1
|
Singh C, Jin B, Shrestha N, Markhard AL, Panda A, Calvo SE, Deik A, Pan X, Zuckerman AL, Ben Saad A, Corey KE, Sjoquist J, Osganian S, AminiTabrizi R, Rhee EP, Shah H, Goldberger O, Mullen AC, Cracan V, Clish CB, Mootha VK, Goodman RP. ChREBP is activated by reductive stress and mediates GCKR-associated metabolic traits. Cell Metab 2024; 36:144-158.e7. [PMID: 38101397 PMCID: PMC10842884 DOI: 10.1016/j.cmet.2023.11.010] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 12/15/2022] [Revised: 07/24/2023] [Accepted: 11/21/2023] [Indexed: 12/17/2023]
Abstract
Common genetic variants in glucokinase regulator (GCKR), which encodes GKRP, a regulator of hepatic glucokinase (GCK), influence multiple metabolic traits in genome-wide association studies (GWASs), making GCKR one of the most pleiotropic GWAS loci in the genome. It is unclear why. Prior work has demonstrated that GCKR influences the hepatic cytosolic NADH/NAD+ ratio, also referred to as reductive stress. Here, we demonstrate that reductive stress is sufficient to activate the transcription factor ChREBP and necessary for its activation by the GKRP-GCK interaction, glucose, and ethanol. We show that hepatic reductive stress induces GCKR GWAS traits such as increased hepatic fat, circulating FGF21, and circulating acylglycerol species, which are also influenced by ChREBP. We define the transcriptional signature of hepatic reductive stress and show its upregulation in fatty liver disease and downregulation after bariatric surgery in humans. These findings highlight how a GCKR-reductive stress-ChREBP axis influences multiple human metabolic traits.
Collapse
Affiliation(s)
- Charandeep Singh
- Liver Center, Division of Gastroenterology, Massachusetts General Hospital, Boston, MA 02114, USA; Endocrine Unit, Massachusetts General Hospital, Boston, MA 02114, USA
| | - Byungchang Jin
- Liver Center, Division of Gastroenterology, Massachusetts General Hospital, Boston, MA 02114, USA; Endocrine Unit, Massachusetts General Hospital, Boston, MA 02114, USA
| | - Nirajan Shrestha
- Liver Center, Division of Gastroenterology, Massachusetts General Hospital, Boston, MA 02114, USA; Endocrine Unit, Massachusetts General Hospital, Boston, MA 02114, USA
| | - Andrew L Markhard
- Howard Hughes Medical Institute and Department of Molecular Biology, Massachusetts General Hospital, Boston, MA 02114, USA
| | - Apekshya Panda
- Howard Hughes Medical Institute and Department of Molecular Biology, Massachusetts General Hospital, Boston, MA 02114, USA; Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA; Department of Systems Biology, Harvard Medical School, Boston, MA 02115, USA
| | - Sarah E Calvo
- Howard Hughes Medical Institute and Department of Molecular Biology, Massachusetts General Hospital, Boston, MA 02114, USA; Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA; Department of Systems Biology, Harvard Medical School, Boston, MA 02115, USA
| | - Amy Deik
- Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA
| | - Xingxiu Pan
- The Scintillon Institute, San Diego, CA 92121, USA
| | - Austin L Zuckerman
- The Scintillon Institute, San Diego, CA 92121, USA; Program in Mathematics and Science Education, University of California, San Diego, La Jolla, CA 92093; Program in Mathematics and Science Education, San Diego State University, San Diego, CA 92120
| | - Amel Ben Saad
- Division of Gastroenterology, University of Massachusetts Chan Medical School, Worcester, MA 01655, USA
| | - Kathleen E Corey
- Liver Center, Division of Gastroenterology, Massachusetts General Hospital, Boston, MA 02114, USA
| | - Julia Sjoquist
- Liver Center, Division of Gastroenterology, Massachusetts General Hospital, Boston, MA 02114, USA
| | - Stephanie Osganian
- Liver Center, Division of Gastroenterology, Massachusetts General Hospital, Boston, MA 02114, USA
| | - Roya AminiTabrizi
- Metabolomics Platform, Comprehensive Cancer Center, the University of Chicago, Chicago, IL 60637, USA
| | - Eugene P Rhee
- Endocrine Unit, Massachusetts General Hospital, Boston, MA 02114, USA; Nephrology Division, Massachusetts General Hospital, Boston, MA 02114, USA
| | - Hardik Shah
- Metabolomics Platform, Comprehensive Cancer Center, the University of Chicago, Chicago, IL 60637, USA
| | - Olga Goldberger
- Howard Hughes Medical Institute and Department of Molecular Biology, Massachusetts General Hospital, Boston, MA 02114, USA
| | - Alan C Mullen
- Division of Gastroenterology, University of Massachusetts Chan Medical School, Worcester, MA 01655, USA
| | - Valentin Cracan
- The Scintillon Institute, San Diego, CA 92121, USA; Department of Chemistry, the Scripps Research Institute, La Jolla, CA 92037, USA
| | - Clary B Clish
- Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA
| | - Vamsi K Mootha
- Howard Hughes Medical Institute and Department of Molecular Biology, Massachusetts General Hospital, Boston, MA 02114, USA; Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA; Department of Systems Biology, Harvard Medical School, Boston, MA 02115, USA
| | - Russell P Goodman
- Liver Center, Division of Gastroenterology, Massachusetts General Hospital, Boston, MA 02114, USA; Endocrine Unit, Massachusetts General Hospital, Boston, MA 02114, USA.
| |
Collapse
|
2
|
Gopal RK, Vantaku VR, Panda A, Reimer B, Rath S, To TL, Fisch AS, Cetinbas M, Livneh M, Calcaterra MJ, Gigliotti BJ, Pierce KA, Clish CB, Dias-Santagata D, Sadow PM, Wirth LJ, Daniels GH, Sadreyev RI, Calvo SE, Parangi S, Mootha VK. Effectors Enabling Adaptation to Mitochondrial Complex I Loss in Hürthle Cell Carcinoma. Cancer Discov 2023; 13:1904-1921. [PMID: 37262067 PMCID: PMC10401073 DOI: 10.1158/2159-8290.cd-22-0976] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/01/2022] [Revised: 04/05/2023] [Accepted: 05/30/2023] [Indexed: 06/03/2023]
Abstract
Oncocytic (Hürthle cell) carcinoma of the thyroid (HCC) is genetically characterized by complex I mitochondrial DNA mutations and widespread chromosomal losses. Here, we utilize RNA sequencing and metabolomics to identify candidate molecular effectors activated by these genetic drivers. We find glutathione biosynthesis, amino acid metabolism, mitochondrial unfolded protein response, and lipid peroxide scavenging to be increased in HCC. A CRISPR-Cas9 knockout screen in a new HCC model reveals which pathways are key for fitness, and highlights loss of GPX4, a defense against lipid peroxides and ferroptosis, as a strong liability. Rescuing complex I redox activity with the yeast NADH dehydrogenase (NDI1) in HCC cells diminishes ferroptosis sensitivity, while inhibiting complex I in normal thyroid cells augments ferroptosis induction. Our work demonstrates unmitigated lipid peroxide stress to be an HCC vulnerability that is mechanistically coupled to the genetic loss of mitochondrial complex I activity. SIGNIFICANCE HCC harbors abundant mitochondria, mitochondrial DNA mutations, and chromosomal losses. Using a CRISPR-Cas9 screen inspired by transcriptomic and metabolomic profiling, we identify molecular effectors essential for cell fitness. We uncover lipid peroxide stress as a vulnerability coupled to mitochondrial complex I loss in HCC. See related article by Frank et al., p. 1884. This article is highlighted in the In This Issue feature, p. 1749.
Collapse
Affiliation(s)
- Raj K. Gopal
- Howard Hughes Medical Institute and Department of Molecular Biology, Massachusetts General Hospital, Boston, Massachusetts
- Broad Institute of MIT and Harvard, Cambridge, Massachusetts
- Department of Medicine, Massachusetts General Hospital, Boston, Massachusetts
- Cancer Center, Massachusetts General Hospital, Boston, Massachusetts
- Harvard Medical School, Boston, Massachusetts
| | - Venkata R. Vantaku
- Harvard Medical School, Boston, Massachusetts
- Department of Surgery, Massachusetts General Hospital, Boston, Massachusetts
| | - Apekshya Panda
- Howard Hughes Medical Institute and Department of Molecular Biology, Massachusetts General Hospital, Boston, Massachusetts
- Broad Institute of MIT and Harvard, Cambridge, Massachusetts
| | - Bryn Reimer
- Howard Hughes Medical Institute and Department of Molecular Biology, Massachusetts General Hospital, Boston, Massachusetts
- Broad Institute of MIT and Harvard, Cambridge, Massachusetts
| | - Sneha Rath
- Howard Hughes Medical Institute and Department of Molecular Biology, Massachusetts General Hospital, Boston, Massachusetts
- Broad Institute of MIT and Harvard, Cambridge, Massachusetts
| | - Tsz-Leung To
- Howard Hughes Medical Institute and Department of Molecular Biology, Massachusetts General Hospital, Boston, Massachusetts
- Broad Institute of MIT and Harvard, Cambridge, Massachusetts
| | - Adam S. Fisch
- Department of Pathology, Massachusetts General Hospital, Boston, Massachusetts
| | - Murat Cetinbas
- Howard Hughes Medical Institute and Department of Molecular Biology, Massachusetts General Hospital, Boston, Massachusetts
- Harvard Medical School, Boston, Massachusetts
| | - Maia Livneh
- Department of Pathology, Massachusetts General Hospital, Boston, Massachusetts
| | | | | | - Kerry A. Pierce
- Broad Institute of MIT and Harvard, Cambridge, Massachusetts
| | - Clary B. Clish
- Broad Institute of MIT and Harvard, Cambridge, Massachusetts
| | - Dora Dias-Santagata
- Harvard Medical School, Boston, Massachusetts
- Department of Pathology, Massachusetts General Hospital, Boston, Massachusetts
| | - Peter M. Sadow
- Cancer Center, Massachusetts General Hospital, Boston, Massachusetts
- Harvard Medical School, Boston, Massachusetts
- Department of Pathology, Massachusetts General Hospital, Boston, Massachusetts
| | - Lori J. Wirth
- Department of Medicine, Massachusetts General Hospital, Boston, Massachusetts
- Cancer Center, Massachusetts General Hospital, Boston, Massachusetts
- Harvard Medical School, Boston, Massachusetts
| | - Gilbert H. Daniels
- Department of Medicine, Massachusetts General Hospital, Boston, Massachusetts
- Cancer Center, Massachusetts General Hospital, Boston, Massachusetts
- Harvard Medical School, Boston, Massachusetts
- Thyroid Unit, Massachusetts General Hospital, Boston, Massachusetts
| | - Ruslan I. Sadreyev
- Howard Hughes Medical Institute and Department of Molecular Biology, Massachusetts General Hospital, Boston, Massachusetts
- Harvard Medical School, Boston, Massachusetts
- Department of Pathology, Massachusetts General Hospital, Boston, Massachusetts
| | - Sarah E. Calvo
- Howard Hughes Medical Institute and Department of Molecular Biology, Massachusetts General Hospital, Boston, Massachusetts
- Broad Institute of MIT and Harvard, Cambridge, Massachusetts
| | - Sareh Parangi
- Cancer Center, Massachusetts General Hospital, Boston, Massachusetts
- Harvard Medical School, Boston, Massachusetts
- Department of Surgery, Massachusetts General Hospital, Boston, Massachusetts
| | - Vamsi K. Mootha
- Howard Hughes Medical Institute and Department of Molecular Biology, Massachusetts General Hospital, Boston, Massachusetts
- Broad Institute of MIT and Harvard, Cambridge, Massachusetts
- Department of Medicine, Massachusetts General Hospital, Boston, Massachusetts
- Department of Systems Biology, Harvard Medical School, Boston, Massachusetts
| |
Collapse
|
3
|
Gupta R, Kanai M, Durham TJ, Tsuo K, McCoy JG, Kotrys AV, Zhou W, Chinnery PF, Karczewski KJ, Calvo SE, Neale BM, Mootha VK. Nuclear genetic control of mtDNA copy number and heteroplasmy in humans. Nature 2023; 620:839-848. [PMID: 37587338 PMCID: PMC10447254 DOI: 10.1038/s41586-023-06426-5] [Citation(s) in RCA: 12] [Impact Index Per Article: 12.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/29/2022] [Accepted: 07/11/2023] [Indexed: 08/18/2023]
Abstract
Mitochondrial DNA (mtDNA) is a maternally inherited, high-copy-number genome required for oxidative phosphorylation1. Heteroplasmy refers to the presence of a mixture of mtDNA alleles in an individual and has been associated with disease and ageing. Mechanisms underlying common variation in human heteroplasmy, and the influence of the nuclear genome on this variation, remain insufficiently explored. Here we quantify mtDNA copy number (mtCN) and heteroplasmy using blood-derived whole-genome sequences from 274,832 individuals and perform genome-wide association studies to identify associated nuclear loci. Following blood cell composition correction, we find that mtCN declines linearly with age and is associated with variants at 92 nuclear loci. We observe that nearly everyone harbours heteroplasmic mtDNA variants obeying two principles: (1) heteroplasmic single nucleotide variants tend to arise somatically and accumulate sharply after the age of 70 years, whereas (2) heteroplasmic indels are maternally inherited as mixtures with relative levels associated with 42 nuclear loci involved in mtDNA replication, maintenance and novel pathways. These loci may act by conferring a replicative advantage to certain mtDNA alleles. As an illustrative example, we identify a length variant carried by more than 50% of humans at position chrM:302 within a G-quadruplex previously proposed to mediate mtDNA transcription/replication switching2,3. We find that this variant exerts cis-acting genetic control over mtDNA abundance and is itself associated in-trans with nuclear loci encoding machinery for this regulatory switch. Our study suggests that common variation in the nuclear genome can shape variation in mtCN and heteroplasmy dynamics across the human population.
Collapse
Affiliation(s)
- Rahul Gupta
- Howard Hughes Medical Institute and Department of Molecular Biology, Massachusetts General Hospital, Boston, MA, USA.
- Broad Institute of MIT and Harvard, Cambridge, MA, USA.
- Analytic and Translational Genetics Unit, Center for Genomic Medicine, Massachusetts General Hospital, Boston, MA, USA.
| | - Masahiro Kanai
- Broad Institute of MIT and Harvard, Cambridge, MA, USA
- Analytic and Translational Genetics Unit, Center for Genomic Medicine, Massachusetts General Hospital, Boston, MA, USA
| | - Timothy J Durham
- Howard Hughes Medical Institute and Department of Molecular Biology, Massachusetts General Hospital, Boston, MA, USA
- Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | - Kristin Tsuo
- Broad Institute of MIT and Harvard, Cambridge, MA, USA
- Analytic and Translational Genetics Unit, Center for Genomic Medicine, Massachusetts General Hospital, Boston, MA, USA
| | - Jason G McCoy
- Howard Hughes Medical Institute and Department of Molecular Biology, Massachusetts General Hospital, Boston, MA, USA
- Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | - Anna V Kotrys
- Howard Hughes Medical Institute and Department of Molecular Biology, Massachusetts General Hospital, Boston, MA, USA
- Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | - Wei Zhou
- Broad Institute of MIT and Harvard, Cambridge, MA, USA
- Analytic and Translational Genetics Unit, Center for Genomic Medicine, Massachusetts General Hospital, Boston, MA, USA
| | - Patrick F Chinnery
- Department of Clinical Neurosciences, University of Cambridge, Cambridge, UK
- MRC Mitochondrial Biology Unit, University of Cambridge, Cambridge, UK
| | - Konrad J Karczewski
- Broad Institute of MIT and Harvard, Cambridge, MA, USA
- Analytic and Translational Genetics Unit, Center for Genomic Medicine, Massachusetts General Hospital, Boston, MA, USA
| | - Sarah E Calvo
- Howard Hughes Medical Institute and Department of Molecular Biology, Massachusetts General Hospital, Boston, MA, USA
- Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | - Benjamin M Neale
- Broad Institute of MIT and Harvard, Cambridge, MA, USA.
- Analytic and Translational Genetics Unit, Center for Genomic Medicine, Massachusetts General Hospital, Boston, MA, USA.
| | - Vamsi K Mootha
- Howard Hughes Medical Institute and Department of Molecular Biology, Massachusetts General Hospital, Boston, MA, USA.
- Broad Institute of MIT and Harvard, Cambridge, MA, USA.
- Department of Systems Biology, Harvard Medical School, Boston, MA, USA.
| |
Collapse
|
4
|
Amarasekera SSC, Hock DH, Lake NJ, Calvo SE, Grønborg SW, Krzesinski EI, Amor DJ, Fahey MC, Simons C, Wibrand F, Mootha VK, Lek M, Lunke S, Stark Z, Østergaard E, Christodoulou J, Thorburn DR, Stroud DA, Compton AG. Multi-omics identifies large mitoribosomal subunit instability caused by pathogenic MRPL39 variants as a cause of pediatric onset mitochondrial disease. Hum Mol Genet 2023; 32:2441-2454. [PMID: 37133451 PMCID: PMC10360397 DOI: 10.1093/hmg/ddad069] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/24/2022] [Revised: 03/20/2023] [Accepted: 04/24/2023] [Indexed: 05/04/2023] Open
Abstract
MRPL39 encodes one of 52 proteins comprising the large subunit of the mitochondrial ribosome (mitoribosome). In conjunction with 30 proteins in the small subunit, the mitoribosome synthesizes the 13 subunits of the mitochondrial oxidative phosphorylation (OXPHOS) system encoded by mitochondrial Deoxyribonucleic acid (DNA). We used multi-omics and gene matching to identify three unrelated individuals with biallelic variants in MRPL39 presenting with multisystem diseases with severity ranging from lethal, infantile-onset (Leigh syndrome spectrum) to milder with survival into adulthood. Clinical exome sequencing of known disease genes failed to diagnose these patients; however quantitative proteomics identified a specific decrease in the abundance of large but not small mitoribosomal subunits in fibroblasts from the two patients with severe phenotype. Re-analysis of exome sequencing led to the identification of candidate single heterozygous variants in mitoribosomal genes MRPL39 (both patients) and MRPL15. Genome sequencing identified a shared deep intronic MRPL39 variant predicted to generate a cryptic exon, with transcriptomics and targeted studies providing further functional evidence for causation. The patient with the milder disease was homozygous for a missense variant identified through trio exome sequencing. Our study highlights the utility of quantitative proteomics in detecting protein signatures and in characterizing gene-disease associations in exome-unsolved patients. We describe Relative Complex Abundance analysis of proteomics data, a sensitive method that can identify defects in OXPHOS disorders to a similar or greater sensitivity to the traditional enzymology. Relative Complex Abundance has potential utility for functional validation or prioritization in many hundreds of inherited rare diseases where protein complex assembly is disrupted.
