Luigi Bisceglia

Idiopathic achalasia is a rare esophageal motility disorder characterized by the selective degeneration of inhibitory myenteric neurons. Its genetic basis remains poorly defined. We investigated whether rare coding variants may contribute to disease susceptibility. Exome sequencing was performed in 31 individuals with idiopathic achalasia and seven unaffected relatives. Candidate variants were prioritized using phenotype-driven filtering and assessed through in silico and structural analysis of publicly available gene expression and single-cell transcriptomic datasets. No pathogenic or likely pathogenic variants were identified in achalasia-associated genes. A gene-agnostic analysis identified two rare heterozygous missense variants in unrelated patients: AFG3L2 c.2105G>A (p.Arg702Gln) and POLG c.1760C>T (p.Pro587Leu). Both genes encode mitochondrial proteins involved in neuronal homeostasis. The variants affected conserved residues, mapped to functionally relevant protein regions, and were predicted by multiple computational approaches to affect protein stability and function. Both genes were highly expressed in esophageal tissue, with AFG3L2 showing enrichment in enteric neuronal populations. These exploratory findings support a potential link between mitochondrial dysfunction, enteric neurodegeneration, and idiopathic achalasia. Rare mitochondrial-related variants may contribute to disease susceptibility in selected individuals by increasing vulnerability of inhibitory enteric neurons, although functional validation and larger studies are required. Accordingly, our findings should be considered hypothesis-generating rather than evidence of causality.

Rare diseases impact ~6%–8% of the population, thus constituting an issue for public health worldwide. The increasing application of genomic technologies in the routine diagnosis of these conditions is documenting the need to integrate multiple techniques in the most complex cases. We describe a 14‐year‐old boy and his 4‐year‐old sister, both presenting with neonatal hypotonia, severe global developmental delay, major feeding difficulties with the need for assisted nutrition, inability to speak and walk autonomously, epilepsy, central sleep apnea, and facial dysmorphism, in whom exome sequencing revealed the novel c.798 + 1G>T variant in the UNC80 gene at the heterozygous state. While reverse phenotyping was compatible with a clinical diagnosis of infantile hypotonia, psychomotor retardation, and characteristic facies type 2 syndrome, chromosomal microarray disclosed a microdeletion involving 5 exons (40–44) in the other allele. Our findings expand the mutational repertoire of UNC80 and demonstrate that infantile hypotonia, psychomotor retardation, and characteristic facies type 2 syndrome may also be caused by intragenic copy number variations. The combination of multiple techniques, also comprising exon‐level resolution array, is a resource in real‐world diagnostics of rare diseases.

Neurodevelopmental disorders are a challenge in medical genetics due to genetic heterogeneity and complex genotype-phenotype correlations. For this reason, the resolution of single cases not belonging to well-defined syndromes often requires an integrated approach of multiple whole-genome technologies. Such an approach has also unexpectedly revealed a complex molecular basis in an increasing number of patients, for whom the original suspect of a pleiotropic syndrome has been resolved as the summation effect of multiple genes. We describe a 10-year-old boy, the third son of first-cousin parents, with global developmental delay, facial dysmorphism, and bilateral deafness. SNP-array analysis revealed regions of homozygosity (ROHs) in multiple chromosome regions. Whole-exome sequencing prioritized on gene-mapping into the ROHs showed homozygosity for the likely pathogenic c.1097_1098delAG p. (Arg366Thrfs*2) frameshift substitution in LARP7 and the likely pathogenic c.5743C>T p.(Arg1915*) nonsense variant in OTOG. Recessive variants in LARP7 cause Alazami syndrome, while variants in OTOG cause an extremely rare autosomal recessive form of neurosensorial deafness. Previously unreported features were acrocyanosis and palmoplantar hyperhidrosis. This case highlights the utility of encouraging technological updates in medical genetics laboratories involved in the study of neurodevelopmental disorders and integrating laboratory outputs with the competencies of next-generation clinicians.

Leber’s hereditary optic neuropathy (LHON) is a mitochondrial genetic disease characterized by a variable and reduced penetrance. Individuals carrying a primary LHON-causing mitochondrial DNA (mtDNA) mutation may either remain asymptomatic lifelong, as unaffected carriers, or develop sudden central visual loss that rapidly aggravates over some weeks. Over the years several genetic/environmental triggers able to modulate the risk of developing LHON have been proposed. We provided data supporting a possible correlation between LHON penetrance and the mtDNA copy number, a raw index of mitochondrial mass, whose increase could represent a compensatory response that cells implement to alleviate the pathogenic effect of the primary LHON-causing mtDNA mutations. We collected Italian and Spanish subjects harboring one of the three common LHON primary mutations, either in heteroplasmic or homoplasmic status. For each population we were able to discriminate between affected subjects presenting typical clinical tracts of LHON and LHON-causing mutation carriers showing no symptoms correlated with vision loss. Each subject has been characterized for the presence of a LHON primary mutation, for its status of homoplasmy or heteroplasmy, and for the mtDNA content per cell, expressed as relative mtDNA/nDNA ratio respect to controls. Additional clinical information is present for all the Italian subjects.

