1
|
Zeng X, Wang Y, Dai M, Li W, Huang Q, Qin L, Li Y, Yan Y, Xue X, Yi F, Li W, He L, Liu Q, Qi L. Single-cell transcriptomics dissects the transcriptome alterations of hematopoietic stem cells in myelodysplastic neoplasms. J Transl Med 2024; 22:359. [PMID: 38632656 PMCID: PMC11022353 DOI: 10.1186/s12967-024-05165-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/26/2024] [Accepted: 04/04/2024] [Indexed: 04/19/2024] Open
Abstract
BACKGROUND Myelodysplastic neoplasms (MDS) are myeloid neoplasms characterized by disordered differentiation of hematopoietic stem cells and a predisposition to acute myeloid leukemia (AML). The underline pathogenesis remains unclear. METHODS In this study, the trajectory of differentiation and mechanisms of leukemic transformation were explored through bioinformatics analysis of single-cell RNA-Seq data from hematopoietic stem and progenitor cells (HSPCs) in MDS patients. RESULTS Among the HSPC clusters, the proportion of common myeloid progenitor (CMP) was the main cell cluster in the patients with excess blasts (EB)/ secondary AML. Cell cycle analysis indicated the CMP of MDS patients were in an active proliferative state. The genes involved in the cell proliferation, such as MAML3 and PLCB1, were up-regulated in MDS CMP. Further validation analysis indicated that the expression levels of MAML3 and PLCB1 in patients with MDS-EB were significantly higher than those without EB. Patients with high expression of PLCB1 had a higher risk of transformation to AML. PLCB1 inhibitor can suppress proliferation, induce cell cycle arrest, and activate apoptosis of leukemic cells in vitro. CONCLUSION This study revealed the transcriptomic change of HSPCs in MDS patients along the pseudotime and indicated that PLCB1 plays a key role in the transformation of MDS into leukemia.
Collapse
Affiliation(s)
- Xiangzong Zeng
- Department of Hematology, Affiliated Qingyuan Hospital, Guangzhou Medical University, Qingyuan People's Hospital, Qingyuan, 511518, China
- Division of Gastroenterology, Institute of Digestive Disease, Affiliated Qingyuan Hospital, Guangzhou Medical University, Qingyuan People's Hospital, Qingyuan, 511518, China
| | - Yichen Wang
- Division of Gastroenterology, Institute of Digestive Disease, Affiliated Qingyuan Hospital, Guangzhou Medical University, Qingyuan People's Hospital, Qingyuan, 511518, China
| | - Min Dai
- Department of Hematology, Nanfang Hospital, Southern Medical University, Guangzhou, 510515, China
| | - Wei Li
- Division of Gastroenterology, Institute of Digestive Disease, Affiliated Qingyuan Hospital, Guangzhou Medical University, Qingyuan People's Hospital, Qingyuan, 511518, China
| | - Qingtian Huang
- Division of Gastroenterology, Institute of Digestive Disease, Affiliated Qingyuan Hospital, Guangzhou Medical University, Qingyuan People's Hospital, Qingyuan, 511518, China
| | - Lingsha Qin
- Division of Gastroenterology, Institute of Digestive Disease, Affiliated Qingyuan Hospital, Guangzhou Medical University, Qingyuan People's Hospital, Qingyuan, 511518, China
| | - Yuquan Li
- Department of Hematology, Affiliated Qingyuan Hospital, Guangzhou Medical University, Qingyuan People's Hospital, Qingyuan, 511518, China
| | - Yanwen Yan
- Department of Hematology, Affiliated Qingyuan Hospital, Guangzhou Medical University, Qingyuan People's Hospital, Qingyuan, 511518, China
| | - Xiangjun Xue
- Department of Hematology, Affiliated Qingyuan Hospital, Guangzhou Medical University, Qingyuan People's Hospital, Qingyuan, 511518, China
| | - Fang Yi
- Department of Hematology, Affiliated Qingyuan Hospital, Guangzhou Medical University, Qingyuan People's Hospital, Qingyuan, 511518, China
| | - Wenhao Li
- Department of Hematology, Affiliated Qingyuan Hospital, Guangzhou Medical University, Qingyuan People's Hospital, Qingyuan, 511518, China
| | - Langyu He
- Department of Blood Transfusion, Affiliated Qingyuan Hospital, Guangzhou Medical University, Qingyuan People's Hospital, Qingyuan, 511518, China
| | - Qifa Liu
- Department of Hematology, Nanfang Hospital, Southern Medical University, Guangzhou, 510515, China.
