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Buradagunta CS, Arsang-Jang S, Massat B, Thapa B, Patek V, D'Souza A, Auer P, Urrutia R, Janz S, Dhakal B, Hari P, Dong J. Identification of novel loci for multiple myeloma when comparing with its precursor condition monoclonal gammopathy of unknown significance. Leukemia 2024; 38:383-385. [PMID: 37919604 PMCID: PMC11326531 DOI: 10.1038/s41375-023-02078-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/18/2023] [Revised: 10/23/2023] [Accepted: 10/27/2023] [Indexed: 11/04/2023]
Affiliation(s)
| | - Shahram Arsang-Jang
- Division of Hematology Oncology, Department of Medicine, Medical College of Wisconsin, Milwaukee, WI, USA
| | - Ben Massat
- Division of Hematology Oncology, Department of Medicine, Medical College of Wisconsin, Milwaukee, WI, USA
| | - Bicky Thapa
- Division of Hematology Oncology, Department of Medicine, Medical College of Wisconsin, Milwaukee, WI, USA
| | - Victoria Patek
- Division of Hematology Oncology, Department of Medicine, Medical College of Wisconsin, Milwaukee, WI, USA
| | - Anita D'Souza
- Division of Hematology Oncology, Department of Medicine, Medical College of Wisconsin, Milwaukee, WI, USA
| | - Paul Auer
- Division of Biostatistics, Institute for Health & Equity, and Cancer Center, Medical College of Wisconsin, Milwaukee, WI, USA
| | - Raul Urrutia
- Linda T. and John A. Mellowes Center for Genomic Sciences and Precision Medicine, Medical College of Wisconsin, Milwaukee, WI, USA
| | - Siegfried Janz
- Division of Hematology Oncology, Department of Medicine, Medical College of Wisconsin, Milwaukee, WI, USA
| | - Binod Dhakal
- Division of Hematology Oncology, Department of Medicine, Medical College of Wisconsin, Milwaukee, WI, USA
| | - Parameswaran Hari
- Division of Hematology Oncology, Department of Medicine, Medical College of Wisconsin, Milwaukee, WI, USA
| | - Jing Dong
- Division of Hematology Oncology, Department of Medicine, Medical College of Wisconsin, Milwaukee, WI, USA.
- Linda T. and John A. Mellowes Center for Genomic Sciences and Precision Medicine, Medical College of Wisconsin, Milwaukee, WI, USA.
- Medical College of Wisconsin Cancer Center, Milwaukee, WI, USA.
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Koller A, Filosi M, Weissensteiner H, Fazzini F, Gorski M, Pattaro C, Schönherr S, Forer L, Herold JM, Stark KJ, Döttelmayer P, Hicks AA, Pramstaller PP, Würzner R, Eckardt KU, Heid IM, Fuchsberger C, Lamina C, Kronenberg F. Nuclear and mitochondrial genetic variants associated with mitochondrial DNA copy number. Sci Rep 2024; 14:2083. [PMID: 38267512 PMCID: PMC10808213 DOI: 10.1038/s41598-024-52373-0] [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: 08/29/2023] [Accepted: 01/17/2024] [Indexed: 01/26/2024] Open
Abstract
Mitochondrial DNA copy number (mtDNA-CN) is a biomarker for mitochondrial dysfunction associated with several diseases. Previous genome-wide association studies (GWAS) have been performed to unravel underlying mechanisms of mtDNA-CN regulation. However, the identified gene regions explain only a small fraction of mtDNA-CN variability. Most of this data has been estimated from microarrays based on various pipelines. In the present study we aimed to (1) identify genetic loci for qPCR-measured mtDNA-CN from three studies (16,130 participants) using GWAS, (2) identify potential systematic differences between our qPCR derived mtDNA-CN measurements compared to the published microarray intensity-based estimates, and (3) disentangle the nuclear from mitochondrial regulation of the mtDNA-CN phenotype. We identified two genome-wide significant autosomal loci associated with qPCR-measured mtDNA-CN: at HBS1L (rs4895440, p = 3.39 × 10-13) and GSDMA (rs56030650, p = 4.85 × 10-08) genes. Moreover, 113/115 of the previously published SNPs identified by microarray-based analyses were significantly equivalent with our findings. In our study, the mitochondrial genome itself contributed only marginally to mtDNA-CN regulation as we only detected a single rare mitochondrial variant associated with mtDNA-CN. Furthermore, we incorporated mitochondrial haplogroups into our analyses to explore their potential impact on mtDNA-CN. However, our findings indicate that they do not exert any significant influence on our results.