Collapse
Affiliation(s)
- Sumudu S C Amarasekera
- Murdoch Children’s Research Institute, Royal Children's Hospital, Melbourne, VIC 3052, Australia
- Department of Paediatrics, University of Melbourne, Melbourne, VIC 3010, Australia
| | - Daniella H Hock
- Department of Biochemistry and Pharmacology, Bio21 Molecular Science and Biotechnology Institute, University of Melbourne, Parkville, VIC 3010, Australia
| | - Nicole J Lake
- Murdoch Children’s Research Institute, Royal Children's Hospital, Melbourne, VIC 3052, Australia
- Department of Genetics, Yale School of Medicine, New Haven, CT 06510 USA
| | - Sarah E Calvo
- Broad Institute, Cambridge, MA 02142, USA
- Howard Hughes Medical Institute and Department of Molecular Biology, Massachusetts General Hospital, Boston, MA 02114, USA
- Department of Systems Biology, Harvard Medical School, Boston, MA 02446, USA
| | - Sabine W Grønborg
- Department of Genetics, Copenhagen University Hospital Rigshospitalet, Copenhagen 2100, Denmark
- Center for Inherited Metabolic Disease, Department of Pediatrics and Adolescent Medicine, Copenhagen University Hospital Rigshospitalet, Copenhagen 2100, Denmark
| | - Emma I Krzesinski
- Monash Genetics, Monash Health, Melbourne, VIC 3168 Australia
- Department of Paediatrics, Monash University, Melbourne, VIC 3168 Australia
| | - David J Amor
- Murdoch Children’s Research Institute, Royal Children's Hospital, Melbourne, VIC 3052, Australia
- Department of Paediatrics, University of Melbourne, Melbourne, VIC 3010, Australia
| | - Michael C Fahey
- Monash Genetics, Monash Health, Melbourne, VIC 3168 Australia
- Department of Paediatrics, Monash University, Melbourne, VIC 3168 Australia
| | - Cas Simons
- Murdoch Children’s Research Institute, Royal Children's Hospital, Melbourne, VIC 3052, Australia
| | - Flemming Wibrand
- Department of Genetics, Copenhagen University Hospital Rigshospitalet, Copenhagen 2100, Denmark
| | - Vamsi K Mootha
- Broad Institute, Cambridge, MA 02142, USA
- Howard Hughes Medical Institute and Department of Molecular Biology, Massachusetts General Hospital, Boston, MA 02114, USA
- Department of Systems Biology, Harvard Medical School, Boston, MA 02446, USA
| | - Monkol Lek
- Department of Genetics, Yale School of Medicine, New Haven, CT 06510 USA
| | - Sebastian Lunke
- Victorian Clinical Genetics Services, Murdoch Children’s Research Institute, Melbourne, VIC 3052, Australia
- Australian Genomics Health Alliance, Melbourne, VIC 3052, Australia
- Department of Pathology, University of Melbourne, Melbourne, VIC 3010, Australia
| | - Zornitza Stark
- Department of Paediatrics, University of Melbourne, Melbourne, VIC 3010, Australia
- Victorian Clinical Genetics Services, Murdoch Children’s Research Institute, Melbourne, VIC 3052, Australia
- Australian Genomics Health Alliance, Melbourne, VIC 3052, Australia
| | - Elsebet Østergaard
- Department of Genetics, Copenhagen University Hospital Rigshospitalet, Copenhagen 2100, Denmark
- Department of Clinical Medicine, University of Copenhagen, Copenhagen 2200, Denmark
| | - John Christodoulou
- Murdoch Children’s Research Institute, Royal Children's Hospital, Melbourne, VIC 3052, Australia
- Department of Paediatrics, University of Melbourne, Melbourne, VIC 3010, Australia
- Victorian Clinical Genetics Services, Murdoch Children’s Research Institute, Melbourne, VIC 3052, Australia
- Australian Genomics Health Alliance, Melbourne, VIC 3052, Australia
- Discipline of Child & Adolescent Health, Sydney Medical School, University of Sydney, Sydney, NSW 2006, Australia
| | - David R Thorburn
- Murdoch Children’s Research Institute, Royal Children's Hospital, Melbourne, VIC 3052, Australia
- Department of Paediatrics, University of Melbourne, Melbourne, VIC 3010, Australia
- Victorian Clinical Genetics Services, Murdoch Children’s Research Institute, Melbourne, VIC 3052, Australia
- Australian Genomics Health Alliance, Melbourne, VIC 3052, Australia
| | - David A Stroud
- Murdoch Children’s Research Institute, Royal Children's Hospital, Melbourne, VIC 3052, Australia
- Department of Biochemistry and Pharmacology, Bio21 Molecular Science and Biotechnology Institute, University of Melbourne, Parkville, VIC 3010, Australia
- Victorian Clinical Genetics Services, Murdoch Children’s Research Institute, Melbourne, VIC 3052, Australia
| | - Alison G Compton
- Murdoch Children’s Research Institute, Royal Children's Hospital, Melbourne, VIC 3052, Australia
- Department of Paediatrics, University of Melbourne, Melbourne, VIC 3010, Australia
- Victorian Clinical Genetics Services, Murdoch Children’s Research Institute, Melbourne, VIC 3052, Australia
| |
Collapse
|
5
|
Gupta R, Kanai M, Durham TJ, Tsuo K, McCoy JG, Chinnery PF, Karczewski KJ, Calvo SE, Neale BM, Mootha VK. Nuclear genetic control of mtDNA copy number and heteroplasmy in humans. medRxiv 2023:2023.01.19.23284696. [PMID: 36711677 PMCID: PMC9882621 DOI: 10.1101/2023.01.19.23284696] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Indexed: 01/21/2023]
Abstract
Human mitochondria contain a high copy number, maternally transmitted genome (mtDNA) that encodes 13 proteins required for oxidative phosphorylation. Heteroplasmy arises when multiple mtDNA variants co-exist in an individual and can exhibit complex dynamics in disease and in aging. As all proteins involved in mtDNA replication and maintenance are nuclear-encoded, heteroplasmy levels can, in principle, be under nuclear genetic control, however this has never been shown in humans. Here, we develop algorithms to quantify mtDNA copy number (mtCN) and heteroplasmy levels using blood-derived whole genome sequences from 274,832 individuals of diverse ancestry and perform GWAS to identify nuclear loci controlling these traits. After careful correction for blood cell composition, we observe that mtCN declines linearly with age and is associated with 92 independent nuclear genetic loci. We find that nearly every individual carries heteroplasmic variants that obey two key patterns: (1) heteroplasmic single nucleotide variants are somatic mutations that accumulate sharply after age 70, while (2) heteroplasmic indels are maternally transmitted as mtDNA mixtures with resulting levels influenced by 42 independent nuclear loci involved in mtDNA replication, maintenance, and novel pathways. These nuclear loci do not appear to act by mtDNA mutagenesis, but rather, likely act by conferring a replicative advantage to specific mtDNA molecules. As an illustrative example, the most common heteroplasmy we identify is a length variant carried by >50% of humans at position m.302 within a G-quadruplex known to serve as a replication switch. We find that this heteroplasmic variant exerts cis -acting genetic control over mtDNA abundance and is itself under trans -acting genetic control of nuclear loci encoding protein components of this regulatory switch. Our study showcases how nuclear haplotype can privilege the replication of specific mtDNA molecules to shape mtCN and heteroplasmy dynamics in the human population.
Collapse
Affiliation(s)
- Rahul Gupta
- Howard Hughes Medical Institute and Department of Molecular Biology, Massachusetts General Hospital, United States
- Broad Institute of MIT and Harvard, United States
- Analytic and Translational Genetics Unit, Center for Genomic Medicine, Massachusetts General Hospital, United States
| | - Masahiro Kanai
- Broad Institute of MIT and Harvard, United States
- Analytic and Translational Genetics Unit, Center for Genomic Medicine, Massachusetts General Hospital, United States
| | - Timothy J Durham
- Howard Hughes Medical Institute and Department of Molecular Biology, Massachusetts General Hospital, United States
- Broad Institute of MIT and Harvard, United States
| | - Kristin Tsuo
- Broad Institute of MIT and Harvard, United States
- Analytic and Translational Genetics Unit, Center for Genomic Medicine, Massachusetts General Hospital, United States
| | - Jason G McCoy
- Howard Hughes Medical Institute and Department of Molecular Biology, Massachusetts General Hospital, United States
- Broad Institute of MIT and Harvard, United States
| | - Patrick F Chinnery
- Department of Clinical Neurosciences & MRC Mitochondrial Biology Unit, University of Cambridge, United Kingdom
| | - Konrad J Karczewski
- Broad Institute of MIT and Harvard, United States
- Analytic and Translational Genetics Unit, Center for Genomic Medicine, Massachusetts General Hospital, United States
| | - Sarah E Calvo
- Howard Hughes Medical Institute and Department of Molecular Biology, Massachusetts General Hospital, United States
- Broad Institute of MIT and Harvard, United States
| | - Benjamin M Neale
- Broad Institute of MIT and Harvard, United States
- Analytic and Translational Genetics Unit, Center for Genomic Medicine, Massachusetts General Hospital, United States
| | - Vamsi K Mootha
- Howard Hughes Medical Institute and Department of Molecular Biology, Massachusetts General Hospital, United States
- Broad Institute of MIT and Harvard, United States
- Department of Systems Biology, Harvard Medical School, United States
| |
Collapse
|
6
|
Shi X, Reinstadler B, Shah H, To TL, Byrne K, Summer L, Calvo SE, Goldberger O, Doench JG, Mootha VK, Shen H. Combinatorial GxGxE CRISPR screen identifies SLC25A39 in mitochondrial glutathione transport linking iron homeostasis to OXPHOS. Nat Commun 2022; 13:2483. [PMID: 35513392 PMCID: PMC9072411 DOI: 10.1038/s41467-022-30126-9] [Citation(s) in RCA: 28] [Impact Index Per Article: 14.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/04/2021] [Accepted: 04/18/2022] [Indexed: 12/18/2022] Open
Abstract
The SLC25 carrier family consists of 53 transporters that shuttle nutrients and co-factors across mitochondrial membranes. The family is highly redundant and their transport activities coupled to metabolic state. Here, we use a pooled, dual CRISPR screening strategy that knocks out pairs of transporters in four metabolic states - glucose, galactose, OXPHOS inhibition, and absence of pyruvate - designed to unmask the inter-dependence of these genes. In total, we screen 63 genes in four metabolic states, corresponding to 2016 single and pair-wise genetic perturbations. We recover 19 gene-by-environment (GxE) interactions and 9 gene-by-gene (GxG) interactions. One GxE interaction hit illustrates that the fitness defect in the mitochondrial folate carrier (SLC25A32) KO cells is genetically buffered in galactose due to a lack of substrate in de novo purine biosynthesis. GxG analysis highlights a buffering interaction between the iron transporter SLC25A37 (A37) and the poorly characterized SLC25A39 (A39). Mitochondrial metabolite profiling, organelle transport assays, and structure-guided mutagenesis identify A39 as critical for mitochondrial glutathione (GSH) import. Functional studies reveal that A39-mediated glutathione homeostasis and A37-mediated mitochondrial iron uptake operate jointly to support mitochondrial OXPHOS. Our work underscores the value of studying family-wide genetic interactions across different metabolic environments.
Collapse
Affiliation(s)
- Xiaojian Shi
- Cellular and Molecular Physiology Department, Yale School of Medicine, New Haven, CT, USA
- Systems Biology Institute, Yale West Campus, West Haven, CT, USA
| | - Bryn Reinstadler
- Howard Hughes Medical Institute and Department of Molecular Biology, Massachusetts General Hospital, Boston, MA, USA
- Department of Systems Biology, Harvard Medical School, Boston, MA, USA
- Broad Institute, Cambridge, MA, USA
| | - Hardik Shah
- Howard Hughes Medical Institute and Department of Molecular Biology, Massachusetts General Hospital, Boston, MA, USA
- Department of Systems Biology, Harvard Medical School, Boston, MA, USA
- Broad Institute, Cambridge, MA, USA
| | - Tsz-Leung To
- Howard Hughes Medical Institute and Department of Molecular Biology, Massachusetts General Hospital, Boston, MA, USA
- Department of Systems Biology, Harvard Medical School, Boston, MA, USA
- Broad Institute, Cambridge, MA, USA
| | - Katie Byrne
- Cellular and Molecular Physiology Department, Yale School of Medicine, New Haven, CT, USA
- Systems Biology Institute, Yale West Campus, West Haven, CT, USA
| | - Luanna Summer
- Cellular and Molecular Physiology Department, Yale School of Medicine, New Haven, CT, USA
- Systems Biology Institute, Yale West Campus, West Haven, CT, USA
| | - Sarah E Calvo
- Howard Hughes Medical Institute and Department of Molecular Biology, Massachusetts General Hospital, Boston, MA, USA
- Department of Systems Biology, Harvard Medical School, Boston, MA, USA
- Broad Institute, Cambridge, MA, USA
| | - Olga Goldberger
- Howard Hughes Medical Institute and Department of Molecular Biology, Massachusetts General Hospital, Boston, MA, USA
- Department of Systems Biology, Harvard Medical School, Boston, MA, USA
| | | | - Vamsi K Mootha
- Howard Hughes Medical Institute and Department of Molecular Biology, Massachusetts General Hospital, Boston, MA, USA
- Department of Systems Biology, Harvard Medical School, Boston, MA, USA
- Broad Institute, Cambridge, MA, USA
| | - Hongying Shen
- Cellular and Molecular Physiology Department, Yale School of Medicine, New Haven, CT, USA.
- Systems Biology Institute, Yale West Campus, West Haven, CT, USA.
| |
Collapse
|
7
|
Laricchia KM, Lake NJ, Watts NA, Shand M, Haessly A, Gauthier L, Benjamin D, Banks E, Soto J, Garimella K, Emery J, Rehm HL, MacArthur DG, Tiao G, Lek MV, Mootha VK, Calvo SE. Mitochondrial DNA variation across 56,434 individuals in gnomAD. Genome Res 2022; 32:569-582. [PMID: 35074858 PMCID: PMC8896463 DOI: 10.1101/gr.276013.121] [Citation(s) in RCA: 27] [Impact Index Per Article: 13.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/23/2021] [Accepted: 01/19/2022] [Indexed: 11/25/2022]
Abstract
Genomic databases of allele frequency are extremely helpful for evaluating clinical variants of unknown significance; however, until now, databases such as the Genome Aggregation Database (gnomAD) have focused on nuclear DNA and have ignored the mitochondrial genome (mtDNA). Here we present a pipeline to call mtDNA variants that addresses three technical challenges: (i) detecting homoplasmic and heteroplasmic variants, present respectively in all or a fraction of mtDNA molecules, (ii) circular mtDNA genome, and (iii) misalignment of nuclear sequences of mitochondrial origin (NUMTs). We observed that mtDNA copy number per cell varied across gnomAD cohorts and influenced the fraction of NUMT-derived false-positive variant calls, which can account for the majority of putative heteroplasmies. To avoid false positives, we excluded contaminated samples, cell lines, and samples prone to NUMT misalignment due to few mtDNA copies. Furthermore, we report variants with heteroplasmy greater than 10%. We applied this pipeline to 56,434 whole genome sequences in the gnomAD v3.1 database that includes individuals of European (58%), African (25%), Latino (10%), and Asian (5%) ancestry. Our gnomAD v3.1 release contains population frequencies for 10,850 unique mtDNA variants at more than half of all mtDNA bases. We report frequencies within each nuclear ancestral population and mitochondrial haplogroup. Homoplasmic variants account for most variant calls (98%) and unique variants (85%). We observed that 1/250 individuals carry a pathogenic mtDNA variant with heteroplasmy above 10%. These mtDNA population allele frequencies are freely accessible and will aid in diagnostic interpretation and research studies.
Collapse
|
8
|
Jourdain AA, Begg BE, Mick E, Shah H, Calvo SE, Skinner OS, Sharma R, Blue SM, Yeo GW, Burge CB, Mootha VK. Loss of LUC7L2 and U1 snRNP subunits shifts energy metabolism from glycolysis to OXPHOS. Mol Cell 2021; 81:1905-1919.e12. [PMID: 33852893 DOI: 10.1016/j.molcel.2021.02.033] [Citation(s) in RCA: 26] [Impact Index Per Article: 8.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/21/2020] [Revised: 12/18/2020] [Accepted: 02/22/2021] [Indexed: 12/17/2022]
Abstract
Oxidative phosphorylation (OXPHOS) and glycolysis are the two major pathways for ATP production. The reliance on each varies across tissues and cell states, and can influence susceptibility to disease. At present, the full set of molecular mechanisms governing the relative expression and balance of these two pathways is unknown. Here, we focus on genes whose loss leads to an increase in OXPHOS activity. Unexpectedly, this class of genes is enriched for components of the pre-mRNA splicing machinery, in particular for subunits of the U1 snRNP. Among them, we show that LUC7L2 represses OXPHOS and promotes glycolysis by multiple mechanisms, including (1) splicing of the glycolytic enzyme PFKM to suppress glycogen synthesis, (2) splicing of the cystine/glutamate antiporter SLC7A11 (xCT) to suppress glutamate oxidation, and (3) secondary repression of mitochondrial respiratory supercomplex formation. Our results connect LUC7L2 expression and, more generally, the U1 snRNP to cellular energy metabolism.
Collapse
Affiliation(s)
- Alexis A Jourdain
- Department of Molecular Biology and Howard Hughes Medical Institute, Massachusetts General Hospital, Boston, MA 02114, USA; Department of Systems Biology, Harvard Medical School, Boston, MA 02115, USA; Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA.
| | | | - Eran Mick
- Department of Molecular Biology and Howard Hughes Medical Institute, Massachusetts General Hospital, Boston, MA 02114, USA; Department of Systems Biology, Harvard Medical School, Boston, MA 02115, USA; Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA
| | - Hardik Shah
- Department of Molecular Biology and Howard Hughes Medical Institute, Massachusetts General Hospital, Boston, MA 02114, USA; Department of Systems Biology, Harvard Medical School, Boston, MA 02115, USA; Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA
| | - Sarah E Calvo
- Department of Molecular Biology and Howard Hughes Medical Institute, Massachusetts General Hospital, Boston, MA 02114, USA; Department of Systems Biology, Harvard Medical School, Boston, MA 02115, USA; Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA
| | - Owen S Skinner
- Department of Molecular Biology and Howard Hughes Medical Institute, Massachusetts General Hospital, Boston, MA 02114, USA; Department of Systems Biology, Harvard Medical School, Boston, MA 02115, USA; Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA
| | - Rohit Sharma
- Department of Molecular Biology and Howard Hughes Medical Institute, Massachusetts General Hospital, Boston, MA 02114, USA; Department of Systems Biology, Harvard Medical School, Boston, MA 02115, USA; Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA
| | - Steven M Blue
- Department of Cellular and Molecular Medicine, Institute for Genomic Medicine, University of California, San Diego, La Jolla, CA 92093, USA
| | - Gene W Yeo
- Department of Cellular and Molecular Medicine, Institute for Genomic Medicine, University of California, San Diego, La Jolla, CA 92093, USA
| | | | - Vamsi K Mootha
- Department of Molecular Biology and Howard Hughes Medical Institute, Massachusetts General Hospital, Boston, MA 02114, USA; Department of Systems Biology, Harvard Medical School, Boston, MA 02115, USA; Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA.
| |
Collapse
|
9
|
Rath S, Sharma R, Gupta R, Ast T, Chan C, Durham TJ, Goodman RP, Grabarek Z, Haas ME, Hung WHW, Joshi PR, Jourdain AA, Kim SH, Kotrys AV, Lam SS, McCoy JG, Meisel JD, Miranda M, Panda A, Patgiri A, Rogers R, Sadre S, Shah H, Skinner OS, To TL, Walker M, Wang H, Ward PS, Wengrod J, Yuan CC, Calvo SE, Mootha VK. MitoCarta3.0: an updated mitochondrial proteome now with sub-organelle localization and pathway annotations. Nucleic Acids Res 2020; 49:D1541-D1547. [PMID: 33174596 PMCID: PMC7778944 DOI: 10.1093/nar/gkaa1011] [Citation(s) in RCA: 586] [Impact Index Per Article: 146.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/18/2020] [Revised: 10/12/2020] [Accepted: 10/14/2020] [Indexed: 02/04/2023] Open
Abstract
The mammalian mitochondrial proteome is under dual genomic control, with 99% of proteins encoded by the nuclear genome and 13 originating from the mitochondrial DNA (mtDNA). We previously developed MitoCarta, a catalogue of over 1000 genes encoding the mammalian mitochondrial proteome. This catalogue was compiled using a Bayesian integration of multiple sequence features and experimental datasets, notably protein mass spectrometry of mitochondria isolated from fourteen murine tissues. Here, we introduce MitoCarta3.0. Beginning with the MitoCarta2.0 inventory, we performed manual review to remove 100 genes and introduce 78 additional genes, arriving at an updated inventory of 1136 human genes. We now include manually curated annotations of sub-mitochondrial localization (matrix, inner membrane, intermembrane space, outer membrane) as well as assignment to 149 hierarchical 'MitoPathways' spanning seven broad functional categories relevant to mitochondria. MitoCarta3.0, including sub-mitochondrial localization and MitoPathway annotations, is freely available at http://www.broadinstitute.org/mitocarta and should serve as a continued community resource for mitochondrial biology and medicine.
