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Zhou R, Lu D, Mi J, Wang C, Lu W, Wang Z, Li X, Wei C, Zhang H, Ji J, Zhang Y, Zhang D, Wang F. Disulfidptosis-related genes serve as potential prognostic biomarkers and indicate tumor microenvironment characteristics and immunotherapy response in prostate cancer. Sci Rep 2024; 14:14107. [PMID: 38898043 PMCID: PMC11187134 DOI: 10.1038/s41598-024-61679-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/07/2024] [Accepted: 05/08/2024] [Indexed: 06/21/2024] Open
Abstract
Disulfidptosis, a newly identified programmed cell death pathway in prostate cancer (PCa), is closely associated with intracellular disulfide stress and glycolysis. This study aims to elucidate the roles of disulfidptosis-related genes (DRGs) in the pathogenesis and progression of PCa, with the goal of improving diagnostic and therapeutic approaches. We analyzed PCa datasets and normal tissue transcriptome data from TCGA, GEO, and MSKCC. Using consensus clustering analysis and LASSO regression, we developed a risk scoring model, which was validated in an independent cohort. The model's predictive accuracy was confirmed through Kaplan-Meier curves, receiver operating characteristic (ROC) curves, and nomograms. Additionally, we explored the relationship between the risk score and immune cell infiltration, and examined the tumor microenvironment and somatic mutations across different risk groups. We also investigated responses to immunotherapy and drug sensitivity. Our analysis identified two disulfidosis subtypes with significant differences in survival, immune environments, and treatment responses. According to our risk score, the high-risk group exhibited poorer progression-free survival (PFS) and higher tumor mutational burden (TMB), associated with increased immune suppression. Functional enrichment analysis linked high-risk features to key cancer pathways, including the IL-17 signaling pathway. Moreover, drug sensitivity analysis revealed varied responses to chemotherapy, suggesting the potential for disulfidosis-based personalized treatment strategies. Notably, we identified PROK1 as a crucial prognostic marker in PCa, with its reduced expression correlating with disease progression. In summary, our study comprehensively assessed the clinical implications of DRGs in PCa progression and prognosis, offering vital insights for tailored precision medicine approaches.
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Affiliation(s)
- Rongbin Zhou
- Collaborative Innovation Centre of Regenerative Medicine and Medical BioResource Development and Application Co-Constructed By the Province and Ministry, Guangxi Medical University, No. 22, Shuangyong Road, Qingxiu District, Nanning, 530021, Guangxi Zhuang Autonomous Region, China
- Center for Genomic and Personalized Medicine, Guangxi Key Laboratory for Genomic and Personalized Medicine, Guangxi Collaborative Innovation Center for Genomic and Personalized Medicine, Guangxi Medical University, Nanning, 530021, Guangxi, China
| | - Dingjin Lu
- Department of Urology, People's Hospital of Beihai, Beihai, 536000, Guangxi, China
| | - Junhao Mi
- Collaborative Innovation Centre of Regenerative Medicine and Medical BioResource Development and Application Co-Constructed By the Province and Ministry, Guangxi Medical University, No. 22, Shuangyong Road, Qingxiu District, Nanning, 530021, Guangxi Zhuang Autonomous Region, China
| | - Chengbang Wang
- Center for Genomic and Personalized Medicine, Guangxi Key Laboratory for Genomic and Personalized Medicine, Guangxi Collaborative Innovation Center for Genomic and Personalized Medicine, Guangxi Medical University, Nanning, 530021, Guangxi, China
- Department of Urology, The First Affiliated Hospital of Guangxi Medical University, Guangxi Medical University, Nanning, 530021, Guangxi, China
| | - Wenhao Lu
- Collaborative Innovation Centre of Regenerative Medicine and Medical BioResource Development and Application Co-Constructed By the Province and Ministry, Guangxi Medical University, No. 22, Shuangyong Road, Qingxiu District, Nanning, 530021, Guangxi Zhuang Autonomous Region, China
- Center for Genomic and Personalized Medicine, Guangxi Key Laboratory for Genomic and Personalized Medicine, Guangxi Collaborative Innovation Center for Genomic and Personalized Medicine, Guangxi Medical University, Nanning, 530021, Guangxi, China
| | - Zuheng Wang
- Department of Urology, The First Affiliated Hospital of Guangxi Medical University, Guangxi Medical University, Nanning, 530021, Guangxi, China
| | - Xiao Li
- School of Life Sciences, Guangxi Medical University, Nanning, 530021, Guangxi, China
| | - Chunmeng Wei
- Center for Genomic and Personalized Medicine, Guangxi Key Laboratory for Genomic and Personalized Medicine, Guangxi Collaborative Innovation Center for Genomic and Personalized Medicine, Guangxi Medical University, Nanning, 530021, Guangxi, China
- Department of Urology, The First Affiliated Hospital of Guangxi Medical University, Guangxi Medical University, Nanning, 530021, Guangxi, China
| | - Huiyong Zhang
- Center for Genomic and Personalized Medicine, Guangxi Key Laboratory for Genomic and Personalized Medicine, Guangxi Collaborative Innovation Center for Genomic and Personalized Medicine, Guangxi Medical University, Nanning, 530021, Guangxi, China
| | - Jin Ji
- Department of Urology, Shanghai Changhai Hospital, Naval Medical University, Shanghai, 200433, China
- Department of Urology, Naval Medical Center, Naval Medical Univiersiy, 338 Huaihai West Road, Shanghai, 200433, China
| | - Yifeng Zhang
- Department of Urology, Naval Medical Center, Naval Medical Univiersiy, 338 Huaihai West Road, Shanghai, 200433, China.
