourth Military Medical University, Xi'an, Shaanxi 710032, China
| | - Wen Yin
- Department of Blood Transfusion, Xijing Hospital, Fourth Military Medical University, Xi'an, Shaanxi 710032, China
| | - Jing Yi
- Department of Blood Transfusion, Xijing Hospital, Fourth Military Medical University, Xi'an, Shaanxi 710032, China
| | - Hao Guo
- Simcere Diagnostics Co., Ltd., Nanjing, Jiangsu 210042, China
| | - Hua Han
- Department of Biochemistry and Molecular Biology, Fourth Military Medical University, Xi'an, Shaanxi 710032, China
| | - Baojun Zhang
- Department of Pathogenic Microbiology and Immunology, Xi'an Jiaotong University, Xi'an, Shaanxi 710049, China
| | - Kaichun Wu
- State Key Laboratory of Holistic Integrative Management of Gastrointestinal Cancers, National Clinical Research Center for Digestive Diseases, Xijing Hospital, Fourth Military Medical University, Xi'an, Shaanxi 710032, China
| | - Daiming Fan
- State Key Laboratory of Holistic Integrative Management of Gastrointestinal Cancers, National Clinical Research Center for Digestive Diseases, Xijing Hospital, Fourth Military Medical University, Xi'an, Shaanxi 710032, China
| | - Xin Wang
- State Key Laboratory of Holistic Integrative Management of Gastrointestinal Cancers, National Clinical Research Center for Digestive Diseases, Xijing Hospital, Fourth Military Medical University, Xi'an, Shaanxi 710032, China; Department of Gastroenterology, Tangdu Hospital, Fourth Military Medical University, Xi'an, Shaanxi 710038, China.
| | - Yongzhan Nie
- State Key Laboratory of Holistic Integrative Management of Gastrointestinal Cancers, National Clinical Research Center for Digestive Diseases, Xijing Hospital, Fourth Military Medical University, Xi'an, Shaanxi 710032, China.
| | - Yuanyuan Lu
- State Key Laboratory of Holistic Integrative Management of Gastrointestinal Cancers, National Clinical Research Center for Digestive Diseases, Xijing Hospital, Fourth Military Medical University, Xi'an, Shaanxi 710032, China.
| | - Xiaodi Zhao
- State Key Laboratory of Holistic Integrative Management of Gastrointestinal Cancers, National Clinical Research Center for Digestive Diseases, Xijing Hospital, Fourth Military Medical University, Xi'an, Shaanxi 710032, China.
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Lin S, Dai Y, Han C, Han T, Zhao L, Wu R, Liu J, Zhang B, Huang N, Liu Y, Lai S, Shi J, Wang Y, Lou M, Xie J, Cheng Y, Tang H, Yao H, Fang H, Zhang Y, Wu X, Shen L, Ye Y, Xue L, Wu ZB. Single-cell transcriptomics reveal distinct immune-infiltrating phenotypes and macrophage-tumor interaction axes among different lineages of pituitary neuroendocrine tumors. Genome Med 2024; 16:60. [PMID: 38658971 PMCID: PMC11040908 DOI: 10.1186/s13073-024-01325-4] [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: 10/14/2023] [Accepted: 03/26/2024] [Indexed: 04/26/2024] Open
Abstract
BACKGROUND Pituitary neuroendocrine tumors (PitNETs) are common gland neoplasms demonstrating distinctive transcription factors. Although the role of immune cells in PitNETs has been widely recognized, the precise immunological environment and its control over tumor cells are poorly understood. METHODS The heterogeneity, spatial distribution, and clinical significance of macrophages in PitNETs were analyzed using single-cell RNA sequencing (scRNA-seq), bulk RNA-seq, spatial transcriptomics, immunohistochemistry, and multiplexed quantitative immunofluorescence (QIF). Cell viability, cell apoptosis assays, and in vivo subcutaneous xenograft experiments have confirmed that INHBA-ACVR1B influences the process of tumor cell apoptosis. RESULTS The present study evaluated scRNA-seq data from 23 PitNET samples categorized into 3 primary lineages. The objective was to explore the diversity of tumors and the composition of immune cells across these lineages. Analyzed data from scRNA-seq and 365 bulk RNA sequencing samples conducted in-house revealed the presence of three unique subtypes of tumor immune microenvironment (TIME) in PitNETs. These subtypes were characterized by varying levels of immune infiltration, ranging from low to intermediate to high. In addition, the NR5A1 lineage is primarily associated with the subtype characterized by limited infiltration of immune cells. Tumor-associated macrophages (TAMs) expressing CX3CR1+, C1Q+, and GPNMB+ showed enhanced contact with tumor cells expressing NR5A1 + , TBX19+, and POU1F1+, respectively. This emphasizes the distinct interaction axes between TAMs and tumor cells based on their lineage. Moreover, the connection between CX3CR1+ macrophages and tumor cells via INHBA-ACVR1B regulates tumor cell apoptosis. CONCLUSIONS In summary, the different subtypes of TIME and the interaction between TAM and tumor cells offer valuable insights into the control of TIME that affects the development of PitNET. These findings can be utilized as prospective targets for therapeutic interventions.
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Affiliation(s)
- Shaojian Lin
- Department of Neurosurgery, Center of Pituitary Tumor, Ruijin Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, China
- Department of Neurosurgery, Center for Immune-Related Diseases at Shanghai Institute of Immunology, Ruijin Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, China
- Department of Neurosurgery, First Affiliated Hospital of Wenzhou Medical University, Wenzhou, China
| | - Yuting Dai
- Shanghai Institute of Hematology, State Key Laboratory of Medical Genomics, National Research Center for Translational Medicine at Shanghai, Rujin Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, China
| | - Changxi Han
- Department of Neurosurgery, Center of Pituitary Tumor, Ruijin Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, China
| | - Tianyi Han
- Department of Neurosurgery, Center of Pituitary Tumor, Ruijin Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, China
| | - Linfeng Zhao
- Shanghai Key Laboratory of Tumor Microenvironment and Inflammation, Shanghai Jiao Tong University School of Medicine, Shanghai, China
| | - Renyan Wu
- Shanghai Institute of Immunology, Department of Immunology and Microbiology, Shanghai Jiao Tong University School of Medicine, Shanghai, China
| | - Jianyue Liu
- Shanghai Key Laboratory of Tumor Microenvironment and Inflammation, Shanghai Jiao Tong University School of Medicine, Shanghai, China
| | - Bo Zhang
- Department of Neurosurgery, Center of Pituitary Tumor, Ruijin Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, China
| | - Ning Huang
- Department of Neurosurgery, First Affiliated Hospital of Wenzhou Medical University, Wenzhou, China
| | - Yanting Liu
- Department of Neurosurgery, Center of Pituitary Tumor, Ruijin Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, China
| | - Shujing Lai
- Shanghai Institute of Immunology, Department of Immunology and Microbiology, Shanghai Jiao Tong University School of Medicine, Shanghai, China
| | - Jintong Shi
- Shanghai Institute of Immunology, Department of Immunology and Microbiology, Shanghai Jiao Tong University School of Medicine, Shanghai, China
| | - Yu Wang
- Department of Neurosurgery, Ren Ji Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, China
| | - Meiqing Lou
- Department of Neurosurgery, Shanghai General Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, China
| | - Jing Xie
- Department of Pathology, Ruijin Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, China
| | - Yijun Cheng
- Department of Neurosurgery, Center of Pituitary Tumor, Ruijin Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, China
| | - Hao Tang
- Department of Neurosurgery, Center of Pituitary Tumor, Ruijin Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, China
| | - Hong Yao
- Department of Neurosurgery, Center of Pituitary Tumor, Ruijin Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, China
| | - Hai Fang
- Shanghai Institute of Hematology, State Key Laboratory of Medical Genomics, National Research Center for Translational Medicine at Shanghai, Rujin Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, China
| | - Yan Zhang
- Med-X Research Institute and School of Biomedical Engineering, Shanghai Jiao Tong University, Shanghai, China
| | - Xuefeng Wu
- Department of Neurosurgery, Center for Immune-Related Diseases at Shanghai Institute of Immunology, Ruijin Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, China
- Shanghai Institute of Immunology, Department of Immunology and Microbiology and the Ministry of Education Key Laboratory of Cell Death and Differentiation, Shanghai Jiao Tong University School of Medicine, Shanghai, China
| | - Lei Shen
- Department of Neurosurgery, Center for Immune-Related Diseases at Shanghai Institute of Immunology, Ruijin Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, China.
- Shanghai Key Laboratory of Tumor Microenvironment and Inflammation, Shanghai Jiao Tong University School of Medicine, Shanghai, China.
| | - Youqiong Ye
- Department of Neurosurgery, Center for Immune-Related Diseases at Shanghai Institute of Immunology, Ruijin Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, China.
- Shanghai Key Laboratory of Tumor Microenvironment and Inflammation, Shanghai Jiao Tong University School of Medicine, Shanghai, China.
- Shanghai Institute of Immunology, Department of Immunology and Microbiology, State Key Laboratory of Systems Medicine for Cancer, Shanghai Jiao Tong University School of Medicine, Shanghai, China.
| | - Li Xue
- Department of Neurosurgery, Center of Pituitary Tumor, Ruijin Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, China.
- Department of Neurosurgery, Center for Immune-Related Diseases at Shanghai Institute of Immunology, Ruijin Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, China.
- Shanghai Center for Brain Science and Brain-Inspired Technology, Shanghai, China.
| | - Zhe Bao Wu
- Department of Neurosurgery, Center of Pituitary Tumor, Ruijin Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, China.
- Department of Neurosurgery, Center for Immune-Related Diseases at Shanghai Institute of Immunology, Ruijin Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, China.
- Department of Neurosurgery, First Affiliated Hospital of Wenzhou Medical University, Wenzhou, China.
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Wang SY, Zhang SJ, Meng HF, Xu HQ, Guo ZX, Yan JF, Gao JL, Niu LN, Wang SL, Jiao K. DPSCs regulate epithelial-T cell interactions in oral submucous fibrosis. Stem Cell Res Ther 2024; 15:113. [PMID: 38650025 PMCID: PMC11036714 DOI: 10.1186/s13287-024-03720-5] [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: 10/21/2023] [Accepted: 04/07/2024] [Indexed: 04/25/2024] Open
Abstract
BACKGROUND Oral submucous fibrosis (OSF) is a precancerous lesion characterized by fibrous tissue deposition, the incidence of which correlates positively with the frequency of betel nut chewing. Prolonged betel nut chewing can damage the integrity of the oral mucosal epithelium, leading to chronic inflammation and local immunological derangement. However, currently, the underlying cellular events driving fibrogenesis and dysfunction are incompletely understood, such that OSF has few treatment options with limited therapeutic effectiveness. Dental pulp stem cells (DPSCs) have been recognized for their anti-inflammatory and anti-fibrosis capabilities, making them promising candidates to treat a range of immune, inflammatory, and fibrotic diseases. However, the application of DPSCs in OSF is inconclusive. Therefore, this study aimed to explore the pathogenic mechanism of OSF and, based on this, to explore new treatment options. METHODS A human cell atlas of oral mucosal tissues was compiled using single-cell RNA sequencing to delve into the underlying mechanisms. Epithelial cells were reclustered to observe the heterogeneity of OSF epithelial cells and their communication with immune cells. The results were validated in vitro, in clinicopathological sections, and in animal models. In vivo, the therapeutic effect and mechanism of DPSCs were characterized by histological staining, immunohistochemical staining, scanning electron microscopy, and atomic force microscopy. RESULTS A unique epithelial cell population, Epi1.2, with proinflammatory and profibrotic functions, was predominantly found in OSF. Epi1.2 cells also induced the fibrotic process in fibroblasts by interacting with T cells through receptor-ligand crosstalk between macrophage migration inhibitory factor (MIF)-CD74 and C-X-C motif chemokine receptor 4 (CXCR4). Furthermore, we developed OSF animal models and simulated the clinical local injection process in the rat buccal mucosa using DPSCs to assess their therapeutic impact and mechanism. In the OSF rat model, DPSCs demonstrated superior therapeutic effects compared with the positive control (glucocorticoids), including reducing collagen deposition and promoting blood vessel regeneration. DPSCs mediated immune homeostasis primarily by regulating the numbers of KRT19 + MIF + epithelial cells and via epithelial-stromal crosstalk. CONCLUSIONS Given the current ambiguity surrounding the cause of OSF and the limited treatment options available, our study reveals that epithelial cells and their crosstalk with T cells play an important role in the mechanism of OSF and suggests the therapeutic promise of DPSCs.
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Affiliation(s)
- S Y Wang
- Department of Stomatology, Tangdu Hospital & State Key Laboratory of Oral and Maxillofacial Reconstruction and Regeneration & School of Stomatology, The Fourth Military Medical University, 169 West Changle Road, Xincheng District, 710032, Xi'an, Shaanxi, P. R. China
| | - S J Zhang
- State Key Laboratory of Oral and Maxillofacial Reconstruction and Regeneration & National Clinical Research Center for Oral Diseases & Shaanxi Key Laboratory of Stomatology, School of Stomatology, The Fourth Military Medical University, 169 West Changle Road, Xincheng District, 710032, Xi'an, Shaanxi, P. R. China
| | - H F Meng
- Beijing SH Bio-tech Co., 100071, Beijing, P.R. China
| | - H Q Xu
- Department of Stomatology, Tangdu Hospital & State Key Laboratory of Oral and Maxillofacial Reconstruction and Regeneration & School of Stomatology, The Fourth Military Medical University, 169 West Changle Road, Xincheng District, 710032, Xi'an, Shaanxi, P. R. China
- The College of Life Science, Northwest University, 710032, Xi'an, Shaanxi, P.R. China
| | - Z X Guo
- Department of Stomatology, Tangdu Hospital & State Key Laboratory of Oral and Maxillofacial Reconstruction and Regeneration & School of Stomatology, The Fourth Military Medical University, 169 West Changle Road, Xincheng District, 710032, Xi'an, Shaanxi, P. R. China
| | - J F Yan
- Department of Stomatology, Tangdu Hospital & State Key Laboratory of Oral and Maxillofacial Reconstruction and Regeneration & School of Stomatology, The Fourth Military Medical University, 169 West Changle Road, Xincheng District, 710032, Xi'an, Shaanxi, P. R. China
| | - J L Gao
- State Key Laboratory of Oral and Maxillofacial Reconstruction and Regeneration & National Clinical Research Center for Oral Diseases & Shaanxi Key Laboratory of Stomatology, School of Stomatology, The Fourth Military Medical University, 169 West Changle Road, Xincheng District, 710032, Xi'an, Shaanxi, P. R. China
| | - L N Niu
- State Key Laboratory of Oral and Maxillofacial Reconstruction and Regeneration & National Clinical Research Center for Oral Diseases & Shaanxi Key Laboratory of Stomatology, School of Stomatology, The Fourth Military Medical University, 169 West Changle Road, Xincheng District, 710032, Xi'an, Shaanxi, P. R. China.
| | - S L Wang
- Beijing Laboratory of Oral Health, Capital Medical University, 10 Xitoutiao, Fengtai District, 100069, Beijing, P.R. China.
- Laboratory of Homeostatic Medicine, School of Medicine, Southern University of Science and Technology, No. 1088 Xueyuan Avenue, Nanshan District, 518055, Shenzhen, P.R. China.
| | - K Jiao
- Department of Stomatology, Tangdu Hospital & State Key Laboratory of Oral and Maxillofacial Reconstruction and Regeneration & School of Stomatology, The Fourth Military Medical University, 169 West Changle Road, Xincheng District, 710032, Xi'an, Shaanxi, P. R. China.
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Zhu W, Zhang Z, Chen J, Chen X, Huang L, Zhang X, Huang X, Ma N, Xu W, Yi X, Lu X, Fu X, Li S, Mo G, Wang Y, Yuan G, Zang M, Li Q, Jiang X, He Y, Wu S, He Y, Li Y, Hou J. A novel engineered IL-21 receptor arms T-cell receptor-engineered T cells (TCR-T cells) against hepatocellular carcinoma. Signal Transduct Target Ther 2024; 9:101. [PMID: 38643203 PMCID: PMC11032311 DOI: 10.1038/s41392-024-01792-6] [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: 07/04/2023] [Revised: 01/30/2024] [Accepted: 03/07/2024] [Indexed: 04/22/2024] Open
Abstract
Strategies to improve T cell therapy efficacy in solid tumors such as hepatocellular carcinoma (HCC) are urgently needed. The common cytokine receptor γ chain (γc) family cytokines such as IL-2, IL-7, IL-15 and IL-21 play fundamental roles in T cell development, differentiation and effector phases. This study aims to determine the combination effects of IL-21 in T cell therapy against HCC and investigate optimized strategies to utilize the effect of IL-21 signal in T cell therapy. The antitumor function of AFP-specific T cell receptor-engineered T cells (TCR-T) was augmented by exogenous IL-21 in vitro and in vivo. IL-21 enhanced proliferation capacity, promoted memory differentiation, downregulated PD-1 expression and alleviated apoptosis in TCR-T after activation. A novel engineered IL-21 receptor was established, and TCR-T armed with the novel engineered IL-21 receptors (IL-21R-TCR-T) showed upregulated phosphorylated STAT3 expression without exogenous IL-21 ligand. IL-21R-TCR-T showed better proliferation upon activation and superior antitumor function in vitro and in vivo. IL-21R-TCR-T exhibited a less differentiated, exhausted and apoptotic phenotype than conventional TCR-T upon repetitive tumor antigen stimulation. The novel IL-21 receptor in our study programs powerful TCR-T and can avoid side effects induced by IL-21 systemic utilization. The novel IL-21 receptor creates new opportunities for next-generation TCR-T against HCC.
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Affiliation(s)
- Wei Zhu
- State Key Laboratory of Organ Failure Research, Guangdong Provincial Key Laboratory of Viral Hepatitis Research, Department of Infectious Diseases, Nanfang Hospital, Southern Medical University, Guangzhou, China
| | - Zhiming Zhang
- State Key Laboratory of Organ Failure Research, Guangdong Provincial Key Laboratory of Viral Hepatitis Research, Department of Infectious Diseases, Nanfang Hospital, Southern Medical University, Guangzhou, China
| | - Jinzhang Chen
- State Key Laboratory of Organ Failure Research, Guangdong Provincial Key Laboratory of Viral Hepatitis Research, Department of Infectious Diseases, Nanfang Hospital, Southern Medical University, Guangzhou, China
| | - Xiaolan Chen
- State Key Laboratory of Organ Failure Research, Guangdong Provincial Key Laboratory of Viral Hepatitis Research, Department of Infectious Diseases, Nanfang Hospital, Southern Medical University, Guangzhou, China
| | - Lei Huang
- Institute of Cellular Medicine, Newcastle University Medical School, Newcastle, UK
| | - Xiaoyong Zhang
- State Key Laboratory of Organ Failure Research, Guangdong Provincial Key Laboratory of Viral Hepatitis Research, Department of Infectious Diseases, Nanfang Hospital, Southern Medical University, Guangzhou, China
| | - Xuan Huang
- State Key Laboratory of Organ Failure Research, Guangdong Provincial Key Laboratory of Viral Hepatitis Research, Department of Infectious Diseases, Nanfang Hospital, Southern Medical University, Guangzhou, China
| | - Na Ma
- Department of Pathology, The First People's Hospital of Foshan, Foshan, China
| | - Weikang Xu
- State Key Laboratory of Organ Failure Research, Guangdong Provincial Key Laboratory of Viral Hepatitis Research, Department of Infectious Diseases, Nanfang Hospital, Southern Medical University, Guangzhou, China
| | - Xuan Yi
- State Key Laboratory of Organ Failure Research, Guangdong Provincial Key Laboratory of Viral Hepatitis Research, Department of Infectious Diseases, Nanfang Hospital, Southern Medical University, Guangzhou, China
- Dermatology Hospital, Southern Medical University, Guangzhou, China
| | - Xinyu Lu
- State Key Laboratory of Organ Failure Research, Guangdong Provincial Key Laboratory of Viral Hepatitis Research, Department of Infectious Diseases, Nanfang Hospital, Southern Medical University, Guangzhou, China
| | - Xin Fu
- State Key Laboratory of Organ Failure Research, Guangdong Provincial Key Laboratory of Viral Hepatitis Research, Department of Infectious Diseases, Nanfang Hospital, Southern Medical University, Guangzhou, China
| | - Siwei Li
- State Key Laboratory of Organ Failure Research, Guangdong Provincial Key Laboratory of Viral Hepatitis Research, Department of Infectious Diseases, Nanfang Hospital, Southern Medical University, Guangzhou, China
| | - Guoheng Mo
- State Key Laboratory of Organ Failure Research, Guangdong Provincial Key Laboratory of Viral Hepatitis Research, Department of Infectious Diseases, Nanfang Hospital, Southern Medical University, Guangzhou, China
| | - Yiyue Wang
- State Key Laboratory of Organ Failure Research, Guangdong Provincial Key Laboratory of Viral Hepatitis Research, Department of Infectious Diseases, Nanfang Hospital, Southern Medical University, Guangzhou, China
| | - Guosheng Yuan
- State Key Laboratory of Organ Failure Research, Guangdong Provincial Key Laboratory of Viral Hepatitis Research, Department of Infectious Diseases, Nanfang Hospital, Southern Medical University, Guangzhou, China
| | - Mengya Zang
- State Key Laboratory of Organ Failure Research, Guangdong Provincial Key Laboratory of Viral Hepatitis Research, Department of Infectious Diseases, Nanfang Hospital, Southern Medical University, Guangzhou, China
| | - Qi Li
- State Key Laboratory of Organ Failure Research, Guangdong Provincial Key Laboratory of Viral Hepatitis Research, Department of Infectious Diseases, Nanfang Hospital, Southern Medical University, Guangzhou, China
| | - Xiaotao Jiang
- Department of Immunology, School of Basic Medical Sciences, Southern Medical University, Guangzhou, China
| | - Yajing He
- State Key Laboratory of Organ Failure Research, Guangdong Provincial Key Laboratory of Viral Hepatitis Research, Department of Infectious Diseases, Nanfang Hospital, Southern Medical University, Guangzhou, China
| | - Sha Wu
- Department of Immunology, School of Basic Medical Sciences, Southern Medical University, Guangzhou, China
- Microbiome Medicine Center, Department of Laboratory Medicine, Zhujiang Hospital, Southern Medical University, Guangzhou, China
- Key Laboratory of Proteomics of Guangdong Province, Demonstration Center for Experimental Education of Basic Medical Sciences of China, Guangzhou, China
| | - Yukai He
- Medical College of Georgia, Augusta University, 1120 15th Street, Augusta, GA, USA
| | - Yongyin Li
- State Key Laboratory of Organ Failure Research, Guangdong Provincial Key Laboratory of Viral Hepatitis Research, Department of Infectious Diseases, Nanfang Hospital, Southern Medical University, Guangzhou, China.
| | - Jinlin Hou
- State Key Laboratory of Organ Failure Research, Guangdong Provincial Key Laboratory of Viral Hepatitis Research, Department of Infectious Diseases, Nanfang Hospital, Southern Medical University, Guangzhou, China.
