1
|
Ma D, Liu S, Liu K, Kong L, Xiao L, Xin Q, Jiang C, Wu J. MDFI promotes the proliferation and tolerance to chemotherapy of colorectal cancer cells by binding ITGB4/LAMB3 to activate the AKT signaling pathway. Cancer Biol Ther 2024; 25:2314324. [PMID: 38375821 PMCID: PMC10880501 DOI: 10.1080/15384047.2024.2314324] [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: 09/21/2023] [Accepted: 01/31/2024] [Indexed: 02/21/2024] Open
Abstract
Colorectal cancer (CRC) is one of the most lethal cancers. Single-cell RNA sequencing (scRNA-seq) and protein-protein interactions (PPIs) have enabled the systematic study of CRC. In our research, the activation of the AKT pathway in CRC was analyzed by KEGG using single-cell sequencing data from the GSE144735 dataset. The correlation and PPIs of MDFI and ITGB4/LAMB3 were examined. The results were verified in the TCGA and CCLE and further tested by coimmunoprecipitation experiments. The effect of MDFI on the AKT pathway via ITGB4/LAMB3 was validated by knockdown and lentiviral overexpression experiments. The effect of MDFI on oxaliplatin/fluorouracil sensitivity was probed by colony formation assay and CCK8 assay. We discovered that MDFI was positively associated with ITGB4/LAMB3. In addition, MDFI was negatively associated with oxaliplatin/fluorouracil sensitivity. MDFI upregulated the AKT pathway by directly interacting with LAMB3 and ITGB4 in CRC cells, and enhanced the proliferation of CRC cells via the AKT pathway. Finally, MDFI reduced the sensitivity of CRC cells to oxaliplatin and fluorouracil. In conclusion, MDFI promotes the proliferation and tolerance to chemotherapy of colorectal cancer cells, partially through the activation of the AKT signaling pathway by the binding to ITGB4/LAMB3. Our findings provide a possible molecular target for CRC therapy.
Collapse
Affiliation(s)
- Ding Ma
- State Key Laboratory of Pharmaceutical Biotechnology, National Institute of Healthcare Data Science at Nanjing University, Jiangsu Key Laboratory of Molecular Medicine, Medical School, Nanjing University, Nanjing, Jiangsu, China
- Department of Gastroenterology, Third Xiangya Hospital, Central South University, Changsha, Hunan, China
| | - Shuwen Liu
- State Key Laboratory of Pharmaceutical Biotechnology, National Institute of Healthcare Data Science at Nanjing University, Jiangsu Key Laboratory of Molecular Medicine, Medical School, Nanjing University, Nanjing, Jiangsu, China
| | - Kua Liu
- State Key Laboratory of Pharmaceutical Biotechnology, National Institute of Healthcare Data Science at Nanjing University, Jiangsu Key Laboratory of Molecular Medicine, Medical School, Nanjing University, Nanjing, Jiangsu, China
| | - Lingkai Kong
- State Key Laboratory of Pharmaceutical Biotechnology, National Institute of Healthcare Data Science at Nanjing University, Jiangsu Key Laboratory of Molecular Medicine, Medical School, Nanjing University, Nanjing, Jiangsu, China
| | - Lingjun Xiao
- State Key Laboratory of Pharmaceutical Biotechnology, National Institute of Healthcare Data Science at Nanjing University, Jiangsu Key Laboratory of Molecular Medicine, Medical School, Nanjing University, Nanjing, Jiangsu, China
| | - Qilei Xin
- Jinan Microecological Biomedicine Shandong Laboratory, Shounuo City Light West Block, Jinan City, Shandong Province, China
| | - Chunping Jiang
- State Key Laboratory of Pharmaceutical Biotechnology, National Institute of Healthcare Data Science at Nanjing University, Jiangsu Key Laboratory of Molecular Medicine, Medical School, Nanjing University, Nanjing, Jiangsu, China
- Jinan Microecological Biomedicine Shandong Laboratory, Shounuo City Light West Block, Jinan City, Shandong Province, China
| | - Junhua Wu
- State Key Laboratory of Pharmaceutical Biotechnology, National Institute of Healthcare Data Science at Nanjing University, Jiangsu Key Laboratory of Molecular Medicine, Medical School, Nanjing University, Nanjing, Jiangsu, China
- Jinan Microecological Biomedicine Shandong Laboratory, Shounuo City Light West Block, Jinan City, Shandong Province, China
| |
Collapse
|
2
|
Ravindran A, Holappa L, Niskanen H, Skovorodkin I, Kaisto S, Beter M, Kiema M, Selvarajan I, Nurminen V, Aavik E, Aherrahrou R, Pasonen-Seppänen S, Fortino V, Laakkonen JP, Ylä-Herttuala S, Vainio S, Örd T, Kaikkonen MU. Translatome profiling reveals Itih4 as a novel smooth muscle cell-specific gene in atherosclerosis. Cardiovasc Res 2024; 120:869-882. [PMID: 38289873 PMCID: PMC11218691 DOI: 10.1093/cvr/cvae028] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 03/29/2023] [Revised: 12/01/2023] [Accepted: 12/12/2023] [Indexed: 02/01/2024] Open
Abstract
AIMS Vascular smooth muscle cells (SMCs) and their derivatives are key contributors to the development of atherosclerosis. However, studying changes in SMC gene expression in heterogeneous vascular tissues is challenging due to the technical limitations and high cost associated with current approaches. In this paper, we apply translating ribosome affinity purification sequencing to profile SMC-specific gene expression directly from tissue. METHODS AND RESULTS To facilitate SMC-specific translatome analysis, we generated SMCTRAP mice, a transgenic mouse line expressing enhanced green fluorescent protein (EGFP)-tagged ribosomal protein L10a (EGFP-L10a) under the control of the SMC-specific αSMA promoter. These mice were further crossed with the atherosclerosis model Ldlr-/-, ApoB100/100 to generate SMCTRAP-AS mice and used to profile atherosclerosis-associated SMCs in thoracic aorta samples of 15-month-old SMCTRAP and SMCTRAP-AS mice. Our analysis of SMCTRAP-AS mice showed that EGFP-L10a expression was localized to SMCs in various tissues, including the aortic wall and plaque. The TRAP fraction demonstrated high enrichment of known SMC-specific genes, confirming the specificity of our approach. We identified several genes, including Cemip, Lum, Mfge8, Spp1, and Serpina3, which are known to be involved in atherosclerosis-induced gene expression. Moreover, we identified several novel genes not previously linked to SMCs in atherosclerosis, such as Anxa4, Cd276, inter-alpha-trypsin inhibitor-4 (Itih4), Myof, Pcdh11x, Rab31, Serpinb6b, Slc35e4, Slc8a3, and Spink5. Among them, we confirmed the SMC-specific expression of Itih4 in atherosclerotic lesions using immunofluorescence staining of mouse aortic roots and spatial transcriptomics of human carotid arteries. Furthermore, our more detailed analysis of Itih4 showed its link to coronary artery disease through the colocalization of genome-wide association studies, splice quantitative trait loci (QTL), and protein QTL signals. CONCLUSION We generated a SMC-specific TRAP mouse line to study atherosclerosis and identified Itih4 as a novel SMC-expressed gene in atherosclerotic plaques, warranting further investigation of its putative function in extracellular matrix stability and genetic evidence of causality.
Collapse
MESH Headings
- Animals
- Myocytes, Smooth Muscle/metabolism
- Myocytes, Smooth Muscle/pathology
- Atherosclerosis/genetics
- Atherosclerosis/metabolism
- Atherosclerosis/pathology
- Muscle, Smooth, Vascular/metabolism
- Muscle, Smooth, Vascular/pathology
- Disease Models, Animal
- Aortic Diseases/genetics
- Aortic Diseases/pathology
- Aortic Diseases/metabolism
- Ribosomal Proteins/genetics
- Ribosomal Proteins/metabolism
- Plaque, Atherosclerotic
- Mice, Inbred C57BL
- Male
- Gene Expression Regulation
- Gene Expression Profiling
- Phenotype
- Transcriptome
- Receptors, LDL/genetics
- Receptors, LDL/metabolism
- Apolipoprotein B-100/genetics
- Apolipoprotein B-100/metabolism
- Mice, Knockout
- Humans
- Green Fluorescent Proteins/genetics
- Green Fluorescent Proteins/metabolism
- Mice
- Mice, Transgenic
- Aorta/metabolism
- Aorta/pathology
- Female
Collapse
Affiliation(s)
- Aarthi Ravindran
- A.I.Virtanen Institute for Molecular Sciences, University of Eastern Finland, Neulaniementie 2, 70211 Kuopio, Finland
| | - Lari Holappa
- A.I.Virtanen Institute for Molecular Sciences, University of Eastern Finland, Neulaniementie 2, 70211 Kuopio, Finland
| | - Henri Niskanen
- A.I.Virtanen Institute for Molecular Sciences, University of Eastern Finland, Neulaniementie 2, 70211 Kuopio, Finland
| | - Ilya Skovorodkin
- Disease networks research unit, Faculty of Biochemistry and Molecular Medicine, Kvantum Institute, Infotech Oulu, University of Oulu, Oulu, Finland
| | - Susanna Kaisto
- Disease networks research unit, Faculty of Biochemistry and Molecular Medicine, Kvantum Institute, Infotech Oulu, University of Oulu, Oulu, Finland
| | - Mustafa Beter
- A.I.Virtanen Institute for Molecular Sciences, University of Eastern Finland, Neulaniementie 2, 70211 Kuopio, Finland
| | - Miika Kiema
- A.I.Virtanen Institute for Molecular Sciences, University of Eastern Finland, Neulaniementie 2, 70211 Kuopio, Finland
| | - Ilakya Selvarajan
- A.I.Virtanen Institute for Molecular Sciences, University of Eastern Finland, Neulaniementie 2, 70211 Kuopio, Finland
| | - Valtteri Nurminen
- A.I.Virtanen Institute for Molecular Sciences, University of Eastern Finland, Neulaniementie 2, 70211 Kuopio, Finland
| | - Einari Aavik
- A.I.Virtanen Institute for Molecular Sciences, University of Eastern Finland, Neulaniementie 2, 70211 Kuopio, Finland
| | - Rédouane Aherrahrou
- A.I.Virtanen Institute for Molecular Sciences, University of Eastern Finland, Neulaniementie 2, 70211 Kuopio, Finland
- Institute for Cardiogenetics, Universität zu Lübeck, 23562 Lübeck, Germany
- DZHK (German Centre for Cardiovascular Research), Partner Site Hamburg/Kiel/Lübeck, University Heart Centre Lübeck, 23562 Lübeck, Germany
| | - Sanna Pasonen-Seppänen
- Institute of Biomedicine, School of Medicine, Faculty of Health Sciences, University of Eastern Finland, Kuopio, Finland
| | - Vittorio Fortino
- Institute of Biomedicine, School of Medicine, Faculty of Health Sciences, University of Eastern Finland, Kuopio, Finland
| | - Johanna P Laakkonen
- A.I.Virtanen Institute for Molecular Sciences, University of Eastern Finland, Neulaniementie 2, 70211 Kuopio, Finland
| | - Seppo Ylä-Herttuala
- A.I.Virtanen Institute for Molecular Sciences, University of Eastern Finland, Neulaniementie 2, 70211 Kuopio, Finland
| | - Seppo Vainio
- Disease networks research unit, Faculty of Biochemistry and Molecular Medicine, Kvantum Institute, Infotech Oulu, University of Oulu, Oulu, Finland
| | - Tiit Örd
- A.I.Virtanen Institute for Molecular Sciences, University of Eastern Finland, Neulaniementie 2, 70211 Kuopio, Finland
| | - Minna U Kaikkonen
- A.I.Virtanen Institute for Molecular Sciences, University of Eastern Finland, Neulaniementie 2, 70211 Kuopio, Finland
| |
Collapse
|
3
|
Chang X, Zheng Y, Xu K. Single-Cell RNA Sequencing: Technological Progress and Biomedical Application in Cancer Research. Mol Biotechnol 2024; 66:1497-1519. [PMID: 37322261 PMCID: PMC11217094 DOI: 10.1007/s12033-023-00777-0] [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: 03/09/2023] [Accepted: 05/23/2023] [Indexed: 06/17/2023]
Abstract
Single-cell RNA-seq (scRNA-seq) is a revolutionary technology that allows for the genomic investigation of individual cells in a population, allowing for the discovery of unusual cells associated with cancer and metastasis. ScRNA-seq has been used to discover different types of cancers with poor prognosis and medication resistance such as lung cancer, breast cancer, ovarian cancer, and gastric cancer. Besides, scRNA-seq is a promising method that helps us comprehend the biological features and dynamics of cell development, as well as other disorders. This review gives a concise summary of current scRNA-seq technology. We also explain the main technological steps involved in implementing the technology. We highlight the present applications of scRNA-seq in cancer research, including tumor heterogeneity analysis in lung cancer, breast cancer, and ovarian cancer. In addition, this review elucidates potential applications of scRNA-seq in lineage tracing, personalized medicine, illness prediction, and disease diagnosis, which reveals that scRNA-seq facilitates these events by producing genetic variations on the single-cell level.
Collapse
Affiliation(s)
- Xu Chang
- Department of Otolaryngology, Head and Neck Surgery, The Second Affiliated Hospital of Nanchang University, Nanchang University, Nanchang, 330006, Jiangxi, People's Republic of China
| | - Yunxi Zheng
- Department of Otolaryngology, Head and Neck Surgery, The Second Affiliated Hospital of Nanchang University, Nanchang University, Nanchang, 330006, Jiangxi, People's Republic of China
| | - Kai Xu
- Department of Otolaryngology, Head and Neck Surgery, The Second Affiliated Hospital of Nanchang University, Nanchang University, Nanchang, 330006, Jiangxi, People's Republic of China.
| |
Collapse
|
4
|
Shen W, Wei W, Wang S, Yang X, Wang R, Tian H. RNA-binding protein AZGP1 inhibits epithelial cell proliferation by regulating the genes of alternative splicing in COPD. Gene 2024; 927:148736. [PMID: 38950687 DOI: 10.1016/j.gene.2024.148736] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/09/2024] [Revised: 05/22/2024] [Accepted: 06/26/2024] [Indexed: 07/03/2024]
Abstract
BACKGROUND Chronic Obstructive Pulmonary Disease (COPD) is characterized by high morbidity, disability, and mortality rates worldwide. RNA-binding proteins (RBPs) might regulate genes involved in oxidative stress and inflammation in COPD patients. Single-cell transcriptome sequencing (scRNA-seq) offers an accurate tool for identifying intercellular heterogeneity and the diversity of immune cells. However, the role of RBPs in the regulation of various cells, especially AT2 cells, remains elusive. MATERIALS AND METHODS A scRNA-seq dataset (GSE173896) and a bulk RNA-seq dataset acquired from airway tissues (GSE124180) were employed for data mining. Next, RNA-seq analysis was performed in both COPD and control patients. Differentially expressed genes (DEGs) were identified using criteria of fold change (FC ≥ 1.5 or ≤ 1.5) and P value ≤ 0.05. Lastly, Gene Ontology (GO), Kyoto Encyclopedia of Genes and Genomes (KEGG), and alternative splicing identification analyses were carried out. RESULTS RBP genes exhibited specific expression patterns across different cell groups and participated in cell proliferation and mitochondrial dysfunction in AT2 cells. As an RBP, AZGP1 expression was upregulated in both the scRNA-seq and RNA-seq datasets. It might potentially be a candidate immune biomarker that regulates COPD progression by modulating AT2 cell proliferation and adhesion by regulating the expression of SAMD5, DNER, DPYSL3, GBP5, GBP3, and KCNJ2. Moreover, AZGP1 regulated alternative splicing events in COPD, particularly DDAH1 and SFRP1, holding significant implications in COPD. CONCLUSION RBP gene AZGP1 inhibits epithelial cell proliferation by regulating genes participating in alternative splicing in COPD.
Collapse
Affiliation(s)
- Wen Shen
- General Medicine Department, The Second Affiliated Hospital of Kunming Medical University, China.
| | - Wei Wei
- General Medicine Department, The Second Affiliated Hospital of Kunming Medical University, China
| | - Shukun Wang
- General Medicine Department, The Second Affiliated Hospital of Kunming Medical University, China
| | - Xiaolei Yang
- General Medicine Department, The Second Affiliated Hospital of Kunming Medical University, China
| | - Ruili Wang
- General Medicine Department, The Second Affiliated Hospital of Kunming Medical University, China
| | - Hong Tian
- General Medicine Department, The Second Affiliated Hospital of Kunming Medical University, China
| |
Collapse
|
5
|
Nishide M, Shimagami H, Kumanogoh A. Single-cell analysis in rheumatic and allergic diseases: insights for clinical practice. Nat Rev Immunol 2024:10.1038/s41577-024-01043-3. [PMID: 38914790 DOI: 10.1038/s41577-024-01043-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 05/08/2024] [Indexed: 06/26/2024]
Abstract
Since the advent of single-cell RNA sequencing (scRNA-seq) methodology, single-cell analysis has become a powerful tool for exploration of cellular networks and dysregulated immune responses in disease pathogenesis. Advanced bioinformatics tools have enabled the combined analysis of scRNA-seq data and information on various cell properties, such as cell surface molecular profiles, chromatin accessibility and spatial information, leading to a deeper understanding of pathology. This Review provides an overview of the achievements in single-cell analysis applied to clinical samples of rheumatic and allergic diseases, including rheumatoid arthritis, systemic lupus erythematosus, systemic sclerosis, allergic airway diseases and atopic dermatitis, with an expanded scope beyond peripheral blood cells to include local diseased tissues. Despite the valuable insights that single-cell analysis has provided into disease pathogenesis, challenges remain in translating single-cell findings into clinical practice and developing personalized treatment strategies. Beyond understanding the atlas of cellular diversity, we discuss the application of data obtained in each study to clinical practice, with a focus on identifying biomarkers and therapeutic targets.
Collapse
Affiliation(s)
- Masayuki Nishide
- Department of Respiratory Medicine and Clinical Immunology, Graduate School of Medicine, Osaka University, Suita, Osaka, Japan.
- Department of Immunopathology, World Premier International Research Center Initiative (WPI), Immunology Frontier Research Center (IFReC), Osaka University, Suita, Osaka, Japan.
- Department of Advanced Clinical and Translational Immunology, Graduate School of Medicine, Osaka University, Suita, Osaka, Japan.
| | - Hiroshi Shimagami
- Department of Respiratory Medicine and Clinical Immunology, Graduate School of Medicine, Osaka University, Suita, Osaka, Japan
- Department of Immunopathology, World Premier International Research Center Initiative (WPI), Immunology Frontier Research Center (IFReC), Osaka University, Suita, Osaka, Japan
- Department of Advanced Clinical and Translational Immunology, Graduate School of Medicine, Osaka University, Suita, Osaka, Japan
| | - Atsushi Kumanogoh
- Department of Respiratory Medicine and Clinical Immunology, Graduate School of Medicine, Osaka University, Suita, Osaka, Japan.
- Department of Immunopathology, World Premier International Research Center Initiative (WPI), Immunology Frontier Research Center (IFReC), Osaka University, Suita, Osaka, Japan.
- Integrated Frontier Research for Medical Science Division, Institute for Open and Transdisciplinary Research Initiatives (OTRI), Osaka University, Suita, Osaka, Japan.
- Center for Infectious Diseases for Education and Research (CiDER), Osaka University, Suita, Osaka, Japan.
