Biallelic variants in LIG3 cause a novel mitochondrial neurogastrointestinal encephalomyopathy

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. Bonora et al. identify a new mitochondrial recessive disorder caused by biallelic variants in the LIG3 gene encoding DNA ligase III, which is responsible for mitochondrial DNA repair. Clinical signs include gut dysmotility and neurological features such as leucoencephalopathy, epilepsy and stroke-like episodes.

Therapy Prospects for Mitochondrial DNA Maintenance Disorders

“…Interestingly, mutations in genes encoding most of the factors constituting the mtDNA replisome [ 48 , 49 ] have been associated with MDDS ( Table 1 ). Since the first identification of mutations in POLG [ 16 ] and TWNK [ 18 ] as causative of MDDS in 2001, a total of 10 genes encoding proteins directly involved in mtDNA replication and repair machinery have been incorporated in this list to date, including the recent identification of mutations in LIG3 causing a mitochondrial neurogastrointestinal encephalomyopathy (MNGIE) like phenotype [ 25 ].…”

“…As shown in Table 1 , mutations in many other proteins belonging to the mtDNA replication/repair machinery have been gradually identified since 2013 [ 19 , 20 , 21 , 22 , 23 , 24 , 25 , 64 , 65 ], probably owing to the widespread introduction of deep sequencing methodology for genetics diagnostic. The group includes genes involved in mtDNA repair ( DNA2 , and possibly MGME1 ) and other long-ago known proteins participating in mtDNA replication such as mtSSB and TFAM.…”

Myopathic mitochondrial DNA depletion syndrome associated with biallelic variants in LIG3

“… 3 In Patient S1 fibroblasts treated with ethidium bromide, mutant cells showed impaired recovery of induced mtDNA depletion, 3 as also reported by Bonora et al . 1 for other LIG3 -mutant fibroblasts. Finally, genetic screening in the family confirmed segregation, with Patient S2 carrying both variants, and the intronic variant present in the mother and absent in the two healthy siblings ( Fig.…”

“…Bonora et al . 1 reported three families with subjects affected by a mitochondrial neurogastrointestinal encephalopathy (MNGIE) phenotype due to recessive mutations of LIG3 , encoding ligase III, an enzyme present in both nucleus and mitochondria. A common molecular feature was reduced amount of mitochondrial DNA (i.e.…”

“…Variants identified in our family are in red, variants described by Bonora et al . 1 are in black. Arrows indicate the positions in genomic DNA (gDNA) or protein sequence.…”