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Affiliation(s)
- Adriana Koller
- Institute of Genetic Epidemiology, Medical University of Innsbruck, Schöpfstrasse 41, 6020, Innsbruck, Austria
| | - Michele Filosi
- Eurac Research, Institute for Biomedicine, Affiliated Institute of the University of Lübeck, Bolzano, Italy
| | - Hansi Weissensteiner
- Institute of Genetic Epidemiology, Medical University of Innsbruck, Schöpfstrasse 41, 6020, Innsbruck, Austria
| | - Federica Fazzini
- Institute of Genetic Epidemiology, Medical University of Innsbruck, Schöpfstrasse 41, 6020, Innsbruck, Austria
| | - Mathias Gorski
- Department of Genetic Epidemiology, University of Regensburg, Regensburg, Germany
| | - Cristian Pattaro
- Eurac Research, Institute for Biomedicine, Affiliated Institute of the University of Lübeck, Bolzano, Italy
| | - Sebastian Schönherr
- Institute of Genetic Epidemiology, Medical University of Innsbruck, Schöpfstrasse 41, 6020, Innsbruck, Austria
| | - Lukas Forer
- Institute of Genetic Epidemiology, Medical University of Innsbruck, Schöpfstrasse 41, 6020, Innsbruck, Austria
| | - Janina M Herold
- Department of Genetic Epidemiology, University of Regensburg, Regensburg, Germany
| | - Klaus J Stark
- Department of Genetic Epidemiology, University of Regensburg, Regensburg, Germany
| | - Patricia Döttelmayer
- Institute of Genetic Epidemiology, Medical University of Innsbruck, Schöpfstrasse 41, 6020, Innsbruck, Austria
| | - Andrew A Hicks
- Eurac Research, Institute for Biomedicine, Affiliated Institute of the University of Lübeck, Bolzano, Italy
| | - Peter P Pramstaller
- Eurac Research, Institute for Biomedicine, Affiliated Institute of the University of Lübeck, Bolzano, Italy
| | - Reinhard Würzner
- Institute of Hygiene and Medical Microbiology, Medical University of Innsbruck, Innsbruck, Austria
| | - Kai-Uwe Eckardt
- Department of Nephrology and Hypertension, University Hospital Erlangen, Friedrich-Alexander-Universität Erlangen-Nürnberg, Erlangen, Germany
- German Chronic Kidney Disease Study, Erlangen, Germany
- Department of Nephrology and Medical Intensive Care, Charité-Universitätsmedizin Berlin, Berlin, Germany
| | - Iris M Heid
- Department of Genetic Epidemiology, University of Regensburg, Regensburg, Germany
| | - Christian Fuchsberger
- Eurac Research, Institute for Biomedicine, Affiliated Institute of the University of Lübeck, Bolzano, Italy
| | - Claudia Lamina
- Institute of Genetic Epidemiology, Medical University of Innsbruck, Schöpfstrasse 41, 6020, Innsbruck, Austria
| | - Florian Kronenberg
- Institute of Genetic Epidemiology, Medical University of Innsbruck, Schöpfstrasse 41, 6020, Innsbruck, Austria.
