Biallelic variants in LIG3 cause a novel mitochondrial neurogastrointestinal encephalomyopathy

  • Brain. 2021 Jun 22;144(5):1451-1466. doi: 10.1093/brain/awab056.
Elena Bonora  1 ,  Sanjiban Chakrabarty  2 ,  Georgios Kellaris  3 ,  Makiko Tsutsumi  4 ,  Francesca Bianco  1 ,  Christian Bergamini  5 ,  Farid Ullah  3 ,  Federica Isidori  1 ,  Irene Liparulo  5 ,  Chiara Diquigiovanni  1 ,  Luca Masin  5 ,  Nicola Rizzardi  5 ,  Mariapia Giuditta Cratere  1  6 ,  Elisa Boschetti  1 ,  Valentina Papa  7 ,  Alessandra Maresca  8 ,  Giovanna Cenacchi  7 ,  Rita Casadio  9 ,  Pierluigi Martelli  9 ,  Ivana Matera  10 ,  Isabella Ceccherini  10 ,  Romana Fato  5 ,  Giuseppe Raiola  11 ,  Serena Arrigo  10 ,  Sara Signa  10 ,  Angela Rita Sementa  10 ,  Mariasavina Severino  10 ,  Pasquale Striano  10 ,  Chiara Fiorillo  10 ,  Tsuyoshi Goto  12 ,  Shumpei Uchino  13  14 ,  Yoshinobu Oyazato  15 ,  Hisayoshi Nakamura  16 ,  Sushil K Mishra  17 ,  Yu-Sheng Yeh  12 ,  Takema Kato  4 ,  Kandai Nozu  18 ,  Jantima Tanboon  16 ,  Ichiro Morioka  19 ,  Ichizo Nishino  16 ,  Tatsushi Toda  20 ,  Yu-Ichi Goto  21 ,  Akira Ohtake  22 ,  Kenjiro Kosaki  23 ,  Yoshiki Yamaguchi  24 ,  Ikuya Nonaka  16 ,  Kazumoto Iijima  18 ,  Masakazu Mimaki  13 ,  Hiroki Kurahashi  4 ,  Anja Raams  2 ,  Alyson MacInnes  25 ,  Mariel Alders  26 ,  Marc Engelen  27 ,  Gabor Linthorst  25 ,  Tom de Koning  28 ,  Wilfred den Dunnen  29 ,  Gerard Dijkstra  30 ,  Karin van Spaendonck  26 ,  Dik C van Gent  2 ,  Eleonora M Aronica  31 ,  Paolo Picco  10 ,  Valerio Carelli  7  8 ,  Marco Seri  1 ,  Nicholas Katsanis  3 ,  Floor A M Duijkers  26 ,  Mariko Taniguchi-Ikeda  4  18  32 ,  Roberto De Giorgio  33
Affiliations
  • 1. Department of Medical and Surgical Sciences, St. Orsola-Malpighi Hospital, University of Bologna, Bologna, 40138, Italy.
  • 2. Department of Molecular Genetics, Erasmus MC, Rotterdam, 3000 CA, The Netherlands.
  • 3. Center for Human Disease Modeling, Duke University, Durham, NC 27710, USA.
  • 4. Division of Molecular Genetics, Institute for Comprehensive Medical Science, Fujita Health University, Aichi, 470-1192, Japan.
  • 5. Department of Pharmacy and Biotechnology, University of Bologna, Bologna, 40126, Italy.
  • 6. Division of Genetics and Cell Biology, San Raffaele Scientific Institute, Milan, 20132, Italy.
  • 7. Department of Biomedical and Neuromotor Sciences, University of Bologna, Bologna, 40123, Italy.
  • 8. IRCCS Istituto delle Scienze Neurologiche di Bologna, Programma di Neurogenetica, Bologna, 40139, Italy.
  • 9. Biocomputing Group, Department of Biological, Geological, Environmental Sciences, University of Bologna, Bologna, 40126, Italy.
  • 10. IRCCS Istituto Giannina Gaslini, Genova, 16128, Italy.
  • 11. Department of Paediatrics, Pugliese-Ciaccio Hospital, Catanzaro, 88100, Italy.
  • 12. Laboratory of Molecular Function of Food, Division of Food Science and Biotechnology, Graduate School of Agriculture, Kyoto University, Uji, 611-0011, Japan.
  • 13. Department of Pediatrics, Teikyo University School of Medicine, Tokyo, 173-8605, Japan.
  • 14. Department of Pediatrics, Graduate School of Medicine, The University of Tokyo, Tokyo, 113-0033, Japan.
  • 15. Department of Pediatrics, Kakogawa Central City Hospital, Kakogawa, Hyogo, 675-8611, Japan.
  • 16. Department of Neuromuscular Research, National Institute of Neuroscience, National Center of Neurology and Psychiatry, Tokyo, 187-8502, Japan.
  • 17. Glycoscience Group, National University of Ireland, Galway, H91 CF50, Ireland.
  • 18. Department of Pediatrics, Kobe University Graduate School of Medicine, Hyogo, 650-0017, Japan.
  • 19. Department of Pediatrics and Child Health, Nihon University School of Medicine, Tokyo, 173-8610, Japan.
  • 20. Department of Neurology, Graduate School of Medicine, The University of Tokyo, Tokyo, 113-0033, Japan.
  • 21. Department of Mental Retardation and Birth Defect Research, National Institute of Neuroscience, National Center of Neurology and Psychiatry, Tokyo, 187-8502, Japan.
  • 22. Department of Pediatrics & Clinical Genomics, Faculty of Medicine, Saitama Medical University, Saitama, 350-0495, Japan.
  • 23. Center for Medical Genetics, Keio University School of Medicine, Tokyo, 160-8582, Japan.
  • 24. Laboratory of Pharmaceutical Physical Chemistry, Tohoku Medical and Pharmaceutical University, Miyagi, 981-8558, Japan.
  • 25. Department of Metabolic Diseases, Amsterdam UMC, University of Amsterdam, Amsterdam, 1100 DD, The Netherlands.
  • 26. Department of Clinical Genetics, Amsterdam UMC, University of Amsterdam, Amsterdam, 1100 DD, The Netherlands.
  • 27. Department of Neurology, Amsterdam UMC, University of Amsterdam, Amsterdam, 1100 DD, The Netherlands.
  • 28. Department of Metabolic Diseases, UMCG, Groningen, 9700 RB, The Netherlands.
  • 29. Department of Pathology, UMCG, Groningen, 9700 RB, The Netherlands.
  • 30. Department of Gastroenterology, UMCG, Groningen, 9700 RB, The Netherlands.
  • 31. Department of Pathology, Amsterdam UMC, University of Amsterdam, Amsterdam, 1100 DD, The Netherlands.
  • 32. Department of Clinical Genetics, Fujita Health University Hospital, Aichi, 470-1192, Japan.
  • 33. Department of Morphology, Surgery and Experimental Medicine, St. Anna Hospital, University of Ferrara, Ferrara, 44124, Italy.
PMID: 33855352 DOI: 10.1093/brain/awab056
Abstract