| | - Duobing Zhang
- Department of Urology, Suzhou Hospital of Anhui Medical University, 616 The Third Bianyang Road, Yongqiao District, Suzhou, 234000, Anhui, China.
| | - Fubo Wang
- Collaborative Innovation Centre of Regenerative Medicine and Medical BioResource Development and Application Co-Constructed By the Province and Ministry, Guangxi Medical University, No. 22, Shuangyong Road, Qingxiu District, Nanning, 530021, Guangxi Zhuang Autonomous Region, China.
- Center for Genomic and Personalized Medicine, Guangxi Key Laboratory for Genomic and Personalized Medicine, Guangxi Collaborative Innovation Center for Genomic and Personalized Medicine, Guangxi Medical University, Nanning, 530021, Guangxi, China.
- Department of Urology, The First Affiliated Hospital of Guangxi Medical University, Guangxi Medical University, Nanning, 530021, Guangxi, China.
- School of Life Sciences, Guangxi Medical University, Nanning, 530021, Guangxi, China.
- Department of Urology, Affiliated Tumor Hospital of Guangxi Medical University, Guangxi Medical University, Nanning, 530021, Guangxi, China.
- School of Public Health, Guangxi Medical University, Nanning, 530021, Guangxi, China.
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Tsai YG, Liao PF, Hsiao KH, Wu HM, Lin CY, Yang KD. Pathogenesis and novel therapeutics of regulatory T cell subsets and interleukin-2 therapy in systemic lupus erythematosus. Front Immunol 2023; 14:1230264. [PMID: 37771588 PMCID: PMC10522836 DOI: 10.3389/fimmu.2023.1230264] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/28/2023] [Accepted: 08/15/2023] [Indexed: 09/30/2023] Open
Abstract
Systemic lupus erythematosus (SLE) is a heterogeneous multisystem inflammatory disease with wide variability in clinical manifestations. Natural arising CD4+ regulatory T cells (Tregs) play a critical role in maintaining peripheral tolerance by suppressing inflammation and preventing autoimmune responses in SLE. Additionally, CD8+ regulatory T cells, type 1 regulatory T cells (Tr1), and B regulatory cells also have a less well-defined role in the pathogenesis of SLE. Elucidation of the roles of various Treg subsets dedicated to immune homeostasis will provide a novel therapeutic approach that governs immune tolerance for the remission of active lupus. Diminished interleukin (IL)-2 production is associated with a depleted Treg cell population, and its reversibility by IL-2 therapy provides important reasons for the treatment of lupus. This review focuses on the pathogenesis and new therapeutics of human Treg subsets and low-dose IL-2 therapy in clinical benefits with SLE.
