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Cheng S, Li S, Yang P, Wang R, Zhou P, Li J. Dissecting the tumour immune microenvironment in merkel cell carcinoma based on a machine learning framework. ARTIFICIAL CELLS, NANOMEDICINE, AND BIOTECHNOLOGY 2023; 51:397-407. [PMID: 37676035 DOI: 10.1080/21691401.2023.2244998] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/11/2023] [Revised: 07/13/2023] [Accepted: 08/02/2023] [Indexed: 09/08/2023]
Abstract
Merkel cell carcinoma (MCC) is a primary cutaneous neoplasm of neuroendocrine carcinoma of the skin, which is characterized by molecular heterogeneity with diverse tumour microenvironment (TME). However, we are still lack knowledge of the cellular states and ecosystems in MCC. Here, we systematically identified and characterized the landscape of cellular states and ecotypes in MCC based on a machine learning framework. We obtained 30 distinct cellular states from 9 immune cell types and investigated the B cell, CD8 T cell, fibroblast, and monocytes/macrophage cellular states in detail. The functional profiling of cellular states were investigated and found the genes highly expressed in cellular states were significantly enriched in immune- and cancer hallmark-related pathways. In addition, four ecotypes were further identified which were with different patient compositions. Transcriptional regulation analysis revealed the critical transcription factors (i.e. E2F1, E2F3 and E2F7), which play important roles in regulating the TME of MCC. In summary, the findings of this study may provide rich knowledge to understand the intrinsic subtypes of MCCs and the pathways involved in distinct subtype oncogenesis, and will further advance the knowledge in developing a specific therapeutic strategy for these MCC subtypes.
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Affiliation(s)
- Shaowen Cheng
- Department of Wound Repair, The First Affiliated Hospital of Hainan Medical University, Haikou, China
| | - Si Li
- College of Biomedical Information and Engineering, Hainan Medical University, Haikou, China
| | - Ping Yang
- Department of Radiotherapy, The First Affiliated Hospital of Hainan Medical University, Haikou, China
| | - Rong Wang
- Department of Wound Repair, The First Affiliated Hospital of Hainan Medical University, Haikou, China
| | - Ping Zhou
- Department of Radiotherapy, The First Affiliated Hospital of Hainan Medical University, Haikou, China
| | - Jingquan Li
- The First Affiliated Hospital of Hainan Medical University, Haikou, China
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Wang L, Wu Z, Xia Y, Lu X, Li J, Fan L, Qiao C, Qiu H, Gu D, Xu W, Li J, Jin H. Single-cell profiling-guided combination therapy of c-Fos and histone deacetylase inhibitors in diffuse large B-cell lymphoma. Clin Transl Med 2022; 12:e798. [PMID: 35522945 PMCID: PMC9076017 DOI: 10.1002/ctm2.798] [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] [Subscribe] [Scholar Register] [Received: 11/06/2021] [Revised: 03/15/2022] [Accepted: 03/18/2022] [Indexed: 12/31/2022] Open
Abstract
Background Diffuse large B‐cell lymphoma (DLBCL) is the most common subtype of non‐Hodgkin lymphoma. Histone deacetylase inhibitors (HDACis) have been widely applied in multiple tumours, but the expected efficacy was not observed in DLBCL. Therefore, this study is aimed to explore superior HDACis and optimise a relative combinational therapeutic strategy. Methods The antitumour effects of the drug were evaluated by Cell Counting Kit‐8 (CCK‐8) assay and apoptosis analysis. Single‐cell RNA sequencing (scRNA‐Seq) was used to analyse the intratumoural heterogeneity of DLBCL cells. Whole‐exome sequencing and RNA sequencing were performed to analyse the genetic and transcriptional features. Western blotting, qRT–PCR, protein array, immunohistochemistry, and chromatin immunoprecipitation assays were applied to explore the involved pathways. The antitumour effects of the compounds were assessed using subcutaneous xenograft tumour models. Results LAQ824 was screened and confirmed to kill DLBCL cells effectively. Using scRNA‐Seq, we characterised the heterogeneity of DLBCL cells under different drug pressures, and c‐Fos was identified as a critical factor in the survival of residual tumour cells. Moreover, we demonstrated that combinatorial treatment with LAQ824 and a c‐Fos inhibitor more potently inhibited tumour cells both in vitro and in vivo. Conclusion Altogether, we found an HDACi, LAQ824, with high efficacy in DLBCL and provided a promising HDACi‐based combination therapy strategy.
