1
|
Jiang J, Qian B, Guo Y, He Z. Identification of subgroups and development of prognostic risk models along the glycolysis-cholesterol synthesis axis in lung adenocarcinoma. Sci Rep 2024; 14:14704. [PMID: 38926418 PMCID: PMC11208590 DOI: 10.1038/s41598-024-64602-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/01/2023] [Accepted: 06/11/2024] [Indexed: 06/28/2024] Open
Abstract
Lung cancer is one of the most dangerous malignant tumors affecting human health. Lung adenocarcinoma (LUAD) is the most common subtype of lung cancer. Both glycolytic and cholesterogenic pathways play critical roles in metabolic adaptation to cancer. A dataset of 585 LUAD samples was downloaded from The Cancer Genome Atlas database. We obtained co-expressed glycolysis and cholesterogenesis genes by selecting and clustering genes from Molecular Signatures Database v7.5. We compared the prognosis of different subtypes and identified differentially expressed genes between subtypes. Predictive outcome events were modeled using machine learning, and the top 9 most important prognostic genes were selected by Shapley additive explanation analysis. A risk score model was built based on multivariate Cox analysis. LUAD patients were categorized into four metabolic subgroups: cholesterogenic, glycolytic, quiescent, and mixed. The worst prognosis was the mixed subtype. The prognostic model had great predictive performance in the test set. Patients with LUAD were effectively typed by glycolytic and cholesterogenic genes and were identified as having the worst prognosis in the glycolytic and cholesterogenic enriched gene groups. The prognostic model can provide an essential basis for clinicians to predict clinical outcomes for patients. The model was robust on the training and test datasets and had a great predictive performance.
Collapse
Affiliation(s)
- Jiuzhou Jiang
- Department of Thoracic Surgery, Sir Run Run Shaw Hospital, Medical College of Zhejiang University, Hangzhou, China.
| | - Bao Qian
- Zhejiang University School of Medicine, Hangzhou, China
| | - Yangjie Guo
- Zhejiang University School of Medicine, Hangzhou, China
| | - Zhengfu He
- Department of Thoracic Surgery, Sir Run Run Shaw Hospital, Medical College of Zhejiang University, Hangzhou, China.
| |
Collapse
|
2
|
Castoldi A, Lee J, de Siqueira Carvalho D, Souto FO. CD8 + T cell metabolic changes in breast cancer. Biochim Biophys Acta Mol Basis Dis 2023; 1869:166565. [PMID: 36220587 DOI: 10.1016/j.bbadis.2022.166565] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/22/2022] [Revised: 08/22/2022] [Accepted: 10/03/2022] [Indexed: 11/05/2022]
Abstract
Immunometabolism has advanced our understanding of how the cellular environment and nutrient availability regulates immune cell fate. Not only are metabolic pathways closely tied to cell signaling and differentiation, but can induce different subsets of immune cells to adopt unique metabolic programs, influencing disease progression. Dysregulation of immune cell metabolism plays an essential role in the progression of several diseases including breast cancer (BC). Metabolic reprogramming plays a critical role in regulating T cell functions. CD8+ T cells are an essential cell type within the tumor microenvironment (TME). To induce antitumor responses, CD8+ T cells need to adapt their metabolism to fulfill their energy requirement for effective function. However, different markers and immunologic techniques have made identifying specific CD8+ T cells subtypes in BC a challenge to the field. This review discusses the immunometabolic processes of CD8+ T cell in the TME in the context of BC and highlights the role of CD8+ T cell metabolic changes in tumor progression.
Collapse
Affiliation(s)
- Angela Castoldi
- Instituto Keizo Asami, Universidade Federal de Pernambuco, Recife, Brazil; Núcleo de Ciências da Vida, Centro Acadêmico do Agreste, Universidade Federal de Pernambuco, Caruaru, Brazil; Programa de Pós-Graduação em Biologia Aplicada à Saúde, Universidade Federal de Pernambuco, Recife, Brazil.
| | - Jennifer Lee
- Division of Endocrinology, Diabetes and Metabolism, Department of Medicine, Beth Israel Deaconess Medical Center and Harvard Medical School, 330 Brookline Avenue, Boston, MA 02215, USA
| | | | - Fabrício Oliveira Souto
- Instituto Keizo Asami, Universidade Federal de Pernambuco, Recife, Brazil; Núcleo de Ciências da Vida, Centro Acadêmico do Agreste, Universidade Federal de Pernambuco, Caruaru, Brazil; Programa de Pós-Graduação em Biologia Aplicada à Saúde, Universidade Federal de Pernambuco, Recife, Brazil
| |
Collapse
|
3
|
Li C, Liu D, Yang S, Hua K. Integrated single-cell transcriptome analysis of the tumor ecosystems underlying cervical cancer metastasis. Front Immunol 2022; 13:966291. [PMID: 36569924 PMCID: PMC9780385 DOI: 10.3389/fimmu.2022.966291] [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: 07/07/2022] [Accepted: 11/21/2022] [Indexed: 12/13/2022] Open
Abstract
Cervical cancer (CC) is one of the most frequent female malignancies worldwide. However, the molecular mechanism of lymph node metastasis in CC remains unclear. In this study, we investigated the transcriptome profile of 51,507 single cells from primary tumors, positive lymph nodes (P-LN), and negative lymph nodes (N-LN) using single-cell sequencing. Validation experiments were performed using bulk transcriptomic datasets and immunohistochemical assays. Our results indicated that epithelial cells in metastatic LN were associated with cell- cycle-related signaling pathways, such as E2F targets, and mitotic spindle, and immune response-related signaling pathways, such as allograft rejection, IL2_STAT5_signaling, and inflammatory response. However, epithelial cells in primary tumors exhibited high enrichment of epithelial-mesenchymal translation (EMT), oxidative phosphorylation, and interferon alpha response. Our analysis then indicated that metastasis LN exhibited an early activated tumor microenvironment (TME) characterized by the decrease of naive T cells and an increase of cytotoxicity CD8 T cells, NK cells, FOXP3+ Treg cells compared with normal LN. By comparing the differently expressed gene of macrophages between tumor and metastatic LN, we discovered that C1QA+ MRC1low macrophages were enriched in a tumor, whereas C1QA+ MRC1high macrophages were enriched in metastatic LN. Finally, we demonstrated that cancer-associated fibroblasts (CAFs) in P-LN were associated with immune regulation, while CAFs in tumor underwent EMT. Our findings offered novel insights into the mechanisms of research, diagnosis, and therapy of CC metastasis.