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Fähnrich A, Stephan I, Hirose M, Haarich F, Awadelkareem MA, Ibrahim S, Busch H, Wohlers I. North and East African mitochondrial genetic variation needs further characterization towards precision medicine. J Adv Res 2023; 54:59-76. [PMID: 36736695 DOI: 10.1016/j.jare.2023.01.021] [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: 10/04/2022] [Revised: 01/16/2023] [Accepted: 01/26/2023] [Indexed: 02/05/2023] Open
Abstract
INTRODUCTION Mitochondria are maternally inherited cell organelles with their own genome, and perform various functions in eukaryotic cells such as energy production and cellular homeostasis. Due to their inheritance and manifold biological roles in health and disease, mitochondrial genetics serves a dual purpose of tracing the history as well as disease susceptibility of human populations across the globe. This work requires a comprehensive catalogue of commonly observed genetic variations in the mitochondrial DNAs for all regions throughout the world. So far, however, certain regions, such as North and East Africa have been understudied. OBJECTIVES To address this shortcoming, we have created the most comprehensive quality-controlled North and East African mitochondrial data set to date and use it for characterizing mitochondrial genetic variation in this region. METHODS We compiled 11 published cohorts with novel data for mitochondrial genomes from 159 Sudanese individuals. We combined these 641 mitochondrial sequences with sequences from the 1000 Genomes (n = 2504) and the Human Genome Diversity Project (n = 828) and used the tool haplocheck for extensive quality control and detection of in-sample contamination, as well as Nanopore long read sequencing for haplogroup validation of 18 samples. RESULTS Using a subset of high-coverage mitochondrial sequences, we predict 15 potentially novel haplogroups in North and East African subjects and observe likely phylogenetic deviations from the established PhyloTree reference for haplogroups L0a1 and L2a1. CONCLUSION Our findings demonstrate common hitherto unexplored variants in mitochondrial genomes of North and East Africa that lead to novel phylogenetic relationships between haplogroups present in these regions. These observations call for further in-depth population genetic studies in that region to enable the prospective use of mitochondrial genetic variation for precision medicine.
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Affiliation(s)
- Anke Fähnrich
- Medical Systems Biology Division, Lübeck Institute of Experimental Dermatology and Institute for Cardiogenetics, University of Lübeck, Ratzeburger Allee 160, 23562 Lübeck, Germany
| | - Isabel Stephan
- Medical Systems Biology Division, Lübeck Institute of Experimental Dermatology and Institute for Cardiogenetics, University of Lübeck, Ratzeburger Allee 160, 23562 Lübeck, Germany
| | - Misa Hirose
- Genetics Division, Lübeck Institute of Experimental Dermatology, University of Lübeck, Ratzeburger Allee 160, 23562 Lübeck, Germany
| | - Franziska Haarich
- Institute for Cardiogenetics, University of Lübeck, DZHK (German Research Centre for Cardiovascular Research), Partner Site Hamburg/Lübeck/Kiel, and University Heart Center, Lübeck, Lübeck, Germany
| | - Mosab Ali Awadelkareem
- Faculty of Medical Laboratory Sciences, Al-Neelain University, Khartoum, Sudan; Nuffield Department of Clinical Neurosciences, University of Oxford, Oxford OX3 9DU, United Kingdom
| | - Saleh Ibrahim
- Genetics Division, Lübeck Institute of Experimental Dermatology, University of Lübeck, Ratzeburger Allee 160, 23562 Lübeck, Germany; Khalifa University, Abu Dhabi, United Arab Emirates
| | - Hauke Busch
- Medical Systems Biology Division, Lübeck Institute of Experimental Dermatology and Institute for Cardiogenetics, University of Lübeck, Ratzeburger Allee 160, 23562 Lübeck, Germany; University Cancer Center Schleswig-Holstein, University Hospital of Schleswig-Holstein, Campus Lübeck, 23538 Lübeck, Germany
| | - Inken Wohlers
- Medical Systems Biology Division, Lübeck Institute of Experimental Dermatology and Institute for Cardiogenetics, University of Lübeck, Ratzeburger Allee 160, 23562 Lübeck, Germany; Biomedical Data Science, Research Center Borstel, 23845 Borstel, Germany.