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Affiliation(s)
- Yi-Giien Tsai
- Department of Pediatrics, Changhua Christian Children’s Hospital, Changhua, Taiwan
- School of Medicine, Kaohsiung Medical University, Kaohsiung, Taiwan
- School of Medicine, Chung Shan Medical University, Taichung, Taiwan
- Department of Post-Baccalaureate Medicine, College of Medicine, National Chung Hsing University, Taichung, Taiwan
| | - Pei-Fen Liao
- School of Medicine, Chung Shan Medical University, Taichung, Taiwan
- Division of Allergy, Asthma and Rheumatology, Department of Pediatrics, Chung Shan Medical University Hospital, Taichung, Taiwan
| | - Kai-Hung Hsiao
- Department of Allergy, Immunology and Rheumatology, Changhua Christian Hospital, Changhua, Taiwan
| | - Hung-Ming Wu
- Department of Neurology, Changhua Christian Hospital, Changhua, Taiwan
| | - Ching-Yuang Lin
- Division of Pediatric Nephrology, Children’s Hospital, China Medical University Hospital, Taichung, Taiwan
| | - Kuender D. Yang
- Department of Pediatrics, Mackay Memorial Hospital, New Taipei City, Taiwan
- Institute of Clinical Medicine, National Yang Ming Chiao Tung University, Taipei, Taiwan
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3
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Natoli V, Charras A, Hofmann SR, Northey S, Russ S, Schulze F, McCann L, Abraham S, Hedrich CM. DNA methylation patterns in CD4 + T-cells separate psoriasis patients from healthy controls, and skin psoriasis from psoriatic arthritis. Front Immunol 2023; 14:1245876. [PMID: 37662940 PMCID: PMC10472451 DOI: 10.3389/fimmu.2023.1245876] [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: 06/23/2023] [Accepted: 07/18/2023] [Indexed: 09/05/2023] Open
Abstract
Background Psoriasis is an autoimmune/inflammatory disorder primarily affecting the skin. Chronic joint inflammation triggers the diagnosis of psoriatic arthritis (PsA) in approximately one-third of psoriasis patients. Although joint disease typically follows the onset of skin psoriasis, in around 15% of cases it is the initial presentation, which can result in diagnostic delays. The pathophysiological mechanisms underlying psoriasis and PsA are not yet fully understood, but there is evidence pointing towards epigenetic dysregulation involving CD4+ and CD8+ T-cells. Objectives The aim of this study was to investigate disease-associated DNA methylation patterns in CD4+ T-cells from psoriasis and PsA patients that may represent potential diagnostic and/or prognostic biomarkers. Methods PBMCs were collected from 12 patients with chronic plaque psoriasis and 8 PsA patients, and 8 healthy controls. CD4+ T-cells were separated through FACS sorting, and DNA methylation profiling was performed (Illumina EPIC850K arrays). Bioinformatic analyses, including gene ontology (GO) and KEGG pathway analysis, were performed using R. To identify genes under the control of interferon (IFN), the Interferome database was consulted, and DNA Methylation Scores were calculated. Results Numbers and proportions of CD4+ T-cell subsets (naïve, central memory, effector memory, CD45RA re-expressing effector memory cells) did not vary between controls, skin psoriasis and PsA patients. 883 differentially methylated positions (DMPs) affecting 548 genes were identified between controls and "all" psoriasis patients. Principal component and partial least-squares discriminant analysis separated controls from skin psoriasis and PsA patients. GO analysis considering promoter DMPs delivered hypermethylation of genes involved in "regulation of wound healing, spreading of epidermal cells", "negative regulation of cell-substrate junction organization" and "negative regulation of focal adhesion assembly". Comparing controls and "all" psoriasis, a majority of DMPs mapped to IFN-related genes (69.2%). Notably, DNA methylation profiles also distinguished skin psoriasis from PsA patients (2,949 DMPs/1,084 genes) through genes affecting "cAMP-dependent protein kinase inhibitor activity" and "cAMP-dependent protein kinase regulator activity". Treatment with cytokine inhibitors (IL-17/TNF) corrected DNA methylation patterns of IL-17/TNF-associated genes, and methylation scores correlated with skin disease activity scores (PASI). Conclusion DNA methylation profiles in CD4+ T-cells discriminate between skin psoriasis and PsA. DNA methylation signatures may be applied for quantification of disease activity and patient stratification towards individualized treatment.
