1
|
Bulduk BK, Tortajada J, Valiente-Pallejà A, Callado LF, Torrell H, Vilella E, Meana JJ, Muntané G, Martorell L. High number of mitochondrial DNA alterations in postmortem brain tissue of patients with schizophrenia compared to healthy controls. Psychiatry Res 2024; 337:115928. [PMID: 38759415 DOI: 10.1016/j.psychres.2024.115928] [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: 02/20/2024] [Revised: 04/12/2024] [Accepted: 04/26/2024] [Indexed: 05/19/2024]
Abstract
Previous studies have shown mitochondrial dysfunction in schizophrenia (SZ) patients, which may be caused by mitochondrial DNA (mtDNA) alterations. However, there are few studies in SZ that have analyzed mtDNA in brain samples by next-generation sequencing (NGS). To address this gap, we used mtDNA-targeted NGS and qPCR to characterize mtDNA alterations in brain samples from patients with SZ (n = 40) and healthy controls (HC) (n = 40). 35 % of SZ patients showed mtDNA alterations, a significantly higher prevalence compared to 10 % of HC. Specifically, SZ patients had a significantly higher frequency of deletions (35 vs. 5 in HC), with a mean number of deletions of 3.8 in SZ vs. 1.0 in HC. Likely pathogenic missense variants were also significantly more frequent in patients with SZ than in HC (10 vs. three HC), encompassing 14 variants in patients and three in HC. The pathogenic tRNA variant m.3243A>G was identified in one SZ patient with a high heteroplasmy level of 32.2 %. While no significant differences in mtDNA copy number (mtDNA-CN) were observed between SZ and HC, antipsychotic users had significantly higher mtDNA-CN than non-users. These findings suggest a potential role for mtDNA alterations in the pathophysiology of SZ that require further validation and functional studies.
Collapse
Affiliation(s)
- Bengisu K Bulduk
- Hospital Universitari Institut Pere Mata (HUIPM), Reus, Catalonia, Spain; Institut d'Investigació Sanitària Pere Virgili (IISPV-CERCA), Universitat Rovira i Virgili (URV), Reus, Catalonia, Spain
| | - Juan Tortajada
- Hospital Universitari Institut Pere Mata (HUIPM), Reus, Catalonia, Spain; Institut d'Investigació Sanitària Pere Virgili (IISPV-CERCA), Universitat Rovira i Virgili (URV), Reus, Catalonia, Spain
| | - Alba Valiente-Pallejà
- Hospital Universitari Institut Pere Mata (HUIPM), Reus, Catalonia, Spain; Institut d'Investigació Sanitària Pere Virgili (IISPV-CERCA), Universitat Rovira i Virgili (URV), Reus, Catalonia, Spain; Centro de Investigación Biomédica en Red de Salud Mental (CIBERSAM), Instituto de Salud Carlos III, Madrid, Spain
| | - Luís F Callado
- Centro de Investigación Biomédica en Red de Salud Mental (CIBERSAM), Instituto de Salud Carlos III, Madrid, Spain; Department of Pharmacology, University of the Basque Country, UPV/EHU, Leioa, and BioBizkaia Health Research Institute, Barakaldo, Bizkaia, Spain
| | - Helena Torrell
- Centre for Omic Sciences (COS), Joint Unit URV-EURECAT Technology Centre of Catalonia, Unique Scientific and Technical Infrastructures, Reus, Catalonia, Spain
| | - Elisabet Vilella
- Hospital Universitari Institut Pere Mata (HUIPM), Reus, Catalonia, Spain; Institut d'Investigació Sanitària Pere Virgili (IISPV-CERCA), Universitat Rovira i Virgili (URV), Reus, Catalonia, Spain; Centro de Investigación Biomédica en Red de Salud Mental (CIBERSAM), Instituto de Salud Carlos III, Madrid, Spain
| | - J Javier Meana
- Centro de Investigación Biomédica en Red de Salud Mental (CIBERSAM), Instituto de Salud Carlos III, Madrid, Spain; Department of Pharmacology, University of the Basque Country, UPV/EHU, Leioa, and BioBizkaia Health Research Institute, Barakaldo, Bizkaia, Spain
| | - Gerard Muntané
- Hospital Universitari Institut Pere Mata (HUIPM), Reus, Catalonia, Spain; Institut d'Investigació Sanitària Pere Virgili (IISPV-CERCA), Universitat Rovira i Virgili (URV), Reus, Catalonia, Spain; Centro de Investigación Biomédica en Red de Salud Mental (CIBERSAM), Instituto de Salud Carlos III, Madrid, Spain; Institut de Biologia Evolutiva (UPF-CSIC), Department of Medicine and Life Sciences, Universitat Pompeu Fabra, Parc de Recerca Biomèdica de Barcelona, Barcelona, Catalonia, Spain.
| | - Lourdes Martorell
- Hospital Universitari Institut Pere Mata (HUIPM), Reus, Catalonia, Spain; Institut d'Investigació Sanitària Pere Virgili (IISPV-CERCA), Universitat Rovira i Virgili (URV), Reus, Catalonia, Spain; Centro de Investigación Biomédica en Red de Salud Mental (CIBERSAM), Instituto de Salud Carlos III, Madrid, Spain.
| |
Collapse
|
2
|
Omidsalar AA, McCullough CG, Xu L, Boedijono S, Gerke D, Webb MG, Manojlovic Z, Sequeira A, Lew MF, Santorelli M, Serrano GE, Beach TG, Limon A, Vawter MP, Hjelm BE. Common mitochondrial deletions in RNA-Seq: evaluation of bulk, single-cell, and spatial transcriptomic datasets. Commun Biol 2024; 7:200. [PMID: 38368460 PMCID: PMC10874445 DOI: 10.1038/s42003-024-05877-4] [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: 03/15/2023] [Accepted: 01/31/2024] [Indexed: 02/19/2024] Open
Abstract
Common mitochondrial DNA (mtDNA) deletions are large structural variants in the mitochondrial genome that accumulate in metabolically active tissues with age and have been investigated in various diseases. We applied the Splice-Break2 pipeline (designed for high-throughput quantification of mtDNA deletions) to human RNA-Seq datasets and describe the methodological considerations for evaluating common deletions in bulk, single-cell, and spatial transcriptomics datasets. A robust evaluation of 1570 samples from 14 RNA-Seq studies showed: (i) the abundance of some common deletions detected in PCR-amplified mtDNA correlates with levels observed in RNA-Seq data; (ii) RNA-Seq library preparation method has a strong effect on deletion detection; (iii) deletions had a significant, positive correlation with age in brain and muscle; (iv) deletions were enriched in cortical grey matter, specifically in layers 3 and 5; and (v) brain regions with dopaminergic neurons (i.e., substantia nigra, ventral tegmental area, and caudate nucleus) had remarkable enrichment of common mtDNA deletions.
Collapse
Affiliation(s)
- Audrey A Omidsalar
- Department of Translational Genomics, Keck School of Medicine of USC, Los Angeles, CA, USA
| | - Carmel G McCullough
- Department of Translational Genomics, Keck School of Medicine of USC, Los Angeles, CA, USA
| | - Lili Xu
- Department of Translational Genomics, Keck School of Medicine of USC, Los Angeles, CA, USA
| | - Stanley Boedijono
- Department of Translational Genomics, Keck School of Medicine of USC, Los Angeles, CA, USA
| | - Daniel Gerke
- Department of Translational Genomics, Keck School of Medicine of USC, Los Angeles, CA, USA
| | - Michelle G Webb
- Department of Translational Genomics, Keck School of Medicine of USC, Los Angeles, CA, USA
| | - Zarko Manojlovic
- Department of Translational Genomics, Keck School of Medicine of USC, Los Angeles, CA, USA
| | - Adolfo Sequeira
- Department of Psychiatry and Human Behavior, University of California - Irvine (UCI) School of Medicine, Irvine, CA, USA
| | - Mark F Lew
- Department of Neurology, Keck School of Medicine of USC, Los Angeles, CA, USA
| | - Marco Santorelli
- Department of Stem Cell Biology and Regenerative Medicine, Keck School of Medicine of USC, Los Angeles, CA, USA
| | - Geidy E Serrano
- Banner Sun Health Research Institute (BSHRI), Sun City, AZ, USA
| | - Thomas G Beach
- Banner Sun Health Research Institute (BSHRI), Sun City, AZ, USA
| | - Agenor Limon
- Mitchell Center for Neurodegenerative Diseases, Department of Neurology, School of Medicine, University of Texas Medical Branch, Galveston, TX, USA
| | - Marquis P Vawter
- Department of Psychiatry and Human Behavior, University of California - Irvine (UCI) School of Medicine, Irvine, CA, USA
| | - Brooke E Hjelm
- Department of Translational Genomics, Keck School of Medicine of USC, Los Angeles, CA, USA.