- Center for Advanced Modalities and DDS (CAMaD), Osaka University, Suita, Osaka, Japan.
| |
Collapse
|
6
|
Zhu J, Zhang K, Chen Y, Ge X, Wu J, Xu P, Yao J. Progress of single-cell RNA sequencing combined with spatial transcriptomics in tumour microenvironment and treatment of pancreatic cancer. J Transl Med 2024; 22:563. [PMID: 38867230 PMCID: PMC11167806 DOI: 10.1186/s12967-024-05307-3] [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: 11/27/2023] [Accepted: 05/16/2024] [Indexed: 06/14/2024] Open
Abstract
In recent years, single-cell analyses have revealed the heterogeneity of the tumour microenvironment (TME) at the genomic, transcriptomic, and proteomic levels, further improving our understanding of the mechanisms of tumour development. Single-cell RNA sequencing (scRNA-seq) technology allow analysis of the transcriptome at the single-cell level and have unprecedented potential for exploration of the characteristics involved in tumour development and progression. These techniques allow analysis of transcript sequences at higher resolution, thereby increasing our understanding of the diversity of cells found in the tumour microenvironment and how these cells interact in complex tumour tissue. Although scRNA-seq has emerged as an important tool for studying the tumour microenvironment in recent years, it cannot be used to analyse spatial information for cells. In this regard, spatial transcriptomics (ST) approaches allow researchers to understand the functions of individual cells in complex multicellular organisms by understanding their physical location in tissue sections. In particular, in related research on tumour heterogeneity, ST is an excellent complementary approach to scRNA-seq, constituting a new method for further exploration of tumour heterogeneity, and this approach can also provide unprecedented insight into the development of treatments for pancreatic cancer (PC). In this review, based on the methods of scRNA-seq and ST analyses, research progress on the tumour microenvironment and treatment of pancreatic cancer is further explained.
Collapse
Affiliation(s)
- Jie Zhu
- Department of Hepatobiliary and Pancreatic Surgery, Northern Jiangsu People's Hospital Affiliated Yangzhou University, Jiangsu Province, China
| | - Ke Zhang
- Dalian Medical University, Dalian, China
| | - Yuan Chen
- Department of Hepatobiliary and Pancreatic Surgery, Northern Jiangsu People's Hospital Affiliated Yangzhou University, Jiangsu Province, China
| | - Xinyu Ge
- Dalian Medical University, Dalian, China
| | - Junqing Wu
- Department of Hepatobiliary and Pancreatic Surgery, Northern Jiangsu People's Hospital Affiliated Yangzhou University, Jiangsu Province, China
| | - Peng Xu
- Department of Hepatobiliary and Pancreatic Surgery, Northern Jiangsu People's Hospital Affiliated Yangzhou University, Jiangsu Province, China.
| | - Jie Yao
- Department of Hepatobiliary and Pancreatic Surgery, Northern Jiangsu People's Hospital Affiliated Yangzhou University, Jiangsu Province, China.
| |
Collapse
|
7
|
Patel AS, Yanai I. A developmental constraint model of cancer cell states and tumor heterogeneity. Cell 2024; 187:2907-2918. [PMID: 38848676 DOI: 10.1016/j.cell.2024.04.032] [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: 10/02/2023] [Revised: 12/29/2023] [Accepted: 04/24/2024] [Indexed: 06/09/2024]
Abstract
Cancer is a disease that stems from a fundamental liability inherent to multicellular life forms in which an individual cell is capable of reneging on the interests of the collective organism. Although cancer is commonly described as an evolutionary process, a less appreciated aspect of tumorigenesis may be the constraints imposed by the organism's developmental programs. Recent work from single-cell transcriptomic analyses across a range of cancer types has revealed the recurrence, plasticity, and co-option of distinct cellular states among cancer cell populations. Here, we note that across diverse cancer types, the observed cell states are proximate within the developmental hierarchy of the cell of origin. We thus posit a model by which cancer cell states are directly constrained by the organism's "developmental map." According to this model, a population of cancer cells traverses the developmental map, thereby generating a heterogeneous set of states whose interactions underpin emergent tumor behavior.
Collapse
Affiliation(s)
- Ayushi S Patel
- Institute for Systems Genetics, NYU Grossman School of Medicine, New York, NY, USA; Department of Biochemistry & Molecular Pharmacology, NYU Grossman School of Medicine, New York, NY, USA; Perlmutter Cancer Center, NYU Langone Health, New York, NY, USA
| | - Itai Yanai
- Institute for Systems Genetics, NYU Grossman School of Medicine, New York, NY, USA; Department of Biochemistry & Molecular Pharmacology, NYU Grossman School of Medicine, New York, NY, USA; Perlmutter Cancer Center, NYU Langone Health, New York, NY, USA.
| |
Collapse
|
8
|
Lee H, Kim SY, Kwon NJ, Jo SJ, Kwon O, Kim JI. Single-Cell and Spatial Transcriptome Analysis of Dermal Fibroblast Development in Perinatal Mouse Skin: Dynamic Lineage Differentiation and Key Driver Genes. J Invest Dermatol 2024; 144:1238-1250.e11. [PMID: 38072389 DOI: 10.1016/j.jid.2023.11.008] [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: 02/20/2023] [Revised: 11/13/2023] [Accepted: 11/21/2023] [Indexed: 01/21/2024]
Abstract
Several single-cell RNA studies of developing mouse skin have elucidated the molecular and cellular processes involved in skin development. However, they have primarily focused on either the fetal or early postnatal period, leaving a gap in our understanding of skin development. In this study, we conducted a comprehensive time-series analysis by combining single-cell RNA-sequencing datasets collected at different stages of development (embryonic days 13.5, 14.5, and 16.5 and postnatal days 0, 2, and 4) and validated our findings through multipanel in situ spatial transcriptomics. Our analysis indicated that embryonic fibroblasts exhibit heterogeneity from a very early stage and that the rapid determination of each lineage occurs within days after birth. The expression of putative key driver genes, including Hey1, Ebf1, Runx3, and Sox11 for the dermal papilla trajectory; Lrrc15 for the dermal sheath trajectory; Zfp536 and Nrn1 for the papillary fibroblast trajectory; and Lrrn4cl and Mfap5 for the fascia fibroblast trajectory, was detected in the corresponding, spatially identified cell types. Finally, cell-to-cell interaction analysis indicated that the dermal papilla lineage is the primary source of the noncanonical Wnt pathway during skin development. Together, our study provides a transcriptomic reference for future research in the field of skin development and regeneration.
Collapse
Affiliation(s)
- Hanjae Lee
- Department of Dermatology, Seoul National University College of Medicine, Seoul, Korea; Department of Translational Medicine, Seoul National University College of Medicine, Seoul, Korea; Genomic Medicine Institute, Medical Research Center, Seoul National University, Seoul, Korea
| | - So Young Kim
- Department of Dermatology, Seoul National University College of Medicine, Seoul, Korea; Biomedical Research Institute, Seoul National University Hospital, Seoul, Korea
| | | | - Seong Jin Jo
- Department of Dermatology, Seoul National University College of Medicine, Seoul, Korea; Genomic Medicine Institute, Medical Research Center, Seoul National University, Seoul, Korea; Laboratory of Cutaneous Aging and Hair Research, Clinical Research Institute, Seoul National University Hospital, Seoul, Korea; Institute of Human-Environment Interface Biology, Seoul National University College of Medicine, Seoul, Korea
| | - Ohsang Kwon
- Department of Dermatology, Seoul National University College of Medicine, Seoul, Korea; Genomic Medicine Institute, Medical Research Center, Seoul National University, Seoul, Korea; Laboratory of Cutaneous Aging and Hair Research, Clinical Research Institute, Seoul National University Hospital, Seoul, Korea; Institute of Human-Environment Interface Biology, Seoul National University College of Medicine, Seoul, Korea; Department of Biomedical Sciences, Seoul National University Graduate School, Seoul, Korea.
| | - Jong-Il Kim
- Genomic Medicine Institute, Medical Research Center, Seoul National University, Seoul, Korea; Department of Biomedical Sciences, Seoul National University Graduate School, Seoul, Korea; Department of Biochemistry and Molecular Biology, Seoul National University College of Medicine, Seoul, Korea; Cancer Research Institute, Seoul National University, Seoul, Korea
| |
Collapse
|
9
|
Abe K, Abe N, Sugaya T, Takahata Y, Fujita M, Hayashi M, Takahashi A, Ohira H. Characteristics of peripheral blood mononuclear cells and potential related molecular mechanisms in patients with autoimmune hepatitis: a single-cell RNA sequencing analysis. Med Mol Morphol 2024; 57:110-123. [PMID: 38340154 DOI: 10.1007/s00795-024-00380-5] [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: 11/17/2023] [Accepted: 01/03/2024] [Indexed: 02/12/2024]
Abstract
Autoimmune hepatitis (AIH) is an immune disorder characterized by hypergammaglobulinemia, autoantibodies, and chronic active hepatitis on liver histology. However, immune cell population characteristics in AIH patients remain poorly understood. This study was designed to analyze peripheral blood mononuclear cell (PBMC) characteristics in AIH through single-cell RNA sequencing (scRNA-seq) and explore potential AIH-related molecular mechanisms. We generated 3690 and 3511 single-cell transcriptomes of PBMCs pooled from 4 healthy controls (HCs) and 4 AIH patients, respectively, by scRNA-seq. These pooled PBMC transcriptomes were used for cell cluster identification and differentially expressed gene (DEG) identification. GO functional enrichment analysis was performed on the DEGs to determine the most active AIH immune cell biological functions. Although the PCA-based uniform manifold approximation and projection (UMAP) algorithm was used to cluster cells with similar expression patterns in the two samples, 87 up- and 12 downregulated DEGs were retained in monocytes and 101 up- and 15 downregulated DEGs were retained in NK cells from AIH PBMCs. Moreover, enriched GO terms in the PBMC-derived monocyte and NK cell clusters were related mainly to antigen processing and presentation, IFN-γ-mediated signaling, and neutrophil degranulation and activation. These potential molecular mechanisms may be important targets for AIH treatment.
Collapse
Affiliation(s)
- Kazumichi Abe
- Department of Gastroenterology, Fukushima Medical University, 1 Hikarigaoka, Fukushima City, Fukushima, 960-1295, Japan.
| | - Naoto Abe
- Department of Gastroenterology, Fukushima Medical University, 1 Hikarigaoka, Fukushima City, Fukushima, 960-1295, Japan
| | - Tatsuro Sugaya
- Department of Gastroenterology, Fukushima Medical University, 1 Hikarigaoka, Fukushima City, Fukushima, 960-1295, Japan
| | - Yosuke Takahata
- Department of Gastroenterology, Fukushima Medical University, 1 Hikarigaoka, Fukushima City, Fukushima, 960-1295, Japan
| | - Masashi Fujita
- Department of Gastroenterology, Fukushima Medical University, 1 Hikarigaoka, Fukushima City, Fukushima, 960-1295, Japan
| | - Manabu Hayashi
- Department of Gastroenterology, Fukushima Medical University, 1 Hikarigaoka, Fukushima City, Fukushima, 960-1295, Japan
| | - Atsushi Takahashi
- Department of Gastroenterology, Fukushima Medical University, 1 Hikarigaoka, Fukushima City, Fukushima, 960-1295, Japan
| | - Hiromasa Ohira
- Department of Gastroenterology, Fukushima Medical University, 1 Hikarigaoka, Fukushima City, Fukushima, 960-1295, Japan
| |
Collapse
|
10
|
Zhong T, Cheng X, Gu Q, Fu G, Wang Y, Jiang Y, Xu J, Jiang Z. Integrated analyses reveal the diagnostic and predictive values of COL5A2 and association with immune environment in Crohn's disease. Genes Immun 2024; 25:209-218. [PMID: 38789829 PMCID: PMC11178494 DOI: 10.1038/s41435-024-00276-5] [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: 09/18/2023] [Revised: 05/03/2024] [Accepted: 05/13/2024] [Indexed: 05/26/2024]
Abstract
The pathogenesis of Crohn's disease (CD) involves abnormal immune cell infiltration and dysregulated immune response. Therefore, thorough research on immune cell abnormalities in CD is crucial for improved treatment of this disease. Single-cell RNA sequencing (scRNA-seq) and bulk RNA-seq data of CD were obtained from the Gene Expression Omnibus (GEO) database. Cell-type identification by estimating relative subsets of RNA transcripts (CIBERSORT), weighted gene co-expression network analysis (WGCNA), protein-protein interaction (PPI) networks evaluated the proportion of immune infiltrating cells, constructed co-expression network and identified key genes, respectively. Based on the dataset (GSE134809), 15 cell clusters were defined and labeled as different cell types. Among the 11 modules, the yellow module had the closest relationship with plasma cells (cluster 5). Confirmed using RNA sequencing and IHC assay, the expression of COL5A2 in CD samples was higher than that in control samples. Furthermore, the COL5A2 protein expression remarkably decreased in the group of patients who responded to anti-tumor necrosis factor (TNF) treatments, compared to the non-response group. The comprehensive analyses described here provided novel insight into the landscape of CD-associated immune environment. In addition, COL5A2 were identified as potential diagnostic indicators for CD, as well as promising predictive markers for CD patients.
Collapse
Affiliation(s)
- Tingting Zhong
- Department of Pathology, Sir Run Run Shaw Hospital, Zhejiang University School of Medicine, Hangzhou, China
| | - Xiaoqing Cheng
- Department of Pathology, Sir Run Run Shaw Hospital, Zhejiang University School of Medicine, Hangzhou, China
| | - Qianru Gu
- Department of Pathology, Sir Run Run Shaw Hospital, Zhejiang University School of Medicine, Hangzhou, China
| | - Guoxiang Fu
- Department of Pathology, Sir Run Run Shaw Hospital, Zhejiang University School of Medicine, Hangzhou, China
| | - Yihong Wang
- Department of Pathology, Sir Run Run Shaw Hospital, Zhejiang University School of Medicine, Hangzhou, China
| | - Yujie Jiang
- Department of Pathology, Sir Run Run Shaw Hospital, Zhejiang University School of Medicine, Hangzhou, China
| | - Jiaqi Xu
- Department of Pathology, Sir Run Run Shaw Hospital, Zhejiang University School of Medicine, Hangzhou, China.
| | - Zhinong Jiang
- Department of Pathology, Sir Run Run Shaw Hospital, Zhejiang University School of Medicine, Hangzhou, China.
| |
Collapse
|
11
|
Wan Z, Bai X, Wang X, Guo X, Wang X, Zhai M, Fu Y, Liu Y, Zhang P, Zhang X, Yang R, Liu Y, Lv L, Zhou Y. Mgp High-Expressing MSCs Orchestrate the Osteoimmune Microenvironment of Collagen/Nanohydroxyapatite-Mediated Bone Regeneration. ADVANCED SCIENCE (WEINHEIM, BADEN-WURTTEMBERG, GERMANY) 2024; 11:e2308986. [PMID: 38588510 PMCID: PMC11187922 DOI: 10.1002/advs.202308986] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/23/2023] [Revised: 03/22/2024] [Indexed: 04/10/2024]
Abstract
Activating autologous stem cells after the implantation of biomaterials is an important process to initiate bone regeneration. Although several studies have demonstrated the mechanism of biomaterial-mediated bone regeneration, a comprehensive single-cell level transcriptomic map revealing the influence of biomaterials on regulating the temporal and spatial expression patterns of mesenchymal stem cells (MSCs) is still lacking. Herein, the osteoimmune microenvironment is depicted around the classical collagen/nanohydroxyapatite-based bone repair materials via combining analysis of single-cell RNA sequencing and spatial transcriptomics. A group of functional MSCs with high expression of matrix Gla protein (Mgp) is identified, which may serve as a pioneer subpopulation involved in bone repair. Remarkably, these Mgp high-expressing MSCs (MgphiMSCs) exhibit efficient osteogenic differentiation potential and orchestrate the osteoimmune microenvironment around implanted biomaterials, rewiring the polarization and osteoclastic differentiation of macrophages through the Mdk/Lrp1 ligand-receptor pair. The inhibition of Mdk/Lrp1 activates the pro-inflammatory programs of macrophages and osteoclastogenesis. Meanwhile, multiple immune-cell subsets also exhibit close crosstalk between MgphiMSCs via the secreted phosphoprotein 1 (SPP1) signaling pathway. These cellular profiles and interactions characterized in this study can broaden the understanding of the functional MSC subpopulations at the early stage of biomaterial-mediated bone regeneration and provide the basis for materials-designed strategies that target osteoimmune modulation.