| | - Ling Qi
- Division of Gastroenterology, Institute of Digestive Disease, Affiliated Qingyuan Hospital, Guangzhou Medical University, Qingyuan People's Hospital, Qingyuan, 511518, China.
| |
Collapse
|
2
|
Xie Z, Huang J, Li Y, Zhu Q, Huang X, Chen J, Wei C, Luo S, Yang S, Gao J. Single-cell RNA sequencing revealed potential targets for immunotherapy studies in hepatocellular carcinoma. Sci Rep 2023; 13:18799. [PMID: 37914817 PMCID: PMC10620237 DOI: 10.1038/s41598-023-46132-w] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/28/2023] [Accepted: 10/27/2023] [Indexed: 11/03/2023] Open
Abstract
Hepatocellular carcinoma (HCC) is a solid tumor prone to chemotherapy resistance, and combined immunotherapy is expected to bring a breakthrough in HCC treatment. However, the tumor and tumor microenvironment (TME) of HCC is highly complex and heterogeneous, and there are still many unknowns regarding tumor cell stemness and metabolic reprogramming in HCC. In this study, we combined single-cell RNA sequencing data from 27 HCC tumor tissues and 4 adjacent non-tumor tissues, and bulk RNA sequencing data from 374 of the Cancer Genome Atlas (TCGA)-liver hepatocellular carcinoma (LIHC) samples to construct a global single-cell landscape atlas of HCC. We analyzed the enrichment of signaling pathways of different cells in HCC, and identified the developmental trajectories of cell subpopulations in the TME using pseudotime analysis. Subsequently, we performed transcription factors regulating different subpopulations and gene regulatory network analysis, respectively. In addition, we estimated the stemness index of tumor cells and analyzed the intercellular communication between tumors and key TME cell clusters. We identified novel HCC cell clusters that specifically express HP (HCC_HP), which may lead to higher tumor differentiation and tumor heterogeneity. In addition, we found that the HP gene expression-positive neutrophil cluster (Neu_AIF1) had extensive and strong intercellular communication with HCC cells, tumor endothelial cells (TEC) and cancer-associated fibroblasts (CAF), suggesting that clearance of this new cluster may inhibit HCC progression. Furthermore, ErbB signaling pathway and GnRH signaling pathway were found to be upregulated in almost all HCC tumor-associated stromal cells and immune cells, except NKT cells. Moreover, the high intercellular communication between HCC and HSPA1-positive TME cells suggests that the immune microenvironment may be reprogrammed. In summary, our present study depicted the single-cell landscape heterogeneity of human HCC, identified new cell clusters in tumor cells and neutrophils with potential implications for immunotherapy research, discovered complex intercellular communication between tumor cells and TME cells.
Collapse
Affiliation(s)
- Zhouhua Xie
- Laboratory of Infectious Disease, HIV/AIDS Clinical Treatment Center of Guangxi (Nanning) and The Fourth People's Hospital of Nanning, Nanning, 530023, Guangxi Zhuang Autonomous Region, China
- Department of Tuberculosis, HIV/AIDS Clinical Treatment Center of Guangxi (Nanning) and The Fourth People's Hospital of Nanning, Nanning, 530023, China
| | - Jinping Huang
- Laboratory of Infectious Disease, HIV/AIDS Clinical Treatment Center of Guangxi (Nanning) and The Fourth People's Hospital of Nanning, Nanning, 530023, Guangxi Zhuang Autonomous Region, China
- Department of Infectious Diseases, HIV/AIDS Clinical Treatment Center of Guangxi (Nanning) and The Fourth People's Hospital of Nanning, Nanning, 530023, China
| | - Yanjun Li
- Laboratory of Infectious Disease, HIV/AIDS Clinical Treatment Center of Guangxi (Nanning) and The Fourth People's Hospital of Nanning, Nanning, 530023, Guangxi Zhuang Autonomous Region, China
- Department of Infectious Diseases, HIV/AIDS Clinical Treatment Center of Guangxi (Nanning) and The Fourth People's Hospital of Nanning, Nanning, 530023, China
| | - Qingdong Zhu
- Department of Tuberculosis, HIV/AIDS Clinical Treatment Center of Guangxi (Nanning) and The Fourth People's Hospital of Nanning, Nanning, 530023, China
| | - Xianzhen Huang
- Department of Tuberculosis, HIV/AIDS Clinical Treatment Center of Guangxi (Nanning) and The Fourth People's Hospital of Nanning, Nanning, 530023, China
| | - Jieling Chen
- Laboratory of Infectious Disease, HIV/AIDS Clinical Treatment Center of Guangxi (Nanning) and The Fourth People's Hospital of Nanning, Nanning, 530023, Guangxi Zhuang Autonomous Region, China
| | - Cailing Wei
- Laboratory of Infectious Disease, HIV/AIDS Clinical Treatment Center of Guangxi (Nanning) and The Fourth People's Hospital of Nanning, Nanning, 530023, Guangxi Zhuang Autonomous Region, China
| | - Shunda Luo
- Department of Clinical Laboratory, HIV/AIDS Clinical Treatment Center of Guangxi (Nanning) and The Fourth People's Hospital of Nanning, Nanning, 530023, China
| | - Shixiong Yang
- Laboratory of Infectious Disease, HIV/AIDS Clinical Treatment Center of Guangxi (Nanning) and The Fourth People's Hospital of Nanning, Nanning, 530023, Guangxi Zhuang Autonomous Region, China.
