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Zhu C, Baumgarten N, Wu M, Wang Y, Das AP, Kaur J, Ardakani FB, Duong TT, Pham MD, Duda M, Dimmeler S, Yuan T, Schulz MH, Krishnan J. CVD-associated SNPs with regulatory potential reveal novel non-coding disease genes. Hum Genomics 2023; 17:69. [PMID: 37491351 PMCID: PMC10369730 DOI: 10.1186/s40246-023-00513-4] [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: 02/26/2023] [Accepted: 07/12/2023] [Indexed: 07/27/2023] Open
Abstract
BACKGROUND Cardiovascular diseases (CVDs) are the leading cause of death worldwide. Genome-wide association studies (GWAS) have identified many single nucleotide polymorphisms (SNPs) appearing in non-coding genomic regions in CVDs. The SNPs may alter gene expression by modifying transcription factor (TF) binding sites and lead to functional consequences in cardiovascular traits or diseases. To understand the underlying molecular mechanisms, it is crucial to identify which variations are involved and how they affect TF binding. METHODS The SNEEP (SNP exploration and analysis using epigenomics data) pipeline was used to identify regulatory SNPs, which alter the binding behavior of TFs and link GWAS SNPs to their potential target genes for six CVDs. The human-induced pluripotent stem cells derived cardiomyocytes (hiPSC-CMs), monoculture cardiac organoids (MCOs) and self-organized cardiac organoids (SCOs) were used in the study. Gene expression, cardiomyocyte size and cardiac contractility were assessed. RESULTS By using our integrative computational pipeline, we identified 1905 regulatory SNPs in CVD GWAS data. These were associated with hundreds of genes, half of them non-coding RNAs (ncRNAs), suggesting novel CVD genes. We experimentally tested 40 CVD-associated non-coding RNAs, among them RP11-98F14.11, RPL23AP92, IGBP1P1, and CTD-2383I20.1, which were upregulated in hiPSC-CMs, MCOs and SCOs under hypoxic conditions. Further experiments showed that IGBP1P1 depletion rescued expression of hypertrophic marker genes, reduced hypoxia-induced cardiomyocyte size and improved hypoxia-reduced cardiac contractility in hiPSC-CMs and MCOs. CONCLUSIONS IGBP1P1 is a novel ncRNA with key regulatory functions in modulating cardiomyocyte size and cardiac function in our disease models. Our data suggest ncRNA IGBP1P1 as a potential therapeutic target to improve cardiac function in CVDs.
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Affiliation(s)
- Chaonan Zhu
- Institute for Cardiovascular Regeneration, Goethe University, 60590, Frankfurt Am Main, Germany
- Cardio-Pulmonary Institute, Goethe University Hospital, 60590, Frankfurt Am Main, Germany
| | - Nina Baumgarten
- Institute for Cardiovascular Regeneration, Goethe University, 60590, Frankfurt Am Main, Germany
- German Center for Cardiovascular Research, Partner Site Rhein-Main, 60590, Frankfurt Am Main, Germany
- Cardio-Pulmonary Institute, Goethe University Hospital, 60590, Frankfurt Am Main, Germany
| | - Meiqian Wu
- Institute for Cardiovascular Regeneration, Goethe University, 60590, Frankfurt Am Main, Germany
| | - Yue Wang
- Institute for Cardiovascular Regeneration, Goethe University, 60590, Frankfurt Am Main, Germany
| | - Arka Provo Das
- Institute for Cardiovascular Regeneration, Goethe University, 60590, Frankfurt Am Main, Germany
- Cardio-Pulmonary Institute, Goethe University Hospital, 60590, Frankfurt Am Main, Germany
| | - Jaskiran Kaur
- Institute for Cardiovascular Regeneration, Goethe University, 60590, Frankfurt Am Main, Germany
| | - Fatemeh Behjati Ardakani
- Institute for Cardiovascular Regeneration, Goethe University, 60590, Frankfurt Am Main, Germany
- German Center for Cardiovascular Research, Partner Site Rhein-Main, 60590, Frankfurt Am Main, Germany
- Cardio-Pulmonary Institute, Goethe University Hospital, 60590, Frankfurt Am Main, Germany
| | - Thanh Thuy Duong
- Genome Biologics, Theodor-Stern-Kai 7, 60590, Frankfurt Am Main, Germany
| | - Minh Duc Pham
- Institute for Cardiovascular Regeneration, Goethe University, 60590, Frankfurt Am Main, Germany
- Cardio-Pulmonary Institute, Goethe University Hospital, 60590, Frankfurt Am Main, Germany
- Department of Medicine III, Cardiology/Angiology/ Nephrology, Goethe University Hospital, Frankfurt, Germany
