1
|
He XY, Que LY, Yang F, Feng Y, Ren D, Song X. Single-cell transcriptional profiling in osteosarcoma and the effect of neoadjuvant chemotherapy on the tumor microenvironment. J Bone Oncol 2024; 46:100604. [PMID: 38765702 PMCID: PMC11101886 DOI: 10.1016/j.jbo.2024.100604] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/11/2023] [Revised: 04/28/2024] [Accepted: 04/29/2024] [Indexed: 05/22/2024] Open
Abstract
Osteosarcoma (OS), a malignant tumor, originates from the bone marrow. Currently, treatment for OS remains limited, making it urgent to understand the immune response in the tumor microenvironment of patients with OS. A comprehensive bioinformatics analysis was performed, including cell clustering subgroups, differential expression genes screening, proposed temporal order, and genomic variant analysis on single-cell RNA-sequencing data, from ten pre-chemotherapy patients and eleven post-chemotherapy patients. Subsequently, we analyzed the differentiation trajectories of osteoblasts, osteoclasts, fibroblasts, myeloid cells, and tumor-infiltrating lymphocytes (TILs) in detail to compare the changes in cell proportions and differential genes pre- and post-chemotherapy. The nine cell types were identified, including fibroblasts, myeloid cells, osteoblasts, TILs, osteoclasts, proliferative osteoblasts, pericytes, endothelial cells, and B cells. Post-chemotherapy treatment, the proportions of myeloid cells and TILs in OS were declined, while the number of osteoblasts was elevated. Besides, a decrease was observed in CD74, FTL, FTH1, MT1X and MT2A, and an increase in PTN, COL3A1, COL1A1, IGFBP7 and FN1. Meanwhile, EMT, DNA repair, G2M checkpoint, and E2F targets were highly enriched post-chemotherapy. Furthermore, there was a down-regulation in the proportions of CD14 monocytes, Tregs, NK cells and CD1C-/CD141-DCs, while an up-regulation was observed in the proportions of SELENOP macrophages, IL7R macrophages, COL1A1 macrophages, CD1C DCs, CD4+ T cells and CD8+ T cells. Overall, these findings revealed changes in the tumor microenvironment of OS post-chemotherapy treatment, providing a new direction for investigating OS treatment.
Collapse
Affiliation(s)
- Xiao-yu He
- Department of Oncology, Second Hospital of Shanxi Medical University, Taiyuan, Shanxi 030001, China
| | - Liu-yi Que
- Department of Oncology, Second Hospital of Shanxi Medical University, Taiyuan, Shanxi 030001, China
| | - Fan Yang
- Department of Oncology, Second Hospital of Shanxi Medical University, Taiyuan, Shanxi 030001, China
| | - Yi Feng
- Department of Orthopedic Surgery, Second Hospital of Shanxi Medical University, Taiyuan, Shanxi 030001, China
| | - Dong Ren
- Department of Oncology, Second Hospital of Shanxi Medical University, Taiyuan, Shanxi 030001, China
| | - Xiang Song
- Department of Oncology, Second Hospital of Shanxi Medical University, Taiyuan, Shanxi 030001, China
| |
Collapse
|
2
|
Gu Y, Hu Y, Zhang H, Wang S, Xu K, Su J. Single-cell RNA sequencing in osteoarthritis. Cell Prolif 2023; 56:e13517. [PMID: 37317049 PMCID: PMC10693192 DOI: 10.1111/cpr.13517] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/28/2023] [Revised: 04/30/2023] [Accepted: 05/26/2023] [Indexed: 06/16/2023] Open
Abstract
Osteoarthritis is a progressive and heterogeneous joint disease with complex pathogenesis. The various phenotypes associated with each patient suggest that better subgrouping of tissues associated with genotypes in different phases of osteoarthritis may provide new insights into the onset and progression of the disease. Recently, single-cell RNA sequencing was used to describe osteoarthritis pathogenesis on a high-resolution view surpassing traditional technologies. Herein, this review summarizes the microstructural changes in articular cartilage, meniscus, synovium and subchondral bone that are mainly due to crosstalk amongst chondrocytes, osteoblasts, fibroblasts and endothelial cells during osteoarthritis progression. Next, we focus on the promising targets discovered by single-cell RNA sequencing and its potential applications in target drugs and tissue engineering. Additionally, the limited amount of research on the evaluation of bone-related biomaterials is reviewed. Based on the pre-clinical findings, we elaborate on the potential clinical values of single-cell RNA sequencing for the therapeutic strategies of osteoarthritis. Finally, a perspective on the future development of patient-centred medicine for osteoarthritis therapy combining other single-cell multi-omics technologies is discussed. This review will provide new insights into osteoarthritis pathogenesis on a cellular level and the field of applications of single-cell RNA sequencing in personalized therapeutics for osteoarthritis in the future.