Collapse
Affiliation(s)
- Zhuqing Wan
- Department of ProsthodonticsPeking University School and Hospital of StomatologyHaidian DistrictBeijing100081China
- National Center for Stomatology, National Clinical Research Center for Oral Disease, National Engineering Research Center of Oral Biomaterials and Digital Medical Devices, Beijing Key Laboratory of Digital Stomatology, NHC Key Laboratory of Digital Stomatology, Key Laboratory of Digital StomatologyChinese Academy of Medical SciencesHaidian DistrictBeijing100081China
| | - Xiaoqiang Bai
- Department of ProsthodonticsPeking University School and Hospital of StomatologyHaidian DistrictBeijing100081China
- National Center for Stomatology, National Clinical Research Center for Oral Disease, National Engineering Research Center of Oral Biomaterials and Digital Medical Devices, Beijing Key Laboratory of Digital Stomatology, NHC Key Laboratory of Digital Stomatology, Key Laboratory of Digital StomatologyChinese Academy of Medical SciencesHaidian DistrictBeijing100081China
| | - Xin Wang
- Department of ProsthodonticsPeking University School and Hospital of StomatologyHaidian DistrictBeijing100081China
- National Center for Stomatology, National Clinical Research Center for Oral Disease, National Engineering Research Center of Oral Biomaterials and Digital Medical Devices, Beijing Key Laboratory of Digital Stomatology, NHC Key Laboratory of Digital Stomatology, Key Laboratory of Digital StomatologyChinese Academy of Medical SciencesHaidian DistrictBeijing100081China
| | - Xiaodong Guo
- Department of ProsthodonticsPeking University School and Hospital of StomatologyHaidian DistrictBeijing100081China
- National Center for Stomatology, National Clinical Research Center for Oral Disease, National Engineering Research Center of Oral Biomaterials and Digital Medical Devices, Beijing Key Laboratory of Digital Stomatology, NHC Key Laboratory of Digital Stomatology, Key Laboratory of Digital StomatologyChinese Academy of Medical SciencesHaidian DistrictBeijing100081China
| | - Xu Wang
- Department of ProsthodonticsPeking University School and Hospital of StomatologyHaidian DistrictBeijing100081China
- National Center for Stomatology, National Clinical Research Center for Oral Disease, National Engineering Research Center of Oral Biomaterials and Digital Medical Devices, Beijing Key Laboratory of Digital Stomatology, NHC Key Laboratory of Digital Stomatology, Key Laboratory of Digital StomatologyChinese Academy of Medical SciencesHaidian DistrictBeijing100081China
| | - Mo Zhai
- Department of ProsthodonticsPeking University School and Hospital of StomatologyHaidian DistrictBeijing100081China
- National Center for Stomatology, National Clinical Research Center for Oral Disease, National Engineering Research Center of Oral Biomaterials and Digital Medical Devices, Beijing Key Laboratory of Digital Stomatology, NHC Key Laboratory of Digital Stomatology, Key Laboratory of Digital StomatologyChinese Academy of Medical SciencesHaidian DistrictBeijing100081China
| | - Yang Fu
- Department of ProsthodonticsPeking University School and Hospital of StomatologyHaidian DistrictBeijing100081China
- National Center for Stomatology, National Clinical Research Center for Oral Disease, National Engineering Research Center of Oral Biomaterials and Digital Medical Devices, Beijing Key Laboratory of Digital Stomatology, NHC Key Laboratory of Digital Stomatology, Key Laboratory of Digital StomatologyChinese Academy of Medical SciencesHaidian DistrictBeijing100081China
| | - Yunsong Liu
- Department of ProsthodonticsPeking University School and Hospital of StomatologyHaidian DistrictBeijing100081China
- National Center for Stomatology, National Clinical Research Center for Oral Disease, National Engineering Research Center of Oral Biomaterials and Digital Medical Devices, Beijing Key Laboratory of Digital Stomatology, NHC Key Laboratory of Digital Stomatology, Key Laboratory of Digital StomatologyChinese Academy of Medical SciencesHaidian DistrictBeijing100081China
| | - Ping Zhang
- Department of ProsthodonticsPeking University School and Hospital of StomatologyHaidian DistrictBeijing100081China
- National Center for Stomatology, National Clinical Research Center for Oral Disease, National Engineering Research Center of Oral Biomaterials and Digital Medical Devices, Beijing Key Laboratory of Digital Stomatology, NHC Key Laboratory of Digital Stomatology, Key Laboratory of Digital StomatologyChinese Academy of Medical SciencesHaidian DistrictBeijing100081China
| | - Xiao Zhang
- Department of ProsthodonticsPeking University School and Hospital of StomatologyHaidian DistrictBeijing100081China
- National Center for Stomatology, National Clinical Research Center for Oral Disease, National Engineering Research Center of Oral Biomaterials and Digital Medical Devices, Beijing Key Laboratory of Digital Stomatology, NHC Key Laboratory of Digital Stomatology, Key Laboratory of Digital StomatologyChinese Academy of Medical SciencesHaidian DistrictBeijing100081China
| | - Ruili Yang
- National Center for Stomatology, National Clinical Research Center for Oral Disease, National Engineering Research Center of Oral Biomaterials and Digital Medical Devices, Beijing Key Laboratory of Digital Stomatology, NHC Key Laboratory of Digital Stomatology, Key Laboratory of Digital StomatologyChinese Academy of Medical SciencesHaidian DistrictBeijing100081China
- Department of OrthodonticsPeking University School and Hospital of StomatologyHaidian DistrictBeijing100081China
| | - Yan Liu
- National Center for Stomatology, National Clinical Research Center for Oral Disease, National Engineering Research Center of Oral Biomaterials and Digital Medical Devices, Beijing Key Laboratory of Digital Stomatology, NHC Key Laboratory of Digital Stomatology, Key Laboratory of Digital StomatologyChinese Academy of Medical SciencesHaidian DistrictBeijing100081China
- Department of OrthodonticsPeking University School and Hospital of StomatologyHaidian DistrictBeijing100081China
| | - Longwei Lv
- Department of ProsthodonticsPeking University School and Hospital of StomatologyHaidian DistrictBeijing100081China
- National Center for Stomatology, National Clinical Research Center for Oral Disease, National Engineering Research Center of Oral Biomaterials and Digital Medical Devices, Beijing Key Laboratory of Digital Stomatology, NHC Key Laboratory of Digital Stomatology, Key Laboratory of Digital StomatologyChinese Academy of Medical SciencesHaidian DistrictBeijing100081China
| | - Yongsheng Zhou
- Department of ProsthodonticsPeking University School and Hospital of StomatologyHaidian DistrictBeijing100081China
- National Center for Stomatology, National Clinical Research Center for Oral Disease, National Engineering Research Center of Oral Biomaterials and Digital Medical Devices, Beijing Key Laboratory of Digital Stomatology, NHC Key Laboratory of Digital Stomatology, Key Laboratory of Digital StomatologyChinese Academy of Medical SciencesHaidian DistrictBeijing100081China
| |
Collapse
|
12
|
Hong H, Wang Y, Menard M, Buckley J, Zhou L, Volpicelli-Daley L, Standaert D, Qin H, Benveniste E. Suppression of the JAK/STAT Pathway Inhibits Neuroinflammation in the Line 61-PFF Mouse Model of Parkinson's Disease. RESEARCH SQUARE 2024:rs.3.rs-4307273. [PMID: 38766241 PMCID: PMC11100885 DOI: 10.21203/rs.3.rs-4307273/v1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/22/2024]
Abstract
Parkinson's disease (PD) is characterized by neuroinflammation, progressive loss of dopaminergic neurons, and accumulation of a-synuclein (a-Syn) into insoluble aggregates called Lewy pathology. The Line 61 a-Syn mouse is an established preclinical model of PD; Thy-1 is used to promote human a-Syn expression, and features of sporadic PD develop at 9-18 months of age. To accelerate the PD phenotypes, we injected sonicated human a-Syn preformed fibrils (PFFs) into the striatum, which produced phospho-Syn (p-a-Syn) inclusions in the substantia nigra pars compacta and significantly increased MHC Class II-positive immune cells. Additionally, there was enhanced infiltration and activation of innate and adaptive immune cells in the midbrain. We then used this new model, Line 61-PFF, to investigate the effect of inhibiting the JAK/STAT signaling pathway, which is critical for regulation of innate and adaptive immune responses. After administration of the JAK1/2 inhibitor AZD1480, immunofluorescence staining showed a significant decrease in p-a-Syn inclusions and MHC Class II expression. Flow cytometry showed reduced infiltration of CD4+ T-cells, CD8+ T-cells, CD19+ B-cells, dendritic cells, macrophages, and endogenous microglia into the midbrain. Importantly, single-cell RNA-Sequencing analysis of CD45+ cells from the midbrain identified 9 microglia clusters, 5 monocyte/macrophage (MM) clusters, and 5 T-cell (T) clusters, in which potentially pathogenic MM4 and T3 clusters were associated with neuroinflammatory responses in Line 61-PFF mice. AZD1480 treatment reduced cell numbers and cluster-specific expression of the antigen-presentation genes H2-Eb1, H2-Aa, H2-Ab1, and Cd74 in the MM4 cluster and proinflammatory genes such as Tnf, Il1b, C1qa, and C1qc in the T3 cluster. Together, these results indicate that inhibiting the JAK/STAT pathway suppresses the activation and infiltration of innate and adaptive cells, reducing neuroinflammation in the Line 61-PFF mouse model.
Collapse
|
13
|
Ren Z, Li C, Wang J, Sui J, Ma Y. Single-cell transcriptome revealed dysregulated RNA-binding protein expression patterns and functions in human ankylosing spondylitis. Front Med (Lausanne) 2024; 11:1369341. [PMID: 38770048 PMCID: PMC11104332 DOI: 10.3389/fmed.2024.1369341] [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: 01/12/2024] [Accepted: 04/22/2024] [Indexed: 05/22/2024] Open
Abstract
Objective To explore the expression characteristics and regulatory patterns of RBPs in different immune cell types of AS, and to clarify the potential key role of RBPs in the occurrence and development of AS disease. Methods PBMC sample data from scRNA-seq (HC*29, AS*10) and bulk RNA-seq (NC*3, AS*5) were selected for correlation analysis. Results (1) Compared with the HC group, the numbers of B, DC (dendritic cells), CD14+ Mono and CD8+ T cells were increased in AS group, while the numbers of platelet (platelets), CD8+ NKT, CD16+ Mono (non-classical monocytes), Native CD4+ T and NK were decreased. (2) Through the analysis of RBP genes in B cells, some RBPs were found to play an important role in B cell differentiation and function, such as DDX3X, SFPQ, SRRM1, UPF2. (3) It may be related to B-cell receptor, IgA immunity, NOD-like receptor and other signaling pathways; Through the analysis of RBP genes in CD8+ T cells, some RBPs that play an important role in the immune regulation of CD8+ T were found, such as EIF2S3, EIF4B, HSPA5, MSL3, PABPC1 and SRSF7; It may be related to T cell receptor, TNF, IL17 and other signaling pathways. (4) Based on bulk RNA-seq, it was found that compared with HC and AS patients, differentially expressed variable splicing genes (RASGs) may play an important role in the occurrence and development of AS by participating in transcriptional regulation, protein phosphorylation and ubiquitination, DNA replication, angiogenesis, intracellular signal transduction and other related pathways. Conclusion RBPs has specific expression characteristics in different immune cell types of AS patients, and has important regulatory functions. Its abnormal expression and regulation may be closely related to the occurrence and development of AS.
Collapse
Affiliation(s)
- Zheng Ren
- Xinjiang Institute of Spinal Surgery, Sixth Affiliated Hospital of Xinjiang Medical University, Ürümqi, Xinjiang, China
| | - Chenyang Li
- Microsurgery Unit, The Third People’s Hospital of Xinjiang, Ürümqi, Xinjiang, China
| | - Jing Wang
- Xinjiang Institute of Spinal Surgery, Sixth Affiliated Hospital of Xinjiang Medical University, Ürümqi, Xinjiang, China
| | - Jiangtao Sui
- Xinjiang Institute of Spinal Surgery, Sixth Affiliated Hospital of Xinjiang Medical University, Ürümqi, Xinjiang, China
| | - Yuan Ma
- Xinjiang Institute of Spinal Surgery, Sixth Affiliated Hospital of Xinjiang Medical University, Ürümqi, Xinjiang, China
| |
Collapse
|
14
|
Tan L, Zhou J, Nie Z, Li D, Wang B. EPHB2 as a key mediator of glioma progression: Insights from microenvironmental receptor ligand-related prognostic gene signature. Genomics 2024; 116:110799. [PMID: 38286348 DOI: 10.1016/j.ygeno.2024.110799] [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: 11/05/2023] [Revised: 01/05/2024] [Accepted: 01/22/2024] [Indexed: 01/31/2024]
Abstract
Malignant gliomas, characterized by pronounced heterogeneity, a complex microenvironment, and a propensity for relapse and drug resistaniguree, pose significant challenges in oncology. This study aimed to investigate the prognostic value of Ligand and Receptor related genes (LRRGs) within the glioma microenvironment. An intersection of 71 ligand-related genes (LRGs) and 2628 receptor-related genes (RRGs) yielded a total of 69 LRRGs. Utilizing the least absolute shrinkage and selection operator (LASSO) regression analysis, a prognostic RiskScore model comprising 28 LRRGs was constructed. The model demonstrated robust prognostic value, further validated in the TCGA-GBMLGG dataset. Subsequent analyses included differential gene expression, Gene Ontology (GO), Kyoto Encyclopedia of Genes and Genomes (KEGG), gene set enrichment (GSEA), and gene set variation (GSVA) within RiskScore groups. Additionally, evaluations of PPI, mRNA-RBP, mRNA-TF, and mRNA-drug interaction networks were conducted. Four hub genes were identified through differential expression analysis of the 28 LRRGs across various GSE datasets. A multivariate Cox prognostic model was constructed for nomogram analysis, gene mutation analysis, and related expression distribution. This study underscores the role of LRRGs in intercellular communication within the glioma microenvironment and identifies four hub genes crucial for prognostic assessment in clinical glioma patients. These findings offer a potential evaluation framework for glioma patients, enhancing our understanding of the disease and informing future therapeutic strategies.
Collapse
Affiliation(s)
- Liming Tan
- The Second Affiliated Hospital, Department of Neurosurgery, Hengyang Medical School, University of South China, Hengyang, Hunan 421001, China
| | - Jingyuan Zhou
- The Second Affiliated Hospital, Department of Neurosurgery, Hengyang Medical School, University of South China, Hengyang, Hunan 421001, China
| | - Zhenyu Nie
- The Second Affiliated Hospital, Department of Neurosurgery, Hengyang Medical School, University of South China, Hengyang, Hunan 421001, China
| | - Ding Li
- The Second Affiliated Hospital, Department of Neurosurgery, Hengyang Medical School, University of South China, Hengyang, Hunan 421001, China
| | - Bing Wang
- The Second Affiliated Hospital, Department of Neurosurgery, Hengyang Medical School, University of South China, Hengyang, Hunan 421001, China.
| |
Collapse
|
15
|
Selman M, Pardo A. Idiopathic Pulmonary Fibrosis: From Common Microscopy to Single-Cell Biology and Precision Medicine. Am J Respir Crit Care Med 2024; 209:1074-1081. [PMID: 38289233 DOI: 10.1164/rccm.202309-1573pp] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/07/2023] [Accepted: 01/29/2024] [Indexed: 05/02/2024] Open
Affiliation(s)
- Moisés Selman
- Instituto Nacional de Enfermedades Respiratorias "Ismael Cosío Villegas", Mexico City, Mexico; and
| | - Annie Pardo
- Facultad de Ciencias, Universidad Nacional Autónoma de México, Mexico City, Mexico
| |
Collapse
|
16
|
Huang L, Zuo Y, Li S, Li C. Melanocyte stem cells in the skin: Origin, biological characteristics, homeostatic maintenance and therapeutic potential. Clin Transl Med 2024; 14:e1720. [PMID: 38778457 PMCID: PMC11111606 DOI: 10.1002/ctm2.1720] [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: 01/19/2024] [Revised: 05/07/2024] [Accepted: 05/12/2024] [Indexed: 05/25/2024] Open
Abstract
Melanocyte stem cells (MSCs), melanocyte lineage-specific skin stem cells derived from the neural crest, are observed in the mammalian hair follicle, the epidermis or the sweat gland. MSCs differentiate into mature melanin-producing melanocytes, which confer skin and hair pigmentation and uphold vital skin functions. In controlling and coordinating the homeostasis, repair and regeneration of skin tissue, MSCs play a vital role. Decreased numbers or impaired functions of MSCs are closely associated with the development and therapy of many skin conditions, such as hair graying, vitiligo, wound healing and melanoma. With the advancement of stem cell technology, the relevant features of MSCs have been further elaborated. In this review, we provide an exhaustive overview of cutaneous MSCs and highlight the latest advances in MSC research. A better understanding of the biological characteristics and micro-environmental regulatory mechanisms of MSCs will help to improve clinical applications in regenerative medicine, skin pigmentation disorders and cancer therapy. KEY POINTS: This review provides a concise summary of the origin, biological characteristics, homeostatic maintenance and therapeutic potential of cutaneous MSCs. The role and potential application value of MSCs in skin pigmentation disorders are discussed. The significance of single-cell RNA sequencing, CRISPR-Cas9 technology and practical models in MSCs research is highlighted.
Collapse
Affiliation(s)
- Luling Huang
- Department of DermatologyXijing HospitalFourth Military Medical UniversityXi'anChina
| | - Yuzhi Zuo
- Department of Plastic and Burns SurgeryThe Affiliated Hospital of Southwest Medical UniversityLuzhouChina
| | - Shuli Li
- Department of DermatologyXijing HospitalFourth Military Medical UniversityXi'anChina
| | - Chunying Li
- Department of DermatologyXijing HospitalFourth Military Medical UniversityXi'anChina
| |
Collapse
|
17
|
Park J, Kadam PS, Atiyas Y, Chhay B, Tsourkas A, Eberwine JH, Issadore DA. High-Throughput Single-Cell, Single-Mitochondrial DNA Assay Using Hydrogel Droplet Microfluidics. Angew Chem Int Ed Engl 2024; 63:e202401544. [PMID: 38470412 DOI: 10.1002/anie.202401544] [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: 01/23/2024] [Revised: 03/06/2024] [Accepted: 03/08/2024] [Indexed: 03/13/2024]
Abstract
There is growing interest in understanding the biological implications of single cell heterogeneity and heteroplasmy of mitochondrial DNA (mtDNA), but current methodologies for single-cell mtDNA analysis limit the scale of analysis to small cell populations. Although droplet microfluidics have increased the throughput of single-cell genomic, RNA, and protein analysis, their application to sub-cellular organelle analysis has remained a largely unsolved challenge. Here, we introduce an agarose-based droplet microfluidic approach for single-cell, single-mtDNA analysis, which allows simultaneous processing of hundreds of individual mtDNA molecules within >10,000 individual cells. Our microfluidic chip encapsulates individual cells in agarose beads, designed to have a sufficiently dense hydrogel network to retain mtDNA after lysis and provide a robust scaffold for subsequent multi-step processing and analysis. To mitigate the impact of the high viscosity of agarose required for mtDNA retention on the throughput of microfluidics, we developed a parallelized device, successfully achieving ~95 % mtDNA retention from single cells within our microbeads at >700,000 drops/minute. To demonstrate utility, we analyzed specific regions of the single-mtDNA using a multiplexed rolling circle amplification (RCA) assay. We demonstrated compatibility with both microscopy, for digital counting of individual RCA products, and flow cytometry for higher throughput analysis.
Collapse
Affiliation(s)
- Juhwan Park
- Department of Bioengineering, School of Engineering and Applied Science, University of Pennsylvania, Philadelphia, Pennsylvania, 19104, USA
| | - Parnika S Kadam
- Department of Pharmacology, Perelman School of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania, 19104, USA
| | - Yasemin Atiyas
- Department of Bioengineering, School of Engineering and Applied Science, University of Pennsylvania, Philadelphia, Pennsylvania, 19104, USA
| | - Bonirath Chhay
- Department of Bioengineering, School of Engineering and Applied Science, University of Pennsylvania, Philadelphia, Pennsylvania, 19104, USA
| | - Andrew Tsourkas
- Department of Bioengineering, School of Engineering and Applied Science, University of Pennsylvania, Philadelphia, Pennsylvania, 19104, USA
| | - James H Eberwine
- Department of Pharmacology, Perelman School of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania, 19104, USA
| | - David A Issadore
- Department of Bioengineering, School of Engineering and Applied Science, University of Pennsylvania, Philadelphia, Pennsylvania, 19104, USA
| |
Collapse
|
18
|
Wang P, Li Z, Ye D. Single-cell RNA-seq analysis reveals the Wnt/Ca 2+ signaling pathway with inflammation, apoptosis in nucleus pulposus degeneration. BMC Musculoskelet Disord 2024; 25:321. [PMID: 38654287 PMCID: PMC11036596 DOI: 10.1186/s12891-024-07368-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 09/15/2023] [Accepted: 03/20/2024] [Indexed: 04/25/2024] Open
Abstract
BACKGROUND Increasing studies have shown degeneration of nucleus pulposus cells (NPCs) as an critical part of the progression of intervertebral disc degeneration (IVDD). However, there are relatively few studies on single-cell transcriptome contrasts in human degenerated NPCs. Moreover, differences in Wnt/Ca2+ signaling in human degenerated nucleus pulposus cells have not been elucidated. The aim of this study is to investigate the differential expression of Wnt/Ca2+ signaling pathway between normal and degenerated nucleus pulposus cells in humans and try to investigate its mechanism. METHODS We performed bioinformatics analysis using our previously published findings to construct single cell expression profiles of normal and degenerated nucleus pulposus. Then, in-depth differential analysis was used to characterize the expression of Wnt/Ca2+ signaling pathway between normal and degenerated nucleus pulposus cells in humans. RESULTS The obtained cell data were clustered into five different chondrocytes clusters, which chondrocyte 4 and chondrocyte 5 mainly accounted for a high proportion in degenerated nucleus pulposus tissues, but rarely in normal nucleus pulposus tissues. Genes associated within the Wnt/Ca2+ signaling pathway, such as Wnt5B, FZD1, PLC (PLCB1), CaN (PPP3CA) and NAFATC1 are mainly present in chondrocyte 3, chondrocyte 4 and chondrocyte 5 from degenerated nucleus pulposus tissues. In addition, as a receptor that activates Wnt signaling pathway, LRP5 is mainly highly expressed in chondrocyte 5 of degenerated nucleus pulposus cells. Six genes, ANGPTL4, PTGES, IGFBP3, GDF15, TRIB3 and TNFRSF10B, which are associated with apoptosis and inflammatory responses, and are widespread in chondrocyte 4 and chondrocyte 5, may be closely related to degenerative of nucleus pulposus cells. CONCLUSIONS Single-cell RNA sequencing revealed differential expression of Wnt/Ca2+ signaling in human normal and degenerated nucleus pulposus cells, and this differential expression may be closely related to the abundance of chondrocyte 4 and chondrocyte 5 in degenerated nucleus pulposus cells. In degenerated nucleus pulposus cells, LRP5 activate Wnt5B, which promotes nucleus pulposus cell apoptosis and inflammatory response by regulating the Wnt/Ca2+ signaling pathway, thereby promoting disc degeneration. ANGPTL4, IGFBP3, PTGES in chondrocyte 4 and TRIB3, GDF15, TNFRSF10B in chondrocyte 5 may play an important role in this process.
Collapse
Affiliation(s)
- Peigeng Wang
- Guangzhou Red Cross Hospital, Guangzhou Red Cross Hospital of Jinan University, Guangzhou, Guangdong Province, 510220, China
- Guizhou Medical University, Guizhou Medical University, Guiyang, Guizhou Province, 550025, China
| | - Zhencong Li
- Department of Spinal Degeneration and Deformity Surgery, Affiliated Hospital of Guangdong Medical University, Zhanjiang, Guangdong Province, 524001, China
| | - Dongping Ye
- Guangzhou Red Cross Hospital, Guangzhou Red Cross Hospital of Jinan University, Guangzhou, Guangdong Province, 510220, China.