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Affiliation(s)
- Valentina Natoli
- Department of Women’s & Children’s Health, Institute of Life Course and Medical Sciences, University of Liverpool, Liverpool, United Kingdom
- Università degli Studi di Genova, Dipartimento di Neuroscienze, Riabilitazione, Oftalmologia, Genetica e Scienze Materno-infantili (DINOGMI), Genoa, Italy
| | - Amandine Charras
- Department of Women’s & Children’s Health, Institute of Life Course and Medical Sciences, University of Liverpool, Liverpool, United Kingdom
| | - Sigrun R. Hofmann
- Klinik und Poliklinik für Kinder- und Jugendmedizin, Universitätsklinikum Carl Gustav Carus, TU Dresden, Dresden, Germany
| | - Sarah Northey
- Department of Women’s & Children’s Health, Institute of Life Course and Medical Sciences, University of Liverpool, Liverpool, United Kingdom
| | - Susanne Russ
- Klinik und Poliklinik für Kinder- und Jugendmedizin, Universitätsklinikum Carl Gustav Carus, TU Dresden, Dresden, Germany
| | - Felix Schulze
- Klinik und Poliklinik für Kinder- und Jugendmedizin, Universitätsklinikum Carl Gustav Carus, TU Dresden, Dresden, Germany
| | - Liza McCann
- Department of Paediatric Rheumatology, Alder Hey Children’s NHS Foundation Trust Hospital, Liverpool, United Kingdom
| | - Susanne Abraham
- Department of Dermatology, University Hospital Carl Gustav Carus, TU Dresden, Dresden, Germany
| | - Christian M. Hedrich
- Department of Women’s & Children’s Health, Institute of Life Course and Medical Sciences, University of Liverpool, Liverpool, United Kingdom
- Department of Paediatric Rheumatology, Alder Hey Children’s NHS Foundation Trust Hospital, Liverpool, United Kingdom
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Li Z, Wang Z, Sun T, Liu S, Ding S, Sun L. Identifying key genes in CD4+ T cells of systemic lupus erythematosus by integrated bioinformatics analysis. Front Genet 2022; 13:941221. [PMID: 36046235 PMCID: PMC9420982 DOI: 10.3389/fgene.2022.941221] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/11/2022] [Accepted: 07/11/2022] [Indexed: 11/13/2022] Open
Abstract
Systemic lupus erythematosus (SLE) is a chronic autoimmune disease characterized by excessive activation of T and B lymphocytes and breakdown of immune tolerance to autoantigens. Despite several mechanisms including the genetic alterations and inflammatory responses have been reported, the overall signature genes in CD4+ T cells and how they affect the pathological process of SLE remain to be elucidated. This study aimed to identify the crucial genes, potential biological processes and pathways underlying SLE pathogenesis by integrated bioinformatics. The gene expression profiles of isolated peripheral CD4+ T cells from SLE patients with different disease activity and healthy controls (GSE97263) were analyzed, and 14 co-expression modules were identified using weighted gene co-expression network analysis (WGCNA). Some of these modules showed significantly positive or negative correlations with SLE disease activity, and primarily enriched in the regulation of type I interferon and immune responses. Next, combining time course sequencing (TCseq) with differentially expressed gene (DEG) analysis, crucial genes in lupus CD4+ T cells were revealed, including some interferon signature genes (ISGs). Among these genes, we identified 4 upregulated genes (PLSCR1, IFI35, BATF2 and CLDN5) and 2 downregulated genes (GDF7 and DERL3) as newfound key genes. The elevated genes showed close relationship with the SLE disease activity. In general, our study identified 6 novel biomarkers in CD4+ T cells that might contribute to the diagnosis and treatment of SLE.
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Affiliation(s)
- Zutong Li
- Department of Rheumatology and Immunology, The Affiliated Drum Tower Hospital of Nanjing University Medical School, Nanjing, China
| | - Zhilong Wang
- Department of Reproductive Medicine Center, The Affiliated Drum Tower Hospital of Nanjing University Medical School, Nanjing, China
| | - Tian Sun
- Department of Rheumatology and Immunology, The Affiliated Drum Tower Hospital of Nanjing University Medical School, Nanjing, China
| | - Shanshan Liu
- Department of Rheumatology and Immunology, The Affiliated Drum Tower Hospital of Nanjing University Medical School, Nanjing, China
| | - Shuai Ding
- Department of Rheumatology and Immunology, The Affiliated Drum Tower Hospital of Nanjing University Medical School, Nanjing, China
- *Correspondence: Lingyun Sun, ; Shuai Ding,
| | - Lingyun Sun
- Department of Rheumatology and Immunology, The Affiliated Drum Tower Hospital of Nanjing University Medical School, Nanjing, China
- *Correspondence: Lingyun Sun, ; Shuai Ding,
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Cury SS, Kuasne H, Souza JDS, Muñoz JJM, da Silva JP, Lopes A, Scapulatempo-Neto C, Faria EF, Delaissé JM, Marchi FA, Rogatto SR. Interplay Between Immune and Cancer-Associated Fibroblasts: A Path to Target Metalloproteinases in Penile Cancer. Front Oncol 2022; 12:935093. [PMID: 35928876 PMCID: PMC9343588 DOI: 10.3389/fonc.2022.935093] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/03/2022] [Accepted: 05/30/2022] [Indexed: 11/13/2022] Open
Abstract
Extracellular matrix (ECM) remodeling and inflammation have been reported in penile carcinomas (PeCa). However, the cell types and cellular crosstalk involved in PeCa are unexplored. We aimed to characterize the complexity of cells and pathways involved in the tumor microenvironment (TME) in PeCa and propose target molecules associated with the TME. We first investigated the prognostic impact of cell types with a secretory profile to identify drug targets that modulate TME-enriched cells. The secretome analysis using the PeCa transcriptome revealed the enrichment of inflammation and extracellular matrix pathways. Twenty-three secreted factors were upregulated, mainly collagens and matrix metalloproteinases (MMPs). The deregulation of collagens and MMPs was confirmed by Quantitative reverse transcription - polymerase chain reaction (RT-qPCR). Further, the deconvolution method (digital cytometry) of the bulk samples revealed a high proportion of macrophages and dendritic cells (DCs) and B cells. Increased DCs and B cells were associated with better survival. A high proportion of cancer-associated fibroblasts (CAFs) was observed in low-survival patients. Patients with increased CAFs had decreased immune cell proportions. The treatment with the MMP inhibitor GM6001 in CAF cells derived from PeCa resulted in altered cell viability. We reported a crosstalk between immune cells and CAFs, and the proportion of these cell populations was associated with prognosis. We demonstrate that a drug targeting MMPs modulates CAFs, expanding the therapeutic options of PeCa.