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Association analyses of the autosomal genome and mitochondrial DNA with accelerometry-derived sleep parameters in depressed UK biobank subjects. J Psychiatr Res 2023; 157:152-161. [PMID: 36463630 DOI: 10.1016/j.jpsychires.2022.11.010] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 04/11/2022] [Revised: 09/01/2022] [Accepted: 11/12/2022] [Indexed: 11/19/2022]
Abstract
BACKGROUND The bidirectional relationship between sleep disturbances and depression is well documented, yet the biology of sleep is not fully understood. Mitochondria have become of interest not only because of the connection between sleep and metabolism but also because of mitochondria's involvement in the production of reactive oxygen species, which are largely scavenged during sleep. METHODS Genome-wide association studies (GWAS) of eight accelerometry-derived sleep measures were performed across both the autosomal and mitochondrial DNA (mtDNA) among two severity levels of depression in UK Biobank participants. We calculated SNP heritability for each of the sleep measures. Linear regression was performed to test associations and mitochondrial haplogroups. RESULTS Variants included in the GWAS accounted for moderate heritability of bedtime (19.6%, p = 4.75 × 10-7), sleep duration (16.6%, p = 8.58 × 10-6) and duration of longest sleep bout (22.6%, p = 4.64 × 10-4). No variants passed genome-wide significance in the autosomal genome. The top hit in the severe depression sample was rs145019802, near GOLGA8B, for sleep efficiency (p = 1.17 × 10-7), and the top hit in the broad depression sample was rs7100859, an intergenic SNP, and nap duration (p = 1.25 × 10-7). Top mtDNA loci were m.12633C > A of MT-ND5 with bedtime (p = 0.002) in the severe sample and m.16186C > T of the control region with nap duration (p = 0.002) in the broad sample. CONCLUSION SNP heritability estimates support the involvement of common SNPs in specific sleep measures among depressed individuals. This is the first study to analyze mtDNA variance in sleep measures in depressed individuals. Our mtDNA findings, although nominally significant, provide preliminary suggestion that mitochondria are involved in sleep.
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Non-B DNA conformations analysis through molecular dynamics simulations. Biochim Biophys Acta Gen Subj 2022; 1866:130252. [DOI: 10.1016/j.bbagen.2022.130252] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/02/2022] [Revised: 09/30/2022] [Accepted: 10/03/2022] [Indexed: 03/13/2023]
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Genome-wide post-transcriptional regulation of bovine mammary gland response to Streptococcus uberis. J Appl Genet 2022; 63:771-782. [PMID: 36066834 DOI: 10.1007/s13353-022-00722-y] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/24/2022] [Revised: 08/30/2022] [Accepted: 08/31/2022] [Indexed: 01/17/2023]
Abstract
MicroRNAs (miRNAs) as post-transcriptionally regulators of gene expression have been shown to be critical regulators to fine-tuning immune responses, besides their criteria for being an ideal biomarker. The regulatory role of miRNAs in responses to most mastitis-causing pathogens is not well understood. Gram-positive Streptococcus uberis (Str. uberis), the leading pathogen in dairy herds, cause both clinical and subclinical infections. In this study, a system biology approach was used to better understand the main post-transcriptional regulatory functions and elements of bovine mammary gland response to Str. uberis infection. Publicly available miRNA-Seq data containing 50 milk samples of the ten dairy cows (five controls and five infected) were retrieved for this current research. Functional enrichment analysis of predicted targets revealed that highly confident responsive miRNAs (4 up- and 19 downregulated) mainly regulate genes involved in the regulation of transcription, apoptotic process, regulation of cell adhesion, and pro-inflammatory signaling pathways. Time series analysis showed that six gene clusters significantly differed in comparisons between Str. uberis-induced samples with controls. Additionally, other bioinformatic analysis, including upstream network analysis, showed essential genes, including TP53 and TGFB1 and some small molecules, including glucose, curcumin, and LPS, commonly regulate most of the downregulated miRNAs. Upregulated miRNAs are commonly controlled by the most important genes, including IL1B, NEAT1, DICER1 enzyme and small molecules including estradiol, tamoxifen, estrogen, LPS, and epigallocatechin. Our study used results of next-generation sequencing to reveal key miRNAs as the main regulator of gene expression responses to a Gram-positive bacterial infection. Furthermore, by gene regulatory network (GRN) analysis, we can introduce the common upregulator transcription factor of these miRNAs. Such milk-based miRNA signature(s) would facilitate risk stratification for large-scale prevention programs and provide an opportunity for early diagnosis and therapeutic intervention.