- Guizhou Medical University, Guizhou Medical University, Guiyang, Guizhou Province, 550025, China.
| |
Collapse
|
19
|
Nakagawa T, Santos J, Nasamran CA, Sen P, Sadat S, Monther A, Bendik J, Ebisumoto K, Hu J, Preissl S, Guo T, Vavinskaya V, Fisch KM, Califano JA. Defining the relationship of salivary gland malignancies to novel cell subpopulations in human salivary glands using single nucleus RNA-sequencing. Int J Cancer 2024; 154:1492-1503. [PMID: 37971144 DOI: 10.1002/ijc.34790] [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: 02/20/2023] [Revised: 09/26/2023] [Accepted: 10/17/2023] [Indexed: 11/19/2023]
Abstract
Salivary glands have essential roles in maintaining oral health, mastication, taste and speech, by secreting saliva. Salivary glands are composed of several types of cells, and each cell type is predicted to be involved in the carcinogenesis of different types of cancers including adenoid cystic carcinoma (ACC), acinic cell carcinoma (AciCC), salivary duct carcinoma (SDC), myoepithelial carcinoma (MECA) and other histology. In our study, we performed single nucleus RNA-seq on three human salivary gland samples to clarify the gene expression profile of each complex cellular component of the salivary glands and related these expression patterns to expression found in salivary gland cancers (SGC) to infer cell of origin. By single nucleus RNA-seq, salivary gland cells were stratified into four clusters: acinar cells, ductal cells 1, ductal cells 2 and myoepithelial cells/stromal cells. The localization of each cell group was verified by IHC of each cluster marker gene, and one group of ductal cells was found to represent intercalated ductal cells labeled with HES1. Furthermore, in comparison with SGC RNA-seq data, acinar cell markers were upregulated in AciCC, but downregulated in ACC and ductal cell markers were upregulated in SDC but downregulated in MECA, suggesting that markers of origin are highly expressed in some SGC. Cell type expressions in specific SGC histology are similar to those found in normal salivary gland populations, indicating a potential etiologic relationship.
Collapse
Affiliation(s)
- Takuya Nakagawa
- Moores Cancer Center, University of California San Diego, La Jolla, California, USA
| | - Jessica Santos
- Moores Cancer Center, University of California San Diego, La Jolla, California, USA
| | - Chanond A Nasamran
- Center for Computational Biology and Bioinformatics, University of California San Diego, La Jolla, California, USA
| | - Prakriti Sen
- Moores Cancer Center, University of California San Diego, La Jolla, California, USA
| | - Sayed Sadat
- Moores Cancer Center, University of California San Diego, La Jolla, California, USA
| | - Abdula Monther
- Moores Cancer Center, University of California San Diego, La Jolla, California, USA
| | - Joseph Bendik
- Moores Cancer Center, University of California San Diego, La Jolla, California, USA
| | - Koji Ebisumoto
- Moores Cancer Center, University of California San Diego, La Jolla, California, USA
| | - Jingjing Hu
- Department of Pathology, University of California San Diego, San Diego, California, USA
| | - Sebastian Preissl
- Center for Epigenomics, Department of Cellular and Molecular Medicine, University of California San Diego, La Jolla, California, USA
| | - Theresa Guo
- Division of Otolaryngology - Head and Neck Surgery, Department of Surgery, University of California San Diego, La Jolla, California, USA
| | - Vera Vavinskaya
- Department of Pathology, University of California San Diego, San Diego, California, USA
| | - Kathleen M Fisch
- Center for Computational Biology and Bioinformatics, University of California San Diego, La Jolla, California, USA
| | - Joseph A Califano
- Moores Cancer Center, University of California San Diego, La Jolla, California, USA
- Division of Otolaryngology - Head and Neck Surgery, Department of Surgery, University of California San Diego, La Jolla, California, USA
| |
Collapse
|
20
|
Chen F, Liu K, Shang L, Wang Y, Tang X, Liang P, Li B. Precision isolation and cultivation of single cells by vortex and flat-top laser ejection. Front Microbiol 2024; 15:1369506. [PMID: 38659989 PMCID: PMC11039905 DOI: 10.3389/fmicb.2024.1369506] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/12/2024] [Accepted: 03/19/2024] [Indexed: 04/26/2024] Open
Abstract
Single-cell isolation stands as a critical step in single-cell studies, and single-cell ejection technology based on laser induced forward transfer technology (LIFT) is considered one of the most promising methods in this regard for its ability of visible isolating single cell from complex samples. In this study, we improve the LIFT technology and introduce optical vortex laser-induced forward transfer (OV-LIFT) and flat-top laser-induced forward transfer (FT-LIFT) by utilizing spatial light modulator (SLM), aiming to enhance the precision of single-cell sorting and the cell's viability after ejection. Experimental results demonstrate that applying vortex and flat-top beams during the sorting and collection process enables precise retrieval of single cells within diameter ranges of 50 μm and 100 μm, respectively. The recovery rates of Saccharomyces cerevisiae and Escherichia coli DH5α single cell ejected by vortex beam are 89 and 78%, by flat-top beam are 85 and 57%. When employing Gaussian beam sorting, the receiving range extends to 400 μm, with cultivation success rates of S. cerevisiae and E. coli DH5α single cell are 48 and 19%, respectively. This marks the first application of different mode beams in the ejection and cultivation of single cells, providing a novel and effective approach for the precise isolation and improving the viability of single cells.
Collapse
Affiliation(s)
- Fuyuan Chen
- Key Laboratory of Optical System Advanced Manufacturing Technology, Changchun Institute of Optics, Fine Mechanics and Physics, Chinese Academy of Sciences, Changchun, China
- University of Chinese Academy of Sciences, Beijing, China
| | - Kunxiang Liu
- Key Laboratory of Optical System Advanced Manufacturing Technology, Changchun Institute of Optics, Fine Mechanics and Physics, Chinese Academy of Sciences, Changchun, China
- University of Chinese Academy of Sciences, Beijing, China
| | - Lindong Shang
- Key Laboratory of Optical System Advanced Manufacturing Technology, Changchun Institute of Optics, Fine Mechanics and Physics, Chinese Academy of Sciences, Changchun, China
- University of Chinese Academy of Sciences, Beijing, China
| | - Yuntong Wang
- Key Laboratory of Optical System Advanced Manufacturing Technology, Changchun Institute of Optics, Fine Mechanics and Physics, Chinese Academy of Sciences, Changchun, China
- University of Chinese Academy of Sciences, Beijing, China
| | - Xusheng Tang
- Key Laboratory of Optical System Advanced Manufacturing Technology, Changchun Institute of Optics, Fine Mechanics and Physics, Chinese Academy of Sciences, Changchun, China
- University of Chinese Academy of Sciences, Beijing, China
| | - Peng Liang
- Key Laboratory of Optical System Advanced Manufacturing Technology, Changchun Institute of Optics, Fine Mechanics and Physics, Chinese Academy of Sciences, Changchun, China
- University of Chinese Academy of Sciences, Beijing, China
| | - Bei Li
- Key Laboratory of Optical System Advanced Manufacturing Technology, Changchun Institute of Optics, Fine Mechanics and Physics, Chinese Academy of Sciences, Changchun, China
- University of Chinese Academy of Sciences, Beijing, China
| |
Collapse
|
21
|
Peng QY, An Y, Jiang ZZ, Xu Y. The Role of Immune Cells in DKD: Mechanisms and Targeted Therapies. J Inflamm Res 2024; 17:2103-2118. [PMID: 38601771 PMCID: PMC11005934 DOI: 10.2147/jir.s457526] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/02/2024] [Accepted: 03/19/2024] [Indexed: 04/12/2024] Open
Abstract
Diabetic kidney disease (DKD), is a common microvascular complication and a major cause of death in patients with diabetes. Disorders of immune cells and immune cytokines can accelerate DKD development of in a number of ways. As the kidney is composed of complex and highly differentiated cells, the interactions among different cell types and immune cells play important regulatory roles in disease development. Here, we summarize the latest research into the molecular mechanisms underlying the interactions among various immune and renal cells in DKD. In addition, we discuss the most recent studies related to single cell technology and bioinformatics analysis in the field of DKD. The aims of our review were to explore immune cells as potential therapeutic targets in DKD and provide some guidance for future clinical treatments.
Collapse
Affiliation(s)
- Qiu-Yue Peng
- Department of Endocrinology and Metabolism, the Affiliated Hospital of Southwest Medical University, Luzhou, Sichuan, People’s Republic of China
- Metabolic Vascular Disease Key Laboratory of Sichuan Province, Sichuan, People’s Republic of China
- Sichuan Clinical Research Center for Nephropathy, Luzhou, Sichuan, People’s Republic of China
| | - Ying An
- Department of Endocrinology and Metabolism, the Affiliated Hospital of Southwest Medical University, Luzhou, Sichuan, People’s Republic of China
- Metabolic Vascular Disease Key Laboratory of Sichuan Province, Sichuan, People’s Republic of China
- Sichuan Clinical Research Center for Nephropathy, Luzhou, Sichuan, People’s Republic of China
| | - Zong-Zhe Jiang
- Department of Endocrinology and Metabolism, the Affiliated Hospital of Southwest Medical University, Luzhou, Sichuan, People’s Republic of China
- Metabolic Vascular Disease Key Laboratory of Sichuan Province, Sichuan, People’s Republic of China
- Sichuan Clinical Research Center for Nephropathy, Luzhou, Sichuan, People’s Republic of China
| | - Yong Xu
- Department of Endocrinology and Metabolism, the Affiliated Hospital of Southwest Medical University, Luzhou, Sichuan, People’s Republic of China
- Metabolic Vascular Disease Key Laboratory of Sichuan Province, Sichuan, People’s Republic of China
- Sichuan Clinical Research Center for Nephropathy, Luzhou, Sichuan, People’s Republic of China
| |
Collapse
|
22
|
Dong C, Ma H, Mi N, Fu W, Yi J, Gao L, Wang H, Ren Y, Lin Y, Han F, Chen Z, Zhou W. Integrated analysis of scRNA-seq and bulk RNA-seq reveals that GPRC5A is an important prognostic gene in pancreatic cancer and is associated with B-cell Infiltration in pancreatic cancer. Front Oncol 2024; 14:1283164. [PMID: 38634049 PMCID: PMC11021786 DOI: 10.3389/fonc.2024.1283164] [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: 08/25/2023] [Accepted: 02/23/2024] [Indexed: 04/19/2024] Open
Abstract
Introduction Pancreatic cancer (PC) is a malignancy with poor prognosis. This investigation aimed to determine the relevant genes that affect the prognosis of PC and investigate their relationship with immune infiltration. Methods : First, we acquired PC single-cell chip data from the GEO database to scrutinize dissimilarities in immune cell infiltration and differential genes between cancerous and adjacent tissues. Subsequently, we combined clinical data from TCGA to identify genes relevant to PC prognosis. Employing Cox and Lasso regression analyses, we constructed a multifactorial Cox prognostic model, which we subsequently confirmed. The prognostic gene expression in PC was authenticated using RT-PCR. Moreover, we employed the TIMER online database to examine the relationship between the expression of prognostic genes and T and B cell infiltration. Additionally, the expression of GPRC5A and its correlation with B cells infiltration and patient prognosis were ascertained in tissue chips using multiple immune fluorescence staining. Results The single-cell analysis unveiled dissimilarities in B-cell infiltration between cancerous and neighboring tissues. We developed a prognostic model utilizing three genes, indicating that patients with high-risk scores experienced a more unfavorable prognosis. Immune infiltration analysis revealed a significant correlation among YWHAZ, GPRC5A, and B cell immune infiltration. In tissue samples, GPRC5A exhibited substantial overexpression and a robust association with an adverse prognosis, demonstrating a positive correlation with B cell infiltration. Conclusion GPRC5A is an independent risk factor in PC and correlated with B cell immune infiltration in PC. These outcomes indicated that GPRC5A is a viable target for treating PC.
Collapse
Affiliation(s)
- Chunlu Dong
- The First School of Clinical Medicine of Lanzhou University, Lanzhou, Gansu, China
- The First Hospital of Lanzhou University, Lanzhou, Gansu, China
| | - Haidong Ma
- The First School of Clinical Medicine of Lanzhou University, Lanzhou, Gansu, China
| | - Ningning Mi
- The First School of Clinical Medicine of Lanzhou University, Lanzhou, Gansu, China
| | - Wenkang Fu
- The First School of Clinical Medicine of Lanzhou University, Lanzhou, Gansu, China
| | - Jianfeng Yi
- The First School of Clinical Medicine of Lanzhou University, Lanzhou, Gansu, China
- Department of Surgery, The First School of Clinical Medicine of Gansu University of Chinese Medicine, Lanzhou, Gansu, China
| | - Long Gao
- The First School of Clinical Medicine of Lanzhou University, Lanzhou, Gansu, China
| | - Haiping Wang
- The First School of Clinical Medicine of Lanzhou University, Lanzhou, Gansu, China
- The First Hospital of Lanzhou University, Lanzhou, Gansu, China
| | - Yanxian Ren
- The First School of Clinical Medicine of Lanzhou University, Lanzhou, Gansu, China
- The First Hospital of Lanzhou University, Lanzhou, Gansu, China
| | - Yanyan Lin
- The First School of Clinical Medicine of Lanzhou University, Lanzhou, Gansu, China
- The First Hospital of Lanzhou University, Lanzhou, Gansu, China
| | - Fangfang Han
- The First School of Clinical Medicine of Lanzhou University, Lanzhou, Gansu, China
- The First Hospital of Lanzhou University, Lanzhou, Gansu, China
| | - Zhou Chen
- The First School of Clinical Medicine of Lanzhou University, Lanzhou, Gansu, China
- The First Hospital of Lanzhou University, Lanzhou, Gansu, China
| | - Wence Zhou
- The First School of Clinical Medicine of Lanzhou University, Lanzhou, Gansu, China
- Lanzhou University Second Hospital, Lanzhou, Gansu, China
| |
Collapse
|
23
|
Yang B, Hu S, Jiang Y, Xu L, Shu S, Zhang H. Advancements in Single-Cell RNA Sequencing Research for Neurological Diseases. Mol Neurobiol 2024:10.1007/s12035-024-04126-3. [PMID: 38564138 DOI: 10.1007/s12035-024-04126-3] [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: 11/29/2023] [Accepted: 03/18/2024] [Indexed: 04/04/2024]
Abstract
Neurological diseases are a major cause of the global burden of disease. Although the mechanisms of the occurrence and development of neurological diseases are not fully clear, most of them are associated with cells mediating neuroinflammation. Yet medications and other therapeutic options to improve treatment are still very limited. Single-cell RNA sequencing (scRNA-seq), as a delightfully potent breakthrough technology, not only identifies various cell types and response states but also uncovers cell-specific gene expression changes, gene regulatory networks, intercellular communication, and cellular movement trajectories, among others, in different cell types. In this review, we describe the technology of scRNA-seq in detail and discuss and summarize the application of scRNA-seq in exploring neurological diseases, elaborating the corresponding specific mechanisms of the diseases as well as providing a reliable basis for new therapeutic approaches. Finally, we affirm that scRNA-seq promotes the development of the neuroscience field and enables us to have a deeper cellular understanding of neurological diseases in the future, which provides strong support for the treatment of neurological diseases and the improvement of patients' prognosis.
Collapse
Affiliation(s)
- Bingjie Yang
- Department of Neurology, The Fourth Clinical School of Medicine, Zhejiang Chinese Medical University, Hangzhou, Zhejiang, China
| | - Shuqi Hu
- Zhejiang University School of Medicine, Hangzhou, Zhejiang, China
- Department of Neurology, Affiliated Hangzhou First People's Hospital, Westlake University School of Medicine, Hangzhou, Zhejiang, China
| | - Yiru Jiang
- Department of Neurology, The Fourth Clinical School of Medicine, Zhejiang Chinese Medical University, Hangzhou, Zhejiang, China
| | - Lei Xu
- Department of Neurology, Zhejiang Rongjun Hospital, Jiaxing, Zhejiang, China
| | - Song Shu
- Department of Neurology, Affiliated Hangzhou First People's Hospital, Westlake University School of Medicine, Hangzhou, Zhejiang, China
| | - Hao Zhang
- Department of Neurology, The Fourth Clinical School of Medicine, Zhejiang Chinese Medical University, Hangzhou, Zhejiang, China.
- Department of Neurology, Affiliated Hangzhou First People's Hospital, Westlake University School of Medicine, Hangzhou, Zhejiang, China.
| |
Collapse
|
24
|
Li M. Harnessing atomic force microscopy-based single-cell analysis to advance physical oncology. Microsc Res Tech 2024; 87:631-659. [PMID: 38053519 DOI: 10.1002/jemt.24467] [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: 08/22/2023] [Revised: 11/21/2023] [Accepted: 11/23/2023] [Indexed: 12/07/2023]
Abstract
Single-cell analysis is an emerging and promising frontier in the field of life sciences, which is expected to facilitate the exploration of fundamental laws of physiological and pathological processes. Single-cell analysis allows experimental access to cell-to-cell heterogeneity to reveal the distinctive behaviors of individual cells, offering novel opportunities to dissect the complexity of severe human diseases such as cancers. Among the single-cell analysis tools, atomic force microscopy (AFM) is a powerful and versatile one which is able to nondestructively image the fine topographies and quantitatively measure multiple mechanical properties of single living cancer cells in their native states under aqueous conditions with unprecedented spatiotemporal resolution. Over the past few decades, AFM has been widely utilized to detect the structural and mechanical behaviors of individual cancer cells during the process of tumor formation, invasion, and metastasis, yielding numerous unique insights into tumor pathogenesis from the biomechanical perspective and contributing much to the field of cancer mechanobiology. Here, the achievements of AFM-based analysis of single cancer cells to advance physical oncology are comprehensively summarized, and challenges and future perspectives are also discussed. RESEARCH HIGHLIGHTS: Achievements of AFM in characterizing the structural and mechanical behaviors of single cancer cells are summarized, and future directions are discussed. AFM is not only capable of visualizing cellular fine structures, but can also measure multiple cellular mechanical properties as well as cell-generated mechanical forces. There is still plenty of room for harnessing AFM-based single-cell analysis to advance physical oncology.
Collapse
Affiliation(s)
- Mi Li
- State Key Laboratory of Robotics, Shenyang Institute of Automation, Chinese Academy of Sciences, Shenyang, China
- Institutes for Robotics and Intelligent Manufacturing, Chinese Academy of Sciences, Shenyang, China
- University of Chinese Academy of Sciences, Beijing, China
| |
Collapse
|
25
|
Ling T, Zhang C, Liu Y, Jiang C, Gu L. Single-cell analysis revealed a potential role of T-cell exhaustion in colorectal cancer with liver metastasis. J Cell Mol Med 2024; 28:e18341. [PMID: 38647235 PMCID: PMC11034372 DOI: 10.1111/jcmm.18341] [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: 01/24/2024] [Revised: 03/19/2024] [Accepted: 04/05/2024] [Indexed: 04/25/2024] Open
Abstract
Liver metastasis (LM) is an important factor leading to colorectal cancer (CRC) mortality. However, the effect of T-cell exhaustion on LM in CRC is unclear. Single-cell sequencing data derived from the Gene Expression Omnibus database. Data were normalized using the Seurat package and subsequently clustered and annotated into different cell clusters. The differentiation trajectories of epithelial cells and T cells were characterized based on pseudo-time analysis. Single-sample gene set enrichment analysis (ssGSEA) was used to calculate enrichment scores for different cell clusters and to identify enriched biological pathways. Finally, cell communication analysis was performed. Nine cell subpopulations were identified from CRC samples with LM. The proportion of T cells increased in LM. T cells can be subdivided into NK/T cells, regulatory T cells (Treg) and exhausted T cells (Tex). In LM, cell adhesion and proliferation activity of Tex were promoted. Epithelial cells can be categorized into six subpopulations. The transformation of primary CRC into LM involved two evolutionary branches of Tex cells. Epithelial cells two were at the beginning of the trajectory in CRC but at the end of the trajectory in CRC with LM. The receptor ligands CEACAM5 and ADGRE5-CD55 played critical roles in the interactions between Tex and Treg cell-epithelial cell, which may promote the epithelial-mesenchymal transition process in CRC. Tex cells are able to promote the process of LM in CRC, which in turn promotes tumour development. This provides a new perspective on the treatment and diagnosis of CRC.