Collapse
Affiliation(s)
- Yuyuan Gu
- Institute of Translational MedicineShanghai UniversityShanghaiChina
- Organoid Research CenterShanghai UniversityShanghaiChina
- School of MedicineShanghai UniversityShanghaiChina
| | - Yan Hu
- Institute of Translational MedicineShanghai UniversityShanghaiChina
- Organoid Research CenterShanghai UniversityShanghaiChina
| | - Hao Zhang
- Institute of Translational MedicineShanghai UniversityShanghaiChina
- Organoid Research CenterShanghai UniversityShanghaiChina
| | - Sicheng Wang
- Institute of Translational MedicineShanghai UniversityShanghaiChina
- Organoid Research CenterShanghai UniversityShanghaiChina
- Department of OrthopedicsShanghai Zhongye HospitalShanghaiChina
| | - Ke Xu
- Institute of Translational MedicineShanghai UniversityShanghaiChina
- Organoid Research CenterShanghai UniversityShanghaiChina
- Wenzhou Institute of Shanghai UniversityWenzhouChina
| | - Jiacan Su
- Institute of Translational MedicineShanghai UniversityShanghaiChina
- Organoid Research CenterShanghai UniversityShanghaiChina
| |
Collapse
|
3
|
Yang Y, Huang Z, Yuan M, Rui J, Chen R, Jin T, Sun Y, Deng Z, Shan H, Niu X, Liu W. Genomic and transcriptomic characterization of pre-operative chemotherapy response in patients with osteosarcoma. Sci Rep 2023; 13:20914. [PMID: 38017005 PMCID: PMC10684554 DOI: 10.1038/s41598-023-46857-8] [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: 07/05/2023] [Accepted: 11/06/2023] [Indexed: 11/30/2023] Open
Abstract
Osteosarcoma is a heterogeneous disease with regard to its chemotherapy response and clinical outcomes. This study aims to investigate the genomic and transcriptomic characteristics related to pre-operative chemotherapy response. Samples from 25 osteosarcoma patients were collected to perform both whole exome and transcriptome sequencing. Osteosarcoma had significant amount of chromosomal copy number variants (CNVs). Chemotherapy responders showed the higher chromosomal CNV burden than non-responders (p = 0.0775), but the difference was not significant. The percentage of COSMIC signature 3, associated with homologous recombination repair deficiency, was higher in responders (56%) than in non-responders (45%). Transcriptomic analysis suggested that 11 genes were significantly up-regulated in responders and 18 genes were up-regulated in non-responders. Both GSEA and KEGG enrichment analysis indicted that four pathways related to cardiomyopathy were up-regulated in responders, while neuroactive ligand - receptor interaction was up-regulated in non-responders. Finally, a previously published chemoresistant model was validated using our dataset, with the area under the curve of 0.796 (95% CI, 0.583-1.000). Osteosarcoma had the heterogeneous mutational profile with frequent occurrence of CNVs. Transcriptomic analysis identified several signaling pathways associated with chemotherapy responsiveness to osteosarcoma. Transcriptomic signatures provides a potential research direction for predicting the chemotherapy response.
