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Mimpen JY, Ramos-Mucci L, Paul C, Kurjan A, Hulley PA, Ikwuanusi CT, Cohen CJ, Gwilym SE, Baldwin MJ, Cribbs AP, Snelling SJB. Single nucleus and spatial transcriptomic profiling of healthy human hamstring tendon. FASEB J 2024; 38:e23629. [PMID: 38742770 DOI: 10.1096/fj.202300601rrr] [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: 03/29/2023] [Revised: 04/03/2024] [Accepted: 04/11/2024] [Indexed: 05/16/2024]
Abstract
The molecular and cellular basis of health in human tendons remains poorly understood. Among human tendons, hamstring tendon has markedly low pathology and can provide a prototypic healthy tendon reference. The aim of this study was to determine the transcriptomes and location of all cell types in healthy hamstring tendon. Using single nucleus RNA sequencing, we profiled the transcriptomes of 10 533 nuclei from four healthy donors and identified 12 distinct cell types. We confirmed the presence of two fibroblast cell types, endothelial cells, mural cells, and immune cells, and identified cell types previously unreported in tendons, including different skeletal muscle cell types, satellite cells, adipocytes, and undefined nervous system cells. The location of these cell types within tendon was defined using spatial transcriptomics and imaging, and potential transcriptional networks and cell-cell interactions were analyzed. We demonstrate that fibroblasts have the highest number of potential cell-cell interactions in our dataset, are present throughout the tendon, and play an important role in the production and organization of extracellular matrix, thus confirming their role as key regulators of hamstring tendon homeostasis. Overall, our findings underscore the complexity of the cellular networks that underpin healthy human tendon function and the central role of fibroblasts as key regulators of hamstring tendon tissue homeostasis.
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Affiliation(s)
- Jolet Y Mimpen
- The Botnar Institute of Musculoskeletal Sciences, Nuffield Department of Orthopaedics Rheumatology and Musculoskeletal Sciences, University of Oxford, Oxford, UK
| | - Lorenzo Ramos-Mucci
- The Botnar Institute of Musculoskeletal Sciences, Nuffield Department of Orthopaedics Rheumatology and Musculoskeletal Sciences, University of Oxford, Oxford, UK
| | - Claudia Paul
- The Botnar Institute of Musculoskeletal Sciences, Nuffield Department of Orthopaedics Rheumatology and Musculoskeletal Sciences, University of Oxford, Oxford, UK
| | - Alina Kurjan
- The Botnar Institute of Musculoskeletal Sciences, Nuffield Department of Orthopaedics Rheumatology and Musculoskeletal Sciences, University of Oxford, Oxford, UK
| | - Philippa A Hulley
- The Botnar Institute of Musculoskeletal Sciences, Nuffield Department of Orthopaedics Rheumatology and Musculoskeletal Sciences, University of Oxford, Oxford, UK
| | | | - Carla J Cohen
- Centre for Computational Biology, MRC Weatherall Institute of Molecular Medicine, University of Oxford, Oxford, United Kingdom of Great Britain and Northern Ireland
| | - Stephen E Gwilym
- The Botnar Institute of Musculoskeletal Sciences, Nuffield Department of Orthopaedics Rheumatology and Musculoskeletal Sciences, University of Oxford, Oxford, UK
| | - Mathew J Baldwin
- The Botnar Institute of Musculoskeletal Sciences, Nuffield Department of Orthopaedics Rheumatology and Musculoskeletal Sciences, University of Oxford, Oxford, UK
| | - Adam P Cribbs
- The Botnar Institute of Musculoskeletal Sciences, Nuffield Department of Orthopaedics Rheumatology and Musculoskeletal Sciences, University of Oxford, Oxford, UK
| | - Sarah J B Snelling
- The Botnar Institute of Musculoskeletal Sciences, Nuffield Department of Orthopaedics Rheumatology and Musculoskeletal Sciences, University of Oxford, Oxford, UK
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Wu Z, Wang X, Wu H, Du S, Wang Z, Xie S, Zhang R, Chen G, Chen H. Identification of CREB5 as a prognostic and immunotherapeutic biomarker in glioma through multi-omics pan-cancer analysis. Comput Biol Med 2024; 173:108307. [PMID: 38547657 DOI: 10.1016/j.compbiomed.2024.108307] [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: 10/15/2023] [Revised: 02/27/2024] [Accepted: 03/12/2024] [Indexed: 04/17/2024]
Abstract
BACKGROUND The functional relevance of cyclic adenosine monophosphate (cAMP)-response element-binding protein 5 (CREB5) in cancers remains elusive, despite its significance as a member of the CREB family. The current research aims to explore the role of CREB5 in multiple cancers. METHODS Pan-cancer analysis was performed to explore the expression patterns, prognostic value, mutational landscape as well as single-cell omic, immunologic, and drug sensitivity profiles of CREB5. Furthermore, we incorporated five distinct machine learning algorithms and determined that the least absolute shrinkage and selection operator-COX (LASSO-COX) algorithm, which exhibited the highest C index, was the optimal selection. Subsequently, we constructed a prognostic model centered around CREB5-associated genes. To elucidate the biological function of CREB5 in glioma cells, several assays including cell counting kit-8 (CCK-8), wound healing, transwell, flow cytometric were performed. RESULTS CREB5 was overexpressed in pan-cancer and was linked to unfavorable prognosis, particularly in glioma. Furthermore, genetic alterations were determined in various types of cancer, and modifications in the CREB5 gene were linked to the prognosis. The single-cell omics and enrichment analyses showed that CREB5 was predominantly expressed in malignant glioma cells and was critically involved in the regulation of various oncogenic processes. Elevated levels of CREB5 were strongly linked with the infiltration of cancer-associated fibroblasts and the Th1 subset of CD4+ T cells. The validated CREB5-associated prognostic model reliably predicted the prognosis and drug response of glioma patients. The in vitro experiments showed that CREB5 promoted glioma cell proliferation, invasion, migration, and gap phase 2/mitotic (G2/M) phase arrest and recruited M2 macrophages into glioma cells. CONCLUSION CREB5 has the potential to act as an oncogene and a biological marker in multiple cancers, particularly glioma.