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167
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Zhao J, Wang X, Zhu H, Wei S, Zhang H, Ma L, Zhu W. Exploring natural killer cell-related biomarkers in multiple myeloma: a novel nature killer cell-related model predicting prognosis and immunotherapy response using single-cell study. Clin Exp Med 2024; 24:79. [PMID: 38634972 PMCID: PMC11026209 DOI: 10.1007/s10238-024-01322-2] [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: 01/12/2024] [Accepted: 03/03/2024] [Indexed: 04/19/2024]
Abstract
BACKGROUND Natural killer cells (NKs) may be involved in multiple myeloma (MM) progression. The present study elucidated the correlation between NKs and the progression of MM using single-cell binding transcriptome probes to identify NK cell-related biomarkers. METHODS Single-cell analysis was performed including cell and subtype annotation, cell communication, and pseudotime analysis. Hallmark pathway enrichment analysis of NKs and NKs-related differentially expressed genes (DEGs) were conducted using Gene Ontology, Kyoto Encyclopedia of Genes and Genomes, and protein-protein interaction (PPI) networks. Then, a risk model was structured based on biomarkers identified through univariate Cox regression analysis and least absolute shrinkage and selection operator regression analysis and subsequently validated. Additionally, correlation of clinical characteristics, gene set enrichment analysis, immune analysis, regulatory network, and drug forecasting were explored. RESULTS A total of 13 cell clusters were obtained and annotated, including 8 cell populations that consisted of NKs. Utilizing 123 PPI network node genes, 8 NK-related DEGs were selected to construct a prognostic model. Immune cell infiltration results suggested that 11 immune cells exhibited marked differences in the high and low-risk groups. Finally, the model was used to screen potential drug targets to enhance immunotherapy efficacy. CONCLUSION A new prognostic model for MM associated with NKs was constructed and validated. This model provides a fresh perspective for predicting patient outcomes, immunotherapeutic response, and candidate drugs.
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Affiliation(s)
- Jing Zhao
- Department of Hematology, The First Affiliated Hospital of Xi'an Jiaotong University, 277 Yanta West Road, Xi'an, 710061, Shaanxi, People's Republic of China.
| | - Xiaoning Wang
- Department of Hematology, The First Affiliated Hospital of Xi'an Jiaotong University, 277 Yanta West Road, Xi'an, 710061, Shaanxi, People's Republic of China
| | - Huachao Zhu
- Department of Hematology, The First Affiliated Hospital of Xi'an Jiaotong University, 277 Yanta West Road, Xi'an, 710061, Shaanxi, People's Republic of China
| | - Suhua Wei
- Department of Hematology, The First Affiliated Hospital of Xi'an Jiaotong University, 277 Yanta West Road, Xi'an, 710061, Shaanxi, People's Republic of China
| | - Hailing Zhang
- Department of Hematology, The First Affiliated Hospital of Xi'an Jiaotong University, 277 Yanta West Road, Xi'an, 710061, Shaanxi, People's Republic of China
| | - Le Ma
- Department of Hematology, The First Affiliated Hospital of Xi'an Jiaotong University, 277 Yanta West Road, Xi'an, 710061, Shaanxi, People's Republic of China
| | - Wenjuan Zhu
- Department of Medical, Xi'an Gem Flower Changqing Hospital, No. 20 Changqing West Road, Xi'an, 710201, Shaanxi, People's Republic of China
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168
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Zeng X, Wang Y, Dai M, Li W, Huang Q, Qin L, Li Y, Yan Y, Xue X, Yi F, Li W, He L, Liu Q, Qi L. Single-cell transcriptomics dissects the transcriptome alterations of hematopoietic stem cells in myelodysplastic neoplasms. J Transl Med 2024; 22:359. [PMID: 38632656 PMCID: PMC11022353 DOI: 10.1186/s12967-024-05165-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: 02/26/2024] [Accepted: 04/04/2024] [Indexed: 04/19/2024] Open
Abstract
BACKGROUND Myelodysplastic neoplasms (MDS) are myeloid neoplasms characterized by disordered differentiation of hematopoietic stem cells and a predisposition to acute myeloid leukemia (AML). The underline pathogenesis remains unclear. METHODS In this study, the trajectory of differentiation and mechanisms of leukemic transformation were explored through bioinformatics analysis of single-cell RNA-Seq data from hematopoietic stem and progenitor cells (HSPCs) in MDS patients. RESULTS Among the HSPC clusters, the proportion of common myeloid progenitor (CMP) was the main cell cluster in the patients with excess blasts (EB)/ secondary AML. Cell cycle analysis indicated the CMP of MDS patients were in an active proliferative state. The genes involved in the cell proliferation, such as MAML3 and PLCB1, were up-regulated in MDS CMP. Further validation analysis indicated that the expression levels of MAML3 and PLCB1 in patients with MDS-EB were significantly higher than those without EB. Patients with high expression of PLCB1 had a higher risk of transformation to AML. PLCB1 inhibitor can suppress proliferation, induce cell cycle arrest, and activate apoptosis of leukemic cells in vitro. CONCLUSION This study revealed the transcriptomic change of HSPCs in MDS patients along the pseudotime and indicated that PLCB1 plays a key role in the transformation of MDS into leukemia.
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Affiliation(s)
- Xiangzong Zeng
- Department of Hematology, Affiliated Qingyuan Hospital, Guangzhou Medical University, Qingyuan People's Hospital, Qingyuan, 511518, China
- Division of Gastroenterology, Institute of Digestive Disease, Affiliated Qingyuan Hospital, Guangzhou Medical University, Qingyuan People's Hospital, Qingyuan, 511518, China
| | - Yichen Wang
- Division of Gastroenterology, Institute of Digestive Disease, Affiliated Qingyuan Hospital, Guangzhou Medical University, Qingyuan People's Hospital, Qingyuan, 511518, China
| | - Min Dai
- Department of Hematology, Nanfang Hospital, Southern Medical University, Guangzhou, 510515, China
| | - Wei Li
- Division of Gastroenterology, Institute of Digestive Disease, Affiliated Qingyuan Hospital, Guangzhou Medical University, Qingyuan People's Hospital, Qingyuan, 511518, China
| | - Qingtian Huang
- Division of Gastroenterology, Institute of Digestive Disease, Affiliated Qingyuan Hospital, Guangzhou Medical University, Qingyuan People's Hospital, Qingyuan, 511518, China
| | - Lingsha Qin
- Division of Gastroenterology, Institute of Digestive Disease, Affiliated Qingyuan Hospital, Guangzhou Medical University, Qingyuan People's Hospital, Qingyuan, 511518, China
| | - Yuquan Li
- Department of Hematology, Affiliated Qingyuan Hospital, Guangzhou Medical University, Qingyuan People's Hospital, Qingyuan, 511518, China
| | - Yanwen Yan
- Department of Hematology, Affiliated Qingyuan Hospital, Guangzhou Medical University, Qingyuan People's Hospital, Qingyuan, 511518, China
| | - Xiangjun Xue
- Department of Hematology, Affiliated Qingyuan Hospital, Guangzhou Medical University, Qingyuan People's Hospital, Qingyuan, 511518, China
| | - Fang Yi
- Department of Hematology, Affiliated Qingyuan Hospital, Guangzhou Medical University, Qingyuan People's Hospital, Qingyuan, 511518, China
| | - Wenhao Li
- Department of Hematology, Affiliated Qingyuan Hospital, Guangzhou Medical University, Qingyuan People's Hospital, Qingyuan, 511518, China
| | - Langyu He
- Department of Blood Transfusion, Affiliated Qingyuan Hospital, Guangzhou Medical University, Qingyuan People's Hospital, Qingyuan, 511518, China
| | - Qifa Liu
- Department of Hematology, Nanfang Hospital, Southern Medical University, Guangzhou, 510515, China.
| | - Ling Qi
- Division of Gastroenterology, Institute of Digestive Disease, Affiliated Qingyuan Hospital, Guangzhou Medical University, Qingyuan People's Hospital, Qingyuan, 511518, China.
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169
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Noh SU, Lim J, Shin SW, Kim Y, Park WY, Batinic-Haberle I, Choi C, Park W. Single-Cell Profiling Reveals Immune-Based Mechanisms Underlying Tumor Radiosensitization by a Novel Mn Porphyrin Clinical Candidate, MnTnBuOE-2-PyP 5+ (BMX-001). Antioxidants (Basel) 2024; 13:477. [PMID: 38671924 PMCID: PMC11047573 DOI: 10.3390/antiox13040477] [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: 02/04/2024] [Revised: 04/08/2024] [Accepted: 04/12/2024] [Indexed: 04/28/2024] Open
Abstract
Manganese porphyrins reportedly exhibit synergic effects when combined with irradiation. However, an in-depth understanding of intratumoral heterogeneity and immune pathways, as affected by Mn porphyrins, remains limited. Here, we explored the mechanisms underlying immunomodulation of a clinical candidate, MnTnBuOE-2-PyP5+ (BMX-001, MnBuOE), using single-cell analysis in a murine carcinoma model. Mice bearing 4T1 tumors were divided into four groups: control, MnBuOE, radiotherapy (RT), and combined MnBuOE and radiotherapy (MnBuOE/RT). In epithelial cells, the epithelial-mesenchymal transition, TNF-α signaling via NF-кB, angiogenesis, and hypoxia-related genes were significantly downregulated in the MnBuOE/RT group compared with the RT group. All subtypes of cancer-associated fibroblasts (CAFs) were clearly reduced in MnBuOE and MnBuOE/RT. Inhibitory receptor-ligand interactions, in which epithelial cells and CAFs interacted with CD8+ T cells, were significantly lower in the MnBuOE/RT group than in the RT group. Trajectory analysis showed that dendritic cells maturation-associated markers were increased in MnBuOE/RT. M1 macrophages were significantly increased in the MnBuOE/RT group compared with the RT group, whereas myeloid-derived suppressor cells were decreased. CellChat analysis showed that the number of cell-cell communications was the lowest in the MnBuOE/RT group. Our study is the first to provide evidence for the combined radiotherapy with a novel Mn porphyrin clinical candidate, BMX-001, from the perspective of each cell type within the tumor microenvironment.
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Affiliation(s)
- Sun Up Noh
- Department of Radiation Oncology, Samsung Medical Center, Seoul 06351, Republic of Korea; (S.U.N.); (S.-W.S.); (Y.K.)
- Sungkyunkwan University School of Medicine, Seoul 06351, Republic of Korea
| | - Jinyeong Lim
- Department of Health Sciences and Technology, Samsung Advanced Institute for Health Sciences and Technology, Sungkyunkwan University, Seoul 06351, Republic of Korea; (J.L.); (W.-Y.P.)
- Samsung Genome Institute, Samsung Medical Center, Seoul 06351, Republic of Korea
| | - Sung-Won Shin
- Department of Radiation Oncology, Samsung Medical Center, Seoul 06351, Republic of Korea; (S.U.N.); (S.-W.S.); (Y.K.)
| | - Yeeun Kim
- Department of Radiation Oncology, Samsung Medical Center, Seoul 06351, Republic of Korea; (S.U.N.); (S.-W.S.); (Y.K.)
| | - Woong-Yang Park
- Department of Health Sciences and Technology, Samsung Advanced Institute for Health Sciences and Technology, Sungkyunkwan University, Seoul 06351, Republic of Korea; (J.L.); (W.-Y.P.)
- Samsung Genome Institute, Samsung Medical Center, Seoul 06351, Republic of Korea
| | - Ines Batinic-Haberle
- Department of Radiation Oncology, Duke University School of Medicine, Durham, NC 27710, USA;
| | - Changhoon Choi
- Department of Radiation Oncology, Samsung Medical Center, Seoul 06351, Republic of Korea; (S.U.N.); (S.-W.S.); (Y.K.)
| | - Won Park
- Department of Radiation Oncology, Samsung Medical Center, Seoul 06351, Republic of Korea; (S.U.N.); (S.-W.S.); (Y.K.)
- Sungkyunkwan University School of Medicine, Seoul 06351, Republic of Korea
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170
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Liu X, Wang X, Yang Q, Luo L, Liu Z, Ren X, Lei K, Li S, Xie Z, Zheng G, Zhang Y, Hao Y, Zhou Q, Hou Y, Fang F, Song W, Cui J, Ma J, Xie W, Shen S, Tang C, Peng S, Yu J, Kuang M, Song X, Wang F, Xu L. Th17 Cells Secrete TWEAK to Trigger Epithelial-Mesenchymal Transition and Promote Colorectal Cancer Liver Metastasis. Cancer Res 2024; 84:1352-1371. [PMID: 38335276 DOI: 10.1158/0008-5472.can-23-2123] [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: 07/16/2023] [Revised: 11/28/2023] [Accepted: 02/07/2024] [Indexed: 02/12/2024]
Abstract
Liver metastasis is the leading cause of mortality in patients with colorectal cancer. Given the significance of both epithelial-mesenchymal transition (EMT) of tumor cells and the immune microenvironment in colorectal cancer liver metastasis (CRLM), the interplay between them could hold the key for developing improved treatment options. We employed multiomics analysis of 130 samples from 18 patients with synchronous CRLM integrated with external datasets to comprehensively evaluate the interaction between immune cells and EMT of tumor cells in liver metastasis. Single-cell RNA sequencing analysis revealed distinct distributions of nonmalignant cells between primary tumors from patients with metastatic colorectal cancer (mCRC) and non-metastatic colorectal cancer, showing that Th17 cells were predominantly enriched in the primary lesion of mCRC. TWEAK, a cytokine secreted by Th17 cells, promoted EMT by binding to receptor Fn14 on tumor cells, and the TWEAK-Fn14 interaction enhanced tumor migration and invasion. In mouse models, targeting Fn14 using CRISPR-induced knockout or lipid nanoparticle-encapsulated siRNA alleviated metastasis and prolonged survival. Mice lacking Il17a or Tnfsf12 (encoding TWEAK) exhibited fewer metastases compared with wild-type mice, while cotransfer of Th17 with tumor cells promoted liver metastasis. Higher TWEAK expression was associated with a worse prognosis in patients with colorectal cancer. In addition, CD163L1+ macrophages interacted with Th17 cells, recruiting Th17 via the CCL4-CCR5 axis. Collectively, this study unveils the role of immune cells in the EMT process and identifies TWEAK secreted by Th17 as a driver of CRLM. SIGNIFICANCE TWEAK secreted by Th17 cells promotes EMT by binding to Fn14 on colorectal cancer cells, suggesting that blocking the TWEAK-Fn14 interaction may be a promising therapeutic approach to inhibit liver metastasis.
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Affiliation(s)
- Xin Liu
- Center of Hepato-Pancreato-Biliary Surgery, The First Affiliated Hospital, Sun Yat-sen University, Guangzhou, P.R. China
| | - Xin Wang
- Institute of Precision Medicine, The First Affiliated Hospital, Sun Yat-sen University, Guangzhou, P.R. China
| | - Qingxia Yang
- Department of Oncology, The First Affiliated Hospital, Sun Yat-sen University, Guangzhou, P.R. China
| | - Li Luo
- Department of Oncology, The First Affiliated Hospital, Sun Yat-sen University, Guangzhou, P.R. China
| | - Ziqin Liu
- Department of Oncology, The First Affiliated Hospital, Sun Yat-sen University, Guangzhou, P.R. China
| | - Xiaoxue Ren
- Department of Oncology, The First Affiliated Hospital, Sun Yat-sen University, Guangzhou, P.R. China
| | - Kai Lei
- Center of Gastrointestinal Surgery, The First Affiliated Hospital, Sun Yat-sen University, Guangzhou, P.R. China
| | - Shangru Li
- Department of Oncology, The First Affiliated Hospital, Sun Yat-sen University, Guangzhou, P.R. China
| | - Zonglin Xie
- Department of Oncology, The First Affiliated Hospital, Sun Yat-sen University, Guangzhou, P.R. China
| | - Gaomin Zheng
- Department of Oncology, The First Affiliated Hospital, Sun Yat-sen University, Guangzhou, P.R. China
| | - Yifan Zhang
- Center of Hepato-Pancreato-Biliary Surgery, The First Affiliated Hospital, Sun Yat-sen University, Guangzhou, P.R. China
| | - Yijie Hao
- Center of Hepato-Pancreato-Biliary Surgery, The First Affiliated Hospital, Sun Yat-sen University, Guangzhou, P.R. China
| | - Qianying Zhou
- Department of Oncology, The First Affiliated Hospital, Sun Yat-sen University, Guangzhou, P.R. China
| | - Yingdong Hou
- Center of Hepato-Pancreato-Biliary Surgery, The First Affiliated Hospital, Sun Yat-sen University, Guangzhou, P.R. China
| | - Fei Fang
- Institute of Precision Medicine, The First Affiliated Hospital, Sun Yat-sen University, Guangzhou, P.R. China
| | - Wu Song
- Center of Gastrointestinal Surgery, The First Affiliated Hospital, Sun Yat-sen University, Guangzhou, P.R. China
| | - Ji Cui
- Center of Gastrointestinal Surgery, The First Affiliated Hospital, Sun Yat-sen University, Guangzhou, P.R. China
| | - Jinping Ma
- Center of Gastrointestinal Surgery, The First Affiliated Hospital, Sun Yat-sen University, Guangzhou, P.R. China
| | - Wenxuan Xie
- Center of Hepato-Pancreato-Biliary Surgery, The First Affiliated Hospital, Sun Yat-sen University, Guangzhou, P.R. China
| | - Shunli Shen
- Center of Hepato-Pancreato-Biliary Surgery, The First Affiliated Hospital, Sun Yat-sen University, Guangzhou, P.R. China
| | - Ce Tang
- Institute of Precision Medicine, The First Affiliated Hospital, Sun Yat-sen University, Guangzhou, P.R. China
| | - Sui Peng
- Institute of Precision Medicine, The First Affiliated Hospital, Sun Yat-sen University, Guangzhou, P.R. China
- Department of Gastroenterology and Hepatology, The First Affiliated Hospital, Sun Yat-sen University, Guangzhou, P.R. China
- Clinical Trial Unit, The First Affiliated Hospital, Sun Yat-sen University, Guangzhou, P.R. China
| | - Jun Yu
- Institute of Precision Medicine, The First Affiliated Hospital, Sun Yat-sen University, Guangzhou, P.R. China
- Department of Medicine and Therapeutics, State Key Laboratory of Digestive Disease, The Chinese University of Hong Kong, Hong Kong SAR, P.R. China
| | - Ming Kuang
- Center of Hepato-Pancreato-Biliary Surgery, The First Affiliated Hospital, Sun Yat-sen University, Guangzhou, P.R. China
- Institute of Precision Medicine, The First Affiliated Hospital, Sun Yat-sen University, Guangzhou, P.R. China
| | - Xinming Song
- Center of Gastrointestinal Surgery, The First Affiliated Hospital, Sun Yat-sen University, Guangzhou, P.R. China
| | - Fang Wang
- Institute of Precision Medicine, The First Affiliated Hospital, Sun Yat-sen University, Guangzhou, P.R. China
| | - Lixia Xu
- Institute of Precision Medicine, The First Affiliated Hospital, Sun Yat-sen University, Guangzhou, P.R. China
- Department of Oncology, The First Affiliated Hospital, Sun Yat-sen University, Guangzhou, P.R. China
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171
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Sun X, Nong M, Meng F, Sun X, Jiang L, Li Z, Zhang P. Architecting the metabolic reprogramming survival risk framework in LUAD through single-cell landscape analysis: three-stage ensemble learning with genetic algorithm optimization. J Transl Med 2024; 22:353. [PMID: 38622716 PMCID: PMC11017668 DOI: 10.1186/s12967-024-05138-2] [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: 01/26/2024] [Accepted: 03/27/2024] [Indexed: 04/17/2024] Open
Abstract
Recent studies have increasingly revealed the connection between metabolic reprogramming and tumor progression. However, the specific impact of metabolic reprogramming on inter-patient heterogeneity and prognosis in lung adenocarcinoma (LUAD) still requires further exploration. Here, we introduced a cellular hierarchy framework according to a malignant and metabolic gene set, named malignant & metabolism reprogramming (MMR), to reanalyze 178,739 single-cell reference profiles. Furthermore, we proposed a three-stage ensemble learning pipeline, aided by genetic algorithm (GA), for survival prediction across 9 LUAD cohorts (n = 2066). Throughout the pipeline of developing the three stage-MMR (3 S-MMR) score, double training sets were implemented to avoid over-fitting; the gene-pairing method was utilized to remove batch effect; GA was harnessed to pinpoint the optimal basic learner combination. The novel 3 S-MMR score reflects various aspects of LUAD biology, provides new insights into precision medicine for patients, and may serve as a generalizable predictor of prognosis and immunotherapy response. To facilitate the clinical adoption of the 3 S-MMR score, we developed an easy-to-use web tool for risk scoring as well as therapy stratification in LUAD patients. In summary, we have proposed and validated an ensemble learning model pipeline within the framework of metabolic reprogramming, offering potential insights for LUAD treatment and an effective approach for developing prognostic models for other diseases.
