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Birker K, Ge S, Kirkland NJ, Theis JL, Marchant J, Fogarty ZC, Missinato MA, Kalvakuri S, Grossfeld P, Engler AJ, Ocorr K, Nelson TJ, Colas AR, Olson TM, Vogler G, Bodmer R. Mitochondrial MICOS complex genes, implicated in hypoplastic left heart syndrome, maintain cardiac contractility and actomyosin integrity. eLife 2023; 12:e83385. [PMID: 37404133 PMCID: PMC10361721 DOI: 10.7554/elife.83385] [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] [Grants] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/14/2022] [Accepted: 07/04/2023] [Indexed: 07/06/2023] Open
Abstract
Hypoplastic left heart syndrome (HLHS) is a severe congenital heart disease (CHD) with a likely oligogenic etiology, but our understanding of the genetic complexities and pathogenic mechanisms leading to HLHS is limited. We therefore performed whole genome sequencing (WGS) on a large cohort of HLHS patients and their families to identify candidate genes that were then tested in Drosophila heart model for functional and structural requirements. Bioinformatic analysis of WGS data from an index family comprised of a HLHS proband born to consanguineous parents and postulated to have a homozygous recessive disease etiology, prioritized 9 candidate genes with rare, predicted damaging homozygous variants. Of the candidate HLHS gene homologs tested, cardiac-specific knockdown (KD) of mitochondrial MICOS complex subunit Chchd3/6 resulted in drastically compromised heart contractility, diminished levels of sarcomeric actin and myosin, reduced cardiac ATP levels, and mitochondrial fission-fusion defects. Interestingly, these heart defects were similar to those inflicted by cardiac KD of ATP synthase subunits of the electron transport chain (ETC), consistent with the MICOS complex's role in maintaining cristae morphology and ETC complex assembly. Analysis of 183 genomes of HLHS patient-parent trios revealed five additional HLHS probands with rare, predicted damaging variants in CHCHD3 or CHCHD6. Hypothesizing an oligogenic basis for HLHS, we tested 60 additional prioritized candidate genes in these cases for genetic interactions with Chchd3/6 in sensitized fly hearts. Moderate KD of Chchd3/6 in combination with Cdk12 (activator of RNA polymerase II), RNF149 (goliath, gol, E3 ubiquitin ligase), or SPTBN1 (β Spectrin, β-Spec, scaffolding protein) caused synergistic heart defects, suggesting the potential involvement of a diverse set of pathways in HLHS. Further elucidation of novel candidate genes and genetic interactions of potentially disease-contributing pathways is expected to lead to a better understanding of HLHS and other CHDs.
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Affiliation(s)
- Katja Birker
- Development, Aging and Regeneration Program, Sanford Burnham Prebys Medical Discovery Institute, La Jolla, United States
| | - Shuchao Ge
- Development, Aging and Regeneration Program, Sanford Burnham Prebys Medical Discovery Institute, La Jolla, United States
| | - Natalie J Kirkland
- Department of Bioengineering, University of California, San Diego, San Diego, United States
| | - Jeanne L Theis
- Cardiovascular Genetics Research Laboratory, Mayo Clinic, Rochester, United States
| | - James Marchant
- Development, Aging and Regeneration Program, Sanford Burnham Prebys Medical Discovery Institute, La Jolla, United States
| | - Zachary C Fogarty
- Department of Quantitative Health Sciences, Mayo Clinic, Rochester, United States
| | - Maria A Missinato
- Development, Aging and Regeneration Program, Sanford Burnham Prebys Medical Discovery Institute, La Jolla, United States
| | - Sreehari Kalvakuri
- Development, Aging and Regeneration Program, Sanford Burnham Prebys Medical Discovery Institute, La Jolla, United States
| | - Paul Grossfeld
- Department of Pediatrics, University of California, San Diego, San Diego, United States
| | - Adam J Engler
- Department of Bioengineering, University of California, San Diego, San Diego, United States
| | - Karen Ocorr
- Development, Aging and Regeneration Program, Sanford Burnham Prebys Medical Discovery Institute, La Jolla, United States
| | - Timothy J Nelson
- Center for Regenerative Medicine, Mayo Clinic, Rochester, United States
| | - Alexandre R Colas
- Development, Aging and Regeneration Program, Sanford Burnham Prebys Medical Discovery Institute, La Jolla, United States
| | - Timothy M Olson
- Department of Cardiovascular Medicine, Mayo Clinic, Rochester, United States
| | - Georg Vogler
- Development, Aging and Regeneration Program, Sanford Burnham Prebys Medical Discovery Institute, La Jolla, United States