Collapse
Affiliation(s)
- Yongkun Yang
- Department of Orthopaedic Oncology Surgery, Beijing Jishuitan Hospital, Capital Medical University, No. 31, Xinjiekou East Street, Xicheng District, Beijing, 100035, China
- Fourth Medical College of Peking University, Beijing, 100035, China
| | - Zhen Huang
- Department of Orthopaedic Oncology Surgery, Beijing Jishuitan Hospital, Capital Medical University, No. 31, Xinjiekou East Street, Xicheng District, Beijing, 100035, China
- Fourth Medical College of Peking University, Beijing, 100035, China
| | | | - Jinqiu Rui
- Geneplus-Beijing, Beijing, 102206, China
| | | | - Tao Jin
- Department of Orthopaedic Oncology Surgery, Beijing Jishuitan Hospital, Capital Medical University, No. 31, Xinjiekou East Street, Xicheng District, Beijing, 100035, China
- Fourth Medical College of Peking University, Beijing, 100035, China
| | - Yang Sun
- Department of Orthopaedic Oncology Surgery, Beijing Jishuitan Hospital, Capital Medical University, No. 31, Xinjiekou East Street, Xicheng District, Beijing, 100035, China
- Fourth Medical College of Peking University, Beijing, 100035, China
| | - Zhiping Deng
- Department of Orthopaedic Oncology Surgery, Beijing Jishuitan Hospital, Capital Medical University, No. 31, Xinjiekou East Street, Xicheng District, Beijing, 100035, China
- Fourth Medical College of Peking University, Beijing, 100035, China
| | - Huachao Shan
- Department of Orthopaedic Oncology Surgery, Beijing Jishuitan Hospital, Capital Medical University, No. 31, Xinjiekou East Street, Xicheng District, Beijing, 100035, China
- Fourth Medical College of Peking University, Beijing, 100035, China
| | - Xiaohui Niu
- Department of Orthopaedic Oncology Surgery, Beijing Jishuitan Hospital, Capital Medical University, No. 31, Xinjiekou East Street, Xicheng District, Beijing, 100035, China
- Fourth Medical College of Peking University, Beijing, 100035, China
| | - Weifeng Liu
- Department of Orthopaedic Oncology Surgery, Beijing Jishuitan Hospital, Capital Medical University, No. 31, Xinjiekou East Street, Xicheng District, Beijing, 100035, China.
- Fourth Medical College of Peking University, Beijing, 100035, China.
| |
Collapse
|
4
|
Huang L, Zhong L, Cheng R, Chang L, Qin M, Liang H, Liao Z. Ferroptosis and WDFY4 as novel targets for immunotherapy of lung adenocarcinoma. Aging (Albany NY) 2023; 15:9676-9694. [PMID: 37728413 PMCID: PMC10564425 DOI: 10.18632/aging.205042] [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: 02/22/2023] [Accepted: 08/21/2023] [Indexed: 09/21/2023]
Abstract
BACKGROUND Lung cancer exhibits the world's highest mortality rate among malignant cancers worldwide, thereby presenting a significant global challenge in terms of reducing patient mortality. In the field of oncology, targeted immunotherapy has emerged as a novel therapeutic approach for lung cancer. This study aims to explore potential targets for immunotherapy in lung adenocarcinoma (LUAD) through the analysis of Ferroptosis Index (FPI) and Single Cell RNA-Sequencing (scRNA-seq) data. The findings of this research can potentially offer valuable insights for improving LUAD immunotherapy strategies and informing clinical decision-making. METHODS Firstly, the relationship between survival and ferroptosis in LUAD patients was analyzed by FPI. Subsequently, the association between ferroptosis and infiltration and regulation of immune cells was explored by immune infiltration analysis and correlation statistics. Lastly, the relationship between major infiltrating immune cell populations and related pathways and prognosis of LUAD patients was analyzed by GSEA and GSVA. To screen out core genes regulating infiltration of immune cell populations, scRNA-seq data of cancer and para-cancerous tissues of LUAD patients were downloaded, followed by cell clustering analysis, cell identification of core subpopulations, pseudotime analysis, single-cell GSVA and pathway enrichment analysis, and identification and functional analysis of core regulatory genes. Moreover, the expression levels of core functional genes in LUAD tissue microarray were detected by immunohistochemistry, and its relationship with the prognosis of LUAD patients was verified. Finally, we used lentivirus with WDFY4 to transfect LUAD A549 cells. CCK-8, flow cytometry apoptosis detection, Scratch wound healing assay, Transwell migration assay, Xenograft nude mice model, immunohistochemical analysis and other experimental methods were used to explore the biological effects of WDFY4 on