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Wu C, Li Y, Luo Y, Dai Y, Qin J, Liu N, Xu R, Li X, Zhang P. Analysis of glutathione Stransferase mu class 5 gene methylation as a prognostic indicator in low-grade gliomas. Technol Health Care 2024:THC231316. [PMID: 39031395 DOI: 10.3233/thc-231316] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 07/22/2024]
Abstract
BACKGROUND Low-grade gliomas (LGG) are a variety of brain tumors that show different clinical outcomes. The methylation of the GSTM5 gene has been noted in the development of LGG, however, its prognostic importance remains uncertain. OBJECTIVE The objective of this study was to examine the correlation between GSTM5 DNA methylation and clinical outcomes in individuals diagnosed with LGG. METHODS Analysis of GSTM5 methylation levels in LGG samples was conducted using data from The Cancer Genome Atlas (TCGA) and Gene Expression Omnibus (GEO) datasets. The overall survival based on GSTM5 methylation status was evaluated using Kaplan-Meier curves. The DNA methylation heatmap for particular CpG sites in the GSTM5 gene was visualized using the "pheatmap" R package. RESULTS The study analyzed that LGG tumors had higher levels of GSTM5 methylation than normal tissues. There was an inverse relationship discovered between GSTM5 expression and methylation. LGG patients with hypermethylation of GSTM5 promoter experienced a positive outcome. Age, grade, and GSTM5 methylation were determined as independent prognostic factors in LGG through both univariate and multivariate Cox regression analyses. CONCLUSION Methylation of GSTM5 DNA, specifically at certain CpG sites, is linked to a positive outlook in patients with LGG. Utilizing the "pheatmap" R package to visualize GSTM5 methylation patterns offers important information for identifying prognostic markers and therapeutic targets in low-grade gliomas.
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Affiliation(s)
- Cuiying Wu
- Department of Neurosurgery, The Seventh Medical Centre of PLA General Hospital, Beijing, China
- Department of Neurobiology, Beijing Institute of Basic Medical Sciences, Beijing, China
- Department of Neurosurgery, The Seventh Medical Centre of PLA General Hospital, Beijing, China
| | - Yunjun Li
- Department of Neurosurgery, Senior Department of Neurosurgery, The First Medical Centre of PLA General Hospital, Beijing, China
- Department of Neurosurgery, The Seventh Medical Centre of PLA General Hospital, Beijing, China
| | - Yongchun Luo
- Department of Neurosurgery, Senior Department of Neurosurgery, The First Medical Centre of PLA General Hospital, Beijing, China
| | - Yiwu Dai
- Department of Neurosurgery, Senior Department of Neurosurgery, The First Medical Centre of PLA General Hospital, Beijing, China
| | - Jiazhen Qin
- Department of Neurosurgery, Senior Department of Neurosurgery, The First Medical Centre of PLA General Hospital, Beijing, China
| | - Ning Liu
- Department of Neurosurgery, The Seventh Medical Centre of PLA General Hospital, Beijing, China
| | - Ruxiang Xu
- Department of Neurosurgery, Sichuan Academy of Medical Science and Sichuan Provincial People's Hospital, School of Medicine, University of Electronic Science and Technology of China, Chengdu, China
| | - Xuezhen Li
- Department of Neurosurgery, Beijing Tiantan Hospital, Capital Medical University, Beijing, China
| | - Peng Zhang
- Department of Neurosurgery, The Seventh Medical Centre of PLA General Hospital, Beijing, China
- Department of Neurosurgery, Senior Department of Neurosurgery, The First Medical Centre of PLA General Hospital, Beijing, China
