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Miraki Feriz A, Khosrojerdi A, Erfanian N, Azarkar S, Sajjadi SM, Shojaei MJ, Vaferi MJ, Safarpour H, Racanelli V. Targeting the dynamic transcriptional landscape of Treg subpopulations in pancreatic ductal adenocarcinoma: Insights from single-cell RNA sequencing analysis with a focus on CTLA4 and TIGIT. Immunobiology 2024; 229:152822. [PMID: 38852289 DOI: 10.1016/j.imbio.2024.152822] [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: 12/30/2023] [Revised: 05/12/2024] [Accepted: 06/03/2024] [Indexed: 06/11/2024]
Abstract
Pancreatic ductal adenocarcinoma (PDAC) is a highly lethal malignancy that represents a significant challenge in cancer research and clinical management. In this study, we reanalyzed a published single-cell RNA sequencing (scRNA-seq) dataset from PDAC and adjacent tissues to investigate the heterogeneity of tumor and normal tissue, specifically focusing on the regulatory T cells (Tregs) and their interactions with other cells in the tumor microenvironment (TME). Treg cells were identified and clustered into natural Tregs (nTreg) and induced Tregs (iTreg) based on the expression of specific genes. It was found that the number of iTregs was higher in the tumor than in healthy tissues, while the number of n Tregs was higher in healthy tissues. Differential gene expression analysis was performed, and biological process analysis revealed that the Tregs in PDAC were mostly involved in protein targeting and translation pathways. In addition, ligand-receptor pairs between Tregs and other cell types were identified, and the critical communication pathways between Tregs and endothelial and ductal cells were revealed, which could potentially contribute to the immunosuppressive TME of PDAC. These findings provide insights into the role of Tregs in PDAC and their interactions with other cell types in the TME, highlighting potential targets for immunotherapy, such as the inhibitory immune checkpoint receptors CTLA4 and TIGIT, which are known to be expressed on Tregs and have been shown to play a role in suppressing anti-tumor immune responses.
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Affiliation(s)
- Adib Miraki Feriz
- Student Research Committee, Birjand University of Medical Sciences (BUMS), Birjand, Iran
| | | | - Nafiseh Erfanian
- Student Research Committee, Birjand University of Medical Sciences (BUMS), Birjand, Iran
| | - Setareh Azarkar
- Student Research Committee, Birjand University of Medical Sciences (BUMS), Birjand, Iran
| | | | | | - Mohammad Javad Vaferi
- Student Research Committee, Birjand University of Medical Sciences (BUMS), Birjand, Iran
| | | | - Vito Racanelli
- Centre for Medical Sciences (CISMed), University of Trento and Internal Medicine Division, Santa Chiara Hospital, Provincial Health Care Agency (APSS), 38122, Trento, Italy.
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Miraki Feriz A, Bahraini F, Khosrojerdi A, Azarkar S, Sajjadi SM, HosseiniGol E, Honardoost MA, Saghafi S, Silvestris N, Leone P, Safarpour H, Racanelli V. Deciphering the immune landscape of head and neck squamous cell carcinoma: A single-cell transcriptomic analysis of regulatory T cell responses to PD-1 blockade therapy. PLoS One 2023; 18:e0295863. [PMID: 38096229 PMCID: PMC10721039 DOI: 10.1371/journal.pone.0295863] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/11/2023] [Accepted: 11/30/2023] [Indexed: 12/17/2023] Open
Abstract
Immunotherapy is changing the Head and Neck Squamous Cell Carcinoma (HNSCC) landscape and improving outcomes for patients with recurrent or metastatic HNSCC. A deeper understanding of the tumor microenvironment (TME) is required in light of the limitations of patients' responses to immunotherapy. Here, we aimed to examine how Nivolumab affects infiltrating Tregs in the HNSCC TME. We used single-cell RNA sequencing data from eight tissues isolated from four HNSCC donors before and after Nivolumab treatment. Interestingly, the study found that Treg counts and suppressive activity increased following Nivolumab therapy. We also discovered that changes in the CD44-SSP1 axis, NKG2C/D-HLA-E axis, and KRAS signaling may have contributed to the increase in Treg numbers. Furthermore, our study suggests that decreasing the activity of the KRAS and Notch signaling pathways, and increasing FOXP3, CTLA-4, LAG-3, and GZMA expression, may be mechanisms that enhance the killing and suppressive capacity of Tregs. Additionally, the result of pseudo-temporal analysis of the HNSCC TME indicated that after Nivolumab therapy, the expression of certain inhibitory immune checkpoints including TIGIT, ENTPD1, and CD276 and LY9, were decreased in Tregs, while LAG-3 showed an increased expression level. The study also found that Tregs had a dense communication network with cluster two, and that certain ligand-receptor pairs, including SPP1/CD44, HLA-E/KLRC2, HLA-E/KLRK1, ANXA1/FPR3, and CXCL9/FCGR2A, had notable changes after the therapy. These changes in gene expression and cell interactions may have implications for the role of Tregs in the TME and in response to Nivolumab therapy.
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Affiliation(s)
- Adib Miraki Feriz
- Student Research Committee, Birjand University of Medical Sciences (BUMS), Birjand, Iran
| | - Fatemeh Bahraini
- Student Research Committee, Birjand University of Medical Sciences (BUMS), Birjand, Iran
| | | | - Setareh Azarkar
- Student Research Committee, Birjand University of Medical Sciences (BUMS), Birjand, Iran
| | | | - Edris HosseiniGol
- Department of Computer Engineering, University of Birjand, Birjand, Iran
| | - Mohammad Amin Honardoost
- Laboratory of Systems Biology and Data Analytics, Genome Institute of Singapore, A*STAR, Singapore, Singapore
| | - Samira Saghafi
- Cellular and Molecular Research Center (CMRC), BUMS, Birjand, Iran
- Department of Internal Medicine, School of Medicine, BUMS, Birjand, Iran
| | - Nicola Silvestris
- Medical Oncology Unit, Department of Human Pathology “G. Barresi”, University of Messina, Messina, Italy
| | - Patrizia Leone
- Department of Biomedical Sciences and Human Oncology, University of Bari "Aldo Moro", Bari, Italy
| | | | - Vito Racanelli
- Centre for Medical Sciences (CISMed), University of Trento and Internal Medicine Division, Santa Chiara Hospital, Provincial Health Care Agency (APSS), Trento, Italy
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