- Genome Biologics, Theodor-Stern-Kai 7, 60590, Frankfurt Am Main, Germany
| | - Maria Duda
- Genome Biologics, Theodor-Stern-Kai 7, 60590, Frankfurt Am Main, Germany
| | - Stefanie Dimmeler
- Institute for Cardiovascular Regeneration, Goethe University, 60590, Frankfurt Am Main, Germany
- German Center for Cardiovascular Research, Partner Site Rhein-Main, 60590, Frankfurt Am Main, Germany
- Cardio-Pulmonary Institute, Goethe University Hospital, 60590, Frankfurt Am Main, Germany
| | - Ting Yuan
- Institute for Cardiovascular Regeneration, Goethe University, 60590, Frankfurt Am Main, Germany.
- Cardio-Pulmonary Institute, Goethe University Hospital, 60590, Frankfurt Am Main, Germany.
- Department of Medicine III, Cardiology/Angiology/ Nephrology, Goethe University Hospital, Frankfurt, Germany.
| | - Marcel H Schulz
- Institute for Cardiovascular Regeneration, Goethe University, 60590, Frankfurt Am Main, Germany.
- German Center for Cardiovascular Research, Partner Site Rhein-Main, 60590, Frankfurt Am Main, Germany.
- Cardio-Pulmonary Institute, Goethe University Hospital, 60590, Frankfurt Am Main, Germany.
| | - Jaya Krishnan
- Institute for Cardiovascular Regeneration, Goethe University, 60590, Frankfurt Am Main, Germany.
- German Center for Cardiovascular Research, Partner Site Rhein-Main, 60590, Frankfurt Am Main, Germany.
- Cardio-Pulmonary Institute, Goethe University Hospital, 60590, Frankfurt Am Main, Germany.
- Department of Medicine III, Cardiology/Angiology/ Nephrology, Goethe University Hospital, Frankfurt, Germany.
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Ebaid AM, Ezzeldin N, Abdelhady EI, Mohammed HA, Abdallah AL. Validity of immunoglobulin-binding protein 1 as a biomarker for lupus nephritis. Lupus 2023; 32:101-110. [PMID: 36418233 DOI: 10.1177/09612033221141278] [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: 11/27/2022]
Abstract
BACKGROUND Lupus nephritis (LN) is a major issue that adds a burden on patients with systemic lupus erythematosus (SLE). Immunoglobulin-binding protein 1 (IGBP1) is identified as a phosphoprotein that has been recently reported to be linked to the B-cell receptor complex and regulates differentiation, proliferation, apoptosis, and tolerance of B cells. Its diagnostic and/or prognostic role in LN has been highlighted only recently. OBJECTIVES This study aims to evaluate the relation between serum IGBP1 and SLE disease activity and/or renal activity and to investigate the validity of IGBP1 as a biomarker for LN. METHODS 96 participants were enrolled and divided into three groups: nephritis, nonnephritis, and control groups. The patients with SLE were diagnosed according to the Systemic Lupus International Collaborating Clinics classification (SLICC) criteria. The serum IGBP1 level was assayed using an enzyme-linked immunosorbent assay (ELISA). Assessments were conducted using the Systemic Lupus Erythematosus Disease Activity Index 2000 (SLEDAI-2k) and renal biopsy for LN patients. RESULTS The nephritis and nonnephritis groups had higher IGBP1 levels than the controls; the nephritis group had the highest serum IGBP1 levels (p < .001). Significant correlations were found between IGBP1 levels and proteinuria (r = 0.568, p = .001) and renal SLEDAI (r = 0.475, p = .006) in the nephritis group; on the other hand, the correlation of serum IGBP1 levels with SLEDAI-2K was non-significant for both groups (nephritis and nonnephritis groups). The IGBP1 levels were significantly different among histopathologic classes (p < .001), with class V showing the highest level. Moreover, it showed a significant positive correlation with the pathologic activity index. Compared with renal SLEDAI for identifying active renal affection in patients with SLE, the serum IGBP1 level with a cut-off value of 547.45 ng/mL is a valid biomarker for detecting active nephritis with 93.8% sensitivity and 96.9% specificity. CONCLUSION The serum IGBP1 levels were high in patients with LN and were positively correlated with the pathologic activity index. The serum IGBP1 level of 547.45 ng/mL is a valid biomarker for detecting active nephritis. Thus, we recommend that clinicians monitor the serum IGBP1 level of patients with SLE to detect LN.