LUAD in vitro and in vivo. RESULTS Survival analysis of FPI values in LUAD patients revealed a positive correlation between smaller FPI values and longer overall survival. Immuno-infiltration analysis and its correlation with FPI values revealed that B cells were most strongly associated with ferroptosis. Ferroptosis of cancer cells could promote infiltration and activation of B cell populations, and LUAD patients with more infiltration of B cell populations had longer long-term survival. scRNA-seq data analysis indicated that the B cell population is one of the major cell populations infiltrated by immune cells in LUAD. During the later phases of B cell differentiation in LUAD, there was a decrease in the expression levels of ACAP1, LINC00926, TLR10, MS4A1, WDFY4, and TRIM22 genes, whereas the expression levels of TMEM59, TP53INP1, and METTL7A genes were elevated. The protein-protein interaction (PPI) network analysis indicated that WDFY4 plays a crucial role in regulating B cell differentiation in LUAD. Immunohistochemical analysis of LUAD tissue microarray revealed a significant downregulation of WDFY4 expression, which was closely related to the occurrence sites of LUAD. Moreover, LUAD patients with a low WDFY4 expression exhibited a poorer prognosis. Additionally, experimental findings demonstrated that the overexpression of WDFY4 could inhibit the proliferation and metastasis of A549 cells while promoting apoptosis. It was also confirmed that WDFY4 could inhibit cancer growth in vivo. CONCLUSIONS The results indicate that promoting infiltration and activation of B cell populations could improve the long-term survival of LUAD patients, thereby offering a potential novel immunotherapeutic approach for LUAD. Besides, the promotion of cancer cell ferroptosis and upregulation of WDFY4 expression have been shown to induce the infiltration and activation of B cell populations. Furthermore, the overexpression of WDFY4 can significantly inhibit the growth of lung adenocarcinoma in vitro and in vivo, highlighting its potential as a target for immunotherapy in LUAD.
Collapse
Affiliation(s)
- Ling Huang
- State Key Laboratory of Trauma, Burns and Combined Injury, Department of Wound Infection and Drug, Daping Hospital, Army Medical University, Chongqing, China
- Hainan Center for Drug and Medical Device Evaluation and Service, Hainan Medical Products Administration, Haikou, China
- School of Hainan Provincial Drug Safety Evaluation Research Center, Hainan Medical University, Haikou, China
| | - Lifan Zhong
- School of Hainan Provincial Drug Safety Evaluation Research Center, Hainan Medical University, Haikou, China
| | - Ruxin Cheng
- Emergency and Trauma College, Hainan Medical University, Haikou, Hainan, China
| | - Limei Chang
- Hainan Center for Drug and Medical Device Evaluation and Service, Hainan Medical Products Administration, Haikou, China
| | - Mingyan Qin
- Hainan Center for Drug and Medical Device Evaluation and Service, Hainan Medical Products Administration, Haikou, China
| | - Huaping Liang
- State Key Laboratory of Trauma, Burns and Combined Injury, Department of Wound Infection and Drug, Daping Hospital, Army Medical University, Chongqing, China
| | - Zhongkai Liao
- Department of Thoracic Surgery, The Second Affiliated Hospital of Hainan Medical University, Haikou, China
| |
Collapse
|
5
|
Liao P, Huang Q, Zhang J, Su Y, Xiao R, Luo S, Wu Z, Zhu L, Li J, Hu Q. How single-cell techniques help us look into lung cancer heterogeneity and immunotherapy. Front Immunol 2023; 14:1238454. [PMID: 37671151 PMCID: PMC10475738 DOI: 10.3389/fimmu.2023.1238454] [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: 06/11/2023] [Accepted: 08/03/2023] [Indexed: 09/07/2023] Open
Abstract
Lung cancer patients tend to have strong intratumoral and intertumoral heterogeneity and complex tumor microenvironment, which are major contributors to the efficacy of and drug resistance to immunotherapy. From a new perspective, single-cell techniques offer an innovative way to look at the intricate cellular interactions between tumors and the immune system and help us gain insights into lung cancer and its response to immunotherapy. This article reviews the application of single-cell techniques in lung cancer, with focuses directed on the heterogeneity of lung cancer and the efficacy of immunotherapy. This review provides both theoretical and experimental information for the future development of immunotherapy and personalized treatment for the management of lung cancer.