| | - Rolf Bodmer
- Development, Aging and Regeneration Program, Sanford Burnham Prebys Medical Discovery Institute, La Jolla, United States
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2
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Pineda S, Nikolova-Krstevski V, Leimena C, Atkinson AJ, Altekoester AK, Cox CD, Jacoby A, Huttner IG, Ju YK, Soka M, Ohanian M, Trivedi G, Kalvakuri S, Birker K, Johnson R, Molenaar P, Kuchar D, Allen DG, van Helden DF, Harvey RP, Hill AP, Bodmer R, Vogler G, Dobrzynski H, Ocorr K, Fatkin D. Conserved Role of the Large Conductance Calcium-Activated Potassium Channel, K Ca1.1, in Sinus Node Function and Arrhythmia Risk. Circ Genom Precis Med 2021; 14:e003144. [PMID: 33629867 DOI: 10.1161/circgen.120.003144] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
Abstract
BACKGROUND KCNMA1 encodes the α-subunit of the large-conductance Ca2+-activated K+ channel, KCa1.1, and lies within a linkage interval for atrial fibrillation (AF). Insights into the cardiac functions of KCa1.1 are limited, and KCNMA1 has not been investigated as an AF candidate gene. METHODS The KCNMA1 gene was sequenced in 118 patients with familial AF. The role of KCa1.1 in normal cardiac structure and function was evaluated in humans, mice, zebrafish, and fly. A novel KCNMA1 variant was functionally characterized. RESULTS A complex KCNMA1 variant was identified in 1 kindred with AF. To evaluate potential disease mechanisms, we first evaluated the distribution of KCa1.1 in normal hearts using immunostaining and immunogold electron microscopy. KCa1.1 was seen throughout the atria and ventricles in humans and mice, with strong expression in the sinus node. In an ex vivo murine sinoatrial node preparation, addition of the KCa1.1 antagonist, paxilline, blunted the increase in beating rate induced by adrenergic receptor stimulation. Knockdown of the KCa1.1 ortholog, kcnma1b, in zebrafish embryos resulted in sinus bradycardia with dilatation and reduced contraction of the atrium and ventricle. Genetic inactivation of the Drosophila KCa1.1 ortholog, slo, systemically or in adult stages, also slowed the heartbeat and produced fibrillatory cardiac contractions. Electrophysiological characterization of slo-deficient flies revealed bursts of action potentials, reflecting increased events of fibrillatory arrhythmias. Flies with cardiac-specific overexpression of the human KCNMA1 mutant also showed increased heart period and bursts of action potentials, similar to the KCa1.1 loss-of-function models. CONCLUSIONS Our data point to a highly conserved role of KCa1.1 in sinus node function in humans, mice, zebrafish, and fly and suggest that KCa1.1 loss of function may predispose to AF.
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Affiliation(s)
- Santiago Pineda
- Development, Aging & Regeneration Program, Sanford-Burnham Prebys Medical Discovery Institute, La Jolla, CA (S.P., S.K., K.B., R.B., G.V., K.O.)
| | - Vesna Nikolova-Krstevski
- Victor Chang Cardiac Research Institute, Darlinghurst (V.N.-K., C.L., A.-K.A., C.D.C., A.J., I.G.H., M.S., M.O., G.T., R.J., R.P.H., A.P.H., D.F.).,Faculty of Medicine, UNSW Sydney, Kensington (V.N.-K., I.G.H., R.J., R.P.H., A.P.H., D.F.)
| | - Christiana Leimena
- Victor Chang Cardiac Research Institute, Darlinghurst (V.N.-K., C.L., A.-K.A., C.D.C., A.J., I.G.H., M.S., M.O., G.T., R.J., R.P.H., A.P.H., D.F.)
| | - Andrew J Atkinson
- Institute of Cardiovascular Sciences, University of Manchester, United Kingdom (A.J.A., H.D.)
| | - Ann-Kristin Altekoester
- Victor Chang Cardiac Research Institute, Darlinghurst (V.N.-K., C.L., A.-K.A., C.D.C., A.J., I.G.H., M.S., M.O., G.T., R.J., R.P.H., A.P.H., D.F.)
| | - Charles D Cox
- Victor Chang Cardiac Research Institute, Darlinghurst (V.N.-K., C.L., A.-K.A., C.D.C., A.J., I.G.H., M.S., M.O., G.T., R.J., R.P.H., A.P.H., D.F.)
| | - Arie Jacoby
- Victor Chang Cardiac Research Institute, Darlinghurst (V.N.-K., C.L., A.-K.A., C.D.C., A.J., I.G.H., M.S., M.O., G.T., R.J., R.P.H., A.P.H., D.F.)
| | - Inken G Huttner
- Victor Chang Cardiac Research Institute, Darlinghurst (V.N.-K., C.L., A.-K.A., C.D.C., A.J., I.G.H., M.S., M.O., G.T., R.J., R.P.H., A.P.H., D.F.).,Faculty of Medicine, UNSW Sydney, Kensington (V.N.-K., I.G.H., R.J., R.P.H., A.P.H., D.F.)
| | - Yue-Kun Ju
- Bosch Institute, University of Sydney, Camperdown (Y.-K.J., D.G.A.)
| | - Magdalena Soka
- Victor Chang Cardiac Research Institute, Darlinghurst (V.N.-K., C.L., A.-K.A., C.D.C., A.J., I.G.H., M.S., M.O., G.T., R.J., R.P.H., A.P.H., D.F.)
