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Zhuang BC, Jude MS, Konwar C, Ryan CP, Whitehead J, Engelbrecht HR, MacIsaac JL, Dever K, Toan TK, Korinek K, Zimmer Z, Huffman KM, Lee NR, McDade TW, Kuzawa CW, Belsky DW, Kobor MS. Comparison of Infinium MethylationEPIC v2.0 to v1.0 for human population epigenetics: considerations for addressing EPIC version differences in DNA methylation-based tools. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.07.02.600461. [PMID: 39005299 PMCID: PMC11245009 DOI: 10.1101/2024.07.02.600461] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 07/16/2024]
Abstract
Background The recently launched DNA methylation profiling platform, Illumina MethylationEPIC BeadChip Infinium microarray v2.0 (EPICv2), is highly correlated with measurements obtained from its predecessor MethylationEPIC BeadChip Infinium microarray v1.0 (EPICv1). However, the concordance between the two versions in the context of DNA methylation-based tools, including cell type deconvolution algorithms, epigenetic clocks, and inflammation and lifestyle biomarkers has not yet been investigated. Findings We profiled DNA methylation on both EPIC versions using matched venous blood samples from individuals spanning early to late adulthood across three cohorts. On combining the DNA methylomes of the cohorts, we observed that samples primarily clustered by the EPIC version they were measured on. Within each cohort, when we calculated cell type proportions, epigenetic age acceleration (EAA), rate of aging estimates, and biomarker scores for the matched samples on each version, we noted significant differences between EPICv1 and EPICv2 in the majority of these estimates. These differences were not significant, however, when estimates were adjusted for EPIC version or when EAAs were calculated separately for each EPIC version. Conclusions Our findings indicate that EPIC version differences predominantly explain DNA methylation variation and influence estimates of DNA methylation-based tools, and therefore we recommend caution when combining cohorts run on different versions. We demonstrate the importance of calculating DNA methylation-based estimates separately for each EPIC version or accounting for EPIC version either as a covariate in statistical models or by using version correction algorithms.
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Singh MS, Pyati A, Rubi RD, Subramanian R, Muley VY, Ansari MA, Yellaboina S. Systems-wide view of host-pathogen interactions across COVID-19 severities using integrated omics analysis. iScience 2024; 27:109087. [PMID: 38384846 PMCID: PMC10879696 DOI: 10.1016/j.isci.2024.109087] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/11/2023] [Revised: 11/07/2023] [Accepted: 01/29/2024] [Indexed: 02/23/2024] Open
Abstract
The mechanisms explaining the variability in COVID-19 clinical manifestations (mild, moderate, and severe) are not fully understood. To identify key gene expression markers linked to disease severity, we employed an integrated approach, combining host-pathogen protein-protein interaction data and viral-induced host gene expression data. We analyzed an RNA-seq dataset from peripheral blood mononuclear cells across 12 projects representing the spectrum of disease severity. We identified genes showing differential expression across mild, moderate, and severe conditions. Enrichment analysis of the pathways in host proteins targeted by each of the SARS-CoV-2 proteins revealed a strong association with processes related to ribosomal biogenesis, translation, and translocation. Interestingly, most of these pathways and associated cellular machinery, including ribosomal biogenesis, ribosomal proteins, and translation, were upregulated in mild conditions but downregulated in severe cases. This suggests that COVID-19 exhibits a paradoxical host response, boosting host/viral translation in mild cases but slowing it in severe cases.