Collapse
Affiliation(s)
- Pu Liao
- Department of Pathology, Union Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, Hubei, China
- Key Laboratory of Pulmonary Diseases of Ministry of Health, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China
| | - Qi Huang
- Department of Respiratory and Critical Care Medicine, Hubei Province Clinical Research Center for Major Respiratory Diseases, National Health Commission (NHC) Key Laboratory of Pulmonary Diseases, Union Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, Hubei, China
| | - Jiwei Zhang
- Department of Pathology, Union Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, Hubei, China
- Key Laboratory of Pulmonary Diseases of Ministry of Health, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China
| | - Yuan Su
- Key Laboratory of Pulmonary Diseases of Ministry of Health, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China
- Department of Respiratory and Critical Care Medicine, Hubei Province Clinical Research Center for Major Respiratory Diseases, National Health Commission (NHC) Key Laboratory of Pulmonary Diseases, Union Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, Hubei, China
| | - Rui Xiao
- Key Laboratory of Pulmonary Diseases of Ministry of Health, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China
- Department of Pathophysiology, School of Basic Medicine; Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China
| | - Shengquan Luo
- Key Laboratory of Pulmonary Diseases of Ministry of Health, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China
- Department of Pathophysiology, School of Basic Medicine; Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China
| | - Zengbao Wu
- Department of Neurosurgery, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, Hubei, China
| | - Liping Zhu
- Key Laboratory of Pulmonary Diseases of Ministry of Health, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China
- Department of Pathophysiology, School of Basic Medicine; Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China
| | - Jiansha Li
- Key Laboratory of Pulmonary Diseases of Ministry of Health, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China
- Institute of Pathology, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, Hubei, China
| | - Qinghua Hu
- Key Laboratory of Pulmonary Diseases of Ministry of Health, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China
- Department of Pathophysiology, School of Basic Medicine; Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China
| |
Collapse
|
6
|
Deng H, Chen Y, Liu Y, Liu L, Xu R. Complement C1QC as a potential prognostic marker and therapeutic target in colon carcinoma based on single-cell RNA sequencing and immunohistochemical analysis. Bosn J Basic Med Sci 2022; 22:912-922. [PMID: 35765947 PMCID: PMC9589315 DOI: 10.17305/bjbms.2022.7309] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/02/2022] [Accepted: 06/15/2022] [Indexed: 09/21/2023] Open
Abstract
Immune cell infiltration plays an essential role in the occurrence and development of colon cancer. However, the main tumor-associated immune cell infiltration and its gene regulation in colon cancer still need to be further clarified in order to provide a new perspective for diagnosing and treating this disease. For this study, single-cell RNA sequencing (scRNA-seq) expression profiles and TCGA colon cancer data sets were first acquired from the GEO database. Then, Seurat, Monocle, LIMMA, Clusterprofile, GSVA and GSEABase algorithms were used to systematically examine the data. Potential target drugs corresponding to target genes were analyzed in the Drugbank database and detected by molecular docking. Immunohistochemistry was used to assess the level of C1QC expression in the tissue microarray. Single cell analysis suggested that neutrophil activation might be the critical regulatory pathway in colon cancer and that macrophages were the main cell population involved. Subsequent functional enrichment analysis on differential genes in macrophages suggested that C1QC may be a critical regulatory factor in the occurrence and progression of colon cancer, and was closely related to the survival of patients. According to the drug target prediction, palivizumab is a targeted drug for C1QC, and molecular docking demonstrated that palivizumab binds to C1QC. Additionally, tissue-microarray based immunohistochemical analysis showed that C1QC was highly expressed in colon cancer tissue, and the prognosis of colon cancer patients with high C1QC expression was worse, closely related to age, lymphatic metastasis and the TNM stage (Tumor, Nodes and Metastases). Our findings suggest that C1QC may regulate the macrophages in colon cancer immune infiltration, which is expected to be a potential immunotherapy target for colon cancer, and beneficial for the diagnosis and prognosis of colon cancer patients.