Abnormal gut motility is a feature of several mitochondrial encephalomyopathies, and mutations in genes such as TYMP and POLG, have been linked to these rare diseases. The human genome encodes three DNA ligases, of which only one, Ligase III (LIG3), has a mitochondrial splice variant and is crucial for mitochondrial health. We investigated the effect of reduced LIG3 activity and resulting mitochondrial dysfunction in seven patients from three independent families, who showed the common occurrence of gut dysmotility and neurological manifestations reminiscent of mitochondrial neurogastrointestinal encephalomyopathy. DNA from these patients was subjected to whole exome Sequencing. In all patients, compound heterozygous variants in a new disease gene, LIG3, were identified. All variants were predicted to have a damaging effect on the protein. The LIG3 gene encodes the only mitochondrial DNA (mtDNA) Ligase and therefore plays a pivotal role in mtDNA repair and replication. In vitro assays in patient-derived cells showed a decrease in LIG3 protein levels and Ligase activity. We demonstrated that the LIG3 gene defects affect mtDNA maintenance, leading to mtDNA depletion without the accumulation of multiple deletions as observed in other mitochondrial disorders. This mitochondrial dysfunction is likely to cause the phenotypes observed in these patients. The most prominent and consistent clinical signs were severe gut dysmotility and neurological abnormalities, including leukoencephalopathy, Epilepsy, Migraine, stroke-like episodes, and neurogenic bladder. A decrease in the number of myenteric neurons, and increased fibrosis and elastin levels were the most prominent changes in the gut. Cytochrome c oxidase (COX) deficient fibres in skeletal muscle were also observed. Disruption of lig3 in zebrafish reproduced the brain alterations and impaired gut transit in vivo. In conclusion, we identified variants in the LIG3 gene that result in a mitochondrial disease characterized by predominant gut dysmotility, encephalopathy, and neuromuscular abnormalities.

Keywords
LIG3; CIPO; MNGIE; mtDNA repair; mtDNA replication.