| |
Collapse
|
3
|
Ugrina M, Burkhart I, Müller D, Schwalbe H, Schwierz N. RNA G-quadruplex folding is a multi-pathway process driven by conformational entropy. Nucleic Acids Res 2024; 52:87-100. [PMID: 37986217 PMCID: PMC10783511 DOI: 10.1093/nar/gkad1065] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/10/2023] [Revised: 09/25/2023] [Accepted: 10/25/2023] [Indexed: 11/22/2023] Open
Abstract
The kinetics of folding is crucial for the function of many regulatory RNAs including RNA G-quadruplexes (rG4s). Here, we characterize the folding pathways of a G-quadruplex from the telomeric repeat-containing RNA by combining all-atom molecular dynamics and coarse-grained simulations with circular dichroism experiments. The quadruplex fold is stabilized by cations and thus, the ion atmosphere forming a double layer surrounding the highly charged quadruplex guides the folding process. To capture the ionic double layer in implicit solvent coarse-grained simulations correctly, we develop a matching procedure based on all-atom simulations in explicit water. The procedure yields quantitative agreement between simulations and experiments as judged by the populations of folded and unfolded states at different salt concentrations and temperatures. Subsequently, we show that coarse-grained simulations with a resolution of three interaction sites per nucleotide are well suited to resolve the folding pathways and their intermediate states. The results reveal that the folding progresses from unpaired chain via hairpin, triplex and double-hairpin constellations to the final folded structure. The two- and three-strand intermediates are stabilized by transient Hoogsteen interactions. Each pathway passes through two on-pathway intermediates. We hypothesize that conformational entropy is a hallmark of rG4 folding. Conformational entropy leads to the observed branched multi-pathway folding process for TERRA25. We corroborate this hypothesis by presenting the free energy landscapes and folding pathways of four rG4 systems with varying loop length.
Collapse
Affiliation(s)
- Marijana Ugrina
- Institute of Physics, University of Augsburg, Universitätsstraße 1, 86159 Augsburg, Germany
- Department of Theoretical Biophysics, Max-Planck-Institute of Biophysics, Max-von-Laue-Straße 3, 60438 Frankfurt am Main, Germany
| | - Ines Burkhart
- Institute for Organic Chemistry and Chemical Biology, Center for Biomolecular Magnetic Resonance (BMRZ), Goethe University Frankfurt am Main, Max-von-Laue-Straße 7, 60438 Frankfurt am Main, Germany
| | - Diana Müller
- Institute for Organic Chemistry and Chemical Biology, Center for Biomolecular Magnetic Resonance (BMRZ), Goethe University Frankfurt am Main, Max-von-Laue-Straße 7, 60438 Frankfurt am Main, Germany
| | - Harald Schwalbe
- Institute for Organic Chemistry and Chemical Biology, Center for Biomolecular Magnetic Resonance (BMRZ), Goethe University Frankfurt am Main, Max-von-Laue-Straße 7, 60438 Frankfurt am Main, Germany
| | - Nadine Schwierz
- Institute of Physics, University of Augsburg, Universitätsstraße 1, 86159 Augsburg, Germany
| |
Collapse
|
4
|
Macken WL, Falabella M, Pizzamiglio C, Woodward CE, Scotchman E, Chitty LS, Polke JM, Bugiardini E, Hanna MG, Vandrovcova J, Chandler N, Labrum R, Pitceathly RDS. Enhanced mitochondrial genome analysis: bioinformatic and long-read sequencing advances and their diagnostic implications. Expert Rev Mol Diagn 2023; 23:797-814. [PMID: 37642407 DOI: 10.1080/14737159.2023.2241365] [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: 03/24/2023] [Accepted: 07/24/2023] [Indexed: 08/31/2023]
Abstract
INTRODUCTION Primary mitochondrial diseases (PMDs) comprise a large and heterogeneous group of genetic diseases that result from pathogenic variants in either nuclear DNA (nDNA) or mitochondrial DNA (mtDNA). Widespread adoption of next-generation sequencing (NGS) has improved the efficiency and accuracy of mtDNA diagnoses; however, several challenges remain. AREAS COVERED In this review, we briefly summarize the current state of the art in molecular diagnostics for mtDNA and consider the implications of improved whole genome sequencing (WGS), bioinformatic techniques, and the adoption of long-read sequencing, for PMD diagnostics. EXPERT OPINION We anticipate that the application of PCR-free WGS from blood DNA will increase in diagnostic laboratories, while for adults with myopathic presentations, WGS from muscle DNA may become more widespread. Improved bioinformatic strategies will enhance WGS data interrogation, with more accurate delineation of mtDNA and NUMTs (nuclear mitochondrial DNA segments) in WGS data, superior coverage uniformity, indirect measurement of mtDNA copy number, and more accurate interpretation of heteroplasmic large-scale rearrangements (LSRs). Separately, the adoption of diagnostic long-read sequencing could offer greater resolution of complex LSRs and the opportunity to phase heteroplasmic variants.
Collapse
Affiliation(s)
- William L Macken
- Department of Neuromuscular Diseases, UCL Queen Square Institute of Neurology, London, UK
- NHS Highly Specialised Service for Rare Mitochondrial Disorders, Queen Square Centre for Neuromuscular Diseases, The National Hospital for Neurology and Neurosurgery, London, UK
| | - Micol Falabella
- Department of Neuromuscular Diseases, UCL Queen Square Institute of Neurology, London, UK
| | - Chiara Pizzamiglio
- Department of Neuromuscular Diseases, UCL Queen Square Institute of Neurology, London, UK
- NHS Highly Specialised Service for Rare Mitochondrial Disorders, Queen Square Centre for Neuromuscular Diseases, The National Hospital for Neurology and Neurosurgery, London, UK
| | - Cathy E Woodward
- NHS Highly Specialised Service for Rare Mitochondrial Disorders, Queen Square Centre for Neuromuscular Diseases, The National Hospital for Neurology and Neurosurgery, London, UK
- Rare and Inherited Disease Laboratory, North Thames Genomic Laboratory Hub, Great Ormond Street Hospital for Children NHS Foundation Trust, London, UK
| | - Elizabeth Scotchman
- Rare and Inherited Disease Laboratory, North Thames Genomic Laboratory Hub, Great Ormond Street Hospital for Children NHS Foundation Trust, London, UK
| | - Lyn S Chitty
- Rare and Inherited Disease Laboratory, North Thames Genomic Laboratory Hub, Great Ormond Street Hospital for Children NHS Foundation Trust, London, UK
| | - James M Polke
- NHS Highly Specialised Service for Rare Mitochondrial Disorders, Queen Square Centre for Neuromuscular Diseases, The National Hospital for Neurology and Neurosurgery, London, UK
- Rare and Inherited Disease Laboratory, North Thames Genomic Laboratory Hub, Great Ormond Street Hospital for Children NHS Foundation Trust, London, UK
| | - Enrico Bugiardini
- Department of Neuromuscular Diseases, UCL Queen Square Institute of Neurology, London, UK
- NHS Highly Specialised Service for Rare Mitochondrial Disorders, Queen Square Centre for Neuromuscular Diseases, The National Hospital for Neurology and Neurosurgery, London, UK
| | - Michael G Hanna
- Department of Neuromuscular Diseases, UCL Queen Square Institute of Neurology, London, UK
- NHS Highly Specialised Service for Rare Mitochondrial Disorders, Queen Square Centre for Neuromuscular Diseases, The National Hospital for Neurology and Neurosurgery, London, UK
| | - Jana Vandrovcova
- Department of Neuromuscular Diseases, UCL Queen Square Institute of Neurology, London, UK
| | - Natalie Chandler
- Rare and Inherited Disease Laboratory, North Thames Genomic Laboratory Hub, Great Ormond Street Hospital for Children NHS Foundation Trust, London, UK
| | - Robyn Labrum
- NHS Highly Specialised Service for Rare Mitochondrial Disorders, Queen Square Centre for Neuromuscular Diseases, The National Hospital for Neurology and Neurosurgery, London, UK
- Rare and Inherited Disease Laboratory, North Thames Genomic Laboratory Hub, Great Ormond Street Hospital for Children NHS Foundation Trust, London, UK
| | - Robert D S Pitceathly
- Department of Neuromuscular Diseases, UCL Queen Square Institute of Neurology, London, UK
- NHS Highly Specialised Service for Rare Mitochondrial Disorders, Queen Square Centre for Neuromuscular Diseases, The National Hospital for Neurology and Neurosurgery, London, UK
| |
Collapse
|
5
|
Lareau CA, Dubois SM, Buquicchio FA, Hsieh YH, Garg K, Kautz P, Nitsch L, Praktiknjo SD, Maschmeyer P, Verboon JM, Gutierrez JC, Yin Y, Fiskin E, Luo W, Mimitou EP, Muus C, Malhotra R, Parikh S, Fleming MD, Oevermann L, Schulte J, Eckert C, Kundaje A, Smibert P, Vardhana SA, Satpathy AT, Regev A, Sankaran VG, Agarwal S, Ludwig LS. Single-cell multi-omics of mitochondrial DNA disorders reveals dynamics of purifying selection across human immune cells. Nat Genet 2023; 55:1198-1209. [PMID: 37386249 PMCID: PMC10548551 DOI: 10.1038/s41588-023-01433-8] [Citation(s) in RCA: 9] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/21/2022] [Accepted: 05/24/2023] [Indexed: 07/01/2023]
Abstract
Pathogenic mutations in mitochondrial DNA (mtDNA) compromise cellular metabolism, contributing to cellular heterogeneity and disease. Diverse mutations are associated with diverse clinical phenotypes, suggesting distinct organ- and cell-type-specific metabolic vulnerabilities. Here we establish a multi-omics approach to quantify deletions in mtDNA alongside cell state features in single cells derived from six patients across the phenotypic spectrum of single large-scale mtDNA deletions (SLSMDs). By profiling 206,663 cells, we reveal the dynamics of pathogenic mtDNA deletion heteroplasmy consistent with purifying selection and distinct metabolic vulnerabilities across T-cell states in vivo and validate these observations in vitro. By extending analyses to hematopoietic and erythroid progenitors, we reveal mtDNA dynamics and cell-type-specific gene regulatory adaptations, demonstrating the context-dependence of perturbing mitochondrial genomic integrity. Collectively, we report pathogenic mtDNA heteroplasmy dynamics of individual blood and immune cells across lineages, demonstrating the power of single-cell multi-omics for revealing fundamental properties of mitochondrial genetics.