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Affiliation(s)
- Luqiao Wang
- Department of Hematology, Pukou CLL Center, the First Affiliated Hospital of Nanjing Medical University, Jiangsu Province Hospital, Nanjing, China.,Key Laboratory of Hematology of Nanjing Medical University, Nanjing Medical University, Nanjing, China.,Jiangsu Key Lab of Cancer Biomarkers, Prevention and Treatment, Collaborative Innovation Center for Personalized Cancer Medicine, Nanjing Medical University, Nanjing, China
| | - Zijuan Wu
- Department of Hematology, Pukou CLL Center, the First Affiliated Hospital of Nanjing Medical University, Jiangsu Province Hospital, Nanjing, China.,Key Laboratory of Hematology of Nanjing Medical University, Nanjing Medical University, Nanjing, China.,Jiangsu Key Lab of Cancer Biomarkers, Prevention and Treatment, Collaborative Innovation Center for Personalized Cancer Medicine, Nanjing Medical University, Nanjing, China
| | - Yi Xia
- Department of Hematology, Pukou CLL Center, the First Affiliated Hospital of Nanjing Medical University, Jiangsu Province Hospital, Nanjing, China.,Key Laboratory of Hematology of Nanjing Medical University, Nanjing Medical University, Nanjing, China.,Jiangsu Key Lab of Cancer Biomarkers, Prevention and Treatment, Collaborative Innovation Center for Personalized Cancer Medicine, Nanjing Medical University, Nanjing, China
| | - Xueying Lu
- Department of Hematology, Pukou CLL Center, the First Affiliated Hospital of Nanjing Medical University, Jiangsu Province Hospital, Nanjing, China.,Key Laboratory of Hematology of Nanjing Medical University, Nanjing Medical University, Nanjing, China.,Jiangsu Key Lab of Cancer Biomarkers, Prevention and Treatment, Collaborative Innovation Center for Personalized Cancer Medicine, Nanjing Medical University, Nanjing, China
| | - Ji Li
- Singleron Biotechnologies, Nanjing, China
| | - Lei Fan
- Department of Hematology, Pukou CLL Center, the First Affiliated Hospital of Nanjing Medical University, Jiangsu Province Hospital, Nanjing, China.,Key Laboratory of Hematology of Nanjing Medical University, Nanjing Medical University, Nanjing, China.,Jiangsu Key Lab of Cancer Biomarkers, Prevention and Treatment, Collaborative Innovation Center for Personalized Cancer Medicine, Nanjing Medical University, Nanjing, China
| | - Chun Qiao
- Department of Hematology, Pukou CLL Center, the First Affiliated Hospital of Nanjing Medical University, Jiangsu Province Hospital, Nanjing, China.,Key Laboratory of Hematology of Nanjing Medical University, Nanjing Medical University, Nanjing, China.,Jiangsu Key Lab of Cancer Biomarkers, Prevention and Treatment, Collaborative Innovation Center for Personalized Cancer Medicine, Nanjing Medical University, Nanjing, China
| | - Hairong Qiu
- Department of Hematology, Pukou CLL Center, the First Affiliated Hospital of Nanjing Medical University, Jiangsu Province Hospital, Nanjing, China.,Key Laboratory of Hematology of Nanjing Medical University, Nanjing Medical University, Nanjing, China.,Jiangsu Key Lab of Cancer Biomarkers, Prevention and Treatment, Collaborative Innovation Center for Personalized Cancer Medicine, Nanjing Medical University, Nanjing, China
| | - Danling Gu
- Department of Hematology, Pukou CLL Center, the First Affiliated Hospital of Nanjing Medical University, Jiangsu Province Hospital, Nanjing, China.,Key Laboratory of Hematology of Nanjing Medical University, Nanjing Medical University, Nanjing, China.,Jiangsu Key Lab of Cancer Biomarkers, Prevention and Treatment, Collaborative Innovation Center for Personalized Cancer Medicine, Nanjing Medical University, Nanjing, China
| | - Wei Xu
- Department of Hematology, Pukou CLL Center, the First Affiliated Hospital of Nanjing Medical University, Jiangsu Province Hospital, Nanjing, China.,Key Laboratory of Hematology of Nanjing Medical University, Nanjing Medical University, Nanjing, China.,Jiangsu Key Lab of Cancer Biomarkers, Prevention and Treatment, Collaborative Innovation Center for Personalized Cancer Medicine, Nanjing Medical University, Nanjing, China
| | - Jianyong Li
- Department of Hematology, Pukou CLL Center, the First Affiliated Hospital of Nanjing Medical University, Jiangsu Province Hospital, Nanjing, China.,Key Laboratory of Hematology of Nanjing Medical University, Nanjing Medical University, Nanjing, China.,Jiangsu Key Lab of Cancer Biomarkers, Prevention and Treatment, Collaborative Innovation Center for Personalized Cancer Medicine, Nanjing Medical University, Nanjing, China.,National Clinical Research Center for Hematologic Diseases, the First Affiliated Hospital of Soochow University, Suzhou, China
| | - Hui Jin
- Department of Hematology, Pukou CLL Center, the First Affiliated Hospital of Nanjing Medical University, Jiangsu Province Hospital, Nanjing, China.,Key Laboratory of Hematology of Nanjing Medical University, Nanjing Medical University, Nanjing, China.,Jiangsu Key Lab of Cancer Biomarkers, Prevention and Treatment, Collaborative Innovation Center for Personalized Cancer Medicine, Nanjing Medical University, Nanjing, China
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