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Nan Y, Chen M, Wu W, Huang R, Sun W, Lu Q, Gu Z, Mao X, Xu H, Wang Y. IGF2BP2 regulates the inflammation of fibroblast-like synoviocytes via GSTM5 in rheumatoid arthritis. Cell Death Discov 2024; 10:215. [PMID: 38702323 PMCID: PMC11068746 DOI: 10.1038/s41420-024-01988-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/05/2023] [Revised: 04/19/2024] [Accepted: 04/23/2024] [Indexed: 05/06/2024] Open
Abstract
Rheumatoid arthritis (RA) is a chronic autoimmune disease with an unknown etiology. RA cannot be fully cured and requires lengthy treatment, imposing a significant burden on both individuals and society. Due to the lack of specific drugs available for treating RA, exploring a key new therapeutic target for RA is currently an important task. Activated fibroblast-like synoviocytes (FLSs) play a crucial role in the progression of RA, which release interleukin (IL)-1β, IL-6 and tumor necrosis factor (TNF)-α resulting in abnormal inflammatory reaction in the synovium. A previous study has highlighted the correlation of m6A reader insulin-like growth factor 2 mRNA-binding protein 2 (IGF2BP2) with inflammation-related diseases in human. However, the role of IGF2BP2 in the inflammatory reaction of FLSs during RA progression has not been assessed. In this study, IGF2BP2 expression was decreased in the synovial tissues of RA patients and collagen-induced arthritis (CIA) rats. Intra-articular injection of an adeno-associated virus (AAV) vector overexpressing IGF2BP2 relieved paw swelling, synovial hyperplasia and cartilage destruction in CIA rats. IGF2BP2 overexpression also inhibited lipopolysaccharide (LPS)-mediated RA fibroblast-like synoviocytes (RA-FLSs) migration and invasion accompanied by a decreased level of inflammatory factors in vitro. Conversely, IGF2BP2 suppression promoted RA-FLSs migration and invasion with an elevated level of inflammatory factors in vitro. The sequencing result showed that glutathione S-transferase Mu 5 (GSTM5), a key antioxidant gene, was the target mRNA of IGF2BP2. Further experiments demonstrated that IGF2BP2 strengthened the stability of GSTM5 mRNA, leading to weakened inflammatory reaction and reduced expression of matrix metalloproteinase 9 and 13 (MMP9, MMP13). Therefore, IGF2BP2-GSTM5 axis may represent a potential therapeutic target for RA treatment.
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Affiliation(s)
- Yunyi Nan
- Department of Orthopaedics, Affiliated Hospital of Nantong University, Medical School of Nantong University, 226001, Nantong, China
| | - Minhao Chen
- Department of Orthopaedics, Affiliated Hospital of Nantong University, Medical School of Nantong University, 226001, Nantong, China
| | - Weijie Wu
- Department of Orthopaedics, Affiliated Hospital of Nantong University, Medical School of Nantong University, 226001, Nantong, China
- Department of Orthopaedics, Affiliated Nantong Hospital of Shanghai University, The Sixth People's Hospital of Nantong, 226001, Nantong, China
| | - Rongrong Huang
- Department of Pharmacy, Affiliated Hospital of Nantong University, 226001, Nantong, China
| | - Weiwei Sun
- Department of Orthopaedics, Affiliated Hospital of Nantong University, Medical School of Nantong University, 226001, Nantong, China
| | - Qian Lu
- Department of Rheumatology, Affiliated Hospital of Nantong University, 226001, Nantong, China
| | - Zhifeng Gu
- Department of Rheumatology, Affiliated Hospital of Nantong University, 226001, Nantong, China
| | - Xingxing Mao
- Department of Orthopaedics, Affiliated Nantong Hospital of Shanghai University, The Sixth People's Hospital of Nantong, 226001, Nantong, China.
| | - Hua Xu
- Department of Orthopaedics, Affiliated Hospital of Nantong University, Medical School of Nantong University, 226001, Nantong, China.
| | - Youhua Wang
- Department of Orthopaedics, Affiliated Hospital of Nantong University, Medical School of Nantong University, 226001, Nantong, China.