Collapse
Affiliation(s)
| | | | | | - Tslil Ast
- Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA,Howard Hughes Medical Institute and Departments of Molecular Biology and Medicine, Massachusetts General Hospital, Boston, MA 02114, USA,Department of Systems Biology, Harvard Medical School, Boston, MA 02115, USA
| | - Connie Chan
- Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA,Howard Hughes Medical Institute and Departments of Molecular Biology and Medicine, Massachusetts General Hospital, Boston, MA 02114, USA,Department of Systems Biology, Harvard Medical School, Boston, MA 02115, USA
| | - Timothy J Durham
- Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA,Howard Hughes Medical Institute and Departments of Molecular Biology and Medicine, Massachusetts General Hospital, Boston, MA 02114, USA,Department of Systems Biology, Harvard Medical School, Boston, MA 02115, USA
| | - Russell P Goodman
- Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA,Howard Hughes Medical Institute and Departments of Molecular Biology and Medicine, Massachusetts General Hospital, Boston, MA 02114, USA,Department of Systems Biology, Harvard Medical School, Boston, MA 02115, USA
| | - Zenon Grabarek
- Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA,Howard Hughes Medical Institute and Departments of Molecular Biology and Medicine, Massachusetts General Hospital, Boston, MA 02114, USA,Department of Systems Biology, Harvard Medical School, Boston, MA 02115, USA
| | - Mary E Haas
- Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA,Howard Hughes Medical Institute and Departments of Molecular Biology and Medicine, Massachusetts General Hospital, Boston, MA 02114, USA,Department of Systems Biology, Harvard Medical School, Boston, MA 02115, USA
| | - Wendy H W Hung
- Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA,Howard Hughes Medical Institute and Departments of Molecular Biology and Medicine, Massachusetts General Hospital, Boston, MA 02114, USA,Department of Systems Biology, Harvard Medical School, Boston, MA 02115, USA
| | - Pallavi R Joshi
- Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA,Howard Hughes Medical Institute and Departments of Molecular Biology and Medicine, Massachusetts General Hospital, Boston, MA 02114, USA,Department of Systems Biology, Harvard Medical School, Boston, MA 02115, USA
| | - Alexis A Jourdain
- Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA,Howard Hughes Medical Institute and Departments of Molecular Biology and Medicine, Massachusetts General Hospital, Boston, MA 02114, USA,Department of Systems Biology, Harvard Medical School, Boston, MA 02115, USA
| | - Sharon H Kim
- Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA,Howard Hughes Medical Institute and Departments of Molecular Biology and Medicine, Massachusetts General Hospital, Boston, MA 02114, USA,Department of Systems Biology, Harvard Medical School, Boston, MA 02115, USA
| | - Anna V Kotrys
- Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA,Howard Hughes Medical Institute and Departments of Molecular Biology and Medicine, Massachusetts General Hospital, Boston, MA 02114, USA,Department of Systems Biology, Harvard Medical School, Boston, MA 02115, USA
| | - Stephanie S Lam
- Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA,Howard Hughes Medical Institute and Departments of Molecular Biology and Medicine, Massachusetts General Hospital, Boston, MA 02114, USA,Department of Systems Biology, Harvard Medical School, Boston, MA 02115, USA
| | - Jason G McCoy
- Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA,Howard Hughes Medical Institute and Departments of Molecular Biology and Medicine, Massachusetts General Hospital, Boston, MA 02114, USA,Department of Systems Biology, Harvard Medical School, Boston, MA 02115, USA
| | - Joshua D Meisel
- Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA,Howard Hughes Medical Institute and Departments of Molecular Biology and Medicine, Massachusetts General Hospital, Boston, MA 02114, USA,Department of Systems Biology, Harvard Medical School, Boston, MA 02115, USA
| | - Maria Miranda
- Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA,Howard Hughes Medical Institute and Departments of Molecular Biology and Medicine, Massachusetts General Hospital, Boston, MA 02114, USA,Department of Systems Biology, Harvard Medical School, Boston, MA 02115, USA
| | - Apekshya Panda
- Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA,Howard Hughes Medical Institute and Departments of Molecular Biology and Medicine, Massachusetts General Hospital, Boston, MA 02114, USA,Department of Systems Biology, Harvard Medical School, Boston, MA 02115, USA
| | - Anupam Patgiri
- Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA,Howard Hughes Medical Institute and Departments of Molecular Biology and Medicine, Massachusetts General Hospital, Boston, MA 02114, USA,Department of Systems Biology, Harvard Medical School, Boston, MA 02115, USA
| | - Robert Rogers
- Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA,Howard Hughes Medical Institute and Departments of Molecular Biology and Medicine, Massachusetts General Hospital, Boston, MA 02114, USA,Department of Systems Biology, Harvard Medical School, Boston, MA 02115, USA
| | - Shayan Sadre
- Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA,Howard Hughes Medical Institute and Departments of Molecular Biology and Medicine, Massachusetts General Hospital, Boston, MA 02114, USA,Department of Systems Biology, Harvard Medical School, Boston, MA 02115, USA
| | - Hardik Shah
- Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA,Howard Hughes Medical Institute and Departments of Molecular Biology and Medicine, Massachusetts General Hospital, Boston, MA 02114, USA,Department of Systems Biology, Harvard Medical School, Boston, MA 02115, USA
| | - Owen S Skinner
- Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA,Howard Hughes Medical Institute and Departments of Molecular Biology and Medicine, Massachusetts General Hospital, Boston, MA 02114, USA,Department of Systems Biology, Harvard Medical School, Boston, MA 02115, USA
| | - Tsz-Leung To
- Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA,Howard Hughes Medical Institute and Departments of Molecular Biology and Medicine, Massachusetts General Hospital, Boston, MA 02114, USA,Department of Systems Biology, Harvard Medical School, Boston, MA 02115, USA
| | - Melissa A Walker
- Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA,Howard Hughes Medical Institute and Departments of Molecular Biology and Medicine, Massachusetts General Hospital, Boston, MA 02114, USA,Department of Systems Biology, Harvard Medical School, Boston, MA 02115, USA
| | - Hong Wang
- Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA,Howard Hughes Medical Institute and Departments of Molecular Biology and Medicine, Massachusetts General Hospital, Boston, MA 02114, USA,Department of Systems Biology, Harvard Medical School, Boston, MA 02115, USA
| | - Patrick S Ward
- Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA,Howard Hughes Medical Institute and Departments of Molecular Biology and Medicine, Massachusetts General Hospital, Boston, MA 02114, USA,Department of Systems Biology, Harvard Medical School, Boston, MA 02115, USA
| | - Jordan Wengrod
- Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA,Howard Hughes Medical Institute and Departments of Molecular Biology and Medicine, Massachusetts General Hospital, Boston, MA 02114, USA,Department of Systems Biology, Harvard Medical School, Boston, MA 02115, USA
| | - Chen-Ching Yuan
- Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA,Howard Hughes Medical Institute and Departments of Molecular Biology and Medicine, Massachusetts General Hospital, Boston, MA 02114, USA,Department of Systems Biology, Harvard Medical School, Boston, MA 02115, USA
| | - Sarah E Calvo
- Correspondence may also be addressed to Sarah E. Calvo.
| | - Vamsi K Mootha
- To whom correspondence should be addressed. Tel: +1 617 643 3059;
| |
Collapse
|
10
|
Frazier AE, Compton AG, Kishita Y, Hock DH, Welch AE, Amarasekera SSC, Rius R, Formosa LE, Imai-Okazaki A, Francis D, Wang M, Lake NJ, Tregoning S, Jabbari JS, Lucattini A, Nitta KR, Ohtake A, Murayama K, Amor DJ, McGillivray G, Wong FY, van der Knaap MS, Jeroen Vermeulen R, Wiltshire EJ, Fletcher JM, Lewis B, Baynam G, Ellaway C, Balasubramaniam S, Bhattacharya K, Freckmann ML, Arbuckle S, Rodriguez M, Taft RJ, Sadedin S, Cowley MJ, Minoche AE, Calvo SE, Mootha VK, Ryan MT, Okazaki Y, Stroud DA, Simons C, Christodoulou J, Thorburn DR. Fatal perinatal mitochondrial cardiac failure caused by recurrent de novo duplications in the ATAD3 locus. Med (N Y) 2020; 2:49-73. [PMID: 33575671 DOI: 10.1016/j.medj.2020.06.004] [Citation(s) in RCA: 20] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
Background In about half of all patients with a suspected monogenic disease, genomic investigations fail to identify the diagnosis. A contributing factor is the difficulty with repetitive regions of the genome, such as those generated by segmental duplications. The ATAD3 locus is one such region, in which recessive deletions and dominant duplications have recently been reported to cause lethal perinatal mitochondrial diseases characterized by pontocerebellar hypoplasia or cardiomyopathy, respectively. Methods Whole exome, whole genome and long-read DNA sequencing techniques combined with studies of RNA and quantitative proteomics were used to investigate 17 subjects from 16 unrelated families with suspected mitochondrial disease. Findings We report six different de novo duplications in the ATAD3 gene locus causing a distinctive presentation including lethal perinatal cardiomyopathy, persistent hyperlactacidemia, and frequently corneal clouding or cataracts and encephalopathy. The recurrent 68 Kb ATAD3 duplications are identifiable from genome and exome sequencing but usually missed by microarrays. The ATAD3 duplications result in the formation of identical chimeric ATAD3A/ATAD3C proteins, altered ATAD3 complexes and a striking reduction in mitochondrial oxidative phosphorylation complex I and its activity in heart tissue. Conclusions ATAD3 duplications appear to act in a dominant-negative manner and the de novo inheritance infers a low recurrence risk for families, unlike most pediatric mitochondrial diseases. More than 350 genes underlie mitochondrial diseases. In our experience the ATAD3 locus is now one of the five most common causes of nuclear-encoded pediatric mitochondrial disease but the repetitive nature of the locus means ATAD3 diagnoses may be frequently missed by current genomic strategies. Funding Australian NHMRC, US Department of Defense, Japanese AMED and JSPS agencies, Australian Genomics Health Alliance and Australian Mito Foundation.
Collapse
Affiliation(s)
- Ann E Frazier
- Murdoch Children's Research Institute, Royal Children's Hospital, Melbourne, VIC 3052, Australia.,Department of Paediatrics, University of Melbourne, Melbourne, VIC 3052, Australia.,These authors contributed equally: A.E. Frazier, A.G. Compton
| | - Alison G Compton
- Murdoch Children's Research Institute, Royal Children's Hospital, Melbourne, VIC 3052, Australia.,Department of Paediatrics, University of Melbourne, Melbourne, VIC 3052, Australia.,These authors contributed equally: A.E. Frazier, A.G. Compton
| | - Yoshihito Kishita
- Diagnostics and Therapeutics of Intractable Diseases, Intractable Disease Research Center, Juntendo University, Graduate School of Medicine, Tokyo, 113-8421, Japan
| | - Daniella H Hock
- Department of Biochemistry and Molecular Biology and Bio21 Molecular Science and Biotechnology Institute, University of Melbourne, Melbourne, VIC 3052, Australia
| | - AnneMarie E Welch
- Murdoch Children's Research Institute, Royal Children's Hospital, Melbourne, VIC 3052, Australia
| | - Sumudu S C Amarasekera
- Murdoch Children's Research Institute, Royal Children's Hospital, Melbourne, VIC 3052, Australia.,Department of Paediatrics, University of Melbourne, Melbourne, VIC 3052, Australia
| | - Rocio Rius
- Murdoch Children's Research Institute, Royal Children's Hospital, Melbourne, VIC 3052, Australia.,Department of Paediatrics, University of Melbourne, Melbourne, VIC 3052, Australia
| | - Luke E Formosa
- Department of Biochemistry and Molecular Biology, Monash Biomedicine Discovery Institute, Monash University, Melbourne, VIC 3800, Australia
| | - Atsuko Imai-Okazaki
- Diagnostics and Therapeutics of Intractable Diseases, Intractable Disease Research Center, Juntendo University, Graduate School of Medicine, Tokyo, 113-8421, Japan.,Division of Genomic Medicine Research, Medical Genomics Center, National Center for Global Health and Medicine, Tokyo 162-8655, Japan
| | - David Francis
- Victorian Clinical Genetics Services, Murdoch Children's Research Institute, Royal Children's Hospital, Melbourne, VIC 3052, Australia
| | - Min Wang
- Murdoch Children's Research Institute, Royal Children's Hospital, Melbourne, VIC 3052, Australia
| | - Nicole J Lake
- Murdoch Children's Research Institute, Royal Children's Hospital, Melbourne, VIC 3052, Australia.,Department of Paediatrics, University of Melbourne, Melbourne, VIC 3052, Australia.,Department of Genetics, Yale School of Medicine, New Haven, CT 06510, USA
| | - Simone Tregoning
- Murdoch Children's Research Institute, Royal Children's Hospital, Melbourne, VIC 3052, Australia.,Victorian Clinical Genetics Services, Murdoch Children's Research Institute, Royal Children's Hospital, Melbourne, VIC 3052, Australia
| | - Jafar S Jabbari
- Australian Genome Research Facility Ltd, Victorian Comprehensive Cancer Centre, Melbourne VIC 3052, Australia
| | - Alexis Lucattini
- Australian Genome Research Facility Ltd, Victorian Comprehensive Cancer Centre, Melbourne VIC 3052, Australia
| | - Kazuhiro R Nitta
- Diagnostics and Therapeutics of Intractable Diseases, Intractable Disease Research Center, Juntendo University, Graduate School of Medicine, Tokyo, 113-8421, Japan
| | - Akira Ohtake
- Department of Pediatrics & Clinical Genomics, Saitama Medical University Hospital, Saitama, 350-0495, Japan
| | - Kei Murayama
- Department of Metabolism, Chiba Children's Hospital, Chiba, 266-0007, Japan
| | - David J Amor
- Murdoch Children's Research Institute, Royal Children's Hospital, Melbourne, VIC 3052, Australia.,Department of Paediatrics, University of Melbourne, Melbourne, VIC 3052, Australia
| | - George McGillivray
- Victorian Clinical Genetics Services, Murdoch Children's Research Institute, Royal Children's Hospital, Melbourne, VIC 3052, Australia
| | - Flora Y Wong
- Ritchie Centre, Hudson Institute of Medical Research; Department of Paediatrics, Monash University; and Monash Newborn, Monash Children's Hospital, Melbourne, VIC 3168, Australia
| | - Marjo S van der Knaap
- Child Neurology, Emma Children's Hospital, Amsterdam University Medical Centers, Vrije Universiteit and Amsterdam Neuroscience, 1081 HV Amsterdam, The Netherlands.,Functional Genomics, Center for Neurogenomics and Cognitive Research, Vrije Universiteit and Amsterdam Neuroscience, 1081 HV Amsterdam, The Netherlands
| | - R Jeroen Vermeulen
- Department of Neurology, Maastricht University Medical Center, 6229 HX, Maastricht, The Netherlands
| | - Esko J Wiltshire
- Department of Paediatrics and Child Health, University of Otago Wellington and Capital and Coast District Health Board, Wellington 6021, New Zealand
| | - Janice M Fletcher
- Department of Genetics and Molecular Pathology, SA Pathology, Adelaide, SA 5000, Australia
| | - Barry Lewis
- Department of Clinical Biochemistry, PathWest Laboratory Medicine Western Australia, Nedlands, WA 6009, Australia
| | - Gareth Baynam
- Western Australian Register of Developmental Anomalies and Genetic Services of Western Australia and King Edward Memorial Hospital for Women Perth, Subiaco, WA 6008, Australia.,Telethon Kids Institute and School of Paediatrics and Child Health, The University of Western Australia, Perth, WA 6009, Australia
| | - Carolyn Ellaway
- Genetic Metabolic Disorders Service, Sydney Children's Hospital Network, The Children's Hospital at Westmead, Sydney, NSW 2145, Australia.,Disciplines of Genomic Medicine and Child and Adolescent Health, Sydney Medical School, University of Sydney, NSW 2145, Australia
| | - Shanti Balasubramaniam
- Genetic Metabolic Disorders Service, Sydney Children's Hospital Network, The Children's Hospital at Westmead, Sydney, NSW 2145, Australia
| | - Kaustuv Bhattacharya
- Genetic Metabolic Disorders Service, Sydney Children's Hospital Network, The Children's Hospital at Westmead, Sydney, NSW 2145, Australia.,Disciplines of Genomic Medicine and Child and Adolescent Health, Sydney Medical School, University of Sydney, NSW 2145, Australia
| | | | - Susan Arbuckle
- Department of Histopathology, The Children's Hospital at Westmead, Sydney Children's Hospital Network, Sydney, NSW 2145, Australia
| | - Michael Rodriguez
- Discipline of Pathology, School of Medical Sciences, The University of Sydney, Sydney, NSW 2006, Australia
| | | | - Simon Sadedin
- Murdoch Children's Research Institute, Royal Children's Hospital, Melbourne, VIC 3052, Australia.,Victorian Clinical Genetics Services, Murdoch Children's Research Institute, Royal Children's Hospital, Melbourne, VIC 3052, Australia
| | - Mark J Cowley
- Children's Cancer Institute, Kensington, NSW 2750, Australia; St Vincent's Clinical School, UNSW Sydney, Darlinghurst, NSW 2010, Australia.,Kinghorn Centre for Clinical Genomics, Garvan Institute of Medical Research, Darlinghurst, NSW 2010, Australia
| | - André E Minoche
- Kinghorn Centre for Clinical Genomics, Garvan Institute of Medical Research, Darlinghurst, NSW 2010, Australia
| | - Sarah E Calvo
- Broad Institute, Cambridge, MA 02142, USA; Howard Hughes Medical Institute and Department of Molecular Biology, Massachusetts General Hospital, Boston, MA 02114, USA; Harvard Medical School, Boston, MA 02446, USA
| | - Vamsi K Mootha
- Broad Institute, Cambridge, MA 02142, USA; Howard Hughes Medical Institute and Department of Molecular Biology, Massachusetts General Hospital, Boston, MA 02114, USA; Harvard Medical School, Boston, MA 02446, USA
| | - Michael T Ryan
- Department of Biochemistry and Molecular Biology, Monash Biomedicine Discovery Institute, Monash University, Melbourne, VIC 3800, Australia
| | - Yasushi Okazaki
- Diagnostics and Therapeutics of Intractable Diseases, Intractable Disease Research Center, Juntendo University, Graduate School of Medicine, Tokyo, 113-8421, Japan
| | - David A Stroud
- Department of Biochemistry and Molecular Biology and Bio21 Molecular Science and Biotechnology Institute, University of Melbourne, Melbourne, VIC 3052, Australia
| | - Cas Simons
- Murdoch Children's Research Institute, Royal Children's Hospital, Melbourne, VIC 3052, Australia.,Institute for Molecular Bioscience, The University of Queensland, Brisbane, QLD 4072 Australia
| | - John Christodoulou
- Murdoch Children's Research Institute, Royal Children's Hospital, Melbourne, VIC 3052, Australia.,Department of Paediatrics, University of Melbourne, Melbourne, VIC 3052, Australia.,Victorian Clinical Genetics Services, Murdoch Children's Research Institute, Royal Children's Hospital, Melbourne, VIC 3052, Australia.,Disciplines of Genomic Medicine and Child and Adolescent Health, Sydney Medical School, University of Sydney, NSW 2145, Australia
| | - David R Thorburn
- Murdoch Children's Research Institute, Royal Children's Hospital, Melbourne, VIC 3052, Australia.,Department of Paediatrics, University of Melbourne, Melbourne, VIC 3052, Australia.,Victorian Clinical Genetics Services, Murdoch Children's Research Institute, Royal Children's Hospital, Melbourne, VIC 3052, Australia.,Lead contact
| |
Collapse
|
11
|
Jain IH, Calvo SE, Markhard AL, Skinner OS, To TL, Ast T, Mootha VK. Genetic Screen for Cell Fitness in High or Low Oxygen Highlights Mitochondrial and Lipid Metabolism. Cell 2020; 181:716-727.e11. [PMID: 32259488 PMCID: PMC7293541 DOI: 10.1016/j.cell.2020.03.029] [Citation(s) in RCA: 110] [Impact Index Per Article: 27.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/10/2019] [Revised: 02/13/2020] [Accepted: 03/11/2020] [Indexed: 01/04/2023]
Abstract
Human cells are able to sense and adapt to variations in oxygen levels. Historically, much research in this field has focused on hypoxia-inducible factor (HIF) signaling and reactive oxygen species (ROS). Here, we perform genome-wide CRISPR growth screens at 21%, 5%, and 1% oxygen to systematically identify gene knockouts with relative fitness defects in high oxygen (213 genes) or low oxygen (109 genes), most without known connection to HIF or ROS. Knockouts of many mitochondrial pathways thought to be essential, including complex I and enzymes in Fe-S biosynthesis, grow relatively well at low oxygen and thus are buffered by hypoxia. In contrast, in certain cell types, knockout of lipid biosynthetic and peroxisomal genes causes fitness defects only in low oxygen. Our resource nominates genetic diseases whose severity may be modulated by oxygen and links hundreds of genes to oxygen homeostasis.