Collapse
Affiliation(s)
- Tianlong Ling
- Department of Gastrointestinal Surgery, Renji HospitalShanghai Jiao Tong University School of MedicineShanghaiChina
| | - Cheng Zhang
- Department of Gastrointestinal Surgery, Renji HospitalShanghai Jiao Tong University School of MedicineShanghaiChina
| | - Ye Liu
- Department of Gastrointestinal Surgery, Renji HospitalShanghai Jiao Tong University School of MedicineShanghaiChina
| | - Chunhui Jiang
- Department of Gastrointestinal Surgery, Renji HospitalShanghai Jiao Tong University School of MedicineShanghaiChina
| | - Lei Gu
- Department of Gastrointestinal Surgery, Renji HospitalShanghai Jiao Tong University School of MedicineShanghaiChina
| |
Collapse
|
26
|
Yao Y, Liu Q, Ding S, Chen Y, Song T, Shang Y. Scutellaria baicalensis Georgi stems and leaves flavonoids promote neuroregeneration and ameliorate memory loss in rats through cAMP-PKA-CREB signaling pathway based on network pharmacology and bioinformatics analysis. Heliyon 2024; 10:e27161. [PMID: 38533079 PMCID: PMC10963208 DOI: 10.1016/j.heliyon.2024.e27161] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/22/2023] [Revised: 02/23/2024] [Accepted: 02/26/2024] [Indexed: 03/28/2024] Open
Abstract
The aim of this study was to investigate the possible molecular mechanism of Scutellaria baicalensis Georgi stems and leaves flavonoids (SSF) in Alzheimer's disease (AD). The active ingredients of SSF and their targets were identified via network pharmacology and bioinformatics analysis. To test the successful establishment of a rat model of AD by Aβ25-35 combined with RHTGF-β1 and AlCl3, the Morris water maze test was used. To intervene, three different doses of SSF were administered. The model group and the control group were included among the parallel groups. A shuttle box test, immunohistochemistry, an enzyme-linked immunosorbent assay, qPCR and Western blot were performed to verify the results. Based on the intersection of genes among AD disease targets, SSF component targets, and differentially expressed genes in the single cell dataset GSE138852 and bulk-seq dataset GSE5281, nine genes related to the action of SSF on AD were identified. SSF have an important anti-AD pathway in the cAMP signaling pathway. SSF can ameliorate the conditioned memory impairment, augment Brdu protein expression and cAMP content; and differentially regulate the mRNA and protein expressions of GPCR, Gαs, AC1, PKA, and VEGF. The cAMP-PKA-CREB pathway in the SSF may mediate the ability of the SSF to ameliorate the composite-induced memory loss and nerve regeneration in rats induced by composite Aβ.
Collapse
Affiliation(s)
- Yinhui Yao
- Institute of Traditional Chinese Medicine, Chengde Medical University / Hebei Province Key Research Office of Traditional Chinese Medicine Against Dementia / Hebei Province Key Laboratory of Traditional Chinese Medicine Research and Development / Hebei Key Laboratory of Nerve Injury and Repair, Chengde, China, Chengde, 067000, China
- Faculty of Integrated Traditional Chinese and Western Medicine, Hebei University of Chinese Medicine, Shijiazhuang, China
| | - Qianqian Liu
- Institute of Traditional Chinese Medicine, Chengde Medical University / Hebei Province Key Research Office of Traditional Chinese Medicine Against Dementia / Hebei Province Key Laboratory of Traditional Chinese Medicine Research and Development / Hebei Key Laboratory of Nerve Injury and Repair, Chengde, China, Chengde, 067000, China
| | - Shengkai Ding
- Institute of Traditional Chinese Medicine, Chengde Medical University / Hebei Province Key Research Office of Traditional Chinese Medicine Against Dementia / Hebei Province Key Laboratory of Traditional Chinese Medicine Research and Development / Hebei Key Laboratory of Nerve Injury and Repair, Chengde, China, Chengde, 067000, China
| | - Yan Chen
- Institute of Traditional Chinese Medicine, Chengde Medical University / Hebei Province Key Research Office of Traditional Chinese Medicine Against Dementia / Hebei Province Key Laboratory of Traditional Chinese Medicine Research and Development / Hebei Key Laboratory of Nerve Injury and Repair, Chengde, China, Chengde, 067000, China
| | - Tangtang Song
- Institute of Traditional Chinese Medicine, Chengde Medical University / Hebei Province Key Research Office of Traditional Chinese Medicine Against Dementia / Hebei Province Key Laboratory of Traditional Chinese Medicine Research and Development / Hebei Key Laboratory of Nerve Injury and Repair, Chengde, China, Chengde, 067000, China
| | - Yazhen Shang
- Institute of Traditional Chinese Medicine, Chengde Medical University / Hebei Province Key Research Office of Traditional Chinese Medicine Against Dementia / Hebei Province Key Laboratory of Traditional Chinese Medicine Research and Development / Hebei Key Laboratory of Nerve Injury and Repair, Chengde, China, Chengde, 067000, China
- Faculty of Integrated Traditional Chinese and Western Medicine, Hebei University of Chinese Medicine, Shijiazhuang, China
| |
Collapse
|
27
|
Yin W, Wan Y, Zhou Y. SpatialcoGCN: deconvolution and spatial information-aware simulation of spatial transcriptomics data via deep graph co-embedding. Brief Bioinform 2024; 25:bbae130. [PMID: 38557675 PMCID: PMC10982953 DOI: 10.1093/bib/bbae130] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/18/2023] [Revised: 02/22/2024] [Accepted: 03/08/2024] [Indexed: 04/04/2024] Open
Abstract
Spatial transcriptomics (ST) data have emerged as a pivotal approach to comprehending the function and interplay of cells within intricate tissues. Nonetheless, analyses of ST data are restricted by the low spatial resolution and limited number of ribonucleic acid transcripts that can be detected with several popular ST techniques. In this study, we propose that both of the above issues can be significantly improved by introducing a deep graph co-embedding framework. First, we establish a self-supervised, co-graph convolution network-based deep learning model termed SpatialcoGCN, which leverages single-cell data to deconvolve the cell mixtures in spatial data. Evaluations of SpatialcoGCN on a series of simulated ST data and real ST datasets from human ductal carcinoma in situ, developing human heart and mouse brain suggest that SpatialcoGCN could outperform other state-of-the-art cell type deconvolution methods in estimating per-spot cell composition. Moreover, with competitive accuracy, SpatialcoGCN could also recover the spatial distribution of transcripts that are not detected by raw ST data. With a similar co-embedding framework, we further established a spatial information-aware ST data simulation method, SpatialcoGCN-Sim. SpatialcoGCN-Sim could generate simulated ST data with high similarity to real datasets. Together, our approaches provide efficient tools for studying the spatial organization of heterogeneous cells within complex tissues.
Collapse
Affiliation(s)
- Wang Yin
- Department of Biomedical Informatics, School of Basic Medical Sciences, Peking University, 38 Xueyuan Road, Beijing 100191, China
- State Key Laboratory of Vascular Homeostasis and Remodeling, Peking University, 38 Xueyuan Road, Beijing 100191, China
- Department of Neurobiology, School of Basic Medical Sciences, Neuroscience Research Institute, Peking University, 38 Xueyuan Road, Beijing 100191, China
| | - You Wan
- Department of Neurobiology, School of Basic Medical Sciences, Neuroscience Research Institute, Peking University, 38 Xueyuan Road, Beijing 100191, China
| | - Yuan Zhou
- Department of Biomedical Informatics, School of Basic Medical Sciences, Peking University, 38 Xueyuan Road, Beijing 100191, China
- State Key Laboratory of Vascular Homeostasis and Remodeling, Peking University, 38 Xueyuan Road, Beijing 100191, China
| |
Collapse
|
28
|
Liu Y, Lyons CJ, Ayu C, O'Brien T. Recent advances in endothelial colony-forming cells: from the transcriptomic perspective. J Transl Med 2024; 22:313. [PMID: 38532420 DOI: 10.1186/s12967-024-05108-8] [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: 12/27/2023] [Accepted: 03/18/2024] [Indexed: 03/28/2024] Open
Abstract
Endothelial colony-forming cells (ECFCs) are progenitors of endothelial cells with significant proliferative and angiogenic ability. ECFCs are a promising treatment option for various diseases, such as ischemic heart disease and peripheral artery disease. However, some barriers hinder the clinical application of ECFC therapeutics. One of the current obstacles is that ECFCs are dysfunctional due to the underlying disease states. ECFCs exhibit dysfunctional phenotypes in pathologic states, which include but are not limited to the following: premature neonates and pregnancy-related diseases, diabetes mellitus, cancers, haematological system diseases, hypoxia, pulmonary arterial hypertension, coronary artery diseases, and other vascular diseases. Besides, ECFCs are heterogeneous among donors, tissue sources, and within cell subpopulations. Therefore, it is important to elucidate the underlying mechanisms of ECFC dysfunction and characterize their heterogeneity to enable clinical application. In this review, we summarize the current and potential application of transcriptomic analysis in the field of ECFC biology. Transcriptomic analysis is a powerful tool for exploring the key molecules and pathways involved in health and disease and can be used to characterize ECFC heterogeneity.
Collapse
Affiliation(s)
- Yaqiong Liu
- Regenerative Medicine Institute (REMEDI), Biomedical Sciences Building, University of Galway, Galway, Ireland
| | - Caomhán J Lyons
- Regenerative Medicine Institute (REMEDI), Biomedical Sciences Building, University of Galway, Galway, Ireland
| | - Christine Ayu
- Regenerative Medicine Institute (REMEDI), Biomedical Sciences Building, University of Galway, Galway, Ireland
| | - Timothy O'Brien
- Regenerative Medicine Institute (REMEDI), Biomedical Sciences Building, University of Galway, Galway, Ireland.
| |
Collapse
|
29
|
Qiao X, Sun J, Ren P, Guo H, Xu H, Bao C, Jiang C. Integrated single-cell sequencing, spatial transcriptome sequencing and bulk RNA sequencing highlights the molecular characteristics of parthanatos in gastric cancer. Aging (Albany NY) 2024; 16:5471-5500. [PMID: 38499384 PMCID: PMC11006479 DOI: 10.18632/aging.205658] [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: 10/26/2023] [Accepted: 02/08/2024] [Indexed: 03/20/2024]
Abstract
BACKGROUND Parthanatos is a novel programmatic form of cell death based on DNA damage and PARP-1 dependency. Nevertheless, its specific role in the context of gastric cancer (GC) remains uncertain. METHODS In this study, we integrated multi-omics algorithms to investigate the molecular characteristics of parthanatos in GC. A series of bioinformatics algorithms were utilized to explore clinical heterogeneity of GC and further predict the clinical outcomes. RESULTS Firstly, we conducted a comprehensive analysis of the omics features of parthanatos in various human tumors, including genomic mutations, transcriptome expression, and prognostic relevance. We successfully identified 7 cell types within the GC microenvironment: myeloid cell, epithelial cell, T cell, stromal cell, proliferative cell, B cell, and NK cell. When compared to adjacent non-tumor tissues, single-cell sequencing results from GC tissues revealed elevated scores for the parthanatos pathway across multiple cell types. Spatial transcriptomics, for the first time, unveiled the spatial distribution characteristics of parthanatos signaling. GC patients with different parthanatos signals often exhibited distinct immune microenvironment and metabolic reprogramming features, leading to different clinical outcomes. The integration of parthanatos signaling and clinical indicators enabled the creation of novel survival curves that accurately assess patients' survival times and statuses. CONCLUSIONS In this study, the molecular characteristics of parthanatos' unicellular and spatial transcriptomics in GC were revealed for the first time. Our model based on parthanatos signals can be used to distinguish individual heterogeneity and predict clinical outcomes in patients with GC.
Collapse
Affiliation(s)
- Xiuli Qiao
- Department of Gastroenterology, The Second Affiliated Hospital of Dalian Medical University, Dalian, China
| | - Jiaao Sun
- The First Affiliated Hospital of Dalian Medical University, Dalian, China
| | - Pingping Ren
- Department of Gastroenterology, The Second Affiliated Hospital of Dalian Medical University, Dalian, China
| | - Hui Guo
- The First Affiliated Hospital of Dalian Medical University, Dalian, China
| | - Hua Xu
- Department of Gastroenterology, The Second Affiliated Hospital of Dalian Medical University, Dalian, China
| | - Chongchan Bao
- Department of Breast and Thyroid Surgery, Affiliated Hospital of Youjiang Medical University for Nationalities, Baise, Guangxi, China
- Key Laboratory of Molecular Pathology in Tumors of Guangxi, Affiliated Hospital of Youjiang Medical University for Nationalities, Baise, Guangxi, China
| | - Chunmeng Jiang
- Department of Gastroenterology, The Second Affiliated Hospital of Dalian Medical University, Dalian, China
| |
Collapse
|
30
|
Lyu M, Xu G, Zhou J, Reboud J, Wang Y, Lai H, Chen Y, Zhou Y, Zhu G, Cooper JM, Ying B. Single-Cell Sequencing Reveals Functional Alterations in Tuberculosis. ADVANCED SCIENCE (WEINHEIM, BADEN-WURTTEMBERG, GERMANY) 2024; 11:e2305592. [PMID: 38192178 PMCID: PMC10953544 DOI: 10.1002/advs.202305592] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/10/2023] [Revised: 11/21/2023] [Indexed: 01/10/2024]
Abstract
Despite its importance, the functional heterogeneity surrounding the dynamics of interactions between mycobacterium tuberculosis and human immune cells in determining host immune strength and tuberculosis (TB) outcomes, remains far from understood. This work now describes the development of a new technological platform to elucidate the immune function differences in individuals with TB, integrating single-cell RNA sequencing and cell surface antibody sequencing to provide both genomic and phenotypic information from the same samples. Single-cell analysis of 23 990 peripheral blood mononuclear cells from a new cohort of primary TB patients and healthy controls enables to not only show four distinct immune phenotypes (TB, myeloid, and natural killer (NK) cells), but also determine the dynamic changes in cell population abundance, gene expression, developmental trajectory, transcriptomic regulation, and cell-cell signaling. In doing so, TB-related changes in immune cell functions demonstrate that the immune response is mediated through host T cells, myeloid cells, and NK cells, with TB patients showing decreased naive, cytotoxicity, and memory functions of T cells, rather than their immunoregulatory function. The platform also has the potential to identify new targets for immunotherapeutic treatment strategies to restore T cells from dysfunctional or exhausted states.
Collapse
Affiliation(s)
- Mengyuan Lyu
- Department of Laboratory MedicineWest China HospitalSichuan UniversityChengduSichuan610041P. R. China
| | - Gaolian Xu
- School of Biomedical Engineering/Med‐X Research InstituteShanghai Jiao Tong UniversityShanghai200030P. R. China
| | - Jian Zhou
- Department of Thoracic SurgeryWest China HospitalSichuan UniversityChengduSichuan610041P. R. China
| | - Julien Reboud
- Division of Biomedical EngineeringUniversity of GlasgowGlasgowG12 8LTUnited Kingdom
| | - Yili Wang
- Department of Laboratory MedicineWest China HospitalSichuan UniversityChengduSichuan610041P. R. China
| | - Hongli Lai
- Department of Laboratory MedicineWest China HospitalSichuan UniversityChengduSichuan610041P. R. China
| | - Yi Chen
- Department of Laboratory MedicineWest China HospitalSichuan UniversityChengduSichuan610041P. R. China
| | - Yanbing Zhou
- Department of Laboratory MedicineWest China HospitalSichuan UniversityChengduSichuan610041P. R. China
| | - Guiying Zhu
- School of Biomedical Engineering/Med‐X Research InstituteShanghai Jiao Tong UniversityShanghai200030P. R. China
| | - Jonathan M. Cooper
- Division of Biomedical EngineeringUniversity of GlasgowGlasgowG12 8LTUnited Kingdom
| | - Binwu Ying
- Department of Laboratory MedicineWest China HospitalSichuan UniversityChengduSichuan610041P. R. China
| |
Collapse
|
31
|
Zhang Y, Xu L, Guo C, Li X, Tian Y, Liao L, Dong J. High CD133 expression in proximal tubular cells in diabetic kidney disease: good or bad? J Transl Med 2024; 22:159. [PMID: 38365731 PMCID: PMC10870558 DOI: 10.1186/s12967-024-04950-0] [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: 07/10/2023] [Accepted: 02/03/2024] [Indexed: 02/18/2024] Open
Abstract
BACKGROUND Proximal tubular cells (PTCs) play a critical role in the progression of diabetic kidney disease (DKD). As one of important progenitor markers, CD133 was reported to indicate the regeneration of dedifferentiated PTCs in acute kidney disease. However, its role in chronic DKD is unclear. Therefore, we aimed to investigate the expression patterns and elucidate its functional significance of CD133 in DKD. METHODS Data mining was employed to illustrate the expression and molecular function of CD133 in PTCs in human DKD. Subsequently, rat models representing various stages of DKD progression were established. The expression of CD133 was confirmed in DKD rats, as well as in human PTCs (HK-2 cells) and rat PTCs (NRK-52E cells) exposed to high glucose. The immunofluorescence and flow cytometry techniques were utilized to determine the expression patterns of CD133, utilizing proliferative and injury indicators. After overexpression or knockdown of CD133 in HK-2 cells, the cell proliferation and apoptosis were detected by EdU assay, real-time cell analysis and flow analysis. Additionally, the evaluation of epithelial, progenitor cell, and apoptotic indices was performed through western blot and quantitative RT-PCR analyses. RESULTS The expression of CD133 was notably elevated in both human and rat PTCs in DKD, and this expression increased as DKD progressed. CD133 was found to be co-expressed with CD24, KIM-1, SOX9, and PCNA, suggesting that CD133+ cells were damaged and associated with proliferation. In terms of functionality, the knockdown of CD133 resulted in a significant reduction in proliferation and an increase in apoptosis in HK-2 cells compared to the high glucose stimulus group. Conversely, the overexpression of CD133 significantly mitigated high glucose-induced cell apoptosis, but had no impact on cellular proliferation. Furthermore, the Nephroseq database provided additional evidence to support the correlation between CD133 expression and the progression of DKD. Analysis of single-cell RNA-sequencing data revealed that CD133+ PTCs potentially play a role in the advancement of DKD through multiple mechanisms, including heat damage, cell microtubule stabilization, cell growth inhibition and tumor necrosis factor-mediated signaling pathway. CONCLUSION Our study demonstrates that the upregulation of CD133 is linked to cellular proliferation and protects PTC from apoptosis in DKD and high glucose induced PTC injury. We propose that heightened CD133 expression may facilitate cellular self-protective responses during the initial stages of high glucose exposure. However, its sustained increase is associated with the pathological progression of DKD. In conclusion, CD133 exhibits dual roles in the advancement of DKD, necessitating further investigation.
Collapse
Affiliation(s)
- Yuhan Zhang
- Department of Endocrinology and Metabology, The First Affiliated Hospital of Shandong First Medical University & Shandong Provincial Qianfoshan Hospital, Jinan, 250014, China
- Department of Endocrinology, Shandong Provincial Hospital Affiliated to Shandong First Medical University, Jinan, 250021, Shandong, China
- Shandong Key Laboratory of Endocrinology and Lipid Metabolism, Jinan, 250021, Shandong, China
| | - Lusi Xu
- Department of Endocrinology and Metabology, The First Affiliated Hospital of Shandong First Medical University & Shandong Provincial Qianfoshan Hospital, Jinan, 250014, China
| | - Congcong Guo
- Department of Endocrinology and Metabology, The First Affiliated Hospital of Shandong First Medical University & Shandong Provincial Qianfoshan Hospital, Jinan, 250014, China
| | - Xianzhi Li
- Department of Endocrinology and Metabology, The First Affiliated Hospital of Shandong First Medical University & Shandong Provincial Qianfoshan Hospital, Jinan, 250014, China
| | - Yutian Tian
- Department of Endocrinology and Metabology, The First Affiliated Hospital of Shandong First Medical University & Shandong Provincial Qianfoshan Hospital, Jinan, 250014, China
| | - Lin Liao
- Department of Endocrinology and Metabology, The First Affiliated Hospital of Shandong First Medical University & Shandong Provincial Qianfoshan Hospital, Jinan, 250014, China.
| | - Jianjun Dong
- Division of Endocrinology, Department of Internal Medicine, Qilu Hospital of Shandong University, Jinan, 250012, China.
| |
Collapse
|
32
|
He Z, Chen Q, Wang K, Lin J, Peng Y, Zhang J, Yan X, Jie Y. Single-cell transcriptomics analysis of cellular heterogeneity and immune mechanisms in neurodegenerative diseases. Eur J Neurosci 2024; 59:333-357. [PMID: 38221677 DOI: 10.1111/ejn.16242] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/17/2023] [Revised: 12/04/2023] [Accepted: 12/12/2023] [Indexed: 01/16/2024]
Abstract
Single-cell transcriptomics analysis is an advanced technology that can describe the intracellular transcriptome in complex tissues. It profiles and analyses datasets by single-cell RNA sequencing. Neurodegenerative diseases are identified by the abnormal apoptosis of neurons in the brain with few or no effective therapy strategies at present, which has been a growing healthcare concern and brought a great burden to society. The transcriptome of individual cells provides deep insights into previously unforeseen cellular heterogeneity and gene expression differences in neurodegenerative disorders. It detects multiple cell subsets and functional changes during pathological progression, which deepens the understanding of the molecular underpinnings and cellular basis of neurodegenerative diseases. Furthermore, the transcriptome analysis of immune cells shows the regulation of immune response. Different subtypes of immune cells and their interaction are found to contribute to disease progression. This finding enables the discovery of novel targets and biomarkers for early diagnosis. In this review, we emphasize the principles of the technology, and its recent progress in the study of cellular heterogeneity and immune mechanisms in neurodegenerative diseases. The application of single-cell transcriptomics analysis in neurodegenerative disorders would help explore the pathogenesis of these diseases and develop novel therapeutic methods.
