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Shi M, Chen L, Wei Y, Chen R, Guo R, Luo F. Systematic analysis of prognostic and immunologic characteristics associated with coronavirus disease 2019 regulators in acute myeloid leukemia. Front Genet 2022; 13:959109. [PMID: 36147489 PMCID: PMC9485716 DOI: 10.3389/fgene.2022.959109] [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: 06/09/2022] [Accepted: 08/12/2022] [Indexed: 11/13/2022] Open
Abstract
The coronavirus disease 2019 (COVID-19) pandemic has so far damaged the health of millions and has made the treatment of cancer patients more complicated, and so did acute myeloid leukemia (AML). The current problem is the lack of understanding of their interactions and suggestions of evidence-based guidelines or historical experience for the treatment of such patients. Here, we first identified the COVID-19-related differentially expressed genes (C-DEGs) in AML patients by analyzing RNA-seq from public databases and explored their enrichment pathways and candidate drugs. A total of 76 C-DEGs associated with the progress of AML and COVID-19 infection were ultimately identified, and the functional analysis suggested that there are some shared links between them. Their protein–protein interactions (PPIs) and protein–drug interactions were then recognized by multiple bioinformatics algorithms. Moreover, a COVID-19 gene-associated prognostic model (C-GPM) with riskScore was constructed, patients with a high riskScore had poor survival and apparently immune-activated phenotypes, such as stronger monocyte and neutrophil cell infiltrations and higher immunosuppressants targeting expressions, meaning which may be one of the common denominators between COVID-19 and AML and the reason what complicates the treatment of the latter. Among the study’s drawbacks is that these results relied heavily on publicly available datasets rather than being clinically confirmed. Yet, these findings visualized those C-DEGs’ enrichment pathways and inner associations, and the C-GPM based on them could accurately predict survival outcomes in AML patients, which will be helpful for further optimizing therapies for AML patients with COVID-19 infections.
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Affiliation(s)
- Mingjie Shi
- Key Laboratory of Research in Maternal and Child Medicine and Birth Defects, Guangdong Medical University, Foshan, China
- Matenal and Child Research Institute, Shunde Women and Children’s Hospital (Maternity andChild Healthcare Hospital of Shunde Foshan), Guangdong Medical University, Foshan, China
| | - Lidan Chen
- First College of Clinical Medicine, Guangdong Medical University, Zhanjiang, China
| | - Yue Wei
- Department of Ultrasound, Shunde Women and Children’s Hospital (Maternity and Child Healthcare Hospital of Shunde Foshan), Guangdong Medical University, Foshan, China
| | - Riling Chen
- Key Laboratory of Research in Maternal and Child Medicine and Birth Defects, Guangdong Medical University, Foshan, China
- Matenal and Child Research Institute, Shunde Women and Children’s Hospital (Maternity andChild Healthcare Hospital of Shunde Foshan), Guangdong Medical University, Foshan, China
- Department of Hematology-Oncology, Shunde Women and Children’s Hospital (Maternity and Child Healthcare Hospital of Shunde Foshan), Guangdong Medical University, Foshan, China
| | - Runmin Guo
- Key Laboratory of Research in Maternal and Child Medicine and Birth Defects, Guangdong Medical University, Foshan, China
- Matenal and Child Research Institute, Shunde Women and Children’s Hospital (Maternity andChild Healthcare Hospital of Shunde Foshan), Guangdong Medical University, Foshan, China
- *Correspondence: Fei Luo, ; Runmin Guo,
| | - Fei Luo
- Key Laboratory of Research in Maternal and Child Medicine and Birth Defects, Guangdong Medical University, Foshan, China
- Matenal and Child Research Institute, Shunde Women and Children’s Hospital (Maternity andChild Healthcare Hospital of Shunde Foshan), Guangdong Medical University, Foshan, China
- Department of Hematology-Oncology, Shunde Women and Children’s Hospital (Maternity and Child Healthcare Hospital of Shunde Foshan), Guangdong Medical University, Foshan, China
- *Correspondence: Fei Luo, ; Runmin Guo,
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Lee HW, Chung W, Lee HO, Jeong DE, Jo A, Lim JE, Hong JH, Nam DH, Jeong BC, Park SH, Joo KM, Park WY. Single-cell RNA sequencing reveals the tumor microenvironment and facilitates strategic choices to circumvent treatment failure in a chemorefractory bladder cancer patient. Genome Med 2020; 12:47. [PMID: 32460812 PMCID: PMC7251908 DOI: 10.1186/s13073-020-00741-6] [Citation(s) in RCA: 99] [Impact Index Per Article: 24.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/11/2019] [Accepted: 04/24/2020] [Indexed: 02/08/2023] Open