Collapse
Affiliation(s)
- Isha H Jain
- Howard Hughes Medical Institute, Department of Molecular Biology, Massachusetts General Hospital, Harvard Medical School, Boston, MA 02114, USA; Broad Institute, Cambridge, MA 02142, USA
| | - Sarah E Calvo
- Howard Hughes Medical Institute, Department of Molecular Biology, Massachusetts General Hospital, Harvard Medical School, Boston, MA 02114, USA; Broad Institute, Cambridge, MA 02142, USA
| | - Andrew L Markhard
- Howard Hughes Medical Institute, Department of Molecular Biology, Massachusetts General Hospital, Harvard Medical School, Boston, MA 02114, USA; Broad Institute, Cambridge, MA 02142, USA
| | - Owen S Skinner
- Howard Hughes Medical Institute, Department of Molecular Biology, Massachusetts General Hospital, Harvard Medical School, Boston, MA 02114, USA; Broad Institute, Cambridge, MA 02142, USA
| | - Tsz-Leung To
- Howard Hughes Medical Institute, Department of Molecular Biology, Massachusetts General Hospital, Harvard Medical School, Boston, MA 02114, USA; Broad Institute, Cambridge, MA 02142, USA
| | - Tslil Ast
- Howard Hughes Medical Institute, Department of Molecular Biology, Massachusetts General Hospital, Harvard Medical School, Boston, MA 02114, USA; Broad Institute, Cambridge, MA 02142, USA
| | - Vamsi K Mootha
- Howard Hughes Medical Institute, Department of Molecular Biology, Massachusetts General Hospital, Harvard Medical School, Boston, MA 02114, USA; Broad Institute, Cambridge, MA 02142, USA.
| |
Collapse
|
12
|
Ast T, Meisel JD, Patra S, Wang H, Grange RMH, Kim SH, Calvo SE, Orefice LL, Nagashima F, Ichinose F, Zapol WM, Ruvkun G, Barondeau DP, Mootha VK. Hypoxia Rescues Frataxin Loss by Restoring Iron Sulfur Cluster Biogenesis. Cell 2019; 177:1507-1521.e16. [PMID: 31031004 PMCID: PMC6911770 DOI: 10.1016/j.cell.2019.03.045] [Citation(s) in RCA: 67] [Impact Index Per Article: 13.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/25/2018] [Revised: 02/11/2019] [Accepted: 03/22/2019] [Indexed: 12/16/2022]
Abstract
Friedreich's ataxia (FRDA) is a devastating, multisystemic disorder caused by recessive mutations in the mitochondrial protein frataxin (FXN). FXN participates in the biosynthesis of Fe-S clusters and is considered to be essential for viability. Here we report that when grown in 1% ambient O2, FXN null yeast, human cells, and nematodes are fully viable. In human cells, hypoxia restores steady-state levels of Fe-S clusters and normalizes ATF4, NRF2, and IRP2 signaling events associated with FRDA. Cellular studies and in vitro reconstitution indicate that hypoxia acts through HIF-independent mechanisms that increase bioavailable iron as well as directly activate Fe-S synthesis. In a mouse model of FRDA, breathing 11% O2 attenuates the progression of ataxia, whereas breathing 55% O2 hastens it. Our work identifies oxygen as a key environmental variable in the pathogenesis associated with FXN depletion, with important mechanistic and therapeutic implications.
Collapse
Affiliation(s)
- Tslil Ast
- Broad Institute, Cambridge, MA 02142, USA; Howard Hughes Medical Institute, Howard Hughes Medical Institute, Massachusetts General Hospital, Boston, MA 02114, USA; Department of Molecular Biology, Massachusetts General Hospital, Boston, MA 02114, USA; Harvard Medical School, Boston, MA 02115, USA
| | - Joshua D Meisel
- Broad Institute, Cambridge, MA 02142, USA; Howard Hughes Medical Institute, Howard Hughes Medical Institute, Massachusetts General Hospital, Boston, MA 02114, USA; Department of Molecular Biology, Massachusetts General Hospital, Boston, MA 02114, USA; Harvard Medical School, Boston, MA 02115, USA
| | - Shachin Patra
- Department of Chemistry, Texas A&M University, College Station, TX 77843, USA
| | - Hong Wang
- Broad Institute, Cambridge, MA 02142, USA; Howard Hughes Medical Institute, Howard Hughes Medical Institute, Massachusetts General Hospital, Boston, MA 02114, USA; Department of Molecular Biology, Massachusetts General Hospital, Boston, MA 02114, USA; Harvard Medical School, Boston, MA 02115, USA
| | - Robert M H Grange
- Department of Anesthesia, Critical Care, and Pain Medicine, Massachusetts General Hospital, Boston, MA 02114, USA
| | - Sharon H Kim
- Broad Institute, Cambridge, MA 02142, USA; Howard Hughes Medical Institute, Howard Hughes Medical Institute, Massachusetts General Hospital, Boston, MA 02114, USA; Department of Molecular Biology, Massachusetts General Hospital, Boston, MA 02114, USA; Harvard Medical School, Boston, MA 02115, USA
| | - Sarah E Calvo
- Broad Institute, Cambridge, MA 02142, USA; Howard Hughes Medical Institute, Howard Hughes Medical Institute, Massachusetts General Hospital, Boston, MA 02114, USA; Department of Molecular Biology, Massachusetts General Hospital, Boston, MA 02114, USA; Harvard Medical School, Boston, MA 02115, USA
| | - Lauren L Orefice
- Department of Molecular Biology, Massachusetts General Hospital, Boston, MA 02114, USA; Harvard Medical School, Boston, MA 02115, USA
| | - Fumiaki Nagashima
- Department of Anesthesia, Critical Care, and Pain Medicine, Massachusetts General Hospital, Boston, MA 02114, USA
| | - Fumito Ichinose
- Department of Anesthesia, Critical Care, and Pain Medicine, Massachusetts General Hospital, Boston, MA 02114, USA
| | - Warren M Zapol
- Department of Anesthesia, Critical Care, and Pain Medicine, Massachusetts General Hospital, Boston, MA 02114, USA
| | - Gary Ruvkun
- Department of Molecular Biology, Massachusetts General Hospital, Boston, MA 02114, USA; Harvard Medical School, Boston, MA 02115, USA
| | - David P Barondeau
- Department of Chemistry, Texas A&M University, College Station, TX 77843, USA
| | - Vamsi K Mootha
- Broad Institute, Cambridge, MA 02142, USA; Howard Hughes Medical Institute, Howard Hughes Medical Institute, Massachusetts General Hospital, Boston, MA 02114, USA; Department of Molecular Biology, Massachusetts General Hospital, Boston, MA 02114, USA; Harvard Medical School, Boston, MA 02115, USA.
| |
Collapse
|
13
|
Lake NJ, Formosa LE, Stroud DA, Ryan MT, Calvo SE, Mootha VK, Morar B, Procopis PG, Christodoulou J, Compton AG, Thorburn DR. A patient with homozygous nonsense variants in two Leigh syndrome disease genes: Distinguishing a dual diagnosis from a hypomorphic protein-truncating variant. Hum Mutat 2019; 40:893-898. [PMID: 30981218 DOI: 10.1002/humu.23753] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/02/2018] [Revised: 03/19/2019] [Accepted: 03/24/2019] [Indexed: 01/04/2023]
Abstract
Leigh syndrome is a mitochondrial disease caused by pathogenic variants in over 85 genes. Whole exome sequencing of a patient with Leigh-like syndrome identified homozygous protein-truncating variants in two genes associated with Leigh syndrome; a reported pathogenic variant in PDHX (NP_003468.2:p.(Arg446*)), and an uncharacterized variant in complex I (CI) assembly factor TIMMDC1 (NP_057673.2:p.(Arg225*)). The TIMMDC1 variant was predicted to truncate 61 amino acids at the C-terminus and functional studies demonstrated a hypomorphic impact of the variant on CI assembly. However, the mutant protein could still rescue CI assembly in TIMMDC1 knockout cells and the patient's clinical phenotype was not clearly distinct from that of other patients with the same PDHX defect. Our data suggest that the hypomorphic effect of the TIMMDC1 protein-truncating variant does not constitute a dual diagnosis in this individual. We recommend cautious assessment of variants in the C-terminus of TIMMDC1 and emphasize the need to consider the caveats detailed within the American College of Medical Genetics and Genomics (ACMG) criteria when assessing variants.
Collapse
Affiliation(s)
- Nicole J Lake
- Brain and Mitochondrial Research, Murdoch Children's Research Institute, Royal Children's Hospital, Melbourne, Victoria, Australia.,Department of Paediatrics, University of Melbourne, Melbourne, Victoria, Australia
| | - Luke E Formosa
- Department of Biochemistry and Molecular Biology, Monash Biomedicine Discovery Institute, Monash University, Clayton Campus, Melbourne, Victoria, Australia
| | - David A Stroud
- Department of Biochemistry and Molecular Biology, The Bio21 Molecular Science and Biotechnology Institute, The University of Melbourne, Parkville, Victoria, Australia
| | - Michael T Ryan
- Department of Biochemistry and Molecular Biology, Monash Biomedicine Discovery Institute, Monash University, Clayton Campus, Melbourne, Victoria, Australia
| | - Sarah E Calvo
- Department of Molecular Biology, Howard Hughes Medical Institute, Massachusetts General Hospital, Boston, Massachusetts.,Department of Systems Biology, Harvard Medical School, Boston, Massachusetts.,Metabolism Program, Broad Institute of MIT and Harvard, Cambridge, Massachusetts
| | - Vamsi K Mootha
- Department of Molecular Biology, Howard Hughes Medical Institute, Massachusetts General Hospital, Boston, Massachusetts.,Department of Systems Biology, Harvard Medical School, Boston, Massachusetts.,Metabolism Program, Broad Institute of MIT and Harvard, Cambridge, Massachusetts
| | - Bharti Morar
- Centre for Clinical Research in Neuropsychiatry, School of Psychiatry and Clinical Neurosciences, University of Western Australia, Perth, Western Australia, Australia.,Mitochondrial Medicine and Biology, Harry Perkins Institute of Medical Research and Centre for Medical Research, University of Western Australia, Nedlands, Western Australia, Australia
| | - Peter G Procopis
- Department of Neurology, Children's Hospital at Westmead, Sydney, New South Wales, Australia.,Discipline of Child and Adolescent Health, Sydney Medical School, University of Sydney, Sydney, New South Wales, Australia
| | - John Christodoulou
- Brain and Mitochondrial Research, Murdoch Children's Research Institute, Royal Children's Hospital, Melbourne, Victoria, Australia.,Department of Paediatrics, University of Melbourne, Melbourne, Victoria, Australia.,Discipline of Child and Adolescent Health, Sydney Medical School, University of Sydney, Sydney, New South Wales, Australia.,Mitochondrial Laboratory, Victorian Clinical Genetics Services, Royal Children's Hospital, Melbourne, Victoria, Australia
| | - Alison G Compton
- Brain and Mitochondrial Research, Murdoch Children's Research Institute, Royal Children's Hospital, Melbourne, Victoria, Australia.,Department of Paediatrics, University of Melbourne, Melbourne, Victoria, Australia
| | - David R Thorburn
- Brain and Mitochondrial Research, Murdoch Children's Research Institute, Royal Children's Hospital, Melbourne, Victoria, Australia.,Department of Paediatrics, University of Melbourne, Melbourne, Victoria, Australia.,Mitochondrial Laboratory, Victorian Clinical Genetics Services, Royal Children's Hospital, Melbourne, Victoria, Australia
| |
Collapse
|
14
|
Li Y, Ning S, Calvo SE, Mootha VK, Liu JS. Bayesian hidden Markov tree models for clustering genes with shared evolutionary history. Ann Appl Stat 2019. [DOI: 10.1214/18-aoas1208] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/19/2022]
|
15
|
Gopal RK, Kübler K, Calvo SE, Polak P, Livitz D, Rosebrock D, Sadow PM, Campbell B, Donovan SE, Amin S, Gigliotti BJ, Grabarek Z, Hess JM, Stewart C, Braunstein LZ, Arndt PF, Mordecai S, Shih AR, Chaves F, Zhan T, Lubitz CC, Kim J, Iafrate AJ, Wirth L, Parangi S, Leshchiner I, Daniels GH, Mootha VK, Dias-Santagata D, Getz G, McFadden DG. Widespread Chromosomal Losses and Mitochondrial DNA Alterations as Genetic Drivers in Hürthle Cell Carcinoma. Cancer Cell 2018; 34:242-255.e5. [PMID: 30107175 PMCID: PMC6121811 DOI: 10.1016/j.ccell.2018.06.013] [Citation(s) in RCA: 153] [Impact Index Per Article: 25.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 12/31/2017] [Revised: 03/30/2018] [Accepted: 06/27/2018] [Indexed: 12/24/2022]
Abstract
Hürthle cell carcinoma of the thyroid (HCC) is a form of thyroid cancer recalcitrant to radioiodine therapy that exhibits an accumulation of mitochondria. We performed whole-exome sequencing on a cohort of primary, recurrent, and metastatic tumors, and identified recurrent mutations in DAXX, TP53, NRAS, NF1, CDKN1A, ARHGAP35, and the TERT promoter. Parallel analysis of mtDNA revealed recurrent homoplasmic mutations in subunits of complex I of the electron transport chain. Analysis of DNA copy-number alterations uncovered widespread loss of chromosomes culminating in near-haploid chromosomal content in a large fraction of HCC, which was maintained during metastatic spread. This work uncovers a distinct molecular origin of HCC compared with other thyroid malignancies.
Collapse
Affiliation(s)
- Raj K Gopal
- Department of Medicine, Massachusetts General Hospital, Boston, MA 02114, USA; Cancer Center, Massachusetts General Hospital, Boston, MA 02114, USA; Department of Molecular Biology, Massachusetts General Hospital, Boston, MA 02114, USA; Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA; Howard Hughes Medical Institute, Chevy Chase, MD, USA; Harvard Medical School, Boston, MA 02115, USA
| | - Kirsten Kübler
- Cancer Center, Massachusetts General Hospital, Boston, MA 02114, USA; Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA; Harvard Medical School, Boston, MA 02115, USA
| | - Sarah E Calvo
- Department of Molecular Biology, Massachusetts General Hospital, Boston, MA 02114, USA; Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA; Howard Hughes Medical Institute, Chevy Chase, MD, USA
| | - Paz Polak
- Cancer Center, Massachusetts General Hospital, Boston, MA 02114, USA; Department of Pathology, Massachusetts General Hospital, Boston, MA 02114, USA; Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA; Harvard Medical School, Boston, MA 02115, USA
| | - Dimitri Livitz
- Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA
| | | | - Peter M Sadow
- Cancer Center, Massachusetts General Hospital, Boston, MA 02114, USA; Department of Pathology, Massachusetts General Hospital, Boston, MA 02114, USA; Harvard Medical School, Boston, MA 02115, USA
| | - Braidie Campbell
- Department of Medicine, Massachusetts General Hospital, Boston, MA 02114, USA; Cancer Center, Massachusetts General Hospital, Boston, MA 02114, USA
| | - Samuel E Donovan
- Department of Medicine, Massachusetts General Hospital, Boston, MA 02114, USA; Cancer Center, Massachusetts General Hospital, Boston, MA 02114, USA
| | - Salma Amin
- Cancer Center, Massachusetts General Hospital, Boston, MA 02114, USA; Department of Surgery, Massachusetts General Hospital, Boston, MA 02114, USA
| | | | - Zenon Grabarek
- Department of Molecular Biology, Massachusetts General Hospital, Boston, MA 02114, USA; Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA; Howard Hughes Medical Institute, Chevy Chase, MD, USA
| | - Julian M Hess
- Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA
| | - Chip Stewart
- Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA
| | | | - Peter F Arndt
- Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA
| | - Scott Mordecai
- Department of Pathology, Massachusetts General Hospital, Boston, MA 02114, USA
| | - Angela R Shih
- Department of Pathology, Massachusetts General Hospital, Boston, MA 02114, USA; Harvard Medical School, Boston, MA 02115, USA
| | - Frances Chaves
- Department of Pathology, Massachusetts General Hospital, Boston, MA 02114, USA
| | - Tiannan Zhan
- Institute for Technology Assessment, Massachusetts General Hospital, Boston, MA 02114, USA
| | - Carrie C Lubitz
- Cancer Center, Massachusetts General Hospital, Boston, MA 02114, USA; Department of Surgery, Massachusetts General Hospital, Boston, MA 02114, USA; Institute for Technology Assessment, Massachusetts General Hospital, Boston, MA 02114, USA; Harvard Medical School, Boston, MA 02115, USA
| | - Jiwoong Kim
- Department of Bioinformatics, University of Texas Southwestern Medical Center, Dallas, TX 75390, USA
| | - A John Iafrate
- Department of Pathology, Massachusetts General Hospital, Boston, MA 02114, USA; Harvard Medical School, Boston, MA 02115, USA
| | - Lori Wirth
- Department of Medicine, Massachusetts General Hospital, Boston, MA 02114, USA; Cancer Center, Massachusetts General Hospital, Boston, MA 02114, USA; Harvard Medical School, Boston, MA 02115, USA
| | - Sareh Parangi
- Cancer Center, Massachusetts General Hospital, Boston, MA 02114, USA; Department of Surgery, Massachusetts General Hospital, Boston, MA 02114, USA; Harvard Medical School, Boston, MA 02115, USA
| | | | - Gilbert H Daniels
- Department of Medicine, Massachusetts General Hospital, Boston, MA 02114, USA; Cancer Center, Massachusetts General Hospital, Boston, MA 02114, USA; Thyroid Unit, Massachusetts General Hospital, Boston, MA 02114, USA; Harvard Medical School, Boston, MA 02115, USA
| | - Vamsi K Mootha
- Department of Medicine, Massachusetts General Hospital, Boston, MA 02114, USA; Department of Molecular Biology, Massachusetts General Hospital, Boston, MA 02114, USA; Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA; Howard Hughes Medical Institute, Chevy Chase, MD, USA; Department of Systems Biology, Harvard Medical School, Boston, MA 02115, USA
| | - Dora Dias-Santagata
- Department of Pathology, Massachusetts General Hospital, Boston, MA 02114, USA; Harvard Medical School, Boston, MA 02115, USA
| | - Gad Getz
- Cancer Center, Massachusetts General Hospital, Boston, MA 02114, USA; Department of Pathology, Massachusetts General Hospital, Boston, MA 02114, USA; Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA; Harvard Medical School, Boston, MA 02115, USA.
| | - David G McFadden
- Department of Medicine, Massachusetts General Hospital, Boston, MA 02114, USA; Thyroid Unit, Massachusetts General Hospital, Boston, MA 02114, USA; Department of Internal Medicine, Division of Endocrinology, University of Texas Southwestern Medical Center, Dallas, TX 75390, USA; Department of Biochemistry, University of Texas Southwestern Medical Center, Dallas, TX 75390, USA; Harold C. Simmons Comprehensive Cancer Center, University of Texas Southwestern Medical Center, Dallas, TX 75390, USA.
| |
Collapse
|
16
|
Abstract
Compartmentalization is a fundamental design principle of eukaryotic metabolism. Here, we review the compartmentalization of NAD+/NADH and NADP+/NADPH with a focus on the liver, an organ that experiences the extremes of biochemical physiology each day. Historical studies of the liver, using classical biochemical fractionation and measurements of redox-coupled metabolites, have given rise to the prevailing view that mitochondrial NAD(H) pools tend to be oxidized and important for energy homeostasis, whereas cytosolic NADP(H) pools tend to be highly reduced for reductive biosynthesis. Despite this textbook view, many questions still remain as to the relative size of these subcellular pools and their redox ratios in different physiological states, and to what extent such redox ratios are simply indicators versus drivers of metabolism. By performing a bioinformatic survey, we find that the liver expresses 352 known or predicted enzymes composing the hepatic NAD(P)ome, i.e. the union of all predicted enzymes producing or consuming NADP(H) or NAD(H) or using them as a redox co-factor. Notably, less than half are predicted to be localized within the cytosol or mitochondria, and a very large fraction of these genes exhibit gene expression patterns that vary during the time of day or in response to fasting or feeding. A future challenge lies in applying emerging new genetic tools to measure and manipulate in vivo hepatic NADP(H) and NAD(H) with subcellular and temporal resolution. Insights from such fundamental studies will be crucial in deciphering the pathogenesis of very common diseases known to involve alterations in hepatic NAD(P)H, such as diabetes and fatty liver disease.