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Affiliation(s)
- Xinti Sun
- Department of Cardiothoracic Surgery, Tianjin Medical University General Hospital, Tianjin, China
| | - Minyu Nong
- School of Clinical Medicine, Youjiang Medical University for Nationalities, Baise, Guangxi, China
| | - Fei Meng
- Department of Cardiothoracic Surgery, Tianjin Medical University General Hospital, Tianjin, China
| | - Xiaojuan Sun
- Department of Oncology, Qingdao University Affiliated Hospital, Qingdao, Shandong, China
| | - Lihe Jiang
- School of Clinical Medicine, Youjiang Medical University for Nationalities, Baise, Guangxi, China
| | - Zihao Li
- Department of Cardiothoracic Surgery, Tianjin Medical University General Hospital, Tianjin, China
| | - Peng Zhang
- Department of Cardiothoracic Surgery, Tianjin Medical University General Hospital, Tianjin, China.
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172
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Yao J, Dai S, Zhu R, Tan J, Zhao Q, Yin Y, Sun J, Du X, Ge L, Xu J, Hou C, Li N, Li J, Ji W, Zhu C, Zhang R, Li T. Deciphering molecular heterogeneity and dynamics of human hippocampal neural stem cells at different ages and injury states. eLife 2024; 12:RP89507. [PMID: 38607670 PMCID: PMC11014727 DOI: 10.7554/elife.89507] [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: 04/13/2024] Open
Abstract
While accumulated publications support the existence of neurogenesis in the adult human hippocampus, the homeostasis and developmental potentials of neural stem cells (NSCs) under different contexts remain unclear. Based on our generated single-nucleus atlas of the human hippocampus across neonatal, adult, aging, and injury, we dissected the molecular heterogeneity and transcriptional dynamics of human hippocampal NSCs under different contexts. We further identified new specific neurogenic lineage markers that overcome the lack of specificity found in some well-known markers. Based on developmental trajectory and molecular signatures, we found that a subset of NSCs exhibit quiescent properties after birth, and most NSCs become deep quiescence during aging. Furthermore, certain deep quiescent NSCs are reactivated following stroke injury. Together, our findings provide valuable insights into the development, aging, and reactivation of the human hippocampal NSCs, and help to explain why adult hippocampal neurogenesis is infrequently observed in humans.
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Affiliation(s)
- Junjun Yao
- State Key Laboratory of Primate Biomedical Research, Institute of Primate Translational Medicine, Kunming University of Science and TechnologyKunmingChina
- Yunnan Key Laboratory of Primate Biomedical ResearchKunmingChina
| | - Shaoxing Dai
- State Key Laboratory of Primate Biomedical Research, Institute of Primate Translational Medicine, Kunming University of Science and TechnologyKunmingChina
- Yunnan Key Laboratory of Primate Biomedical ResearchKunmingChina
| | - Ran Zhu
- State Key Laboratory of Primate Biomedical Research, Institute of Primate Translational Medicine, Kunming University of Science and TechnologyKunmingChina
- Yunnan Key Laboratory of Primate Biomedical ResearchKunmingChina
| | - Ju Tan
- Department of Anatomy, National and Regional Engineering Laboratory of Tissue Engineering, State Key Laboratory of Trauma, Burn and Combined Injury, Key Lab for Biomechanics and Tissue Engineering of Chongqing, Third Military Medical UniversityChongqingChina
| | - Qiancheng Zhao
- State Key Laboratory of Primate Biomedical Research, Institute of Primate Translational Medicine, Kunming University of Science and TechnologyKunmingChina
- Yunnan Key Laboratory of Primate Biomedical ResearchKunmingChina
| | - Yu Yin
- State Key Laboratory of Primate Biomedical Research, Institute of Primate Translational Medicine, Kunming University of Science and TechnologyKunmingChina
- Yunnan Key Laboratory of Primate Biomedical ResearchKunmingChina
| | - Jiansen Sun
- Zhong-Zhi- Yi-Gu Research InstituteChongqingChina
| | - Xuewei Du
- State Key Laboratory of Primate Biomedical Research, Institute of Primate Translational Medicine, Kunming University of Science and TechnologyKunmingChina
- Yunnan Key Laboratory of Primate Biomedical ResearchKunmingChina
| | - Longjiao Ge
- State Key Laboratory of Primate Biomedical Research, Institute of Primate Translational Medicine, Kunming University of Science and TechnologyKunmingChina
- Yunnan Key Laboratory of Primate Biomedical ResearchKunmingChina
| | - Jianhua Xu
- Department of Anatomy, National and Regional Engineering Laboratory of Tissue Engineering, State Key Laboratory of Trauma, Burn and Combined Injury, Key Lab for Biomechanics and Tissue Engineering of Chongqing, Third Military Medical UniversityChongqingChina
| | - Chunli Hou
- Department of Anatomy, National and Regional Engineering Laboratory of Tissue Engineering, State Key Laboratory of Trauma, Burn and Combined Injury, Key Lab for Biomechanics and Tissue Engineering of Chongqing, Third Military Medical UniversityChongqingChina
| | - Nan Li
- State Key Laboratory of Primate Biomedical Research, Institute of Primate Translational Medicine, Kunming University of Science and TechnologyKunmingChina
- Yunnan Key Laboratory of Primate Biomedical ResearchKunmingChina
| | - Jun Li
- Yunnan Key Laboratory of Primate Biomedical ResearchKunmingChina
| | - Weizhi Ji
- State Key Laboratory of Primate Biomedical Research, Institute of Primate Translational Medicine, Kunming University of Science and TechnologyKunmingChina
- Yunnan Key Laboratory of Primate Biomedical ResearchKunmingChina
| | - Chuhong Zhu
- Department of Anatomy, National and Regional Engineering Laboratory of Tissue Engineering, State Key Laboratory of Trauma, Burn and Combined Injury, Key Lab for Biomechanics and Tissue Engineering of Chongqing, Third Military Medical UniversityChongqingChina
| | - Runrui Zhang
- State Key Laboratory of Primate Biomedical Research, Institute of Primate Translational Medicine, Kunming University of Science and TechnologyKunmingChina
- Yunnan Key Laboratory of Primate Biomedical ResearchKunmingChina
| | - Tianqing Li
- State Key Laboratory of Primate Biomedical Research, Institute of Primate Translational Medicine, Kunming University of Science and TechnologyKunmingChina
- Yunnan Key Laboratory of Primate Biomedical ResearchKunmingChina
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173
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Li J, Ma R, Wang X, Lu Y, Chen J, Feng D, Zhou J, Xia K, Klein O, Xie H, Lu P. Sprouty genes regulate activated fibroblasts in mammary epithelial development and breast cancer. Cell Death Dis 2024; 15:256. [PMID: 38600092 PMCID: PMC11006910 DOI: 10.1038/s41419-024-06637-2] [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: 09/15/2023] [Revised: 03/27/2024] [Accepted: 04/02/2024] [Indexed: 04/12/2024]
Abstract
Stromal fibroblasts are a major stem cell niche component essential for organ formation and cancer development. Fibroblast heterogeneity, as revealed by recent advances in single-cell techniques, has raised important questions about the origin, differentiation, and function of fibroblast subtypes. In this study, we show in mammary stromal fibroblasts that loss of the receptor tyrosine kinase (RTK) negative feedback regulators encoded by Spry1, Spry2, and Spry4 causes upregulation of signaling in multiple RTK pathways and increased extracellular matrix remodeling, resulting in accelerated epithelial branching. Single-cell transcriptomic analysis demonstrated that increased production of FGF10 due to Sprouty (Spry) loss results from expansion of a functionally distinct subgroup of fibroblasts with the most potent branching-promoting ability. Compared to their three independent lineage precursors, fibroblasts in this subgroup are "activated," as they are located immediately adjacent to the epithelium that is actively undergoing branching and invasion. Spry genes are downregulated, and activated fibroblasts are expanded, in all three of the major human breast cancer subtypes. Together, our data highlight the regulation of a functional subtype of mammary fibroblasts by Spry genes and their essential role in epithelial morphogenesis and cancer development.
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Affiliation(s)
- Jiyong Li
- MOE Key Lab of Rare Pediatric Diseases & Hunan Key Laboratory of Medical Genetics of the School of Life Sciences, Hu Nan Sheng, China
- Institute of Cell Biology, University of South China, Hu Nan Sheng, China
- Institute for Future Sciences, Hengyang Medical School, University of South China, Hu Nan Sheng, China
| | - Rongze Ma
- MOE Key Lab of Rare Pediatric Diseases & Hunan Key Laboratory of Medical Genetics of the School of Life Sciences, Hu Nan Sheng, China
- Institute of Cell Biology, University of South China, Hu Nan Sheng, China
- Institute for Future Sciences, Hengyang Medical School, University of South China, Hu Nan Sheng, China
| | - Xuebing Wang
- Institute of Aix-Marseille, Wuhan University of Technology, Wuhan, 430070, China
- School of Chemistry, Chemical Engineering and Life Sciences, Wuhan University of Technology, Wuhan, 430070, China
| | - Yunzhe Lu
- School of Life Science and Technology, ShanghaiTech University, Shanghai, 201210, China
| | - Jing Chen
- MOE Key Lab of Rare Pediatric Diseases & Hunan Key Laboratory of Medical Genetics of the School of Life Sciences, Hu Nan Sheng, China
- Institute of Cell Biology, University of South China, Hu Nan Sheng, China
- Institute for Future Sciences, Hengyang Medical School, University of South China, Hu Nan Sheng, China
| | - Deyi Feng
- MOE Key Lab of Rare Pediatric Diseases & Hunan Key Laboratory of Medical Genetics of the School of Life Sciences, Hu Nan Sheng, China
- Institute of Cell Biology, University of South China, Hu Nan Sheng, China
- Institute for Future Sciences, Hengyang Medical School, University of South China, Hu Nan Sheng, China
| | - Jiecan Zhou
- MOE Key Lab of Rare Pediatric Diseases & Hunan Key Laboratory of Medical Genetics of the School of Life Sciences, Hu Nan Sheng, China
- The First Affiliated Hospital, Pharmacy Department, Hengyang Medical School, University of South China, Hu Nan Sheng, China
| | - Kun Xia
- MOE Key Lab of Rare Pediatric Diseases & Hunan Key Laboratory of Medical Genetics of the School of Life Sciences, Hu Nan Sheng, China
- Institute of Cell Biology, University of South China, Hu Nan Sheng, China
| | - Ophir Klein
- Department of Orofacial Sciences and Program in Craniofacial Biology, University of California, San Francisco, UCSF Box 0422, 513 Parnassus Avenue, HSE1508, San Francisco, CA, 94143, California, USA
- Department of Pediatrics and Guerin Children's, Cedars-Sinai Medical Center, 8700 Gracie Allen Dr., Los Angeles, CA, USA
| | - Hao Xie
- Institute of Aix-Marseille, Wuhan University of Technology, Wuhan, 430070, China
- School of Chemistry, Chemical Engineering and Life Sciences, Wuhan University of Technology, Wuhan, 430070, China
| | - Pengfei Lu
- MOE Key Lab of Rare Pediatric Diseases & Hunan Key Laboratory of Medical Genetics of the School of Life Sciences, Hu Nan Sheng, China.
- Institute of Cell Biology, University of South China, Hu Nan Sheng, China.
- Institute for Future Sciences, Hengyang Medical School, University of South China, Hu Nan Sheng, China.
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174
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Shea JM, Villeda SA. MICROGLIA AGING IN THE HIPPOCAMPUS ADVANCES THROUGH INTERMEDIATE STATES THAT DRIVE INFLAMMATORY ACTIVATION AND COGNITIVE DECLINE. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.04.09.588665. [PMID: 38645176 PMCID: PMC11030314 DOI: 10.1101/2024.04.09.588665] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 04/23/2024]
Abstract
During aging, microglia - the resident macrophages of the brain - exhibit dystrophic phenotypes and contribute to age-related neuroinflammation. While numerous hallmarks of age-related microglia dystrophy have been elucidated, the progression from homeostasis to dysfunction during the aging process remains unresolved. To bridge this gap in knowledge, we undertook complementary cellular and molecular analyses of microglia in the mouse hippocampus across the adult lifespan and in the experimental aging model of heterochronic parabiosis. Single-cell RNA-Seq and pseudotime analysis revealed age-related transcriptional heterogeneity in hippocampal microglia and identified intermediate states of microglial aging that also emerge following heterochronic parabiosis. We tested the functionality of intermediate stress response states via TGFβ1 and translational states using pharmacological approaches in vitro to reveal their modulation of the progression to an inflammatory state. Furthermore, we utilized single-cell RNA-Seq in conjunction with an in vivo adult microglia-specific Tgfb1 conditional genetic knockout mouse model, to demonstrate that microglia advancement through intermediate aging states drives inflammatory activation and associated hippocampal-dependent cognitive decline.
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Affiliation(s)
- Jeremy M. Shea
- Department of Anatomy, University of California San Francisco, San Francisco, California 94143, USA
| | - Saul A. Villeda
- Department of Anatomy, University of California San Francisco, San Francisco, California 94143, USA
- Department of Physical Therapy and Rehabilitation Science, University of California San Francisco, San Francisco, California 94143, USA
- Bakar Aging Research Institute, University of California San Francisco, San Francisco, California, 94143, USA
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175
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Wu S, Qin X, Huang L. The role of alternative polyadenylation in epithelial-mesenchymal transition of non-small cell lung cancer. Hum Mol Genet 2024; 33:677-686. [PMID: 38224682 DOI: 10.1093/hmg/ddae001] [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: 12/20/2023] [Accepted: 12/24/2023] [Indexed: 01/17/2024] Open
Abstract
The metastatic non-small cell lung cancer (NSCLC) is one of the cancers with high incidence, poor survival, and limited treatment. Epithelial-mesenchymal transition (EMT) is the first step by which an early tumor converts to an invasive one. Studying the underlying mechanisms of EMT can help the understanding of cancer metastasis and improve the treatment. In this study, 1013 NSCLC patients and 123 NSCLC cell lines are deeply analyzed for the potential roles of alternative polyadenylation (APA) in the EMT process. A trend of shorter 3'-UTRs (three prime untranslated region) is discovered in the mesenchymal samples. The identification of EMT-related APA events highlights the proximal poly(A) selection of CARM1. It is a pathological biomarker of mesenchymal tumor and cancer metastasis through losing miRNA binding to upregulate the EMT inducer of CARM1 and releasing miRNAs to downregulate the EMT inhibitor of RBM47. The crucial role of this APA event in EMT also guides its effect on drug responses. The patients with shorter 3'-UTR of CARM1 are more benefit from chemotherapy drugs, especially cisplatin. A stratification of NSCLC patients based on this APA event is useful for chemotherapy design in future clinics.
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Affiliation(s)
- Sijia Wu
- School of Life Science and Technology, Xidian University, No. 2, South Taibai Road, Yanta district, Xi'an 710071, China
| | - Xinyu Qin
- School of Life Science and Technology, Xidian University, No. 2, South Taibai Road, Yanta district, Xi'an 710071, China
| | - Liyu Huang
- School of Life Science and Technology, Xidian University, No. 2, South Taibai Road, Yanta district, Xi'an 710071, China
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176
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Ji G, Yang Q, Wang S, Yan X, Ou Q, Gong L, Zhao J, Zhou Y, Tian F, Lei J, Mu X, Wang J, Wang T, Wang X, Sun J, Zhang J, Jia C, Jiang T, Zhao MG, Lu Q. Single-cell profiling of response to neoadjuvant chemo-immunotherapy in surgically resectable esophageal squamous cell carcinoma. Genome Med 2024; 16:49. [PMID: 38566201 PMCID: PMC10985969 DOI: 10.1186/s13073-024-01320-9] [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: 06/16/2023] [Accepted: 03/21/2024] [Indexed: 04/04/2024] Open
Abstract
BACKGROUND The efficacy of neoadjuvant chemo-immunotherapy (NAT) in esophageal squamous cell carcinoma (ESCC) is challenged by the intricate interplay within the tumor microenvironment (TME). Unveiling the immune landscape of ESCC in the context of NAT could shed light on heterogeneity and optimize therapeutic strategies for patients. METHODS We analyzed single cells from 22 baseline and 24 post-NAT treatment samples of stage II/III ESCC patients to explore the association between the immune landscape and pathological response to neoadjuvant anti-PD-1 combination therapy, including pathological complete response (pCR), major pathological response (MPR), and incomplete pathological response (IPR). RESULTS Single-cell profiling identified 14 major cell subsets of cancer, immune, and stromal cells. Trajectory analysis unveiled an interesting link between cancer cell differentiation and pathological response to NAT. ESCC tumors enriched with less differentiated cancer cells exhibited a potentially favorable pathological response to NAT, while tumors enriched with clusters of more differentiated cancer cells may resist treatment. Deconvolution of transcriptomes in pre-treatment tumors identified gene signatures in response to NAT contributed by specific immune cell populations. Upregulated genes associated with better pathological responses in CD8 + effector T cells primarily involved interferon-gamma (IFNγ) signaling, neutrophil degranulation, and negative regulation of the T cell apoptotic process, whereas downregulated genes were dominated by those in the immune response-activating cell surface receptor signaling pathway. Natural killer cells in pre-treatment tumors from pCR patients showed a similar upregulation of gene expression in response to IFNγ but a downregulation of genes in the neutrophil-mediated immunity pathways. A decreased cellular contexture of regulatory T cells in ESCC TME indicated a potentially favorable pathological response to NAT. Cell-cell communication analysis revealed extensive interactions between CCL5 and its receptor CCR5 in various immune cells of baseline pCR tumors. Immune checkpoint interaction pairs, including CTLA4-CD86, TIGIT-PVR, LGALS9-HAVCR2, and TNFSF4-TNFRSF4, might serve as additional therapeutic targets for ICI therapy in ESCC. CONCLUSIONS This pioneering study unveiled an intriguing association between cancer cell differentiation and pathological response in esophageal cancer patients, revealing distinct subgroups of tumors for which neoadjuvant chemo-immunotherapy might be effective. We also delineated the immune landscape of ESCC tumors in the context of clinical response to NAT, which provides clinical insights for better understanding how patients respond to the treatment and further identifying novel therapeutic targets for ESCC patients in the future.
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Affiliation(s)
- Gang Ji
- Department of Digestive Surgery, Xijing Hospital, Air Force Medical University, No. 169 Changle West Road, Xi'an, 710032, China
| | - Qi Yang
- Precision Pharmacy & Drug Development Center, Department of Pharmacy, Tangdu Hospital, Air Force Medical University, No. 569 Xinsi Road, Xi'an, 710038, China
| | - Song Wang
- Geneseeq Research Institute, Nanjing Geneseeq Technology Inc, Nanjing, 210000, Jiangsu, China
| | - Xiaolong Yan
- Department of Thoracic Surgery, Tangdu Hospital, Air Force Medical University, No. 569 Xinsi Road, Xi'an, 710038, China
| | - Qiuxiang Ou
- Geneseeq Research Institute, Nanjing Geneseeq Technology Inc, Nanjing, 210000, Jiangsu, China
| | - Li Gong
- Department of Pathology, Tangdu Hospital, Air Force Medical University, No. 569 Xinsi Road, Xi'an, 710038, China
| | - Jinbo Zhao
- Department of Thoracic Surgery, Tangdu Hospital, Air Force Medical University, No. 569 Xinsi Road, Xi'an, 710038, China
| | - Yongan Zhou
- Department of Thoracic Surgery, Tangdu Hospital, Air Force Medical University, No. 569 Xinsi Road, Xi'an, 710038, China
| | - Feng Tian
- Department of Thoracic Surgery, Tangdu Hospital, Air Force Medical University, No. 569 Xinsi Road, Xi'an, 710038, China
| | - Jie Lei
- Department of Thoracic Surgery, Tangdu Hospital, Air Force Medical University, No. 569 Xinsi Road, Xi'an, 710038, China
| | - Xiaorong Mu
- Department of Pathology, Tangdu Hospital, Air Force Medical University, No. 569 Xinsi Road, Xi'an, 710038, China
| | - Jian Wang
- Department of Thoracic Surgery, Tangdu Hospital, Air Force Medical University, No. 569 Xinsi Road, Xi'an, 710038, China
| | - Tao Wang
- Department of Thoracic Surgery, Tangdu Hospital, Air Force Medical University, No. 569 Xinsi Road, Xi'an, 710038, China
| | - Xiaoping Wang
- Department of Thoracic Surgery, Tangdu Hospital, Air Force Medical University, No. 569 Xinsi Road, Xi'an, 710038, China
| | - Jianyong Sun
- Department of Thoracic Surgery, Tangdu Hospital, Air Force Medical University, No. 569 Xinsi Road, Xi'an, 710038, China
| | - Jipeng Zhang
- Department of Thoracic Surgery, Tangdu Hospital, Air Force Medical University, No. 569 Xinsi Road, Xi'an, 710038, China
| | - Chenghui Jia
- Department of Thoracic Surgery, The First Affiliated Hospital of Xi'an Medical College, Xi'an, 710000, China
| | - Tao Jiang
- Department of Thoracic Surgery, Tangdu Hospital, Air Force Medical University, No. 569 Xinsi Road, Xi'an, 710038, China.
| | - Ming-Gao Zhao
- Precision Pharmacy & Drug Development Center, Department of Pharmacy, Tangdu Hospital, Air Force Medical University, No. 569 Xinsi Road, Xi'an, 710038, China.
| | - Qiang Lu
- Department of Thoracic Surgery, Tangdu Hospital, Air Force Medical University, No. 569 Xinsi Road, Xi'an, 710038, China.