| | - Monique Ohanian
- Victor Chang Cardiac Research Institute, Darlinghurst (V.N.-K., C.L., A.-K.A., C.D.C., A.J., I.G.H., M.S., M.O., G.T., R.J., R.P.H., A.P.H., D.F.)
| | - Gunjan Trivedi
- Victor Chang Cardiac Research Institute, Darlinghurst (V.N.-K., C.L., A.-K.A., C.D.C., A.J., I.G.H., M.S., M.O., G.T., R.J., R.P.H., A.P.H., D.F.)
| | - Sreehari Kalvakuri
- Development, Aging & Regeneration Program, Sanford-Burnham Prebys Medical Discovery Institute, La Jolla, CA (S.P., S.K., K.B., R.B., G.V., K.O.)
| | - Katja Birker
- Development, Aging & Regeneration Program, Sanford-Burnham Prebys Medical Discovery Institute, La Jolla, CA (S.P., S.K., K.B., R.B., G.V., K.O.)
| | - Renee Johnson
- Victor Chang Cardiac Research Institute, Darlinghurst (V.N.-K., C.L., A.-K.A., C.D.C., A.J., I.G.H., M.S., M.O., G.T., R.J., R.P.H., A.P.H., D.F.).,Faculty of Medicine, UNSW Sydney, Kensington (V.N.-K., I.G.H., R.J., R.P.H., A.P.H., D.F.)
| | - Peter Molenaar
- Faculty of Health, Queensland University of Technology (P.M.).,School of Medicine, University of Queensland, Prince Charles Hospital, Brisbane, Queensland, Australia (P.M.)
| | - Dennis Kuchar
- Cardiology Department, St Vincent's Hospital, Darlinghurst (D.K., D.F.)
| | - David G Allen
- Bosch Institute, University of Sydney, Camperdown (Y.-K.J., D.G.A.)
| | - Dirk F van Helden
- University of Newcastle and Hunter Medical Research Institute, NSW, Australia (D.F.v.H.)
| | - Richard P Harvey
- Victor Chang Cardiac Research Institute, Darlinghurst (V.N.-K., C.L., A.-K.A., C.D.C., A.J., I.G.H., M.S., M.O., G.T., R.J., R.P.H., A.P.H., D.F.).,Faculty of Medicine, UNSW Sydney, Kensington (V.N.-K., I.G.H., R.J., R.P.H., A.P.H., D.F.)
| | - Adam P Hill
- Victor Chang Cardiac Research Institute, Darlinghurst (V.N.-K., C.L., A.-K.A., C.D.C., A.J., I.G.H., M.S., M.O., G.T., R.J., R.P.H., A.P.H., D.F.).,Faculty of Medicine, UNSW Sydney, Kensington (V.N.-K., I.G.H., R.J., R.P.H., A.P.H., D.F.)
| | - Rolf Bodmer
- Development, Aging & Regeneration Program, Sanford-Burnham Prebys Medical Discovery Institute, La Jolla, CA (S.P., S.K., K.B., R.B., G.V., K.O.)
| | - Georg Vogler
- Development, Aging & Regeneration Program, Sanford-Burnham Prebys Medical Discovery Institute, La Jolla, CA (S.P., S.K., K.B., R.B., G.V., K.O.)
| | - Halina Dobrzynski
- Institute of Cardiovascular Sciences, University of Manchester, United Kingdom (A.J.A., H.D.).,Jagiellonian University Medical College, Cracow, Poland (H.D.)
| | - Karen Ocorr
- Development, Aging & Regeneration Program, Sanford-Burnham Prebys Medical Discovery Institute, La Jolla, CA (S.P., S.K., K.B., R.B., G.V., K.O.)
| | - Diane Fatkin
- Victor Chang Cardiac Research Institute, Darlinghurst (V.N.-K., C.L., A.-K.A., C.D.C., A.J., I.G.H., M.S., M.O., G.T., R.J., R.P.H., A.P.H., D.F.).,Faculty of Medicine, UNSW Sydney, Kensington (V.N.-K., I.G.H., R.J., R.P.H., A.P.H., D.F.).,Cardiology Department, St Vincent's Hospital, Darlinghurst (D.K., D.F.)
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3
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Walls S, Diop S, Birse R, Elmen L, Gan Z, Kalvakuri S, Pineda S, Reddy C, Taylor E, Trinh B, Vogler G, Zarndt R, McCulloch A, Lee P, Bhattacharya S, Bodmer R, Ocorr K. Prolonged Exposure to Microgravity Reduces Cardiac Contractility and Initiates Remodeling in Drosophila. Cell Rep 2020; 33:108445. [PMID: 33242407 PMCID: PMC7787258 DOI: 10.1016/j.celrep.2020.108445] [Citation(s) in RCA: 19] [Impact Index Per Article: 4.8] [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: 07/30/2020] [Revised: 11/01/2020] [Accepted: 11/06/2020] [Indexed: 01/08/2023] Open
Abstract
Understanding the effects of microgravity on human organs is crucial to exploration of low-earth orbit, the moon, and beyond. Drosophila can be sent to space in large numbers to examine the effects of microgravity on heart structure and function, which is fundamentally conserved from flies to humans. Flies reared in microgravity exhibit cardiac constriction with myofibrillar remodeling and diminished output. RNA sequencing (RNA-seq) in isolated hearts revealed reduced expression of sarcomeric/extracellular matrix (ECM) genes and dramatically increased proteasomal gene expression, consistent with the observed compromised, smaller hearts and suggesting abnormal proteostasis. This was examined further on a second flight in which we found dramatically elevated proteasome aggregates co-localizing with increased amyloid and polyQ deposits. Remarkably, in long-QT causing sei/hERG mutants, proteasomal gene expression at 1g, although less than the wild-type expression, was nevertheless increased in microgravity. Therefore, cardiac remodeling and proteostatic stress may be a fundamental response of heart muscle to microgravity.