Collapse
Affiliation(s)
- Caleb A Lareau
- Department of Pathology, Stanford University, Stanford, CA, USA.
- Parker Institute of Cancer Immunotherapy, San Francisco, CA, USA.
- Department of Genetics, Stanford University, Stanford, CA, USA.
- Broad Institute of MIT and Harvard, Cambridge, MA, USA.
- Division of Hematology/Oncology, Boston Children's Hospital and Department of Pediatric Oncology, Dana-Farber Cancer Institute, Harvard Medical School, Boston, MA, USA.
| | - Sonia M Dubois
- Division of Hematology/Oncology, Boston Children's Hospital and Department of Pediatric Oncology, Dana-Farber Cancer Institute, Harvard Medical School, Boston, MA, USA
| | | | - Yu-Hsin Hsieh
- Max-Delbrück-Center for Molecular Medicine in the Helmholtz Association (MDC), Berlin Institute for Medical Systems Biology (BIMSB), Berlin, Germany
| | - Kopal Garg
- Broad Institute of MIT and Harvard, Cambridge, MA, USA
- Division of Hematology/Oncology, Boston Children's Hospital and Department of Pediatric Oncology, Dana-Farber Cancer Institute, Harvard Medical School, Boston, MA, USA
| | - Pauline Kautz
- Max-Delbrück-Center for Molecular Medicine in the Helmholtz Association (MDC), Berlin Institute for Medical Systems Biology (BIMSB), Berlin, Germany
- Berlin Institute of Health at Charité-Universitätsmedizin Berlin, Berlin, Germany
- Technische Universität Berlin, Institute of Biotechnology, Berlin, Germany
| | - Lena Nitsch
- Max-Delbrück-Center for Molecular Medicine in the Helmholtz Association (MDC), Berlin Institute for Medical Systems Biology (BIMSB), Berlin, Germany
- Berlin Institute of Health at Charité-Universitätsmedizin Berlin, Berlin, Germany
- Department of Biology, Chemistry, Pharmacy, Freie Universität Berlin, Berlin, Germany
| | - Samantha D Praktiknjo
- Max-Delbrück-Center for Molecular Medicine in the Helmholtz Association (MDC), Berlin Institute for Medical Systems Biology (BIMSB), Berlin, Germany
- Berlin Institute of Health at Charité-Universitätsmedizin Berlin, Berlin, Germany
| | - Patrick Maschmeyer
- Max-Delbrück-Center for Molecular Medicine in the Helmholtz Association (MDC), Berlin Institute for Medical Systems Biology (BIMSB), Berlin, Germany
- Berlin Institute of Health at Charité-Universitätsmedizin Berlin, Berlin, Germany
| | - Jeffrey M Verboon
- Broad Institute of MIT and Harvard, Cambridge, MA, USA
- Division of Hematology/Oncology, Boston Children's Hospital and Department of Pediatric Oncology, Dana-Farber Cancer Institute, Harvard Medical School, Boston, MA, USA
| | | | - Yajie Yin
- Department of Pathology, Stanford University, Stanford, CA, USA
| | | | - Wendy Luo
- Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | - Eleni P Mimitou
- Technology Innovation Lab, New York Genome Center, New York City, NY, USA
- Immunai, New York City, NY, USA
| | - Christoph Muus
- Broad Institute of MIT and Harvard, Cambridge, MA, USA
- Paulson School of Engineering and Applied Sciences, Harvard University, Cambridge, MA, USA
| | - Rhea Malhotra
- Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | - Sumit Parikh
- Center for Pediatric Neurosciences, Mitochondrial Medicine, Cleveland Clinic, Cleveland, OH, USA
| | - Mark D Fleming
- Department of Pathology, Boston Children's Hospital, Harvard Medical School, Boston, MA, USA
| | - Lena Oevermann
- Department of Pediatric Oncology, Charité-Universitätsmedizin Berlin, Campus Virchow Klinikum, Berlin, Germany
| | - Johannes Schulte
- Department of Pediatric Oncology, Charité-Universitätsmedizin Berlin, Campus Virchow Klinikum, Berlin, Germany
| | - Cornelia Eckert
- Department of Pediatric Oncology, Charité-Universitätsmedizin Berlin, Campus Virchow Klinikum, Berlin, Germany
| | - Anshul Kundaje
- Department of Genetics, Stanford University, Stanford, CA, USA
- Department of Computer Science, Stanford University, Stanford, CA, USA
| | - Peter Smibert
- Technology Innovation Lab, New York Genome Center, New York City, NY, USA
- 10x Genomics, San Francisco, CA, USA
| | | | - Ansuman T Satpathy
- Department of Pathology, Stanford University, Stanford, CA, USA
- Parker Institute of Cancer Immunotherapy, San Francisco, CA, USA
| | - Aviv Regev
- Broad Institute of MIT and Harvard, Cambridge, MA, USA.
- Department of Biology and Koch Institute, Massachusetts Institute of Technology, Cambridge, MA, USA.
- Genentech, San Francisco, CA, USA.
| | - Vijay G Sankaran
- Broad Institute of MIT and Harvard, Cambridge, MA, USA.
- Division of Hematology/Oncology, Boston Children's Hospital and Department of Pediatric Oncology, Dana-Farber Cancer Institute, Harvard Medical School, Boston, MA, USA.
| | - Suneet Agarwal
- Division of Hematology/Oncology, Boston Children's Hospital and Department of Pediatric Oncology, Dana-Farber Cancer Institute, Harvard Medical School, Boston, MA, USA.
| | - Leif S Ludwig
- Broad Institute of MIT and Harvard, Cambridge, MA, USA.
- Division of Hematology/Oncology, Boston Children's Hospital and Department of Pediatric Oncology, Dana-Farber Cancer Institute, Harvard Medical School, Boston, MA, USA.
- Max-Delbrück-Center for Molecular Medicine in the Helmholtz Association (MDC), Berlin Institute for Medical Systems Biology (BIMSB), Berlin, Germany.
- Berlin Institute of Health at Charité-Universitätsmedizin Berlin, Berlin, Germany.
| |
Collapse
|
6
|
Liu L, Cheng S, Qi X, Meng P, Yang X, Pan C, Chen Y, Zhang H, Zhang Z, Zhang J, Li C, Wen Y, Jia Y, Cheng B, Zhang F. Mitochondria-wide association study observed significant interactions of mitochondrial respiratory and the inflammatory in the development of anxiety and depression. Transl Psychiatry 2023; 13:216. [PMID: 37344456 DOI: 10.1038/s41398-023-02518-y] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 02/08/2023] [Revised: 06/08/2023] [Accepted: 06/12/2023] [Indexed: 06/23/2023] Open
Abstract
The aim of this study was to investigate the possible interaction of mitochondrial dysfunction and inflammatory cytokines in the risk of anxiety and depression. We utilized the UK Biobank for the sample of this study. A mitochondria-wide association(MiWAS) and interaction analysis was performed to investigate the interaction effects of mitochondrial DNA (mtDNA)×C-reactive protein (CRP) on the risks of self-reported anxiety (N = 72,476), general anxiety disorder (GAD-7) scores (N = 80,853), self-reported depression (N = 80,778), Patient Health Questionnaire (PHQ-9) scores (N = 80,520) in total samples, females and males, respectively, adjusting for sex, age, Townsend deprivation index (TDI), education score, alcohol intake, smoking and 10 principal components. In all, 25 mtSNPs and 10 mtSNPs showed significant level of association with self-reported anxiety and GAD-7 score respectively. A total of seven significant mtDNA × CRP interactions were found for anxiety, such as m.3915G>A(MT-ND1) for self-reported anxiety in total subjects (P = 6.59 × 10-3), m.4561T>C(MT-ND2) (P = 3.04 × 10-3) for GAD-7 score in total subjects. For depression, MiWAS identified 17 significant mtSNPs for self-reported depression and 14 significant mtSNPs for PHQ-9 scores. 17 significant mtDNA associations (2 for self-reported depression and 15 for PHQ-9 score) was identified, such as m.14869G>A(MT-CYB; P = 2.22 × 10-3) associated with self-reported depression and m.4561T>C (MT-ND2; P value = 3.02 × 10-8) associated with PHQ-9 score in all subjects. In addition, 5 common mtDNA shared with anxiety and depression were found in MiWAS, and 4 common mtDNA variants were detected to interact with CRP for anxiety and depression, such as m.9899T>C(MT-CO3). Our study suggests the important interaction effects of mitochondrial function and CRP on the risks of anxiety and depression.