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Affiliation(s)
- Mairembam Stelin Singh
- Department of Biochemistry, SCLS, Jamia Hamdard, New Delhi, India
- Department of Zoology, Rajiv Gandhi University, Itanagar, Arunachal Pradesh, India
| | - Anand Pyati
- All India Institute of Medical Sciences, Bibinagar, Hyderabad, Telangana 508126, India
| | - R. Devika Rubi
- Department of Computer Science and Engineering, Keshav Memorial Institute of Technology, Hyderabad, Telangana State, India
| | - Rajasekaran Subramanian
- Department of Computer Science and Engineering, Keshav Memorial Institute of Technology, Hyderabad, Telangana State, India
| | | | - Mairaj Ahmed Ansari
- Department of Biotechnology, SCLS, Jamia Hamdard, New Delhi, India
- Centre for Virology, SIST, Jamia Hamdard, New Delhi, India
| | - Sailu Yellaboina
- All India Institute of Medical Sciences, Bibinagar, Hyderabad, Telangana 508126, India
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Chen W, Li X, Jiang Y, Ni D, Yang L, Wu J, Gao M, Wang J, Song J, Shi W. Pancancer analysis of the correlations of HS6ST2 with prognosis, tumor immunity, and drug resistance. Sci Rep 2023; 13:19209. [PMID: 37932473 PMCID: PMC10628205 DOI: 10.1038/s41598-023-46525-x] [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: 04/27/2023] [Accepted: 11/02/2023] [Indexed: 11/08/2023] Open
Abstract
HS6ST2 has ability to encodes a member of the heparan sulfate (HS) sulfotransferase gene family, which catalyze the transfer of sulfate to HS and a crucial regulator of cell growth, differentiation, adhesion, and migration. Although mounting evidence supports a vital role for HS6ST2 in tumorigenesis of some cancers, no pan-cancer analysis of HS6ST2 has been reported. Therefore, we aimed to explore the prognostic value of HS6ST2 in 33 cancer types and investigate its potential immune function. Based on data from The Cancer Genome Atlas, Cancer Cell Lines Encyclopedia, Genotype Tissue Expression, and GSCA, we used a range of bioinformatics approaches to explore the potential carcinogenic role of HS6ST2, analysis of HS6ST2 and prognosis, DNA methylation, RNA methylation, microsatellite instability (MSI), tumor mutation burden (TMB), and immune cell infiltration in different tumors. The results show that HS6ST2 was highly expressed in most cancers but lower in Breast invasive carcinoma, Kidney Chromophobe, Kidney renal clear cell carcinoma, Kidney renal papillary cell carcinoma, and Uterine Corpus Endometrial Carcinoma. Moreover, HS6ST2 is positively or negatively associated with prognosis in different cancers. HS6ST2 expression was not only associated with MSI in 5 cancer types and associated with TMB in 10 cancer types, and it's significantly correlated with DNA methylation in 13 types of cancer, but it's correlated with RNA methylation related genes in most cancer. HS6ST2 expression was correlated with immune cell infiltration, immune-related genes, tumor immune microenvironment, and drug resistance in various cancers. Eventually, HS6ST2 was validated in human lung adenocarcinoma tissues. Our study reveals that HS6ST2 can function as a prognostic marker in various malignant tumors because of its role in tumorigenesis and tumor immunity.
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Affiliation(s)
- Weiwei Chen
- Medical School of Nantong University, Nantong, 226007, China
- Department of Oncology, Affiliated Hospital of Nantong University, Nantong, 226001, China
- Department of Radiotherapy, The Sixth Affiliated Hospital of Nantong University, Yancheng Third People's Hospital, The Yancheng School of Clinical Medicine of Nanjing Medical University, Yancheng, 224002, China
| | - Xia Li
- Department of General Medicine, The Sixth Affiliated Hospital of Nantong University, Yancheng Third People's Hospital, The Yancheng School of Clinical Medicine of Nanjing Medical University, Yancheng, 224002, China
| | - Youqin Jiang
- Department of Radiotherapy, The Sixth Affiliated Hospital of Nantong University, Yancheng Third People's Hospital, The Yancheng School of Clinical Medicine of Nanjing Medical University, Yancheng, 224002, China
| | - Daguang Ni
- Department of Radiotherapy, The Sixth Affiliated Hospital of Nantong University, Yancheng Third People's Hospital, The Yancheng School of Clinical Medicine of Nanjing Medical University, Yancheng, 224002, China
| | - Longfei Yang
- Medical School of Nantong University, Nantong, 226007, China
| | - Jixiang Wu
- Department of Cardiothoracic Surgery, The Sixth Affiliated Hospital of Nantong University, Yancheng Third People's Hospital, The Yancheng School of Clinical Medicine of Nanjing Medical University, Yancheng, 224002, China
| | - Mingcheng Gao
- Department of Cardiothoracic Surgery, The Sixth Affiliated Hospital of Nantong University, Yancheng Third People's Hospital, The Yancheng School of Clinical Medicine of Nanjing Medical University, Yancheng, 224002, China
| | - Jin Wang
- Department of Cardiothoracic Surgery, The Sixth Affiliated Hospital of Nantong University, Yancheng Third People's Hospital, The Yancheng School of Clinical Medicine of Nanjing Medical University, Yancheng, 224002, China.