Abstract
BACKGROUND Tumor cell-intrinsic mechanisms and complex interactions with the tumor microenvironment contribute to therapeutic failure via tumor evolution. It may be possible to overcome treatment resistance by developing a personalized approach against relapsing cancers based on a comprehensive analysis of cell type-specific transcriptomic changes over the clinical course of the disease using single-cell RNA sequencing (scRNA-seq). METHODS Here, we used scRNA-seq to depict the tumor landscape of a single case of chemo-resistant metastatic, muscle-invasive urothelial bladder cancer (MIUBC) addicted to an activating Harvey rat sarcoma viral oncogene homolog (HRAS) mutation. In order to analyze tumor evolution and microenvironmental changes upon treatment, we also applied scRNA-seq to the corresponding patient-derived xenograft (PDX) before and after treatment with tipifarnib, a HRAS-targeting agent under clinical evaluation. RESULTS In the parallel analysis of the human MIUBC and the PDX, diverse stromal and immune cell populations recapitulated the cellular composition in the human and mouse tumor microenvironment. Treatment with tipifarnib showed dramatic anticancer effects but was unable to achieve a complete response. Importantly, the comparative scRNA-seq analysis between pre- and post-tipifarnib-treated PDX revealed the nature of tipifarnib-refractory tumor cells and the tumor-supporting microenvironment. Based on the upregulation of programmed death-ligand 1 (PD-L1) in surviving tumor cells, and the accumulation of multiple immune-suppressive subsets from post-tipifarnib-treated PDX, a PD-L1 inhibitor, atezolizumab, was clinically applied; this resulted in a favorable response from the patient with acquired resistance to tipifarnib. CONCLUSION We presented a single case report demonstrating the power of scRNA-seq for visualizing the tumor microenvironment and identifying molecular and cellular therapeutic targets in a treatment-refractory cancer patient.
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Affiliation(s)
- Hye Won Lee
- Department of Anatomy and Cell Biology, Sungkyunkwan University School of Medicine, Suwon, 16419, Republic of Korea
- Single Cell Network Research Center, Sungkyunkwan University School of Medicine, Suwon, 16419, Republic of Korea
- Samsung Advanced Institute of Health Science and Technology, Sungkyunkwan University, Seoul, 06351, Republic of Korea
- Department of Molecular Cell Biology, Sungkyunkwan University School of Medicine, Suwon, 16419, Republic of Korea
- Department of Hospital Medicine, Yonsei University College of Medicine, Seoul, 03722, Republic of Korea
| | - Woosung Chung
- Samsung Advanced Institute of Health Science and Technology, Sungkyunkwan University, Seoul, 06351, Republic of Korea
- Department of Molecular Cell Biology, Sungkyunkwan University School of Medicine, Suwon, 16419, Republic of Korea
- Samsung Genome Institute, Samsung Medical Center, Seoul, 06351, Republic of Korea
- DCGen Co., Ltd, Seoul, 03170, Republic of Korea
| | - Hae-Ock Lee
- Department of Molecular Cell Biology, Sungkyunkwan University School of Medicine, Suwon, 16419, Republic of Korea
- Samsung Genome Institute, Samsung Medical Center, Seoul, 06351, Republic of Korea
| | - Da Eun Jeong
- Department of Anatomy and Cell Biology, Sungkyunkwan University School of Medicine, Suwon, 16419, Republic of Korea
- Single Cell Network Research Center, Sungkyunkwan University School of Medicine, Suwon, 16419, Republic of Korea
| | - Areum Jo
- Samsung Genome Institute, Samsung Medical Center, Seoul, 06351, Republic of Korea
| | - Joung Eun Lim
- Department of Urology, Samsung Medical Center, Sungkyunkwan University School of Medicine, Seoul, 06351, Republic of Korea
| | - Jeong Hee Hong
- Department of Urology, Dankook University College of Medicine, Cheonan, 31116, Republic of Korea
| | - Do-Hyun Nam
- Samsung Advanced Institute of Health Science and Technology, Sungkyunkwan University, Seoul, 06351, Republic of Korea
- Department of Neurosurgery, Samsung Medical Center, Sungkyunkwan University School of Medicine, Seoul, 06351, Republic of Korea
| | - Byong Chang Jeong
- Samsung Advanced Institute of Health Science and Technology, Sungkyunkwan University, Seoul, 06351, Republic of Korea.
- Department of Urology, Samsung Medical Center, Sungkyunkwan University School of Medicine, Seoul, 06351, Republic of Korea.
| | - Se Hoon Park
- Division of Hematology and Oncology, Department of Medicine, Samsung Medical Center, Sungkyunkwan University School of Medicine, Seoul, 06351, Republic of Korea.
| | - Kyeung-Min Joo
- Department of Anatomy and Cell Biology, Sungkyunkwan University School of Medicine, Suwon, 16419, Republic of Korea.
- Single Cell Network Research Center, Sungkyunkwan University School of Medicine, Suwon, 16419, Republic of Korea.