Collapse
Affiliation(s)
- Ziping He
- Department of Forensic Science, School of Basic Medical Science, Central South University, Changsha, China
- Clinical Medicine Eight-Year Program, Xiangya School of Medicine, Central South University, Changsha, China
| | - Qianqian Chen
- Department of Forensic Science, School of Basic Medical Science, Central South University, Changsha, China
| | - Kaiyue Wang
- Department of Forensic Science, School of Basic Medical Science, Central South University, Changsha, China
- Clinical Medicine Eight-Year Program, Xiangya School of Medicine, Central South University, Changsha, China
| | - Jiang Lin
- Department of Forensic Science, School of Basic Medical Science, Central South University, Changsha, China
| | - Yilin Peng
- Department of Forensic Science, School of Basic Medical Science, Central South University, Changsha, China
| | - Jinlong Zhang
- Department of Forensic Science, School of Basic Medical Science, Central South University, Changsha, China
- Department of Forensic Science, School of Basic Medical Science, Xinjiang Medical University, Urumqi, China
| | - Xisheng Yan
- Department of Cardiovascular Medicine, Wuhan Third Hospital & Tongren Hospital of Wuhan University, Wuhan, China
| | - Yan Jie
- Department of Forensic Science, School of Basic Medical Science, Central South University, Changsha, China
- Department of Forensic Science, School of Basic Medical Science, Xinjiang Medical University, Urumqi, China
| |
Collapse
|
33
|
Yang S, Liu C, Jiang M, Liu X, Geng L, Zhang Y, Sun S, Wang K, Yin J, Ma S, Wang S, Belmonte JCI, Zhang W, Qu J, Liu GH. A single-nucleus transcriptomic atlas of primate liver aging uncovers the pro-senescence role of SREBP2 in hepatocytes. Protein Cell 2024; 15:98-120. [PMID: 37378670 PMCID: PMC10833472 DOI: 10.1093/procel/pwad039] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/02/2023] [Accepted: 05/19/2023] [Indexed: 06/29/2023] Open
Abstract
Aging increases the risk of liver diseases and systemic susceptibility to aging-related diseases. However, cell type-specific changes and the underlying mechanism of liver aging in higher vertebrates remain incompletely characterized. Here, we constructed the first single-nucleus transcriptomic landscape of primate liver aging, in which we resolved cell type-specific gene expression fluctuation in hepatocytes across three liver zonations and detected aberrant cell-cell interactions between hepatocytes and niche cells. Upon in-depth dissection of this rich dataset, we identified impaired lipid metabolism and upregulation of chronic inflammation-related genes prominently associated with declined liver functions during aging. In particular, hyperactivated sterol regulatory element-binding protein (SREBP) signaling was a hallmark of the aged liver, and consequently, forced activation of SREBP2 in human primary hepatocytes recapitulated in vivo aging phenotypes, manifesting as impaired detoxification and accelerated cellular senescence. This study expands our knowledge of primate liver aging and informs the development of diagnostics and therapeutic interventions for liver aging and associated diseases.
Collapse
Affiliation(s)
- Shanshan Yang
- Advanced Innovation Center for Human Brain Protection and National Clinical Research Center for Geriatric Disorders, Xuanwu Hospital Capital Medical University, Beijing 100053, China
- Aging Translational Medicine Center, International Center for Aging and Cancer, Beijing Municipal Geriatric Medical Research Center, Xuanwu Hospital, Capital Medical University, Beijing 100053, China
- Xuanwu Hospital Capital Medical University, Beijing 100053, China
| | - Chengyu Liu
- State Key Laboratory of Stem Cell and Reproductive Biology, Institute of Zoology, Chinese Academy of Sciences, Beijing 100101, China
- University of Chinese Academy of Sciences, Beijing 100049, China
| | - Mengmeng Jiang
- State Key Laboratory of Membrane Biology, Institute of Zoology, Chinese Academy of Sciences, Beijing 100101, China
- Institute for Stem Cell and Regeneration, Chinese Academy of Sciences, Beijing 100101, China
- Beijing Institute for Stem Cell and Regenerative Medicine, Beijing 100101, China
| | - Xiaoqian Liu
- State Key Laboratory of Stem Cell and Reproductive Biology, Institute of Zoology, Chinese Academy of Sciences, Beijing 100101, China
- Institute for Stem Cell and Regeneration, Chinese Academy of Sciences, Beijing 100101, China
- Beijing Institute for Stem Cell and Regenerative Medicine, Beijing 100101, China
| | - Lingling Geng
- Advanced Innovation Center for Human Brain Protection and National Clinical Research Center for Geriatric Disorders, Xuanwu Hospital Capital Medical University, Beijing 100053, China
- Aging Translational Medicine Center, International Center for Aging and Cancer, Beijing Municipal Geriatric Medical Research Center, Xuanwu Hospital, Capital Medical University, Beijing 100053, China
| | - Yiyuan Zhang
- State Key Laboratory of Membrane Biology, Institute of Zoology, Chinese Academy of Sciences, Beijing 100101, China
- Beijing Institute for Stem Cell and Regenerative Medicine, Beijing 100101, China
| | - Shuhui Sun
- State Key Laboratory of Membrane Biology, Institute of Zoology, Chinese Academy of Sciences, Beijing 100101, China
- Institute for Stem Cell and Regeneration, Chinese Academy of Sciences, Beijing 100101, China
- Beijing Institute for Stem Cell and Regenerative Medicine, Beijing 100101, China
| | - Kang Wang
- State Key Laboratory of Membrane Biology, Institute of Zoology, Chinese Academy of Sciences, Beijing 100101, China
- University of Chinese Academy of Sciences, Beijing 100049, China
| | - Jian Yin
- State Key Laboratory of Membrane Biology, Institute of Zoology, Chinese Academy of Sciences, Beijing 100101, China
- University of Chinese Academy of Sciences, Beijing 100049, China
| | - Shuai Ma
- State Key Laboratory of Membrane Biology, Institute of Zoology, Chinese Academy of Sciences, Beijing 100101, China
- Institute for Stem Cell and Regeneration, Chinese Academy of Sciences, Beijing 100101, China
- Beijing Institute for Stem Cell and Regenerative Medicine, Beijing 100101, China
| | - Si Wang
- Advanced Innovation Center for Human Brain Protection and National Clinical Research Center for Geriatric Disorders, Xuanwu Hospital Capital Medical University, Beijing 100053, China
- Aging Translational Medicine Center, International Center for Aging and Cancer, Beijing Municipal Geriatric Medical Research Center, Xuanwu Hospital, Capital Medical University, Beijing 100053, China
| | | | - Weiqi Zhang
- CAS Key Laboratory of Genomic and Precision Medicine, Beijing Institute of Genomics, Chinese Academy of Sciences and China National Center for Bioinformation, Beijing 100101, China
- University of Chinese Academy of Sciences, Beijing 100049, China
- Institute for Stem Cell and Regeneration, Chinese Academy of Sciences, Beijing 100101, China
- Aging Biomarker Consortium, Beijing 100101, China
| | - Jing Qu
- State Key Laboratory of Stem Cell and Reproductive Biology, Institute of Zoology, Chinese Academy of Sciences, Beijing 100101, China
- University of Chinese Academy of Sciences, Beijing 100049, China
- Institute for Stem Cell and Regeneration, Chinese Academy of Sciences, Beijing 100101, China
- Beijing Institute for Stem Cell and Regenerative Medicine, Beijing 100101, China
- Aging Biomarker Consortium, Beijing 100101, China
| | - Guang-Hui Liu
- Advanced Innovation Center for Human Brain Protection and National Clinical Research Center for Geriatric Disorders, Xuanwu Hospital Capital Medical University, Beijing 100053, China
- State Key Laboratory of Membrane Biology, Institute of Zoology, Chinese Academy of Sciences, Beijing 100101, China
- Aging Translational Medicine Center, International Center for Aging and Cancer, Beijing Municipal Geriatric Medical Research Center, Xuanwu Hospital, Capital Medical University, Beijing 100053, China
- Xuanwu Hospital Capital Medical University, Beijing 100053, China
- University of Chinese Academy of Sciences, Beijing 100049, China
- Institute for Stem Cell and Regeneration, Chinese Academy of Sciences, Beijing 100101, China
- Beijing Institute for Stem Cell and Regenerative Medicine, Beijing 100101, China
- Aging Biomarker Consortium, Beijing 100101, China
| |
Collapse
|
34
|
Su Z, You L, He Y, Chen J, Zhang G, Liu Z. Multi-omics reveals the role of ENO1 in bladder cancer and constructs an epithelial-related prognostic model to predict prognosis and efficacy. Sci Rep 2024; 14:2189. [PMID: 38273010 PMCID: PMC10811216 DOI: 10.1038/s41598-024-52573-8] [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: 09/18/2023] [Accepted: 01/20/2024] [Indexed: 01/27/2024] Open
Abstract
α-Enolase (ENO1) is a crucial molecular target for tumor therapy and has emerged as a research hotspot in recent decades. Here, we aimed to explore the role of ENO1 in bladder cancer (BLCA) and then construct a signature to predict the prognosis and treatment response of BLCA. Firstly, we found ENO1 was highly expressed in BLCA tissues, as verified by IHC, and was associated with poor prognosis. The analysis of the tumor immune microenvironment by bulk RNA-seq and scRNA-seq showed that ENO1 was associated with CD8+ T-cell exhaustion. Additionally, the results in vitro showed that ENO1 could promote the proliferation and invasion of BLCA cells. Then, the analysis of epithelial cells (ECs) revealed that ENO1 might promote BLCA progression by metabolism, the cell cycle and some carcinogenic pathways. A total of 249 hub genes were obtained from differentially expressed genes between ENO1-related ECs, and we used LASSO analysis to construct a novel signature that not only accurately predicted the prognosis of BLCA patients but also predicted the response to treatment for BLCA. Finally, we constructed a nomogram to better guide clinical application. In conclusion, through multi-omics analysis, we found that ENO1 was overexpressed in bladder cancer and associated with poor prognosis, CD8+ T-cell exhaustion and epithelial heterogeneity. Moreover, the prognosis and treatment of patients can be well predicted by constructing an epithelial-related prognostic signature.
Collapse
Affiliation(s)
- Zhixiong Su
- Department of Oncology, Shengli Clinical Medical College of Fujian Medical University, Fujian Provincial Hospital, No. 134, East Street, Fuzhou, 350001, Fujian, People's Republic of China
| | - Lijie You
- Department of Oncology, Shengli Clinical Medical College of Fujian Medical University, Fujian Provincial Hospital, No. 134, East Street, Fuzhou, 350001, Fujian, People's Republic of China
| | - Yufang He
- Department of Oncology, Shengli Clinical Medical College of Fujian Medical University, Fujian Provincial Hospital, No. 134, East Street, Fuzhou, 350001, Fujian, People's Republic of China
| | - Jingbo Chen
- Department of Oncology, Shengli Clinical Medical College of Fujian Medical University, Fujian Provincial Hospital, No. 134, East Street, Fuzhou, 350001, Fujian, People's Republic of China.
| | - Guifeng Zhang
- Department of Oncology, Shengli Clinical Medical College of Fujian Medical University, Fujian Provincial Hospital, No. 134, East Street, Fuzhou, 350001, Fujian, People's Republic of China.
| | - Zhenhua Liu
- Department of Oncology, Shengli Clinical Medical College of Fujian Medical University, Fujian Provincial Hospital, No. 134, East Street, Fuzhou, 350001, Fujian, People's Republic of China.
| |
Collapse
|
35
|
Lin H, Zhang M, Hu M, Zhang Y, Jiang W, Tang W, Ouyang Y, Jiang L, Mi Y, Chen Z, He P, Zhao G, Ouyang X. Emerging applications of single-cell profiling in precision medicine of atherosclerosis. J Transl Med 2024; 22:97. [PMID: 38263066 PMCID: PMC10804726 DOI: 10.1186/s12967-023-04629-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: 06/12/2023] [Accepted: 10/14/2023] [Indexed: 01/25/2024] Open
Abstract
Atherosclerosis is a chronic, progressive, inflammatory disease that occurs in the arterial wall. Despite recent advancements in treatment aimed at improving efficacy and prolonging survival, atherosclerosis remains largely incurable. In this review, we discuss emerging single-cell sequencing techniques and their novel insights into atherosclerosis. We provide examples of single-cell profiling studies that reveal phenotypic characteristics of atherosclerosis plaques, blood, liver, and the intestinal tract. Additionally, we highlight the potential clinical applications of single-cell analysis and propose that combining this approach with other techniques can facilitate early diagnosis and treatment, leading to more accurate medical interventions.
Collapse
Affiliation(s)
- Huiling Lin
- Department of Physiology, Medical College, Institute of Neuroscience Research, Hengyang Key Laboratory of Neurodegeneration and Cognitive Impairment, University of South China, Hengyang, 421001, Hunan, China
- Department of Physiology, School of Medicine, Hunan Normal University, Changsha, 410081, Hunan, China
| | - Ming Zhang
- Affiliated Qingyuan Hospital, Guangzhou Medical University (Qingyuan People's Hospital), Qingyuan, 511518, Guangdong, China
| | - Mi Hu
- Department of Physiology, Medical College, Institute of Neuroscience Research, Hengyang Key Laboratory of Neurodegeneration and Cognitive Impairment, University of South China, Hengyang, 421001, Hunan, China
| | - Yangkai Zhang
- Department of Physiology, Medical College, Institute of Neuroscience Research, Hengyang Key Laboratory of Neurodegeneration and Cognitive Impairment, University of South China, Hengyang, 421001, Hunan, China
| | - WeiWei Jiang
- Department of Organ Transplantation, Zhujiang Hospital, Southern Medical University, Guangzhou, Guangdong, China
| | - Wanying Tang
- Department of Physiology, Medical College, Institute of Neuroscience Research, Hengyang Key Laboratory of Neurodegeneration and Cognitive Impairment, University of South China, Hengyang, 421001, Hunan, China
| | - Yuxin Ouyang
- Department of Physiology, Medical College, Institute of Neuroscience Research, Hengyang Key Laboratory of Neurodegeneration and Cognitive Impairment, University of South China, Hengyang, 421001, Hunan, China
| | - Liping Jiang
- Department of Clinical Pharmacology, Xiangya Hospital, Central South University, Changsha, Hunan, China
| | - Yali Mi
- Affiliated Qingyuan Hospital, Guangzhou Medical University (Qingyuan People's Hospital), Qingyuan, 511518, Guangdong, China
| | - Zhi Chen
- College of Physics and Optoelectronic Engineering, Shenzhen University, Shenzhen, China
| | - Pingping He
- Department of Nursing, School of Medicine, Hunan Normal University, Changsha, 410081, Hunan, China.
| | - Guojun Zhao
- Affiliated Qingyuan Hospital, Guangzhou Medical University (Qingyuan People's Hospital), Qingyuan, 511518, Guangdong, China.
| | - Xinping Ouyang
- Department of Physiology, Medical College, Institute of Neuroscience Research, Hengyang Key Laboratory of Neurodegeneration and Cognitive Impairment, University of South China, Hengyang, 421001, Hunan, China.
- Department of Physiology, School of Medicine, Hunan Normal University, Changsha, 410081, Hunan, China.
- The Key Laboratory of Model Animals and Stem Cell Biology in Hunan Province, School of Medicine, Hunan Normal University, 410081, Hunan, Changsha, China.
- The Engineering Research Center of Reproduction and Translational Medicine of Hunan Province, School of Medicine, Hunan Normal University, 410081, Hunan, Changsha, China.
| |
Collapse
|
36
|
Tan D, Yang C, Wang J, Su Y, Zheng C. scAMAC: self-supervised clustering of scRNA-seq data based on adaptive multi-scale autoencoder. Brief Bioinform 2024; 25:bbae068. [PMID: 38426327 PMCID: PMC10905526 DOI: 10.1093/bib/bbae068] [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: 10/20/2023] [Revised: 01/15/2024] [Accepted: 01/26/2024] [Indexed: 03/02/2024] Open
Abstract
Cluster assignment is vital to analyzing single-cell RNA sequencing (scRNA-seq) data to understand high-level biological processes. Deep learning-based clustering methods have recently been widely used in scRNA-seq data analysis. However, existing deep models often overlook the interconnections and interactions among network layers, leading to the loss of structural information within the network layers. Herein, we develop a new self-supervised clustering method based on an adaptive multi-scale autoencoder, called scAMAC. The self-supervised clustering network utilizes the Multi-Scale Attention mechanism to fuse the feature information from the encoder, hidden and decoder layers of the multi-scale autoencoder, which enables the exploration of cellular correlations within the same scale and captures deep features across different scales. The self-supervised clustering network calculates the membership matrix using the fused latent features and optimizes the clustering network based on the membership matrix. scAMAC employs an adaptive feedback mechanism to supervise the parameter updates of the multi-scale autoencoder, obtaining a more effective representation of cell features. scAMAC not only enables cell clustering but also performs data reconstruction through the decoding layer. Through extensive experiments, we demonstrate that scAMAC is superior to several advanced clustering and imputation methods in both data clustering and reconstruction. In addition, scAMAC is beneficial for downstream analysis, such as cell trajectory inference. Our scAMAC model codes are freely available at https://github.com/yancy2024/scAMAC.
Collapse
Affiliation(s)
- Dayu Tan
- Key Laboratory of Intelligent Computing and Signal Processing of Ministry of Education, School of Artificial Intelligence, Anhui University, 230601 Hefei, China
| | - Cheng Yang
- Key Laboratory of Intelligent Computing and Signal Processing of Ministry of Education, School of Artificial Intelligence, Anhui University, 230601 Hefei, China
| | - Jing Wang
- Key Laboratory of Intelligent Computing and Signal Processing of Ministry of Education, School of Artificial Intelligence, Anhui University, 230601 Hefei, China
| | - Yansen Su
- Key Laboratory of Intelligent Computing and Signal Processing of Ministry of Education, School of Artificial Intelligence, Anhui University, 230601 Hefei, China
| | - Chunhou Zheng
- Key Laboratory of Intelligent Computing and Signal Processing of Ministry of Education, School of Artificial Intelligence, Anhui University, 230601 Hefei, China
| |
Collapse
|
37
|
Ravaee H, Manshaei MH, Safayani M, Sartakhti JS. Intelligent phenotype-detection and gene expression profile generation with generative adversarial networks. J Theor Biol 2024; 577:111636. [PMID: 37944593 DOI: 10.1016/j.jtbi.2023.111636] [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: 04/16/2023] [Revised: 08/11/2023] [Accepted: 10/05/2023] [Indexed: 11/12/2023]
Abstract
Gene expression analysis is valuable for cancer type classification and identifying diverse cancer phenotypes. The latest high-throughput RNA sequencing devices have enabled access to large volumes of gene expression data. However, we face several challenges, such as data security and privacy, when we develop machine learning-based classifiers for categorizing cancer types with these datasets. To address these issues, we propose IP3G (Intelligent Phenotype-detection and Gene expression profile Generation with Generative adversarial network), a model based on Generative Adversarial Networks. IP3G tackles two major problems: augmenting gene expression data and unsupervised phenotype discovery. By converting gene expression profiles into 2-Dimensional images and leveraging IP3G, we generate new profiles for specific phenotypes. IP3G learns disentangled representations of gene expression patterns and identifies phenotypes without labeled data. We improve the objective function of the GAN used in IP3G by employing the earth mover distance and a novel mutual information function. IP3G outperforms clustering methods like k-Means, DBSCAN, and GMM in unsupervised phenotype discovery, while also surpassing SVM and CNN classification accuracy by up to 6% through gene expression profile augmentation. The source code for the developed IP3G is accessible to the public on GitHub.