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Lo Faro V, Nolte IM, Ten Brink JB, Snieder H, Jansonius NM, Bergen AA. Mitochondrial Genome Study Identifies Association Between Primary Open-Angle Glaucoma and Variants in MT-CYB, MT-ND4 Genes and Haplogroups. Front Genet 2021; 12:781189. [PMID: 34976016 PMCID: PMC8719162 DOI: 10.3389/fgene.2021.781189] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/22/2021] [Accepted: 11/29/2021] [Indexed: 11/21/2022] Open
Abstract
Background and purpose: Primary open-angle glaucoma (POAG) is an optic neuropathy characterized by death of retinal ganglion cells and atrophy of the optic nerve head. The susceptibility of the optic nerve to damage has been shown to be mediated by mitochondrial dysfunction. In this study, we aimed to determine a possible association between mitochondrial SNPs or haplogroups and POAG. Methods: Mitochondrial DNA single nucleotide polymorphisms (mtSNPs) were genotyped using the Illumina Infinium Global Screening Array-24 (GSA) 700K array set. Genetic analyses were performed in a POAG case-control study involving the cohorts, Groningen Longitudinal Glaucoma Study-Lifelines Cohort Study and Amsterdam Glaucoma Study, including 721 patients and 1951 controls in total. We excluded samples not passing quality control for nuclear genotypes and samples with low call rate for mitochondrial variation. The mitochondrial variants were analyzed both as SNPs and haplogroups. These were determined with the bioinformatics software HaploGrep, and logistic regression analysis was used for the association, as well as for SNPs. Results: Meta-analysis of the results from both cohorts revealed a significant association between POAG and the allele A of rs2853496 [odds ratio (OR) = 0.64; p = 0.006] within the MT-ND4 gene, and for the T allele of rs35788393 (OR = 0.75; p = 0.041) located in the MT-CYB gene. In the mitochondrial haplogroup analysis, the most significant p-value was reached by haplogroup K (p = 1.2 × 10−05), which increases the risk of POAG with an OR of 5.8 (95% CI 2.7–13.1). Conclusion: We identified an association between POAG and polymorphisms in the mitochondrial genes MT-ND4 (rs2853496) and MT-CYB (rs35788393), and with haplogroup K. The present study provides further evidence that mitochondrial genome variations are implicated in POAG. Further genetic and functional studies are required to substantiate the association between mitochondrial gene polymorphisms and POAG and to define the pathophysiological mechanisms of mitochondrial dysfunction in glaucoma.
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Affiliation(s)
- Valeria Lo Faro
- Department of Ophthalmology, University of Groningen, University Medical Center Groningen, Groningen, Netherlands
- Department of Clinical Genetics, Amsterdam University Medical Center (AMC), Amsterdam, Netherlands
| | - Ilja M. Nolte
- Department of Epidemiology, University of Groningen, University Medical Center Groningen, Groningen, Netherlands
| | - Jacoline B. Ten Brink
- Department of Clinical Genetics, Amsterdam University Medical Center (AMC), Amsterdam, Netherlands
| | - Harold Snieder
- Department of Epidemiology, University of Groningen, University Medical Center Groningen, Groningen, Netherlands
| | - Nomdo M. Jansonius
- Department of Ophthalmology, University of Groningen, University Medical Center Groningen, Groningen, Netherlands
| | - Arthur A. Bergen
- Department of Clinical Genetics, Amsterdam University Medical Center (AMC), Amsterdam, Netherlands
- Department of Ophthalmology, Amsterdam UMC, Amsterdam, Netherlands
- *Correspondence: Arthur A. Bergen,
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