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177
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Zhang X, Xiao Q, Zhang C, Zhou Q, Xu T. Construction of a prognostic model with CAFs for predicting the prognosis and immunotherapeutic response of lung squamous cell carcinoma. J Cell Mol Med 2024; 28:e18262. [PMID: 38520221 PMCID: PMC10960179 DOI: 10.1111/jcmm.18262] [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: 12/18/2023] [Revised: 02/29/2024] [Accepted: 03/04/2024] [Indexed: 03/25/2024] Open
Abstract
Lung squamous cell carcinoma (LUSC) is one of the subtypes of lung cancer (LC) that contributes to approximately 25%-30% of its prevalence. Cancer-associated fibroblasts (CAFs) are key cellular components of the TME, and the large number of CAFs in tumour tissues creates a favourable environment for tumour development. However, the function of CAFs in the LUSC is complex and uncertain. First, we processed the scRNA-seq data and classified distinct types of CAFs. We also identified prognostic CAFRGs using univariate Cox analysis and conducted survival analysis. Additionally, we assessed immune cell infiltration in CAF clusters using ssGSEA. We developed a model with a significant prognostic correlation and verified the prognostic model. Furthermore, we explored the immune landscape of LUSC and further investigated the correlation between malignant features and LUSC. We identified CAFs and classified them into three categories: iCAFs, mCAFs and apCAFs. The survival analysis showed a significant correlation between apCAFs and iCAFs and LUSC patient prognosis. Kaplan-Meier analysis showed that patients in CAF cluster C showed a better survival probability compared to clusters A and B. In addition, we identified nine significant prognostic CAFRGs (CLDN1, TMX4, ALPL, PTX3, BHLHE40, TNFRSF12A, VKORC1, CST3 and ADD3) and subsequently employed multivariate Cox analysis to develop a signature and validate the model. Lastly, the correlation between CAFRG and malignant features indicates the potential role of CAFRG in promoting tumour angiogenesis, EMT and cell cycle alterations. We constructed a CAF prognostic signature for identifying potential prognostic CAFRGs and predicting the prognosis and immunotherapeutic response for LUSC. Our study may provide a more accurate prognostic assessment and immunotherapy targeting strategies for LUSC.
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Affiliation(s)
- Xiang Zhang
- Lung cancer center, West China hospitalSichuan universityChengduChina
| | - Qingqing Xiao
- Division of Abdominal Tumor Multimodality Treatment, Cancer Center, West China HospitalSichuan UniversityChengduChina
| | - Cong Zhang
- Department of Thoracic surgeryChengdu Seventh People's Hospital (Affiliated Cancer Hospital of Chengdu Medical College)ChengduChina
| | - Qinghua Zhou
- Lung cancer center, West China hospitalSichuan universityChengduChina
| | - Tao Xu
- Department of Thoracic SurgeryThe Affiliated Hospital, Southwest Medical UniversityLuzhouChina
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178
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Liu J, Liao X, Li N, Xu Z, Yang W, Zhou H, Liu Y, Zhang Z, Wang G, Hou S. Single‐cell RNA sequencing reveals inflammatory retinal microglia in experimental autoimmune uveitis. MedComm (Beijing) 2024; 5:e534. [PMID: 38585235 PMCID: PMC10999176 DOI: 10.1002/mco2.534] [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: 06/29/2023] [Revised: 03/13/2024] [Accepted: 03/13/2024] [Indexed: 04/09/2024] Open
Abstract
Autoimmune uveitis (AU) is a kind of immune-mediated disease resulting in irreversible ocular damage and even permanent vision loss. However, the precise mechanism underlying dynamic immune changes contributing to disease initiation and progression of AU remains unclear. Here, we induced an experimental AU (EAU) model with IRBP651-670 and found that day[D]14 was the inflammatory summit with remarking clinical and histopathological manifestations and the activation of retinal microglia exhibited a time-dependent pattern in the EAU course. We conducted single-cell RNA sequencing of retinal immune cells in EAU mice at four time points and found microglia constituting the largest proportion, especially on D14. A novel inflammatory subtype (Cd74high Ccl5high) of retinal microglia was identified at the disease peak that was closely associated with modulating immune responses. In vitro experiments indicated that inflammatory stimuli induced proinflammatory microglia with the upregulation of CD74 and CCL5, and CD74 overexpression in microglia elicited their proinflammatory phenotype via nuclear factor-kappa B signaling that could be attenuated by the treatment of neutralizing CCL5 antibody to a certain extent. In-vivo blockade of Cd74 and Ccl5 effectively alleviated retinal microglial activation and disease phenotype of EAU. Therefore, we propose targeting CD74 and CCL5 of retinal microglia as promising strategies for AU treatment.
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Affiliation(s)
- Jiangyi Liu
- The First Affiliated Hospital of Chongqing Medical UniversityChongqing Key Laboratory for the Prevention and Treatment of Major Blinding Eye DiseasesChongqing Eye InstituteChongqingChina
| | - Xingyun Liao
- The First Affiliated Hospital of Chongqing Medical UniversityChongqing Key Laboratory for the Prevention and Treatment of Major Blinding Eye DiseasesChongqing Eye InstituteChongqingChina
- Department of Medical OncologyChongqing University Cancer HospitalChongqingChina
| | - Na Li
- Department of Laboratory MedicineBeijing Tongren HospitalCapital Medical UniversityBeijingChina
| | - Zongren Xu
- The First Affiliated Hospital of Chongqing Medical UniversityChongqing Key Laboratory for the Prevention and Treatment of Major Blinding Eye DiseasesChongqing Eye InstituteChongqingChina
| | - Wang Yang
- Department of KidneyFirst Affiliated HospitalThird Military Medical University (Army Medical University)ChongqingChina
| | - Hongxiu Zhou
- The First Affiliated Hospital of Chongqing Medical UniversityChongqing Key Laboratory for the Prevention and Treatment of Major Blinding Eye DiseasesChongqing Eye InstituteChongqingChina
| | - Yusen Liu
- The First Affiliated Hospital of Chongqing Medical UniversityChongqing Key Laboratory for the Prevention and Treatment of Major Blinding Eye DiseasesChongqing Eye InstituteChongqingChina
| | - Zhi Zhang
- The First Affiliated Hospital of Chongqing Medical UniversityChongqing Key Laboratory for the Prevention and Treatment of Major Blinding Eye DiseasesChongqing Eye InstituteChongqingChina
| | - Guoqing Wang
- The First Affiliated Hospital of Chongqing Medical UniversityChongqing Key Laboratory for the Prevention and Treatment of Major Blinding Eye DiseasesChongqing Eye InstituteChongqingChina
| | - Shengping Hou
- The First Affiliated Hospital of Chongqing Medical UniversityChongqing Key Laboratory for the Prevention and Treatment of Major Blinding Eye DiseasesChongqing Eye InstituteChongqingChina
- Beijing Institute of OphthalmologyBeijing Tongren Eye CenterBeijing Tongren HospitalCapital Medical UniversityBeijing Ophthalmology and Visual Sciences Key LaboratoryBeijingChina
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179
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Lee Y, Chowdhury T, Kim S, Yu HJ, Kim KM, Kang H, Kim MS, Kim JW, Kim YH, Ji SY, Hwang K, Han JH, Hwang J, Yoo SK, Lee KS, Choe G, Won JK, Park SH, Lee YK, Shin JH, Park CK, Kim CY, Kim JI. Central neurocytoma exhibits radial glial cell signatures with FGFR3 hypomethylation and overexpression. Exp Mol Med 2024; 56:975-986. [PMID: 38609519 PMCID: PMC11059271 DOI: 10.1038/s12276-024-01204-3] [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: 07/12/2023] [Revised: 12/01/2023] [Accepted: 01/30/2024] [Indexed: 04/14/2024] Open
Abstract
We explored the genomic events underlying central neurocytoma (CN), a rare neoplasm of the central nervous system, via multiomics approaches, including whole-exome sequencing, bulk and single-nuclei RNA sequencing, and methylation sequencing. We identified FGFR3 hypomethylation leading to FGFR3 overexpression as a major event in the ontogeny of CN that affects crucial downstream events, such as aberrant PI3K-AKT activity and neuronal development pathways. Furthermore, we found similarities between CN and radial glial cells based on analyses of gene markers and CN tumor cells and postulate that CN tumorigenesis is due to dysregulation of radial glial cell differentiation into neurons. Our data demonstrate the potential role of FGFR3 as one of the leading drivers of tumorigenesis in CN.
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Affiliation(s)
- Yeajina Lee
- Department of Biomedical Sciences, Seoul National University Graduate School, Seoul, Republic of Korea
- Genomic Medicine Institute, Medical Research Center, Seoul National University, Seoul, Republic of Korea
| | - Tamrin Chowdhury
- Department of Neurosurgery, Seoul National University College of Medicine, Seoul National University Hospital, Seoul, Republic of Korea
| | - Sojin Kim
- Department of Neurosurgery, Seoul National University College of Medicine, Seoul National University Hospital, Seoul, Republic of Korea
| | - Hyeon Jong Yu
- Department of Neurosurgery, Seoul National University College of Medicine, Seoul National University Hospital, Seoul, Republic of Korea
| | - Kyung-Min Kim
- Department of Neurosurgery, Seoul National University College of Medicine, Seoul National University Hospital, Seoul, Republic of Korea
| | - Ho Kang
- Department of Neurosurgery, Seoul National University College of Medicine, Seoul National University Hospital, Seoul, Republic of Korea
| | - Min-Sung Kim
- Department of Neurosurgery, Seoul National University College of Medicine, Seoul National University Hospital, Seoul, Republic of Korea
| | - Jin Wook Kim
- Department of Neurosurgery, Seoul National University College of Medicine, Seoul National University Hospital, Seoul, Republic of Korea
| | - Yong-Hwy Kim
- Department of Neurosurgery, Seoul National University College of Medicine, Seoul National University Hospital, Seoul, Republic of Korea
| | - So Young Ji
- Department of Neurosurgery, Seoul National University College of Medicine, Seoul National University Bundang Hospital, Seongnam-si, Gyeonggi-do, Republic of Korea
| | - Kihwan Hwang
- Department of Neurosurgery, Seoul National University College of Medicine, Seoul National University Bundang Hospital, Seongnam-si, Gyeonggi-do, Republic of Korea
| | - Jung Ho Han
- Department of Neurosurgery, Seoul National University College of Medicine, Seoul National University Bundang Hospital, Seongnam-si, Gyeonggi-do, Republic of Korea
| | - Jinha Hwang
- Department of Laboratory Medicine, Korea University Anam Hospital, Seoul, Republic of Korea
| | - Seong-Keun Yoo
- The Marc and Jennifer Lipschultz Precision Immunology Institute, Icahn School of Medicine at Mount Sinai, New York, NY, 10029, USA
| | - Kyu Sang Lee
- Department of Pathology, Seoul National University College of Medicine, Seoul National University Bundang Hospital, Seongnam-si, Gyeonggi-do, Republic of Korea
| | - Gheeyoung Choe
- Department of Pathology, Seoul National University College of Medicine, Seoul National University Bundang Hospital, Seongnam-si, Gyeonggi-do, Republic of Korea
| | - Jae-Kyung Won
- Department of Pathology, Seoul National University College of Medicine, Seoul National University Hospital, Seoul, Republic of Korea
| | - Sung-Hye Park
- Department of Pathology, Seoul National University College of Medicine, Seoul National University Hospital, Seoul, Republic of Korea
| | - Yong Kyu Lee
- Lieber Institute for Brain Development, Johns Hopkins Medical Campus, Baltimore, MD, 21205, USA
| | - Joo Heon Shin
- Lieber Institute for Brain Development, Johns Hopkins Medical Campus, Baltimore, MD, 21205, USA
- Department of Neurology, Johns Hopkins School of Medicine, Baltimore, MD, USA
| | - Chul-Kee Park
- Genomic Medicine Institute, Medical Research Center, Seoul National University, Seoul, Republic of Korea.
- Department of Neurosurgery, Seoul National University College of Medicine, Seoul National University Hospital, Seoul, Republic of Korea.
| | - Chae-Yong Kim
- Department of Neurosurgery, Seoul National University College of Medicine, Seoul National University Bundang Hospital, Seongnam-si, Gyeonggi-do, Republic of Korea.
| | - Jong-Il Kim
- Department of Biomedical Sciences, Seoul National University Graduate School, Seoul, Republic of Korea.
- Genomic Medicine Institute, Medical Research Center, Seoul National University, Seoul, Republic of Korea.
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180
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Su XT, Reyes JV, Lackey AE, Demirci H, Bachmann S, Maeoka Y, Cornelius RJ, McCormick JA, Yang CL, Jung HJ, Welling PA, Nelson JW, Ellison DH. Enriched Single-Nucleus RNA-Sequencing Reveals Unique Attributes of Distal Convoluted Tubule Cells. J Am Soc Nephrol 2024; 35:426-440. [PMID: 38238903 PMCID: PMC11000721 DOI: 10.1681/asn.0000000000000297] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/10/2023] [Accepted: 12/17/2023] [Indexed: 01/24/2024] Open
Abstract
SIGNIFICANCE STATEMENT High-resolution single-nucleus RNA-sequencing data indicate a clear separation between primary sites of calcium and magnesium handling within distal convoluted tubule (DCT). Both DCT1 and DCT2 express Slc12a3, but these subsegments serve distinctive functions, with more abundant magnesium-handling genes along DCT1 and more calcium-handling genes along DCT2. The data also provide insight into the plasticity of the distal nephron-collecting duct junction, formed from cells of separate embryonic origins. By focusing/changing gradients of gene expression, the DCT can morph into different physiological cell states on demand. BACKGROUND The distal convoluted tubule (DCT) comprises two subsegments, DCT1 and DCT2, with different functional and molecular characteristics. The functional and molecular distinction between these segments, however, has been controversial. METHODS To understand the heterogeneity within the DCT population with better clarity, we enriched for DCT nuclei by using a mouse line combining "Isolation of Nuclei Tagged in specific Cell Types" and sodium chloride cotransporter-driven inducible Cre recombinase. We sorted the fluorescently labeled DCT nuclei using Fluorescence-Activated Nucleus Sorting and performed single-nucleus transcriptomics. RESULTS Among 25,183 DCT cells, 75% were from DCT1 and 25% were from DCT2. In addition, there was a small population (<1%) enriched in proliferation-related genes, such as Top2a , Cenpp , and Mki67 . Although both DCT1 and DCT2 expressed sodium chloride cotransporter, magnesium transport genes were predominantly expressed along DCT1, whereas calcium, electrogenic sodium, and potassium transport genes were more abundant along DCT2. The transition between these two segments was gradual, with a transitional zone in which DCT1 and DCT2 cells were interspersed. The expression of the homeobox genes by DCT cells suggests that they develop along different trajectories. CONCLUSIONS Transcriptomic analysis of an enriched rare cell population using a genetically targeted approach clarifies the function and classification of distal cells. The DCT segment is short, can be separated into two subsegments that serve distinct functions, and is speculated to derive from different origins during development.
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Affiliation(s)
- Xiao-Tong Su
- Division of Hypertension and Nephrology, School of Medicine, Oregon Health & Science University, Portland, Oregon
| | - Jeremiah V. Reyes
- Division of Hypertension and Nephrology, School of Medicine, Oregon Health & Science University, Portland, Oregon
- Department of Biochemistry and Molecular Biology, College of Medicine, University of the Philippines Manila, Manila, Philippines
| | - Anne E. Lackey
- Division of Hypertension and Nephrology, School of Medicine, Oregon Health & Science University, Portland, Oregon
| | - Hasan Demirci
- Department of Anatomy, Charité-Universitätsmedizin Berlin, Berlin, Germany
| | - Sebastian Bachmann
- Department of Anatomy, Charité-Universitätsmedizin Berlin, Berlin, Germany
| | - Yujiro Maeoka
- Division of Hypertension and Nephrology, School of Medicine, Oregon Health & Science University, Portland, Oregon
| | - Ryan J. Cornelius
- Division of Hypertension and Nephrology, School of Medicine, Oregon Health & Science University, Portland, Oregon
| | - James A. McCormick
- Division of Hypertension and Nephrology, School of Medicine, Oregon Health & Science University, Portland, Oregon
| | - Chao-Ling Yang
- Division of Hypertension and Nephrology, School of Medicine, Oregon Health & Science University, Portland, Oregon
| | - Hyun Jun Jung
- Division of Nephrology, Department of Medicine, Johns Hopkins University School of Medicine, Baltimore, Maryland
| | - Paul A. Welling
- Division of Nephrology, Department of Medicine, Johns Hopkins University School of Medicine, Baltimore, Maryland
- Department of Physiology, Johns Hopkins University School of Medicine, Baltimore, Maryland
| | - Jonathan W. Nelson
- Division of Hypertension and Nephrology, School of Medicine, Oregon Health & Science University, Portland, Oregon
| | - David H. Ellison
- Division of Hypertension and Nephrology, School of Medicine, Oregon Health & Science University, Portland, Oregon
- Oregon Clinical and Translational Research Institute, Oregon Health & Science University, Portland, Oregon
- Renal Section, VA Portland Healthcare System, Portland, Oregon
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181
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LeFever NM, Katreddi RR, Dolphin NM, Mathias NA, Forni PE. Following the p63/Keratin5 basal cells in the sensory and non-sensory epithelia of the vomeronasal organ. Genesis 2024; 62:e23596. [PMID: 38665067 PMCID: PMC11141727 DOI: 10.1002/dvg.23596] [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: 11/16/2023] [Revised: 02/27/2024] [Accepted: 03/19/2024] [Indexed: 05/01/2024]
Abstract
The vomeronasal organ (VNO) is a part of the accessory olfactory system, which detects pheromones and chemical factors that trigger a spectrum of sexual and social behaviors. The vomeronasal epithelium (VNE) shares several features with the epithelium of the main olfactory epithelium (MOE). However, it is a distinct neuroepithelium populated by chemosensory neurons that differ from the olfactory sensory neurons in cellular structure, receptor expression, and connectivity. The vomeronasal organ of rodents comprises a sensory epithelium (SE) and a thin non-sensory epithelium (NSE) that morphologically resembles the respiratory epithelium. Sox2-positive cells have been previously identified as the stem cell population that gives rise to neuronal progenitors in MOE and VNE. In addition, the MOE also comprises p63 positive horizontal basal cells, a second pool of quiescent stem cells that become active in response to injury. Immunolabeling against the transcription factor p63, Keratin-5 (Krt5), Krt14, NrCAM, and Krt5Cre tracing experiments highlighted the existence of horizontal basal cells distributed along the basal lamina of SE of the VNO. Single cell sequencing and genetic lineage tracing suggest that the vomeronasal horizontal basal cells arise from basal progenitors at the boundary between the SE and NSE proximal to the marginal zones. Moreover, our experiments revealed that the NSE of rodents is, like the respiratory epithelium, a stratified epithelium where the p63/Krt5+ basal progenitor cells self-replicate and give rise to the apical columnar cells facing the lumen of the VNO.
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Affiliation(s)
- Noah M LeFever
- Department of Biological Sciences, University at Albany, State University of New York, Albany, New York, USA
- The RNA Institute, University at Albany, State University of New York, Albany, New York, USA
| | - Raghu Ram Katreddi
- Department of Biological Sciences, University at Albany, State University of New York, Albany, New York, USA
- The RNA Institute, University at Albany, State University of New York, Albany, New York, USA
| | - Nikki M Dolphin
- Department of Biological Sciences, University at Albany, State University of New York, Albany, New York, USA
- The RNA Institute, University at Albany, State University of New York, Albany, New York, USA
| | - Nick A Mathias
- Department of Biological Sciences, University at Albany, State University of New York, Albany, New York, USA
- The RNA Institute, University at Albany, State University of New York, Albany, New York, USA
| | - Paolo E Forni
- Department of Biological Sciences, University at Albany, State University of New York, Albany, New York, USA
- The RNA Institute, University at Albany, State University of New York, Albany, New York, USA
- The Center for Neuroscience Research, University at Albany, State University of New York, Albany, New York, USA
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182
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Zhao Z, Fan C, Wang S, Wang H, Deng H, Zeng S, Tang S, Li L, Xiong Z, Qiu X. Single-nucleus RNA and multiomics in situ pairwise sequencing reveals cellular heterogeneity of the abnormal ligamentum teres in patients with developmental dysplasia of the hip. Heliyon 2024; 10:e27803. [PMID: 38524543 PMCID: PMC10958365 DOI: 10.1016/j.heliyon.2024.e27803] [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: 09/02/2023] [Revised: 02/22/2024] [Accepted: 03/06/2024] [Indexed: 03/26/2024] Open
Abstract
Developmental dysplasia of the hip (DDH) is the most common hip deformity in pediatric orthopedics. One of the common pathological changes in DDH is the thickening and hypertrophy of the ligamentum teres. However, the underlying pathogenic mechanism responsible for these changes remains unclear. This study represents the first time that the heterogeneity of cell subsets in the abnormal ligamentum teres of patients with DDH has been resolved at the single-cell and spatial levels by snRNA-Seq and MiP-Seq. Through gene set enrichment and intercellular communication network analyses, we found that receptor-like cells and ligament stem cells may play an essential role in the pathological changes resulting in ligamentum teres thickening and hypertrophy. Eight ligand-receptor pairs related to the ECM-receptor pathway were observed to be closely associated with DDH. Further, using the Monocle R package, we predicted a differentiation trajectory of pericytes into two branches, leading to junctional ligament stem cells or fibroblasts. The expression of extracellular matrix-related genes along pseudotemporal trajectories was also investigated. Using MiP-Seq, we determined the expression distribution of marker genes specific to different cell types within the ligamentum teres, as well as differentially expressed DDH-associated genes at the spatial level.