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3
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Shao J, Xu Y, Olsen RJ, Kasparian S, Sun K, Mathur S, Zhang J, He C, Chen SH, Bernicker EH, Li Z. 5-Hydroxymethylcytosine in Cell-Free DNA Predicts Immunotherapy Response in Lung Cancer. Cells 2024; 13:715. [PMID: 38667328 PMCID: PMC11049556 DOI: 10.3390/cells13080715] [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: 02/21/2024] [Revised: 04/04/2024] [Accepted: 04/17/2024] [Indexed: 04/28/2024] Open
Abstract
Immune checkpoint inhibitors (ICIs) drastically improve therapeutic outcomes for lung cancer, but accurately predicting individual patient responses to ICIs remains a challenge. We performed the genome-wide profiling of 5-hydroxymethylcytosine (5hmC) in 85 plasma cell-free DNA (cfDNA) samples from lung cancer patients and developed a 5hmC signature that was significantly associated with progression-free survival (PFS). We built a 5hmC predictive model to quantify the 5hmC level and validated the model in the validation, test, and control sets. Low weighted predictive scores (wp-scores) were significantly associated with a longer PFS compared to high wp-scores in the validation [median 7.6 versus 1.8 months; p = 0.0012; hazard ratio (HR) 0.12; 95% confidence interval (CI), 0.03-0.54] and test (median 14.9 versus 3.3 months; p = 0.00074; HR 0.10; 95% CI, 0.02-0.50) sets. Objective response rates in patients with a low or high wp-score were 75.0% (95% CI, 42.8-94.5%) versus 0.0% (95% CI, 0.0-60.2%) in the validation set (p = 0.019) and 80.0% (95% CI, 44.4-97.5%) versus 0.0% (95% CI, 0.0-36.9%) in the test set (p = 0.0011). The wp-scores were also significantly associated with PFS in patients receiving single-agent ICI treatment (p < 0.05). In addition, the 5hmC predictive signature demonstrated superior predictive capability to tumor programmed death-ligand 1 and specificity to ICI treatment response prediction. Moreover, we identified novel 5hmC-associated genes and signaling pathways integral to ICI treatment response in lung cancer. This study provides proof-of-concept evidence that the cfDNA 5hmC signature is a robust biomarker for predicting ICI treatment response in lung cancer.
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Affiliation(s)
- Jianming Shao
- Department of Pathology and Genomic Medicine, Houston Methodist Hospital, Houston, TX 77030, USA (R.J.O.)
- Houston Methodist Research Institute, Houston, TX 77030, USA (S.M.); (S.-H.C.)
| | - Yitian Xu
- Houston Methodist Research Institute, Houston, TX 77030, USA (S.M.); (S.-H.C.)
| | - Randall J. Olsen
- Department of Pathology and Genomic Medicine, Houston Methodist Hospital, Houston, TX 77030, USA (R.J.O.)
- Houston Methodist Research Institute, Houston, TX 77030, USA (S.M.); (S.-H.C.)
- Weill Cornell Medical College, New York, NY 10065, USA
| | - Saro Kasparian
- Neal Cancer Center, Houston Methodist Hospital, Houston, TX 77030, USA (E.H.B.)
- Department of Medical Oncology, City of Hope Comprehensive Cancer Center, Duarte, CA 91010, USA
| | - Kai Sun
- Weill Cornell Medical College, New York, NY 10065, USA
- Neal Cancer Center, Houston Methodist Hospital, Houston, TX 77030, USA (E.H.B.)
| | - Sunil Mathur
- Houston Methodist Research Institute, Houston, TX 77030, USA (S.M.); (S.-H.C.)
- Neal Cancer Center, Houston Methodist Hospital, Houston, TX 77030, USA (E.H.B.)
| | - Jun Zhang
- Weill Cornell Medical College, New York, NY 10065, USA
- Neal Cancer Center, Houston Methodist Hospital, Houston, TX 77030, USA (E.H.B.)
| | - Chuan He
- Department of Chemistry, Department of Biochemistry and Molecular Biology, Institute for Biophysical Dynamics, The University of Chicago, Chicago, IL 60637, USA
- Howard Hughes Medical Institute, The University of Chicago, Chicago, IL 60637, USA
| | - Shu-Hsia Chen
- Houston Methodist Research Institute, Houston, TX 77030, USA (S.M.); (S.-H.C.)