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Affiliation(s)
- Stanley Walls
- Development, Aging & Regeneration Program, Sanford Burnham Prebys Medical Discovery Institute, 10901 N. Torrey Pines Rd., La Jolla, CA 92037, USA
| | - Soda Diop
- Development, Aging & Regeneration Program, Sanford Burnham Prebys Medical Discovery Institute, 10901 N. Torrey Pines Rd., La Jolla, CA 92037, USA
| | - Ryan Birse
- Development, Aging & Regeneration Program, Sanford Burnham Prebys Medical Discovery Institute, 10901 N. Torrey Pines Rd., La Jolla, CA 92037, USA
| | - Lisa Elmen
- Development, Aging & Regeneration Program, Sanford Burnham Prebys Medical Discovery Institute, 10901 N. Torrey Pines Rd., La Jolla, CA 92037, USA
| | - Zhuohui Gan
- Department of Bioengineering, University of California, San Diego, 9500 Gilman Drive, La Jolla, CA 92093, USA
| | - Sreehari Kalvakuri
- Development, Aging & Regeneration Program, Sanford Burnham Prebys Medical Discovery Institute, 10901 N. Torrey Pines Rd., La Jolla, CA 92037, USA
| | - Santiago Pineda
- Development, Aging & Regeneration Program, Sanford Burnham Prebys Medical Discovery Institute, 10901 N. Torrey Pines Rd., La Jolla, CA 92037, USA
| | - Curran Reddy
- Space Biosciences Division, NASA Ames Research Center, Mailstop 236-5, Moffett Field, CA 94035, USA
| | - Erika Taylor
- Development, Aging & Regeneration Program, Sanford Burnham Prebys Medical Discovery Institute, 10901 N. Torrey Pines Rd., La Jolla, CA 92037, USA
| | - Bosco Trinh
- Development, Aging & Regeneration Program, Sanford Burnham Prebys Medical Discovery Institute, 10901 N. Torrey Pines Rd., La Jolla, CA 92037, USA
| | - Georg Vogler
- Development, Aging & Regeneration Program, Sanford Burnham Prebys Medical Discovery Institute, 10901 N. Torrey Pines Rd., La Jolla, CA 92037, USA
| | - Rachel Zarndt
- Development, Aging & Regeneration Program, Sanford Burnham Prebys Medical Discovery Institute, 10901 N. Torrey Pines Rd., La Jolla, CA 92037, USA
| | - Andrew McCulloch
- Department of Bioengineering, University of California, San Diego, 9500 Gilman Drive, La Jolla, CA 92093, USA
| | - Peter Lee
- Department of Pathology and Laboratory Medicine, Brown University, 69 Brown Street, Providence, RI 02912, USA
| | - Sharmila Bhattacharya
- Space Biosciences Division, NASA Ames Research Center, Mailstop 236-5, Moffett Field, CA 94035, USA
| | - Rolf Bodmer
- Development, Aging & Regeneration Program, Sanford Burnham Prebys Medical Discovery Institute, 10901 N. Torrey Pines Rd., La Jolla, CA 92037, USA.
| | - Karen Ocorr
- Development, Aging & Regeneration Program, Sanford Burnham Prebys Medical Discovery Institute, 10901 N. Torrey Pines Rd., La Jolla, CA 92037, USA.