Collapse
Affiliation(s)
- Huiming Deng
- Department of Gastrointestinal Surgery, Huazhong University of Science and Technology Union Shenzhen Hospital, Shenzhen, China
- Molecular Pharmacology Research Center, School of Pharmaceutical Science, Wenzhou Medical University, Wenzhou, China
| | - Yan Chen
- Department of Ultrasound, Hainan General Hospital, Hainan Affiliated Hospital of Hainan Medical University, Haikou, China
| | - Yong Liu
- Department of Gastrointestinal Surgery, Huazhong University of Science and Technology Union Shenzhen Hospital, Shenzhen, China
| | - Li Liu
- Department of Gastrointestinal Surgery, Huazhong University of Science and Technology Union Shenzhen Hospital, Shenzhen, China
| | - Ronghua Xu
- Department of Gastrointestinal Surgery, Huazhong University of Science and Technology Union Shenzhen Hospital, Shenzhen, China
| |
Collapse
|
7
|
Xu N, Wang X, Wang L, Song Y, Zheng X, Hu H. Comprehensive analysis of potential cellular communication networks in advanced osteosarcoma using single-cell RNA sequencing data. Front Genet 2022; 13:1013737. [PMID: 36303551 PMCID: PMC9592772 DOI: 10.3389/fgene.2022.1013737] [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: 08/07/2022] [Accepted: 09/26/2022] [Indexed: 11/23/2022] Open
Abstract
Osteosarcoma (OS) is a common bone cancer in children and adolescents, and metastasis and recurrence are the major causes of poor treatment outcomes. A better understanding of the tumor microenvironment is required to develop an effective treatment for OS. In this paper, a single-cell RNA sequencing dataset was taken to a systematic genetic analysis, and potential signaling pathways linked with osteosarcoma development were explored. Our findings revealed 25 clusters across 11 osteosarcoma tissues, with 11 cell types including “Chondroblastic cells”, “Osteoblastic cells”, “Myeloid cells”, “Pericytes”, “Fibroblasts”, “Proliferating osteoblastic cells”, “Osteoclasts”, “TILs”, “Endothelial cells”, “Mesenchymal stem cells”, and “Myoblasts”. The results of Cell communication analysis showed 17 potential cellular communication networks including “COLLAGEN signaling pathway network”, “CD99 signaling pathway network”, “PTN signaling pathway network”, “MIF signaling pathway network”, “SPP1 signaling pathway network”, “FN1 signaling pathway network”, “LAMININ signaling pathway network”, “FGF signaling pathway network”, “VEGF signaling pathway network”, “GALECTIN signaling pathway network”, “PERIOSTIN signaling pathway network”, “VISFATIN signaling pathway network”, “ITGB2 signaling pathway network”, “NOTCH signaling pathway network”, “IGF signaling pathway network”, “VWF signaling pathway network”, “PDGF signaling pathway network”. This research may provide novel insights into the pathophysiology of OS’s molecular processes.
Collapse
Affiliation(s)
- Ning Xu
- Departments of Orthopedics, Shanghai Eighth People’s Hospital, Shanghai, China
| | - Xiaojing Wang
- Department of Neurology, The First Affiliated Hospital of Anhui Medical University, Hefei, China
| | - Lili Wang
- Departments of Orthopedics, Shanghai Eighth People’s Hospital, Shanghai, China
| | - Yuan Song
- Departments of Orthopedics, Shanghai Eighth People’s Hospital, Shanghai, China
- *Correspondence: Yuan Song, ; Xianyou Zheng, ; Hai Hu,
| | - Xianyou Zheng
- Departments of Orthopedics, Sixth People’s Hospital Affiliated to Shanghai Jiao Tong University, Shanghai, China
- *Correspondence: Yuan Song, ; Xianyou Zheng, ; Hai Hu,
| | - Hai Hu
- Departments of Orthopedics, Shanghai Eighth People’s Hospital, Shanghai, China
- Departments of Orthopedics, Sixth People’s Hospital Affiliated to Shanghai Jiao Tong University, Shanghai, China
- *Correspondence: Yuan Song, ; Xianyou Zheng, ; Hai Hu,
| |
Collapse
|
8
|
Jiang H, Du H, Liu Y, Tian X, Xia J, Yang S. Identification of novel prognostic biomarkers for osteosarcoma: a bioinformatics analysis of differentially expressed genes in the mesenchymal stem cells from single-cell sequencing data set. Transl Cancer Res 2022; 11:3841-3852. [PMID: 36388032 PMCID: PMC9641133 DOI: 10.21037/tcr-22-2370] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/21/2022] [Accepted: 10/19/2022] [Indexed: 11/25/2022]
Abstract