- Administrative Office, HIV/AIDS Clinical Treatment Center of Guangxi (Nanning) and The Fourth People's Hospital of Nanning, Nanning, 530023, China.
| | - Jiamin Gao
- Laboratory of Infectious Disease, HIV/AIDS Clinical Treatment Center of Guangxi (Nanning) and The Fourth People's Hospital of Nanning, Nanning, 530023, Guangxi Zhuang Autonomous Region, China.
- Department of Infectious Diseases, HIV/AIDS Clinical Treatment Center of Guangxi (Nanning) and The Fourth People's Hospital of Nanning, Nanning, 530023, China.
| |
Collapse
|
3
|
Li H, Qu L, Yang Y, Zhang H, Li X, Zhang X. Single-cell Transcriptomic Architecture Unraveling the Complexity of Tumor Heterogeneity in Distal Cholangiocarcinoma. Cell Mol Gastroenterol Hepatol 2022; 13:1592-1609.e9. [PMID: 35219893 PMCID: PMC9043309 DOI: 10.1016/j.jcmgh.2022.02.014] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 11/16/2021] [Revised: 02/17/2022] [Accepted: 02/17/2022] [Indexed: 01/03/2023]
Abstract
BACKGROUND & AIMS Distal cholangiocarcinoma (dCCA) are a group of epithelial cell malignancies that occurs at the distal common bile duct, and account for approximately 40% of all cholangiocarcinoma cases. dCCA remains a highly lethal disease as it typically features remarkable cellular heterogeneity. A comprehensive exploration of cellular diversity and the tumor microenvironment is essential to depict the mechanisms driving dCCA progression. METHODS Single-cell RNA sequencing was used here to dissect the heterogeneity landscape and tumor microenvironment composition of human dCCAs. Seven human dCCAs and adjacent normal bile duct samples were included in the current study for single-cell RNA sequencing and subsequent validation approaches. Additionally, the results of the analyses were compared with bulk transcriptomic datasets from extrahepatic cholangiocarcinoma and single-cell RNA data from intrahepatic cholangiocarcinoma. RESULTS We sequenced a total of 49,717 single cells derived from human dCCAs and adjacent tissues, identifying 11 distinct cell types. Malignant cells displayed remarkable inter- and intra-tumor heterogeneity with 5 distinct subsets were defined in tumor samples. The malignant cells displayed variable degree of aneuploidy, which can be classified into low- and high-copy number variation groups based on either amplification or deletion of chr17q12 - chr17q21.2. Additionally, we identified 4 distinct T lymphocytes subsets, of which cytotoxic CD8+ T cells predominated as effectors in tumor tissues, whereas tumor infiltrating FOXP3+ CD4+ regulatory T cells exhibited highly immunosuppressive characteristics. CONCLUSION Our single-cell transcriptomic dataset depicts the inter- and intra-tumor heterogeneity of human dCCAs at the expression level.
Collapse
Affiliation(s)
- Hongguang Li
- Department of Hepatobiliary Surgery, Shandong Provincial Hospital, Cheeloo College of Medicine, Shandong University, Jinan, Shandong, China
| | - Lingxin Qu
- Department of Physiology and Pathophysiology, School of Basic Medical Sciences, Cheeloo College of Medicine, Shandong University, Jinan, Shandong, China
| | - Yongheng Yang
- Department of Physiology and Pathophysiology, School of Basic Medical Sciences, Cheeloo College of Medicine, Shandong University, Jinan, Shandong, China
| | - Haibin Zhang
- Department of Physiology and Pathophysiology, School of Basic Medical Sciences, Cheeloo College of Medicine, Shandong University, Jinan, Shandong, China
| | - Xuexin Li
- Division of Genome Biology, Department of Medical Biochemistry and Biophysics, Karolinska Institutet, Stockholm, Sweden
| | - Xiaolu Zhang
- Department of Physiology and Pathophysiology, School of Basic Medical Sciences, Cheeloo College of Medicine, Shandong University, Jinan, Shandong, China,Correspondence Address correspondence to: Xiaolu Zhang, Department of Physiology and Pathophysiology, School of Basic Medical Sciences, Cheeloo College of Medicine, Shandong University, Jinan, Shandong, 250012, China. tel: (+86) 17862933917; fax: (+86) 53188565657.