| | - Jianxiang Song
- Department of Cardiothoracic Surgery, The Sixth Affiliated Hospital of Nantong University, Yancheng Third People's Hospital, The Yancheng School of Clinical Medicine of Nanjing Medical University, Yancheng, 224002, China.
| | - Wenyu Shi
- Medical School of Nantong University, Nantong, 226007, China.
- Department of Oncology, Affiliated Hospital of Nantong University, Nantong, 226001, China.
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Immune Functions of Astrocytes in Viral Neuroinfections. Int J Mol Sci 2023; 24:ijms24043514. [PMID: 36834929 PMCID: PMC9960577 DOI: 10.3390/ijms24043514] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/14/2022] [Revised: 02/07/2023] [Accepted: 02/08/2023] [Indexed: 02/12/2023] Open
Abstract
Neuroinfections of the central nervous system (CNS) can be triggered by various pathogens. Viruses are the most widespread and have the potential to induce long-term neurologic symptoms with potentially lethal outcomes. In addition to directly affecting their host cells and inducing immediate changes in a plethora of cellular processes, viral infections of the CNS also trigger an intense immune response. Regulation of the innate immune response in the CNS depends not only on microglia, which are fundamental immune cells of the CNS, but also on astrocytes. These cells align blood vessels and ventricle cavities, and consequently, they are one of the first cell types to become infected after the virus breaches the CNS. Moreover, astrocytes are increasingly recognized as a potential viral reservoir in the CNS; therefore, the immune response initiated by the presence of intracellular virus particles may have a profound effect on cellular and tissue physiology and morphology. These changes should be addressed in terms of persisting infections because they may contribute to recurring neurologic sequelae. To date, infections of astrocytes with different viruses originating from genetically distinct families, including Flaviviridae, Coronaviridae, Retroviridae, Togaviridae, Paramyxoviridae, Picomaviridae, Rhabdoviridae, and Herpesviridae, have been confirmed. Astrocytes express a plethora of receptors that detect viral particles and trigger signaling cascades, leading to an innate immune response. In this review, we summarize the current knowledge on virus receptors that initiate the release of inflammatory cytokines from astrocytes and depict the involvement of astrocytes in immune functions of the CNS.
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Ma Y, Shi J, Zhang Y, Chen Z, Jia G. Titanium Dioxide Nanoparticles Altered the lncRNA Expression Profile in Human Lung Cells. INTERNATIONAL JOURNAL OF ENVIRONMENTAL RESEARCH AND PUBLIC HEALTH 2023; 20:1059. [PMID: 36673815 PMCID: PMC9858630 DOI: 10.3390/ijerph20021059] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 11/25/2022] [Revised: 12/30/2022] [Accepted: 01/04/2023] [Indexed: 06/17/2023]
Abstract
Respiration is considered to be the main occupational or environmental exposure pathway of titanium dioxide nanoparticles (TiO2 NPs), and the lung is considered to be the target organ of respiratory exposure; however, the mechanism of respiratory toxicity is not fully understood. In this study, the effect of TiO2 NPs on the expression profile of long non-coding RNA (lncRNA) in bronchial epithelial cells (BEAS-2B) was investigated to understand their potential toxic mechanism. BEAS-2B cells were treated with 100 μg/mL TiO2 NPs for 48 h, then RNA sequencing was performed to screen the differential lncRNAs compared with the control group, and the enrichment pathways of the differentially expressed lncRNAs were further analyzed using the Kyoto Encyclopedia of Genes and Genomes (KEGG). The results identified a total of 45,769 lncRNAs, and 277 different lncRNAs were screened. KEGG pathway analysis showed that the targeted mRNAs of these different lncRNAs were enriched in the pyrimidine metabolism pathway. This work demonstrates that TiO2 NPs could alter the lncRNA expression profile in BEAS-2B cells, and epigenetics may play a role in the mechanism of respiratory toxicity induced by TiO2 NPs.