- Neal Cancer Center, Houston Methodist Hospital, Houston, TX 77030, USA (E.H.B.)
| | - Eric H. Bernicker
- Neal Cancer Center, Houston Methodist Hospital, Houston, TX 77030, USA (E.H.B.)
| | - Zejuan Li
- Department of Pathology and Genomic Medicine, Houston Methodist Hospital, Houston, TX 77030, USA (R.J.O.)
- Houston Methodist Research Institute, Houston, TX 77030, USA (S.M.); (S.-H.C.)
- Weill Cornell Medical College, New York, NY 10065, USA
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4
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Advani J, Mehta PA, Hamel AR, Mehrotra S, Kiel C, Strunz T, Corso-Díaz X, Kwicklis M, van Asten F, Ratnapriya R, Chew EY, Hernandez DG, Montezuma SR, Ferrington DA, Weber BHF, Segrè AV, Swaroop A. QTL mapping of human retina DNA methylation identifies 87 gene-epigenome interactions in age-related macular degeneration. Nat Commun 2024; 15:1972. [PMID: 38438351 PMCID: PMC10912779 DOI: 10.1038/s41467-024-46063-8] [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: 06/08/2023] [Accepted: 02/12/2024] [Indexed: 03/06/2024] Open
Abstract
DNA methylation provides a crucial epigenetic mark linking genetic variations to environmental influence. We have analyzed array-based DNA methylation profiles of 160 human retinas with co-measured RNA-seq and >8 million genetic variants, uncovering sites of genetic regulation in cis (37,453 methylation quantitative trait loci and 12,505 expression quantitative trait loci) and 13,747 DNA methylation loci affecting gene expression, with over one-third specific to the retina. Methylation and expression quantitative trait loci show non-random distribution and enrichment of biological processes related to synapse, mitochondria, and catabolism. Summary data-based Mendelian randomization and colocalization analyses identify 87 target genes where methylation and gene-expression changes likely mediate the genotype effect on age-related macular degeneration. Integrated pathway analysis reveals epigenetic regulation of immune response and metabolism including the glutathione pathway and glycolysis. Our study thus defines key roles of genetic variations driving methylation changes, prioritizes epigenetic control of gene expression, and suggests frameworks for regulation of macular degeneration pathology by genotype-environment interaction in retina.
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Affiliation(s)
- Jayshree Advani
- Neurobiology, Neurodegeneration and Repair Laboratory, National Eye Institute, National Institutes of Health, Bethesda, MD, USA
| | - Puja A Mehta
- Ocular Genomics Institute, Department of Ophthalmology, Massachusetts Eye and Ear, Boston, MA, USA
- Department of Ophthalmology, Harvard Medical School, Boston, MA, USA
- Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | - Andrew R Hamel
- Ocular Genomics Institute, Department of Ophthalmology, Massachusetts Eye and Ear, Boston, MA, USA
- Department of Ophthalmology, Harvard Medical School, Boston, MA, USA
- Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | - Sudeep Mehrotra
- Ocular Genomics Institute, Department of Ophthalmology, Massachusetts Eye and Ear, Boston, MA, USA
- Department of Ophthalmology, Harvard Medical School, Boston, MA, USA
- Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | - Christina Kiel
- Institute of Human Genetics, University of Regensburg, Regensburg, Germany
| | - Tobias Strunz
- Institute of Human Genetics, University of Regensburg, Regensburg, Germany
| | - Ximena Corso-Díaz
- Neurobiology, Neurodegeneration and Repair Laboratory, National Eye Institute, National Institutes of Health, Bethesda, MD, USA
| | - Madeline Kwicklis
- Neurobiology, Neurodegeneration and Repair Laboratory, National Eye Institute, National Institutes of Health, Bethesda, MD, USA
| | - Freekje van Asten
- Neurobiology, Neurodegeneration and Repair Laboratory, National Eye Institute, National Institutes of Health, Bethesda, MD, USA
| | - Rinki Ratnapriya
- Neurobiology, Neurodegeneration and Repair Laboratory, National Eye Institute, National Institutes of Health, Bethesda, MD, USA
| | - Emily Y Chew
- Division of Epidemiology and Clinical Applications, Clinical Trials Branch, National Eye Institute, National Institutes of Health, Bethesda, MD, USA
| | - Dena G Hernandez
- Laboratory of Neurogenetics, National Institute of Aging, National Institutes of Health, Bethesda, MD, USA
| | - Sandra R Montezuma
- Department of Ophthalmology and Visual Neurosciences, University of Minnesota, Minneapolis, MN, USA
| | - Deborah A Ferrington
- Department of Ophthalmology and Visual Neurosciences, University of Minnesota, Minneapolis, MN, USA
- Doheny Eye Institute, Pasadena, CA, USA
| | - Bernhard H F Weber
- Institute of Human Genetics, University of Regensburg, Regensburg, Germany
- Institute of Clinical Human Genetics, University Hospital Regensburg, Regensburg, Germany
| | - Ayellet V Segrè
- Ocular Genomics Institute, Department of Ophthalmology, Massachusetts Eye and Ear, Boston, MA, USA.