Collapse
Affiliation(s)
- Hamid Ravaee
- Department of Electrical and Computer Engineering, Isfahan University of Technology, Isfahan, 84156-83111, Iran
| | - Mohammad Hossein Manshaei
- Department of Electrical and Computer Engineering, Isfahan University of Technology, Isfahan, 84156-83111, Iran.
| | - Mehran Safayani
- Department of Electrical and Computer Engineering, Isfahan University of Technology, Isfahan, 84156-83111, Iran
| | | |
Collapse
|
38
|
Xiao W, Jiang N, Ji Z, Ni M, Zhang Z, Zhao Q, Huang R, Li P, Hou L. Single-Cell RNA Sequencing Reveals the Cellular Landscape of Longissimus Dorsi in a Newborn Suhuai Pig. Int J Mol Sci 2024; 25:1204. [PMID: 38256277 PMCID: PMC10816681 DOI: 10.3390/ijms25021204] [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: 11/19/2023] [Revised: 01/13/2024] [Accepted: 01/15/2024] [Indexed: 01/24/2024] Open
Abstract
The introduction of single-cell RNA sequencing (scRNA-seq) technology has spurred additional advancements in analyzing the cellular composition of tissues. The longissimus dorsi (LD) in pigs serves as the primary skeletal muscle for studying meat quality in the pig industry. However, the single-cell profile of porcine LD is still in its infancy stage. In this study, we profiled the transcriptomes of 16,018 cells in the LD of a newborn Suhuai pig at single-cell resolution. Subsequently, we constructed a cellular atlas of the LD, identifying 11 distinct cell populations, including endothelial cells (24.39%), myotubes (18.82%), fibro-adipogenic progenitors (FAPs, 18.11%), satellite cells (16.74%), myoblasts (3.99%), myocytes (5.74%), Schwann cells (3.81%), smooth muscle cells (3.22%), dendritic cells (2.99%), pericytes (1.86%), and neutrophils (0.33%). CellChat was employed to deduce the cell-cell interactions by evaluating the gene expression of receptor-ligand pairs across different cell types. The results show that FAPs and pericytes are the primary signal contributors in LD. In addition, we delineated the developmental trajectory of myogenic cells and examined alterations in the expression of various marker genes and molecular events throughout various stages of differentiation. Moreover, we found that FAPs can be divided into three subclusters (NR2F2-FAPs, LPL-FAPs, and TNMD-FAPs) according to their biological functions, suggesting that the FAPs could be associated with the differentiation of tendon cell. Taken together, we constructed the cellular atlas and cell communication network in LD of a newborn Suhuai pig, and analyzed the developmental trajectory of myogenic cells and the heterogeneity of FAPs subpopulation cells. This enhances our comprehension of the molecular features involved in skeletal muscle development and the meat quality control in pigs.
Collapse
Affiliation(s)
- Wei Xiao
- College of Animal Science and Technology, Nanjing Agricultural University, Nanjing 210095, China; (W.X.); (N.J.); (Z.J.); (M.N.); (Z.Z.); (Q.Z.); (R.H.); (P.L.)
- Institute of Swine Science, Nanjing Agricultural University, Nanjing 210095, China
- Key Laboratory of Pig Genetic Resources Evaluation and Utilization (Nanjing) of Ministry of Agriculture and Rural Affairs, Nanjing Agricultural University, Nanjing 210095, China
| | - Nengjing Jiang
- College of Animal Science and Technology, Nanjing Agricultural University, Nanjing 210095, China; (W.X.); (N.J.); (Z.J.); (M.N.); (Z.Z.); (Q.Z.); (R.H.); (P.L.)
- Institute of Swine Science, Nanjing Agricultural University, Nanjing 210095, China
- Key Laboratory of Pig Genetic Resources Evaluation and Utilization (Nanjing) of Ministry of Agriculture and Rural Affairs, Nanjing Agricultural University, Nanjing 210095, China
| | - Zhengyu Ji
- College of Animal Science and Technology, Nanjing Agricultural University, Nanjing 210095, China; (W.X.); (N.J.); (Z.J.); (M.N.); (Z.Z.); (Q.Z.); (R.H.); (P.L.)
- Institute of Swine Science, Nanjing Agricultural University, Nanjing 210095, China
- Key Laboratory of Pig Genetic Resources Evaluation and Utilization (Nanjing) of Ministry of Agriculture and Rural Affairs, Nanjing Agricultural University, Nanjing 210095, China
| | - Mengru Ni
- College of Animal Science and Technology, Nanjing Agricultural University, Nanjing 210095, China; (W.X.); (N.J.); (Z.J.); (M.N.); (Z.Z.); (Q.Z.); (R.H.); (P.L.)
- Institute of Swine Science, Nanjing Agricultural University, Nanjing 210095, China
- Key Laboratory of Pig Genetic Resources Evaluation and Utilization (Nanjing) of Ministry of Agriculture and Rural Affairs, Nanjing Agricultural University, Nanjing 210095, China
| | - Zhaobo Zhang
- College of Animal Science and Technology, Nanjing Agricultural University, Nanjing 210095, China; (W.X.); (N.J.); (Z.J.); (M.N.); (Z.Z.); (Q.Z.); (R.H.); (P.L.)
- Institute of Swine Science, Nanjing Agricultural University, Nanjing 210095, China
| | - Qingbo Zhao
- College of Animal Science and Technology, Nanjing Agricultural University, Nanjing 210095, China; (W.X.); (N.J.); (Z.J.); (M.N.); (Z.Z.); (Q.Z.); (R.H.); (P.L.)
- Institute of Swine Science, Nanjing Agricultural University, Nanjing 210095, China
- Key Laboratory of Pig Genetic Resources Evaluation and Utilization (Nanjing) of Ministry of Agriculture and Rural Affairs, Nanjing Agricultural University, Nanjing 210095, China
- Huai’an Academy, Nanjing Agricultural University, Huai’an 223001, China
| | - Ruihua Huang
- College of Animal Science and Technology, Nanjing Agricultural University, Nanjing 210095, China; (W.X.); (N.J.); (Z.J.); (M.N.); (Z.Z.); (Q.Z.); (R.H.); (P.L.)
- Institute of Swine Science, Nanjing Agricultural University, Nanjing 210095, China
- Key Laboratory of Pig Genetic Resources Evaluation and Utilization (Nanjing) of Ministry of Agriculture and Rural Affairs, Nanjing Agricultural University, Nanjing 210095, China
- Huai’an Academy, Nanjing Agricultural University, Huai’an 223001, China
| | - Pinghua Li
- College of Animal Science and Technology, Nanjing Agricultural University, Nanjing 210095, China; (W.X.); (N.J.); (Z.J.); (M.N.); (Z.Z.); (Q.Z.); (R.H.); (P.L.)
- Institute of Swine Science, Nanjing Agricultural University, Nanjing 210095, China
- Key Laboratory of Pig Genetic Resources Evaluation and Utilization (Nanjing) of Ministry of Agriculture and Rural Affairs, Nanjing Agricultural University, Nanjing 210095, China
- Huai’an Academy, Nanjing Agricultural University, Huai’an 223001, China
| | - Liming Hou
- College of Animal Science and Technology, Nanjing Agricultural University, Nanjing 210095, China; (W.X.); (N.J.); (Z.J.); (M.N.); (Z.Z.); (Q.Z.); (R.H.); (P.L.)
- Institute of Swine Science, Nanjing Agricultural University, Nanjing 210095, China
- Key Laboratory of Pig Genetic Resources Evaluation and Utilization (Nanjing) of Ministry of Agriculture and Rural Affairs, Nanjing Agricultural University, Nanjing 210095, China
- Huai’an Academy, Nanjing Agricultural University, Huai’an 223001, China
| |
Collapse
|
39
|
Dong S, Liu Y, Gong Y, Dong X, Zeng X. scCAN: Clustering With Adaptive Neighbor-Based Imputation Method for Single-Cell RNA-Seq Data. IEEE/ACM TRANSACTIONS ON COMPUTATIONAL BIOLOGY AND BIOINFORMATICS 2024; 21:95-105. [PMID: 38285569 DOI: 10.1109/tcbb.2023.3337231] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/31/2024]
Abstract
Single-cell RNA sequencing (scRNA-seq) is widely used to study cellular heterogeneity in different samples. However, due to technical deficiencies, dropout events often result in zero gene expression values in the gene expression matrix. In this paper, we propose a new imputation method called scCAN, based on adaptive neighborhood clustering, to estimate the zero value of dropouts. Our method continuously updates cell-cell similarity information by simultaneously learning similarity relationships, clustering structures, and imposing new rank constraints on the Laplacian matrix of the similarity matrix, improving the imputation of dropout zero values. To evaluate the performance of this method, we used four simulated and eight real scRNA-seq data for downstream analyses, including cell clustering, recovered gene expression, and reconstructed cell trajectories. Our method improves the performance of the downstream analysis and is better than other imputation methods.
Collapse
|
40
|
Peng Q, Wang L, Zuo L, Gao S, Jiang X, Han Y, Lin J, Peng M, Wu N, Tang Y, Tian H, Zhou Y, Liao Q. HPV E6/E7: insights into their regulatory role and mechanism in signaling pathways in HPV-associated tumor. Cancer Gene Ther 2024; 31:9-17. [PMID: 38102462 DOI: 10.1038/s41417-023-00682-3] [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: 05/29/2023] [Revised: 10/09/2023] [Accepted: 10/24/2023] [Indexed: 12/17/2023]
Abstract
Human papillomavirus (HPV) is a class of envelope-free double-stranded DNA virus. HPV infection has been strongly associated with the development of many malignancies, such as cervical, anal and oral cancers. The viral oncoproteins E6 and E7 perform central roles on HPV-induced carcinogenic processes. During tumor development, it usually goes along with the activation of abnormal signaling pathways. E6 and E7 induces changes in cell cycle, proliferation, invasion, metastasis and other biological behaviors by affecting downstream tumor-related signaling pathways, thus promoting malignant transformation of cells and ultimately leading to tumorigenesis and progression. Here, we summarized that E6 and E7 proteins promote HPV-associated tumorigenesis and development by regulating the activation of various tumor-related signaling pathways, for example, the Wnt/β-catenin, PI3K/Akt, and NF-kB signaling pathway. We also discussed the importance of HPV-encoded E6 and E7 and their regulated tumor-related signaling pathways for the diagnosis and effective treatment of HPV-associated tumors.
Collapse
Affiliation(s)
- Qiu Peng
- Hunan Key Laboratory of Cancer Metabolism, Hunan Cancer Hospital and the Affiliated Cancer Hospital of Xiangya School of Medicine, Central South University, Changsha, 410013, Hunan, China.
| | - Lujuan Wang
- Hunan Key Laboratory of Tumor Models and Individualized Medicine, The Second Xiangya Hospital of Central South University, Changsha, 410011, Hunan, China
| | - Liang Zuo
- Hunan Key Laboratory of Cancer Metabolism, Hunan Cancer Hospital and the Affiliated Cancer Hospital of Xiangya School of Medicine, Central South University, Changsha, 410013, Hunan, China
| | - Shuichao Gao
- Hunan Key Laboratory of Cancer Metabolism, Hunan Cancer Hospital and the Affiliated Cancer Hospital of Xiangya School of Medicine, Central South University, Changsha, 410013, Hunan, China
| | - Xianjie Jiang
- Hunan Key Laboratory of Cancer Metabolism, Hunan Cancer Hospital and the Affiliated Cancer Hospital of Xiangya School of Medicine, Central South University, Changsha, 410013, Hunan, China
| | - Yaqian Han
- Hunan Key Laboratory of Cancer Metabolism, Hunan Cancer Hospital and the Affiliated Cancer Hospital of Xiangya School of Medicine, Central South University, Changsha, 410013, Hunan, China
| | - Jinguan Lin
- Hunan Key Laboratory of Cancer Metabolism, Hunan Cancer Hospital and the Affiliated Cancer Hospital of Xiangya School of Medicine, Central South University, Changsha, 410013, Hunan, China
| | - Mingjing Peng
- Hunan Key Laboratory of Cancer Metabolism, Hunan Cancer Hospital and the Affiliated Cancer Hospital of Xiangya School of Medicine, Central South University, Changsha, 410013, Hunan, China
| | - Nayiyuan Wu
- Hunan Key Laboratory of Cancer Metabolism, Hunan Cancer Hospital and the Affiliated Cancer Hospital of Xiangya School of Medicine, Central South University, Changsha, 410013, Hunan, China
| | - Yanyan Tang
- Hunan Key Laboratory of Cancer Metabolism, Hunan Cancer Hospital and the Affiliated Cancer Hospital of Xiangya School of Medicine, Central South University, Changsha, 410013, Hunan, China
| | - Hao Tian
- Hunan Key Laboratory of Cancer Metabolism, Hunan Cancer Hospital and the Affiliated Cancer Hospital of Xiangya School of Medicine, Central South University, Changsha, 410013, Hunan, China.
| | - Yujuan Zhou
- Hunan Key Laboratory of Cancer Metabolism, Hunan Cancer Hospital and the Affiliated Cancer Hospital of Xiangya School of Medicine, Central South University, Changsha, 410013, Hunan, China.
- University of South China, Hengyang, 421001, Hunan, China.
- Public Service Platform of Tumor organoids Technology, 283 Tongzipo Road, Changsha, 410013, Hunan, China.
| | - Qianjin Liao
- Hunan Key Laboratory of Cancer Metabolism, Hunan Cancer Hospital and the Affiliated Cancer Hospital of Xiangya School of Medicine, Central South University, Changsha, 410013, Hunan, China.
- University of South China, Hengyang, 421001, Hunan, China.
- Public Service Platform of Tumor organoids Technology, 283 Tongzipo Road, Changsha, 410013, Hunan, China.
| |
Collapse
|
41
|
Kang MJ, Ioannou S, Lougheide Q, Dittmar M, Hsu Y, Pastor-Soler NM. The study of intercalated cells using ex vivo techniques: primary cell culture, cell lines, kidney slices, and organoids. Am J Physiol Cell Physiol 2024; 326:C229-C251. [PMID: 37899748 DOI: 10.1152/ajpcell.00479.2022] [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: 10/27/2022] [Revised: 10/23/2023] [Accepted: 10/24/2023] [Indexed: 10/31/2023]
Abstract
This review summarizes methods to study kidney intercalated cell (IC) function ex vivo. While important for acid-base homeostasis, IC dysfunction is often not recognized clinically until it becomes severe. The advantage of using ex vivo techniques is that they allow for the differential evaluation of IC function in controlled environments. Although in vitro kidney tubular perfusion is a classical ex vivo technique to study IC, here we concentrate on primary cell cultures, immortalized cell lines, and ex vivo kidney slices. Ex vivo techniques are useful in evaluating IC signaling pathways that allow rapid responses to extracellular changes in pH, CO2, and bicarbonate (HCO3-). However, these methods for IC work can also be challenging, as cell lines that recapitulate IC do not proliferate easily in culture. Moreover, a "pure" IC population in culture does not necessarily replicate its collecting duct (CD) environment, where ICs are surrounded by the more abundant principal cells (PCs). It is reassuring that many findings obtained in ex vivo IC systems signaling have been largely confirmed in vivo. Some of these newly identified signaling pathways reveal that ICs are important for regulating NaCl reabsorption, thus suggesting new frontiers to target antihypertensive treatments. Moreover, recent single-cell characterization studies of kidney epithelial cells revealed a dual developmental origin of IC, as well as the presence of novel CD cell types with certain IC characteristics. These exciting findings present new opportunities for the study of IC ex vivo and will likely rediscover the importance of available tools in this field.NEW & NOTEWORTHY The study of kidney intercalated cells has been limited by current cell culture and kidney tissue isolation techniques. This review is to be used as a reference to select ex vivo techniques to study intercalated cells. We focused on the use of cell lines and kidney slices as potential useful models to study membrane transport proteins. We also review how novel collecting duct organoids may help better elucidate the role of these intriguing cells.
Collapse
Affiliation(s)
- Min Ju Kang
- Division of Nephrology and Hypertension, Department of Medicine, Keck School of Medicine of USC, Los Angeles, California, United States
| | - Silvia Ioannou
- Division of Nephrology and Hypertension, Department of Medicine, Keck School of Medicine of USC, Los Angeles, California, United States
| | - Quinn Lougheide
- Division of Nephrology and Hypertension, Department of Medicine, Keck School of Medicine of USC, Los Angeles, California, United States
| | - Michael Dittmar
- Division of Nephrology and Hypertension, Department of Medicine, Keck School of Medicine of USC, Los Angeles, California, United States
| | - Young Hsu
- Division of Nephrology and Hypertension, Department of Medicine, Keck School of Medicine of USC, Los Angeles, California, United States
| | - Nuria M Pastor-Soler
- Division of Nephrology and Hypertension, Department of Medicine, Keck School of Medicine of USC, Los Angeles, California, United States
| |
Collapse
|
42
|
Liang Q, Huang Y, He S, Chen K. Pathway centric analysis for single-cell RNA-seq and spatial transcriptomics data with GSDensity. Nat Commun 2023; 14:8416. [PMID: 38110427 PMCID: PMC10728201 DOI: 10.1038/s41467-023-44206-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: 06/26/2023] [Accepted: 12/04/2023] [Indexed: 12/20/2023] Open
Abstract
Advances in single-cell technology have enabled molecular dissection of heterogeneous biospecimens at unprecedented scales and resolutions. Cluster-centric approaches are widely applied in analyzing single-cell data, however they have limited power in dissecting and interpreting highly heterogenous, dynamically evolving data. Here, we present GSDensity, a graph-modeling approach that allows users to obtain pathway-centric interpretation and dissection of single-cell and spatial transcriptomics (ST) data without performing clustering. Using pathway gene sets, we show that GSDensity can accurately detect biologically distinct cells and reveal novel cell-pathway associations ignored by existing methods. Moreover, GSDensity, combined with trajectory analysis can identify curated pathways that are active at various stages of mouse brain development. Finally, GSDensity can identify spatially relevant pathways in mouse brains and human tumors including those following high-order organizational patterns in the ST data. Particularly, we create a pan-cancer ST map revealing spatially relevant and recurrently active pathways across six different tumor types.
Collapse
Affiliation(s)
- Qingnan Liang
- Department of Bioinformatics and Computational Biology, UT MD Anderson Cancer Center, Houston, TX, USA
| | - Yuefan Huang
- Department of Bioinformatics and Computational Biology, UT MD Anderson Cancer Center, Houston, TX, USA
| | - Shan He
- Department of Bioinformatics and Computational Biology, UT MD Anderson Cancer Center, Houston, TX, USA
| | - Ken Chen
- Department of Bioinformatics and Computational Biology, UT MD Anderson Cancer Center, Houston, TX, USA.
| |
Collapse
|
43
|
Guo ZH, Wu Y, Wang S, Zhang Q, Shi JM, Wang YB, Chen ZH. scInterpreter: a knowledge-regularized generative model for interpretably integrating scRNA-seq data. BMC Bioinformatics 2023; 24:481. [PMID: 38104057 PMCID: PMC10724984 DOI: 10.1186/s12859-023-05579-4] [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: 09/29/2023] [Accepted: 11/23/2023] [Indexed: 12/19/2023] Open
Abstract
BACKGROUND The rapid emergence of single-cell RNA-seq (scRNA-seq) data presents remarkable opportunities for broad investigations through integration analyses. However, most integration models are black boxes that lack interpretability or are hard to train. RESULTS To address the above issues, we propose scInterpreter, a deep learning-based interpretable model. scInterpreter substantially outperforms other state-of-the-art (SOTA) models in multiple benchmark datasets. In addition, scInterpreter is extensible and can integrate and annotate atlas scRNA-seq data. We evaluated the robustness of scInterpreter in a variety of situations. Through comparison experiments, we found that with a knowledge prior, the training process can be significantly accelerated. Finally, we conducted interpretability analysis for each dimension (pathway) of cell representation in the embedding space. CONCLUSIONS The results showed that the cell representations obtained by scInterpreter are full of biological significance. Through weight sorting, we found several new genes related to pathways in PBMC dataset. In general, scInterpreter is an effective and interpretable integration tool. It is expected that scInterpreter will bring great convenience to the study of single-cell transcriptomics.