Collapse
Affiliation(s)
- Chunbo Li
- Department of Obstetrics and Gynecology, Obstetrics and Gynecology Hospital of Fudan University, Shanghai, China
| | - Danyang Liu
- Department of Pathology, Obstetrics and Gynecology Hospital of Fudan University, Shanghai, China
| | - Shimin Yang
- Department of Obstetrics and Gynecology, Obstetrics and Gynecology Hospital of Fudan University, Shanghai, China
| | - Keqin Hua
- Department of Obstetrics and Gynecology, Obstetrics and Gynecology Hospital of Fudan University, Shanghai, China,*Correspondence: Keqin Hua,
| |
Collapse
|
4
|
Zhao S, Ji W, Shen Y, Fan Y, Huang H, Huang J, Lai G, Yuan K, Cheng C. Expression of hub genes of endothelial cells in glioblastoma-A prognostic model for GBM patients integrating single-cell RNA sequencing and bulk RNA sequencing. BMC Cancer 2022; 22:1274. [PMID: 36474171 PMCID: PMC9724299 DOI: 10.1186/s12885-022-10305-z] [Citation(s) in RCA: 21] [Impact Index Per Article: 10.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/28/2022] [Accepted: 11/10/2022] [Indexed: 12/12/2022] Open
Abstract
BACKGROUND This study aimed to use single-cell RNA-seq (scRNA-seq) to discover marker genes in endothelial cells (ECs) and construct a prognostic model for glioblastoma multiforme (GBM) patients in combination with traditional high-throughput RNA sequencing (bulk RNA-seq). METHODS Bulk RNA-seq data was downloaded from The Cancer Genome Atlas (TCGA) and The China Glioma Genome Atlas (CGGA) databases. 10x scRNA-seq data for GBM were obtained from the Gene Expression Omnibus (GEO) database. The uniform manifold approximation and projection (UMAP) were used for downscaling and cluster identification. Key modules and differentially expressed genes (DEGs) were identified by weighted gene correlation network analysis (WGCNA). A non-negative matrix decomposition (NMF) algorithm was used to identify the different subtypes based on DEGs, and multivariate cox regression analysis to model the prognosis. Finally, differences in mutational landscape, immune cell abundance, immune checkpoint inhibitors (ICIs)-associated genes, immunotherapy effects, and enriched pathways were investigated between different risk groups. RESULTS The analysis of scRNA-seq data from eight samples revealed 13 clusters and four cell types. After applying Fisher's exact test, ECs were identified as the most important cell type. The NMF algorithm identified two clusters with different prognostic and immunological features based on DEGs. We finally built a prognostic model based on the expression levels of four key genes. Higher risk scores were significantly associated with poorer survival outcomes, low mutation rates in IDH genes, and upregulation of immune checkpoints such as PD-L1 and CD276. CONCLUSION We built and validated a 4-gene signature for GBM using 10 scRNA-seq and bulk RNA-seq data in this work.
Collapse
Affiliation(s)
- Songyun Zhao
- grid.460176.20000 0004 1775 8598Department of Neurosurgery, Wuxi People’s Hospital Affiliated to Nanjing Medical University, No. 299 Qing Yang Road, 214023 Wuxi, Jiangsu China
| | - Wei Ji
- grid.460176.20000 0004 1775 8598Department of Neurosurgery, Wuxi People’s Hospital Affiliated to Nanjing Medical University, No. 299 Qing Yang Road, 214023 Wuxi, Jiangsu China
| | - Yifan Shen
- grid.460176.20000 0004 1775 8598Department of Neurosurgery, Wuxi People’s Hospital Affiliated to Nanjing Medical University, No. 299 Qing Yang Road, 214023 Wuxi, Jiangsu China
| | - Yuansheng Fan
- grid.460176.20000 0004 1775 8598Department of Neurosurgery, Wuxi People’s Hospital Affiliated to Nanjing Medical University, No. 299 Qing Yang Road, 214023 Wuxi, Jiangsu China
| | - Hui Huang
- grid.460176.20000 0004 1775 8598Department of Neurosurgery, Wuxi People’s Hospital Affiliated to Nanjing Medical University, No. 299 Qing Yang Road, 214023 Wuxi, Jiangsu China
| | - Jin Huang
- grid.460176.20000 0004 1775 8598Department of Neurosurgery, Wuxi People’s Hospital Affiliated to Nanjing Medical University, No. 299 Qing Yang Road, 214023 Wuxi, Jiangsu China
| | - Guichuan Lai
- grid.203458.80000 0000 8653 0555Department of Epidemiology and Health Statistics, School of Public Health, Chongqing Medical University, Yixue Road, 400016 Chongqing, China
| | - Kemiao Yuan
- Department of Oncology, Traditional Chinese Medicine Hospital of Wuxi, No.8, West Zhongnan Road, 214071 Wuxi, China
| | - Chao Cheng
- grid.460176.20000 0004 1775 8598Department of Neurosurgery, Wuxi People’s Hospital Affiliated to Nanjing Medical University, No. 299 Qing Yang Road, 214023 Wuxi, Jiangsu China
| |
Collapse
|
5
|
Rong H, Peng J, Ma K, Zhu J, He JT. Ttc39c is a potential target for the treatment of lung cancer. BMC Pulm Med 2022; 22:391. [PMID: 36303158 PMCID: PMC9615393 DOI: 10.1186/s12890-022-02173-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/08/2022] [Revised: 08/18/2022] [Accepted: 09/19/2022] [Indexed: 11/16/2022] Open
Abstract
BACKGROUND The novel TTC gene, tetratricopeptide repeat domain 39 C (Ttc39c), mainly mediates the interaction between proteins. It is involved in the progression of various tumors. In this study, we determined the effect of Ttc39c on lung adenocarcinoma and found that it might be used as a potential intervention target. METHODS We performed a difference analysis of Ttc39c samples from the TCGA database. Transwell experiments were conducted to determine the ability of cell metastasis. Celigo and MTT assays were performed to determine the effect of Ttc39c gene subtraction on cell proliferation. FACS was performed to determine the effect of Ttc39c gene subtraction on apoptosis. Clone-formation experiments were conducted to determine the effect of Ttc39c gene subtraction on cloning ability. Transcriptomics, proteomics, and metabolomics were used to elucidate the enrichment pathway of the Ttc39c gene in the progression of lung adenocarcinoma. RESULTS The expression of Ttc39c increased significantly in lung adenocarcinoma. The proliferation, metastasis, and cloning ability of human lung cancer cells were inhibited, while the apoptosis of cells increased significantly after the depletion of Ttc39c. Our results based on the transcriptomics, proteomics, and metabolomics analyses indicated that Ttc39c might be involved in the progression of lung adenocarcinoma (LUAD) mainly through the metabolic pathway and the p53 pathway. CONCLUSION To summarize, Ttc39c strongly regulates the proliferation and metastasis of lung adenocarcinoma cells. The main pathways involved in Ttc39c in lung adenocarcinoma include the energy metabolism and p53 pathways.