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Affiliation(s)
- Ying Ma
- Department of Occupational and Environmental Health Sciences, School of Public Health, Peking University, Beijing 100191, China
- Beijing Key Laboratory of Toxicological Research and Risk Assessment for Food Safety, School of Public Health, Peking University, Beijing 100191, China
| | - Jiaqi Shi
- Department of Occupational and Environmental Health Sciences, School of Public Health, Peking University, Beijing 100191, China
- Beijing Key Laboratory of Toxicological Research and Risk Assessment for Food Safety, School of Public Health, Peking University, Beijing 100191, China
| | - Yi Zhang
- Department of Occupational and Environmental Health Sciences, School of Public Health, Peking University, Beijing 100191, China
- Beijing Key Laboratory of Toxicological Research and Risk Assessment for Food Safety, School of Public Health, Peking University, Beijing 100191, China
| | - Zhangjian Chen
- Department of Occupational and Environmental Health Sciences, School of Public Health, Peking University, Beijing 100191, China
- Beijing Key Laboratory of Toxicological Research and Risk Assessment for Food Safety, School of Public Health, Peking University, Beijing 100191, China
| | - Guang Jia
- Department of Occupational and Environmental Health Sciences, School of Public Health, Peking University, Beijing 100191, China
- Beijing Key Laboratory of Toxicological Research and Risk Assessment for Food Safety, School of Public Health, Peking University, Beijing 100191, China
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Huoman J, Sayyab S, Apostolou E, Karlsson L, Porcile L, Rizwan M, Sharma S, Das J, Rosén A, Lerm M. Epigenetic rewiring of pathways related to odour perception in immune cells exposed to SARS-CoV-2 in vivo and in vitro. Epigenetics 2022; 17:1875-1891. [PMID: 35758003 PMCID: PMC9665140 DOI: 10.1080/15592294.2022.2089471] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022] Open
Abstract
A majority of SARS-CoV-2 recoverees develop only mild-to-moderate symptoms, while some remain completely asymptomatic. Although viruses, including SARS-CoV-2, may evade host immune responses by epigenetic mechanisms including DNA methylation, little is known about whether these modifications are important in defence against and healthy recovery from COVID-19 in the host. To this end, epigenome-wide DNA methylation patterns from COVID-19 convalescents were compared to uninfected controls from before and after the pandemic. Peripheral blood mononuclear cell (PBMC) DNA was extracted from uninfected controls, COVID-19 convalescents, and symptom-free individuals with SARS-CoV-2-specific T cell-responses, as well as from PBMCs stimulated in vitro with SARS-CoV-2. Subsequently, the Illumina MethylationEPIC 850K array was performed, and statistical/bioinformatic analyses comprised differential DNA methylation, pathway over-representation, and module identification analyses. Differential DNA methylation patterns distinguished COVID-19 convalescents from uninfected controls, with similar results in an experimental SARS-CoV-2 infection model. A SARS-CoV-2-induced module was identified in vivo, comprising 66 genes of which six (TP53, INS, HSPA4, SP1, ESR1, and FAS) were present in corresponding in vitro analyses. Over-representation analyses revealed involvement in Wnt, muscarinic acetylcholine receptor signalling, and gonadotropin-releasing hormone receptor pathways. Furthermore, numerous differentially methylated and network genes from both settings interacted with the SARS-CoV-2 interactome. Altered DNA methylation patterns of COVID-19 convalescents suggest recovery from mild-to-moderate SARS-CoV-2 infection leaves longstanding epigenetic traces. Both in vitro and in vivo exposure caused epigenetic modulation of pathways thataffect odour perception. Future studies should determine whether this reflects host-induced protective antiviral defense or targeted viral hijacking to evade host defence.