Collapse
Affiliation(s)
- Li Liu
- Key Laboratory of Trace Elements and Endemic Diseases, Collaborative Innovation Center of Endemic Disease and Health Promotion for Silk Road Region, School of Public Health, Health Science Center, Xi'an Jiaotong University, Xi'an, 710061, P. R. China
| | - Shiqiang Cheng
- Key Laboratory of Trace Elements and Endemic Diseases, Collaborative Innovation Center of Endemic Disease and Health Promotion for Silk Road Region, School of Public Health, Health Science Center, Xi'an Jiaotong University, Xi'an, 710061, P. R. China
| | - Xin Qi
- Precision Medicine Center, The First Affiliated Hospital of Xi'an Jiaotong University, Xi'an, P. R. China
| | - Peilin Meng
- Key Laboratory of Trace Elements and Endemic Diseases, Collaborative Innovation Center of Endemic Disease and Health Promotion for Silk Road Region, School of Public Health, Health Science Center, Xi'an Jiaotong University, Xi'an, 710061, P. R. China
| | - Xuena Yang
- Key Laboratory of Trace Elements and Endemic Diseases, Collaborative Innovation Center of Endemic Disease and Health Promotion for Silk Road Region, School of Public Health, Health Science Center, Xi'an Jiaotong University, Xi'an, 710061, P. R. China
| | - Chuyu Pan
- Key Laboratory of Trace Elements and Endemic Diseases, Collaborative Innovation Center of Endemic Disease and Health Promotion for Silk Road Region, School of Public Health, Health Science Center, Xi'an Jiaotong University, Xi'an, 710061, P. R. China
| | - Yujing Chen
- Key Laboratory of Trace Elements and Endemic Diseases, Collaborative Innovation Center of Endemic Disease and Health Promotion for Silk Road Region, School of Public Health, Health Science Center, Xi'an Jiaotong University, Xi'an, 710061, P. R. China
| | - Huijie Zhang
- Key Laboratory of Trace Elements and Endemic Diseases, Collaborative Innovation Center of Endemic Disease and Health Promotion for Silk Road Region, School of Public Health, Health Science Center, Xi'an Jiaotong University, Xi'an, 710061, P. R. China
| | - Zhen Zhang
- Key Laboratory of Trace Elements and Endemic Diseases, Collaborative Innovation Center of Endemic Disease and Health Promotion for Silk Road Region, School of Public Health, Health Science Center, Xi'an Jiaotong University, Xi'an, 710061, P. R. China
| | - Jingxi Zhang
- Key Laboratory of Trace Elements and Endemic Diseases, Collaborative Innovation Center of Endemic Disease and Health Promotion for Silk Road Region, School of Public Health, Health Science Center, Xi'an Jiaotong University, Xi'an, 710061, P. R. China
| | - Chune Li
- Key Laboratory of Trace Elements and Endemic Diseases, Collaborative Innovation Center of Endemic Disease and Health Promotion for Silk Road Region, School of Public Health, Health Science Center, Xi'an Jiaotong University, Xi'an, 710061, P. R. China
| | - Yan Wen
- Key Laboratory of Trace Elements and Endemic Diseases, Collaborative Innovation Center of Endemic Disease and Health Promotion for Silk Road Region, School of Public Health, Health Science Center, Xi'an Jiaotong University, Xi'an, 710061, P. R. China
| | - Yumeng Jia
- Key Laboratory of Trace Elements and Endemic Diseases, Collaborative Innovation Center of Endemic Disease and Health Promotion for Silk Road Region, School of Public Health, Health Science Center, Xi'an Jiaotong University, Xi'an, 710061, P. R. China
| | - Bolun Cheng
- Key Laboratory of Trace Elements and Endemic Diseases, Collaborative Innovation Center of Endemic Disease and Health Promotion for Silk Road Region, School of Public Health, Health Science Center, Xi'an Jiaotong University, Xi'an, 710061, P. R. China
| | - Feng Zhang
- Key Laboratory of Trace Elements and Endemic Diseases, Collaborative Innovation Center of Endemic Disease and Health Promotion for Silk Road Region, School of Public Health, Health Science Center, Xi'an Jiaotong University, Xi'an, 710061, P. R. China.
- Department of Psychiatry, The First Affiliated Hospital of Xi'an Jiaotong University, Xi'an, China.
| |
Collapse
|
7
|
Zhang H, Chen Y, Zhang J, Li C, Zhang Z, Pan C, Cheng S, Yang X, Meng P, Jia Y, Wen Y, Liu H, Zhang F. Assessing the joint effects of mitochondrial function and human behavior on the risks of anxiety and depression. J Affect Disord 2023; 320:561-567. [PMID: 36206883 DOI: 10.1016/j.jad.2022.09.157] [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: 08/17/2022] [Revised: 09/24/2022] [Accepted: 09/30/2022] [Indexed: 11/17/2022]
Abstract
BACKGROUND Psychiatric disorders have great health hazards and the exact pathogeny remains elusive now. We aim to explore the potential interaction effects of mitochondrial function and human behavior on the risks of anxiety and depression. METHODS The genome-wide association study (GWAS) data of mitochondrial function (N = 383,476-982,072) were obtained from published studies. Individual level genotype and phenotype data of anxiety, depression and behavioral factors (including drinking, smoking and physical activity) were all from the UK Biobank (N = 84,805-85,164). We first calculated the polygenic risk scores (PRS) of mitochondrial function as the instrumental variables, and then constructed linear regression analyses to systematically explore the potential interaction effects of mitochondrial function and human behavior on anxiety and depression. RESULTS In total samples, we observed mitochondrial heteroplasmy (MtHz) vs. Drinking (PGAD-7 = 6.49 × 10-3; PPHQ-9 = 1.89 × 10-3) was positively associated with both anxiety and depression. In males, MtHz vs. Drinking (PMale = 3.46 × 10-5) was positively correlated with depression. In females, blood mitochondrial DNA copy number (mtDNA-CN) vs. Drinking (PFemale = 8.63 × 10-3) was negatively related to anxiety. Furthermore, we identified additional 6 suggestive interaction effects (P < 0.05) for anxiety and depression. LIMITATIONS Considering all subjects were from UK Biobank, it should be careful to extrapolate our findings to other populations with different genetic background. CONCLUSIONS Our results suggest the significant impacts of mitochondrial function and human behavior interactions on the development of anxiety and depression, providing new clues for clarifying the pathogenesis of anxiety and depression.
Collapse
Affiliation(s)
- Huijie Zhang
- Key Laboratory of Trace Elements and Endemic Diseases, National Health and Family Planning Commission, School of Public Health, Health Science Center, Xi'an Jiaotong University, 710061 Xi'an, People's Republic of China
| | - Yujing Chen
- Key Laboratory of Trace Elements and Endemic Diseases, National Health and Family Planning Commission, School of Public Health, Health Science Center, Xi'an Jiaotong University, 710061 Xi'an, People's Republic of China
| | - Jingxi Zhang
- Key Laboratory of Trace Elements and Endemic Diseases, National Health and Family Planning Commission, School of Public Health, Health Science Center, Xi'an Jiaotong University, 710061 Xi'an, People's Republic of China
| | - Chun'e Li
- Key Laboratory of Trace Elements and Endemic Diseases, National Health and Family Planning Commission, School of Public Health, Health Science Center, Xi'an Jiaotong University, 710061 Xi'an, People's Republic of China
| | - Zhen Zhang
- Key Laboratory of Trace Elements and Endemic Diseases, National Health and Family Planning Commission, School of Public Health, Health Science Center, Xi'an Jiaotong University, 710061 Xi'an, People's Republic of China
| | - Chuyu Pan
- Key Laboratory of Trace Elements and Endemic Diseases, National Health and Family Planning Commission, School of Public Health, Health Science Center, Xi'an Jiaotong University, 710061 Xi'an, People's Republic of China
| | - Shiqiang Cheng
- Key Laboratory of Trace Elements and Endemic Diseases, National Health and Family Planning Commission, School of Public Health, Health Science Center, Xi'an Jiaotong University, 710061 Xi'an, People's Republic of China
| | - Xuena Yang
- Key Laboratory of Trace Elements and Endemic Diseases, National Health and Family Planning Commission, School of Public Health, Health Science Center, Xi'an Jiaotong University, 710061 Xi'an, People's Republic of China
| | - Peilin Meng
- Key Laboratory of Trace Elements and Endemic Diseases, National Health and Family Planning Commission, School of Public Health, Health Science Center, Xi'an Jiaotong University, 710061 Xi'an, People's Republic of China
| | - Yumeng Jia
- Key Laboratory of Trace Elements and Endemic Diseases, National Health and Family Planning Commission, School of Public Health, Health Science Center, Xi'an Jiaotong University, 710061 Xi'an, People's Republic of China
| | - Yan Wen
- Key Laboratory of Trace Elements and Endemic Diseases, National Health and Family Planning Commission, School of Public Health, Health Science Center, Xi'an Jiaotong University, 710061 Xi'an, People's Republic of China
| | - Huan Liu
- Key Laboratory of Trace Elements and Endemic Diseases, National Health and Family Planning Commission, School of Public Health, Health Science Center, Xi'an Jiaotong University, 710061 Xi'an, People's Republic of China
| | - Feng Zhang
- Key Laboratory of Trace Elements and Endemic Diseases, National Health and Family Planning Commission, School of Public Health, Health Science Center, Xi'an Jiaotong University, 710061 Xi'an, People's Republic of China.