- Department of Ophthalmology, Harvard Medical School, Boston, MA, USA.
- Broad Institute of MIT and Harvard, Cambridge, MA, USA.
| | - Anand Swaroop
- Neurobiology, Neurodegeneration and Repair Laboratory, National Eye Institute, National Institutes of Health, Bethesda, MD, USA.
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5
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Cheng Y, Liang X, Bi X, Liu C, Yang Y. Identification ATP5F1D as a Biomarker Linked to Diagnosis, Prognosis, and Immune Infiltration in Endometrial Cancer Based on Data-Independent Acquisition (DIA) Analysis. Biochem Genet 2024:10.1007/s10528-023-10646-9. [PMID: 38265620 DOI: 10.1007/s10528-023-10646-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/12/2023] [Accepted: 12/19/2023] [Indexed: 01/25/2024]
Abstract
In developed countries, endometrial cancer (EC) is the most prevalent gynecological cancer. ATP5F1D is a subunit of ATP synthase, as well as an important component of the mitochondrial electron transport chain (ETC). ETC plays a compelling role in carcinogenesis. To date, little is known about the role of ATP5F1D in EC. We undertook data-independent acquisition mass spectrometry (DIA-MS) of 20 EC patients, comprising 10 high-grade and 10 low-grade cancer tissues. Biological functions of differentially expressed genes (DEGs) were analyzed by GO and KEGG. The expression level, clinicopathological features, diagnostic potency, prognostic value, RNA modifications, immune characteristics, and therapy response of ATP5F1D were investigated. In total, 77 DEGs were acquired by DIA analysis, which were closely related to regulating immune response and metabolic pathways. Among the five genes (NDUFB8, SLC26A2, RAF1, ATP5F1D, and GSTM5) involving in reactive oxygen species pathway, ATP5F1D showed the most significant differential expression (2.903-fold change). We found ATP5F1D had a high diagnostic value and was associated with a favorable prognosis in EC patients. After analyzing the RNA modifications of ATP5F1D, revealing a negative regulation between them. Additionally, ATP5F1D was closely related to tumor immune infiltration. Our results suggested T-cell dysfunction and TAM-M2 polarization might be the important mechanisms of ATP5F1D to facilitate tumor immune escape. Noticeably, EC patients with ATP5F1D-high expression had better immune treatment responses and were more sensitive to chemotherapy drugs. ATP5F1D can be used as a biomarker for diagnosis, prognosis, and immune infiltration of EC, and offers a crucial reference for personalized treatment of EC patients.
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Affiliation(s)
- Yuemei Cheng
- The First Clinical Medical College of Lanzhou University, Department of Obstetrics and Gynecology, Gansu Provincial Clinical Research Center for Gynecological Oncology, Lanzhou, 730000, Gansu, China
| | - Xiaolei Liang
- Department of Obstetrics and Gynecology, The First Hospital of Lanzhou University, Gansu Provincial Clinical Research Center for Gynecological Oncology, Lanzhou, 730000, Gansu, China
| | - Xuehan Bi
- Department of Obstetrics and Gynecology, The First Hospital of Lanzhou University, Gansu Provincial Clinical Research Center for Gynecological Oncology, Lanzhou, 730000, Gansu, China
| | - Chang Liu
- Department of Obstetrics and Gynecology, The First Hospital of Lanzhou University, Gansu Provincial Clinical Research Center for Gynecological Oncology, Lanzhou, 730000, Gansu, China
| | - Yongxiu Yang
- Department of Obstetrics and Gynecology, The First Hospital of Lanzhou University, Gansu Provincial Clinical Research Center for Gynecological Oncology, Lanzhou, 730000, Gansu, China.