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Affiliation(s)
- Sarah Santiloni Cury
- Department of Clinical Genetics, University Hospital of Southern Denmark, Vejle, Denmark
- Institute of Regional Health Research, University of Southern Denmark, Odense, Denmark
- Department of Structural and Functional Biology, São Paulo State University (UNESP), Botucatu, Brazil
| | - Hellen Kuasne
- Department of Clinical Genetics, University Hospital of Southern Denmark, Vejle, Denmark
- Rosalind and Morris Goodman Cancer Institute, McGill University, Montreal, QC, Canada
- International Research Center (CIPE), A. C. Camargo Cancer Center, São Paulo, Brazil
| | - Jeferson dos Santos Souza
- Department of Structural and Functional Biology, São Paulo State University (UNESP), Botucatu, Brazil
| | - Juan Jose Moyano Muñoz
- International Research Center (CIPE), A. C. Camargo Cancer Center, São Paulo, Brazil
- Universidad Señor de Sipán, Chiclayo, Peru
| | | | - Ademar Lopes
- Pelvic Surgery Department, A. C. Camargo Cancer Center, São Paulo, Brazil
| | - Cristovam Scapulatempo-Neto
- Molecular Oncology Research Center, Barretos Cancer Hospital, Barretos, Brazil
- Department of Pathology, Diagnósticos da América - DASA, Barueri, Brazil
| | - Eliney Ferreira Faria
- Molecular Oncology Research Center, Barretos Cancer Hospital, Barretos, Brazil
- Uro-oncology and Robotic Surgery, Hospital Felicio Rocho, Belo Horizonte, Brazil
| | - Jean-Marie Delaissé
- Clinical Cell Biology, Lillebaelt Hospital, University Hospital of Southern Denmark, Vejle, Denmark
- Department of Clinical Research, Clinical Cell Biology, University of Southern Denmark, Odense, Denmark
| | | | - Silvia Regina Rogatto
- Department of Clinical Genetics, University Hospital of Southern Denmark, Vejle, Denmark
- Institute of Regional Health Research, University of Southern Denmark, Odense, Denmark
- *Correspondence: Silvia Regina Rogatto,
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Bednar KJ, Lee JH, Ort T. Tregs in Autoimmunity: Insights Into Intrinsic Brake Mechanism Driving Pathogenesis and Immune Homeostasis. Front Immunol 2022; 13:932485. [PMID: 35844555 PMCID: PMC9280893 DOI: 10.3389/fimmu.2022.932485] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/29/2022] [Accepted: 05/16/2022] [Indexed: 11/16/2022] Open
Abstract
CD4+CD25highFoxp3+ regulatory T-cells (Tregs) are functionally characterized for their ability to suppress the activation of multiple immune cell types and are indispensable for maintaining immune homeostasis and tolerance. Disruption of this intrinsic brake system assessed by loss of suppressive capacity, cell numbers, and Foxp3 expression, leads to uncontrolled immune responses and tissue damage. The conversion of Tregs to a pathogenic pro-inflammatory phenotype is widely observed in immune mediated diseases. However, the molecular mechanisms that underpin the control of Treg stability and suppressive capacity are incompletely understood. This review summarizes the concepts of Treg cell stability and Treg cell plasticity highlighting underlying mechanisms including translational and epigenetic regulators that may enable translation to new therapeutic strategies. Our enhanced understanding of molecular mechanism controlling Tregs will have important implications into immune homeostasis and therapeutic potential for the treatment of immune-mediated diseases.
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