Collapse
Affiliation(s)
- Russell P Goodman
- From the Division of Gastroenterology and
- Howard Hughes Medical Institute, and Department of Molecular Biology, Massachusetts General Hospital, Boston, Massachusetts 02114 and
| | - Sarah E Calvo
- Howard Hughes Medical Institute, and Department of Molecular Biology, Massachusetts General Hospital, Boston, Massachusetts 02114 and
- the Broad Institute, Cambridge, Massachusetts 02142
| | - Vamsi K Mootha
- Howard Hughes Medical Institute, and Department of Molecular Biology, Massachusetts General Hospital, Boston, Massachusetts 02114 and
- the Broad Institute, Cambridge, Massachusetts 02142
| |
Collapse
|
17
|
Lake NJ, Webb BD, Stroud DA, Richman TR, Ruzzenente B, Compton AG, Mountford HS, Pulman J, Zangarelli C, Rio M, Boddaert N, Assouline Z, Sherpa MD, Schadt EE, Houten SM, Byrnes J, McCormick EM, Zolkipli-Cunningham Z, Haude K, Zhang Z, Retterer K, Bai R, Calvo SE, Mootha VK, Christodoulou J, Rötig A, Filipovska A, Cristian I, Falk MJ, Metodiev MD, Thorburn DR. Biallelic Mutations in MRPS34 Lead to Instability of the Small Mitoribosomal Subunit and Leigh Syndrome. Am J Hum Genet 2018; 102:713. [PMID: 29625026 DOI: 10.1016/j.ajhg.2018.03.015] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/17/2022] Open
|
18
|
Garone C, D’Souza AR, Dallabona C, Lodi T, Rebelo-Guiomar P, Rorbach J, Donati MA, Procopio E, Montomoli M, Guerrini R, Zeviani M, Calvo SE, Mootha VK, DiMauro S, Ferrero I, Minczuk M. Defective mitochondrial rRNA methyltransferase MRM2 causes MELAS-like clinical syndrome. Hum Mol Genet 2017; 26:4257-4266. [PMID: 28973171 PMCID: PMC5886288 DOI: 10.1093/hmg/ddx314] [Citation(s) in RCA: 56] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/13/2017] [Revised: 08/01/2017] [Accepted: 08/03/2017] [Indexed: 02/02/2023] Open
Abstract
Defects in nuclear-encoded proteins of the mitochondrial translation machinery cause early-onset and tissue-specific deficiency of one or more OXPHOS complexes. Here, we report a 7-year-old Italian boy with childhood-onset rapidly progressive encephalomyopathy and stroke-like episodes. Multiple OXPHOS defects and decreased mtDNA copy number (40%) were detected in muscle homogenate. Clinical features combined with low level of plasma citrulline were highly suggestive of mitochondrial encephalopathy, lactic acidosis and stroke-like episodes (MELAS) syndrome, however, the common m.3243 A > G mutation was excluded. Targeted exome sequencing of genes encoding the mitochondrial proteome identified a damaging mutation, c.567 G > A, affecting a highly conserved amino acid residue (p.Gly189Arg) of the MRM2 protein. MRM2 has never before been linked to a human disease and encodes an enzyme responsible for 2'-O-methyl modification at position U1369 in the human mitochondrial 16S rRNA. We generated a knockout yeast model for the orthologous gene that showed a defect in respiration and the reduction of the 2'-O-methyl modification at the equivalent position (U2791) in the yeast mitochondrial 21S rRNA. Complementation with the mrm2 allele carrying the equivalent yeast mutation failed to rescue the respiratory phenotype, which was instead completely rescued by expressing the wild-type allele. Our findings establish that defective MRM2 causes a MELAS-like phenotype, and suggests the genetic screening of the MRM2 gene in patients with a m.3243 A > G negative MELAS-like presentation.
Collapse
Affiliation(s)
- Caterina Garone
- Medical Research Council Mitochondrial Biology Unit, University of Cambridge, Cambridge CB2 0XY, UK
- Department of Neurology, Columbia University Medical Center, New York, NY 10032, USA
| | - Aaron R D’Souza
- Medical Research Council Mitochondrial Biology Unit, University of Cambridge, Cambridge CB2 0XY, UK
| | - Cristina Dallabona
- Department of Chemistry, Life Sciences and Environmental Sustainability - University of Parma, Parma 43121, Italy
| | - Tiziana Lodi
- Department of Chemistry, Life Sciences and Environmental Sustainability - University of Parma, Parma 43121, Italy
| | - Pedro Rebelo-Guiomar
- Medical Research Council Mitochondrial Biology Unit, University of Cambridge, Cambridge CB2 0XY, UK
- Graduate Program in Areas of Basic and Applied Biology (GABBA), University of Porto, 4099-002, Portugal
| | - Joanna Rorbach
- Medical Research Council Mitochondrial Biology Unit, University of Cambridge, Cambridge CB2 0XY, UK
| | | | - Elena Procopio
- Metabolic Unit, A. Meyer Children's Hospital, Florence 50139, Italy
| | - Martino Montomoli
- Pediatric Neurology Unit and Laboratories, “A. Meyer” Children's Hospital, University of Florence, 50139, Italy
| | - Renzo Guerrini
- Pediatric Neurology Unit and Laboratories, “A. Meyer” Children's Hospital, University of Florence, 50139, Italy
| | - Massimo Zeviani
- Medical Research Council Mitochondrial Biology Unit, University of Cambridge, Cambridge CB2 0XY, UK
| | - Sarah E Calvo
- Broad Institute of MIT & Harvard, Cambridge, MA 02142, USA
- Department of Molecular Biology and Howard Hughes Medical Institute, Massachusetts General Hospital, and Department of Systems Biology, Harvard Medical School, Boston, MA 02115, USA
| | - Vamsi K Mootha
- Department of Molecular Biology and Howard Hughes Medical Institute, Massachusetts General Hospital, and Department of Systems Biology, Harvard Medical School, Boston, MA 02115, USA
| | - Salvatore DiMauro
- Department of Neurology, Columbia University Medical Center, New York, NY 10032, USA
| | - Ileana Ferrero
- Department of Chemistry, Life Sciences and Environmental Sustainability - University of Parma, Parma 43121, Italy
| | - Michal Minczuk
- Medical Research Council Mitochondrial Biology Unit, University of Cambridge, Cambridge CB2 0XY, UK
| |
Collapse
|
19
|
Feichtinger RG, Oláhová M, Kishita Y, Garone C, Kremer LS, Yagi M, Uchiumi T, Jourdain AA, Thompson K, D'Souza AR, Kopajtich R, Alston CL, Koch J, Sperl W, Mastantuono E, Strom TM, Wortmann SB, Meitinger T, Pierre G, Chinnery PF, Chrzanowska-Lightowlers ZM, Lightowlers RN, DiMauro S, Calvo SE, Mootha VK, Moggio M, Sciacco M, Comi GP, Ronchi D, Murayama K, Ohtake A, Rebelo-Guiomar P, Kohda M, Kang D, Mayr JA, Taylor RW, Okazaki Y, Minczuk M, Prokisch H. Biallelic C1QBP Mutations Cause Severe Neonatal-, Childhood-, or Later-Onset Cardiomyopathy Associated with Combined Respiratory-Chain Deficiencies. Am J Hum Genet 2017; 101:525-538. [PMID: 28942965 PMCID: PMC5630164 DOI: 10.1016/j.ajhg.2017.08.015] [Citation(s) in RCA: 47] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/16/2017] [Accepted: 08/11/2017] [Indexed: 11/16/2022] Open
Abstract
Complement component 1 Q subcomponent-binding protein (C1QBP; also known as p32) is a multi-compartmental protein whose precise function remains unknown. It is an evolutionary conserved multifunctional protein localized primarily in the mitochondrial matrix and has roles in inflammation and infection processes, mitochondrial ribosome biogenesis, and regulation of apoptosis and nuclear transcription. It has an N-terminal mitochondrial targeting peptide that is proteolytically processed after import into the mitochondrial matrix, where it forms a homotrimeric complex organized in a doughnut-shaped structure. Although C1QBP has been reported to exert pleiotropic effects on many cellular processes, we report here four individuals from unrelated families where biallelic mutations in C1QBP cause a defect in mitochondrial energy metabolism. Infants presented with cardiomyopathy accompanied by multisystemic involvement (liver, kidney, and brain), and children and adults presented with myopathy and progressive external ophthalmoplegia. Multiple mitochondrial respiratory-chain defects, associated with the accumulation of multiple deletions of mitochondrial DNA in the later-onset myopathic cases, were identified in all affected individuals. Steady-state C1QBP levels were decreased in all individuals' samples, leading to combined respiratory-chain enzyme deficiency of complexes I, III, and IV. C1qbp-/- mouse embryonic fibroblasts (MEFs) resembled the human disease phenotype by showing multiple defects in oxidative phosphorylation (OXPHOS). Complementation with wild-type, but not mutagenized, C1qbp restored OXPHOS protein levels and mitochondrial enzyme activities in C1qbp-/- MEFs. C1QBP deficiency represents an important mitochondrial disorder associated with a clinical spectrum ranging from infantile lactic acidosis to childhood (cardio)myopathy and late-onset progressive external ophthalmoplegia.
Collapse
Affiliation(s)
- René G Feichtinger
- Department of Pediatrics, University Hospital Salzburg, Paracelsus Medical University, 5020 Salzburg, Austria
| | - Monika Oláhová
- Wellcome Centre for Mitochondrial Research, Institute of Neuroscience and Institute for Cell and Molecular Biosciences, Newcastle University, Newcastle upon Tyne NE2 4HH, UK
| | - Yoshihito Kishita
- Research Center for Genomic Medicine, Saitama Medical University, Saitama 350-1241, Japan; Diagnostics and Therapeutics of Intractable Diseases, Intractable Disease Research Center, Juntendo University, Graduate School of Medicine, Tokyo 113-8421, Japan
| | - Caterina Garone
- Medical Research Council Mitochondrial Biology Unit, University of Cambridge, Wellcome Trust, MRC Building, Cambridge CB2 0XY, UK; Department of Neurology, Columbia University Medical Center, New York, NY 10032-3784, USA
| | - Laura S Kremer
- Institute of Human Genetics, Technische Universität München, 81675 Munich, Germany; Institute of Human Genetics, Helmholtz Zentrum München, 85764 Neuherberg, Germany
| | - Mikako Yagi
- Department of Clinical Chemistry and Laboratory Medicine, Graduate School of Medical Sciences, Kyushu University, 3-1-1 Maidashi, Higashi-ku, Fukuoka 812-8582, Japan
| | - Takeshi Uchiumi
- Department of Clinical Chemistry and Laboratory Medicine, Graduate School of Medical Sciences, Kyushu University, 3-1-1 Maidashi, Higashi-ku, Fukuoka 812-8582, Japan
| | - Alexis A Jourdain
- Howard Hughes Medical Institute, Department of Molecular Biology, Center for Genome Medicine, Massachusetts General Hospital, Boston, MA 02114, USA; Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA
| | - Kyle Thompson
- Wellcome Centre for Mitochondrial Research, Institute of Neuroscience and Institute for Cell and Molecular Biosciences, Newcastle University, Newcastle upon Tyne NE2 4HH, UK
| | - Aaron R D'Souza
- Medical Research Council Mitochondrial Biology Unit, University of Cambridge, Wellcome Trust, MRC Building, Cambridge CB2 0XY, UK
| | - Robert Kopajtich
- Institute of Human Genetics, Technische Universität München, 81675 Munich, Germany
| | - Charlotte L Alston
- Wellcome Centre for Mitochondrial Research, Institute of Neuroscience and Institute for Cell and Molecular Biosciences, Newcastle University, Newcastle upon Tyne NE2 4HH, UK
| | - Johannes Koch
- Department of Pediatrics, University Hospital Salzburg, Paracelsus Medical University, 5020 Salzburg, Austria
| | - Wolfgang Sperl
- Department of Pediatrics, University Hospital Salzburg, Paracelsus Medical University, 5020 Salzburg, Austria
| | - Elisa Mastantuono
- Institute of Human Genetics, Technische Universität München, 81675 Munich, Germany; Institute of Human Genetics, Helmholtz Zentrum München, 85764 Neuherberg, Germany
| | - Tim M Strom
- Institute of Human Genetics, Technische Universität München, 81675 Munich, Germany; Institute of Human Genetics, Helmholtz Zentrum München, 85764 Neuherberg, Germany
| | - Saskia B Wortmann
- Department of Pediatrics, University Hospital Salzburg, Paracelsus Medical University, 5020 Salzburg, Austria; Institute of Human Genetics, Technische Universität München, 81675 Munich, Germany; Institute of Human Genetics, Helmholtz Zentrum München, 85764 Neuherberg, Germany
| | - Thomas Meitinger
- Institute of Human Genetics, Technische Universität München, 81675 Munich, Germany; Institute of Human Genetics, Helmholtz Zentrum München, 85764 Neuherberg, Germany; DZHK (German Centre for Cardiovascular Research), partner site Munich Heart Alliance, 80802 Munich, Germany
| | - Germaine Pierre
- South West Regional Metabolic Department, Bristol Royal Hospital for Children, Bristol BS1 3NU, UK
| | - Patrick F Chinnery
- Medical Research Council Mitochondrial Biology Unit, University of Cambridge, Wellcome Trust, MRC Building, Cambridge CB2 0XY, UK
| | - Zofia M Chrzanowska-Lightowlers
- Wellcome Centre for Mitochondrial Research, Institute of Neuroscience and Institute for Cell and Molecular Biosciences, Newcastle University, Newcastle upon Tyne NE2 4HH, UK
| | - Robert N Lightowlers
- Wellcome Centre for Mitochondrial Research, Institute of Neuroscience and Institute for Cell and Molecular Biosciences, Newcastle University, Newcastle upon Tyne NE2 4HH, UK
| | - Salvatore DiMauro
- Department of Neurology, Columbia University Medical Center, New York, NY 10032-3784, USA
| | - Sarah E Calvo
- Howard Hughes Medical Institute, Department of Molecular Biology, Center for Genome Medicine, Massachusetts General Hospital, Boston, MA 02114, USA; Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA
| | - Vamsi K Mootha
- Howard Hughes Medical Institute, Department of Molecular Biology, Center for Genome Medicine, Massachusetts General Hospital, Boston, MA 02114, USA; Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA
| | - Maurizio Moggio
- Neuromuscular Unit, Fondazione IRCCS Ca' Granda, Ospedale Maggiore Policlinico, 20122 Milan, Italy
| | - Monica Sciacco
- Neuromuscular Unit, Fondazione IRCCS Ca' Granda, Ospedale Maggiore Policlinico, 20122 Milan, Italy
| | - Giacomo P Comi
- Neuroscience Section, Department of Pathophysiology and Transplantation, Dino Ferrari Center, University of Milan, IRCCS Foundation Ca' Granda, Ospedale Maggiore Policlinico, 20122 Milan, Italy
| | - Dario Ronchi
- Neuroscience Section, Department of Pathophysiology and Transplantation, Dino Ferrari Center, University of Milan, IRCCS Foundation Ca' Granda, Ospedale Maggiore Policlinico, 20122 Milan, Italy
| | - Kei Murayama
- Department of Metabolism, Chiba Children's Hospital, Chiba 266-0007, Japan
| | - Akira Ohtake
- Department of Pediatrics, Faculty of Medicine, Saitama Medical University, Saitama 350-0495, Japan
| | - Pedro Rebelo-Guiomar
- Medical Research Council Mitochondrial Biology Unit, University of Cambridge, Wellcome Trust, MRC Building, Cambridge CB2 0XY, UK; Graduate Program in Areas of Basic and Applied Biology, University of Porto, 4099-002 Porto, Portugal
| | - Masakazu Kohda
- Research Center for Genomic Medicine, Saitama Medical University, Saitama 350-1241, Japan; Diagnostics and Therapeutics of Intractable Diseases, Intractable Disease Research Center, Juntendo University, Graduate School of Medicine, Tokyo 113-8421, Japan
| | - Dongchon Kang
- Department of Clinical Chemistry and Laboratory Medicine, Graduate School of Medical Sciences, Kyushu University, 3-1-1 Maidashi, Higashi-ku, Fukuoka 812-8582, Japan
| | - Johannes A Mayr
- Department of Pediatrics, University Hospital Salzburg, Paracelsus Medical University, 5020 Salzburg, Austria
| | - Robert W Taylor
- Wellcome Centre for Mitochondrial Research, Institute of Neuroscience and Institute for Cell and Molecular Biosciences, Newcastle University, Newcastle upon Tyne NE2 4HH, UK
| | - Yasushi Okazaki
- Research Center for Genomic Medicine, Saitama Medical University, Saitama 350-1241, Japan; Diagnostics and Therapeutics of Intractable Diseases, Intractable Disease Research Center, Juntendo University, Graduate School of Medicine, Tokyo 113-8421, Japan
| | - Michal Minczuk
- Medical Research Council Mitochondrial Biology Unit, University of Cambridge, Wellcome Trust, MRC Building, Cambridge CB2 0XY, UK
| | - Holger Prokisch
- Institute of Human Genetics, Technische Universität München, 81675 Munich, Germany; Institute of Human Genetics, Helmholtz Zentrum München, 85764 Neuherberg, Germany.
| |
Collapse
|
20
|
Lake NJ, Webb BD, Stroud DA, Richman TR, Ruzzenente B, Compton AG, Mountford HS, Pulman J, Zangarelli C, Rio M, Boddaert N, Assouline Z, Sherpa MD, Schadt EE, Houten SM, Byrnes J, McCormick EM, Zolkipli-Cunningham Z, Haude K, Zhang Z, Retterer K, Bai R, Calvo SE, Mootha VK, Christodoulou J, Rötig A, Filipovska A, Cristian I, Falk MJ, Metodiev MD, Thorburn DR. Biallelic Mutations in MRPS34 Lead to Instability of the Small Mitoribosomal Subunit and Leigh Syndrome. Am J Hum Genet 2017; 101:239-254. [PMID: 28777931 DOI: 10.1016/j.ajhg.2017.07.005] [Citation(s) in RCA: 67] [Impact Index Per Article: 9.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/16/2017] [Accepted: 07/09/2017] [Indexed: 12/30/2022] Open
Abstract
The synthesis of all 13 mitochondrial DNA (mtDNA)-encoded protein subunits of the human oxidative phosphorylation (OXPHOS) system is carried out by mitochondrial ribosomes (mitoribosomes). Defects in the stability of mitoribosomal proteins or mitoribosome assembly impair mitochondrial protein translation, causing combined OXPHOS enzyme deficiency and clinical disease. Here we report four autosomal-recessive pathogenic mutations in the gene encoding the small mitoribosomal subunit protein, MRPS34, in six subjects from four unrelated families with Leigh syndrome and combined OXPHOS defects. Whole-exome sequencing was used to independently identify all variants. Two splice-site mutations were identified, including homozygous c.321+1G>T in a subject of Italian ancestry and homozygous c.322-10G>A in affected sibling pairs from two unrelated families of Puerto Rican descent. In addition, compound heterozygous MRPS34 mutations were identified in a proband of French ancestry; a missense (c.37G>A [p.Glu13Lys]) and a nonsense (c.94C>T [p.Gln32∗]) variant. We demonstrated that these mutations reduce MRPS34 protein levels and the synthesis of OXPHOS subunits encoded by mtDNA. Examination of the mitoribosome profile and quantitative proteomics showed that the mitochondrial translation defect was caused by destabilization of the small mitoribosomal subunit and impaired monosome assembly. Lentiviral-mediated expression of wild-type MRPS34 rescued the defect in mitochondrial translation observed in skin fibroblasts from affected subjects, confirming the pathogenicity of MRPS34 mutations. Our data establish that MRPS34 is required for normal function of the mitoribosome in humans and furthermore demonstrate the power of quantitative proteomic analysis to identify signatures of defects in specific cellular pathways in fibroblasts from subjects with inherited disease.