- Samsung Advanced Institute of Health Science and Technology, Sungkyunkwan University, Seoul, 06351, Republic of Korea.
- Stem Cell and Regenerative Medicine Center, Research Institute for Future Medicine, Samsung Medical Center, Seoul, 06351, Republic of Korea.
| | - Woong-Yang Park
- Samsung Advanced Institute of Health Science and Technology, Sungkyunkwan University, Seoul, 06351, Republic of Korea.
- Department of Molecular Cell Biology, Sungkyunkwan University School of Medicine, Suwon, 16419, Republic of Korea.
- Samsung Genome Institute, Samsung Medical Center, Seoul, 06351, Republic of Korea.
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Chen Z, Chen S, Liu J. The role of T cells in the pathogenesis of Parkinson's disease. Prog Neurobiol 2018; 169:1-23. [PMID: 30114440 DOI: 10.1016/j.pneurobio.2018.08.002] [Citation(s) in RCA: 37] [Impact Index Per Article: 6.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/12/2018] [Revised: 06/24/2018] [Accepted: 08/12/2018] [Indexed: 02/06/2023]
Abstract
Recent evidence has shown that neuroinflammation plays a key role in the pathogenesis of Parkinson's disease (PD). However, different components of the brain's immune system may exert diverse effects on neuroinflammatory events in PD. The adaptive immune response, especially the T cell response, can trigger type 1 pro-inflammatory activities and suppress type 2 anti-inflammatory activities, eventually resulting in deregulated neuroinflammation and subsequent dopaminergic neurodegeneration. Additionally, studies have increasingly shown that therapies targeting T cells can alleviate neurodegeneration and motor behavior impairment in animal models of PD. Therefore, we conclude that abnormal T cell-mediated immunity is a fundamental pathological process that may be a promising translational therapeutic target for Parkinson's disease.
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Affiliation(s)
- Zhichun Chen
- Department of Neurology and Institute of Neurology, Ruijin Hospital Affiliated with the Shanghai Jiao Tong University School of Medicine, Shanghai 200025, China
| | - Shengdi Chen
- Department of Neurology and Institute of Neurology, Ruijin Hospital Affiliated with the Shanghai Jiao Tong University School of Medicine, Shanghai 200025, China
| | - Jun Liu
- Department of Neurology and Institute of Neurology, Ruijin Hospital Affiliated with the Shanghai Jiao Tong University School of Medicine, Shanghai 200025, China.
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Shete A, Suryawanshi P, Godbole S, Pawar J, Paranjape R, Thakar M. HIV-infected CD4+ T Cells Use T-bet-dependent Pathway for Production of IL-10 Upon Antigen Recognition. Scand J Immunol 2016; 83:288-96. [PMID: 27028319 DOI: 10.1111/sji.12422] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/27/2015] [Accepted: 02/15/2016] [Indexed: 01/11/2023]
Abstract
Interleukin (IL)-10 has been implicated in persistence of pathogens in a number of chronic infections. Infected CD4+ cells upon reactivation with HIV antigens were also shown to produce IL-10, which might contribute to their persistence. Hence, it is crucial to determine mechanisms regulating IL-10 production after activation with HIV antigens for devising effective blocking strategies. In this study, ERK-, T-bet- and FoxP3-dependent pathways were evaluated for their possible roles in IL-10 production by infected CD4+ cells after reactivation with HIV Env. Intracellular and secreted IL-10 levels were determined by flow cytometry and Bioplex assay after treating PBMCs with PD98059, tipifarnib and cyclosporin A for blocking of ERK-, T-bet-and FoxP3-dependent pathways, respectively. Baseline levels of T-bet, pERK were higher in P24+ CD4+ cells as compared to uninfected CD4+ cells, which increased further after activation with Env. Inhibition of T-bet resulted in 2.3-fold reduction of IL-10 expression whereas ERK and FoxP3 inhibition failed to cause suppression of IL-10 expression. Conversely, IL-10 secreted by PBMCs was inhibited maximally after ERK inhibition suggesting its role in regulation of cytokine secretory pathway. IFN-γ was found to be suppressed after treatment with inhibitors of all these pathways. Thus, the study highlighted need for IL-10 blockade along with the use of antigens for therapeutic vaccinations or latency reversal and identified the T-bet-dependent pathway as an important pathway regulating IL-10 production by infected CD4+ cells. However, simultaneous blockade of IFN-γ precludes use of inhibitor of this pathway as an IL-10 blocking strategy.
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Affiliation(s)
- A Shete
- National AIDS Research Institute, Pune, India
| | | | - S Godbole
- National AIDS Research Institute, Pune, India
| | - J Pawar
- National AIDS Research Institute, Pune, India
| | - R Paranjape
- National AIDS Research Institute, Pune, India
| | - M Thakar
- National AIDS Research Institute, Pune, India
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