Leber’s hereditary optic neuropathy (LHON) associated with mutations in mitochondrial DNA (mtDNA) typically manifests only optic nerve involvement but in some patients may develop additional neurological complications. The cause of this association is not clear. We present a case of a 24-year-old male with a history of subacute, painless, and rapidly progressive bilateral vision loss. We performed ophthalmological, neurological and neuropsychological investigations in the proband and his LHON family. The proband showed optic neuropathy, epilepsy, migraine, and intellectual disability; all the maternal relatives did not manifest optic neuropathy but a moderate to severe intellectual disability. Genetic screening revealed a novel association of the LHON m.3460G > A primary mutation with the m.T961delT + C(n)ins within the mitochondrial encoded 12S RNA (MTRNR1) gene which segregates with the intellectual disability through the maternal branch of the family. We also found a significant increase of mtDNA content in all the unaffected homo/heteroplasmic mutation carriers with respect to either affected or control subjects. This is the first case reporting the co-segregation of a mutation in MTRNR1 gene with a LHON primary mutation, which may be a risk factor of the extraocular signs complicating LHON phenotype. In addition, the data herein reported, confirmed that the key factor modulating the penetrance of optic atrophy in the family is the amount of mtDNA.

Autosomal recessive polycystic kidney disease (ARPKD) is a rare severe genetic disorder arising in the perinatal period, although a late-onset presentation of the disease has been described. Pulmonary hypoplasia is the major cause of morbidity and mortality in the newborn period. ARPKD is caused by mutations in the PKHD1 (polycystic kidney and hepatic disease 1) gene that is among the largest human genes. To achieve a molecular diagnosis of the disease, a large series of Italian affected subjects were recruited. Exhaustive mutation analysis of PKHD1 gene was carried out by Sanger sequencing and multiple ligation probe amplification (MLPA) technique in 110 individuals. A total of 173 mutations resulting in a detection rate of 78.6% were identified. Additional 20 unrelated patients, in whom it was not possible to analyze the whole coding sequence, have been included in this study. Taking into account the total number (n=130) of this cohort of patients, 107 different types of mutations have been detected in 193 mutated alleles. Out of 107 mutations, 62 were novel: 11 nonsense, 6 frameshift, 7 splice site mutations, 2 in-frame deletions and 2 multiexon deletion detected by MLPA. Thirty-four were missense variants. In conclusion, our report expands the spectrum of PKHD1 mutations and confirms the heterogeneity of this disorder. The population under study represents the largest Italian ARPKD cohort reported to date. The estimated costs and the time invested for molecular screening of genes with large size and allelic heterogeneity such as PKHD1 demand the use of next-generation sequencing (NGS) technologies for a faster and cheaper screening of the affected subjects.

Some patients diagnosed as having type 2 diabetes mellitus (T2DM) are, instead, affected by multigenerational diabetes whose clinical characteristics are mostly undefined. 1. To identify among patients who had been previously defined as affected by T2DM those, in fact, affected by multigenerational diabetes; 2. After excluding patients carrying the most common MODY genes and mitochondrial mutations, we compared clinical features of remaining patients with those of patients with T2DM. Among 2,583 consecutive adult patients who had been defined as affected by T2DM, we looked for those with diabetes in ≥3 consecutive generations. All probands were screened for mutations in six MODY genes (HNF4A, GCK, HNF1A, PDX1, HNF1B and NeuroD1) and for the A3243G mitochondrial mutation. After excluding patients with mutations in one of such genes, we compared clinical features of the remaining 67 patients (2.6% of the whole initial sample) affected by multigenerational “familial diabetes of the adulthood” (FDA) and of their diabetic relatives (n = 63) to those with T2DM (n = 1,028) by generalized hierarchical linear models followed by pairwise comparisons. Age, age at diagnosis, proportion of hypertension (all p<0.001), and waist circumference (p<0.05) were lower in FDA than T2DM. Nonetheless, the two groups had similar age-adjusted incidence rate of all-cause mortality. Beside younger age at diagnosis, FDA patients show lower waist circumference and reduced proportion of hypertension as compared to those with T2DM; despite such reduced potential cardiovascular risk factors, FDA patients did not show a reduced mortality risk than patients with T2DM.

Sir, We read with great interest the article by Giordano and colleagues (2014) reporting that cellular activation of compensatory mitochondrial biogenesis, as measured by mitochondrial DNA (mtDNA) copy number, is a major determinant of incomplete penetrance in Leber’s hereditary optic neuropathy (LHON), a mitochondrial disease characterized by bilateral subacute loss of central vision due to optic atrophy (Carelli et al. , 2004; Yu-Wai-Man et al. , 2011). In most known mitochondrial diseases due to mtDNA mutations the penetrance or the severity of the condition depends on the level of heteroplasmy of the mutation (Schon et al. , 2012). However, LHON is due to mtDNA mutations that exemplify a different paradigm. The three primary mutations, namely the m.3460G>A/ND1, m.11778G>A/ND4 and m.14484T>C/ND6, are generally found as homoplasmic. One of the three primary mtDNA mutations is necessary but not sufficient to cause optic neuropathy and disease penetrance can vary in different families harbouring the same mutation, and even within different branches of the same family (Howell and Mackey, 1998). The study by Giordano and colleagues (2014) highlights how in large LHON cohorts of individuals of European descent, higher mtDNA content in blood cells discriminates the unaffected mutation carriers from LHON affected and control subjects. A significantly higher mtDNA copy number was observed in asymptomatic maternal relatives, hereafter called ‘Carriers’, moving progressively towards lower values from carriers to affected subjects to controls. Previously, different data were reported on this …

To report clinical findings and molecular defect in three subjects affected by Biber-Haab-Dimmer dystrophy or Lattice Corneal Dystrophy Type I (LCD1), a corneal dystrophy transmitted as an autosomal dominant tract.