Collapse
Affiliation(s)
- Hao Rong
- Department of Thoracic Surgery, Sichuan Cancer Hospital & Institute, No. 55, 4th section, South Renmin Road, 610054, Chengdu, Sichuan, China
- Sichuan Cancer Center, School of Medicine, No. 55, 4th section, South Renmin Road, 610054, Chengdu, China
- University of Electronic Science and Technology of China, No. 55, 4th section, South Renmin Road, 610054, Chengdu, China
| | - Jun Peng
- Department of Thoracic Surgery, Sichuan Cancer Hospital & Institute, No. 55, 4th section, South Renmin Road, 610054, Chengdu, Sichuan, China
- Sichuan Cancer Center, School of Medicine, No. 55, 4th section, South Renmin Road, 610054, Chengdu, China
- University of Electronic Science and Technology of China, No. 55, 4th section, South Renmin Road, 610054, Chengdu, China
| | - Ke Ma
- Department of Thoracic Surgery, Sichuan Cancer Hospital & Institute, No. 55, 4th section, South Renmin Road, 610054, Chengdu, Sichuan, China
- Sichuan Cancer Center, School of Medicine, No. 55, 4th section, South Renmin Road, 610054, Chengdu, China
- University of Electronic Science and Technology of China, No. 55, 4th section, South Renmin Road, 610054, Chengdu, China
| | - Jiang Zhu
- Department of Thoracic Surgery, Sichuan Cancer Hospital & Institute, No. 55, 4th section, South Renmin Road, 610054, Chengdu, Sichuan, China
- Sichuan Cancer Center, School of Medicine, No. 55, 4th section, South Renmin Road, 610054, Chengdu, China
- University of Electronic Science and Technology of China, No. 55, 4th section, South Renmin Road, 610054, Chengdu, China
| | - Jin-Tao He
- Department of Thoracic Surgery, Sichuan Cancer Hospital & Institute, No. 55, 4th section, South Renmin Road, 610054, Chengdu, Sichuan, China.
- Sichuan Cancer Center, School of Medicine, No. 55, 4th section, South Renmin Road, 610054, Chengdu, China.
- University of Electronic Science and Technology of China, No. 55, 4th section, South Renmin Road, 610054, Chengdu, China.
| |
Collapse
|
6
|
Yu X, Zhang Q, Zhang S, He Y, Guo W. Single-cell sequencing and establishment of an 8-gene prognostic model for pancreatic cancer patients. Front Oncol 2022; 12:1000447. [PMID: 36237305 PMCID: PMC9552769 DOI: 10.3389/fonc.2022.1000447] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/22/2022] [Accepted: 09/05/2022] [Indexed: 11/15/2022] Open
Abstract
Background Single-cell sequencing (SCS) technologies enable analysis of gene structure and expression data at single-cell resolution. However, SCS analysis in pancreatic cancer remains largely unexplored. Methods We downloaded pancreatic cancer SCS data from different databases and applied appropriate dimensionality reduction algorithms. We identified 10 cell types and subsequently screened differentially expressed marker genes of these 10 cell types using FindAllMarkers analysis. Also, we evaluated the tumor immune microenvironment based on ESTIMATE and MCP-counter. Statistical enrichment was evaluated using Gene Ontology and Kyoto Encyclopedia of Genes and Genomes pathway analysis. We used all candidate gene sets in KEGG database to perform gene set enrichment analysis. We used LASSO regression to reduce the number of genes in the pancreatic risk model by R package glmnet, followed by rtPCR to validate the expression of the signature genes in different pancreatic cancer cell lines. Results We identified 15 cell subpopulations by dimension reduction and data clustering. We divided the 15 subpopulations into 10 distinct cell types based on marker gene expression. Then, we performed functional enrichment analysis for the 352 marker genes in pancreatic cancer cells. Based on RNA expression data and prognostic information from TCGA and GEO datasets, we identified 42 prognosis-related genes, including 5 protective genes and 37 high-risk genes, which we used to identified two molecular subtypes. C1 subtype was associated with a better prognosis, whereas C2 subtype was associated with a worse prognosis. Moreover, chemokine and chemokine receptor genes were differentially expressed between C1 and C2 subtypes. Functional and pathway enrichment uncovered functional differences between C1 and C2 subtype. We identified eight genes that could serve as potential biomarkers for prognosis prediction in pancreatic cancer patients. These genes were used to establish an 8-gene pancreatic cancer prognostic model. Conclusions We established an 8-gene pancreatic cancer prognostic model. This model can meaningfully predict prognosis and treatment response in pancreatic cancer patients.
Collapse
Affiliation(s)
- Xiao Yu
- Department of Hepatobiliary and Pancreatic Surgery, The First Affiliated Hospital of Zhengzhou University, Zhengzhou, China
- Key Laboratory of Hepatobiliary and Pancreatic Surgery and Digestive Organ Transplantation of Henan Province, The First Affiliated Hospital of Zhengzhou University, Zhengzhou, China
- Open and Key Laboratory of Hepatobiliary & Pancreatic Surgery and Digestive Organ Transplantation at Henan Universities, The First Affiliated Hospital of Zhengzhou University, Zhengzhou, China
- Henan Key Laboratory of Digestive Organ Transplantation, The First Affiliated Hospital of Zhengzhou University, Zhengzhou, China
| | - Qiyao Zhang
- Department of Hepatobiliary and Pancreatic Surgery, The First Affiliated Hospital of Zhengzhou University, Zhengzhou, China
- Key Laboratory of Hepatobiliary and Pancreatic Surgery and Digestive Organ Transplantation of Henan Province, The First Affiliated Hospital of Zhengzhou University, Zhengzhou, China
- Open and Key Laboratory of Hepatobiliary & Pancreatic Surgery and Digestive Organ Transplantation at Henan Universities, The First Affiliated Hospital of Zhengzhou University, Zhengzhou, China
- Henan Key Laboratory of Digestive Organ Transplantation, The First Affiliated Hospital of Zhengzhou University, Zhengzhou, China
| | - Shuijun Zhang
- Department of Hepatobiliary and Pancreatic Surgery, The First Affiliated Hospital of Zhengzhou University, Zhengzhou, China
- Key Laboratory of Hepatobiliary and Pancreatic Surgery and Digestive Organ Transplantation of Henan Province, The First Affiliated Hospital of Zhengzhou University, Zhengzhou, China
- Open and Key Laboratory of Hepatobiliary & Pancreatic Surgery and Digestive Organ Transplantation at Henan Universities, The First Affiliated Hospital of Zhengzhou University, Zhengzhou, China
- Henan Key Laboratory of Digestive Organ Transplantation, The First Affiliated Hospital of Zhengzhou University, Zhengzhou, China
| | - Yuting He
- Department of Hepatobiliary and Pancreatic Surgery, The First Affiliated Hospital of Zhengzhou University, Zhengzhou, China
- Key Laboratory of Hepatobiliary and Pancreatic Surgery and Digestive Organ Transplantation of Henan Province, The First Affiliated Hospital of Zhengzhou University, Zhengzhou, China
- Open and Key Laboratory of Hepatobiliary & Pancreatic Surgery and Digestive Organ Transplantation at Henan Universities, The First Affiliated Hospital of Zhengzhou University, Zhengzhou, China
- Henan Key Laboratory of Digestive Organ Transplantation, The First Affiliated Hospital of Zhengzhou University, Zhengzhou, China
- *Correspondence: Wenzhi Guo, ; Yuting He,
| | - Wenzhi Guo
- Department of Hepatobiliary and Pancreatic Surgery, The First Affiliated Hospital of Zhengzhou University, Zhengzhou, China
- Key Laboratory of Hepatobiliary and Pancreatic Surgery and Digestive Organ Transplantation of Henan Province, The First Affiliated Hospital of Zhengzhou University, Zhengzhou, China
- Open and Key Laboratory of Hepatobiliary & Pancreatic Surgery and Digestive Organ Transplantation at Henan Universities, The First Affiliated Hospital of Zhengzhou University, Zhengzhou, China
- Henan Key Laboratory of Digestive Organ Transplantation, The First Affiliated Hospital of Zhengzhou University, Zhengzhou, China
- *Correspondence: Wenzhi Guo, ; Yuting He,
| |
Collapse
|
7
|
Expression Analysis of Ligand-Receptor Pairs Identifies Cell-to-Cell Crosstalk between Macrophages and Tumor Cells in Lung Adenocarcinoma. J Immunol Res 2022; 2022:9589895. [PMID: 36249427 PMCID: PMC9553453 DOI: 10.1155/2022/9589895] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/16/2022] [Revised: 08/28/2022] [Accepted: 09/08/2022] [Indexed: 12/24/2022] Open
Abstract
Background Lung adenocarcinoma is one of the most commonly diagnosed malignancies worldwide. Macrophage plays crucial roles in the tumor microenvironment, but its autocrine network and communications with tumor cell are still unclear. Methods We acquired single-cell RNA sequencing (scRNA-seq) (n = 30) and bulk RNA sequencing (n = 1480) samples of lung adenocarcinoma patients from previous literatures and publicly available databases. Various cell subtypes were identified, including macrophages. Differentially expressed ligand-receptor gene pairs were obtained to explore cell-to-cell communications between macrophages and tumor cells. Furthermore, a machine-learning predictive model based on ligand-receptor interactions was built and validated. Results A total of 159,219 single cells (18,248 tumor cells and 29,520 macrophages) were selected in this study. We identified significantly correlated autocrine ligand-receptor gene pairs in tumor cells and macrophages, respectively. Furthermore, we explored the cell-to-cell communications between macrophages and tumor cells and detected significantly correlated ligand-receptor signaling pairs. We determined that some of the hub gene pairs were associated with patient prognosis and constructed a machine-learning model based on the intercellular interaction network. Conclusion We revealed significant cell-to-cell communications (both autocrine and paracrine network) within macrophages and tumor cells in lung adenocarcinoma. Hub genes with prognostic significance in the network were also identified.