Collapse
|
21
|
Li Y, Jourdain AA, Calvo SE, Liu JS, Mootha VK. CLIC, a tool for expanding biological pathways based on co-expression across thousands of datasets. PLoS Comput Biol 2017; 13:e1005653. [PMID: 28719601 PMCID: PMC5546725 DOI: 10.1371/journal.pcbi.1005653] [Citation(s) in RCA: 28] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/05/2016] [Revised: 08/07/2017] [Accepted: 06/21/2017] [Indexed: 12/31/2022] Open
Abstract
In recent years, there has been a huge rise in the number of publicly available transcriptional profiling datasets. These massive compendia comprise billions of measurements and provide a special opportunity to predict the function of unstudied genes based on co-expression to well-studied pathways. Such analyses can be very challenging, however, since biological pathways are modular and may exhibit co-expression only in specific contexts. To overcome these challenges we introduce CLIC, CLustering by Inferred Co-expression. CLIC accepts as input a pathway consisting of two or more genes. It then uses a Bayesian partition model to simultaneously partition the input gene set into coherent co-expressed modules (CEMs), while assigning the posterior probability for each dataset in support of each CEM. CLIC then expands each CEM by scanning the transcriptome for additional co-expressed genes, quantified by an integrated log-likelihood ratio (LLR) score weighted for each dataset. As a byproduct, CLIC automatically learns the conditions (datasets) within which a CEM is operative. We implemented CLIC using a compendium of 1774 mouse microarray datasets (28628 microarrays) or 1887 human microarray datasets (45158 microarrays). CLIC analysis reveals that of 910 canonical biological pathways, 30% consist of strongly co-expressed gene modules for which new members are predicted. For example, CLIC predicts a functional connection between protein C7orf55 (FMC1) and the mitochondrial ATP synthase complex that we have experimentally validated. CLIC is freely available at www.gene-clic.org. We anticipate that CLIC will be valuable both for revealing new components of biological pathways as well as the conditions in which they are active.
Collapse
Affiliation(s)
- Yang Li
- Howard Hughes Medical Institute and Department of Molecular Biology and the Center for Genomic Medicine, Massachusetts General Hospital, Boston, MA, United States of America and Department of Systems Biology, Harvard Medical School, Boston, MA United States of America
- Department of Statistics, Harvard University, Cambridge, MA, United States of America
| | - Alexis A. Jourdain
- Howard Hughes Medical Institute and Department of Molecular Biology and the Center for Genomic Medicine, Massachusetts General Hospital, Boston, MA, United States of America and Department of Systems Biology, Harvard Medical School, Boston, MA United States of America
- Broad Institute, Cambridge, MA, United States of America
| | - Sarah E. Calvo
- Howard Hughes Medical Institute and Department of Molecular Biology and the Center for Genomic Medicine, Massachusetts General Hospital, Boston, MA, United States of America and Department of Systems Biology, Harvard Medical School, Boston, MA United States of America
- Broad Institute, Cambridge, MA, United States of America
- * E-mail: (SEC); (JSL); (VKM)
| | - Jun S. Liu
- Department of Statistics, Harvard University, Cambridge, MA, United States of America
- * E-mail: (SEC); (JSL); (VKM)
| | - Vamsi K. Mootha
- Howard Hughes Medical Institute and Department of Molecular Biology and the Center for Genomic Medicine, Massachusetts General Hospital, Boston, MA, United States of America and Department of Systems Biology, Harvard Medical School, Boston, MA United States of America
- Broad Institute, Cambridge, MA, United States of America
- * E-mail: (SEC); (JSL); (VKM)
| |
Collapse
|
22
|
Calvo SE, Julien O, Clauser KR, Shen H, Kamer KJ, Wells JA, Mootha VK. Comparative Analysis of Mitochondrial N-Termini from Mouse, Human, and Yeast. Mol Cell Proteomics 2017; 16:512-523. [PMID: 28122942 DOI: 10.1074/mcp.m116.063818] [Citation(s) in RCA: 55] [Impact Index Per Article: 7.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/13/2016] [Revised: 01/06/2017] [Indexed: 01/08/2023] Open
Abstract
The majority of mitochondrial proteins are encoded in the nuclear genome, translated in the cytoplasm, and directed to the mitochondria by an N-terminal presequence that is cleaved upon import. Recently, N-proteome catalogs have been generated for mitochondria from yeast and from human U937 cells. Here, we applied the subtiligase method to determine N-termini for 327 proteins in mitochondria isolated from mouse liver and kidney. Comparative analysis between mitochondrial N-termini from mouse, human, and yeast proteins shows that whereas presequences are poorly conserved at the sequence level, other presequence properties are extremely conserved, including a length of ∼20-60 amino acids, a net charge between +3 to +6, and the presence of stabilizing amino acids at the N-terminus of mature proteins that follow the N-end rule from bacteria. As in yeast, ∼80% of mouse presequence cleavage sites match canonical motifs for three mitochondrial peptidases (MPP, Icp55, and Oct1), whereas the remainder do not match any known peptidase motifs. We show that mature mitochondrial proteins often exist with a spectrum of N-termini, consistent with a model of multiple cleavage events by MPP and Icp55. In addition to analysis of canonical targeting presequences, our N-terminal dataset allows the exploration of other cleavage events and provides support for polypeptide cleavage into two distinct enzymes (Hsd17b4), protein cleavages key for signaling (Oma1, Opa1, Htra2, Mavs, and Bcs2l13), and in several cases suggests novel protein isoforms (Scp2, Acadm, Adck3, Hsdl2, Dlst, and Ogdh). We present an integrated catalog of mammalian mitochondrial N-termini that can be used as a community resource to investigate individual proteins, to elucidate mechanisms of mammalian mitochondrial processing, and to allow researchers to engineer tags distally to the presequence cleavage.
Collapse
Affiliation(s)
- Sarah E Calvo
- From the ‡Howard Hughes Medical Institute, Department of Molecular Biology, Massachusetts General Hospital, Boston, Massachusetts 02114; .,§Department of Systems Biology, Harvard Medical School, Boston, Massachusetts 02115.,¶Broad Institute, Cambridge, Massachusetts 02141
| | | | | | - Hongying Shen
- From the ‡Howard Hughes Medical Institute, Department of Molecular Biology, Massachusetts General Hospital, Boston, Massachusetts 02114.,§Department of Systems Biology, Harvard Medical School, Boston, Massachusetts 02115
| | - Kimberli J Kamer
- From the ‡Howard Hughes Medical Institute, Department of Molecular Biology, Massachusetts General Hospital, Boston, Massachusetts 02114.,§Department of Systems Biology, Harvard Medical School, Boston, Massachusetts 02115
| | - James A Wells
- **Departments of Pharmaceutical Chemistry and.,§§Cellular and Molecular Pharmacology, University of California, San Francisco, California 94143
| | - Vamsi K Mootha
- From the ‡Howard Hughes Medical Institute, Department of Molecular Biology, Massachusetts General Hospital, Boston, Massachusetts 02114.,§Department of Systems Biology, Harvard Medical School, Boston, Massachusetts 02115
| |
Collapse
|
23
|
Arroyo JD, Jourdain AA, Calvo SE, Ballarano CA, Doench JG, Root DE, Mootha VK. A Genome-wide CRISPR Death Screen Identifies Genes Essential for Oxidative Phosphorylation. Cell Metab 2016; 24:875-885. [PMID: 27667664 PMCID: PMC5474757 DOI: 10.1016/j.cmet.2016.08.017] [Citation(s) in RCA: 197] [Impact Index Per Article: 24.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 04/19/2016] [Revised: 07/15/2016] [Accepted: 08/24/2016] [Indexed: 12/18/2022]
Abstract
Oxidative phosphorylation (OXPHOS) is the major pathway for ATP production in humans. Deficiencies in OXPHOS can arise from mutations in either mitochondrial or nuclear genomes and comprise the largest collection of inborn errors of metabolism. At present we lack a complete catalog of human genes and pathways essential for OXPHOS. Here we introduce a genome-wide CRISPR "death screen" that actively selects dying cells to reveal human genes required for OXPHOS, inspired by the classic observation that human cells deficient in OXPHOS survive in glucose but die in galactose. We report 191 high-confidence hits essential for OXPHOS, including 72 underlying known OXPHOS diseases. Our screen reveals a functional module consisting of NGRN, WBSCR16, RPUSD3, RPUSD4, TRUB2, and FASTKD2 that regulates the mitochondrial 16S rRNA and intra-mitochondrial translation. Our work yields a rich catalog of genes required for OXPHOS and, more generally, demonstrates the power of death screening for functional genomic analysis.
Collapse
Affiliation(s)
- Jason D Arroyo
- Department of Molecular Biology and Howard Hughes Medical Institute, Massachusetts General Hospital, Boston, MA 02114, USA; Department of Systems Biology, Harvard Medical School, Boston, MA 02115, USA; Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA
| | - Alexis A Jourdain
- Department of Molecular Biology and Howard Hughes Medical Institute, Massachusetts General Hospital, Boston, MA 02114, USA; Department of Systems Biology, Harvard Medical School, Boston, MA 02115, USA; Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA
| | - Sarah E Calvo
- Department of Molecular Biology and Howard Hughes Medical Institute, Massachusetts General Hospital, Boston, MA 02114, USA; Department of Systems Biology, Harvard Medical School, Boston, MA 02115, USA; Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA
| | - Carmine A Ballarano
- Department of Molecular Biology and Howard Hughes Medical Institute, Massachusetts General Hospital, Boston, MA 02114, USA; Department of Systems Biology, Harvard Medical School, Boston, MA 02115, USA; Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA
| | - John G Doench
- Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA
| | - David E Root
- Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA
| | - Vamsi K Mootha
- Department of Molecular Biology and Howard Hughes Medical Institute, Massachusetts General Hospital, Boston, MA 02114, USA; Department of Systems Biology, Harvard Medical School, Boston, MA 02115, USA; Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA.
| |
Collapse
|
24
|
Calvo SE, Clauser KR, Mootha VK. MitoCarta2.0: an updated inventory of mammalian mitochondrial proteins. Nucleic Acids Res 2015; 44:D1251-7. [PMID: 26450961 PMCID: PMC4702768 DOI: 10.1093/nar/gkv1003] [Citation(s) in RCA: 914] [Impact Index Per Article: 101.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/04/2015] [Accepted: 09/23/2015] [Indexed: 01/17/2023] Open
Abstract
Mitochondria are complex organelles that house essential pathways involved in energy metabolism, ion homeostasis, signalling and apoptosis. To understand mitochondrial pathways in health and disease, it is crucial to have an accurate inventory of the organelle's protein components. In 2008, we made substantial progress toward this goal by performing in-depth mass spectrometry of mitochondria from 14 organs, epitope tagging/microscopy and Bayesian integration to assemble MitoCarta (www.broadinstitute.org/pubs/MitoCarta): an inventory of genes encoding mitochondrial-localized proteins and their expression across 14 mouse tissues. Using the same strategy we have now reconstructed this inventory separately for human and for mouse based on (i) improved gene transcript models, (ii) updated literature curation, including results from proteomic analyses of mitochondrial sub-compartments, (iii) improved homology mapping and (iv) updated versions of all seven original data sets. The updated human MitoCarta2.0 consists of 1158 human genes, including 918 genes in the original inventory as well as 240 additional genes. The updated mouse MitoCarta2.0 consists of 1158 genes, including 967 genes in the original inventory plus 191 additional genes. The improved MitoCarta 2.0 inventory provides a molecular framework for system-level analysis of mammalian mitochondria.
Collapse
Affiliation(s)
- Sarah E Calvo
- Howard Hughes Medical Institute and Department of Molecular Biology, Massachusetts General Hospital, Boston, MA 02114, USA Broad Institute, Cambridge, MA 02141, USA Department of Systems Biology, Harvard Medical School, Boston, MA 02115, USA
| | | | - Vamsi K Mootha
- Howard Hughes Medical Institute and Department of Molecular Biology, Massachusetts General Hospital, Boston, MA 02114, USA Broad Institute, Cambridge, MA 02141, USA Department of Systems Biology, Harvard Medical School, Boston, MA 02115, USA
| |
Collapse
|
25
|
Calvo SE, Klauser KR, Mootha VK. MitoCarta2.0: An updated protein inventory of the mammalian mitochondrion. Mitochondrion 2015. [DOI: 10.1016/j.mito.2015.07.068] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
|
26
|
Fassone E, Duncan AJ, Taanman JW, Pagnamenta AT, Sadowski MI, Holand T, Qasim W, Rutland P, Calvo SE, Mootha VK, Bitner-Glindzicz M, Rahman S. FOXRED1, encoding an FAD-dependent oxidoreductase complex-I-specific molecular chaperone, is mutated in infantile-onset mitochondrial encephalopathy. Hum Mol Genet 2015; 24:4183. [PMID: 26022995 DOI: 10.1093/hmg/ddv164] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022] Open
|
27
|
Li Y, Calvo SE, Gutman R, Liu JS, Mootha VK. Expansion of biological pathways based on evolutionary inference. Cell 2014; 158:213-25. [PMID: 24995987 DOI: 10.1016/j.cell.2014.05.034] [Citation(s) in RCA: 81] [Impact Index Per Article: 8.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/22/2013] [Revised: 02/06/2014] [Accepted: 05/12/2014] [Indexed: 01/24/2023]
Abstract
The availability of diverse genomes makes it possible to predict gene function based on shared evolutionary history. This approach can be challenging, however, for pathways whose components do not exhibit a shared history but rather consist of distinct "evolutionary modules." We introduce a computational algorithm, clustering by inferred models of evolution (CLIME), which inputs a eukaryotic species tree, homology matrix, and pathway (gene set) of interest. CLIME partitions the gene set into disjoint evolutionary modules, simultaneously learning the number of modules and a tree-based evolutionary history that defines each module. CLIME then expands each module by scanning the genome for new components that likely arose under the inferred evolutionary model. Application of CLIME to ∼1,000 annotated human pathways and to the proteomes of yeast, red algae, and malaria reveals unanticipated evolutionary modularity and coevolving components. CLIME is freely available and should become increasingly powerful with the growing wealth of eukaryotic genomes.
Collapse
Affiliation(s)
- Yang Li
- Howard Hughes Medical Institute and Department of Molecular Biology, Massachusetts General Hospital, Boston, MA 02114, USA; Department of Statistics, Harvard University, Cambridge, MA 02138, USA
| | - Sarah E Calvo
- Howard Hughes Medical Institute and Department of Molecular Biology, Massachusetts General Hospital, Boston, MA 02114, USA; Broad Institute, Cambridge, MA 02141, USA
| | - Roee Gutman
- Department of Biostatistics, Brown University, Providence, RI 02912, USA
| | - Jun S Liu
- Department of Statistics, Harvard University, Cambridge, MA 02138, USA.
| | - Vamsi K Mootha
- Howard Hughes Medical Institute and Department of Molecular Biology, Massachusetts General Hospital, Boston, MA 02114, USA; Broad Institute, Cambridge, MA 02141, USA; Department of Systems Biology, Harvard Medical School, Boston, MA 02115, USA.
| |
Collapse
|
28
|
Ajroud-Driss S, Fecto F, Ajroud K, Lalani I, Calvo SE, Mootha VK, Deng HX, Siddique N, Tahmoush AJ, Heiman-Patterson TD, Siddique T. Mutation in the novel nuclear-encoded mitochondrial protein CHCHD10 in a family with autosomal dominant mitochondrial myopathy. Neurogenetics 2014; 16:1-9. [PMID: 25193783 DOI: 10.1007/s10048-014-0421-1] [Citation(s) in RCA: 81] [Impact Index Per Article: 8.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/28/2014] [Accepted: 08/21/2014] [Indexed: 12/11/2022]
Abstract
Mitochondrial myopathies belong to a larger group of systemic diseases caused by morphological or biochemical abnormalities of mitochondria. Mitochondrial disorders can be caused by mutations in either the mitochondrial or nuclear genome. Only 5% of all mitochondrial disorders are autosomal dominant. We analyzed DNA from members of the previously reported Puerto Rican kindred with an autosomal dominant mitochondrial myopathy (Heimann-Patterson et al. 1997). Linkage analysis suggested a putative locus on the pericentric region of the long arm of chromosome 22 (22q11). Using the tools of integrative genomics, we established chromosome 22 open reading frame 16 (C22orf16) (later designated as CHCHD10) as the only high-scoring mitochondrial candidate gene in our minimal candidate region. Sequence analysis revealed a double-missense mutation (R15S and G58R) in cis in CHCHD10 which encodes a coiled coil-helix-coiled coil-helix protein of unknown function. These two mutations completely co-segregated with the disease phenotype and were absent in 1,481 Caucasian and 80 Hispanic (including 32 Puerto Rican) controls. Expression profiling showed that CHCHD10 is enriched in skeletal muscle. Mitochondrial localization of the CHCHD10 protein was confirmed using immunofluorescence in cells expressing either wild-type or mutant CHCHD10. We found that the expression of the G58R, but not the R15S, mutation induced mitochondrial fragmentation. Our findings identify a novel gene causing mitochondrial myopathy, thereby expanding the spectrum of mitochondrial myopathies caused by nuclear genes. Our findings also suggest a role for CHCHD10 in the morphologic remodeling of the mitochondria.
Collapse
Affiliation(s)
- Senda Ajroud-Driss
- Division of Neuromuscular Medicine, The Ken and Ruth Davee Department of Neurology and Clinical Neurosciences, Feinberg School of Medicine, Northwestern University, Chicago, IL, 60611, USA,
| | | | | | | | | | | | | | | | | | | | | |
Collapse
|
29
|
Lieber DS, Hershman SG, Slate NG, Calvo SE, Sims KB, Schmahmann JD, Mootha VK. Next generation sequencing with copy number variant detection expands the phenotypic spectrum of HSD17B4-deficiency. BMC Med Genet 2014; 15:30. [PMID: 24602372 PMCID: PMC4015298 DOI: 10.1186/1471-2350-15-30] [Citation(s) in RCA: 37] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 11/06/2013] [Accepted: 02/25/2014] [Indexed: 11/10/2022]
Abstract
Background D-bifunctional protein deficiency, caused by recessive mutations in HSD17B4, is a severe, infantile-onset disorder of peroxisomal fatty acid oxidation. Few affected patients survive past two years of age. Compound heterozygous mutations in HSD17B4 have also been reported in two sisters diagnosed with Perrault syndrome (MIM # 233400), who presented in adolescence with ovarian dysgenesis, hearing loss, and ataxia. Case presentation An adult male presented with cerebellar ataxia, peripheral neuropathy, hearing loss, and azoospermia. The clinical presentation, in combination with biochemical findings in serum, urine, and muscle biopsy, suggested a mitochondrial disorder. Commercial genetic testing of 18 ataxia and mitochondrial disease genes was negative. Targeted exome sequencing followed by analysis of single nucleotide variants and small insertions/deletions failed to reveal a genetic basis of disease. Application of a computational algorithm to infer copy number variants (CNVs) from exome data revealed a heterozygous 12 kb deletion of exons 10–13 of HSD17B4 that was compounded with a rare missense variant (p.A196V) at a highly conserved residue. Retrospective review of patient records revealed mildly elevated ratios of pristanic:phytanic acid and arachidonic:docosahexaenoic acid, consistent with dysfunctional peroxisomal fatty acid oxidation. Conclusion Our case expands the phenotypic spectrum of HSD17B4-deficiency, representing the first male case reported with infertility. Furthermore, it points to crosstalk between mitochondria and peroxisomes in HSD17B4-deficiency and Perrault syndrome.
