Clinical and Genetic Analysis of Patients With TK2 Deficiency

Abstract

Objectives: Thymidine kinase 2 deficiency (TK2d) is a rare autosomal recessive disorder that stems from a perturbation of the mitochondrial DNA maintenance. Nucleoside treatment has recently shown promise as a disease-modifying therapy. TK2d was initially associated with rapidly progressive fatal myopathy in children featuring mitochondrial DNA depletion. Subsequently, less severe variants of the disease were described, with onset of symptoms during adolescence or adulthood and associated with the presence of multiple mtDNA deletions. These less severe phenotypes have been reported in only 15% of the approximately 120 patients described worldwide. However, some reports suggest that these juvenile and adult-onset presentations may be more common. The objective of this study was to describe the clinical phenotype in a sample of patients from Spain.

Methods: This study includes 53 patients harboring biallelic TK2 pathogenic variants, compiling data retrospectively from 7 Spanish centers. We analyzed allele frequency, investigated the most recent common ancestor of core haplotypes, and used the Runs of Homozygosity approach to investigate variant coalescence.

Results: Symptom onset distribution revealed that 32 patients (60%) experienced symptoms beyond 12 years of age. Approximately 30% of patients died of respiratory insufficiency, while 56% of surviving patients needed mechanical ventilation. Genetic analysis identified 16 distinct variants in TK2. Two variants, p.Lys202del and p.Thr108Met, exhibited significantly higher prevalence in the Spanish population than that reported in gnomAD database (86-fold and 13-fold, respectively). These variants are estimated to have originated approximately 16.8 generations ago for p.Thr108Met and 95.2 generations ago for p.Lys202del within the Spanish population, with the increase in frequency attributed to various forms of inbreeding. In late-onset cases, 46.9% carried the p.Lys202del variant.

Discussion: The higher frequency of TK2d in Spain can be partially attributed to the increased prevalence of 2 variants and consanguinity. Notably, in 60% of the cohort, the disease was late-onset, emphasizing the potential underdiagnosis of this subgroup of patients in other regions. Raising awareness of this potentially treatable disorder is of utmost importance because early interventions can significantly affect the quality of life and survival of affected individuals.

Figure 1. Main Clinical Characteristics by Age at Onset

Relevant clinical characteristics in different group of ages are represented; ptosis, progressive external ophthalmoplegia (PEO), facial weakness, cervical weakness, dysphagia, and mechanical ventilation.

Figure 2. Distribution of Patients According to the Age at Which the First Symptoms Appeared

Ages less than 1 year, between 1 and 12 years, between 12 and 40 years, and more than 40 years.

Figure 3. TK2 Gene Variants Distribution

TK2 representation showing the distribution of the variants identified in our cohort and the number of alleles identified for each variant (red background for >20 alleles, yellow background for 5–20 alleles, and blue background for ≤4 alleles).

Figure 4. ROH Exploratory Analysis

Different runs of homozygosity (ROH) exploratory analyses are presented in this figure. (A) ROH size distribution by variant. Average total sums are presented over 6 classes of ROH lengths: 0.3 ≤ ROH > 0.5 Mb, 0.5 ≤ ROH > 1 Mb, 1 ≤ ROH > 2 Mb, 2 ≤ ROH > 4 Mb, 4 ≤ ROH > Mb, and ROH ≥8 Mb. (B) Average number and cumulative length of ROH (Runs of Homozygosity) exceeding 1.5 Mb for each individual. The diagonal line on the graph is generated through regression analysis, plotting the number of ROH against the total ROH length. Data for this analysis come from ASW and ACB populations in the 1000 Genomes Project, which are representative of admixed and relatively outbred populations. Consanguinity practices in preceding generations manifest as a rightward shift. Simulated data for the number and total length of ROH (ROH >1.5 Mb) in the offspring resulting from various consanguineous matings are also displayed. Points of varying colors represent offspring from different consanguineous relationships: green for second cousins, yellow for first cousins, orange for avuncular (including uncle-niece, aunt-nephew, and double first cousins), and red for incestuous relationships (such as brother-sister and parent-offspring). Each type of consanguineous mating is depicted through 5,000 simulations. Simulations do not account for genetic drift. However, the extent of the rightward shift can be extrapolated to scenarios where there is some degree of autozygosity due to genetic drift. (C) Population analysis and components of the inbreeding coefficient. Systematic inbreeding coefficient (FIS) vs the inbreeding coefficient obtained from ROH (FROH). In this context, FIS is the average SNP homozygosity within an individual relative to the expected homozygosity of alleles randomly drawn from the population. The diagonal broken line represents FIS = FROH. The horizontal broken line represents FIS = 0. (D) Representation of the ROH physical distribution in the Chr 16 of affected individuals. The broken line shows the TK2 gene physical location.