BACKGROUND Mesenchymal stem cells (MSCs) play a crucial role in osteosarcoma (OS) growth and progression. This study conducted a bioinformatics analysis of a single-cell ribonucleic acid sequencing data set and explored the MSC-specific differentially expressed genes (DEGs) in advanced OS. METHODS MSC-specific DEGs from GSE152048 was extracted using Seurat R package. These DEGs were then subjected to the functional analysis, and several key genes were further identified and underwent a prognosis analysis. RESULTS A total of 234 upregulated and 280 downregulated DEGs were identified between the MSCs and other cells, and a total of 188 upregulated and 158 downregulated DEGs were identified between the MSCs and osteoblastic cells. The Gene Ontology (GO) functional analysis showed that the specific DEGs between the MSCs and osteoblastic cells were enriched in GO terms such as "collagen catabolic process", "positive regulation of pathway-restricted SMAD protein phosphorylation", "osteoblast differentiation", "regulation of release of cytochrome c from mitochondria" and "interleukin-1 production". The specific DEGs between the MSCs and osteoblastic cells were subjected to a protein-protein interaction network analysis. Further, a survival analysis of 20 genes with combined scores >0.94 revealed that the low expression of ANXA1 (annexin A1) and TPM1 (tropomyosin 1) was associated with the shorter overall survival of OS patients, while the high expression of FDPS (farnesyl pyrophosphate synthase), IFITM5 (interferon-induced transmembrane protein 5), FKBP11 (FKBP prolyl isomerase 11), SP7, and SQLE (squalene epoxidase) was associated with the shorter overall survival of OS patients. In a further analysis, we compared the expression of ANXA1, FDPS, IFITM5, FKBP11, SP7, SQLE, and TPM1 between the MSCs and high-grade OS cells. Further validation studies using the GSE42352 data set revealed that ANXA1, FKBP11, SP7, and TPM1 were more upregulated in the MSCs than the high-grade OS cells, while FDPS, IFITM5, and SQLE were more downregulated in the MSCs than the high-grade OS cells. CONCLUSIONS Our bioinformatics analysis revealed 7 hub genes derived from the specific DEGs between the MSCs and osteoblastic cells. The 7 hub genes may serve as potential prognostic biomarkers for patients with OS.
Collapse
Affiliation(s)
- Haoli Jiang
- Department of Orthopaedics, the Third People’s Hospital of Shenzhen, Shenzhen, China
| | - Haoyuan Du
- Department of Orthopaedics, Shenzhen People’s Hospital (The Second Clinical Medical College, Jinan University & the First Affiliated Hospital, Southern University of Science and Technology), Shenzhen, China
| | - Yingnan Liu
- Department of Hand and Micro-Vasscular Surgery, Shenzhen People’s Hospital (The Second Clinical Medical College, Jinan University & the First Affiliated Hospital, Southern University of Science and Technology), Shenzhen, China
| | - Xiao Tian
- Department of Orthopaedics, The Affiliated Huaian No.1 People’s Hospital of Nanjing Medical University, Huaian, China
| | - Jinquan Xia
- Department of Orthopaedics, the Third People’s Hospital of Shenzhen, Shenzhen, China
| | - Shucai Yang
- Department of Clinical Laboratory, Pingshan District People’s Hospital of Shenzhen (Pingshan General Hospital of Southern Medical University), Shenzhen, China
| |
Collapse
|
9
|
Liu X, Xu X, Wu Z, Shan Q, Wang Z, Wu Z, Ding X, Huang W, Wang Z. Integrated single-cell RNA-seq analysis identifies immune heterogeneity associated with KRAS/TP53 mutation status and tumor-sideness in colorectal cancers. Front Immunol 2022; 13:961350. [PMID: 36172359 PMCID: PMC9510840 DOI: 10.3389/fimmu.2022.961350] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/04/2022] [Accepted: 08/23/2022] [Indexed: 11/13/2022] Open
Abstract
BackgroundThe main objective of this study was to analyze the effects of KRAS/TP53 mutation status and tumor sideness on the immune microenvironment of colorectal cancer using integrated scRNA-seq data.MethodsA total of 78 scRNA-seq datasets, comprising 42 treatment-naive colorectal tumors, 13 tumor adjacent tissues and 23 normal mucosa tissues were included. Standardized Seurat procedures were applied to identify cellular components with canonical cell marks. The batch-effect was assessed and corrected using harmony algorithm. The scMetabolism algorithm was used for single-cell metabolic analysis. The results and clinical significance were further validated using immunofluorescent-staining and TCGA-COAD datasets. Immune-infiltration scores of bulk-RNA-seq data were estimated using ssGSEA. The presto-wilcoxauc algorithm was used to identify differentially enriched genes or pathways across different subgroups. Two-sided p-value less than 0.05 was considered statistically significant.ResultsWe refined the landscape of functional