Advances in next-generation sequencing (NGS) promise to facilitate diagnosis of inherited disorders. While 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 utility, we performed targeted NGS in 42 unrelated infants with clinical and biochemical evidence of mitochondrial oxidative phosphorylation disease, who were refractory to traditional molecular diagnosis. These devastating mitochondrial disorders are characterized by phenotypic and genetic heterogeneity, with over 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. Since patients and controls harbored a comparable number of such heterozygous alleles, we could not prioritize dominant acting genes. However, patients showed a five-fold enrichment of genes with two such mutations that could underlie recessive disease. In total, 23/42 (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. 13 patients (31%) had mutations in nuclear genes never linked to disease. The pathogenicity of two such genes, NDUFB3 and AGK, was supported by cDNA complementation and evidence from multiple patients, respectively. The results underscore the immediate potential and challenges of deploying NGS in clinical settings.
The Fabry Registry is a global observational research platform established to define outcome data on the natural and treated course of this rare disorder. Participating physicians submit structured longitudinal data to a centralized, confidential database. This report describes the baseline demographic and clinical characteristics of the first 1765 patients (54% males (16% aged < 20 years) and 46% females (13% < 20 years)) enrolled in the Fabry Registry. The median ages at symptom onset and diagnosis were 9 and 23 years (males) and 13 and 32 years (females), respectively, indicating diagnostic delays in both sexes. Frequent presenting symptoms in males included neurological pain (62%), skin signs (31%), gastroenterological symptoms (19%), renal signs (unspecified) (17%), and ophthalmological signs (11%). First symptoms in females included neurological pain (41%), gastroenterological symptoms (13%), ophthalmological (12%), and skin signs (12%). For those patients reporting renal progression, the median age at occurrence was 38 years for both sexes, but onset of cerebrovascular and cardiovascular events was later in females (median 43 and 47 years, respectively) than in males (38 and 41 years, respectively). This paper demonstrates that in spite of the considerable burden of disease in both sexes that begins to manifest in childhood or adolescence, the recognition of the underlying diagnosis is delayed by 14 years in males and 19 years in females. The Fabry Registry provides data that can increase awareness of common symptoms in all age groups, as well as insight into treated and untreated disease course, leading to improved recognition and earlier treatment, and possibly to improved outcomes for affected individuals.
Selective harvest of large individuals should alter natural adaptive landscapes and drive evolution toward reduced somatic growth and increased reproductive investment. However, few studies have simultaneously considered the relative importance of artificial and natural selection in driving trait changes in wild populations. Using 50 years of individual-based data on Windermere pike (Esox lucius), we show that trait changes tracked the adaptive peak, which moved in the direction imposed by the dominating selective force. Individual lifetime somatic growth decreased at the start of the time series because harvest selection was strong and natural selection was too weak to override the strength of harvest selection. However, natural selection favoring fast somatic growth strengthened across the time series in parallel with the increase in pike abundance and, presumably, cannibalism. Harvest selection was overridden by natural selection when the fishing effort dwindled, triggering a rapid increase in pike somatic growth. The two selective forces appear to have acted in concert during only one short period of prey collapse that favored slow-growing pike. Moreover, increased somatic growth occurred concurrently with a reduction in reproductive investment in young and small female pike, indicating a tradeoff between growth and reproduction. The age-specific amplitude of this change paralleled the age-specific strength of harvest pressure, suggesting that reduced investment was also a response to increased life expectancy. This is the first study to demonstrate that a consideration of both natural selection and artificial selection is needed to fully explain time-varying trait dynamics in harvested populations.adaptive landscapes ͉ conservation ͉ contemporary evolution ͉ fisheries ͉ top predators
The ability of natural selection to drive local adaptation has been appreciated ever since Darwin. Whether human impacts can impede the adaptive process has received less attention. We tested this hypothesis by quantifying natural selection and harvest selection acting on a freshwater fish (pike) over four decades. Across the time series, directional natural selection tended to favour large individuals whereas the fishery targeted large individuals. Moreover, non-linear natural selection tended to favour intermediate sized fish whereas the fishery targeted intermediate sized fish because the smallest and largest individuals were often not captured. Thus, our results unequivocally demonstrate that natural selection and fishery selection often acted in opposite directions within this natural system. Moreover, the two selective factors combined to produce reduced fitness overall and stronger stabilizing selection relative to natural selection acting alone. The long-term ramifications of such human-induced modifications to adaptive landscapes are currently unknown and certainly warrant further investigation.
In humans, complex I of the respiratory chain is composed of seven mitochondrial DNA (mtDNA)-encoded and 38 nuclear-encoded subunits that assemble together in a process that is poorly defined. To date, only two complex I assembly factors have been identified and how each functions is not clear. Here, we show that the human complex I assembly factor CIA30 (complex I intermediate associated protein) associates with newly translated mtDNA-encoded complex I subunits at early stages in their assembly before dissociating at a later stage. Using antibodies we identified a CIA30-deficient patient who presented with cardioencephalomyopathy and reduced levels and activity of complex I. Genetic analysis revealed the patient had mutations in both alleles of the NDUFAF1 gene that encodes CIA30. Complex I assembly in patient cells was defective at early stages with subunits being degraded. Complementing the deficiency in patient fibroblasts with normal CIA30 using a novel lentiviral system restored steady-state complex I levels. Our results indicate that CIA30 is a crucial component in the early assembly of complex I and mutations in its gene can cause mitochondrial disease.
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