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Affiliation(s)
- Zhixuan Wu
- Department of Oncology, The First Affiliated Hospital of Wenzhou Medical University, Wenzhou, 325035, Zhejiang, China; Department of Burns and Skin Repair Surgery, The Third Affiliated Hospital of Wenzhou Medical University, Ruian, 325200, Zhejiang, China; The Quzhou Affiliated Hospital of Wenzhou Medical University, Quzhou People's Hospital, Quzhou, Zhejiang, 324000, China
| | - Xiaowu Wang
- Department of Burns and Skin Repair Surgery, The Third Affiliated Hospital of Wenzhou Medical University, Ruian, 325200, Zhejiang, China
| | - Haodong Wu
- Department of Oncology, The First Affiliated Hospital of Wenzhou Medical University, Wenzhou, 325035, Zhejiang, China
| | - Shengwei Du
- Department of Pathology, The First Affiliated Hospital of Wenzhou Medical University, Wenzhou, 325035, Zhejiang, China
| | - Ziqiong Wang
- Department of Pathology, The First Affiliated Hospital of Wenzhou Medical University, Wenzhou, 325035, Zhejiang, China
| | - Shicheng Xie
- Department of Oncology, The First Affiliated Hospital of Wenzhou Medical University, Wenzhou, 325035, Zhejiang, China
| | - Rongrong Zhang
- Department of Pathology, The First Affiliated Hospital of Wenzhou Medical University, Wenzhou, 325035, Zhejiang, China.
| | - Guorong Chen
- The Quzhou Affiliated Hospital of Wenzhou Medical University, Quzhou People's Hospital, Quzhou, Zhejiang, 324000, China.
| | - Hanbin Chen
- Department of Oncology, The First Affiliated Hospital of Wenzhou Medical University, Wenzhou, 325035, Zhejiang, China.
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Xu W, Wei D, Song X. Identification of SLC40A1, LCN2, CREB5, and SLC7A11 as ferroptosis-related biomarkers in alopecia areata through machine learning. Sci Rep 2024; 14:3800. [PMID: 38360836 PMCID: PMC10869692 DOI: 10.1038/s41598-024-54278-4] [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: 10/21/2023] [Accepted: 02/10/2024] [Indexed: 02/17/2024] Open
Abstract
Alopecia areata (AA) is a common non-scarring hair loss condition driven by the collapse of immune privilege and oxidative stress. The role of ferroptosis, a type of cell death linked to oxidative stress, in AA is yet to be explored, even though it's implicated in various diseases. Using transcriptome data from AA patients and controls from datasets GSE68801 and GSE80342, we aimed to identify AA diagnostic marker genes linked to ferroptosis. We employed Single-sample gene set enrichment analysis (ssGSEA) for immune cell infiltration evaluation. Correlations between ferroptosis-related differentially expressed genes (FRDEGs) and immune cells/functions were identified using Spearman analysis. Feature selection was done through Support vector machine-recursive feature elimination (SVM-RFE) and LASSO regression models. Validation was performed using the GSE80342 dataset, followed by hierarchical internal validation. We also constructed a nomogram to assess the predictive ability of FRDEGs in AA. Furthermore, the expression and distribution of these molecules were confirmed through immunofluorescence. Four genes, namely SLC40A1, LCN2, CREB5, and SLC7A11, were identified as markers for AA. A prediction model based on these genes showed high accuracy (AUC = 0.9052). Immunofluorescence revealed reduced expression of these molecules in AA patients compared to normal controls (NC), with SLC40A1 and CREB5 showing significant differences. Notably, they were primarily localized to the outer root sheath and in proximity to the sebaceous glands. Our study identified several ferroptosis-related genes associated with AA. These findings, emerging from the integration of immune cell infiltration analysis and machine learning, contribute to the evolving understanding of diagnostic and therapeutic strategies in AA. Importantly, this research lays a solid foundation for subsequent studies exploring the intricate relationship between AA and ferroptosis.