| |
Collapse
|
4
|
Chen Y, Sun Y, Luo Z, Lin J, Qi B, Kang X, Ying C, Guo C, Yao M, Chen X, Wang Y, Wang Q, Chen J, Chen S. Potential Mechanism Underlying Exercise Upregulated Circulating Blood Exosome miR-215-5p to Prevent Necroptosis of Neuronal Cells and a Model for Early Diagnosis of Alzheimer's Disease. Front Aging Neurosci 2022; 14:860364. [PMID: 35615585 PMCID: PMC9126031 DOI: 10.3389/fnagi.2022.860364] [Citation(s) in RCA: 18] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/22/2022] [Accepted: 03/21/2022] [Indexed: 02/05/2023] Open
Abstract
Exercise is crucial for preventing Alzheimer's disease (AD), although the exact underlying mechanism remains unclear. The construction of an accurate AD risk prediction model is beneficial as it can provide a theoretical basis for preventive exercise prescription. In recent years, necroptosis has been confirmed as an important manifestation of AD, and exercise is known to inhibit necroptosis of neuronal cells. In this study, we extracted 67 necroptosis-related genes and 32 necroptosis-related lncRNAs and screened for key predictive AD risk genes through a random forest analysis. Based on the neural network Prediction model, we constructed a new logistic regression-based AD risk prediction model in order to provide a visual basis for the formulation of exercise prescription. The prediction model had an area under the curve (AUC) value of 0.979, indicative of strong predictive power and a robust clinical application prospect. In the exercise group, the expression of exosomal miR-215-5p was found to be upregulated; miR-215-5p could potentially inhibit the expressions of IDH1, BCL2L11, and SIRT1. The single-cell SCENIC assay was used to identify key transcriptional regulators in skeletal muscle. Among them, CEBPB and GATA6 were identified as putative transcriptional regulators of miR-215. After "skeletal muscle removal of load," the expressions of CEBPB and GATA6 increased substantially, which in turn led to the elevation of miR-215 expression, thereby suggesting a putative mechanism for negative feedback regulation of exosomal homeostasis.
Collapse
Affiliation(s)
- Yisheng Chen
- Department of Sports Medicine, Huashan Hospital, Fudan University, Shanghai, China
| | - Yaying Sun
- Department of Sports Medicine, Huashan Hospital, Fudan University, Shanghai, China
| | - Zhiwen Luo
- Department of Sports Medicine, Huashan Hospital, Fudan University, Shanghai, China
| | - Jinrong Lin
- Department of Sports Medicine, Huashan Hospital, Fudan University, Shanghai, China
| | - Beijie Qi
- Department of Sports Medicine, Huashan Hospital, Fudan University, Shanghai, China
| | - Xueran Kang
- Shanghai Jiao Tong University School of Medicine, Shanghai Jiao Tong University, Shanghai, China
| | - Chenting Ying
- Department of Orthopaedics, The Second Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, China
| | - Chenyang Guo
- Department of Orthopedics, Shanghai General Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai Jiao Tong University, Shanghai, China
| | - Mengxuan Yao
- Department of Orthopaedic Surgery, The Third Hospital of Hebei Medical University, Shijiazhuang, China
- Key Laboratory of Biomechanics of Hebei Province, Orthopaedic Research Institution of Hebei Province, Shijiazhuang, China
| | | | - Yi Wang
- Huashan Hospital, Fudan University, Shanghai, China
| | - Qian Wang
- Department of Central Laboratory, The Affiliated Taian City Central Hospital of Qingdao University, Tai’an, China
- *Correspondence: Qian Wang,
| | - Jiwu Chen
- Department of Orthopedics, Shanghai General Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai Jiao Tong University, Shanghai, China
- Jiwu Chen,
| | - Shiyi Chen
- Department of Sports Medicine, Huashan Hospital, Fudan University, Shanghai, China
- Shiyi Chen,
| |
Collapse
|