Collapse
|
8
|
Li C, Hua K. Dissecting the Single-Cell Transcriptome Network of Immune Environment Underlying Cervical Premalignant Lesion, Cervical Cancer and Metastatic Lymph Nodes. Front Immunol 2022; 13:897366. [PMID: 35812401 PMCID: PMC9263187 DOI: 10.3389/fimmu.2022.897366] [Citation(s) in RCA: 19] [Impact Index Per Article: 9.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/16/2022] [Accepted: 05/20/2022] [Indexed: 01/09/2023] Open
Abstract
Cervical cancer (CC) is one of the most common malignancy in women worldwide. It is characterized by a natural continuous phenomenon, that is, it is in the initial stage of HPV infection, progresses to intraepithelial neoplasia, and then develops into invasion and metastasis. Determining the complexity of tumor microenvironment (TME) can deepen our understanding of lesion progression and provide novel therapeutic strategies for CC. We performed the single-cell RNA sequencing on the normal cervix, intraepithelial neoplasia, primary tumor and metastatic lymph node tissues to describe the composition, lineage, and functional status of immune cells and mesenchymal cells at different stages of CC progression. A total of 59913 single cells were obtained and divided into 9 cellular clusters, including immune cells (T/NK cells, macrophages, B cells, plasma cells, mast cells and neutrophils) and mesenchymal cells (endothelial cells, smooth muscle cells and fibroblasts). Our results showed that there were distinct cell subpopulations in different stages of CC. High-stage intraepithelial neoplasia (HSIL) tissue exhibited a low, recently activated TME, and it was characterized by high infiltration of tissue-resident CD8 T cell, effector NK cells, Treg, DC1, pDC, and M1-like macrophages. Tumor tissue displayed high enrichment of exhausted CD8 T cells, resident NK cells and M2-like macrophages, suggesting immunosuppressive TME. Metastatic lymph node consisted of naive T cell, central memory T cell, circling NK cells, cytotoxic CD8+ T cells and effector memory CD8 T cells, suggesting an early activated phase of immune response. This study is the first to delineate the transcriptome profile of immune cells during CC progression using single-cell RNA sequencing. Our results indicated that HSIL exhibited a low, recently activated TME, tumor displayed immunosuppressive statue, and metastatic lymph node showed early activated phase of immune response. Our study enhanced the understanding of dynamic change of TME during CC progression and has implications for the development of novel treatments to inhibit the initiation and progression of CC.
Collapse
Affiliation(s)
- Chunbo Li
- Department of Obstetrics and Gynecology, Obstetrics and Gynecology Hospital of Fudan University, Shanghai, China
| | - Keqin Hua
- Department of Obstetrics and Gynecology, Obstetrics and Gynecology Hospital of Fudan University, Shanghai, China
- Shanghai Key Laboratory of Female Reproductive Endocrine Related Diseases, Shanghai, China
| |
Collapse
|
9
|
Jiang A, Wang J, Liu N, Zheng X, Li Y, Ma Y, Zheng H, Chen X, Fan C, Zhang R, Fu X, Yao Y. Integration of Single-Cell RNA Sequencing and Bulk RNA Sequencing Data to Establish and Validate a Prognostic Model for Patients With Lung Adenocarcinoma. Front Genet 2022; 13:833797. [PMID: 35154287 PMCID: PMC8829512 DOI: 10.3389/fgene.2022.833797] [Citation(s) in RCA: 13] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/12/2021] [Accepted: 01/14/2022] [Indexed: 12/27/2022] Open
Abstract
Background: Lung adenocarcinoma (LUAD) remains a lethal disease worldwide, with numerous studies exploring its potential prognostic markers using traditional RNA sequencing (RNA-seq) data. However, it cannot detect the exact cellular and molecular changes in tumor cells. This study aimed to construct a prognostic model for LUAD using single-cell RNA-seq (scRNA-seq) and traditional RNA-seq data. Methods: Bulk RNA-seq data were downloaded from The Cancer Genome Atlas (TCGA) database. LUAD scRNA-seq data were acquired from Gene Expression Omnibus (GEO) database. The uniform manifold approximation and projection (UMAP) was used for dimensionality reduction and cluster identification. Weighted Gene Correlation Network Analysis (WGCNA) was utilized to identify key modules and differentially expressed genes (DEGs). The non-negative Matrix Factorization (NMF) algorithm was used to identify different subtypes based on DEGs. The Cox regression analysis was used to develop the prognostic model. The characteristics of mutation landscape, immune status, and immune checkpoint inhibitors (ICIs) related genes between different risk groups were also investigated. Results: scRNA-seq data of four samples were integrated to identify 13 clusters and 9cell types. After applying differential analysis, NK cells, bladder epithelial cells, and bronchial epithelial cells were identified as significant cell types. Overall, 329 DEGs were selected for prognostic model construction through differential analysis and WGCNA. Besides, NMF identified two clusters based on DEGs in the TCGA cohort, with distinct prognosis and immune characteristics being observed. We developed a prognostic model based on the expression levels of six DEGs. A higher risk score was significantly correlated with poor survival outcomes but was associated with a more frequent TP53 mutation rate, higher tumor mutation burden (TMB), and up-regulation of PD-L1. Two independent external validation cohorts were also adopted to verify our results, with consistent results observed in them. Conclusion: This study constructed and validated a prognostic model for LUAD by integrating 10× scRNA-seq and bulk RNA-seq data. Besides, we observed two distinct subtypes in this population, with different prognosis and immune characteristics.