Collapse
Affiliation(s)
| | | | | | | | | | - Jeremy D Schmahmann
- Ataxia Unit, Cognitive Behavioral Neurology Unit, Laboratory for Neuroanatomy and Cerebellar Neurobiology, Department of Neurology, Massachusetts General Hospital & Harvard Medical School, Boston, MA 02114 USA,
| | | |
Collapse
|
30
|
Strittmatter L, Li Y, Nakatsuka NJ, Calvo SE, Grabarek Z, Mootha VK. CLYBL is a polymorphic human enzyme with malate synthase and β-methylmalate synthase activity. Hum Mol Genet 2013; 23:2313-23. [PMID: 24334609 DOI: 10.1093/hmg/ddt624] [Citation(s) in RCA: 25] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
Abstract
CLYBL is a human mitochondrial enzyme of unknown function that is found in multiple eukaryotic taxa and conserved to bacteria. The protein is expressed in the mitochondria of all mammalian organs, with highest expression in brown fat and kidney. Approximately 5% of all humans harbor a premature stop polymorphism in CLYBL that has been associated with reduced levels of circulating vitamin B12. Using comparative genomics, we now show that CLYBL is strongly co-expressed with and co-evolved specifically with other components of the mitochondrial B12 pathway. We confirm that the premature stop polymorphism in CLYBL leads to a loss of protein expression. To elucidate the molecular function of CLYBL, we used comparative operon analysis, structural modeling and enzyme kinetics. We report that CLYBL encodes a malate/β-methylmalate synthase, converting glyoxylate and acetyl-CoA to malate, or glyoxylate and propionyl-CoA to β-methylmalate. Malate synthases are best known for their established role in the glyoxylate shunt of plants and lower organisms and are traditionally described as not occurring in humans. The broader role of a malate/β-methylmalate synthase in human physiology and its mechanistic link to vitamin B12 metabolism remain unknown.
Collapse
Affiliation(s)
- Laura Strittmatter
- Department of Molecular Biology, Howard Hughes Medical Institute, Massachusetts General Hospital, Boston, MA 02114, USA
| | | | | | | | | | | |
Collapse
|
31
|
Sancak Y, Markhard AL, Kitami T, Kovács-Bogdán E, Kamer KJ, Udeshi ND, Carr SA, Chaudhuri D, Clapham DE, Li AA, Calvo SE, Goldberger O, Mootha VK. EMRE is an essential component of the mitochondrial calcium uniporter complex. Science 2013; 342:1379-82. [PMID: 24231807 DOI: 10.1126/science.1242993] [Citation(s) in RCA: 484] [Impact Index Per Article: 44.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/28/2022]
Abstract
The mitochondrial uniporter is a highly selective calcium channel in the organelle's inner membrane. Its molecular components include the EF-hand-containing calcium-binding proteins mitochondrial calcium uptake 1 (MICU1) and MICU2 and the pore-forming subunit mitochondrial calcium uniporter (MCU). We sought to achieve a full molecular characterization of the uniporter holocomplex (uniplex). Quantitative mass spectrometry of affinity-purified uniplex recovered MICU1 and MICU2, MCU and its paralog MCUb, and essential MCU regulator (EMRE), a previously uncharacterized protein. EMRE is a 10-kilodalton, metazoan-specific protein with a single transmembrane domain. In its absence, uniporter channel activity was lost despite intact MCU expression and oligomerization. EMRE was required for the interaction of MCU with MICU1 and MICU2. Hence, EMRE is essential for in vivo uniporter current and additionally bridges the calcium-sensing role of MICU1 and MICU2 with the calcium-conducting role of MCU.
Collapse
Affiliation(s)
- Yasemin Sancak
- Department of Molecular Biology, Massachusetts General Hospital, Department of Systems Biology, Harvard Medical School, Boston, MA, USA
| | | | | | | | | | | | | | | | | | | | | | | | | |
Collapse
|
32
|
Hildick-Smith GJ, Cooney JD, Garone C, Kremer LS, Haack TB, Thon JN, Miyata N, Lieber DS, Calvo SE, Akman HO, Yien YY, Huston NC, Branco DS, Shah DI, Freedman ML, Koehler CM, Italiano JE, Merkenschlager A, Beblo S, Strom TM, Meitinger T, Freisinger P, Donati MA, Prokisch H, Mootha VK, DiMauro S, Paw BH. Macrocytic anemia and mitochondriopathy resulting from a defect in sideroflexin 4. Am J Hum Genet 2013; 93:906-14. [PMID: 24119684 DOI: 10.1016/j.ajhg.2013.09.011] [Citation(s) in RCA: 45] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/21/2013] [Revised: 09/11/2013] [Accepted: 09/18/2013] [Indexed: 01/19/2023] Open
Abstract
We used exome sequencing to identify mutations in sideroflexin 4 (SFXN4) in two children with mitochondrial disease (the more severe case also presented with macrocytic anemia). SFXN4 is an uncharacterized mitochondrial protein that localizes to the mitochondrial inner membrane. sfxn4 knockdown in zebrafish recapitulated the mitochondrial respiratory defect observed in both individuals and the macrocytic anemia with megaloblastic features of the more severe case. In vitro and in vivo complementation studies with fibroblasts from the affected individuals and zebrafish demonstrated the requirement of SFXN4 for mitochondrial respiratory homeostasis and erythropoiesis. Our findings establish mutations in SFXN4 as a cause of mitochondriopathy and macrocytic anemia.
Collapse
Affiliation(s)
- Gordon J Hildick-Smith
- Division of Hematology, Department of Medicine, Brigham and Women's Hospital and Harvard Medical School, Boston, MA 02115, USA
| | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | |
Collapse
|
33
|
Eran A, Li JB, Vatalaro K, McCarthy J, Rahimov F, Collins C, Markianos K, Margulies DM, Brown EN, Calvo SE, Kohane IS, Kunkel LM. Comparative RNA editing in autistic and neurotypical cerebella. Mol Psychiatry 2013; 18:1041-8. [PMID: 22869036 PMCID: PMC3494744 DOI: 10.1038/mp.2012.118] [Citation(s) in RCA: 54] [Impact Index Per Article: 4.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 02/16/2012] [Revised: 06/29/2012] [Accepted: 06/29/2012] [Indexed: 01/03/2023]
Abstract
Adenosine-to-inosine (A-to-I) RNA editing is a neurodevelopmentally regulated epigenetic modification shown to modulate complex behavior in animals. Little is known about human A-to-I editing, but it is thought to constitute one of many molecular mechanisms connecting environmental stimuli and behavioral outputs. Thus, comprehensive exploration of A-to-I RNA editing in human brains may shed light on gene-environment interactions underlying complex behavior in health and disease. Synaptic function is a main target of A-to-I editing, which can selectively recode key amino acids in synaptic genes, directly altering synaptic strength and duration in response to environmental signals. Here, we performed a high-resolution survey of synaptic A-to-I RNA editing in a human population, and examined how it varies in autism, a neurodevelopmental disorder in which synaptic abnormalities are a common finding. Using ultra-deep (>1000 × ) sequencing, we quantified the levels of A-to-I editing of 10 synaptic genes in postmortem cerebella from 14 neurotypical and 11 autistic individuals. A high dynamic range of editing levels was detected across individuals and editing sites, from 99.6% to below detection limits. In most sites, the extreme ends of the population editing distributions were individuals with autism. Editing was correlated with isoform usage, clusters of correlated sites were identified, and differential editing patterns examined. Finally, a dysfunctional form of the editing enzyme adenosine deaminase acting on RNA B1 was found more commonly in postmortem cerebella from individuals with autism. These results provide a population-level, high-resolution view of A-to-I RNA editing in human cerebella and suggest that A-to-I editing of synaptic genes may be informative for assessing the epigenetic risk for autism.
Collapse
Affiliation(s)
- Alal Eran
- Harvard-MIT Division of Health Sciences and Technology, Cambridge, MA 02139, USA,Program in Genomics, Boston Children’s Hospital, Boston, MA 02115, USA
| | - Jin Billy Li
- Department of Genetics, Stanford University, Stanford, CA 94305, USA
| | - Kayla Vatalaro
- Program in Genomics, Boston Children’s Hospital, Boston, MA 02115, USA
| | - Jillian McCarthy
- Program in Genomics, Boston Children’s Hospital, Boston, MA 02115, USA
| | - Fedik Rahimov
- Program in Genomics, Boston Children’s Hospital, Boston, MA 02115, USA,Department of Genetics, Harvard Medical School, Boston, MA 02115, USA
| | - Christin Collins
- Program in Genomics, Boston Children’s Hospital, Boston, MA 02115, USA,Department of Genetics, Harvard Medical School, Boston, MA 02115, USA
| | - Kyriacos Markianos
- Program in Genomics, Boston Children’s Hospital, Boston, MA 02115, USA,Department of Pediatrics, Harvard Medical School, Boston, MA 02115, USA
| | - David M. Margulies
- Department of Pediatrics, Harvard Medical School, Boston, MA 02115, USA,Correlagen Diagnostics, Waltham, MA 02452, USA,Center for Biomedical Informatics, Harvard Medical School, Boston, MA 02115, USA
| | - Emery N. Brown
- Harvard-MIT Division of Health Sciences and Technology, Cambridge, MA 02139, USA,Neuroscience Statistics Research Laboratory, Department of Anesthesia and Critical Care, Massachusetts General Hospital, Harvard Medical School, Boston, MA 02114, USA,Department of Brain and Cognitive Sciences, MIT, Cambridge, MA 02139, USA
| | - Sarah E. Calvo
- Broad Institute of Harvard and MIT, Cambridge, MA 02139, USA
| | - Isaac S. Kohane
- Harvard-MIT Division of Health Sciences and Technology, Cambridge, MA 02139, USA,Department of Pediatrics, Harvard Medical School, Boston, MA 02115, USA,Center for Biomedical Informatics, Harvard Medical School, Boston, MA 02115, USA,Correspondence: Louis Kunkel, Program in Genomics, Department of Genetics, Boston Children’s Hospital, 3 Blackfan Circle, CLS 15027.1, Boston, MA 02115, USA. Telephone: (617) 355-6279, fax: (617) 730-0253, , Isaac Kohane, Department of Pediatrics, Boston Children's Hospital, 300 Longwood Ave., Enders 144, Boston, MA 02115, USA. Telephone: (617) 919-2182, fax: (617) 730-0921,
| | - Louis M. Kunkel
- Program in Genomics, Boston Children’s Hospital, Boston, MA 02115, USA,Department of Genetics, Harvard Medical School, Boston, MA 02115, USA,Department of Pediatrics, Harvard Medical School, Boston, MA 02115, USA,The Manton Center for Orphan Disease Research, Boston, MA 02115, USA,Correspondence: Louis Kunkel, Program in Genomics, Department of Genetics, Boston Children’s Hospital, 3 Blackfan Circle, CLS 15027.1, Boston, MA 02115, USA. Telephone: (617) 355-6279, fax: (617) 730-0253, , Isaac Kohane, Department of Pediatrics, Boston Children's Hospital, 300 Longwood Ave., Enders 144, Boston, MA 02115, USA. Telephone: (617) 919-2182, fax: (617) 730-0921,
| |
Collapse
|
34
|
Lieber DS, Calvo SE, Shanahan K, Slate NG, Liu S, Hershman SG, Gold NB, Chapman BA, Thorburn DR, Berry GT, Schmahmann JD, Borowsky ML, Mueller DM, Sims KB, Mootha VK. Targeted exome sequencing of suspected mitochondrial disorders. Neurology 2013; 80:1762-70. [PMID: 23596069 DOI: 10.1212/wnl.0b013e3182918c40] [Citation(s) in RCA: 127] [Impact Index Per Article: 11.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/04/2023] Open
Abstract
OBJECTIVE To evaluate the utility of targeted exome sequencing for the molecular diagnosis of mitochondrial disorders, which exhibit marked phenotypic and genetic heterogeneity. METHODS We considered a diverse set of 102 patients with suspected mitochondrial disorders based on clinical, biochemical, and/or molecular findings, and whose disease ranged from mild to severe, with varying age at onset. We sequenced the mitochondrial genome (mtDNA) and the exons of 1,598 nuclear-encoded genes implicated in mitochondrial biology, mitochondrial disease, or monogenic disorders with phenotypic overlap. We prioritized variants likely to underlie disease and established molecular diagnoses in accordance with current clinical genetic guidelines. RESULTS Targeted exome sequencing yielded molecular diagnoses in established disease loci in 22% of cases, including 17 of 18 (94%) with prior molecular diagnoses and 5 of 84 (6%) without. The 5 new diagnoses implicated 2 genes associated with canonical mitochondrial disorders (NDUFV1, POLG2), and 3 genes known to underlie other neurologic disorders (DPYD, KARS, WFS1), underscoring the phenotypic and biochemical overlap with other inborn errors. We prioritized variants in an additional 26 patients, including recessive, X-linked, and mtDNA variants that were enriched 2-fold over background and await further support of pathogenicity. In one case, we modeled patient mutations in yeast to provide evidence that recessive mutations in ATP5A1 can underlie combined respiratory chain deficiency. CONCLUSION The results demonstrate that targeted exome sequencing is an effective alternative to the sequential testing of mtDNA and individual nuclear genes as part of the investigation of mitochondrial disease. Our study underscores the ongoing challenge of variant interpretation in the clinical setting.
Collapse
Affiliation(s)
- Daniel S Lieber
- Department of Molecular Biology, Massachusetts General Hospital, Boston, MA, USA
| | | | | | | | | | | | | | | | | | | | | | | | | | | | | |
Collapse
|
35
|
Garone C, Rubio JC, Calvo SE, Naini A, Tanji K, Dimauro S, Mootha VK, Hirano M. MPV17 Mutations Causing Adult-Onset Multisystemic Disorder With Multiple Mitochondrial DNA Deletions. ACTA ACUST UNITED AC 2013; 69:1648-51. [PMID: 22964873 DOI: 10.1001/archneurol.2012.405] [Citation(s) in RCA: 59] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/13/2023]
Abstract
OBJECTIVE To identify the cause of an adult-onset multisystemic disease with multiple deletions of mitochondrial DNA (mtDNA). DESIGN Case report. SETTING University hospitals. PATIENT A 65-year-old man with axonal sensorimotor peripheral neuropathy, ptosis, ophthalmoparesis, diabetes mellitus, exercise intolerance, steatohepatopathy, depression, parkinsonism, and gastrointestinal dysmotility. RESULTS Skeletal muscle biopsy revealed ragged-red and cytochrome- c oxidase-deficient fibers, and Southern blot analysis showed multiple mtDNA deletions. No deletions were detected in fibroblasts, and the results of quantitative polymerase chain reaction showed that the amount of mtDNA was normal in both muscle and fibroblasts. Exome sequencing using a mitochondrial library revealed compound heterozygous MPV17 mutations (p.LysMet88-89MetLeu and p.Leu143*), a novel cause of mtDNA multiple deletions. CONCLUSIONS In addition to causing juvenile-onset disorders with mtDNA depletion, MPV17 mutations can cause adult-onset multisystemic disease with multiple mtDNA deletions.
Collapse
|
36
|
Ronchi D, Garone C, Bordoni A, Gutierrez Rios P, Calvo SE, Ripolone M, Ranieri M, Rizzuti M, Villa L, Magri F, Corti S, Bresolin N, Mootha VK, Moggio M, DiMauro S, Comi GP, Sciacco M. Next-generation sequencing reveals DGUOK mutations in adult patients with mitochondrial DNA multiple deletions. Brain 2012; 135:3404-15. [PMID: 23043144 DOI: 10.1093/brain/aws258] [Citation(s) in RCA: 70] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/31/2023] Open
Abstract
The molecular diagnosis of mitochondrial disorders still remains elusive in a large proportion of patients, but advances in next generation sequencing are significantly improving our chances to detect mutations even in sporadic patients. Syndromes associated with mitochondrial DNA multiple deletions are caused by different molecular defects resulting in a wide spectrum of predominantly adult-onset clinical presentations, ranging from progressive external ophthalmoplegia to multi-systemic disorders of variable severity. The mutations underlying these conditions remain undisclosed in half of the affected subjects. We applied next-generation sequencing of known mitochondrial targets (MitoExome) to probands presenting with adult-onset mitochondrial myopathy and harbouring mitochondrial DNA multiple deletions in skeletal muscle. We identified autosomal recessive mutations in the DGUOK gene (encoding mitochondrial deoxyguanosine kinase), which has previously been associated with an infantile hepatocerebral form of mitochondrial DNA depletion. Mutations in DGUOK occurred in five independent subjects, representing 5.6% of our cohort of patients with mitochondrial DNA multiple deletions, and impaired both muscle DGUOK activity and protein stability. Clinical presentations were variable, including mitochondrial myopathy with or without progressive external ophthalmoplegia, recurrent rhabdomyolysis in a young female who had received a liver transplant at 9 months of age and adult-onset lower motor neuron syndrome with mild cognitive impairment. These findings reinforce the concept that mutations in genes involved in deoxyribonucleotide metabolism can cause diverse clinical phenotypes and suggest that DGUOK should be screened in patients harbouring mitochondrial DNA deletions in skeletal muscle.
Collapse
Affiliation(s)
- Dario Ronchi
- Dino Ferrari Centre, Neuroscience Section, Department of Pathophysiology and Transplantation, University of Milan, Neurology Unit, IRCCS Foundation Ca' Granda Ospedale Maggiore Policlinico, 20122 Milan, Italy.
| | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | |
Collapse
|
37
|
Calvo SE, Compton AG, Hershman SG, Lim SC, Lieber DS, Tucker EJ, Laskowski A, Garone C, Liu S, Jaffe DB, Christodoulou J, Fletcher JM, Bruno DL, Goldblatt J, Dimauro S, Thorburn DR, Mootha VK. Molecular diagnosis of infantile mitochondrial disease with targeted next-generation sequencing. Sci Transl Med 2012; 4:118ra10. [PMID: 22277967 DOI: 10.1126/scitranslmed.3003310] [Citation(s) in RCA: 338] [Impact Index Per Article: 28.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Abstract
Advances in next-generation sequencing (NGS) promise to facilitate diagnosis of inherited disorders. Although in research settings NGS has pinpointed causal alleles using segregation in large families, the key challenge for clinical diagnosis is application to single individuals. To explore its diagnostic use, we performed targeted NGS in 42 unrelated infants with clinical and biochemical evidence of mitochondrial oxidative phosphorylation disease. These devastating mitochondrial disorders are characterized by phenotypic and genetic heterogeneity, with more than 100 causal genes identified to date. We performed "MitoExome" sequencing of the mitochondrial DNA (mtDNA) and exons of ~1000 nuclear genes encoding mitochondrial proteins and prioritized rare mutations predicted to disrupt function. Because patients and healthy control individuals harbored a comparable number of such heterozygous alleles, we could not prioritize dominant-acting genes. However, patients showed a fivefold enrichment of genes with two such mutations that could underlie recessive disease. In total, 23 of 42 (55%) patients harbored such recessive genes or pathogenic mtDNA variants. Firm diagnoses were enabled in 10 patients (24%) who had mutations in genes previously linked to disease. Thirteen patients (31%) had mutations in nuclear genes not previously linked to disease. The pathogenicity of two such genes, NDUFB3 and AGK, was supported by complementation studies and evidence from multiple patients, respectively. The results underscore the potential and challenges of deploying NGS in clinical settings.
Collapse
Affiliation(s)
- Sarah E Calvo
- Center for Human Genetic Research and Department of Molecular Biology, Massachusetts General Hospital, 185 Cambridge Street, Sixth Floor, Boston, MA 02114, USA
| | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | |
Collapse
|
38
|
Lieber DS, Calvo SE, Slate NG, Liu S, Borowsky ML, Hershman SG, Gold NB, Berry GT, Mueller DM, Schmahmann JD, Sims KB, Mootha VK. Targeted exome sequencing of suspected mitochondrial disorders in a hospital-based cohort. Mitochondrion 2012. [DOI: 10.1016/j.mito.2012.07.065] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
|
39
|
Abstract
Calcium uptake into mitochondria occurs via a recently identified ion channel called the uniporter. Here, we characterize the phylogenomic distribution of the uniporter's membrane-spanning pore subunit (MCU) and regulatory partner (MICU1). Homologs of both components tend to co-occur in all major branches of eukaryotic life, but both have been lost along certain protozoan and fungal lineages. Several bacterial genomes also contain putative MCU homologs that may represent prokaryotic calcium channels. The analyses indicate that the uniporter may have been an early feature of mitochondria.