immune cell subtypes, especially T cells and myeloid cells, across normal mucosa, tumor adjacent and tumor tissue. The existence and function of two states of exhausted CD8+ T (Tex) subtypes in colorectal cancer, and FOLR2+ LYVE1+ macrophages indicating unfavorable prognosis in colorectal cancer were identified and validated. The diverse tumor mutation status reshaped the immune cell function and immune checkpoint ligands/receptors (ICLs/ICRs) expression pattern. Importantly, the KRAS/TP53 dual mutations significantly reduced the major energy metabolic functions in immune cells, and promoted the cell-to-cell communications towards immunosuppression in colorectal cancers. The results revealed LAG3, CD24-SIGLEC10 and HBEGF-CD9 pathways as potential therapeutic targets for dual mutant colorectal cancers.ConclusionsWe revealed that the immune microenvironment underwent a gradual remodeling with an enrichment of immunosuppressive myeloid cells from normal mucosa to tumor regions in colorectal cancers. Moreover, we revealed the metabolic heterogeneity of tumor-infiltrating immune cells and suggested that the KRAS/TP53 dual mutation may impair antitumor immunity by reducing T and myeloid cell energy metabolism and reshaping cellular interactions toward immunosuppression.
Collapse
Affiliation(s)
- Xiaoyu Liu
- Department of Radiology, Ruijin Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, China
| | - Xu Xu
- Department of Pediatrics, Ruijin Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, China
| | - Zhuozhuo Wu
- Department of Radiology, Ruijin Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, China
| | - Qungang Shan
- Department of Radiology, Ruijin Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, China
| | - Ziyin Wang
- Department of Radiology, Ruijin Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, China
| | - Zhiyuan Wu
- Department of Radiology, Ruijin Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, China
| | - Xiaoyi Ding
- Department of Radiology, Ruijin Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, China
| | - Wei Huang
- Department of Radiology, Ruijin Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, China
- *Correspondence: Zhongmin Wang, ; Wei Huang,
| | - Zhongmin Wang
- Department of Radiology, Ruijin Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, China
- Department of Radiology, Ruijin Hospital Luwan Branch, Shanghai Jiao Tong University School of Medicine, Shanghai, China
- *Correspondence: Zhongmin Wang, ; Wei Huang,
| |
Collapse
|
10
|
Integrated Single-Cell RNA-Sequencing Analysis of Gastric Cancer Identifies FABP1 as a Novel Prognostic Biomarker. JOURNAL OF ONCOLOGY 2022; 2022:4761403. [PMID: 35799608 PMCID: PMC9256400 DOI: 10.1155/2022/4761403] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 03/24/2022] [Revised: 05/03/2022] [Accepted: 05/31/2022] [Indexed: 12/25/2022]
Abstract
Gastric cancer (GC) is usually diagnosed in an advanced stage at the first visit due to the atypical clinical symptoms. The low surgical resection rate and chemotherapy sensitivity result in dismal survival. Therefore, it is urgent to develop novel biomarkers with high sensitivity and specificity to accurately assess the prognosis of GC patients. In the present study, 3385 differentially expressed genes (DEGs) were obtained from the single-cell RNA sequencing data of GC specimens. Using the unsupervised dimensionality reduction, we further found 3 subsets of cells including gastric cells, plasmacytoid dendritic cells, and memory T cells. Based on the cell clustering, we explored the key regulatory genes for GC progression by pseudo-time analysis and functional enrichment analysis. According to the results, the significant differentially expressed fatty acid-binding protein 1 (FABP1) verified by pseudo-time analysis was identified as the hub gene of GC progression. FABP1 was shown to be closely related to the long-term survival and the age at diagnosis of patients with GC in analysis based on the TCGA (The Cancer Genome Atlas) database. To further verify the role of FABP1 in GC, we performed immunohistochemical (IHC) analysis using the GC tissue microarray and found that the expression level of FABP1 was higher in GC tissues than in the adjacent tissues. Moreover, GC patients with higher expression of FABP1 had a worse clinical outcome. In summary, our study revealed that FABP1 is a potential effective biomarker for the prognosis of GC, and high expression of FABP1 predicts unsatisfactory survival.
Collapse
|