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Affiliation(s)
- Zhenhui Zhao
- Shenzhen Children's Hospital, Shenzhen, Guangdong Province, China
- China Medical University, Shenyang, Liaoning Province, China
| | - Chuiqin Fan
- Shenzhen Children's Hospital, Shenzhen, Guangdong Province, China
- China Medical University, Shenyang, Liaoning Province, China
| | - Shiyou Wang
- Key Laboratory of Synthetic Biology Regulatory Elements, Institute of Systems Medicine, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing, China
- Suzhou Institute of Systems Medicine, Suzhou, China
| | - Haoyu Wang
- Key Laboratory of Synthetic Biology Regulatory Elements, Institute of Systems Medicine, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing, China
- Suzhou Institute of Systems Medicine, Suzhou, China
| | - Hansheng Deng
- Shenzhen Children's Hospital, Shenzhen, Guangdong Province, China
| | - Shuaidan Zeng
- Shenzhen Children's Hospital, Shenzhen, Guangdong Province, China
| | - Shengping Tang
- Shenzhen Children's Hospital, Shenzhen, Guangdong Province, China
| | - Li Li
- Shenzhen Luohu Maternity and Child Healthcare Hospital, Shenzhen, Guangdong Province, China
| | - Zhu Xiong
- Shenzhen Children's Hospital, Shenzhen, Guangdong Province, China
- China Medical University, Shenyang, Liaoning Province, China
| | - Xin Qiu
- Shenzhen Children's Hospital, Shenzhen, Guangdong Province, China
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183
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Jiang A, Han K, Wei J, Su X, Wang R, Zhang W, Liu X, Qiao J, Liu P, Liu Q, Zhang J, Zhang N, Ge Y, Zhuang Y, Yu H, Wang S, Chen K, Lu W, Xu X, Yang H, Fan G, Dong B. Spatially resolved single-cell atlas of ascidian endostyle provides insight into the origin of vertebrate pharyngeal organs. SCIENCE ADVANCES 2024; 10:eadi9035. [PMID: 38552007 PMCID: PMC10980280 DOI: 10.1126/sciadv.adi9035] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 05/26/2023] [Accepted: 02/26/2024] [Indexed: 04/01/2024]
Abstract
The pharyngeal endoderm, an innovation of deuterostome ancestors, contributes to pharyngeal development by influencing the patterning and differentiation of pharyngeal structures in vertebrates; however, the evolutionary origin of the pharyngeal organs in vertebrates is largely unknown. The endostyle, a distinct pharyngeal organ exclusively present in basal chordates, represents a good model for understanding pharyngeal organ origins. Using Stereo-seq and single-cell RNA sequencing, we constructed aspatially resolved single-cell atlas for the endostyle of the ascidian Styela clava. We determined the cell composition of the hemolymphoid region, which illuminates a mixed ancestral structure for the blood and lymphoid system. In addition, we discovered a cluster of hair cell-like cells in zone 3, which has transcriptomic similarity with the hair cells of the vertebrate acoustico-lateralis system. These findings reshape our understanding of the pharynx of the basal chordate and provide insights into the evolutionary origin of multiplexed pharyngeal organs.
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Affiliation(s)
- An Jiang
- Fang Zongxi Center for Marine EvoDevo, MoE Key Laboratory of Marine Genetics and Breeding, College of Marine Life Sciences, Ocean University of China, Qingdao 266003, China
| | - Kai Han
- BGI Research, Qingdao 266555, China
| | - Jiankai Wei
- Fang Zongxi Center for Marine EvoDevo, MoE Key Laboratory of Marine Genetics and Breeding, College of Marine Life Sciences, Ocean University of China, Qingdao 266003, China
- Laboratory for Marine Biology and Biotechnology, Qingdao Marine Science and Technology Center, Qingdao 266237, China
| | | | - Rui Wang
- BGI Research, Qingdao 266555, China
| | - Wei Zhang
- Fang Zongxi Center for Marine EvoDevo, MoE Key Laboratory of Marine Genetics and Breeding, College of Marine Life Sciences, Ocean University of China, Qingdao 266003, China
| | | | - Jinghan Qiao
- Fang Zongxi Center for Marine EvoDevo, MoE Key Laboratory of Marine Genetics and Breeding, College of Marine Life Sciences, Ocean University of China, Qingdao 266003, China
| | - Penghui Liu
- Fang Zongxi Center for Marine EvoDevo, MoE Key Laboratory of Marine Genetics and Breeding, College of Marine Life Sciences, Ocean University of China, Qingdao 266003, China
| | - Qun Liu
- BGI Research, Qingdao 266555, China
| | - Jin Zhang
- Fang Zongxi Center for Marine EvoDevo, MoE Key Laboratory of Marine Genetics and Breeding, College of Marine Life Sciences, Ocean University of China, Qingdao 266003, China
| | | | - Yonghang Ge
- Fang Zongxi Center for Marine EvoDevo, MoE Key Laboratory of Marine Genetics and Breeding, College of Marine Life Sciences, Ocean University of China, Qingdao 266003, China
| | - Yuan Zhuang
- Fang Zongxi Center for Marine EvoDevo, MoE Key Laboratory of Marine Genetics and Breeding, College of Marine Life Sciences, Ocean University of China, Qingdao 266003, China
| | - Haiyan Yu
- Fang Zongxi Center for Marine EvoDevo, MoE Key Laboratory of Marine Genetics and Breeding, College of Marine Life Sciences, Ocean University of China, Qingdao 266003, China
| | - Shi Wang
- Fang Zongxi Center for Marine EvoDevo, MoE Key Laboratory of Marine Genetics and Breeding, College of Marine Life Sciences, Ocean University of China, Qingdao 266003, China
- Laboratory for Marine Biology and Biotechnology, Qingdao Marine Science and Technology Center, Qingdao 266237, China
| | - Kai Chen
- State Key Laboratory of Primate Biomedical Research and Institute of Primate Translational Medicine, Kunming University of Science and Technology, Kunming, Yunnan 650500, China
| | - Wange Lu
- State Key Laboratory of Medicinal Chemical Biology and College of Life Sciences, Nankai University, 94 Weijin Road, Tianjin 300071, China
| | - Xun Xu
- BGI Research, Shenzhen 518083, China
| | | | - Guangyi Fan
- BGI Research, Qingdao 266555, China
- BGI Research, Shenzhen 518083, China
- Qingdao Key Laboratory of Marine Genomics BGI Research, Qingdao 266555, China
| | - Bo Dong
- Fang Zongxi Center for Marine EvoDevo, MoE Key Laboratory of Marine Genetics and Breeding, College of Marine Life Sciences, Ocean University of China, Qingdao 266003, China
- Laboratory for Marine Biology and Biotechnology, Qingdao Marine Science and Technology Center, Qingdao 266237, China
- MoE Key Laboratory of Evolution and Marine Biodiversity, Institute of Evolution and Marine Biodiversity, Ocean University of China, Qingdao 266003, China
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184
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Kang Y, Zhang H, Guan J. scINRB: single-cell gene expression imputation with network regularization and bulk RNA-seq data. Brief Bioinform 2024; 25:bbae148. [PMID: 38600665 PMCID: PMC11006796 DOI: 10.1093/bib/bbae148] [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: 01/09/2024] [Revised: 02/26/2024] [Accepted: 03/18/2024] [Indexed: 04/12/2024] Open
Abstract
Single-cell RNA sequencing (scRNA-seq) facilitates the study of cell type heterogeneity and the construction of cell atlas. However, due to its limitations, many genes may be detected to have zero expressions, i.e. dropout events, leading to bias in downstream analyses and hindering the identification and characterization of cell types and cell functions. Although many imputation methods have been developed, their performances are generally lower than expected across different kinds and dimensions of data and application scenarios. Therefore, developing an accurate and robust single-cell gene expression data imputation method is still essential. Considering to maintain the original cell-cell and gene-gene correlations and leverage bulk RNA sequencing (bulk RNA-seq) data information, we propose scINRB, a single-cell gene expression imputation method with network regularization and bulk RNA-seq data. scINRB adopts network-regularized non-negative matrix factorization to ensure that the imputed data maintains the cell-cell and gene-gene similarities and also approaches the gene average expression calculated from bulk RNA-seq data. To evaluate the performance, we test scINRB on simulated and experimental datasets and compare it with other commonly used imputation methods. The results show that scINRB recovers gene expression accurately even in the case of high dropout rates and dimensions, preserves cell-cell and gene-gene similarities and improves various downstream analyses including visualization, clustering and trajectory inference.
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Affiliation(s)
- Yue Kang
- Department of Automation, Xiamen University, Xiamen, Fujian, China
| | - Hongyu Zhang
- Department of Automation, Xiamen University, Xiamen, Fujian, China
| | - Jinting Guan
- Department of Automation, Xiamen University, Xiamen, Fujian, China
- National Institute for Data Science in Health and Medicine, Xiamen University, Xiamen, Fujian, China
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185
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Hu X, Zhang Z, Long L, Gu M, Chen W, Pan B, Wu X, Wang C, Li C, Zheng L, Sheng P. Deconvolution of synovial myeloid cell subsets across pathotypes and role of COL3A1+ macrophages in rheumatoid arthritis remission. Front Immunol 2024; 15:1307748. [PMID: 38601143 PMCID: PMC11005452 DOI: 10.3389/fimmu.2024.1307748] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/05/2023] [Accepted: 03/08/2024] [Indexed: 04/12/2024] Open
Abstract
Background Monocyte/macrophage (Mo/Mp) is a critical cell population involved in immune modulation of rheumatoid synovitis (RA) across different pathotypes. This study aims to investigate the contribution of Mo/Mp clusters to RA activity, and the biological function of particular subtypes in RA remission. Methods We integrated single-cell RNA sequencing datasets from 4 published and 1 in-house studies using Liger selected by comparison. We estimated the abundance of Mo/Mp subtypes in bulk RNA-seq data from the 81 patients of the Pathobiology of Early Arthritis Cohort (PEAC) using deconvolution analysis. Correlations between Mo/Mp subtypes and RA clinical metrics were assessed. A particular cell type was identified using multicolor immunofluorescence and flow cytometry in vivo and successfully induced from a cell line in vitro. Potential immune modulation function of it was performed using immunohistochemical staining, adhesion assay, and RT-qPCR. Results We identified 8 Mo/Mp clusters. As a particular subtype among them, COL3A1+ Mp (CD68+, COL3A1+, ACTA2-) enriched in myeloid pathotype and negatively correlated with RA severity metrics in all pathotypes. Flow cytometry and multicolor immunofluorescence evidenced the enrichment and M2-like phenotype of COL3A1+ Mp in the myeloid pathotype. Further assays suggested that COL3A1+ Mp potentially attenuates RA severity via expressing anti-inflammatory cytokines, enhancing Mp adhesion, and forming a physical barrier at the synovial lining. Conclusion This study reported unexplored associations between different pathologies and myeloid cell subtypes. We also identified a fibroblast-and-M2-like cluster named COL3A1+ Mp, which potentially contributes to synovial immune homeostasis. Targeting the development of COL3A1+ Mp may hold promise for inducing RA remission.
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Affiliation(s)
- Xuantao Hu
- Department of Joint Surgery, The First Affiliated Hospital of Sun Yat-Sen University, Guangzhou, China
- Guangdong Provincial Key Laboratory of Orthopaedics and Traumatology, The First Affiliated Hospital of Sun Yat-sen University, Guangzhou, China
| | - Ziji Zhang
- Department of Joint Surgery, The First Affiliated Hospital of Sun Yat-Sen University, Guangzhou, China
- Guangdong Provincial Key Laboratory of Orthopaedics and Traumatology, The First Affiliated Hospital of Sun Yat-sen University, Guangzhou, China
| | - Lingli Long
- Research Center of Translational Medicine, The First Affiliated Hospital of Sun Yat-sen University, Guangzhou, China
| | - Minghu Gu
- Department of Joint Surgery, The First Affiliated Hospital of Sun Yat-Sen University, Guangzhou, China
- Guangdong Provincial Key Laboratory of Orthopaedics and Traumatology, The First Affiliated Hospital of Sun Yat-sen University, Guangzhou, China
| | - Weishen Chen
- Department of Joint Surgery, The First Affiliated Hospital of Sun Yat-Sen University, Guangzhou, China
- Guangdong Provincial Key Laboratory of Orthopaedics and Traumatology, The First Affiliated Hospital of Sun Yat-sen University, Guangzhou, China
| | - Baiqi Pan
- Department of Joint Surgery, The First Affiliated Hospital of Sun Yat-Sen University, Guangzhou, China
- Guangdong Provincial Key Laboratory of Orthopaedics and Traumatology, The First Affiliated Hospital of Sun Yat-sen University, Guangzhou, China
| | - Xiaoyu Wu
- Department of Joint Surgery, The First Affiliated Hospital of Sun Yat-Sen University, Guangzhou, China
- Guangdong Provincial Key Laboratory of Orthopaedics and Traumatology, The First Affiliated Hospital of Sun Yat-sen University, Guangzhou, China
| | - Chao Wang
- Department of Joint Surgery, The First Affiliated Hospital of Sun Yat-Sen University, Guangzhou, China
- Guangdong Provincial Key Laboratory of Orthopaedics and Traumatology, The First Affiliated Hospital of Sun Yat-sen University, Guangzhou, China
| | - Chengxin Li
- Department of Joint Surgery, The First Affiliated Hospital of Sun Yat-Sen University, Guangzhou, China
- Guangdong Provincial Key Laboratory of Orthopaedics and Traumatology, The First Affiliated Hospital of Sun Yat-sen University, Guangzhou, China
| | - Linli Zheng
- Department of Joint Surgery, The First Affiliated Hospital of Sun Yat-Sen University, Guangzhou, China
- Guangdong Provincial Key Laboratory of Orthopaedics and Traumatology, The First Affiliated Hospital of Sun Yat-sen University, Guangzhou, China
| | - Puyi Sheng
- Department of Joint Surgery, The First Affiliated Hospital of Sun Yat-Sen University, Guangzhou, China
- Guangdong Provincial Key Laboratory of Orthopaedics and Traumatology, The First Affiliated Hospital of Sun Yat-sen University, Guangzhou, China
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186
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Smith JJ, Taylor SR, Blum JA, Feng W, Collings R, Gitler AD, Miller DM, Kratsios P. A molecular atlas of adult C. elegans motor neurons reveals ancient diversity delineated by conserved transcription factor codes. Cell Rep 2024; 43:113857. [PMID: 38421866 PMCID: PMC11091551 DOI: 10.1016/j.celrep.2024.113857] [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: 08/18/2023] [Revised: 01/17/2024] [Accepted: 02/08/2024] [Indexed: 03/02/2024] Open
Abstract
Motor neurons (MNs) constitute an ancient cell type targeted by multiple adult-onset diseases. It is therefore important to define the molecular makeup of adult MNs in animal models and extract organizing principles. Here, we generate a comprehensive molecular atlas of adult Caenorhabditis elegans MNs and a searchable database. Single-cell RNA sequencing of 13,200 cells reveals that ventral nerve cord MNs cluster into 29 molecularly distinct subclasses. Extending C. elegans Neuronal Gene Expression Map and Network (CeNGEN) findings, all MN subclasses are delineated by distinct expression codes of either neuropeptide or transcription factor gene families. Strikingly, combinatorial codes of homeodomain transcription factor genes succinctly delineate adult MN diversity in both C. elegans and mice. Further, molecularly defined MN subclasses in C. elegans display distinct patterns of connectivity. Hence, our study couples the connectivity map of the C. elegans motor circuit with a molecular atlas of its constituent MNs and uncovers organizing principles and conserved molecular codes of adult MN diversity.
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Affiliation(s)
- Jayson J Smith
- Department of Neurobiology, University of Chicago, Chicago, IL 60637, USA; University of Chicago Neuroscience Institute, Chicago, IL 60637, USA
| | - Seth R Taylor
- Department of Cell and Developmental Biology, Vanderbilt University School of Medicine, Nashville, TN 37240, USA; Department of Cell Biology and Physiology, Brigham Young University, Provo, UT 84602, USA
| | - Jacob A Blum
- Department of Genetics, Stanford University School of Medicine, Stanford, CA, USA
| | - Weidong Feng
- Department of Neurobiology, University of Chicago, Chicago, IL 60637, USA; University of Chicago Neuroscience Institute, Chicago, IL 60637, USA
| | - Rebecca Collings
- Department of Cell and Developmental Biology, Vanderbilt University School of Medicine, Nashville, TN 37240, USA
| | - Aaron D Gitler
- Department of Genetics, Stanford University School of Medicine, Stanford, CA, USA
| | - David M Miller
- Department of Cell and Developmental Biology, Vanderbilt University School of Medicine, Nashville, TN 37240, USA; Program in Neuroscience, Vanderbilt University, Nashville, TN 37240, USA.
| | - Paschalis Kratsios
- Department of Neurobiology, University of Chicago, Chicago, IL 60637, USA; University of Chicago Neuroscience Institute, Chicago, IL 60637, USA.
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187
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Srirat T, Hayakawa T, Mise-Omata S, Nakagawara K, Ando M, Shichino S, Ito M, Yoshimura A. NR4a1/2 deletion promotes accumulation of TCF1 + stem-like precursors of exhausted CD8 + T cells in the tumor microenvironment. Cell Rep 2024; 43:113898. [PMID: 38451819 DOI: 10.1016/j.celrep.2024.113898] [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: 07/18/2023] [Revised: 11/28/2023] [Accepted: 02/15/2024] [Indexed: 03/09/2024] Open
Abstract
T cell exhaustion impairs tumor immunity and contributes to resistance against immune checkpoint inhibitors. The nuclear receptor subfamily 4 group A (NR4a) family of nuclear receptors plays a crucial role in driving T cell exhaustion. In this study, we observe that NR4a1 and NR4a2 deficiency in CD8+ tumor-infiltrating lymphocytes (TILs) results in potent tumor eradication and exhibits not only reduced exhaustion characteristics but also an increase in the precursors/progenitors of exhausted T (Pre-Tex) cell fraction. Serial transfers of NR4a1-/-NR4a2-/-CD8+ TILs into tumor-bearing mice result in the expansion of TCF1+ (Tcf7+) stem-like Pre-Tex cells, whereas wild-type TILs are depleted upon secondary transfer. NR4a1/2-deficient CD8+ T cells express higher levels of stemness/memory-related genes and illustrate potent mitochondrial oxidative phosphorylation. Collectively, these findings suggest that inhibiting NR4a in tumors represents a potent immuno-oncotherapy strategy by increasing stem-like Pre-Tex cells and reducing exhaustion of CD8+ T cells.
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Affiliation(s)
- Tanakorn Srirat
- Department of Microbiology and Immunology, Keio University School of Medicine, 35 Shinanomachi, Shinjuku-ku, Tokyo 160-8582, Japan.
| | - Taeko Hayakawa
- Department of Microbiology and Immunology, Keio University School of Medicine, 35 Shinanomachi, Shinjuku-ku, Tokyo 160-8582, Japan
| | - Setsuko Mise-Omata
- Department of Microbiology and Immunology, Keio University School of Medicine, 35 Shinanomachi, Shinjuku-ku, Tokyo 160-8582, Japan
| | - Kensuke Nakagawara
- Department of Microbiology and Immunology, Keio University School of Medicine, 35 Shinanomachi, Shinjuku-ku, Tokyo 160-8582, Japan
| | - Makoto Ando
- Department of Microbiology and Immunology, Keio University School of Medicine, 35 Shinanomachi, Shinjuku-ku, Tokyo 160-8582, Japan
| | - Shigeyuki Shichino
- Division of Molecular Regulation of Inflammatory and Immune Diseases, Research Institute for Biomedical Sciences, Tokyo University of Science, 2669 Yamazaki, Noda City, Chiba 278-0022, Japan
| | - Minako Ito
- Division of Allergy and Immunology, Medical Institute of Bioregulation, Kyushu University, 3-1-1 Maidashi, Higashi-ku, Fukuoka 812-8582, Japan
| | - Akihiko Yoshimura
- Department of Microbiology and Immunology, Keio University School of Medicine, 35 Shinanomachi, Shinjuku-ku, Tokyo 160-8582, Japan.