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6
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Ke C, Chen C, Yang M, Chen H, Li L, Ke Y. Revealing the mechanism of 755-nm long-pulsed alexandrite laser in inhibiting infantile hemangioma endothelial cells through transcriptome sequencing. Lasers Med Sci 2024; 39:37. [PMID: 38236327 PMCID: PMC10796541 DOI: 10.1007/s10103-023-03967-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: 09/12/2023] [Accepted: 12/27/2023] [Indexed: 01/19/2024]
Abstract
Laser therapy has shown promising outcomes in treating infantile hemangiomas. However, the molecular mechanisms underlying laser treatment for IH remain incompletely elucidated. This study aimed to unravel the molecular mechanisms of laser therapy in IH treatment. We evaluated the inhibitory effects of laser treatment on the proliferation and promotion of apoptosis in human hemangioma endothelial cells (HemECs) through cell counting kit-8 (CCK-8) assay, Hoechst 33342 staining, and flow cytometric analysis. Transcriptome sequencing analysis of HemECs following laser treatment revealed a significant decrease in the expression level of the GSTM5 gene. The qRT-PCR and western blot analysis also showed that GSTM5 expression in HemECs was downregulated compared to human umbilical vein endothelial cells (HUVECs), and concomitantly, the p62-Nrf2 pathway was suppressed. Using siRNA to downregulate GSTM5 expression, we observed that inhibiting GSTM5 expression could restrain cell proliferation, elevate intracellular ROS levels, and induce apoptosis in HemECs. Furthermore, upon inhibition of the p62-Nrf2 pathway using p62-specific siRNA, a significant decrease in GSTM5 expression and an elevation in intracellular ROS levels were noted in laser-treated HemECs. These findings suggested that laser treatment may operate by inhibiting the p62-Nrf2 pathway, thereby downregulating GSTM5 expression, elevating ROS levels, and consequently inducing apoptosis in HemECs.
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Affiliation(s)
- Chen Ke
- Plastic Surgery, The First Affiliated Hospital of Wenzhou Medical University, Nanbaixiang, Wenzhou, 325000, Zhejiang, China
| | - Changhan Chen
- Department of Cosmetology, Wenzhou Hospital of Integrated Traditional Chinese and Western Medicine, Wenzhou, 325000, Zhejiang, China
| | - Ming Yang
- Department of Cosmetology, Wenzhou Hospital of Integrated Traditional Chinese and Western Medicine, Wenzhou, 325000, Zhejiang, China
| | - Hao Chen
- Department of Cosmetology, Wenzhou Hospital of Integrated Traditional Chinese and Western Medicine, Wenzhou, 325000, Zhejiang, China
| | - Liqun Li
- Plastic Surgery, The First Affiliated Hospital of Wenzhou Medical University, Nanbaixiang, Wenzhou, 325000, Zhejiang, China.
| | - Youhui Ke
- Department of Cosmetology, Wenzhou Hospital of Integrated Traditional Chinese and Western Medicine, Wenzhou, 325000, Zhejiang, China.
- Wenzhou Key Laboratory of Laser Cosmetology, Wenzhou, 325000, Zhejiang, China.