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4
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Elmén L, Volpato CB, Kervadec A, Pineda S, Kalvakuri S, Alayari NN, Foco L, Pramstaller PP, Ocorr K, Rossini A, Cammarato A, Colas AR, Hicks AA, Bodmer R. Silencing of CCR4-NOT complex subunits affects heart structure and function. Dis Model Mech 2020; 13:dmm044727. [PMID: 32471864 PMCID: PMC7390626 DOI: 10.1242/dmm.044727] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/28/2020] [Accepted: 05/19/2020] [Indexed: 12/12/2022] Open
Abstract
The identification of genetic variants that predispose individuals to cardiovascular disease and a better understanding of their targets would be highly advantageous. Genome-wide association studies have identified variants that associate with QT-interval length (a measure of myocardial repolarization). Three of the strongest associating variants (single-nucleotide polymorphisms) are located in the putative promotor region of CNOT1, a gene encoding the central CNOT1 subunit of CCR4-NOT: a multifunctional, conserved complex regulating gene expression and mRNA stability and turnover. We isolated the minimum fragment of the CNOT1 promoter containing all three variants from individuals homozygous for the QT risk alleles and demonstrated that the haplotype associating with longer QT interval caused reduced reporter expression in a cardiac cell line, suggesting that reduced CNOT1 expression might contribute to abnormal QT intervals. Systematic siRNA-mediated knockdown of CCR4-NOT components in human induced pluripotent stem cell-derived cardiomyocytes (hiPSC-CMs) revealed that silencing CNOT1 and other CCR4-NOT genes reduced their proliferative capacity. Silencing CNOT7 also shortened action potential duration. Furthermore, the cardiac-specific knockdown of Drosophila orthologs of CCR4-NOT genes in vivo (CNOT1/Not1 and CNOT7/8/Pop2) was either lethal or resulted in dilated cardiomyopathy, reduced contractility or a propensity for arrhythmia. Silencing CNOT2/Not2, CNOT4/Not4 and CNOT6/6L/twin also affected cardiac chamber size and contractility. Developmental studies suggested that CNOT1/Not1 and CNOT7/8/Pop2 are required during cardiac remodeling from larval to adult stages. To summarize, we have demonstrated how disease-associated genes identified by GWAS can be investigated by combining human cardiomyocyte cell-based and whole-organism in vivo heart models. Our results also suggest a potential link of CNOT1 and CNOT7/8 to QT alterations and further establish a crucial role of the CCR4-NOT complex in heart development and function.This article has an associated First Person interview with the first author of the paper.
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Affiliation(s)
- Lisa Elmén
- Development Aging and Regeneration Program, Sanford Burnham Prebys Medical Discovery Institute, 10901 N Torrey Pines Rd, La Jolla, CA 92037, USA
| | - Claudia B Volpato
- Institute for Biomedicine, Eurac Research, Affiliated Institute of the University of Lübeck, Via Galvani 31, 39100 Bolzano, Italy
| | - Anaïs Kervadec
- Development Aging and Regeneration Program, Sanford Burnham Prebys Medical Discovery Institute, 10901 N Torrey Pines Rd, La Jolla, CA 92037, USA
| | - Santiago Pineda
- Development Aging and Regeneration Program, Sanford Burnham Prebys Medical Discovery Institute, 10901 N Torrey Pines Rd, La Jolla, CA 92037, USA
| | - Sreehari Kalvakuri
- Development Aging and Regeneration Program, Sanford Burnham Prebys Medical Discovery Institute, 10901 N Torrey Pines Rd, La Jolla, CA 92037, USA
| | - Nakissa N Alayari
- Development Aging and Regeneration Program, Sanford Burnham Prebys Medical Discovery Institute, 10901 N Torrey Pines Rd, La Jolla, CA 92037, USA
| | - Luisa Foco
- Institute for Biomedicine, Eurac Research, Affiliated Institute of the University of Lübeck, Via Galvani 31, 39100 Bolzano, Italy
| | - Peter P Pramstaller
- Institute for Biomedicine, Eurac Research, Affiliated Institute of the University of Lübeck, Via Galvani 31, 39100 Bolzano, Italy
| | - Karen Ocorr
- Development Aging and Regeneration Program, Sanford Burnham Prebys Medical Discovery Institute, 10901 N Torrey Pines Rd, La Jolla, CA 92037, USA
| | - Alessandra Rossini
- Institute for Biomedicine, Eurac Research, Affiliated Institute of the University of Lübeck, Via Galvani 31, 39100 Bolzano, Italy
| | - Anthony Cammarato
- Johns Hopkins University, Division of Cardiology, 720 Rutland Ave., Baltimore, MD 21205, USA
| | - Alexandre R Colas
- Development Aging and Regeneration Program, Sanford Burnham Prebys Medical Discovery Institute, 10901 N Torrey Pines Rd, La Jolla, CA 92037, USA
| | - Andrew A Hicks
- Institute for Biomedicine, Eurac Research, Affiliated Institute of the University of Lübeck, Via Galvani 31, 39100 Bolzano, Italy
| | - Rolf Bodmer
- Development Aging and Regeneration Program, Sanford Burnham Prebys Medical Discovery Institute, 10901 N Torrey Pines Rd, La Jolla, CA 92037, USA
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5