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Affiliation(s)
- Amany M Ebaid
- Faculty of Medicine, Rheumatology & Rehabilitation Department, Faculty of Medicine, 68865Zagazig University, Zagazig, Egypt
| | - Nillie Ezzeldin
- Faculty of Medicine, Rheumatology & Rehabilitation Department, Faculty of Medicine, 68865Zagazig University, Zagazig, Egypt
| | - Enas I Abdelhady
- Faculty of Medicine, Rheumatology & Rehabilitation Department, Faculty of Medicine, 68865Zagazig University, Zagazig, Egypt
| | - Heba A Mohammed
- Medical Microbiology and Immunology Department, Faculty of Medicine, 68865Zagazig University, Zagazig, Egypt
| | - Alshimaa L Abdallah
- Medical Microbiology and Immunology Department, Faculty of Medicine, 68865Zagazig University, Zagazig, Egypt
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Lindblom J, Mohan C, Parodis I. Diagnostic, predictive and prognostic biomarkers in systemic lupus erythematosus: current insights. Curr Opin Rheumatol 2022; 34:139-149. [PMID: 35013077 DOI: 10.1097/bor.0000000000000862] [Citation(s) in RCA: 14] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/25/2022]
Abstract
PURPOSE OF REVIEW Biomarkers for diagnosis, monitoring and prognosis still constitute an unmet need for systemic lupus erythematosus (SLE). Focusing on recent findings, this review summarises the current landscape of biomarkers in lupus. RECENT FINDINGS Urine activated leukocyte cell adhesion molecule (ALCAM) exhibited good diagnostic ability in SLE and lupus nephritis (LN) whereas cerebrospinal fluid neutrophil gelatinase-associated lipocalin (NGAL) showed promise in neuropsychiatric SLE. Urine ALCAM, CD163 and vascular cell adhesion molecule 1 (VCAM-1) may be useful in surveillance of LN. Urine monocyte chemoattractant protein 1 was found to predict treatment response in SLE, and urine CD163 and NGAL treatment response in LN. Serum complement component 3 (C3) and urinary VCAM-1 have been reported to portend long-term renal prognosis in LN. SUMMARY NGAL holds promise as a versatile biomarker in SLE whereas urine ALCAM, CD163 and VCAM-1 displayed good performance as biomarkers in LN. The overall lack of concerted corroboration of leading candidates across multiple cohorts and diverse populations leaves the current biomarker landscape in SLE in an urgent need for further survey and systematic validation.
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Affiliation(s)
- Julius Lindblom
- Division of Rheumatology, Department of Medicine Solna, Karolinska Institutet and Karolinska University Hospital, Stockholm, Sweden
| | - Chandra Mohan
- Department Biomedical Engineering, University of Houston, Houston, Texas, USA
| | - Ioannis Parodis
- Division of Rheumatology, Department of Medicine Solna, Karolinska Institutet and Karolinska University Hospital, Stockholm, Sweden
- Department of Rheumatology, Faculty of Medicine and Health, Örebro University, Örebro, Sweden
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