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7
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Shi H, Yuan X, Liu G, Fan W. Identifying and Validating GSTM5 as an Immunogenic Gene in Diabetic Foot Ulcer Using Bioinformatics and Machine Learning. J Inflamm Res 2023; 16:6241-6256. [PMID: 38145013 PMCID: PMC10748866 DOI: 10.2147/jir.s442388] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/31/2023] [Accepted: 12/12/2023] [Indexed: 12/26/2023] Open
Abstract
Background A diabetic foot ulcer (DFU) is a serious, long-term condition associated with a significant risk of disability and mortality. However, research on its biomarkers is still limited. This study utilizes bioinformatics and machine learning methods to identify immune-related biomarkers for DFU and validates them through external datasets and animal experiments. Methods This study used bioinformatics and machine learning to analyze microarray data from the Gene Expression Omnibus (GEO) database to identify key genes associated with DFU. Animal experiments were conducted to validate these findings. This research employs the datasets GSE68183 and GSE80178 retrieved from the GEO database as the training dataset for building a gene machine learning model, and after conducting differential analysis on the data, this study used package glmnet and package e1071 to construct LASSO and SVM-RFE machine learning models, respectively. Subsequently, we validated the model using the training set and validation set (GSE134431). We conducted enrichment analysis, including GSEA and GSVA, on the model genes. We also performed immune functional analysis and immune-related analysis on the model genes. Finally, we conducted immunohistochemistry (IHC) validation on the model genes. Results This study identifies GSTM5 as a potential immune-related key target in DFU using machine learning and bioinformatics methods. Subsequent validation through external datasets and IHC experiments also confirms GSTM5 as a critical biomarker for DFU. The gene may be associated with T cells regulatory (Tregs) and T cells follicular helper, and it influences the NF-κB, GnRH, and MAPK signaling pathway. Conclusion This study identified and validated GSTM5 as a biomarker for DFU. This finding may potentially provide a target for immune therapy for DFU.
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Affiliation(s)
- Hongshuo Shi
- Department of Peripheral Vascular Surgery, Institute of Surgery of Traditional Chinese Medicine, Shuguang Hospital Affiliated to Shanghai University of Traditional Chinese Medicine, Shanghai, People’s Republic of China
| | - Xin Yuan
- Department of Peripheral Vascular Surgery, Institute of Surgery of Traditional Chinese Medicine, Shuguang Hospital Affiliated to Shanghai University of Traditional Chinese Medicine, Shanghai, People’s Republic of China
| | - Guobin Liu
- Department of Peripheral Vascular Surgery, Institute of Surgery of Traditional Chinese Medicine, Shuguang Hospital Affiliated to Shanghai University of Traditional Chinese Medicine, Shanghai, People’s Republic of China
| | - Weijing Fan
- Department of Peripheral Vascular Surgery, Institute of Surgery of Traditional Chinese Medicine, Shuguang Hospital Affiliated to Shanghai University of Traditional Chinese Medicine, Shanghai, People’s Republic of China
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8
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Advani J, Corso-Diaz X, Kwicklis M, van Asten F, Ratnapriya R, Mehta P, Hamel A, Mahrotra S, Segrè A, Kiel C, Strunz T, Weber B, Chew E, Hernandez D, Montezuma S, Ferrington D, Swaroop A. QTL mapping of human retina DNA methylation identifies 87 gene-epigenome interactions in age-related macular degeneration. RESEARCH SQUARE 2023:rs.3.rs-3011096. [PMID: 37398472 PMCID: PMC10312909 DOI: 10.21203/rs.3.rs-3011096/v1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 07/04/2023]
Abstract
DNA methylation (DNAm) provides a crucial epigenetic mark linking genetic variations to environmental influence. We analyzed array-based DNAm profiles of 160 human retinas with co-measured RNA-seq and > 8 million genetic variants, uncovering sites of genetic regulation in cis (37,453 mQTLs and 12,505 eQTLs) and 13,747 eQTMs (DNAm loci affecting gene expression), with over one-third specific to the retina. mQTLs and eQTMs show non-random distribution and enrichment of biological processes related to synapse, mitochondria, and catabolism. Summary data-based Mendelian randomization and colocalization analyses identify 87 target genes where methylation and gene-expression changes likely mediate the genotype effect on age-related macular degeneration (AMD). Integrated pathway analysis reveals epigenetic regulation of immune response and metabolism including the glutathione pathway and glycolysis. Our study thus defines key roles of genetic variations driving methylation changes, prioritizes epigenetic control of gene expression, and suggests frameworks for regulation of AMD pathology by genotype-environment interaction in retina.