Collapse
Affiliation(s)
- Aimin Jiang
- Department of Medical Oncology, The First Affiliated Hospital of Xi'an Jiaotong University, Xi'an, China
| | - Jingjing Wang
- Department of Medical Oncology, The First Affiliated Hospital of Xi'an Jiaotong University, Xi'an, China
| | - Na Liu
- Department of Medical Oncology, The First Affiliated Hospital of Xi'an Jiaotong University, Xi'an, China
| | - Xiaoqiang Zheng
- Department of Medical Oncology, The First Affiliated Hospital of Xi'an Jiaotong University, Xi'an, China
| | - Yimeng Li
- Department of Medical Oncology, The First Affiliated Hospital of Xi'an Jiaotong University, Xi'an, China
| | - Yuyan Ma
- Department of Medical Oncology, The First Affiliated Hospital of Xi'an Jiaotong University, Xi'an, China
| | - Haoran Zheng
- Department of Medical Oncology, The First Affiliated Hospital of Xi'an Jiaotong University, Xi'an, China
| | - Xue Chen
- Department of Medical Oncology, The First Affiliated Hospital of Xi'an Jiaotong University, Xi'an, China
| | - Chaoxin Fan
- Department of Medical Oncology, The First Affiliated Hospital of Xi'an Jiaotong University, Xi'an, China
| | - Rui Zhang
- Department of Medical Oncology, The First Affiliated Hospital of Xi'an Jiaotong University, Xi'an, China
| | - Xiao Fu
- Department of Medical Oncology, The First Affiliated Hospital of Xi'an Jiaotong University, Xi'an, China
| | - Yu Yao
- Department of Medical Oncology, The First Affiliated Hospital of Xi'an Jiaotong University, Xi'an, China
| |
Collapse
|
10
|
Liang J, Chen Z, Huang Y, Bi G, Bian Y, Jin X, Zhang H, Sui Q, Zhan C, Wang Q. Signatures of malignant cells and novel therapeutic targets revealed by single-cell sequencing in lung adenocarcinoma. Cancer Med 2022; 11:2244-2258. [PMID: 35102706 PMCID: PMC9160812 DOI: 10.1002/cam4.4547] [Citation(s) in RCA: 12] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/13/2021] [Revised: 12/11/2021] [Accepted: 12/12/2021] [Indexed: 02/06/2023] Open
Abstract
Background Single‐cell transcriptomics has been used to investigate various tumors to elucidate the molecular distinction of all cell type compositions of a complex mix. Aims This study aimed to investigate malignant‐cell‐specific genes to explore diagnostic and therapeutic biomarkers using single‐cell transcriptomic data of lung adenocarcinoma. Materials & Methods 10X single‐cell RNA‐seq data of fourteen patients with lung adenocarcinoma were analyzed. Genes that expressed differentially and those with higher confidence to distinguish tumor cells from normal cells were picked out using the ROC curves. The LASSO regression method was used to select most markedly correlated genes to predict the malignancy of every single cell within a model. We also conducted further experiments to determine their roles in lung cancer in vitro. Results Twenty two thousand four hundred and ninety one tumor and 181 666 normal single cells were analyzed where 369 genes were found to be specifically expressed in single malignant cells. Seventy of them, encoding secreted or membrane‐bound proteins, showed involvement in cell‐to‐cell communications in tumor biology. KRT18 and the other six genes were identified as predictors to distinguish single malignant cells and were integrated to construct an accurate (96.1%) predicting model. Notably, IRX2, SPINK13, and CAPN8 outperformed the other four genes. Further experiments confirmed the upregulation of them in lung adenocarcinoma at both tissue and cell levels. Proliferative capacities of lung adenocarcinoma cells were attenuated by knocking‐down of either of them. However, targeting CAPN8, IRX2, or SPINK13 hardly exerted a cytotoxic effect on these cells. Discussion Apart from the current model, similar tools were still warranted using single‐cell RNA‐seq data of more types of tumors. The three genes identified as potential therapeutic targets in the present study still need to be validated in more in lung cancer. Conclusion Our model can aid the analyses of single‐cell sequencing data. CAPN8, IRX2, and SPINK13 may serve as novel targets of targeted and immune‐based therapies in lung adenocarcinoma.
Collapse
Affiliation(s)
- Jiaqi Liang
- Department of Thoracic Surgery, Zhongshan Hospital, Fudan University, Shanghai, China
| | - Zhencong Chen
- Department of Thoracic Surgery, Zhongshan Hospital, Fudan University, Shanghai, China
| | - Yiwei Huang
- Department of Thoracic Surgery, Zhongshan Hospital, Fudan University, Shanghai, China
| | - Guoshu Bi
- Department of Thoracic Surgery, Zhongshan Hospital, Fudan University, Shanghai, China
| | - Yunyi Bian
- Department of Thoracic Surgery, Zhongshan Hospital, Fudan University, Shanghai, China
| | - Xing Jin
- Department of Thoracic Surgery, Zhongshan Hospital, Fudan University, Shanghai, China
| | - Huan Zhang
- Department of Thoracic Surgery, Zhongshan Hospital, Fudan University, Shanghai, China
| | - Qihai Sui
- Department of Thoracic Surgery, Zhongshan Hospital, Fudan University, Shanghai, China
| | - Cheng Zhan
- Department of Thoracic Surgery, Zhongshan Hospital, Fudan University, Shanghai, China
| | - Qun Wang
- Department of Thoracic Surgery, Zhongshan Hospital, Fudan University, Shanghai, China
| |
Collapse
|
11
|
Huang RH, Wang LX, He J, Gao W. Application and prospects of single cell sequencing in tumors. Biomark Res 2021; 9:88. [PMID: 34895349 PMCID: PMC8665603 DOI: 10.1186/s40364-021-00336-2] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/30/2021] [Accepted: 10/18/2021] [Indexed: 02/06/2023] Open
Abstract
Cancer is an intricate disease with inherent intra-tumor heterogeneity at the cellular level because of genetic changes and environmental differences. Cellular heterogeneity exists even within the same tumor type. Small deviations in a genome or transcriptome can lead to significant differences in function. Conventional bulk population sequencing, which produces admixed populations of cells, can only provide an average expression signal for one cell population, ignoring differences between individual cells. Important advances in sequencing have been made in recent years. Single cell sequencing starts in a single cell, thereby increasing our capability to characterize intratumor heterogeneity. This technology has been used to analyze genetic variation, specific metabolic activity, and evolutionary processes in tumors, which may help us understand tumor occurrence and development and improve our understanding of the tumor microenvironment. In addition, it provides a theoretical basis for the development of clinical treatments, especially for personalized medicine. In this article, we briefly introduce Single cell sequencing technology, summarize the application of Single cell sequencing to study the tumor microenvironment, as well as its therapeutic application in different clinical procedures.