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Vissers LE, Kalvakuri S, de Boer E, Geuer S, Oud M, van Outersterp I, Kwint M, Witmond M, Kersten S, Polla DL, Weijers D, Begtrup A, McWalter K, Ruiz A, Gabau E, Morton JE, Griffith C, Weiss K, Gamble C, Bartley J, Vernon HJ, Brunet K, Ruivenkamp C, Kant SG, Kruszka P, Larson A, Afenjar A, Billette de Villemeur T, Nugent K, Raymond FL, Venselaar H, Demurger F, Soler-Alfonso C, Li D, Bhoj E, Hayes I, Hamilton NP, Ahmad A, Fisher R, van den Born M, Willems M, Sorlin A, Delanne J, Moutton S, Christophe P, Mau-Them FT, Vitobello A, Goel H, Massingham L, Phornphutkul C, Schwab J, Keren B, Charles P, Vreeburg M, De Simone L, Hoganson G, Iascone M, Milani D, Evenepoel L, Revencu N, Ward DI, Burns K, Krantz I, Raible SE, Murrell JR, Wood K, Cho MT, van Bokhoven H, Muenke M, Kleefstra T, Bodmer R, de Brouwer AP, de Brouwer APM. De Novo Variants in CNOT1, a Central Component of the CCR4-NOT Complex Involved in Gene Expression and RNA and Protein Stability, Cause Neurodevelopmental Delay. Am J Hum Genet 2020; 107:164-172. [PMID: 32553196 DOI: 10.1016/j.ajhg.2020.05.017] [Citation(s) in RCA: 26] [Impact Index Per Article: 6.5] [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: 04/09/2020] [Accepted: 05/26/2020] [Indexed: 11/27/2022] Open
Abstract
CNOT1 is a member of the CCR4-NOT complex, which is a master regulator, orchestrating gene expression, RNA deadenylation, and protein ubiquitination. We report on 39 individuals with heterozygous de novo CNOT1 variants, including missense, splice site, and nonsense variants, who present with a clinical spectrum of intellectual disability, motor delay, speech delay, seizures, hypotonia, and behavioral problems. To link CNOT1 dysfunction to the neurodevelopmental phenotype observed, we generated variant-specific Drosophila models, which showed learning and memory defects upon CNOT1 knockdown. Introduction of human wild-type CNOT1 was able to rescue this phenotype, whereas mutants could not or only partially, supporting our hypothesis that CNOT1 impairment results in neurodevelopmental delay. Furthermore, the genetic interaction with autism-spectrum genes, such as ASH1L, DYRK1A, MED13, and SHANK3, was impaired in our Drosophila models. Molecular characterization of CNOT1 variants revealed normal CNOT1 expression levels, with both mutant and wild-type alleles expressed at similar levels. Analysis of protein-protein interactions with other members indicated that the CCR4-NOT complex remained intact. An integrated omics approach of patient-derived genomics and transcriptomics data suggested only minimal effects on endonucleolytic nonsense-mediated mRNA decay components, suggesting that de novo CNOT1 variants are likely haploinsufficient hypomorph or neomorph, rather than dominant negative. In summary, we provide strong evidence that de novo CNOT1 variants cause neurodevelopmental delay with a wide range of additional co-morbidities. Whereas the underlying pathophysiological mechanism warrants further analysis, our data demonstrate an essential and central role of the CCR4-NOT complex in human brain development.
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Affiliation(s)
| | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | - Arjan P M de Brouwer
- Department of Human Genetics, Donders Institute for Brain, Cognition and Behaviour, Radboud University Medical Center, PO Box 9101, 6500 HB Nijmegen, the Netherlands
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6
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Zanon A, Kalvakuri S, Rakovic A, Foco L, Guida M, Schwienbacher C, Serafin A, Rudolph F, Trilck M, Grünewald A, Stanslowsky N, Wegner F, Giorgio V, Lavdas AA, Bodmer R, Pramstaller PP, Klein C, Hicks AA, Pichler I, Philip S. Corrigendum: SLP-2 interacts with Parkin in mitochondria and prevents mitochondrial dysfunction in Parkin-deficient human iPSC-derived neurons and Drosophila. Hum Mol Genet 2018; 28:1225. [PMID: 30517638 DOI: 10.1093/hmg/ddy408] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022] Open
Affiliation(s)
- Alessandra Zanon
- Institute for Biomedicine, Eurac Research, Affiliated Institute of the University of Lübeck, Bolzano, Italy
| | - Sreehari Kalvakuri
- Development, Aging and Regeneration Program, Sanford Burnham Prebys Medical Discovery Institute, La Jolla, CA, USA
| | | | - Luisa Foco
- Institute for Biomedicine, Eurac Research, Affiliated Institute of the University of Lübeck, Bolzano, Italy
| | - Marianna Guida
- Institute for Biomedicine, Eurac Research, Affiliated Institute of the University of Lübeck, Bolzano, Italy
| | - Christine Schwienbacher
- Institute for Biomedicine, Eurac Research, Affiliated Institute of the University of Lübeck, Bolzano, Italy
| | - Alice Serafin
- Institute for Biomedicine, Eurac Research, Affiliated Institute of the University of Lübeck, Bolzano, Italy
| | | | - Michaela Trilck
- Institute of Neurogenetics, University of Lübeck, Lübeck, Germany
| | - Anne Grünewald
- Institute of Neurogenetics, University of Lübeck, Lübeck, Germany.,Molecular and Functional Neurobiology Group, Luxembourg Centre for Systems Biomedicine, University of Luxembourg, Belvaux, Luxembourg
| | | | - Florian Wegner