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Li S, Mi T, Jin L, Liu Y, Zhang Z, Wang J, Wu X, Ren C, Wang Z, Kong X, Liu J, Luo J, He D. Integrative analysis with machine learning identifies diagnostic and prognostic signatures in neuroblastoma based on differentially DNA methylated enhancers between INSS stage 4 and 4S neuroblastoma. J Cancer Res Clin Oncol 2024; 150:148. [PMID: 38512513 PMCID: PMC10957705 DOI: 10.1007/s00432-024-05650-4] [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: 01/09/2024] [Accepted: 02/10/2024] [Indexed: 03/23/2024]
Abstract
INTRODUCTION Accumulating evidence demonstrates that aberrant methylation of enhancers is crucial in gene expression profiles across several cancers. However, the latent effect of differently expressed enhancers between INSS stage 4S and 4 neuroblastoma (NB) remains elusive. METHODS We utilized the transcriptome and methylation data of stage 4S and 4 NB patients to perform Enhancer Linking by Methylation/Expression Relationships (ELMER) analysis, discovering a differently expressed motif within 67 enhancers between stage 4S and 4 NB. Harnessing the 67 motif genes, we established the INSS stage related signature (ISRS) by amalgamating 12 and 10 distinct machine learning (ML) algorithms across 113 and 101 ML combinations to precisely diagnose stage 4 NB among all NB patients and to predict the prognosis of NB patients. Based on risk scores calculated by prognostic ISRS, patients were categorized into high and low-risk groups according to median risk score. We conducted comprehensive comparisons between two risk groups, in terms of clinical applications, immune microenvironment, somatic mutations, immunotherapy, chemotherapy and single-cell analysis. Ultimately, we empirically validated the differential expressions of two ISRS model genes, CAMTA2 and FOXD1, through immunochemistry staining. RESULTS Through leave-one-out cross-validation, in both feature selection and model construction, we selected the random forest algorithm to diagnose stage 4 NB, and Enet algorithm to develop prognostic ISRS, due to their highest average C-index across five NB cohorts. After validations, the ISRS demonstrated a stable predictive capability, outperforming the previously published NB signatures and several clinic variables. We stratified NB patients into high and low-risk group based on median risk score, which showed the low-risk group with a superior survival outcome, an abundant immune infiltration, a decreased mutation landscape, and an enhanced sensitivity to immunotherapy. Single-cell analysis between two risk groups reveals biologically cellular variations underlying ISRS. Finally, we verified the significantly higher protein levels of CAMTA2 and FOXD1 in stage 4S NB, as well as their protective prognosis value in NB. CONCLUSION Based on multi-omics data and ML algorithms, we successfully developed the ISRS to enable accurate diagnosis and prognostic stratification in NB, which shed light on molecular mechanisms of spontaneous regression and clinical utilization of ISRS.
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Affiliation(s)
- Shan Li
- Department of Urology, Children's Hospital of Chongqing Medical University, Zhongshan 2nd Road, No. 136, Yuzhong District, Chongqing, 400014, China
- Chongqing Key Laboratory of Children Urogenital Development and Tissue Engineering, Chongqing, 400014, China
- China International Science and Technology Cooperation Base of Child Development and Critical Disorders, National Clinical Research Center for Child Health and Disorders, Ministry of Education Key Laboratory of Child Development and Disorders, Chongqing Key Laboratory of Pediatrics, Children's Hospital of Chongqing Medical University, Chongqing, 400014, China
| | - Tao Mi
- Department of Urology, Children's Hospital of Chongqing Medical University, Zhongshan 2nd Road, No. 136, Yuzhong District, Chongqing, 400014, China
- Chongqing Key Laboratory of Children Urogenital Development and Tissue Engineering, Chongqing, 400014, China
- China International Science and Technology Cooperation Base of Child Development and Critical Disorders, National Clinical Research Center for Child Health and Disorders, Ministry of Education Key Laboratory of Child Development and Disorders, Chongqing Key Laboratory of Pediatrics, Children's Hospital of Chongqing Medical University, Chongqing, 400014, China
| | - Liming Jin
- Department of Urology, Children's Hospital of Chongqing Medical University, Zhongshan 2nd Road, No. 136, Yuzhong District, Chongqing, 400014, China
- Chongqing Key Laboratory of Children Urogenital Development and Tissue Engineering, Chongqing, 400014, China
- China International Science and Technology Cooperation Base of Child Development and Critical Disorders, National Clinical Research Center for Child Health and Disorders, Ministry of Education Key Laboratory of Child Development and Disorders, Chongqing Key Laboratory of Pediatrics, Children's Hospital of Chongqing Medical University, Chongqing, 400014, China
| | - Yimeng Liu
- Department of Urology, Children's Hospital of Chongqing Medical University, Zhongshan 2nd Road, No. 136, Yuzhong District, Chongqing, 400014, China
- Chongqing Key Laboratory of Children Urogenital Development and Tissue Engineering, Chongqing, 400014, China
- China International Science and Technology Cooperation Base of Child Development and Critical Disorders, National Clinical Research Center for Child Health and Disorders, Ministry of Education Key Laboratory of Child Development and Disorders, Chongqing Key Laboratory of Pediatrics, Children's Hospital of Chongqing Medical University, Chongqing, 400014, China
| | - Zhaoxia Zhang
- Department of Urology, Children's Hospital of Chongqing Medical University, Zhongshan 2nd Road, No. 136, Yuzhong District, Chongqing, 400014, China
- Chongqing Key Laboratory of Children Urogenital Development and Tissue Engineering, Chongqing, 400014, China
- China International Science and Technology Cooperation Base of Child Development and Critical Disorders, National Clinical Research Center for Child Health and Disorders, Ministry of Education Key Laboratory of Child Development and Disorders, Chongqing Key Laboratory of Pediatrics, Children's Hospital of Chongqing Medical University, Chongqing, 400014, China
| | - Jinkui Wang
- Department of Urology, Children's Hospital of Chongqing Medical University, Zhongshan 2nd Road, No. 136, Yuzhong District, Chongqing, 400014, China
- Chongqing Key Laboratory of Children Urogenital Development and Tissue Engineering, Chongqing, 400014, China
- China International Science and Technology Cooperation Base of Child Development and Critical Disorders, National Clinical Research Center for Child Health and Disorders, Ministry of Education Key Laboratory of Child Development and Disorders, Chongqing Key Laboratory of Pediatrics, Children's Hospital of Chongqing Medical University, Chongqing, 400014, China
| | - Xin Wu
- Department of Urology, Children's Hospital of Chongqing Medical University, Zhongshan 2nd Road, No. 136, Yuzhong District, Chongqing, 400014, China
- Chongqing Key Laboratory of Children Urogenital Development and Tissue Engineering, Chongqing, 400014, China
- China International Science and Technology Cooperation Base of Child Development and Critical Disorders, National Clinical Research Center for Child Health and Disorders, Ministry of Education Key Laboratory of Child Development and Disorders, Chongqing Key Laboratory of Pediatrics, Children's Hospital of Chongqing Medical University, Chongqing, 400014, China
| | - Chunnian Ren
- Department of Urology, Children's Hospital of Chongqing Medical University, Zhongshan 2nd Road, No. 136, Yuzhong District, Chongqing, 400014, China
- Chongqing Key Laboratory of Children Urogenital Development and Tissue Engineering, Chongqing, 400014, China
- China International Science and Technology Cooperation Base of Child Development and Critical Disorders, National Clinical Research Center for Child Health and Disorders, Ministry of Education Key Laboratory of Child Development and Disorders, Chongqing Key Laboratory of Pediatrics, Children's Hospital of Chongqing Medical University, Chongqing, 400014, China
| | - Zhaoying Wang
- Department of Urology, Children's Hospital of Chongqing Medical University, Zhongshan 2nd Road, No. 136, Yuzhong District, Chongqing, 400014, China
- Chongqing Key Laboratory of Children Urogenital Development and Tissue Engineering, Chongqing, 400014, China
- China International Science and Technology Cooperation Base of Child Development and Critical Disorders, National Clinical Research Center for Child Health and Disorders, Ministry of Education Key Laboratory of Child Development and Disorders, Chongqing Key Laboratory of Pediatrics, Children's Hospital of Chongqing Medical University, Chongqing, 400014, China
| | - Xiangpan Kong
- Department of Urology, Children's Hospital of Chongqing Medical University, Zhongshan 2nd Road, No. 136, Yuzhong District, Chongqing, 400014, China
- Chongqing Key Laboratory of Children Urogenital Development and Tissue Engineering, Chongqing, 400014, China
- China International Science and Technology Cooperation Base of Child Development and Critical Disorders, National Clinical Research Center for Child Health and Disorders, Ministry of Education Key Laboratory of Child Development and Disorders, Chongqing Key Laboratory of Pediatrics, Children's Hospital of Chongqing Medical University, Chongqing, 400014, China
| | - Jiayan Liu
- Department of Urology, Children's Hospital of Chongqing Medical University, Zhongshan 2nd Road, No. 136, Yuzhong District, Chongqing, 400014, China
- Chongqing Key Laboratory of Children Urogenital Development and Tissue Engineering, Chongqing, 400014, China
- China International Science and Technology Cooperation Base of Child Development and Critical Disorders, National Clinical Research Center for Child Health and Disorders, Ministry of Education Key Laboratory of Child Development and Disorders, Chongqing Key Laboratory of Pediatrics, Children's Hospital of Chongqing Medical University, Chongqing, 400014, China
| | - Junyi Luo
- Department of Urology, Children's Hospital of Chongqing Medical University, Zhongshan 2nd Road, No. 136, Yuzhong District, Chongqing, 400014, China
- Chongqing Key Laboratory of Children Urogenital Development and Tissue Engineering, Chongqing, 400014, China
- China International Science and Technology Cooperation Base of Child Development and Critical Disorders, National Clinical Research Center for Child Health and Disorders, Ministry of Education Key Laboratory of Child Development and Disorders, Chongqing Key Laboratory of Pediatrics, Children's Hospital of Chongqing Medical University, Chongqing, 400014, China
| | - Dawei He
- Department of Urology, Children's Hospital of Chongqing Medical University, Zhongshan 2nd Road, No. 136, Yuzhong District, Chongqing, 400014, China.
- Chongqing Key Laboratory of Children Urogenital Development and Tissue Engineering, Chongqing, 400014, China.
- China International Science and Technology Cooperation Base of Child Development and Critical Disorders, National Clinical Research Center for Child Health and Disorders, Ministry of Education Key Laboratory of Child Development and Disorders, Chongqing Key Laboratory of Pediatrics, Children's Hospital of Chongqing Medical University, Chongqing, 400014, China.
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189
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Guo X, Ning J, Chen Y, Liu G, Zhao L, Fan Y, Sun S. Recent advances in differential expression analysis for single-cell RNA-seq and spatially resolved transcriptomic studies. Brief Funct Genomics 2024; 23:95-109. [PMID: 37022699 DOI: 10.1093/bfgp/elad011] [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: 07/08/2022] [Revised: 12/09/2022] [Accepted: 03/10/2023] [Indexed: 04/07/2023] Open
Abstract
Differential expression (DE) analysis is a necessary step in the analysis of single-cell RNA sequencing (scRNA-seq) and spatially resolved transcriptomics (SRT) data. Unlike traditional bulk RNA-seq, DE analysis for scRNA-seq or SRT data has unique characteristics that may contribute to the difficulty of detecting DE genes. However, the plethora of DE tools that work with various assumptions makes it difficult to choose an appropriate one. Furthermore, a comprehensive review on detecting DE genes for scRNA-seq data or SRT data from multi-condition, multi-sample experimental designs is lacking. To bridge such a gap, here, we first focus on the challenges of DE detection, then highlight potential opportunities that facilitate further progress in scRNA-seq or SRT analysis, and finally provide insights and guidance in selecting appropriate DE tools or developing new computational DE methods.
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Affiliation(s)
- Xiya Guo
- School of Public Health, Xi'an Jiaotong University, Xi'an, Shaanxi 710061, P.R. China
- Key Laboratory of Trace Elements and Endemic Diseases, Center for Single Cell Omics and Health, Xi'an Jiaotong University, Xi'an, Shaanxi 710061, P.R. China
| | - Jin Ning
- School of Public Health, Xi'an Jiaotong University, Xi'an, Shaanxi 710061, P.R. China
- Key Laboratory of Trace Elements and Endemic Diseases, Center for Single Cell Omics and Health, Xi'an Jiaotong University, Xi'an, Shaanxi 710061, P.R. China
| | - Yuanze Chen
- School of Public Health, Xi'an Jiaotong University, Xi'an, Shaanxi 710061, P.R. China
- Key Laboratory of Trace Elements and Endemic Diseases, Center for Single Cell Omics and Health, Xi'an Jiaotong University, Xi'an, Shaanxi 710061, P.R. China
| | - Guoliang Liu
- School of Public Health, Xi'an Jiaotong University, Xi'an, Shaanxi 710061, P.R. China
- Key Laboratory of Trace Elements and Endemic Diseases, Center for Single Cell Omics and Health, Xi'an Jiaotong University, Xi'an, Shaanxi 710061, P.R. China
| | - Liyan Zhao
- School of Public Health, Xi'an Jiaotong University, Xi'an, Shaanxi 710061, P.R. China
- Key Laboratory of Trace Elements and Endemic Diseases, Center for Single Cell Omics and Health, Xi'an Jiaotong University, Xi'an, Shaanxi 710061, P.R. China
| | - Yue Fan
- School of Public Health, Xi'an Jiaotong University, Xi'an, Shaanxi 710061, P.R. China
- Key Laboratory of Trace Elements and Endemic Diseases, Center for Single Cell Omics and Health, Xi'an Jiaotong University, Xi'an, Shaanxi 710061, P.R. China
| | - Shiquan Sun
- School of Public Health, Xi'an Jiaotong University, Xi'an, Shaanxi 710061, P.R. China
- Key Laboratory of Trace Elements and Endemic Diseases, Center for Single Cell Omics and Health, Xi'an Jiaotong University, Xi'an, Shaanxi 710061, P.R. China
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190
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Jones EF, Haldar A, Oza VH, Lasseigne BN. Quantifying transcriptome diversity: a review. Brief Funct Genomics 2024; 23:83-94. [PMID: 37225889 PMCID: PMC11484519 DOI: 10.1093/bfgp/elad019] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/18/2023] [Revised: 04/14/2023] [Accepted: 05/05/2023] [Indexed: 05/26/2023] Open
Abstract
Following the central dogma of molecular biology, gene expression heterogeneity can aid in predicting and explaining the wide variety of protein products, functions and, ultimately, heterogeneity in phenotypes. There is currently overlapping terminology used to describe the types of diversity in gene expression profiles, and overlooking these nuances can misrepresent important biological information. Here, we describe transcriptome diversity as a measure of the heterogeneity in (1) the expression of all genes within a sample or a single gene across samples in a population (gene-level diversity) or (2) the isoform-specific expression of a given gene (isoform-level diversity). We first overview modulators and quantification of transcriptome diversity at the gene level. Then, we discuss the role alternative splicing plays in driving transcript isoform-level diversity and how it can be quantified. Additionally, we overview computational resources for calculating gene-level and isoform-level diversity for high-throughput sequencing data. Finally, we discuss future applications of transcriptome diversity. This review provides a comprehensive overview of how gene expression diversity arises, and how measuring it determines a more complete picture of heterogeneity across proteins, cells, tissues, organisms and species.
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Affiliation(s)
- Emma F Jones
- The Department of Cell, Developmental and Integrative Biology, Heersink School of Medicine, The University of Alabama at Birmingham, Birmingham, AL, USA
| | - Anisha Haldar
- The Department of Cell, Developmental and Integrative Biology, Heersink School of Medicine, The University of Alabama at Birmingham, Birmingham, AL, USA
| | - Vishal H Oza
- The Department of Cell, Developmental and Integrative Biology, Heersink School of Medicine, The University of Alabama at Birmingham, Birmingham, AL, USA
| | - Brittany N Lasseigne
- The Department of Cell, Developmental and Integrative Biology, Heersink School of Medicine, The University of Alabama at Birmingham, Birmingham, AL, USA
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191
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Li R, Du Y, Li K, Xiong X, Zhang L, Guo C, Gao S, Yao Y, Xu Y, Yang J. Single-cell transcriptome profiling implicates the psychological stress-induced disruption of spermatogenesis. MOLECULAR THERAPY. NUCLEIC ACIDS 2024; 35:102158. [PMID: 38439912 PMCID: PMC10910125 DOI: 10.1016/j.omtn.2024.102158] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 09/24/2023] [Accepted: 02/15/2024] [Indexed: 03/06/2024]
Abstract
Male infertility has emerged as a global issue, partly attributed to psychological stress. However, the cellular and molecular mechanisms underlying the adverse effects of psychological stress on male reproductive function remain elusive. We created a psychologically stressed model using terrified-sound and profiled the testes from stressed and control rats using single-cell RNA sequencing. Comparative and comprehensive transcriptome analyses of 11,744 testicular cells depicted the cellular landscape of spermatogenesis and revealed significant molecular alterations of spermatogenesis suffering from psychological stress. At the cellular level, stressed rats exhibited delayed spermatogenesis at the spermatogonia and pachytene phases, resulting in reduced sperm production. Additionally, psychological stress rewired cellular interactions among germ cells, negatively impacting reproductive development. Molecularly, we observed the down-regulation of anti-oxidation-related genes and up-regulation of genes promoting reactive oxygen species (ROS) generation in the stress group. These alterations led to elevated ROS levels in testes, affecting the expression of key regulators such as ATF2 and STAR, which caused reproductive damage through apoptosis or inhibition of testosterone synthesis. Overall, our study aimed to uncover the cellular and molecular mechanisms by which psychological stress disrupts spermatogenesis, offering insights into the mechanisms of psychological stress-induced male infertility in other species and promises in potential therapeutic targets.
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Affiliation(s)
- Rufeng Li
- Department of Cell Biology and Genetics, School of Basic Medical Sciences, Xi’an Jiaotong University Health Science Center, Xi’an 710061, P.R. China
| | - Yuefeng Du
- Department of Urology, the First Affiliated Hospital of Xi’an Jiaotong University, Xi’an 710061, P.R. China
| | - Kang Li
- Department of Cell Biology and Genetics, School of Basic Medical Sciences, Xi’an Jiaotong University Health Science Center, Xi’an 710061, P.R. China
| | - Xiaofan Xiong
- Center for Tumor and Immunology, the Precision Medical Institute, the Second Affiliated Hospital of Xi’an Jiaotong University, Xi’an 710004, P.R. China
| | - Lingyu Zhang
- Department of Cell Biology and Genetics, School of Basic Medical Sciences, Xi’an Jiaotong University Health Science Center, Xi’an 710061, P.R. China
| | - Chen Guo
- Department of Cell Biology and Genetics, School of Basic Medical Sciences, Xi’an Jiaotong University Health Science Center, Xi’an 710061, P.R. China
| | - Shanfeng Gao
- Department of Cell Biology and Genetics, School of Basic Medical Sciences, Xi’an Jiaotong University Health Science Center, Xi’an 710061, P.R. China
| | - Yufei Yao
- Department of Cell Biology and Genetics, School of Basic Medical Sciences, Xi’an Jiaotong University Health Science Center, Xi’an 710061, P.R. China
| | - Yungang Xu
- Department of Cell Biology and Genetics, School of Basic Medical Sciences, Xi’an Jiaotong University Health Science Center, Xi’an 710061, P.R. China
| | - Juan Yang
- Department of Cell Biology and Genetics, School of Basic Medical Sciences, Xi’an Jiaotong University Health Science Center, Xi’an 710061, P.R. China
- Key Laboratory of Environment and Genes Related to Diseases (Xi’an Jiaotong University), Ministry of Education of China, Xi’an 710061, P.R. China
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192
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Patton MH, Thomas KT, Bayazitov IT, Newman KD, Kurtz NB, Robinson CG, Ramirez CA, Trevisan AJ, Bikoff JB, Peters ST, Pruett-Miller SM, Jiang Y, Schild AB, Nityanandam A, Zakharenko SS. Synaptic plasticity in human thalamocortical assembloids. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.02.01.578421. [PMID: 38352415 PMCID: PMC10862901 DOI: 10.1101/2024.02.01.578421] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 02/25/2024]
Abstract
Synaptic plasticities, such as long-term potentiation (LTP) and depression (LTD), tune synaptic efficacy and are essential for learning and memory. Current studies of synaptic plasticity in humans are limited by a lack of adequate human models. Here, we modeled the thalamocortical system by fusing human induced pluripotent stem cell-derived thalamic and cortical organoids. Single-nucleus RNA-sequencing revealed that most cells in mature thalamic organoids were glutamatergic neurons. When fused to form thalamocortical assembloids, thalamic and cortical organoids formed reciprocal long-range axonal projections and reciprocal synapses detectable by light and electron microscopy, respectively. Using whole-cell patch-clamp electrophysiology and two-photon imaging, we characterized glutamatergic synaptic transmission. Thalamocortical and corticothalamic synapses displayed short-term plasticity analogous to that in animal models. LTP and LTD were reliably induced at both synapses; however, their mechanisms differed from those previously described in rodents. Thus, thalamocortical assembloids provide a model system for exploring synaptic plasticity in human circuits.