Collapse
Affiliation(s)
- Ruo Han Huang
- Department of Oncology, The First Affiliated Hospital of Nanjing Medical University, 300 Guangzhou Road, Nanjing, 210029, China
| | - Le Xin Wang
- Department of Oncology, The First Affiliated Hospital of Nanjing Medical University, 300 Guangzhou Road, Nanjing, 210029, China
| | - Jing He
- Department of Oncology, The First Affiliated Hospital of Nanjing Medical University, 300 Guangzhou Road, Nanjing, 210029, China.
| | - Wen Gao
- Department of Oncology, The First Affiliated Hospital of Nanjing Medical University, 300 Guangzhou Road, Nanjing, 210029, China.
| |
Collapse
|
12
|
Zhong H, Wang J, Zhu Y, Shen Y. Comprehensive Analysis of a Nine-Gene Signature Related to Tumor Microenvironment in Lung Adenocarcinoma. Front Cell Dev Biol 2021; 9:700607. [PMID: 34540825 PMCID: PMC8440811 DOI: 10.3389/fcell.2021.700607] [Citation(s) in RCA: 21] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/26/2021] [Accepted: 08/04/2021] [Indexed: 01/29/2023] Open
Abstract
Lung adenocarcinoma (LUAD) is the most common malignancy, leading to more than 1 million related deaths each year. Due to low long-term survival rates, the exploration of molecular mechanisms underlying LUAD progression and novel prognostic predictors is urgently needed to improve LUAD treatment. In our study, cancer-specific differentially expressed genes (DEGs) were identified using the robust rank aggregation (RRA) method between tumor and normal tissues from six Gene Expression Omnibus databases (GSE43458, GSE62949, GSE68465, GSE115002, GSE116959, and GSE118370), followed by a selection of prognostic modules using weighted gene co-expression network analysis. Univariate Cox regression, least absolute shrinkage and selection operator (LASSO), and multivariate Cox regression analyses were applied to identify nine hub genes (CBFA2T3, CR2, SEL1L3, TM6SF1, TSPAN32, ITGA6, MAPK11, RASA3, and TLR6) that constructed a prognostic risk model. The RNA expressions of nine hub genes were validated in tumor and normal tissues by RNA-sequencing and single-cell RNA-sequencing, while immunohistochemistry staining from the Human Protein Atlas database showed consistent results in the protein levels. The risk model revealed that high-risk patients were associated with poor prognoses, including advanced stages and low survival rates. Furthermore, a multivariate Cox regression analysis suggested that the prognostic risk model could be an independent prognostic factor for LUAD patients. A nomogram that incorporated the signature and clinical features was additionally built for prognostic prediction. Moreover, the levels of hub genes were related to immune cell infiltration in LUAD microenvironments. A CMap analysis identified 13 small molecule drugs as potential agents based on the risk model for LUAD treatment. Thus, we identified a prognostic risk model including CBFA2T3, CR2, SEL1L3, TM6SF1, TSPAN32, ITGA6, MAPK11, RASA3, and TLR6 as novel biomarkers and validated their prognostic and predicted values for LUAD.
Collapse
Affiliation(s)
- Haihui Zhong
- Department of Thoracic Surgery, Meizhou People's Hospital (Huangtang Hospital), Meizhou Hospital Affiliated to Sun Yat-sen University, Meizhou Academy of Medical Sciences, Meizhou, China
| | - Jie Wang
- Institute for Pathology, University Hospital of Cologne, Cologne, Germany
| | - Yaru Zhu
- Department of Critical Care Medicine, Zhujiang Hospital, Southern Medical University, Guangzhou, China
| | - Yefeng Shen
- Institute for Pathology, University Hospital of Cologne, Cologne, Germany
| |
Collapse
|
13
|
Bi G, Liang J, Shan G, Zhan C, Wang Q. Some Thoughts Concerning the Mutational Background of Cell Lines and Heterogeneity of Bulk Tumor. J Thorac Oncol 2021; 16:e67-e68. [PMID: 34425999 DOI: 10.1016/j.jtho.2021.05.009] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/01/2021] [Accepted: 05/02/2021] [Indexed: 11/27/2022]
Affiliation(s)
- Guoshu Bi
- Department of Thoracic Surgery, Zhongshan Hospital, Fudan University, Shanghai, People's Republic of China
| | - Jiaqi Liang
- Department of Thoracic Surgery, Zhongshan Hospital, Fudan University, Shanghai, People's Republic of China
| | - Guangyao Shan
- Department of Thoracic Surgery, Zhongshan Hospital, Fudan University, Shanghai, People's Republic of China
| | - Cheng Zhan
- Department of Thoracic Surgery, Zhongshan Hospital, Fudan University, Shanghai, People's Republic of China.
| | - Qun Wang
- Department of Thoracic Surgery, Zhongshan Hospital, Fudan University, Shanghai, People's Republic of China
| |
Collapse
|
14
|
Du Y, Hu Z, Liang J, Zhan C, Qiao T. Noncancer Cells in Tumor Samples May Bias the Predictive Genomic-Adjusted Radiation Dose. J Thorac Oncol 2021; 16:e47. [PMID: 34034893 DOI: 10.1016/j.jtho.2021.01.1625] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/17/2021] [Accepted: 01/25/2021] [Indexed: 10/21/2022]
Affiliation(s)
- Yajing Du
- Center for Tumor Diagnosis and Therapy, Jinshan Hospital, Fudan University, Shanghai, People's Republic of China
| | - Zhengyang Hu
- Department of Thoracic Surgery, Zhongshan Hospital, Fudan University, Shanghai, People's republic of China
| | - Jiaqi Liang
- Department of Thoracic Surgery, Zhongshan Hospital, Fudan University, Shanghai, People's republic of China
| | - Cheng Zhan
- Department of Thoracic Surgery, Zhongshan Hospital, Fudan University, Shanghai, People's republic of China
| | - Tiankui Qiao
- Center for Tumor Diagnosis and Therapy, Jinshan Hospital, Fudan University, Shanghai, People's Republic of China.
| |
Collapse
|
15
|
He J, Zhang W, Li F, Yu Y. Development of metastasis-associated seven gene signature for predicting lung adenocarcinoma prognosis using single-cell RNA sequencing data. MATHEMATICAL BIOSCIENCES AND ENGINEERING : MBE 2021; 18:5959-5977. [PMID: 34517518 DOI: 10.3934/mbe.2021298] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/13/2023]
Abstract
Metastasis is the primary cause of lung adenocarcinoma (LUAD)-related death. This study evaluated the metastasis-associated genes (MAGs) in single-cell RNA sequencing (scRNA-seq) data from LUAD tissues and developed a MAG signature to predict overall survival (OS) of LUAD patients. The LUAD scRNA-seq data was downloaded from the Gene Expression Omnibus (GEO) Database and MAGs were identified from LUAD scRNA-seq data. The LUAD transcriptomic and clinical data were obtained from The Cancer Genome Atlas (TCGA). Cox and LASSO regression analyses were performed to identify differentially expressed MAGs (DEMAGs) with prognostic value that were then used to construct a MAG signature and MAG-nomogram model. Finally, a functional enrichment analysis was performed via Gene Set Enrichment Analysis (GSEA). 414 MAGs and 22 prognostic DEMAGs were revealed in the study. Multivariate Cox proportional hazards regression analysis was utilized to construct a 7-MAG signature for predicting the OS of LUAD patients. Patients with high risk scores had a significantly worse OS than those with low risk scores in the training group (n = 236), and the 7-MAG signature was successfully confirmed in the testing group (n = 232) and the entire TCGA-LUAD cohort (n = 468). Furthermore, univariate and multivariate Cox regression suggested that the 7-MAG signature was an independent prognostic indicator. Additionally, based on the 7-MAG signature, a nomogram was established that could more intuitively help to predict the OS of LUAD patients. The GSEA revealed the underlying molecular mechanisms of the 7-MAG signature in LUAD metastasis. In conclusion, a 7-MAG signature was developed based on LUAD scRNA-seq data that could effectively predict LUAD patient prognosis and provide novel insights for therapeutic targets and the potential molecular mechanism of metastatic LUAD.