- Department of Neurology, Hannover Medical School, Hannover, Germany
| | | | - Alexandros A Lavdas
- Institute for Biomedicine, Eurac Research, Affiliated Institute of the University of Lübeck, Bolzano, Italy
| | - Rolf Bodmer
- Development, Aging and Regeneration Program, Sanford Burnham Prebys Medical Discovery Institute, La Jolla, CA, USA
| | - Peter P Pramstaller
- Institute for Biomedicine, Eurac Research, Affiliated Institute of the University of Lübeck, Bolzano, Italy.,Department of Neurology, General Central Hospital, Bolzano, Italy.,Department of Neurology, University of Lübeck, Lübeck, Germany
| | - Christine Klein
- Institute of Neurogenetics, University of Lübeck, Lübeck, Germany
| | - Andrew A Hicks
- Institute for Biomedicine, Eurac Research, Affiliated Institute of the University of Lübeck, Bolzano, Italy
| | - Irene Pichler
- Institute for Biomedicine, Eurac Research, Affiliated Institute of the University of Lübeck, Bolzano, Italy
| | - Seibler Philip
- Institute of Neurogenetics, University of Lübeck, Lübeck, Germany
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7
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Zanon A, Kalvakuri S, Rakovic A, Foco L, Guida M, Schwienbacher C, Serafin A, Rudolph F, Trilck M, Grünewald A, Stanslowsky N, Wegner F, Giorgio V, Lavdas AA, Bodmer R, Pramstaller PP, Klein C, Hicks AA, Pichler I, Seibler P. SLP-2 interacts with Parkin in mitochondria and prevents mitochondrial dysfunction in Parkin-deficient human iPSC-derived neurons and Drosophila. Hum Mol Genet 2017; 26:2412-2425. [PMID: 28379402 DOI: 10.1093/hmg/ddx132] [Citation(s) in RCA: 41] [Impact Index Per Article: 5.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/16/2016] [Accepted: 03/16/2017] [Indexed: 12/26/2022] Open
Abstract
Mutations in the Parkin gene (PARK2) have been linked to a recessive form of Parkinson's disease (PD) characterized by the loss of dopaminergic neurons in the substantia nigra. Deficiencies of mitochondrial respiratory chain complex I activity have been observed in the substantia nigra of PD patients, and loss of Parkin results in the reduction of complex I activity shown in various cell and animal models. Using co-immunoprecipitation and proximity ligation assays on endogenous proteins, we demonstrate that Parkin interacts with mitochondrial Stomatin-like protein 2 (SLP-2), which also binds the mitochondrial lipid cardiolipin and functions in the assembly of respiratory chain proteins. SH-SY5Y cells with a stable knockdown of Parkin or SLP-2, as well as induced pluripotent stem cell-derived neurons from Parkin mutation carriers, showed decreased complex I activity and altered mitochondrial network morphology. Importantly, induced expression of SLP-2 corrected for these mitochondrial alterations caused by reduced Parkin function in these cells. In-vivo Drosophila studies showed a genetic interaction of Parkin and SLP-2, and further, tissue-specific or global overexpression of SLP-2 transgenes rescued parkin mutant phenotypes, in particular loss of dopaminergic neurons, mitochondrial network structure, reduced ATP production, and flight and motor dysfunction. The physical and genetic interaction between Parkin and SLP-2 and the compensatory potential of SLP-2 suggest a functional epistatic relationship to Parkin and a protective role of SLP-2 in neurons. This finding places further emphasis on the significance of Parkin for the maintenance of mitochondrial function in neurons and provides a novel target for therapeutic strategies.
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Affiliation(s)
- Alessandra Zanon
- Institute for Biomedicine, Eurac Research, Affiliated Institute of the University of Lübeck, 39100 Bolzano, Italy
| | - Sreehari Kalvakuri
- Development, Aging and Regeneration Program, Sanford Burnham Prebys Medical Discovery Institute, La Jolla, CA 92037, USA
| | | | - Luisa Foco
- Institute for Biomedicine, Eurac Research, Affiliated Institute of the University of Lübeck, 39100 Bolzano, Italy
| | - Marianna Guida
- Institute for Biomedicine, Eurac Research, Affiliated Institute of the University of Lübeck, 39100 Bolzano, Italy
| | - Christine Schwienbacher
- Institute for Biomedicine, Eurac Research, Affiliated Institute of the University of Lübeck, 39100 Bolzano, Italy
| | - Alice Serafin
- Institute for Biomedicine, Eurac Research, Affiliated Institute of the University of Lübeck, 39100 Bolzano, Italy
| | - Franziska Rudolph
- Institute of Neurogenetics, University of Lübeck, 23562 Lübeck, Germany
| | - Michaela Trilck
- Institute of Neurogenetics, University of Lübeck, 23562 Lübeck, Germany
| | - Anne Grünewald
- Institute of Neurogenetics, University of Lübeck, 23562 Lübeck, Germany.,Molecular and Functional Neurobiology Group, Luxembourg Centre for Systems Biomedicine, University of Luxembourg, L-4367 Belvaux, Luxembourg
| | - Nancy Stanslowsky
- Department of Neurology, Hannover Medical School, 30625 Hannover, Germany
| | - Florian Wegner
- Department of Neurology, Hannover Medical School, 30625 Hannover, Germany
| | | | - Alexandros A Lavdas