Collapse
Affiliation(s)
- Alexander G Bick
- Department of Molecular Biology, Massachusetts General Hospital, Boston, MA 02114, USA
| | | | | |
Collapse
|
40
|
Lieber DS, Vafai SB, Horton LC, Slate NG, Liu S, Borowsky ML, Calvo SE, Schmahmann JD, Mootha VK. Atypical case of Wolfram syndrome revealed through targeted exome sequencing in a patient with suspected mitochondrial disease. BMC Med Genet 2012; 13:3. [PMID: 22226368 PMCID: PMC3281774 DOI: 10.1186/1471-2350-13-3] [Citation(s) in RCA: 25] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 09/06/2011] [Accepted: 01/06/2012] [Indexed: 11/10/2022]
Abstract
BACKGROUND Mitochondrial diseases comprise a diverse set of clinical disorders that affect multiple organ systems with varying severity and age of onset. Due to their clinical and genetic heterogeneity, these diseases are difficult to diagnose. We have developed a targeted exome sequencing approach to improve our ability to properly diagnose mitochondrial diseases and apply it here to an individual patient. Our method targets mitochondrial DNA (mtDNA) and the exons of 1,600 nuclear genes involved in mitochondrial biology or Mendelian disorders with multi-system phenotypes, thereby allowing for simultaneous evaluation of multiple disease loci. CASE PRESENTATION Targeted exome sequencing was performed on a patient initially suspected to have a mitochondrial disorder. The patient presented with diabetes mellitus, diffuse brain atrophy, autonomic neuropathy, optic nerve atrophy, and a severe amnestic syndrome. Further work-up revealed multiple heteroplasmic mtDNA deletions as well as profound thiamine deficiency without a clear nutritional cause. Targeted exome sequencing revealed a homozygous c.1672C > T (p.R558C) missense mutation in exon 8 of WFS1 that has previously been reported in a patient with Wolfram syndrome. CONCLUSION This case demonstrates how clinical application of next-generation sequencing technology can enhance the diagnosis of patients suspected to have rare genetic disorders. Furthermore, the finding of unexplained thiamine deficiency in a patient with Wolfram syndrome suggests a potential link between WFS1 biology and thiamine metabolism that has implications for the clinical management of Wolfram syndrome patients.
Collapse
Affiliation(s)
- Daniel S Lieber
- Department of Molecular Biology, Massachusetts General Hospital, Boston, MA 02114, USA
| | | | | | | | | | | | | | | | | |
Collapse
|
41
|
Tucker EJ, Hershman SG, Köhrer C, Belcher-Timme CA, Patel J, Goldberger OA, Christodoulou J, Silberstein JM, McKenzie M, Ryan MT, Compton AG, Jaffe JD, Carr SA, Calvo SE, RajBhandary UL, Thorburn DR, Mootha VK. Mutations in MTFMT underlie a human disorder of formylation causing impaired mitochondrial translation. Cell Metab 2011; 14:428-34. [PMID: 21907147 PMCID: PMC3486727 DOI: 10.1016/j.cmet.2011.07.010] [Citation(s) in RCA: 121] [Impact Index Per Article: 9.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 04/22/2011] [Revised: 07/06/2011] [Accepted: 07/26/2011] [Indexed: 01/19/2023]
Abstract
The metazoan mitochondrial translation machinery is unusual in having a single tRNA(Met) that fulfills the dual role of the initiator and elongator tRNA(Met). A portion of the Met-tRNA(Met) pool is formylated by mitochondrial methionyl-tRNA formyltransferase (MTFMT) to generate N-formylmethionine-tRNA(Met) (fMet-tRNA(met)), which is used for translation initiation; however, the requirement of formylation for initiation in human mitochondria is still under debate. Using targeted sequencing of the mtDNA and nuclear exons encoding the mitochondrial proteome (MitoExome), we identified compound heterozygous mutations in MTFMT in two unrelated children presenting with Leigh syndrome and combined OXPHOS deficiency. Patient fibroblasts exhibit severe defects in mitochondrial translation that can be rescued by exogenous expression of MTFMT. Furthermore, patient fibroblasts have dramatically reduced fMet-tRNA(Met) levels and an abnormal formylation profile of mitochondrially translated COX1. Our findings demonstrate that MTFMT is critical for efficient human mitochondrial translation and reveal a human disorder of Met-tRNA(Met) formylation.
Collapse
Affiliation(s)
- Elena J. Tucker
- Murdoch Childrens Research Institute, Royal Children's Hospital, Melbourne, VIC, 3052, Australia
- Department of Paediatrics, University of Melbourne, Melbourne, VIC, 3052, Australia
| | - Steven G. Hershman
- Center for Human Genetic Research, Massachusetts General Hospital, Boston, MA, 02114, USA
- Department of Systems Biology, Harvard Medical School, Boston, MA, 02115, USA
- Broad Institute, Cambridge, MA, 02142, USA
| | - Caroline Köhrer
- Department of Biology, Massachusetts Institute of Technology, Cambridge, MA, 02142, USA
| | - Casey A. Belcher-Timme
- Center for Human Genetic Research, Massachusetts General Hospital, Boston, MA, 02114, USA
- Department of Systems Biology, Harvard Medical School, Boston, MA, 02115, USA
- Broad Institute, Cambridge, MA, 02142, USA
| | | | - Olga A. Goldberger
- Center for Human Genetic Research, Massachusetts General Hospital, Boston, MA, 02114, USA
- Department of Systems Biology, Harvard Medical School, Boston, MA, 02115, USA
- Broad Institute, Cambridge, MA, 02142, USA
| | - John Christodoulou
- Genetic Metabolic Disorders Research Unit, Children's Hospital at Westmead, Sydney, NSW, 2006, Australia
- Discipline of Paediatrics & Child Health, University of Sydney, Sydney, NSW, 2006, Australia
- Discipline of Genetic Medicine, University of Sydney, Sydney, NSW, 2006, Australia
| | - Jonathon M. Silberstein
- Department of Neurology, Princess Margaret Hospital for Children, Perth, WA, 6008, Australia
| | - Matthew McKenzie
- Centre for Reproduction and Development, Monash Institute of Medical Research, Monash University, Melbourne, Australia
| | - Michael T. Ryan
- Department of Biochemistry, La Trobe University, Melbourne, VIC, 3086, Australia
- ARC Centre of Excellence for Coherent X-ray Science, La Trobe University, Melbourne, VIC, 3086, Australia
| | - Alison G. Compton
- Murdoch Childrens Research Institute, Royal Children's Hospital, Melbourne, VIC, 3052, Australia
| | | | | | - Sarah E. Calvo
- Center for Human Genetic Research, Massachusetts General Hospital, Boston, MA, 02114, USA
- Department of Systems Biology, Harvard Medical School, Boston, MA, 02115, USA
- Broad Institute, Cambridge, MA, 02142, USA
| | - Uttam L. RajBhandary
- Department of Biology, Massachusetts Institute of Technology, Cambridge, MA, 02142, USA
| | - David R. Thorburn
- Murdoch Childrens Research Institute, Royal Children's Hospital, Melbourne, VIC, 3052, Australia
- Department of Paediatrics, University of Melbourne, Melbourne, VIC, 3052, Australia
- Genetic Health Services Victoria, Royal Children's Hospital, Melbourne, VIC, 3052, Australia
| | - Vamsi K. Mootha
- Center for Human Genetic Research, Massachusetts General Hospital, Boston, MA, 02114, USA
- Department of Systems Biology, Harvard Medical School, Boston, MA, 02115, USA
- Broad Institute, Cambridge, MA, 02142, USA
| |
Collapse
|
42
|
Tucker EJ, Compton AG, Calvo SE, Thorburn DR. The molecular basis of human complex I deficiency. IUBMB Life 2011; 63:669-77. [PMID: 21766414 DOI: 10.1002/iub.495] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/23/2011] [Accepted: 04/18/2011] [Indexed: 12/18/2022]
Abstract
Disorders of oxidative phosphorylation (OXPHOS) have a birth prevalence of ∼1/5,000 and are the most common inborn errors of metabolism. The most common OXPHOS disorder is complex I deficiency. Patients with complex I deficiency present with variable symptoms, such as muscle weakness, cardiomyopathy, developmental delay or regression, blindness, seizures, failure to thrive, liver dysfunction or ataxia. Molecular diagnosis of patients with complex I deficiency is a challenging task due to the clinical heterogeneity of patients and the large number of candidate disease genes, both nuclear-encoded and mitochondrial DNA (mtDNA)-encoded. In this review, we have thoroughly surveyed the literature to identify 149 patients described with both isolated complex I deficiency and pathogenic mutations within nuclear genes. In total, 115 different pathogenic mutations have been reported in 22 different nuclear genes encoding complex I subunits or assembly factors, highlighting the allelic and locus heterogeneity of this disorder. Missense mutations predominate in genes encoding core subunits and some assembly factors while null-type mutations are common in the genes encoding supernumerary subunits and other assembly factors. Despite developments in molecular technology, many patients do not receive molecular diagnosis and no gene has yet been identified that accounts for more than 5% of cases, suggesting that there are likely many disease genes that await discovery.
Collapse
Affiliation(s)
- Elena J Tucker
- Murdoch Childrens Research Institute, Royal Children's Hospital, Melbourne, Australia.
| | | | | | | |
Collapse
|
43
|
Abstract
For nearly three decades, the sequence of the human mitochondrial genome (mtDNA) has provided a molecular framework for understanding maternally inherited diseases. However, the vast majority of human mitochondrial disorders are caused by nuclear genome defects, which is not surprising since the mtDNA encodes only 13 proteins. Advances in genomics, mass spectrometry, and computation have only recently made it possible to systematically identify the complement of over 1,000 proteins that comprise the mammalian mitochondrial proteome. Here, we review recent progress in characterizing the mitochondrial proteome and highlight insights into its complexity, tissue heterogeneity, evolutionary origins, and biochemical versatility. We then discuss how this proteome is being used to discover the genetic basis of respiratory chain disorders as well as to expand our definition of mitochondrial disease. Finally, we explore future prospects and challenges for using the mitochondrial proteome as a foundation for systems analysis of the organelle.
Collapse
Affiliation(s)
- Sarah E Calvo
- Broad Institute of MIT and Harvard, Cambridge, Massachusetts 02142, USA
| | | |
Collapse
|
44
|
Fassone E, Duncan AJ, Taanman JW, Pagnamenta AT, Sadowski MI, Holand T, Qasim W, Rutland P, Calvo SE, Mootha VK, Bitner-Glindzicz M, Rahman S. FOXRED1, encoding an FAD-dependent oxidoreductase complex-I-specific molecular chaperone, is mutated in infantile-onset mitochondrial encephalopathy. Hum Mol Genet 2010; 19:4837-47. [PMID: 20858599 DOI: 10.1093/hmg/ddq414] [Citation(s) in RCA: 65] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022] Open
Abstract
Complex I is the first and largest enzyme in the respiratory chain and is located in the inner mitochondrial membrane. Complex I deficiency is the most commonly reported mitochondrial disorder presenting in childhood, but the molecular basis of most cases remains elusive. We describe a patient with complex I deficiency caused by mutation of the molecular chaperone FOXRED1. A combined homozygosity mapping and bioinformatics approach in a consanguineous Iranian-Jewish pedigree led to the identification of a homozygous mutation in FOXRED1 in a child who presented with infantile-onset encephalomyopathy. Silencing of FOXRED1 in human fibroblasts resulted in reduced complex I steady-state levels and activity, while lentiviral-mediated FOXRED1 transgene expression rescued complex I deficiency in the patient fibroblasts. This FAD-dependent oxidoreductase, which has never previously been associated with human disease, is now shown to be a complex I-specific molecular chaperone. The discovery of the c.1054C>T; p.R352W mutation in the FOXRED1 gene is a further contribution towards resolving the complex puzzle of the genetic basis of human mitochondrial disease.
Collapse
Affiliation(s)
- Elisa Fassone
- Clinical and Molecular Genetics Unit, UCL Institute of Child Health, London WC1N 1EH, UK
| | | | | | | | | | | | | | | | | | | | | | | |
Collapse
|
45
|
Calvo SE, Tucker EJ, Compton AG, Kirby DM, Crawford G, Burtt NP, Rivas M, Guiducci C, Bruno DL, Goldberger OA, Redman MC, Wiltshire E, Wilson CJ, Altshuler D, Gabriel SB, Daly MJ, Thorburn DR, Mootha VK. High-throughput, pooled sequencing identifies mutations in NUBPL and FOXRED1 in human complex I deficiency. Nat Genet 2010; 42:851-8. [PMID: 20818383 PMCID: PMC2977978 DOI: 10.1038/ng.659] [Citation(s) in RCA: 284] [Impact Index Per Article: 20.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/02/2010] [Accepted: 08/11/2010] [Indexed: 12/15/2022]
Abstract
Discovering the molecular basis of mitochondrial respiratory chain disease is challenging given the large number of both mitochondrial and nuclear genes that are involved. We report a strategy of focused candidate gene prediction, high-throughput sequencing and experimental validation to uncover the molecular basis of mitochondrial complex I disorders. We created seven pools of DNA from a cohort of 103 cases and 42 healthy controls and then performed deep sequencing of 103 candidate genes to identify 151 rare variants that were predicted to affect protein function. We established genetic diagnoses in 13 of 60 previously unsolved cases using confirmatory experiments, including cDNA complementation to show that mutations in NUBPL and FOXRED1 can cause complex I deficiency. Our study illustrates how large-scale sequencing, coupled with functional prediction and experimental validation, can be used to identify causal mutations in individual cases.
Collapse
Affiliation(s)
- Sarah E Calvo
- Center for Human Genetic Research, Massachusetts General Hospital, Boston, Massachusetts, USA
| | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | |
Collapse
|
46
|
Pagliarini DJ, Calvo SE, Chang B, Sheth SA, Vafai SB, Ong SE, Walford GA, Sugiana C, Boneh A, Chen WK, Hill DE, Vidal M, Evans JG, Thorburn DR, Carr SA, Mootha VK. A mitochondrial protein compendium elucidates complex I disease biology. Cell 2008; 134:112-23. [PMID: 18614015 DOI: 10.1016/j.cell.2008.06.016] [Citation(s) in RCA: 1510] [Impact Index Per Article: 94.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/31/2007] [Revised: 03/06/2008] [Accepted: 06/02/2008] [Indexed: 01/04/2023]
Abstract
Mitochondria are complex organelles whose dysfunction underlies a broad spectrum of human diseases. Identifying all of the proteins resident in this organelle and understanding how they integrate into pathways represent major challenges in cell biology. Toward this goal, we performed mass spectrometry, GFP tagging, and machine learning to create a mitochondrial compendium of 1098 genes and their protein expression across 14 mouse tissues. We link poorly characterized proteins in this inventory to known mitochondrial pathways by virtue of shared evolutionary history. Using this approach, we predict 19 proteins to be important for the function of complex I (CI) of the electron transport chain. We validate a subset of these predictions using RNAi, including C8orf38, which we further show harbors an inherited mutation in a lethal, infantile CI deficiency. Our results have important implications for understanding CI function and pathogenesis and, more generally, illustrate how our compendium can serve as a foundation for systematic investigations of mitochondria.
Collapse
Affiliation(s)
- David J Pagliarini
- Center for Human Genetic Research, Massachusetts General Hospital, Boston, MA 02114, USA
| | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | |
Collapse
|
47
|
Galagan JE, Calvo SE, Cuomo C, Ma LJ, Wortman JR, Batzoglou S, Lee SI, Baştürkmen M, Spevak CC, Clutterbuck J, Kapitonov V, Jurka J, Scazzocchio C, Farman M, Butler J, Purcell S, Harris S, Braus GH, Draht O, Busch S, D'Enfert C, Bouchier C, Goldman GH, Bell-Pedersen D, Griffiths-Jones S, Doonan JH, Yu J, Vienken K, Pain A, Freitag M, Selker EU, Archer DB, Peñalva MA, Oakley BR, Momany M, Tanaka T, Kumagai T, Asai K, Machida M, Nierman WC, Denning DW, Caddick M, Hynes M, Paoletti M, Fischer R, Miller B, Dyer P, Sachs MS, Osmani SA, Birren BW. Sequencing of Aspergillus nidulans and comparative analysis with A. fumigatus and A. oryzae. Nature 2005; 438:1105-15. [PMID: 16372000 DOI: 10.1038/nature04341] [Citation(s) in RCA: 930] [Impact Index Per Article: 48.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/31/2005] [Accepted: 10/19/2005] [Indexed: 11/08/2022]
Abstract
The aspergilli comprise a diverse group of filamentous fungi spanning over 200 million years of evolution. Here we report the genome sequence of the model organism Aspergillus nidulans, and a comparative study with Aspergillus fumigatus, a serious human pathogen, and Aspergillus oryzae, used in the production of sake, miso and soy sauce. Our analysis of genome structure provided a quantitative evaluation of forces driving long-term eukaryotic genome evolution. It also led to an experimentally validated model of mating-type locus evolution, suggesting the potential for sexual reproduction in A. fumigatus and A. oryzae. Our analysis of sequence conservation revealed over 5,000 non-coding regions actively conserved across all three species. Within these regions, we identified potential functional elements including a previously uncharacterized TPP riboswitch and motifs suggesting regulation in filamentous fungi by Puf family genes. We further obtained comparative and experimental evidence indicating widespread translational regulation by upstream open reading frames. These results enhance our understanding of these widely studied fungi as well as provide new insight into eukaryotic genome evolution and gene regulation.
Collapse
Affiliation(s)
- James E Galagan
- The Broad Institute of MIT and Harvard, 320 Charles Street, Cambridge, Massachusetts 02142, USA
| | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | |
Collapse
|
48
|
Galagan JE, Calvo SE, Borkovich KA, Selker EU, Read ND, Jaffe D, FitzHugh W, Ma LJ, Smirnov S, Purcell S, Rehman B, Elkins T, Engels R, Wang S, Nielsen CB, Butler J, Endrizzi M, Qui D, Ianakiev P, Bell-Pedersen D, Nelson MA, Werner-Washburne M, Selitrennikoff CP, Kinsey JA, Braun EL, Zelter A, Schulte U, Kothe GO, Jedd G, Mewes W, Staben C, Marcotte E, Greenberg D, Roy A, Foley K, Naylor J, Stange-Thomann N, Barrett R, Gnerre S, Kamal M, Kamvysselis M, Mauceli E, Bielke C, Rudd S, Frishman D, Krystofova S, Rasmussen C, Metzenberg RL, Perkins DD, Kroken S, Cogoni C, Macino G, Catcheside D, Li W, Pratt RJ, Osmani SA, DeSouza CPC, Glass L, Orbach MJ, Berglund JA, Voelker R, Yarden O, Plamann M, Seiler S, Dunlap J, Radford A, Aramayo R, Natvig DO, Alex LA, Mannhaupt G, Ebbole DJ, Freitag M, Paulsen I, Sachs MS, Lander ES, Nusbaum C, Birren B. The genome sequence of the filamentous fungus Neurospora crassa. Nature 2003; 422:859-68. [PMID: 12712197 DOI: 10.1038/nature01554] [Citation(s) in RCA: 1129] [Impact Index Per Article: 53.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/24/2002] [Accepted: 03/14/2003] [Indexed: 11/09/2022]
Abstract
Neurospora crassa is a central organism in the history of twentieth-century genetics, biochemistry and molecular biology. Here, we report a high-quality draft sequence of the N. crassa genome. The approximately 40-megabase genome encodes about 10,000 protein-coding genes--more than twice as many as in the fission yeast Schizosaccharomyces pombe and only about 25% fewer than in the fruitfly Drosophila melanogaster. Analysis of the gene set yields insights into unexpected aspects of Neurospora biology including the identification of genes potentially associated with red light photobiology, genes implicated in secondary metabolism, and important differences in Ca2+ signalling as compared with plants and animals. Neurospora possesses the widest array of genome defence mechanisms known for any eukaryotic organism, including a process unique to fungi called repeat-induced point mutation (RIP). Genome analysis suggests that RIP has had a profound impact on genome evolution, greatly slowing the creation of new genes through genomic duplication and resulting in a genome with an unusually low proportion of closely related genes.
Collapse
Affiliation(s)
- James E Galagan
- Whitehead Institute Center for Genome Research, 320 Charles Street, Cambridge, Massachusetts 02141, USA.
| | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | |
Collapse
|