Collapse
Affiliation(s)
- Jinqi He
- Department of Medical Oncology, Harbin Medical University Cancer Hospital, Harbin 150081, China
| | - Wenjing Zhang
- Department of Hematology Oncology, The Central Hospital of Shaoyang, Shaoyang 422000, China
| | - Faxiang Li
- Department of Hematology Oncology, The Central Hospital of Shaoyang, Shaoyang 422000, China
| | - Yan Yu
- Department of Medical Oncology, Harbin Medical University Cancer Hospital, Harbin 150081, China
| |
Collapse
|
16
|
Chen Z, Zhao M, Liang J, Hu Z, Huang Y, Li M, Pang Y, Lu T, Sui Q, Zhan C, Lin M, Guo W, Wang Q, Tan L. Dissecting the single-cell transcriptome network underlying esophagus non-malignant tissues and esophageal squamous cell carcinoma. EBioMedicine 2021; 69:103459. [PMID: 34192657 PMCID: PMC8253912 DOI: 10.1016/j.ebiom.2021.103459] [Citation(s) in RCA: 57] [Impact Index Per Article: 19.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/13/2021] [Revised: 06/07/2021] [Accepted: 06/08/2021] [Indexed: 02/06/2023] Open
Abstract
BACKGROUND Esophageal squamous cell carcinoma (ESCC) is among the most prevalent causes of cancer-related death in adults. Tumor microenvironment (TME) has been associated with therapeutic failure and lethal outcomes for patients. However, published reports on the heterogeneity and TME in ESCC are scanty. METHODS Five tumor samples and five corresponding non-malignant samples were subjected to scRNA-seq analysis. Bulk RNA sequencing data were retrieved in publicly available databases. FINDINGS From the scRNA-seq data, a total of 128,688 cells were enrolled for subsequent analyses. Gene expression and CNV status exhibited high heterogeneity of tumor cells. We further identified a list of tumor-specific genes and four malignant signatures, which are potential new markers for ESCC. Metabolic analysis revealed that energy supply-related pathways are pivotal in cancer metabolic reprogramming. Moreover, significant differences were found in stromal and immune cells between the esophagus normal and tumor tissues, which promoted carcinogenesis at both cellular and molecular levels in ESCC. Immune checkpoints, regarded as potential targets for immunotherapy in ESCC were significantly highly expressed in ESCC, including LAG3 and HAVCR2. Eventually, we constructed a cell-to-cell communication atlas based on cancer cells and immune cells and performed the flow cytometry, qRT-PCR, immunofluorescence, and immunohistochemistry analyses to validate the results. INTERPRETATION This study demonstrates a widespread reprogramming across multiple cellular elements within the TME in ESCC, particularly in transcriptional states, cellular functions, and cell-to-cell interactions. The findings offer an insight into the exploration of TME and heterogeneity in the ESCC and provide new therapeutic targets for its clinical management in the future. FUNDING The work was supported by the Shanghai Pujiang Program (2020PJD009) and Research Development Fund of Zhongshan Hospital, Fudan University (2019ZSFZ002 and 2019ZSFZ19).
Collapse
Affiliation(s)
- Zhencong Chen
- Department of Thoracic Surgery, Zhongshan Hospital, Fudan University, No. 180, Fenglin Road, Shanghai 200032, China
| | - Mengnan Zhao
- Department of Thoracic Surgery, Zhongshan Hospital, Fudan University, No. 180, Fenglin Road, Shanghai 200032, China
| | - Jiaqi Liang
- Department of Thoracic Surgery, Zhongshan Hospital, Fudan University, No. 180, Fenglin Road, Shanghai 200032, China
| | - Zhengyang Hu
- Department of Thoracic Surgery, Zhongshan Hospital, Fudan University, No. 180, Fenglin Road, Shanghai 200032, China
| | - Yiwei Huang
- Department of Thoracic Surgery, Zhongshan Hospital, Fudan University, No. 180, Fenglin Road, Shanghai 200032, China
| | - Ming Li
- Department of Thoracic Surgery, Zhongshan Hospital, Fudan University, No. 180, Fenglin Road, Shanghai 200032, China
| | - Yanrui Pang
- Department of Pathology of Zhongshan Hospital, Fudan University, No. 180, Fenglin Road, Shanghai 200032, China
| | - Tao Lu
- Department of Thoracic Surgery, Zhongshan Hospital, Fudan University, No. 180, Fenglin Road, Shanghai 200032, China
| | - Qihai Sui
- Department of Thoracic Surgery, Zhongshan Hospital, Fudan University, No. 180, Fenglin Road, Shanghai 200032, China
| | - Cheng Zhan
- Department of Thoracic Surgery, Zhongshan Hospital, Fudan University, No. 180, Fenglin Road, Shanghai 200032, China.
| | - Miao Lin
- Department of Thoracic Surgery, Zhongshan Hospital, Fudan University, No. 180, Fenglin Road, Shanghai 200032, China.
| | - Weigang Guo
- Department of Thoracic Surgery, Zhongshan Hospital, Fudan University, No. 180, Fenglin Road, Shanghai 200032, China.
| | - Qun Wang
- Department of Thoracic Surgery, Zhongshan Hospital, Fudan University, No. 180, Fenglin Road, Shanghai 200032, China
| | - Lijie Tan
- Department of Thoracic Surgery, Zhongshan Hospital, Fudan University, No. 180, Fenglin Road, Shanghai 200032, China
| |
Collapse
|
17
|
Zhang L, Zhu J, Wang H, Xia J, Liu P, Chen F, Jiang H, Miao Q, Wu W, Zhang L, Luo L, Jiang X, Bai Y, Sun C, Chen D, Zhang X. A high-resolution cell atlas of the domestic pig lung and an online platform for exploring lung single-cell data. J Genet Genomics 2021; 48:411-425. [PMID: 34144929 DOI: 10.1016/j.jgg.2021.03.012] [Citation(s) in RCA: 15] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/01/2020] [Revised: 03/01/2021] [Accepted: 03/16/2021] [Indexed: 12/28/2022]
Abstract
The genetically engineered pig is regarded as an optimal source of organ transplantation for humans and an excellent model for human disease research, given its comparable physiology to human beings. A myriad of single-cell RNA sequencing (scRNA-seq) data on humans has been reported, but such data on pigs are scarce. Here, we apply scRNA-seq technology to study the cellular heterogeneity of 3-month-old pig lungs, generating the single-cell atlas of 13,580 cells covering 16 major cell types. Based on these data, we systematically characterize the similarities and differences in the cellular cross-talk and expression patterns of respiratory virus receptors in each cell type of pig lungs compared with human lungs. Furthermore, we analyze pig lung xenotransplantation barriers and reported the cell-type expression patterns of 10 genes associated with pig-to-human immunobiological incompatibility and coagulation dysregulation. We also investigate the conserved transcription factors (TFs) and their candidate target genes and constructed five conserved TF regulatory networks in the main cell types shared by pig and human lungs. Finally, we present a comprehensive and openly accessible online platform, ScdbLung. Our scRNA-seq atlas of the domestic pig lung and ScdbLung database can guide pig lung research and clinical applicability.