- Institute for Biomedicine, Eurac Research, Affiliated Institute of the University of Lübeck, 39100 Bolzano, Italy
| | - Rolf Bodmer
- Development, Aging and Regeneration Program, Sanford Burnham Prebys Medical Discovery Institute, La Jolla, CA 92037, USA
| | - Peter P Pramstaller
- Institute for Biomedicine, Eurac Research, Affiliated Institute of the University of Lübeck, 39100 Bolzano, Italy.,Department of Neurology, General Central Hospital, 39100 Bolzano, Italy.,Department of Neurology, University of Lübeck, 23562 Lübeck, Germany
| | - Christine Klein
- Institute of Neurogenetics, University of Lübeck, 23562 Lübeck, Germany
| | - Andrew A Hicks
- Institute for Biomedicine, Eurac Research, Affiliated Institute of the University of Lübeck, 39100 Bolzano, Italy
| | - Irene Pichler
- Institute for Biomedicine, Eurac Research, Affiliated Institute of the University of Lübeck, 39100 Bolzano, Italy
| | - Philip Seibler
- Institute of Neurogenetics, University of Lübeck, 23562 Lübeck, Germany
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8
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Sen A, Kalvakuri S, Bodmer R, Cox RT. Clueless, a protein required for mitochondrial function, interacts with the PINK1-Parkin complex in Drosophila. Dis Model Mech 2015; 8:577-89. [PMID: 26035866 PMCID: PMC4457034 DOI: 10.1242/dmm.019208] [Citation(s) in RCA: 29] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/17/2014] [Accepted: 04/03/2015] [Indexed: 01/22/2023] Open
Abstract
Loss of mitochondrial function often leads to neurodegeneration and is thought to be one of the underlying causes of neurodegenerative diseases such as Parkinson's disease (PD). However, the precise events linking mitochondrial dysfunction to neuronal death remain elusive. PTEN-induced putative kinase 1 (PINK1) and Parkin (Park), either of which, when mutated, are responsible for early-onset PD, mark individual mitochondria for destruction at the mitochondrial outer membrane. The specific molecular pathways that regulate signaling between the nucleus and mitochondria to sense mitochondrial dysfunction under normal physiological conditions are not well understood. Here, we show that Drosophila Clueless (Clu), a highly conserved protein required for normal mitochondrial function, can associate with Translocase of the outer membrane (TOM) 20, Porin and PINK1, and is thus located at the mitochondrial outer membrane. Previously, we found that clu genetically interacts with park in Drosophila female germ cells. Here, we show that clu also genetically interacts with PINK1, and our epistasis analysis places clu downstream of PINK1 and upstream of park. In addition, Clu forms a complex with PINK1 and Park, further supporting that Clu links mitochondrial function with the PINK1-Park pathway. Lack of Clu causes PINK1 and Park to interact with each other, and clu mutants have decreased mitochondrial protein levels, suggesting that Clu can act as a negative regulator of the PINK1-Park pathway. Taken together, these results suggest that Clu directly modulates mitochondrial function, and that Clu's function contributes to the PINK1-Park pathway of mitochondrial quality control. Summary: The protein Clueless is crucial for mitochondrial function and can interact genetically and physically with the PINK1-Parkin mitophagy complex.
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Affiliation(s)
- Aditya Sen
- Department of Biochemistry and Molecular Biology, 4301 Jones Bridge Road, Uniformed Services University, Bethesda, MD 20814, USA
| | - Sreehari Kalvakuri
- Sanford-Burnham Medical Research Institute, 10901 North Torrey Pines Road, La Jolla, CA 92037, USA
| | - Rolf Bodmer
- Sanford-Burnham Medical Research Institute, 10901 North Torrey Pines Road, La Jolla, CA 92037, USA
| | - Rachel T Cox
- Department of Biochemistry and Molecular Biology, 4301 Jones Bridge Road, Uniformed Services University, Bethesda, MD 20814, USA
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9
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Abstract
Neddylation is a posttranslational modification that plays important roles in regulating protein structure and function by covalently conjugating NEDD8, an ubiquitin-like small molecule, to the substrate. Here, we report that Parkinson's disease (PD)-related parkin and PINK1 are NEDD8 conjugated. Neddylation of parkin and PINK1 results in increased E3 ligase activity of parkin and selective stabilization of the 55 kDa PINK1 fragment. Expression of dAPP-BP1, a NEDD8 activation enzyme subunit, in Drosophila suppresses abnormalities induced by dPINK1 RNAi. PD neurotoxin MPP(+) inhibits neddylation of both parkin and PINK1. NEDD8 immunoreactivity is associated with Lewy bodies in midbrain dopaminergic neurons of PD patients. Together, these results suggest that parkin and PINK1 are regulated by neddylation and that impaired NEDD8 modification of these proteins likely contributes to PD pathogenesis.
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Affiliation(s)
- Yeun Su Choo
- Sanford-Burnham Medical Research Institute, 10901 N. Torrey Pines Road, La Jolla, CA 92037, USA
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