| |
Collapse
|
8
|
Hjelm BE, Ramiro C, Rollins BL, Omidsalar AA, Gerke DS, Das SC, Sequeira A, Morgan L, Schatzberg AF, Barchas JD, Lee FS, Myers RM, Watson SJ, Akil H, Bunney WE, Vawter MP. Large Common Mitochondrial DNA Deletions Are Associated with a Mitochondrial SNP T14798C Near the 3' Breakpoints. Complex Psychiatry 2023; 8:90-98. [PMID: 36778651 PMCID: PMC9909249 DOI: 10.1159/000528051] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/02/2022] [Accepted: 10/19/2022] [Indexed: 11/16/2022] Open
Abstract
Introduction Large somatic deletions of mitochondrial DNA (mtDNA) accumulate with aging in metabolically active tissues such as the brain. We have cataloged the breakpoints and frequencies of large mtDNA deletions in the human brain. Methods We quantified 112 high-frequency mtDNA somatic deletions across four human brain regions with the Splice-Break2 pipeline. In addition, we utilized PLINK/Seq to test the association of mitochondrial genotypes with the abundance of these high-frequency mtDNA deletions. A conservative p value threshold of 5E-08 was used to find the significant loci. Results One mtDNA SNP (T14798C) was significantly associated with mtDNA deletions in two brain regions, the dorsolateral prefrontal cortex (DLPFC) and the superior temporal gyrus. Since the DLPFC showed the most robust association between T14798C and two deletion breakpoints (7816-14807 and 5462-14807), this association was tested in the DLPFC of a replication sample and validated the first results. Incorporating the C allele at 14,798 bp increased the perfect/imperfect length of the repeat at the 3' breakpoint of the two associated deletions. Conclusion This is the first study to identify the association of mtDNA SNP with large mtDNA deletions in the human brain. The T14798C allele located in the MT-CYB gene is a common polymorphism that occurs in several mitochondrial haplogroups. We hypothesize that the T14798C association with two deletions occurs by extending the repeat length around the 3' deletion breakpoints. This simple mechanism suggests that mtDNA SNPs can affect the mitochondrial genome structure, especially in brain where high levels of reactive oxygen species lead to deletion accumulation with aging.
Collapse
Affiliation(s)
- Brooke E. Hjelm
- Department of Translational Genomics, Keck School of Medicine, University of Southern California, Los Angeles, California, USA
| | - Christian Ramiro
- Functional Genomics Laboratory, Department of Psychiatry and Human Behavior, University of California, Irvine, California, USA
| | - Brandi L. Rollins
- Functional Genomics Laboratory, Department of Psychiatry and Human Behavior, University of California, Irvine, California, USA
| | - Audrey A. Omidsalar
- Department of Translational Genomics, Keck School of Medicine, University of Southern California, Los Angeles, California, USA
| | - Daniel S. Gerke
- Department of Translational Genomics, Keck School of Medicine, University of Southern California, Los Angeles, California, USA
| | - Sujan C. Das
- Functional Genomics Laboratory, Department of Psychiatry and Human Behavior, University of California, Irvine, California, USA
| | - Adolfo Sequeira
- Functional Genomics Laboratory, Department of Psychiatry and Human Behavior, University of California, Irvine, California, USA
| | - Ling Morgan
- Functional Genomics Laboratory, Department of Psychiatry and Human Behavior, University of California, Irvine, California, USA
| | - Alan F. Schatzberg
- Department of Psychiatry and Behavioral Sciences, Stanford University, Stanford, California, USA
| | - Jack D. Barchas
- Department of Psychiatry, Weill Cornell Medical College, Ithaca, New York, USA
| | - Francis S. Lee
- Department of Psychiatry, Weill Cornell Medical College, Ithaca, New York, USA
| | - Richard M. Myers
- HudsonAlpha Institute for Biotechnology, Huntsville, Alabama, USA
| | - Stanley J. Watson
- The Michigan Neuroscience Institute (MNI), University of Michigan, Ann Arbor, Michigan, USA
| | - Huda Akil
- The Michigan Neuroscience Institute (MNI), University of Michigan, Ann Arbor, Michigan, USA
| | - William E. Bunney
- Department of Psychiatry and Human Behavior, University of California, Irvine, California, USA
| | - Marquis P. Vawter
- Functional Genomics Laboratory, Department of Psychiatry and Human Behavior, University of California, Irvine, California, USA,*Marquis P. Vawter,
| |
Collapse
|
9
|
Das SC, Hjelm BE, Rollins BL, Sequeira A, Morgan L, Omidsalar AA, Schatzberg AF, Barchas JD, Lee FS, Myers RM, Watson SJ, Akil H, Bunney WE, Vawter MP. Mitochondria DNA copy number, mitochondria DNA total somatic deletions, Complex I activity, synapse number, and synaptic mitochondria number are altered in schizophrenia and bipolar disorder. Transl Psychiatry 2022; 12:353. [PMID: 36042222 PMCID: PMC9427957 DOI: 10.1038/s41398-022-02127-1] [Citation(s) in RCA: 11] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 04/04/2022] [Revised: 08/16/2022] [Accepted: 08/18/2022] [Indexed: 11/15/2022] Open
Abstract
Mitochondrial dysfunction is a neurobiological phenomenon implicated in the pathophysiology of schizophrenia and bipolar disorder that can synergistically affect synaptic neurotransmission. We hypothesized that schizophrenia and bipolar disorder share molecular alterations at the mitochondrial and synaptic levels. Mitochondria DNA (mtDNA) copy number (CN), mtDNA common deletion (CD), mtDNA total deletion, complex I activity, synapse number, and synaptic mitochondria number were studied in the postmortem human dorsolateral prefrontal cortex (DLPFC), superior temporal gyrus (STG), primary visual cortex (V1), and nucleus accumbens (NAc) of controls (CON), and subjects with schizophrenia (SZ), and bipolar disorder (BD). The results showed (i) the mtDNA CN is significantly higher in DLPFC of both SZ and BD, decreased in the STG of BD, and unaltered in V1 and NAc of both SZ and BD; (ii) the mtDNA CD is significantly higher in DLPFC of BD while unaltered in STG, V1, and NAc of both SZ and BD; (iii) The total deletion burden is significantly higher in DLPFC in both SZ and BD while unaltered in STG, V1, and NAc of SZ and BD; (iv) Complex I activity is significantly lower in DLPFC of both SZ and BD, which is driven by the presence of medications, with no alteration in STG, V1, and NAc. In addition, complex I protein concentration, by ELISA, was decreased across three cortical regions of SZ and BD subjects; (v) The number of synapses is decreased in DLPFC of both SZ and BD, while the synaptic mitochondria number was significantly lower in female SZ and female BD compared to female controls. Overall, these findings will pave the way to understand better the pathophysiology of schizophrenia and bipolar disorder for therapeutic interventions.
Collapse
Affiliation(s)
- Sujan C. Das
- grid.266093.80000 0001 0668 7243Functional Genomics Laboratory, Department of Psychiatry & Human Behavior, University of California, Irvine, CA USA
| | - Brooke E. Hjelm
- grid.42505.360000 0001 2156 6853Department of Translational Genomics, Keck School of Medicine, University of Southern California, Health Sciences Campus, Los Angeles, CA USA
| | - Brandi L. Rollins
- grid.266093.80000 0001 0668 7243Functional Genomics Laboratory, Department of Psychiatry & Human Behavior, University of California, Irvine, CA USA
| | - Adolfo Sequeira
- grid.266093.80000 0001 0668 7243Functional Genomics Laboratory, Department of Psychiatry & Human Behavior, University of California, Irvine, CA USA
| | - Ling Morgan
- grid.266093.80000 0001 0668 7243Functional Genomics Laboratory, Department of Psychiatry & Human Behavior, University of California, Irvine, CA USA
| | - Audrey A. Omidsalar
- grid.42505.360000 0001 2156 6853Department of Translational Genomics, Keck School of Medicine, University of Southern California, Health Sciences Campus, Los Angeles, CA USA
| | - Alan F. Schatzberg
- grid.168010.e0000000419368956Department of Psychiatry and Behavioral Sciences, Stanford University, Stanford, CA USA
| | - Jack D. Barchas
- grid.5386.8000000041936877XDepartment of Psychiatry, Weill Cornell Medical College, Ithaca, NJ USA
| | - Francis S. Lee
- grid.5386.8000000041936877XDepartment of Psychiatry, Weill Cornell Medical College, Ithaca, NJ USA
| | - Richard M. Myers
- grid.417691.c0000 0004 0408 3720HudsonAlpha Institute for Biotechnology, Huntsville, AL 35806 USA
| | - Stanley J. Watson
- grid.214458.e0000000086837370The Michigan Neuroscience Institute, University of Michigan, Ann Arbor, MI USA
| | - Huda Akil
- grid.214458.e0000000086837370The Michigan Neuroscience Institute, University of Michigan, Ann Arbor, MI USA
| | - William E. Bunney
- grid.266093.80000 0001 0668 7243Department of Psychiatry & Human Behavior, University of California, Irvine, CA USA
| | - Marquis P. Vawter
- grid.266093.80000 0001 0668 7243Functional Genomics Laboratory, Department of Psychiatry & Human Behavior, University of California, Irvine, CA USA
| |
Collapse
|
10
|
Baratta AM, Brandner AJ, Plasil SL, Rice RC, Farris SP. Advancements in Genomic and Behavioral Neuroscience Analysis for the Study of Normal and Pathological Brain Function. Front Mol Neurosci 2022; 15:905328. [PMID: 35813067 PMCID: PMC9259865 DOI: 10.3389/fnmol.2022.905328] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/26/2022] [Accepted: 06/06/2022] [Indexed: 11/16/2022] Open
Abstract
Psychiatric and neurological disorders are influenced by an undetermined number of genes and molecular pathways that may differ among afflicted individuals. Functionally testing and characterizing biological systems is essential to discovering the interrelationship among candidate genes and understanding the neurobiology of behavior. Recent advancements in genetic, genomic, and behavioral approaches are revolutionizing modern neuroscience. Although these tools are often used separately for independent experiments, combining these areas of research will provide a viable avenue for multidimensional studies on the brain. Herein we will briefly review some of the available tools that have been developed for characterizing novel cellular and animal models of human disease. A major challenge will be openly sharing resources and datasets to effectively integrate seemingly disparate types of information and how these systems impact human disorders. However, as these emerging technologies continue to be developed and adopted by the scientific community, they will bring about unprecedented opportunities in our understanding of molecular neuroscience and behavior.