Collapse
Affiliation(s)
- Lijing Zhang
- College of Life Sciences, University of Chinese Academy of Sciences, Beijing 100049, China; MGI, BGI-Shenzhen, Shenzhen 518083, China
| | - Jiacheng Zhu
- College of Life Sciences, University of Chinese Academy of Sciences, Beijing 100049, China; BGI-Shenzhen, Shenzhen 518083, China
| | - Haoyu Wang
- College of Life Sciences, University of Chinese Academy of Sciences, Beijing 100049, China; BGI-Shenzhen, Shenzhen 518083, China
| | - Jun Xia
- College of Life Sciences, University of Chinese Academy of Sciences, Beijing 100049, China; MGI, BGI-Shenzhen, Shenzhen 518083, China
| | - Ping Liu
- MGI, BGI-Shenzhen, Shenzhen 518083, China
| | - Fang Chen
- MGI, BGI-Shenzhen, Shenzhen 518083, China; BGI-Shenzhen, Shenzhen 518083, China
| | - Hui Jiang
- College of Life Sciences, University of Chinese Academy of Sciences, Beijing 100049, China; MGI, BGI-Shenzhen, Shenzhen 518083, China
| | - Qiuling Miao
- Department of Pathology, Shenzhen Children's Hospital, Shenzhen 518038, China
| | - Weiying Wu
- Department of Neurobiology, NHC and CAMS Key Laboratory of Medical Neurobiology, School of Brain Science and Brian Medicine, The MOE Frontier Science Center for Brain Research and Brain-Machine Integration, Zhejiang University School of Medicine, Hangzhou 310031, China
| | - Lingli Zhang
- Department of Pathophysiology, School of Basic Medicine, Guilin Medical University, Guilin 541199, China
| | - Lihua Luo
- College of Life Sciences, University of Chinese Academy of Sciences, Beijing 100049, China; BGI-Shenzhen, Shenzhen 518083, China
| | - Xiaosen Jiang
- College of Life Sciences, University of Chinese Academy of Sciences, Beijing 100049, China; BGI-Shenzhen, Shenzhen 518083, China
| | - Yong Bai
- BGI-Shenzhen, Shenzhen 518083, China
| | - Chengcheng Sun
- College of Life Sciences, University of Chinese Academy of Sciences, Beijing 100049, China; BGI-Shenzhen, Shenzhen 518083, China
| | | | - Xingliang Zhang
- Institute of Pediatrics, Department of Pediatric Surgery, Shenzhen Children's Hospital, Shenzhen 518038, China; Department of Pediatrics, The Affiliated Hospital of Guangdong Medical University, Zhanjiang 524001, China.
| |
Collapse
|
18
|
Chen Z, Huang Y, Hu Z, Zhao M, Li M, Bi G, Zheng Y, Liang J, Lu T, Jiang W, Xu S, Zhan C, Xi J, Wang Q, Tan L. Landscape and dynamics of single tumor and immune cells in early and advanced-stage lung adenocarcinoma. Clin Transl Med 2021; 11:e350. [PMID: 33783985 PMCID: PMC7943914 DOI: 10.1002/ctm2.350] [Citation(s) in RCA: 48] [Impact Index Per Article: 16.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/04/2020] [Revised: 02/18/2021] [Accepted: 02/23/2021] [Indexed: 12/24/2022] Open
Abstract
BACKGROUND Lung adenocarcinoma (LUAD) patients with different American Joint Committee on Cancer stages have different overall 5-year survival rates. The tumor microenvironment (TME) and intra-tumor heterogeneity (ITH) have been shown to play a crucial role in the occurrence and development of tumors. However, the TME and ITH in different lesions of LUAD have not been extensively explored. METHODS We present a 204,157-cell catalog of the TME transcriptome in 29 lung samples to systematically explore the TME and ITH in the different stages of LUAD. Traditional RNA sequencing data and complete clinical information were downloaded from publicly available databases. RESULTS Based on these high-quality cells, we constructed a single-cell network underlying cellular and molecular features of normal lung, early LUAD, and advanced LUAD cells. In contrast with early malignant cells, we noticed that advanced malignant cells had a remarkably more complex TME and higher ITH level. We also found that compared with other immune cells, more differences in CD8+/CTL T cells, regulatory T cells, and follicular B cells were evident between early and advanced LUAD. Additionally, cell-cell communication analyses, revealed great diversity between different lesions of LUAD at the single-cell level. Flow cytometry and qRT-PCR were used to validate our results. CONCLUSION Our results revealed the cellular diversity and molecular complexity of cell lineages in different stages of LUAD. We believe our research, which serves as a basic framework and valuable resource, can facilitate exploration of the pathogenesis of LUAD and identify novel therapeutic targets in the future.
Collapse
Affiliation(s)
- Zhencong Chen
- Department of Thoracic SurgeryZhongshan Hospital, Fudan UniversityShanghaiChina
| | - Yiwei Huang
- Department of Thoracic SurgeryZhongshan Hospital, Fudan UniversityShanghaiChina
| | - Zhengyang Hu
- Department of Thoracic SurgeryZhongshan Hospital, Fudan UniversityShanghaiChina
| | - Mengnan Zhao
- Department of Thoracic SurgeryZhongshan Hospital, Fudan UniversityShanghaiChina
| | - Ming Li
- Department of Thoracic SurgeryZhongshan Hospital, Fudan UniversityShanghaiChina
| | - Guoshu Bi
- Department of Thoracic SurgeryZhongshan Hospital, Fudan UniversityShanghaiChina
| | - Yuansheng Zheng
- Department of Thoracic SurgeryZhongshan Hospital, Fudan UniversityShanghaiChina
| | - Jiaqi Liang
- Department of Thoracic SurgeryZhongshan Hospital, Fudan UniversityShanghaiChina
| | - Tao Lu
- Department of Thoracic SurgeryZhongshan Hospital, Fudan UniversityShanghaiChina
| | - Wei Jiang
- Department of Thoracic SurgeryZhongshan Hospital, Fudan UniversityShanghaiChina
| | - Songtao Xu
- Department of Thoracic SurgeryZhongshan Hospital, Fudan UniversityShanghaiChina
| | - Cheng Zhan
- Department of Thoracic SurgeryZhongshan Hospital, Fudan UniversityShanghaiChina
| | - Junjie Xi
- Department of Thoracic SurgeryZhongshan Hospital, Fudan UniversityShanghaiChina
| | - Qun Wang
- Department of Thoracic SurgeryZhongshan Hospital, Fudan UniversityShanghaiChina
| | - Lijie Tan
- Department of Thoracic SurgeryZhongshan Hospital, Fudan UniversityShanghaiChina
| |
Collapse
|