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Affiliation(s)
- Mary H. Patton
- Department of Developmental Neurobiology, St. Jude Children’s Research Hospital; Memphis, TN 38105, USA
| | - Kristen T. Thomas
- Department of Developmental Neurobiology, St. Jude Children’s Research Hospital; Memphis, TN 38105, USA
| | - Ildar T. Bayazitov
- Department of Developmental Neurobiology, St. Jude Children’s Research Hospital; Memphis, TN 38105, USA
| | - Kyle D. Newman
- Department of Developmental Neurobiology, St. Jude Children’s Research Hospital; Memphis, TN 38105, USA
| | - Nathaniel B. Kurtz
- Cell and Tissue Imaging Center, St. Jude Children’s Research Hospital; Memphis, TN 38105, USA
| | - Camenzind G. Robinson
- Cell and Tissue Imaging Center, St. Jude Children’s Research Hospital; Memphis, TN 38105, USA
| | - Cody A. Ramirez
- Department of Developmental Neurobiology, St. Jude Children’s Research Hospital; Memphis, TN 38105, USA
| | - Alexandra J. Trevisan
- Department of Developmental Neurobiology, St. Jude Children’s Research Hospital; Memphis, TN 38105, USA
| | - Jay B. Bikoff
- Department of Developmental Neurobiology, St. Jude Children’s Research Hospital; Memphis, TN 38105, USA
| | - Samuel T. Peters
- Center for Advanced Genome Engineering, St. Jude Children’s Research Hospital; Memphis, TN 38105, USA
| | - Shondra M. Pruett-Miller
- Center for Advanced Genome Engineering, St. Jude Children’s Research Hospital; Memphis, TN 38105, USA
- Department of Cell & Molecular Biology, St. Jude Children’s Research Hospital; Memphis, TN 38105, USA
| | - Yanbo Jiang
- Department of Developmental Neurobiology, St. Jude Children’s Research Hospital; Memphis, TN 38105, USA
| | - Andrew B. Schild
- Department of Developmental Neurobiology, St. Jude Children’s Research Hospital; Memphis, TN 38105, USA
| | - Anjana Nityanandam
- Department of Developmental Neurobiology, St. Jude Children’s Research Hospital; Memphis, TN 38105, USA
| | - Stanislav S. Zakharenko
- Department of Developmental Neurobiology, St. Jude Children’s Research Hospital; Memphis, TN 38105, USA
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193
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Liu Z, Feng G, Chen Y, Fan J, Liang Z, Bi J, Dai X. Hyperhomocysteinemia may aggravate abdominal aortic aneurysm formation by up-regulating RASSF2. Gene 2024; 898:148036. [PMID: 38036076 DOI: 10.1016/j.gene.2023.148036] [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: 09/09/2023] [Revised: 11/14/2023] [Accepted: 11/24/2023] [Indexed: 12/02/2023]
Abstract
Abdominal aortic aneurysm (AAA) is a fatal cardiovascular disorder with high mortality and morbidity rates. To date, no drug has shown to significantly alleviate the risk of AAA. Previous studies have indicated that hyperhomocysteinemia (HHcy) significantly increases the incidence of AAA by disrupting endothelial cell homeostasis; however, the potential molecular mechanisms require clarification. Herein, we aimed to integrate transcriptomics analysis and molecular biology experiments to explore the potential molecular targets by which HHcy may increase the incidence of AAA. We integrated two AAA data profiles (GSE57691 and GSE7084) based on previously published microarray ribonucleic acid sequencing (RNAseq) data from the GEO database. Additionally, 500 μM homocysteine-treated human aorta endothelium cells microarray dataset (GSE175748) was downloaded and processed. Subsequently, single-cell RNA-seq profiles of the aortic aneurysms (GSE155468) were downloaded, scaled, and processed for further analysis. The microarray profiles analysis demonstrated that the Ras association domain family member 2 (RASSF2) and interleukin (IL)-1β are potentially the target genes involved in the HHcy-mediated aggravation of AAA formation. Single-cell RNAseq analysis revealed that RASSF2 might impair endothelial cell function by increasing inflammatory cell infiltration to participate in AAA formation. Finally, we conducted reverse transcription quantitative polymerase chain reaction and immunofluorescence analysis to validate the up-regulated mRNA expression of RASSF2 (p = 0.008) and IL-1β (p = 0.002) in AAA tissue compared to control tissue. Immunofluorescence staining revealed overexpression of RASSF2 protein in AAA tissue sections compared to control tissue (p = 0.037). Co-localization of RASSF2 and the aortic endothelium cell marker, CD31, was observed in tissue sections, indicating the potential involvement of RASSF2 in aortic endothelial cells. To summarise, our preliminary study revealed that HHcy may worsen AAA formation by up-regulating the expression of RASSF2 and IL-1β in aortic endothelium cells.
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Affiliation(s)
- Zongwei Liu
- Department of Vascular surgery of Tianjin Medical University General Hospital, Tianjin, PR China
| | - Guilin Feng
- Department of Vascular surgery of Tianjin Medical University General Hospital, Tianjin, PR China
| | - Yonghui Chen
- Department of Vascular surgery of Tianjin Medical University General Hospital, Tianjin, PR China
| | - Jibo Fan
- Department of Vascular surgery of Tianjin Medical University General Hospital, Tianjin, PR China
| | - Zhian Liang
- Department of Vascular surgery of Tianjin Medical University General Hospital, Tianjin, PR China
| | - Jiaxue Bi
- Department of Vascular surgery of Tianjin Medical University General Hospital, Tianjin, PR China.
| | - Xiangchen Dai
- Department of Vascular surgery of Tianjin Medical University General Hospital, Tianjin, PR China.
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194
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Zhou Z, Zhou X, Jiang X, Yang B, Lu X, Fei Y, Zhao L, Chen H, Zhang L, Si X, Liang N, Wang Y, Yang D, Peng Y, Yang Y, Yao Z, He Y, Wu X, Zhang W, Wang M, Yang H, Zhang X. Single-cell profiling identifies IL1B hi macrophages associated with inflammation in PD-1 inhibitor-induced inflammatory arthritis. Nat Commun 2024; 15:2107. [PMID: 38453911 PMCID: PMC10920757 DOI: 10.1038/s41467-024-46195-x] [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: 07/08/2023] [Accepted: 02/14/2024] [Indexed: 03/09/2024] Open
Abstract
Inflammatory arthritis (IA) is a common rheumatic adverse event following immune checkpoint inhibitors treatment. The clinical disparities between IA and rheumatoid arthritis (RA) imply disease heterogeneity and distinct mechanisms, which remain elusive. Here, we profile CD45+ cells from the peripheral blood or synovial fluid (SF) of patients with PD-1-induced IA (PD-1-IA) or RA using single-cell RNA sequencing. We report the predominant expansion of IL1Bhi myeloid cells with enhanced NLRP3 inflammasome activity, in both the SF and peripheral blood of PD-1-IA, but not RA. IL1Bhi macrophages in the SF of PD-1-IA shared similar inflammatory signatures and might originate from peripheral IL1Bhi monocytes. Exhausted CD8+ T cells (Texs) significantly accumulated in the SF of patients with PD-1-IA. IL1Bhi myeloid cells communicated with CD8+ Texs possibly via the CCR1-CCL5/CCL3 and CXCL10-CXCR3 axes. Collectively, these results demonstrate different cellular and molecular pathways in PD-1-IA and RA and highlight IL1Bhi macrophages as a possible therapeutic target in PD-1-IA.
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Affiliation(s)
- Ziyue Zhou
- Department of Rheumatology and Clinical Immunology, National Clinical Research Center for Dermatologic and Immunologic Diseases, the Ministry of Education Key Laboratory, Peking Union Medical College Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, 100730, Beijing, China
- Clinical Immunology Center, Chinese Academy of Medical Sciences and Peking Union Medical College, 100730, Beijing, China
- State Key Laboratory of Complex Severe and Rare Diseases, Peking Union Medical College Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, 100730, Beijing, China
| | - Xiaoxiang Zhou
- Department of Thoracic Surgery, National Cancer Center/National Clinical Research Center for Cancer/Cancer Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, 100021, Beijing, China
| | - Xu Jiang
- State Key Laboratory of Complex Severe and Rare Diseases, Peking Union Medical College Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, 100730, Beijing, China
- National Infrastructure for Translational Medicine, Institute of Clinical Medicine, Peking Union Medical College Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, 100730, Beijing, China
| | - Bo Yang
- Department of Orthopedics, Peking Union Medical College Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, 100730, Beijing, China
| | - Xin Lu
- Department of Orthopedics, Peking Union Medical College Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, 100730, Beijing, China
| | - Yunyun Fei
- Department of Rheumatology and Clinical Immunology, National Clinical Research Center for Dermatologic and Immunologic Diseases, the Ministry of Education Key Laboratory, Peking Union Medical College Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, 100730, Beijing, China
- Clinical Immunology Center, Chinese Academy of Medical Sciences and Peking Union Medical College, 100730, Beijing, China
- State Key Laboratory of Complex Severe and Rare Diseases, Peking Union Medical College Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, 100730, Beijing, China
| | - Lidan Zhao
- Department of Rheumatology and Clinical Immunology, National Clinical Research Center for Dermatologic and Immunologic Diseases, the Ministry of Education Key Laboratory, Peking Union Medical College Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, 100730, Beijing, China
- Clinical Immunology Center, Chinese Academy of Medical Sciences and Peking Union Medical College, 100730, Beijing, China
- State Key Laboratory of Complex Severe and Rare Diseases, Peking Union Medical College Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, 100730, Beijing, China
| | - Hua Chen
- Department of Rheumatology and Clinical Immunology, National Clinical Research Center for Dermatologic and Immunologic Diseases, the Ministry of Education Key Laboratory, Peking Union Medical College Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, 100730, Beijing, China
- Clinical Immunology Center, Chinese Academy of Medical Sciences and Peking Union Medical College, 100730, Beijing, China
- State Key Laboratory of Complex Severe and Rare Diseases, Peking Union Medical College Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, 100730, Beijing, China
| | - Li Zhang
- Department of Pulmonary and Critical Care Medicine, Peking Union Medical College Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, 100730, Beijing, China
| | - Xiaoyan Si
- Department of Pulmonary and Critical Care Medicine, Peking Union Medical College Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, 100730, Beijing, China
| | - Naixin Liang
- Department of Thoracic Surgery, Peking Union Medical College Hospital, Chinese Academy of Medical Sciences, 100730, Beijing, China
| | - Yadong Wang
- Department of Thoracic Surgery, Peking Union Medical College Hospital, Chinese Academy of Medical Sciences, 100730, Beijing, China
| | - Dan Yang
- Department of Rheumatology and Clinical Immunology, National Clinical Research Center for Dermatologic and Immunologic Diseases, the Ministry of Education Key Laboratory, Peking Union Medical College Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, 100730, Beijing, China
- Clinical Immunology Center, Chinese Academy of Medical Sciences and Peking Union Medical College, 100730, Beijing, China
- State Key Laboratory of Complex Severe and Rare Diseases, Peking Union Medical College Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, 100730, Beijing, China
| | - Yezi Peng
- Department of Rheumatology and Clinical Immunology, National Clinical Research Center for Dermatologic and Immunologic Diseases, the Ministry of Education Key Laboratory, Peking Union Medical College Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, 100730, Beijing, China
- Clinical Immunology Center, Chinese Academy of Medical Sciences and Peking Union Medical College, 100730, Beijing, China
- State Key Laboratory of Complex Severe and Rare Diseases, Peking Union Medical College Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, 100730, Beijing, China
| | - Yiying Yang
- Department of Rheumatology and Clinical Immunology, National Clinical Research Center for Dermatologic and Immunologic Diseases, the Ministry of Education Key Laboratory, Peking Union Medical College Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, 100730, Beijing, China
- Clinical Immunology Center, Chinese Academy of Medical Sciences and Peking Union Medical College, 100730, Beijing, China
- State Key Laboratory of Complex Severe and Rare Diseases, Peking Union Medical College Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, 100730, Beijing, China
| | - Zhuoran Yao
- Department of Thoracic Oncology, Cancer Center, and Laboratory of Clinical Cell Therapy, West China Hospital, Sichuan University, 610041, Chengdu, China
| | - Yangzhige He
- State Key Laboratory of Complex Severe and Rare Diseases, Peking Union Medical College Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, 100730, Beijing, China
- National Infrastructure for Translational Medicine, Institute of Clinical Medicine, Peking Union Medical College Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, 100730, Beijing, China
| | - Xunyao Wu
- State Key Laboratory of Complex Severe and Rare Diseases, Peking Union Medical College Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, 100730, Beijing, China
| | - Wen Zhang
- Department of Rheumatology and Clinical Immunology, National Clinical Research Center for Dermatologic and Immunologic Diseases, the Ministry of Education Key Laboratory, Peking Union Medical College Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, 100730, Beijing, China
- Clinical Immunology Center, Chinese Academy of Medical Sciences and Peking Union Medical College, 100730, Beijing, China
- State Key Laboratory of Complex Severe and Rare Diseases, Peking Union Medical College Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, 100730, Beijing, China
| | - Min Wang
- Department of Rheumatology, Beijing Hospital, National Center of Gerontology, Institute of Geriatric Medicine, Clinical Immunology Center, Chinese Academy of Medical Sciences, 100730, Beijing, China
| | - Huaxia Yang
- Department of Rheumatology and Clinical Immunology, National Clinical Research Center for Dermatologic and Immunologic Diseases, the Ministry of Education Key Laboratory, Peking Union Medical College Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, 100730, Beijing, China.
- Clinical Immunology Center, Chinese Academy of Medical Sciences and Peking Union Medical College, 100730, Beijing, China.
- State Key Laboratory of Complex Severe and Rare Diseases, Peking Union Medical College Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, 100730, Beijing, China.
| | - Xuan Zhang
- Department of Rheumatology, Beijing Hospital, National Center of Gerontology, Institute of Geriatric Medicine, Clinical Immunology Center, Chinese Academy of Medical Sciences, 100730, Beijing, China.
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Huo Z, Wang Z, Luo H, Maimaitiming D, Yang T, Liu H, Li H, Wu H, Zhang Z. Single-cell transcriptomes reveal the heterogeneity and microenvironment of vestibular schwannoma. Neuro Oncol 2024; 26:444-457. [PMID: 37862593 PMCID: PMC10912001 DOI: 10.1093/neuonc/noad201] [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: 04/30/2023] [Indexed: 10/22/2023] Open
Abstract
BACKGROUND Vestibular schwannoma (VS) is the most common benign tumor in the cerebellopontine angle and internal auditory canal. Illustrating the heterogeneous cellular components of VS could provide insights into its various growth patterns. METHODS Single-cell RNA sequencing was used to profile transcriptomes from 7 VS samples and 2 normal nerves. Multiplex immunofluorescence was employed to verify the data set results. Bulk RNA sequencing was conducted on 5 normal nerves and 44 VS samples to generate a prediction model for VS growth. RESULTS A total of 83 611 cells were annotated as 14 distinct cell types. We uncovered the heterogeneity in distinct VS tumors. A subset of Schwann cells with the vascular endothelial growth factor biomarker was significantly associated with fast VS growth through mRNA catabolism and peptide biosynthesis. The macrophages in the normal nerves were largely of the M2 phenotype, while no significant differences in the proportions of M1 and M2 macrophages were found between slow-growing and fast-growing VS. The normal spatial distribution of fibroblasts and vascular cells was destroyed in VS. The communications between Schwann cells and vascular cells were strengthened in VS compared with those in the normal nerve. Three cell clusters were significantly associated with fast VS growth and could refine the growth classification in bulk RNA. CONCLUSIONS Our findings offer novel insights into the VS microenvironment at the single-cell level. It may enhance our understanding of the different clinical phenotypes of VS and help predict growth characteristics. Molecular subtypes should be included in the treatment considerations.
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Affiliation(s)
- Zirong Huo
- Department of Otolaryngology Head and Neck Surgery, Shanghai Ninth People's Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, China
- Ear Institute, Shanghai Jiao Tong University School of Medicine, Shanghai, China
- Shanghai Key Laboratory of Translational Medicine on Ear and Nose Diseases, Shanghai, China
| | - Zhaohui Wang
- Department of Otolaryngology Head and Neck Surgery, Shanghai Ninth People's Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, China
- Ear Institute, Shanghai Jiao Tong University School of Medicine, Shanghai, China
- Shanghai Key Laboratory of Translational Medicine on Ear and Nose Diseases, Shanghai, China
| | - Huahong Luo
- Department of Otolaryngology Head and Neck Surgery, Shanghai Ninth People's Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, China
- Ear Institute, Shanghai Jiao Tong University School of Medicine, Shanghai, China
- Shanghai Key Laboratory of Translational Medicine on Ear and Nose Diseases, Shanghai, China
| | - Dilihumaer Maimaitiming
- Department of Otolaryngology Head and Neck Surgery, Shanghai Ninth People's Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, China
- Ear Institute, Shanghai Jiao Tong University School of Medicine, Shanghai, China
- Shanghai Key Laboratory of Translational Medicine on Ear and Nose Diseases, Shanghai, China
| | - Tao Yang
- Department of Otolaryngology Head and Neck Surgery, Shanghai Ninth People's Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, China
- Ear Institute, Shanghai Jiao Tong University School of Medicine, Shanghai, China
- Shanghai Key Laboratory of Translational Medicine on Ear and Nose Diseases, Shanghai, China
| | - Huihui Liu
- Department of Otolaryngology Head and Neck Surgery, Shanghai Ninth People's Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, China
- Ear Institute, Shanghai Jiao Tong University School of Medicine, Shanghai, China
- Shanghai Key Laboratory of Translational Medicine on Ear and Nose Diseases, Shanghai, China
| | - Huipeng Li
- Department of Otolaryngology Head and Neck Surgery, Shanghai Ninth People's Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, China
- Ear Institute, Shanghai Jiao Tong University School of Medicine, Shanghai, China
- Shanghai Key Laboratory of Translational Medicine on Ear and Nose Diseases, Shanghai, China
| | - Hao Wu
- Department of Otolaryngology Head and Neck Surgery, Shanghai Ninth People's Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, China
- Ear Institute, Shanghai Jiao Tong University School of Medicine, Shanghai, China
- Shanghai Key Laboratory of Translational Medicine on Ear and Nose Diseases, Shanghai, China
| | - Zhihua Zhang
- Department of Otolaryngology Head and Neck Surgery, Shanghai Ninth People's Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, China
- Ear Institute, Shanghai Jiao Tong University School of Medicine, Shanghai, China
- Shanghai Key Laboratory of Translational Medicine on Ear and Nose Diseases, Shanghai, China
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196
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Wu M, Shi Y, Liu Y, Huang H, Che J, Shi J, Xu C. Exosome-transmitted podoplanin promotes tumor-associated macrophage-mediated immune tolerance in glioblastoma. CNS Neurosci Ther 2024; 30:e14643. [PMID: 38470096 PMCID: PMC10929222 DOI: 10.1111/cns.14643] [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: 11/17/2023] [Revised: 01/11/2024] [Accepted: 01/29/2024] [Indexed: 03/13/2024] Open
Abstract
AIMS Glioblastoma is the most frequent and aggressive primary brain tumor, characterized by rapid disease course and poor treatment responsiveness. The abundance of immunosuppressive macrophages in glioblastoma challenges the efficacy of novel immunotherapy. METHODS Bulk RNA-seq and single-cell RNA-seq of glioma patients from public databases were comprehensively analyzed to illustrate macrophage infiltration patterns and molecular characteristics of podoplanin (PDPN). Multiplexed fluorescence immunohistochemistry staining of PDPN, GFAP, CD68, and CD163 were performed in glioma tissue microarray. The impact of PDPN on macrophage immunosuppressive polarization was investigated using a co-culture system. Bone marrow-derived macrophages (BMDMs) and OT-II T cells isolated from BALB/c and OT-II mice respectively were co-cultured to determine T-cell adherence. Pathway alterations were probed through RNA sequencing and western blot analyses. RESULTS Our findings demonstrated that PDPN is notably correlated with the expression of CD68 and CD163 in glioma tissues. Additionally, macrophages phagocytosing PDPN-containing EVs (EVsPDPN ) from GBM cells presented increased CD163 expression and augmented secretion of immunoregulatory cytokine (IL-6, IL-10, TNF-α, and TGF-β1). PDPN within EVs was also associated with enhanced phagocytic activity and reduced MHC II expression in macrophages, compromising CD4+ T-cell activation. CONCLUSIONS This investigation underscores that EVsPDPN derived from glioblastoma cells contributes to M2 macrophage-mediated immunosuppression and is a potential prognostic marker and therapeutic target in glioblastoma.