Collapse
Affiliation(s)
- Annalisa M. Baratta
- Center for Neuroscience, School of Medicine, University of Pittsburgh, Pittsburgh, PA, United States
| | - Adam J. Brandner
- Center for Neuroscience, School of Medicine, University of Pittsburgh, Pittsburgh, PA, United States
| | - Sonja L. Plasil
- Department of Pharmacology & Chemical Biology, School of Medicine, University of Pittsburgh, Pittsburgh, PA, United States
| | - Rachel C. Rice
- Center for Neuroscience, School of Medicine, University of Pittsburgh, Pittsburgh, PA, United States
| | - Sean P. Farris
- Center for Neuroscience, School of Medicine, University of Pittsburgh, Pittsburgh, PA, United States
- Department of Anesthesiology and Perioperative Medicine, School of Medicine, University of Pittsburgh, Pittsburgh, PA, United States
- Department of Biomedical Informatics, School of Medicine, University of Pittsburgh, Pittsburgh, PA, United States
- *Correspondence: Sean P. Farris,
| |
Collapse
|
11
|
Valiente-Pallejà A, Tortajada J, Bulduk BK, Vilella E, Garrabou G, Muntané G, Martorell L. Comprehensive summary of mitochondrial DNA alterations in the postmortem human brain: A systematic review. EBioMedicine 2022; 76:103815. [PMID: 35085849 PMCID: PMC8790490 DOI: 10.1016/j.ebiom.2022.103815] [Citation(s) in RCA: 13] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/08/2021] [Revised: 12/24/2021] [Accepted: 01/05/2022] [Indexed: 12/12/2022] Open
Abstract
BACKGROUND Mitochondrial DNA (mtDNA) encodes 37 genes necessary for synthesizing 13 essential subunits of the oxidative phosphorylation system. mtDNA alterations are known to cause mitochondrial disease (MitD), a clinically heterogeneous group of disorders that often present with neuropsychiatric symptoms. Understanding the nature and frequency of mtDNA alterations in health and disease could be a cornerstone in disentangling the relationship between biochemical findings and clinical symptoms of brain disorders. This systematic review aimed to summarize the mtDNA alterations in human brain tissue reported to date that have implications for further research on the pathophysiological significance of mtDNA alterations in brain functioning. METHODS We searched the PubMed and Embase databases using distinct terms related to postmortem human brain and mtDNA up to June 10, 2021. Reports were eligible if they were empirical studies analysing mtDNA in postmortem human brains. FINDINGS A total of 158 of 637 studies fulfilled the inclusion criteria and were clustered into the following groups: MitD (48 entries), neurological diseases (NeuD, 55 entries), psychiatric diseases (PsyD, 15 entries), a miscellaneous group with controls and other clinical diseases (5 entries), ageing (20 entries), and technical issues (5 entries). Ten entries were ascribed to more than one group. Pathogenic single nucleotide variants (pSNVs), both homo- or heteroplasmic variants, have been widely reported in MitD, with heteroplasmy levels varying among brain regions; however, pSNVs are rarer in NeuD, PsyD and ageing. A lower mtDNA copy number (CN) in disease was described in most, but not all, of the identified studies. mtDNA deletions were identified in individuals in the four clinical categories and ageing. Notably, brain samples showed significantly more mtDNA deletions and at higher heteroplasmy percentages than blood samples, and several of the deletions present in the brain were not detected in the blood. Finally, mtDNA heteroplasmy, mtDNA CN and the deletion levels varied depending on the brain region studied. INTERPRETATION mtDNA alterations are well known to affect human tissues, including the brain. In general, we found that studies of MitD, NeuD, PsyD, and ageing were highly variable in terms of the type of disease or ageing process investigated, number of screened individuals, studied brain regions and technology used. In NeuD and PsyD, no particular type of mtDNA alteration could be unequivocally assigned to any specific disease or diagnostic group. However, the presence of mtDNA deletions and mtDNA CN variation imply a role for mtDNA in NeuD and PsyD. Heteroplasmy levels and threshold effects, affected brain regions, and mitotic segregation patterns of mtDNA alterations may be involved in the complex inheritance of NeuD and PsyD and in the ageing process. Therefore, more information is needed regarding the type of mtDNA alteration, the affected brain regions, the heteroplasmy levels, and their relationship with clinical phenotypes and the ageing process. FUNDING Hospital Universitari Institut Pere Mata; Institut d'Investigació Sanitària Pere Virgili; Instituto de Salud Carlos III, Ministerio de Ciencia e Innovación (PI18/00514).
Collapse
Affiliation(s)
- Alba Valiente-Pallejà
- Research Department, Hospital Universitari Institut Pere Mata (HUIPM); Institut d'Investigació Sanitària Pere Virgili (IISPV); Faculty of Medicine and Health Sciences, Universitat Rovira i Virgili (URV), 43201 Reus, Catalonia, Spain; Biomedical Network Research Centre on Mental Health (CIBERSAM), 28029 Madrid, Spain
| | - Juan Tortajada
- Research Department, Hospital Universitari Institut Pere Mata (HUIPM); Institut d'Investigació Sanitària Pere Virgili (IISPV); Faculty of Medicine and Health Sciences, Universitat Rovira i Virgili (URV), 43201 Reus, Catalonia, Spain; Biomedical Network Research Centre on Mental Health (CIBERSAM), 28029 Madrid, Spain
| | - Bengisu K Bulduk
- Research Department, Hospital Universitari Institut Pere Mata (HUIPM); Institut d'Investigació Sanitària Pere Virgili (IISPV); Faculty of Medicine and Health Sciences, Universitat Rovira i Virgili (URV), 43201 Reus, Catalonia, Spain; Biomedical Network Research Centre on Mental Health (CIBERSAM), 28029 Madrid, Spain
| | - Elisabet Vilella
- Research Department, Hospital Universitari Institut Pere Mata (HUIPM); Institut d'Investigació Sanitària Pere Virgili (IISPV); Faculty of Medicine and Health Sciences, Universitat Rovira i Virgili (URV), 43201 Reus, Catalonia, Spain; Biomedical Network Research Centre on Mental Health (CIBERSAM), 28029 Madrid, Spain
| | - Glòria Garrabou
- Laboratory of Muscle Research and Mitochondrial Function, Department of Internal Medicine-Hospital Clínic of Barcelona (HCB); Institut d'Investigacions Biomèdiques August Pi i Sunyer (IDIBAPS); Faculty of Medicine and Health Sciences, Universitat de Barcelona (UB), 08036 Barcelona, Catalonia, Spain; Biomedical Network Research Centre on Rare Diseases (CIBERER), 28029 Madrid, Spain
| | - Gerard Muntané
- Research Department, Hospital Universitari Institut Pere Mata (HUIPM); Institut d'Investigació Sanitària Pere Virgili (IISPV); Faculty of Medicine and Health Sciences, Universitat Rovira i Virgili (URV), 43201 Reus, Catalonia, Spain; Biomedical Network Research Centre on Mental Health (CIBERSAM), 28029 Madrid, Spain; Institute of Evolutionary Biology (IBE), Universitat Pompeu Fabra (UPF), 08003 Barcelona, Catalonia, Spain
| | - Lourdes Martorell
- Research Department, Hospital Universitari Institut Pere Mata (HUIPM); Institut d'Investigació Sanitària Pere Virgili (IISPV); Faculty of Medicine and Health Sciences, Universitat Rovira i Virgili (URV), 43201 Reus, Catalonia, Spain; Biomedical Network Research Centre on Mental Health (CIBERSAM), 28029 Madrid, Spain.