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Affiliation(s)
- Johanna Huoman
- Division of Inflammation and Infection, Department of Biomedical and Clinical Sciences, Linköping University, Linköping, Sweden.,Department of Dermatology and Allergy, University Hospital Bonn, Bonn, Germany
| | - Shumaila Sayyab
- Division of Inflammation and Infection, Department of Biomedical and Clinical Sciences, Linköping University, Linköping, Sweden
| | - Eirini Apostolou
- Division of Cell Biology, Department of Biomedical and Clinical Sciences, Linköping University, Linköping, Sweden
| | - Lovisa Karlsson
- Division of Inflammation and Infection, Department of Biomedical and Clinical Sciences, Linköping University, Linköping, Sweden
| | - Lucas Porcile
- Division of Inflammation and Infection, Department of Biomedical and Clinical Sciences, Linköping University, Linköping, Sweden
| | - Muhammad Rizwan
- Division of Cell Biology, Department of Biomedical and Clinical Sciences, Linköping University, Linköping, Sweden
| | - Sumit Sharma
- Division of Molecular Medicine and Virology, Department of Biomedical and Clinical Sciences, Linköping University, Linköping, Sweden
| | - Jyotirmoy Das
- Division of Inflammation and Infection, Department of Biomedical and Clinical Sciences, Linköping University, Linköping, Sweden
| | - Anders Rosén
- Division of Cell Biology, Department of Biomedical and Clinical Sciences, Linköping University, Linköping, Sweden
| | - Maria Lerm
- Division of Inflammation and Infection, Department of Biomedical and Clinical Sciences, Linköping University, Linköping, Sweden
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Sarkar S, Sen R. Insights into Cardiovascular Defects and Cardiac Epigenome in the Context of COVID-19. EPIGENOMES 2022; 6:epigenomes6020013. [PMID: 35645252 PMCID: PMC9150012 DOI: 10.3390/epigenomes6020013] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/08/2022] [Revised: 03/30/2022] [Accepted: 04/06/2022] [Indexed: 02/01/2023] Open
Abstract
Although few in number, studies on epigenome of the heart of COVID-19 patients show that epigenetic signatures such as DNA methylation are significantly altered, leading to changes in expression of several genes. It contributes to pathogenic cardiac phenotypes of COVID-19, e.g., low heart rate, myocardial edema, and myofibrillar disarray. DNA methylation studies reveal changes which likely contribute to cardiac disease through unknown mechanisms. The incidence of severe COVID-19 disease, including hospitalization, requiring respiratory support, morbidity, and mortality, is disproportionately higher in individuals with co-morbidities. This poses unprecedented strains on the global healthcare system. While their underlying conditions make patients more susceptible to severe COVID-19 disease, strained healthcare systems, lack of adequate support, or sedentary lifestyles from ongoing lockdowns have proved detrimental to their underlying health conditions, thus pushing them to severe risk of congenital heart disease (CHD) itself. Prophylactic vaccines against COVID-19 have ushered new hope for CHD. A common connection between COVID-19 and CHD is SARS-CoV-2’s host receptor ACE2, because ACE2 regulates and protects organs, including the heart, in various ways. ACE2 is a common therapeutic target against cardiovascular disease and COVID-19 which damages organs. Hence, this review explores the above regarding CHDs, cardiovascular damage, and cardiac epigenetics, in COVID-19 patients.
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Affiliation(s)
- Shreya Sarkar
- New Brunswick Heart Centre, Saint John Regional Hospital, Saint John, NB E2L 4L2, Canada;
| | - Rwik Sen
- Active Motif, Inc., 1914 Palomar Oaks Way, Suite 150, Carlsbad, CA 92008, USA
- Correspondence:
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