Collapse
Affiliation(s)
- Zhen-Hao Guo
- College of Electronics and Information Engineering, Tongji University, Shanghai, 200000, China
- Department of Clinical Anesthesiology, Faculty of Anesthesiology, Second Military Medical University / Naval Medical University, Shanghai, 200433, China
| | - Yan Wu
- College of Electronics and Information Engineering, Tongji University, Shanghai, 200000, China.
| | - Siguo Wang
- EIT Institute for Advanced Study, Ningbo, 315201, Zhejiang, China
| | - Qinhu Zhang
- EIT Institute for Advanced Study, Ningbo, 315201, Zhejiang, China
- Big Data and Intelligent Computing Research Center, Guangxi Academy of Science, Nanning, 530007, China
| | - Jin-Ming Shi
- Department of Endocrinology, Aviation General Hospital, Beijing, 100000, China
| | - Yan-Bin Wang
- College of Computer Science and Technology, Zhejiang University, Hangzhou, 310027, Zhejiang, China
| | - Zhan-Heng Chen
- Department of Clinical Anesthesiology, Faculty of Anesthesiology, Second Military Medical University / Naval Medical University, Shanghai, 200433, China.
- Big Data and Intelligent Computing Research Center, Guangxi Academy of Science, Nanning, 530007, China.
| |
Collapse
|
44
|
Du ZH, Hu WL, Li JQ, Shang X, You ZH, Chen ZZ, Huang YA. scPML: pathway-based multi-view learning for cell type annotation from single-cell RNA-seq data. Commun Biol 2023; 6:1268. [PMID: 38097699 PMCID: PMC10721875 DOI: 10.1038/s42003-023-05634-z] [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: 05/30/2023] [Accepted: 11/24/2023] [Indexed: 12/17/2023] Open
Abstract
Recent developments in single-cell technology have enabled the exploration of cellular heterogeneity at an unprecedented level, providing invaluable insights into various fields, including medicine and disease research. Cell type annotation is an essential step in its omics research. The mainstream approach is to utilize well-annotated single-cell data to supervised learning for cell type annotation of new singlecell data. However, existing methods lack good generalization and robustness in cell annotation tasks, partially due to difficulties in dealing with technical differences between datasets, as well as not considering the heterogeneous associations of genes in regulatory mechanism levels. Here, we propose the scPML model, which utilizes various gene signaling pathway data to partition the genetic features of cells, thus characterizing different interaction maps between cells. Extensive experiments demonstrate that scPML performs better in cell type annotation and detection of unknown cell types from different species, platforms, and tissues.
Collapse
Affiliation(s)
- Zhi-Hua Du
- College of Computer Science and Software Engineering, ShenZhen University, 3688 Nanhai Avenue, Shenzhen, China
| | - Wei-Lin Hu
- College of Computer Science and Software Engineering, ShenZhen University, 3688 Nanhai Avenue, Shenzhen, China
| | - Jian-Qiang Li
- College of Computer Science and Software Engineering, ShenZhen University, 3688 Nanhai Avenue, Shenzhen, China
| | - Xuequn Shang
- School of Computer Science, Northwestern Polytechnical University, Xi'an, China
| | - Zhu-Hong You
- School of Computer Science, Northwestern Polytechnical University, Xi'an, China
| | - Zhuang-Zhuang Chen
- College of Computer Science and Software Engineering, ShenZhen University, 3688 Nanhai Avenue, Shenzhen, China
| | - Yu-An Huang
- School of Computer Science, Northwestern Polytechnical University, Xi'an, China.
| |
Collapse
|
45
|
Ryabov V, Gombozhapova A, Litviakov N, Ibragimova M, Tsyganov M, Rogovskaya Y, Kzhyshkowska J. Microarray Analysis for Transcriptomic Profiling of Myocardium in Patients with Fatal Myocardial Infarction. Biomedicines 2023; 11:3294. [PMID: 38137515 PMCID: PMC10740899 DOI: 10.3390/biomedicines11123294] [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: 11/08/2023] [Revised: 12/08/2023] [Accepted: 12/10/2023] [Indexed: 12/24/2023] Open
Abstract
Transcriptomic evidence from human myocardium in myocardial infarction (MI) is still not sufficient. Thus, there is a need for studies on human cardiac samples in relation to the clinical data of patients. The purpose of our pilot study was to investigate the transcriptomic profile of myocardium in the infarct zone, in comparison to the remote myocardium, in patients with fatal MI, via microarray analysis. This study included four patients with fatal MI type 1. We selected histologically verified samples from within the infarct area (n = 4) and remote myocardium (n = 4). The whole transcriptome was evaluated using microarray analysis. Differentially expressed genes (DEGs) clustered in the infarct area and in the remote myocardium allowed their differentiation. We identified a total of 1785 DEGs (8.32%) in the infarct area, including 1692 up-regulated (94.79%) and 93 down-regulated (5.21%) genes. The top 10 up-regulated genes were TRAIL, SUCLA2, NAE1, PDCL3, OSBPL5, FCGR2C, SELE, CEP63, ST3GAL3 and C4orf3. In the infarct area, we found up-regulation of seventeen apoptosis-related genes, eleven necroptosis-related, and six necrosis-related genes. Transcriptome profiling of the myocardium in patients with MI remains a relevant area of research for the formation of new scientific hypotheses and a potential way to increase the translational significance of studies into myocardial infarction.
Collapse
Affiliation(s)
- Vyacheslav Ryabov
- Cardiology Research Institute, Tomsk National Research Medical Center, Russian Academy of Sciences, 634012 Tomsk, Russia;
| | - Aleksandra Gombozhapova
- Cardiology Research Institute, Tomsk National Research Medical Center, Russian Academy of Sciences, 634012 Tomsk, Russia;
| | - Nikolai Litviakov
- Cancer Research Institute, Tomsk National Research Medical Center, Russian Academy of Sciences, 634009 Tomsk, Russia; (N.L.); (M.I.); (M.T.)
| | - Marina Ibragimova
- Cancer Research Institute, Tomsk National Research Medical Center, Russian Academy of Sciences, 634009 Tomsk, Russia; (N.L.); (M.I.); (M.T.)
| | - Matvey Tsyganov
- Cancer Research Institute, Tomsk National Research Medical Center, Russian Academy of Sciences, 634009 Tomsk, Russia; (N.L.); (M.I.); (M.T.)
| | | | - Julia Kzhyshkowska
- Institute of Transfusion Medicine and Immunology, Medical Faculty Mannheim, Heidelberg University, 69117 Heidelberg, Germany;
- Laboratory of Translational and Cellular Biomedicine, National Research Tomsk State University, 634050 Tomsk, Russia
| |
Collapse
|
46
|
Liu Z, Zhang Y, Wu C. Single-cell sequencing in pancreatic cancer research: A deeper understanding of heterogeneity and therapy. Biomed Pharmacother 2023; 168:115664. [PMID: 37837881 DOI: 10.1016/j.biopha.2023.115664] [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: 07/05/2023] [Revised: 09/28/2023] [Accepted: 10/06/2023] [Indexed: 10/16/2023] Open
Abstract
Pancreatic cancer, including pancreatic ductal adenocarcinomas (PDACs), is a malignant tumor with characteristics of tumor-stroma interactions. Patients often have a poor prognosis and a poor long-term survival rate. In recent years, rapidly-developing single-cell sequencing techniques have been used to analyze cell populations at a single-cell resolution, so that it is now possible to have a more in-depth and clearer understanding of the genetic composition of pancreatic cancer. In this review, we provide an overview of the current single-cell sequencing techniques and their applications in the exploration of intratumoral heterogeneity, the tumor microenvironment, therapy resistance, and novel treatments. Our hope is to provide new insight into the potential of precision therapy, which will perhaps one day lead to significant advances in PDAC treatment.
Collapse
Affiliation(s)
- Zhuomiao Liu
- Department of Radiation Oncology, the Fourth Affiliated Hospital of China Medical University, Shenyang, China
| | - Yalin Zhang
- Department of Radiation Oncology, the Fourth Affiliated Hospital of China Medical University, Shenyang, China
| | - Chunli Wu
- Department of Radiation Oncology, the Fourth Affiliated Hospital of China Medical University, Shenyang, China.
| |
Collapse
|
47
|
Forston MD, Wei GZ, Chariker JH, Stephenson T, Andres K, Glover C, Rouchka EC, Whittemore SR, Hetman M. Enhanced oxidative phosphorylation, re-organized intracellular signaling, and epigenetic de-silencing as revealed by oligodendrocyte translatome analysis after contusive spinal cord injury. Sci Rep 2023; 13:21254. [PMID: 38040794 PMCID: PMC10692148 DOI: 10.1038/s41598-023-48425-6] [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: 07/12/2023] [Accepted: 11/27/2023] [Indexed: 12/03/2023] Open
Abstract
Reducing the loss of oligodendrocytes (OLs) is a major goal for neuroprotection after spinal cord injury (SCI). Therefore, the OL translatome was determined in Ribotag:Plp1-CreERT2 mice at 2, 10, and 42 days after moderate contusive T9 SCI. At 2 and 42 days, mitochondrial respiration- or actin cytoskeleton/cell junction/cell adhesion mRNAs were upregulated or downregulated, respectively. The latter effect suggests myelin sheath loss/morphological simplification which is consistent with downregulation of cholesterol biosynthesis transcripts on days 10 and 42. Various regulators of pro-survival-, cell death-, and/or oxidative stress response pathways showed peak expression acutely, on day 2. Many acutely upregulated OL genes are part of the repressive SUZ12/PRC2 operon suggesting that epigenetic de-silencing contributes to SCI effects on OL gene expression. Acute OL upregulation of the iron oxidoreductase Steap3 was confirmed at the protein level and replicated in cultured OLs treated with the mitochondrial uncoupler FCCP. Hence, STEAP3 upregulation may mark mitochondrial dysfunction. Taken together, in SCI-challenged OLs, acute and subchronic enhancement of mitochondrial respiration may be driven by axonal loss and subsequent myelin sheath degeneration. Acutely, the OL switch to oxidative phosphorylation may lead to oxidative stress that is further amplified by upregulation of such enzymes as STEAP3.
Collapse
Affiliation(s)
- Michael D Forston
- Kentucky Spinal Cord Injury Research Center, University of Louisville School of Medicine, Louisville, KY, 40202, USA
- Department of Anatomical Sciences & Neurobiology, University of Louisville School of Medicine, Louisville, KY, 40202, USA
| | - George Z Wei
- Kentucky Spinal Cord Injury Research Center, University of Louisville School of Medicine, Louisville, KY, 40202, USA
- Department of Pharmacology & Toxicology, University of Louisville School of Medicine, Louisville, KY, 40202, USA
- MD/PhD Program, University of Louisville School of Medicine, Louisville, KY, 40202, USA
| | - Julia H Chariker
- Kentucky IDeA Networks of Biomedical Research Excellence (KY INBRE) Bioinformatics Core, University of Louisville, Louisville, KY, 40202, USA
- Neuroscience Training, University Louisville School of Medicine, Louisville, KY, 40202, USA
| | - Tyler Stephenson
- Kentucky Spinal Cord Injury Research Center, University of Louisville School of Medicine, Louisville, KY, 40202, USA
- Department of Neurological Surgery, University of Louisville School of Medicine, Louisville, KY, 40202, USA
| | - Kariena Andres
- Kentucky Spinal Cord Injury Research Center, University of Louisville School of Medicine, Louisville, KY, 40202, USA
- Department of Neurological Surgery, University of Louisville School of Medicine, Louisville, KY, 40202, USA
| | - Charles Glover
- Kentucky Spinal Cord Injury Research Center, University of Louisville School of Medicine, Louisville, KY, 40202, USA
- Department of Neurological Surgery, University of Louisville School of Medicine, Louisville, KY, 40202, USA
| | - Eric C Rouchka
- Kentucky IDeA Networks of Biomedical Research Excellence (KY INBRE) Bioinformatics Core, University of Louisville, Louisville, KY, 40202, USA
- Department of Biochemistry and Molecular Genetics, University of Louisville School of Medicine, Louisville, KY, 40202, USA
| | - Scott R Whittemore
- Kentucky Spinal Cord Injury Research Center, University of Louisville School of Medicine, Louisville, KY, 40202, USA
- Department of Neurological Surgery, University of Louisville School of Medicine, Louisville, KY, 40202, USA
- Department of Anatomical Sciences & Neurobiology, University of Louisville School of Medicine, Louisville, KY, 40202, USA
- Department of Pharmacology & Toxicology, University of Louisville School of Medicine, Louisville, KY, 40202, USA
- MD/PhD Program, University of Louisville School of Medicine, Louisville, KY, 40202, USA
| | - Michal Hetman
- Kentucky Spinal Cord Injury Research Center, University of Louisville School of Medicine, Louisville, KY, 40202, USA.
- Department of Neurological Surgery, University of Louisville School of Medicine, Louisville, KY, 40202, USA.
- Department of Anatomical Sciences & Neurobiology, University of Louisville School of Medicine, Louisville, KY, 40202, USA.
- Department of Pharmacology & Toxicology, University of Louisville School of Medicine, Louisville, KY, 40202, USA.
- MD/PhD Program, University of Louisville School of Medicine, Louisville, KY, 40202, USA.
| |
Collapse
|
48
|
Liu Y, Li F, Shang J, Liu J, Wang J, Ge D. scFED: Clustering Identifying Cell Types of scRNA-Seq Data Based on Feature Engineering Denoising. Interdiscip Sci 2023; 15:590-601. [PMID: 37402002 DOI: 10.1007/s12539-023-00574-y] [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: 01/20/2023] [Revised: 05/31/2023] [Accepted: 06/06/2023] [Indexed: 07/05/2023]
Abstract
Recently developed single-cell RNA-seq (scRNA-seq) technology has given researchers the chance to investigate single-cell level of disease development. Clustering is one of the most essential strategies for analyzing scRNA-seq data. Choosing high-quality feature sets can significantly enhance the outcomes of single-cell clustering and classification. But computationally burdensome and highly expressed genes cannot afford a stabilized and predictive feature set for technical reasons. In this study, we introduce scFED, a feature-engineered gene selection framework. scFED identifies prospective feature sets to eliminate the noise fluctuation. And fuse them with existing knowledge from the tissue-specific cellular taxonomy reference database (CellMatch) to avoid the influence of subjective factors. Then present a reconstruction approach for noise reduction and crucial information amplification. We apply scFED on four genuine single-cell datasets and compare it with other techniques. According to the results, scFED improves clustering, decreases dimension of the scRNA-seq data, improves cell type identification when combined with clustering algorithms, and has higher performance than other methods. Therefore, scFED offers certain benefits in scRNA-seq data gene selection.
Collapse
Affiliation(s)
- Yang Liu
- School of Computer Science, Qufu Normal University, Rizhao, 276826, China
| | - Feng Li
- School of Computer Science, Qufu Normal University, Rizhao, 276826, China.
| | - Junliang Shang
- School of Computer Science, Qufu Normal University, Rizhao, 276826, China
| | - Jinxing Liu
- School of Computer Science, Qufu Normal University, Rizhao, 276826, China
| | - Juan Wang
- School of Computer Science, Qufu Normal University, Rizhao, 276826, China
| | - Daohui Ge
- School of Computer Science, Qufu Normal University, Rizhao, 276826, China
| |
Collapse
|
49
|
Huizing GJ, Deutschmann IM, Peyré G, Cantini L. Paired single-cell multi-omics data integration with Mowgli. Nat Commun 2023; 14:7711. [PMID: 38001063 PMCID: PMC10673889 DOI: 10.1038/s41467-023-43019-2] [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: 02/02/2023] [Accepted: 10/30/2023] [Indexed: 11/26/2023] Open
Abstract
The profiling of multiple molecular layers from the same set of cells has recently become possible. There is thus a growing need for multi-view learning methods able to jointly analyze these data. We here present Multi-Omics Wasserstein inteGrative anaLysIs (Mowgli), a novel method for the integration of paired multi-omics data with any type and number of omics. Of note, Mowgli combines integrative Nonnegative Matrix Factorization and Optimal Transport, enhancing at the same time the clustering performance and interpretability of integrative Nonnegative Matrix Factorization. We apply Mowgli to multiple paired single-cell multi-omics data profiled with 10X Multiome, CITE-seq, and TEA-seq. Our in-depth benchmark demonstrates that Mowgli's performance is competitive with the state-of-the-art in cell clustering and superior to the state-of-the-art once considering biological interpretability. Mowgli is implemented as a Python package seamlessly integrated within the scverse ecosystem and it is available at http://github.com/cantinilab/mowgli .
Collapse
Affiliation(s)
- Geert-Jan Huizing
- Institut Pasteur, Université Paris Cité, CNRS UMR 3738, Machine Learning for Integrative Genomics Group, F-75015, Paris, France.
- Institut de Biologie de l'Ecole Normale Supérieure, CNRS, INSERM, Ecole Normale Supérieure, Université PSL, 75005, Paris, France.
| | - Ina Maria Deutschmann
- Institut de Biologie de l'Ecole Normale Supérieure, CNRS, INSERM, Ecole Normale Supérieure, Université PSL, 75005, Paris, France
| | - Gabriel Peyré
- CNRS and DMA de l'Ecole Normale Supérieure, CNRS, Ecole Normale Supérieure, Université PSL, 75005, Paris, France
| | - Laura Cantini
- Institut Pasteur, Université Paris Cité, CNRS UMR 3738, Machine Learning for Integrative Genomics Group, F-75015, Paris, France.
- Institut de Biologie de l'Ecole Normale Supérieure, CNRS, INSERM, Ecole Normale Supérieure, Université PSL, 75005, Paris, France.
| |
Collapse
|
50
|
Rao L, Cai L, Huang L. Single-cell dynamics of liver development in postnatal pigs. Sci Bull (Beijing) 2023; 68:2583-2597. [PMID: 37783617 DOI: 10.1016/j.scib.2023.09.021] [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: 04/24/2023] [Revised: 06/21/2023] [Accepted: 09/14/2023] [Indexed: 10/04/2023]
Abstract
The postnatal development of the liver, an essential organ for metabolism and immunity, remains poorly characterized at the single-cell resolution. Here, we generated single-nucleus and single-cell transcriptomes of 84,824 pig liver cells at four postnatal time points: day 30, 42, 150, and 730. We uncovered 23 cell types, including three rare cell types: plasmacytoid dendritic cells, CAVIN3+IGF2+ endothelial cells, and EBF1+ fibroblasts. The latter two were verified by multiplex immunohistochemistry. Trajectory and gene regulatory analyses revealed 33 genes that encode transcription factors associated with hepatocyte development and function, including NFIL3 involved in regulating hepatic metabolism. We characterized the spatiotemporal heterogeneity of liver endothelial cells, identified and validated leucine zipper protein 2 (LUZP2) as a novel adult liver sinusoidal endothelial cell-specific transcription factor. Lymphoid cells (NK and T cells) governed the immune system of the pig liver since day 30. Furthermore, we identified a cluster of tissue-resident NK cells, which displayed virus defense functions, maintained proliferative features at day 730, and manifested a higher conservative transcription factor expression pattern in humans than in mouse liver. Our study presents the most comprehensive postnatal liver development single-cell atlas and demonstrates the metabolic and immune changes across the four age stages.
Collapse
Affiliation(s)
- Lin Rao
- National Key Laboratory for Swine Genetic Improvement and Germplasm Innovation, Ministry of Science and Technology of China, Jiangxi Agricultural University, Nanchang 330045, China.
| | - Liping Cai
- National Key Laboratory for Swine Genetic Improvement and Germplasm Innovation, Ministry of Science and Technology of China, Jiangxi Agricultural University, Nanchang 330045, China
| | - Lusheng Huang
- National Key Laboratory for Swine Genetic Improvement and Germplasm Innovation, Ministry of Science and Technology of China, Jiangxi Agricultural University, Nanchang 330045, China.
| |
Collapse
|