| |
Collapse
|
12
|
Radecki P, Uppuluri R, Aviran S. Rapid structure-function insights via hairpin-centric analysis of big RNA structure probing datasets. NAR Genom Bioinform 2021; 3:lqab073. [PMID: 34447931 PMCID: PMC8384053 DOI: 10.1093/nargab/lqab073] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/16/2021] [Revised: 07/14/2021] [Accepted: 08/03/2021] [Indexed: 12/23/2022] Open
Abstract
The functions of RNA are often tied to its structure, hence analyzing structure is of significant interest when studying cellular processes. Recently, large-scale structure probing (SP) studies have enabled assessment of global structure-function relationships via standard data summarizations or local folding. Here, we approach structure quantification from a hairpin-centric perspective where putative hairpins are identified in SP datasets and used as a means to capture local structural effects. This has the advantage of rapid processing of big (e.g. transcriptome-wide) data as RNA folding is circumvented, yet it captures more information than simple data summarizations. We reformulate a statistical learning algorithm we previously developed to significantly improve precision of hairpin detection, then introduce a novel nucleotide-wise measure, termed the hairpin-derived structure level (HDSL), which captures local structuredness by accounting for the presence of likely hairpin elements. Applying HDSL to data from recent studies recapitulates, strengthens and expands on their findings which were obtained by more comprehensive folding algorithms, yet our analyses are orders of magnitude faster. These results demonstrate that hairpin detection is a promising avenue for global and rapid structure-function analysis, furthering our understanding of RNA biology and the principal features which drive biological insights from SP data.
Collapse
Affiliation(s)
- Pierce Radecki
- Biomedical Engineering Department and Genome Center, University of California at Davis, Davis, CA 95616, USA
| | - Rahul Uppuluri
- Biomedical Engineering Department and Genome Center, University of California at Davis, Davis, CA 95616, USA
| | - Sharon Aviran
- Biomedical Engineering Department and Genome Center, University of California at Davis, Davis, CA 95616, USA
| |
Collapse
|
13
|
Pabis K. Triplex and other DNA motifs show motif-specific associations with mitochondrial DNA deletions and species lifespan. Mech Ageing Dev 2021; 194:111429. [PMID: 33422563 DOI: 10.1016/j.mad.2021.111429] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/06/2020] [Revised: 01/02/2021] [Accepted: 01/03/2021] [Indexed: 11/20/2022]
Abstract
The "theory of resistant biomolecules" posits that long-lived species show resistance to molecular damage at the level of their biomolecules. Here, we test this hypothesis in the context of mitochondrial DNA (mtDNA) as it implies that predicted mutagenic DNA motifs should be inversely correlated with species maximum lifespan (MLS). First, we confirmed that guanine-quadruplex and direct repeat (DR) motifs are mutagenic, as they associate with mtDNA deletions in the human major arc of mtDNA, while also adding mirror repeat (MR) and intramolecular triplex motifs to a growing list of potentially mutagenic features. What is more, triplex motifs showed disease-specific associations with deletions and an apparent interaction with guanine-quadruplex motifs. Surprisingly, even though DR, MR and guanine-quadruplex motifs were associated with mtDNA deletions, their correlation with MLS was explained by the biased base composition of mtDNA. Only triplex motifs negatively correlated with MLS even after adjusting for body mass, phylogeny, mtDNA base composition and effective number of codons. Taken together, our work highlights the importance of base composition for the comparative biogerontology of mtDNA and suggests that future research on mitochondrial triplex motifs is warranted.
Collapse
Affiliation(s)
- Kamil Pabis
- Georg August University of Göttingen, Göttingen, Germany.
| |
Collapse
|
14
|
Accurate mapping of mitochondrial DNA deletions and duplications using deep sequencing. PLoS Genet 2020; 16:e1009242. [PMID: 33315859 PMCID: PMC7769605 DOI: 10.1371/journal.pgen.1009242] [Citation(s) in RCA: 41] [Impact Index Per Article: 10.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/18/2020] [Revised: 12/28/2020] [Accepted: 11/02/2020] [Indexed: 12/21/2022] Open
Abstract
Deletions and duplications in mitochondrial DNA (mtDNA) cause mitochondrial disease and accumulate in conditions such as cancer and age-related disorders, but validated high-throughput methodology that can readily detect and discriminate between these two types of events is lacking. Here we establish a computational method, MitoSAlt, for accurate identification, quantification and visualization of mtDNA deletions and duplications from genomic sequencing data. Our method was tested on simulated sequencing reads and human patient samples with single deletions and duplications to verify its accuracy. Application to mouse models of mtDNA maintenance disease demonstrated the ability to detect deletions and duplications even at low levels of heteroplasmy.
Collapse
|
15
|
Bagge EK, Fujimori-Tonou N, Kubota-Sakashita M, Kasahara T, Kato T. Unbiased PCR-free spatio-temporal mapping of the mtDNA mutation spectrum reveals brain region-specific responses to replication instability. BMC Biol 2020; 18:150. [PMID: 33097039 PMCID: PMC7585204 DOI: 10.1186/s12915-020-00890-5] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/11/2020] [Accepted: 10/06/2020] [Indexed: 12/24/2022] Open
Abstract
Background The accumulation of mtDNA mutations in different tissues from various mouse models has been widely studied especially in the context of mtDNA mutation-driven ageing but has been confounded by the inherent limitations of the most widely used approaches. By implementing a method to sequence mtDNA without PCR amplification prior to library preparation, we map the full unbiased mtDNA mutation spectrum across six distinct brain regions from mice. Results We demonstrate that ageing-induced levels of mtDNA mutations (single nucleotide variants and deletions) reach stable levels at 50 weeks of age but can be further elevated specifically in the cortex, nucleus accumbens (NAc), and paraventricular thalamic nucleus (PVT) by expression of a proof-reading-deficient mitochondrial DNA polymerase, PolgD181A. The increase in single nucleotide variants increases the fraction of shared SNVs as well as their frequency, while characteristics of deletions remain largely unaffected. In addition, PolgD181A also induces an ageing-dependent accumulation of non-coding control-region multimers in NAc and PVT, a feature that appears almost non-existent in wild-type mice. Conclusions Our data provide a novel view of the spatio-temporal accumulation of mtDNA mutations using very limited tissue input. The differential response of brain regions to a state of replication instability provides insight into a possible heterogenic mitochondrial landscape across the brain that may be involved in the ageing phenotype and mitochondria-associated disorders.
Collapse
Affiliation(s)
- Emilie Kristine Bagge
- Laboratory for Molecular Dynamics of Mental Disorders, RIKEN Center for Brain Science, Wako, Saitama, Japan
| | - Noriko Fujimori-Tonou
- Laboratory for Molecular Dynamics of Mental Disorders, RIKEN Center for Brain Science, Wako, Saitama, Japan.,Current address: Support Unit for Bio-Material Analysis, Research Resources Division, RIKEN Center for Brain Science, Wako, Saitama, Japan
| | - Mie Kubota-Sakashita
- Laboratory for Molecular Dynamics of Mental Disorders, RIKEN Center for Brain Science, Wako, Saitama, Japan
| | - Takaoki Kasahara
- Laboratory for Molecular Dynamics of Mental Disorders, RIKEN Center for Brain Science, Wako, Saitama, Japan.,Current address: Career Development Program, RIKEN Center for Brain Science, Wako, Saitama, Japan
| | - Tadafumi Kato
- Laboratory for Molecular Dynamics of Mental Disorders, RIKEN Center for Brain Science, Wako, Saitama, Japan. .,Department of Psychiatry and Behavioral Science, Juntendo University, Graduate School of Medicine, Hongo 2-1-1, Bunkyo, Tokyo 113-8421, Japan.
| |
Collapse
|
16
|
Lujan SA, Longley MJ, Humble MH, Lavender CA, Burkholder A, Blakely EL, Alston CL, Gorman GS, Turnbull DM, McFarland R, Taylor RW, Kunkel TA, Copeland WC. Ultrasensitive deletion detection links mitochondrial DNA replication, disease, and aging. Genome Biol 2020; 21:248. [PMID: 32943091 PMCID: PMC7500033 DOI: 10.1186/s13059-020-02138-5] [Citation(s) in RCA: 42] [Impact Index Per Article: 10.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/07/2020] [Accepted: 08/07/2020] [Indexed: 12/31/2022] Open
Abstract
BACKGROUND Acquired human mitochondrial genome (mtDNA) deletions are symptoms and drivers of focal mitochondrial respiratory deficiency, a pathological hallmark of aging and late-onset mitochondrial disease. RESULTS To decipher connections between these processes, we create LostArc, an ultrasensitive method for quantifying deletions in circular mtDNA molecules. LostArc reveals 35 million deletions (~ 470,000 unique spans) in skeletal muscle from 22 individuals with and 19 individuals without pathogenic variants in POLG. This nuclear gene encodes the catalytic subunit of replicative mitochondrial DNA polymerase γ. Ablation, the deleted mtDNA fraction, suffices to explain skeletal muscle phenotypes of aging and POLG-derived disease. Unsupervised bioinformatic analyses reveal distinct age- and disease-correlated deletion patterns. CONCLUSIONS These patterns implicate replication by DNA polymerase γ as the deletion driver and suggest little purifying selection against mtDNA deletions by mitophagy in postmitotic muscle fibers. Observed deletion patterns are best modeled as mtDNA deletions initiated by replication fork stalling during strand displacement mtDNA synthesis.