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Affiliation(s)
- Wen Xu
- School of Medicine, Zhejiang University, Hangzhou, 310009, China
- Department of Dermatology, Hangzhou Third People's Hospital, Affiliated Hangzhou Dermatology Hospital, Zhejiang University School of Medicine, West Lake Ave 38, Hangzhou, 310009, China
| | - Dongfan Wei
- School of Medicine, Zhejiang University, Hangzhou, 310009, China
- Department of Dermatology, Hangzhou Third People's Hospital, Affiliated Hangzhou Dermatology Hospital, Zhejiang University School of Medicine, West Lake Ave 38, Hangzhou, 310009, China
| | - Xiuzu Song
- Department of Dermatology, Hangzhou Third People's Hospital, Affiliated Hangzhou Dermatology Hospital, Zhejiang University School of Medicine, West Lake Ave 38, Hangzhou, 310009, China.
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Hao RC, Li ZL, Wang FY, Tang J, Li PL, Yin BF, Li XT, Han MY, Mao N, Liu B, Ding L, Zhu H. Single-cell transcriptomic analysis identifies a highly replicating Cd168 + skeletal stem/progenitor cell population in mouse long bones. J Genet Genomics 2023; 50:702-712. [PMID: 37075860 DOI: 10.1016/j.jgg.2023.04.004] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/23/2023] [Revised: 04/08/2023] [Accepted: 04/09/2023] [Indexed: 04/21/2023]
Abstract
Skeletal stem/progenitor cells (SSPCs) are tissue-specific stem/progenitor cells localized within skeletons and contribute to bone development, homeostasis, and regeneration. However, the heterogeneity of SSPC populations in mouse long bones and their respective regenerative capacity remain to be further clarified. In this study, we perform integrated analysis using single-cell RNA sequencing (scRNA-seq) datasets of mouse hindlimb buds, postnatal long bones, and fractured long bones. Our analyses reveal the heterogeneity of osteochondrogenic lineage cells and recapitulate the developmental trajectories during mouse long bone growth. In addition, we identify a novel Cd168+ SSPC population with highly replicating capacity and osteochondrogenic potential in embryonic and postnatal long bones. Moreover, the Cd168+ SSPCs can contribute to newly formed skeletal tissues during fracture healing. Furthermore, the results of multicolor immunofluorescence show that Cd168+ SSPCs reside in the superficial zone of articular cartilage as well as in growth plates of postnatal mouse long bones. In summary, we identify a novel Cd168+ SSPC population with regenerative potential in mouse long bones, which adds to the knowledge of the tissue-specific stem cells in skeletons.
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Affiliation(s)
- Rui-Cong Hao
- Basic Medical College of Anhui Medical University, Hefei, Anhui 230032, China; Beijing Institute of Radiation Medicine, Beijing 100850, China
| | - Zhi-Ling Li
- Beijing Institute of Radiation Medicine, Beijing 100850, China
| | - Fei-Yan Wang
- Basic Medical College of Anhui Medical University, Hefei, Anhui 230032, China; Beijing Institute of Radiation Medicine, Beijing 100850, China
| | - Jie Tang
- Beijing Institute of Radiation Medicine, Beijing 100850, China
| | - Pei-Lin Li
- Beijing Institute of Radiation Medicine, Beijing 100850, China
| | - Bo-Feng Yin
- Beijing Institute of Radiation Medicine, Beijing 100850, China
| | - Xiao-Tong Li
- Beijing Institute of Radiation Medicine, Beijing 100850, China
| | - Meng-Yue Han
- Basic Medical College of Anhui Medical University, Hefei, Anhui 230032, China; Beijing Institute of Radiation Medicine, Beijing 100850, China
| | - Ning Mao
- Beijing Institute of Basic Medical Sciences, Beijing 100850, China
| | - Bing Liu
- State Key Laboratory of Experimental Hematology, Department of Hematology, Fifth Medical Center of Chinese PLA General Hospital, Beijing 100071, China
| | - Li Ding
- Basic Medical College of Anhui Medical University, Hefei, Anhui 230032, China; Air Force Medical Center, PLA, Beijing 100142, China.
| | - Heng Zhu
- Basic Medical College of Anhui Medical University, Hefei, Anhui 230032, China; Beijing Institute of Radiation Medicine, Beijing 100850, China.
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