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Affiliation(s)
- Mengwan Wu
- Department of Oncology, Sichuan Academy of Medical Sciences, Sichuan Provincial People's Hospital, School of MedicineUniversity of Electronic Science and Technology of ChinaChengduSichuanChina
- Yu‐Yue Pathology Scientific Research CenterChongqingChina
- Jinfeng LaboratoryChongqingChina
| | - Ying Shi
- Department of Oncology, Sichuan Academy of Medical Sciences, Sichuan Provincial People's Hospital, School of MedicineUniversity of Electronic Science and Technology of ChinaChengduSichuanChina
| | - Yuyang Liu
- Department of Neurosurgery920th Hospital of Joint Logistics Support ForceKunmingChina
| | - Hongxiang Huang
- Department of Oncology, The First Affiliated HospitalNanchang UniversityNanchangChina
| | - Jiajia Che
- Department of Oncology, Sichuan Academy of Medical Sciences, Sichuan Provincial People's Hospital, School of MedicineUniversity of Electronic Science and Technology of ChinaChengduSichuanChina
| | - Jing Shi
- Department of Neurosurgery920th Hospital of Joint Logistics Support ForceKunmingChina
| | - Chuan Xu
- Department of Oncology, Sichuan Academy of Medical Sciences, Sichuan Provincial People's Hospital, School of MedicineUniversity of Electronic Science and Technology of ChinaChengduSichuanChina
- Yu‐Yue Pathology Scientific Research CenterChongqingChina
- Jinfeng LaboratoryChongqingChina
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197
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Ji L, Fu G, Huang M, Kao X, Zhu J, Dai Z, Chen Y, Li H, Zhou J, Chu X, Lei Z. scRNA-seq of colorectal cancer shows regional immune atlas with the function of CD20 + B cells. Cancer Lett 2024; 584:216664. [PMID: 38253219 DOI: 10.1016/j.canlet.2024.216664] [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: 10/25/2023] [Revised: 12/25/2023] [Accepted: 01/18/2024] [Indexed: 01/24/2024]
Abstract
Colorectal cancer (CRC) from different regions exhibits different histological, genetic characteristics, and molecular subtypes, even in response to conventional chemotherapies and immunotherapies. To characterize the immune landscape in different regions of CRC and search for potential therapeutic targets, we analyzed 39,484 single-cell transcription data from 19 samples of CRC and paired normal tissues from four regions to identify the immune characteristics of CRC among anatomic locations, especially in B cells. We discovered that immune cell infiltration in tumors significantly varied among different regions of CRC. B cells from right- and left-sided CRC had different development trajectories, but both had extensive interactions with myeloid cells and T cells. Survival analysis suggested that CD20+ B cells correlated with good prognosis in CRC patients, especially on the right side. Furthermore, the depletion of CD20+ B cells demonstrated that anti-CD20 promoted tumor growth progression and reversed the tumor-killing activity of anti-PD-1 treatment in vivo and in vitro. Our results highlight the characterization of the immune landscape of CRC in different regions. CD20+ B-cell infiltration has been associated with CRC patient prognosis and may promote the tumor-killing role of PD-1 antibodies.
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Affiliation(s)
- Linlin Ji
- Department of Medical Oncology, Nanjing Jinling Hospital, Affiliated Hospital of Medical School, Nanjing University, Nanjing, 210000, China
| | - Gongbo Fu
- Department of Medical Oncology, Nanjing Jinling Hospital, Affiliated Hospital of Medical School, Nanjing University, Nanjing, 210000, China; Department of Medical Oncology, Jinling Hospital, The First School of Clinical Medicine, Southern Medical University, Nanjing, 210000, China; Department of Medical Oncology, Jinling Hospital, Nanjing Medical University, Nanjing, 210000, China; Department of Medical Oncology, Jinling Hospital, Nanjing University of Chinese Medicine, Nanjing, 210000, China.
| | - Mengxi Huang
- Department of Medical Oncology, Nanjing Jinling Hospital, Affiliated Hospital of Medical School, Nanjing University, Nanjing, 210000, China
| | - Xiaoming Kao
- Department of General Surgery, Jinling Hospital, Nanjing Medical University, Nanjing, 210002, China
| | - Jialong Zhu
- Department of Medical Oncology, Jinling Hospital, The First School of Clinical Medicine, Southern Medical University, Nanjing, 210000, China
| | - Zhe Dai
- Department of Medical Oncology, Nanjing Jinling Hospital, Affiliated Hospital of Medical School, Nanjing University, Nanjing, 210000, China
| | - Yitian Chen
- Department of Medical Oncology, Nanjing Jinling Hospital, Affiliated Hospital of Medical School, Nanjing University, Nanjing, 210000, China
| | - Huiyu Li
- Department of Medical Oncology, Nanjing Jinling Hospital, Affiliated Hospital of Medical School, Nanjing University, Nanjing, 210000, China
| | - Jie Zhou
- Department of Oncology and Southwest Cancer Center, Southwest Hospital, Army Medical University (Third Military Medical University), Chongqing, 400038, China.
| | - Xiaoyuan Chu
- Department of Medical Oncology, Nanjing Jinling Hospital, Affiliated Hospital of Medical School, Nanjing University, Nanjing, 210000, China; Department of Medical Oncology, Jinling Hospital, The First School of Clinical Medicine, Southern Medical University, Nanjing, 210000, China; Department of Medical Oncology, Jinling Hospital, Nanjing Medical University, Nanjing, 210000, China; Department of Medical Oncology, Jinling Hospital, Nanjing University of Chinese Medicine, Nanjing, 210000, China.
| | - Zengjie Lei
- Department of Medical Oncology, Nanjing Jinling Hospital, Affiliated Hospital of Medical School, Nanjing University, Nanjing, 210000, China; Department of Medical Oncology, Jinling Hospital, The First School of Clinical Medicine, Southern Medical University, Nanjing, 210000, China; Department of Medical Oncology, Jinling Hospital, Nanjing Medical University, Nanjing, 210000, China; Department of Medical Oncology, Jinling Hospital, Nanjing University of Chinese Medicine, Nanjing, 210000, China.
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198
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Hu R, Chen X, Su Q, Wang Z, Wang X, Gong M, Xu M, Le R, Gao Y, Dai P, Zhang ZN, Shao L, Li W. ISR inhibition reverses pancreatic β-cell failure in Wolfram syndrome models. Cell Death Differ 2024; 31:322-334. [PMID: 38321214 PMCID: PMC10923889 DOI: 10.1038/s41418-024-01258-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: 07/25/2023] [Revised: 01/18/2024] [Accepted: 01/22/2024] [Indexed: 02/08/2024] Open
Abstract
Pancreatic β-cell failure by WFS1 deficiency is manifested in individuals with wolfram syndrome (WS). The lack of a suitable human model in WS has impeded progress in the development of new treatments. Here, human pluripotent stem cell derived pancreatic islets (SC-islets) harboring WFS1 deficiency and mouse model of β cell specific Wfs1 knockout were applied to model β-cell failure in WS. We charted a high-resolution roadmap with single-cell RNA-seq (scRNA-seq) to investigate pathogenesis for WS β-cell failure, revealing two distinct cellular fates along pseudotime trajectory: maturation and stress branches. WFS1 deficiency disrupted β-cell fate trajectory toward maturation and directed it towards stress trajectory, ultimately leading to β-cell failure. Notably, further investigation of the stress trajectory identified activated integrated stress response (ISR) as a crucial mechanism underlying WS β-cell failure, characterized by aberrant eIF2 signaling in WFS1-deficient SC-islets, along with elevated expression of genes in regulating stress granule formation. Significantly, we demonstrated that ISRIB, an ISR inhibitor, efficiently reversed β-cell failure in WFS1-deficient SC-islets. We further validated therapeutic efficacy in vivo with β-cell specific Wfs1 knockout mice. Altogether, our study provides novel insights into WS pathogenesis and offers a strategy targeting ISR to treat WS diabetes.
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Affiliation(s)
- Rui Hu
- Medical Innovation Center and State Key Laboratory of Cardiology, Translational Medical Center for Stem Cell Therapy and Institute for Regenerative Medicine, Shanghai East Hospital, Frontier Science Center for Stem Cell Research, School of Life Sciences and Technology, Tongji University, Shanghai, 200092, China
| | - Xiangyi Chen
- Medical Innovation Center and State Key Laboratory of Cardiology, Translational Medical Center for Stem Cell Therapy and Institute for Regenerative Medicine, Shanghai East Hospital, Frontier Science Center for Stem Cell Research, School of Life Sciences and Technology, Tongji University, Shanghai, 200092, China
| | - Qiang Su
- Medical Innovation Center and State Key Laboratory of Cardiology, Translational Medical Center for Stem Cell Therapy and Institute for Regenerative Medicine, Shanghai East Hospital, Frontier Science Center for Stem Cell Research, School of Life Sciences and Technology, Tongji University, Shanghai, 200092, China
| | - Zhaoyue Wang
- Medical Innovation Center and State Key Laboratory of Cardiology, Translational Medical Center for Stem Cell Therapy and Institute for Regenerative Medicine, Shanghai East Hospital, Frontier Science Center for Stem Cell Research, School of Life Sciences and Technology, Tongji University, Shanghai, 200092, China
| | - Xushu Wang
- Medical Innovation Center and State Key Laboratory of Cardiology, Translational Medical Center for Stem Cell Therapy and Institute for Regenerative Medicine, Shanghai East Hospital, Frontier Science Center for Stem Cell Research, School of Life Sciences and Technology, Tongji University, Shanghai, 200092, China
| | - Mengting Gong
- Medical Innovation Center and State Key Laboratory of Cardiology, Translational Medical Center for Stem Cell Therapy and Institute for Regenerative Medicine, Shanghai East Hospital, Frontier Science Center for Stem Cell Research, School of Life Sciences and Technology, Tongji University, Shanghai, 200092, China
| | - Minglu Xu
- Medical Innovation Center and State Key Laboratory of Cardiology, Translational Medical Center for Stem Cell Therapy and Institute for Regenerative Medicine, Shanghai East Hospital, Frontier Science Center for Stem Cell Research, School of Life Sciences and Technology, Tongji University, Shanghai, 200092, China
| | - Rongrong Le
- Clinical and Translational Research Center of Shanghai First Maternity & Infant Hospital, Frontier Science Center for Stem Cells, School of Life Sciences and Technology, Tongji University, Shanghai, 200092, China
| | - Yawei Gao
- Medical Innovation Center and State Key Laboratory of Cardiology, Translational Medical Center for Stem Cell Therapy and Institute for Regenerative Medicine, Shanghai East Hospital, Frontier Science Center for Stem Cell Research, School of Life Sciences and Technology, Tongji University, Shanghai, 200092, China
| | - Peng Dai
- Clinical and Translational Research Center of Shanghai First Maternity & Infant Hospital, Frontier Science Center for Stem Cells, School of Life Sciences and Technology, Tongji University, Shanghai, 200092, China
| | - Zhen-Ning Zhang
- Medical Innovation Center and State Key Laboratory of Cardiology, Translational Medical Center for Stem Cell Therapy and Institute for Regenerative Medicine, Shanghai East Hospital, Frontier Science Center for Stem Cell Research, School of Life Sciences and Technology, Tongji University, Shanghai, 200092, China.
| | - Li Shao
- Department of VIP Clinic, Shanghai East Hospital, Tongji University School of Medicine, No. 1800 Yuntai Road, Pudong District, Shanghai, 200123, China.
| | - Weida Li
- Medical Innovation Center and State Key Laboratory of Cardiology, Translational Medical Center for Stem Cell Therapy and Institute for Regenerative Medicine, Shanghai East Hospital, Frontier Science Center for Stem Cell Research, School of Life Sciences and Technology, Tongji University, Shanghai, 200092, China.
- Reg-Verse Therapeutics (Shanghai) Co. Ltd., Shanghai, 200120, China.
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199
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Li J, Xu Y, Zhang J, Zhang Z, Guo H, Wei D, Wu C, Hai T, Sun HX, Zhao Y. Single-cell transcriptomic analysis reveals transcriptional and cell subpopulation differences between human and pig immune cells. Genes Genomics 2024; 46:303-322. [PMID: 37979077 DOI: 10.1007/s13258-023-01456-9] [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: 08/16/2023] [Accepted: 09/26/2023] [Indexed: 11/19/2023]
Abstract
BACKGROUND The pig is a promising donor candidate for xenotransplantation. Understanding the differences between human and swine immune systems is critical for addressing xenotransplant rejection and hematopoietic reconstitution. The gene transcriptional profile differences between human and pig immune cell subpopulations have not been studied. To assess the similarities and differences between pigs and humans at the levels of gene transcriptional profiles or cell subpopulations are important for better understanding the cross-species similarity of humans and pigs, and it would help establish the fundamental principles necessary to genetically engineer donor pigs and improve xenotransplantation. OBJECTIVE To assess the gene transcriptional similarities and differences between pigs and humans. METHODS Two pigs and two healthy humans' PBMCs were sorted for 10 × genomics single-cell sequence. We generated integrated human-pig scRNA-seq data from human and pig PBMCs and defined the overall gene expression landscape of pig peripheral blood immune cell subpopulations by updating the set of human-porcine homologous genes. The subsets of immune cells were detected by flow cytometry. RESULTS There were significantly less T cells, NK cells and monocytes but more B cells in pig peripheral blood than those in human peripheral blood. High oxidative phosphorylation, HIF-1, glycolysis, and lysosome-related gene expressions in pig CD14+ monocytes were observed, whereas pig CD14+ monocytes exhibited lower levels of cytokine receptors and JAK-STAT-related genes. Pig activated CD4+T cells decreased cell adhesion and inflammation, while enriched for migration and activation processes. Porcine GNLY+CD8+T cells reduced cytotoxicity and increased proliferation compared with human GNLY+CD8+T cells. Pig CD2+CD8+γδT cells were functionally homologous to human CD2+CD4+ γδT cells. Pig CD2-CD8-γδT cells expressed genes with quiescent and precursor characteristics, while CD2-CD8+γδT cells expressed migration and memory-related molecules. Pig CD24+ and CD5+B cells are associated with inflammatory responses. CONCLUSION Our research with integrated scRNA-seq assays identified the different distribution of pig immune cell subpopulations and the different transcriptional profiles of human and pig immune cells. This study enables a deeper understanding of the development and function of porcine immune cells.
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Affiliation(s)
- Jie Li
- State Key Laboratory of Membrane Biology, Institute of Zoology, Chinese Academy of Sciences, Beichen West Road 1-5, Chaoyang District, Beijing, 100101, China
- University of Chinese Academy of Sciences, Beijing, 100049, China
- Beijing Institute for Stem Cell and Regenerative Medicine, Beijing, 100101, China
- BGI-Beijing, Beijing, 102601, China
| | - Yanan Xu
- State Key Laboratory of Membrane Biology, Institute of Zoology, Chinese Academy of Sciences, Beichen West Road 1-5, Chaoyang District, Beijing, 100101, China
- University of Chinese Academy of Sciences, Beijing, 100049, China
- Beijing Institute for Stem Cell and Regenerative Medicine, Beijing, 100101, China
| | - Jiayu Zhang
- State Key Laboratory of Membrane Biology, Institute of Zoology, Chinese Academy of Sciences, Beichen West Road 1-5, Chaoyang District, Beijing, 100101, China
- University of Chinese Academy of Sciences, Beijing, 100049, China
- Department of Immunology, Hebei Medical University, Shijiazhuang, 050017, Hebei, China
| | - Zhaoqi Zhang
- State Key Laboratory of Membrane Biology, Institute of Zoology, Chinese Academy of Sciences, Beichen West Road 1-5, Chaoyang District, Beijing, 100101, China
- University of Chinese Academy of Sciences, Beijing, 100049, China
- CAS Key Laboratory of Quantitative Engineering Biology, Shenzhen Institute of Synthetic Biology, Shenzhen Institute of Advanced Technology, Chinese Academy of Sciences, Shenzhen, 518055, China
| | - Han Guo
- State Key Laboratory of Membrane Biology, Institute of Zoology, Chinese Academy of Sciences, Beichen West Road 1-5, Chaoyang District, Beijing, 100101, China
- University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Dong Wei
- State Key Laboratory of Membrane Biology, Institute of Zoology, Chinese Academy of Sciences, Beichen West Road 1-5, Chaoyang District, Beijing, 100101, China
- University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Changhong Wu
- State Key Laboratory of Membrane Biology, Institute of Zoology, Chinese Academy of Sciences, Beichen West Road 1-5, Chaoyang District, Beijing, 100101, China
- University of Chinese Academy of Sciences, Beijing, 100049, China
- Beijing Institute for Stem Cell and Regenerative Medicine, Beijing, 100101, China
| | - Tang Hai
- Beijing Institute for Stem Cell and Regenerative Medicine, Beijing, 100101, China.
- Beijing Farm Animal Research Center, Institute of Zoology, Chinese Academy of Sciences, Beijing, 100101, China.
- State Key Laboratory of Stem Cell and Reproductive Biology, Institute of Zoology, Chinese Academy of Sciences, Beijing, 100101, China.
| | - Hai-Xi Sun
- University of Chinese Academy of Sciences, Beijing, 100049, China.
- BGI-Beijing, Beijing, 102601, China.
| | - Yong Zhao
- State Key Laboratory of Membrane Biology, Institute of Zoology, Chinese Academy of Sciences, Beichen West Road 1-5, Chaoyang District, Beijing, 100101, China.
- University of Chinese Academy of Sciences, Beijing, 100049, China.
- Beijing Institute for Stem Cell and Regenerative Medicine, Beijing, 100101, China.
- CAS Key Laboratory of Quantitative Engineering Biology, Shenzhen Institute of Synthetic Biology, Shenzhen Institute of Advanced Technology, Chinese Academy of Sciences, Shenzhen, 518055, China.
- Faculty of Synthetic Biology, Shenzhen Institute of Advanced Technology, Shenzhen, 518055, China.
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Shi Y, Huang L, Dong H, Yang M, Ding W, Zhou X, Lu T, Liu Z, Zhou X, Wang M, Zeng B, Sun Y, Zhong S, Wang B, Wang W, Yin C, Wang X, Wu Q. Decoding the spatiotemporal regulation of transcription factors during human spinal cord development. Cell Res 2024; 34:193-213. [PMID: 38177242 PMCID: PMC10907391 DOI: 10.1038/s41422-023-00897-x] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/26/2023] [Accepted: 11/02/2023] [Indexed: 01/06/2024] Open
Abstract
The spinal cord is a crucial component of the central nervous system that facilitates sensory processing and motor performance. Despite its importance, the spatiotemporal codes underlying human spinal cord development have remained elusive. In this study, we have introduced an image-based single-cell transcription factor (TF) expression decoding spatial transcriptome method (TF-seqFISH) to investigate the spatial expression and regulation of TFs during human spinal cord development. By combining spatial transcriptomic data from TF-seqFISH and single-cell RNA-sequencing data, we uncovered the spatial distribution of neural progenitor cells characterized by combinatorial TFs along the dorsoventral axis, as well as the molecular and spatial features governing neuronal generation, migration, and differentiation along the mediolateral axis. Notably, we observed a sandwich-like organization of excitatory and inhibitory interneurons transiently appearing in the dorsal horns of the developing human spinal cord. In addition, we integrated data from 10× Visium to identify early and late waves of neurogenesis in the dorsal horn, revealing the formation of laminas in the dorsal horns. Our study also illuminated the spatial differences and molecular cues underlying motor neuron (MN) diversification, and the enrichment of Amyotrophic Lateral Sclerosis (ALS) risk genes in MNs and microglia. Interestingly, we detected disease-associated microglia (DAM)-like microglia groups in the developing human spinal cord, which are predicted to be vulnerable to ALS and engaged in the TYROBP causal network and response to unfolded proteins. These findings provide spatiotemporal transcriptomic resources on the developing human spinal cord and potential strategies for spinal cord injury repair and ALS treatment.
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Affiliation(s)
- Yingchao Shi
- Guangdong Institute of Intelligence Science and Technology, Guangdong, China.
| | - Luwei Huang
- State Key Laboratory of Brain and Cognitive Science, Institute of Biophysics, Chinese Academy of Sciences, Beijing, China
- University of Chinese Academy of Sciences, Beijing, China
| | - Hao Dong
- State Key Laboratory of Brain and Cognitive Science, Institute of Biophysics, Chinese Academy of Sciences, Beijing, China
- University of Chinese Academy of Sciences, Beijing, China
| | - Meng Yang
- Changping Laboratory, Beijing, China
| | - Wenyu Ding
- State Key Laboratory of Cognitive Neuroscience and Learning, IDG/McGovern Institute for Brain Research, New Cornerstone Science Laboratory, Beijing Normal University, Beijing, China
| | - Xiang Zhou
- State Key Laboratory of Brain and Cognitive Science, Institute of Biophysics, Chinese Academy of Sciences, Beijing, China
- University of Chinese Academy of Sciences, Beijing, China
| | - Tian Lu
- State Key Laboratory of Brain and Cognitive Science, Institute of Biophysics, Chinese Academy of Sciences, Beijing, China
- University of Chinese Academy of Sciences, Beijing, China
| | | | - Xin Zhou
- Changping Laboratory, Beijing, China
- State Key Laboratory of Cognitive Neuroscience and Learning, IDG/McGovern Institute for Brain Research, New Cornerstone Science Laboratory, Beijing Normal University, Beijing, China
| | - Mengdi Wang
- State Key Laboratory of Brain and Cognitive Science, Institute of Biophysics, Chinese Academy of Sciences, Beijing, China
- University of Chinese Academy of Sciences, Beijing, China
| | - Bo Zeng
- Changping Laboratory, Beijing, China
| | - Yinuo Sun
- Changping Laboratory, Beijing, China
| | - Suijuan Zhong
- Changping Laboratory, Beijing, China
- State Key Laboratory of Cognitive Neuroscience and Learning, IDG/McGovern Institute for Brain Research, New Cornerstone Science Laboratory, Beijing Normal University, Beijing, China
| | - Bosong Wang
- State Key Laboratory of Cognitive Neuroscience and Learning, IDG/McGovern Institute for Brain Research, New Cornerstone Science Laboratory, Beijing Normal University, Beijing, China
| | - Wei Wang
- State Key Laboratory of Brain and Cognitive Science, Institute of Biophysics, Chinese Academy of Sciences, Beijing, China
- University of Chinese Academy of Sciences, Beijing, China
| | | | - Xiaoqun Wang
- State Key Laboratory of Brain and Cognitive Science, Institute of Biophysics, Chinese Academy of Sciences, Beijing, China.
- Changping Laboratory, Beijing, China.
- State Key Laboratory of Cognitive Neuroscience and Learning, IDG/McGovern Institute for Brain Research, New Cornerstone Science Laboratory, Beijing Normal University, Beijing, China.
| | - Qian Wu
- Changping Laboratory, Beijing, China.
- State Key Laboratory of Cognitive Neuroscience and Learning, IDG/McGovern Institute for Brain Research, New Cornerstone Science Laboratory, Beijing Normal University, Beijing, China.
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