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Affiliation(s)
| | | | | | | | | | - Puja Mehta
- Department of Ophthalmology, Massachusetts Eye and Ear, Harvard Medical School, Boston, MA, USA
| | - Andrew Hamel
- Department of Ophthalmology, Massachusetts Eye and Ear
| | | | | | | | | | | | - Emily Chew
- National Eye Institute/National Institutes of Health
| | | | | | | | - Anand Swaroop
- National Eye Institute, National Institutes of Health
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9
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Bhat A, Abu R, Jagadesan S, Vellichirammal NN, Pendyala VV, Yu L, Rudebush TL, Guda C, Zucker IH, Kumar V, Gao L. Quantitative Proteomics Identifies Novel Nrf2-Mediated Adaptative Signaling Pathways in Skeletal Muscle Following Exercise Training. Antioxidants (Basel) 2023; 12:151. [PMID: 36671013 PMCID: PMC9854705 DOI: 10.3390/antiox12010151] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/05/2022] [Revised: 12/31/2022] [Accepted: 01/06/2023] [Indexed: 01/11/2023] Open
Abstract
Exercise training (ExT) improves skeletal muscle health via multiple adaptative pathways. Nrf2 is a principal antioxidant transcription factor responsible for maintaining intracellular redox homeostasis. In this study, we hypothesized that Nrf2 is essential for adaptative responses to ExT and thus beneficial for muscle. Experiments were carried out on male wild type (WT) and iMS-Nrf2flox/flox inducible muscle-specific Nrf2 (KO) mice, which were randomly assigned to serve as sedentary controls (Sed) or underwent 3 weeks of treadmill ExT thus generating four groups: WT-Sed, WT-ExT, KO-Sed, and KO-ExT groups. Mice were examined for exercise performance and in situ tibialis anterior (TA) contractility, followed by mass spectrometry-based proteomics and bioinformatics to identify differentially expressed proteins and signaling pathways. We found that maximal running distance was significantly longer in the WT-ExT group compared to the WT-Sed group, whereas this capacity was impaired in KO-ExT mice. Force generation and fatigue tolerance of the TA were enhanced in WT-ExT, but reduced in KO-ExT, compared to Sed controls. Proteomic analysis further revealed that ExT upregulated 576 proteins in WT but downregulated 207 proteins in KO mice. These proteins represent pathways in redox homeostasis, mitochondrial respiration, and proteomic adaptation of muscle to ExT. In summary, our data suggest a critical role of Nrf2 in the beneficial effects of SkM and adaptation to ExT.
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Affiliation(s)
- Anjali Bhat
- Department of Anesthesiology, University of Nebraska Medical Center, Omaha, NE 68198, USA
| | - Rafay Abu
- Mass Spectrometry and Proteomics Core Facility, University of Nebraska Medical Center, Omaha, NE 68198, USA
- Department of Biochemistry, Glocal University, Saharanpur 247121, Uttar Pradesh, India
| | | | | | - Ved Vasishtha Pendyala
- Department of Anesthesiology, University of Nebraska Medical Center, Omaha, NE 68198, USA
| | - Li Yu
- Department of Cellular & Integrative Physiology, University of Nebraska Medical Center, Omaha, NE 68198, USA
| | - Tara L. Rudebush
- Department of Cellular & Integrative Physiology, University of Nebraska Medical Center, Omaha, NE 68198, USA
| | - Chittibabu Guda
- Department of Genetics, Cell Biology & Anatomy, University of Nebraska Medical Center, Omaha, NE 68198, USA
| | - Irving H. Zucker
- Department of Cellular & Integrative Physiology, University of Nebraska Medical Center, Omaha, NE 68198, USA
| | - Vikas Kumar
- Mass Spectrometry and Proteomics Core Facility, University of Nebraska Medical Center, Omaha, NE 68198, USA
- Department of Genetics, Cell Biology & Anatomy, University of Nebraska Medical Center, Omaha, NE 68198, USA
| | - Lie Gao
- Department of Anesthesiology, University of Nebraska Medical Center, Omaha, NE 68198, USA
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