Collapse
Affiliation(s)
- Scott A Lujan
- Genome Integrity and Structural Biology Laboratory, DNA Replication Fidelity Group, National Institute of Environmental Health Sciences, National Institutes of Health, Research Triangle Park, NC, 27709, USA
| | - Matthew J Longley
- Genome Integrity and Structural Biology Laboratory, Mitochondrial DNA Replication Group, National Institute of Environmental Health Sciences, National Institutes of Health, Research Triangle Park, NC, 27709, USA
| | - Margaret H Humble
- Genome Integrity and Structural Biology Laboratory, Mitochondrial DNA Replication Group, National Institute of Environmental Health Sciences, National Institutes of Health, Research Triangle Park, NC, 27709, USA
| | - Christopher A Lavender
- Integrative Bioinformatics, National Institute of Environmental Health Sciences, National Institutes of Health, Research Triangle Park, NC, 27709, USA
| | - Adam Burkholder
- Integrative Bioinformatics, National Institute of Environmental Health Sciences, National Institutes of Health, Research Triangle Park, NC, 27709, USA
| | - Emma L Blakely
- Wellcome Centre for Mitochondrial Research, Translational and Clinical Research Institute, Faculty of Medical Sciences, Newcastle University, Newcastle upon Tyne, NE2 4HH, UK
- NHS Highly Specialised Mitochondrial Diagnostic Laboratory, Newcastle upon Tyne Hospitals NHS Foundation Trust, Newcastle upon Tyne, NE1 4LP, UK
| | - Charlotte L Alston
- Wellcome Centre for Mitochondrial Research, Translational and Clinical Research Institute, Faculty of Medical Sciences, Newcastle University, Newcastle upon Tyne, NE2 4HH, UK
- NHS Highly Specialised Mitochondrial Diagnostic Laboratory, Newcastle upon Tyne Hospitals NHS Foundation Trust, Newcastle upon Tyne, NE1 4LP, UK
| | - Grainne S Gorman
- Wellcome Centre for Mitochondrial Research, Translational and Clinical Research Institute, Faculty of Medical Sciences, Newcastle University, Newcastle upon Tyne, NE2 4HH, UK
| | - Doug M Turnbull
- Wellcome Centre for Mitochondrial Research, Translational and Clinical Research Institute, Faculty of Medical Sciences, Newcastle University, Newcastle upon Tyne, NE2 4HH, UK
| | - Robert McFarland
- Wellcome Centre for Mitochondrial Research, Translational and Clinical Research Institute, Faculty of Medical Sciences, Newcastle University, Newcastle upon Tyne, NE2 4HH, UK
| | - Robert W Taylor
- Wellcome Centre for Mitochondrial Research, Translational and Clinical Research Institute, Faculty of Medical Sciences, Newcastle University, Newcastle upon Tyne, NE2 4HH, UK
- NHS Highly Specialised Mitochondrial Diagnostic Laboratory, Newcastle upon Tyne Hospitals NHS Foundation Trust, Newcastle upon Tyne, NE1 4LP, UK
| | - Thomas A Kunkel
- Genome Integrity and Structural Biology Laboratory, DNA Replication Fidelity Group, National Institute of Environmental Health Sciences, National Institutes of Health, Research Triangle Park, NC, 27709, USA
| | - William C Copeland
- Genome Integrity and Structural Biology Laboratory, Mitochondrial DNA Replication Group, National Institute of Environmental Health Sciences, National Institutes of Health, Research Triangle Park, NC, 27709, USA.
| |
Collapse
|
17
|
Chan ST, McCarthy MJ, Vawter MP. Psychiatric drugs impact mitochondrial function in brain and other tissues. Schizophr Res 2020; 217:136-147. [PMID: 31744750 PMCID: PMC7228833 DOI: 10.1016/j.schres.2019.09.007] [Citation(s) in RCA: 22] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 03/11/2019] [Revised: 09/14/2019] [Accepted: 09/16/2019] [Indexed: 12/31/2022]
Abstract
Mitochondria have been linked to the etiology of schizophrenia (SZ). However, studies of mitochondria in SZ might be confounded by the effects of pharmacological treatment with antipsychotic drugs (APDs) and other common medications. This review summarizes findings on relevant mitochondria mechanisms underlying SZ, and the potential impact of psychoactive drugs including primarily APDs, but also antidepressants and anxiolytics. The summarized data suggest that APDs impair mitochondria function by decreasing Complex I activity and ATP production and dissipation of the mitochondria membrane potential. At the same time, in the brains of patients with SZ, antipsychotic drug treatment normalizes gene expression modules enriched in mitochondrial genes that are decreased in SZ. This indicates that APDs may have both positive and negative effects on mitochondria. The available evidence suggests three conclusions i) alterations in mitochondria functions in SZ exist prior to APD treatment, ii) mitochondria alterations in SZ can be reversed by APD treatment, and iii) APDs directly cause impairment of mitochondria function. Overall, the mechanisms of action of psychiatric drugs on mitochondria are both direct and indirect; we conclude the effects of APDs on mitochondria may contribute to both their therapeutic and metabolic side effects. These studies support the hypothesis that neuronal mitochondria are an etiological factor in SZ. Moreover, APDs and other drugs must be considered in the evaluation of this pathophysiological role of mitochondria in SZ. Considering these effects, pharmacological actions on mitochondria may be a worthwhile target for further APD development.
Collapse
Affiliation(s)
- Shawna T Chan
- Functional Genomics Laboratory, Department of Human Behavior and Psychiatry, University of California, Irvine, USA; School of Medicine University of California, Irvine, USA
| | - Michael J McCarthy
- Psychiatry Service VA San Diego Healthcare System, Department of Psychiatry, University of California, San Diego, USA
| | - Marquis P Vawter
- Functional Genomics Laboratory, Department of Human Behavior and Psychiatry, University of California, Irvine, USA.
| |
Collapse
|
18
|
Schulmann A, Ryu E, Goncalves V, Rollins B, Christiansen M, Frye MA, Biernacka J, Vawter MP. Novel Complex Interactions between Mitochondrial and Nuclear DNA in Schizophrenia and Bipolar Disorder. MOLECULAR NEUROPSYCHIATRY 2019; 5:13-27. [PMID: 31019915 PMCID: PMC6465701 DOI: 10.1159/000495658] [Citation(s) in RCA: 27] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/05/2018] [Accepted: 11/20/2018] [Indexed: 12/21/2022]
Abstract
Mitochondrial dysfunction has been associated with schizophrenia (SZ) and bipolar disorder (BD). This review examines recent publications and novel associations between mitochondrial genes and SZ and BD. Associations of nuclear-encoded mitochondrial variants with SZ were found using gene- and pathway-based approaches. Two control region mitochondrial DNA (mtDNA) SNPs, T16519C and T195C, both showed an association with SZ and BD. A review of 4 studies of A15218G located in the cytochrome B oxidase gene (CYTB, SZ = 11,311, control = 35,735) shows a moderate association with SZ (p = 2.15E-03). Another mtDNA allele A12308G was nominally associated with psychosis in BD type I subjects and SZ. The first published study testing the epistatic interaction between nuclear-encoded and mitochondria-encoded genes demonstrated evidence for potential interactions between mtDNA and the nuclear genome for BD. A similar analysis for the risk of SZ revealed significant joint effects (34 nuclear-mitochondria SNP pairs with joint effect p ≤ 5E-07) and significant enrichment of projection neurons. The mitochondria-encoded gene CYTB was found in both the epistatic interactions for SZ and BD and the single SNP association of SZ. Future efforts considering population stratification and polygenic risk scores will test the role of mitochondrial variants in psychiatric disorders.
Collapse
Affiliation(s)
- Anton Schulmann
- Janelia Research Campus, Howard Hughes Medical Institute, Ashburn, Virginia, USA
| | - Euijung Ryu
- Department of Health Sciences Research, Mayo Clinic, Rochester, Minnesota, USA
| | - Vanessa Goncalves
- Molecular Brain Science Department, Centre for Addiction and Mental Health, Toronto, Ontario, Canada
| | - Brandi Rollins
- Functional Genomics Laboratory, Department of Psychiatry and Human Behavior, School of Medicine, University of California, Irvine, California, USA
| | - Michael Christiansen
- Department for Congenital Disorders, Statens Serum Institut, Copenhagen, Denmark
- Department of Biomedical Science, University of Copenhagen, Copenhagen, Denmark
| | - Mark A. Frye
- Department of Psychiatry and Psychology, Mayo Clinic, Rochester, Minnesota, USA
| | - Joanna Biernacka
- Department of Health Sciences Research, Mayo Clinic, Rochester, Minnesota, USA
- Department of Psychiatry and Psychology, Mayo Clinic, Rochester, Minnesota, USA
| | - Marquis P. Vawter
- Functional Genomics Laboratory, Department of Psychiatry and Human Behavior, School of Medicine, University of California, Irvine, California, USA
| |
Collapse
|