Recessive Phenotype Research Articles

Molecular tool for efficient breeding of DOMINANT Greenshell laying hens and significant refinement of phenotypic selection focused on eggshell color

In recent decades, interest in non-traditionally colored eggs has increased. For breeders, this market interest means breeding lines of laying hens that lay eggs of varied colors, such as the blue-green eggshells (Dominant Greenshell) in this study. This study presents the results of genotyping the polymorphism of the O locus responsible for shell coloration and photometric measurement of eggshell color based on the CIELAb system, which was carried out on the unique Czech breeding population Dominant Greenshell. The aim was to use a combination of phenotyping using the CIELab System method and genotyping of the O locus using the end-point PCR approach with the main focus on the accuracy of distinguishing shell color genotypes, streamlining the selection of dominant homozygotes in the O locus, optimizing this technology for the most efficient and cost-effective selection procedure in practical hen breeding. The optometric method was able to reliably distinguish only dominant and recessive phenotypes and eliminate from the population only undesirable recessive homozygotes with a white colored shell. The parameter a* (redness/greenness) from the CIELab color space turned out to be absolutely key for distinguishing dominant and recessive phenotypes. Using the CART methodology, a classification tree built on discriminating optometric characteristics a-blunt was obtained, however, for the group of desirable O/O homozygotes, the selection approach would result in incorrect genotyping of 31% of individuals. Therefore, a combined approach based on rapid and simple elimination of recessive homozygotes using phenotyping (CIELab photometric measurement) and molecular identification of the EAV-HP insertion in the SLCO1B3 gene in dominant phenotypes, regardless of color intensity affected by laying time/order, and allowing reliable elimination, has proven to be the most effective method to distinguish heterozygotes from the breeding population. The combination of optometric and molecular selection methods then leads to more efficient selection, reduction of overall selection costs. This process led to the stabilization of the breeding population within one generation and the achievement of a pure homozygous line with regard to eggshell color.

Intermediate cystinosis: a case report of 10-year treatment with cysteamine

BackgroundCystinosis is a lysosomal storage disorder characterized by an autosomal recessive phenotype. Intermediate cystinosis, which progresses slowly and causes renal failure, accounts for approximately 5% of all cystinosis cases. Patients with intermediate cystinosis may not exhibit the typical symptoms of cystinosis, such as Fanconi syndrome and ocular symptoms. Because of its diverse clinical presentation and rarity, intermediate cystinosis can be difficult to diagnose. Additionally, few patients can tolerate cystine-depleting drugs, such as cysteamine, because of their complicated administration schedules and side effects. We report a case of intermediate cystinosis that was treated with cysteamine for 10 years.Case presentationUrinary abnormalities were first diagnosed when the patient was 3 years of age during a health examination specifically for 3-year-old children, which is unique to Japan. Cystinosis was diagnosed when the patient was 12 years of age. Cysteamine therapy was initiated and regular cystine concentration measurements were performed. Although proteinuria persisted, the patient’s renal function progressed slowly. Two renal biopsies were performed, and multinucleated podocytes and cystine crystals without focal segmental glomerulosclerosis lesions were observed in the biopsy specimens. The patient’s renal function remained stable.ConclusionsThis case of intermediate cystinosis was treated with cysteamine over the course of 10 years. Intermediate cystinosis requires an appropriate diagnosis and long-term treatment.

Expanding the phenotypes of ABL1 deficiency syndromes: When mutations in different isoforms Lead to different diseases.

All reported ABL1 gain of function and loss of function (LOF) variants, impact both isoforms 1a and 1b. Our findings suggest that LOF variants affecting solely ABL1 isoform 1b may lead to a distinct autosomal recessive new phenotype.

Strain variation in the Candida albicans iron limitation response.

Iron acquisition is critical for pathogens to proliferate during invasive infection, and the human fungal pathogen Candida albicans is no exception. The iron regulatory network, established in reference strain SC5314 and derivatives, includes the central player Sef1, a transcription factor that activates iron acquisition genes in response to iron limitation. Here, we explored potential variation in this network among five diverse C. albicans strains through mutant analysis, Nanostring gene expression profiling, and, for two strains, RNA-Seq. Our findings highlight four features that may inform future studies of natural variation and iron acquisition in this species. (i) Conformity: In all strains, major iron acquisition genes are upregulated during iron limitation, and a sef1Δ/Δ mutation impairs that response and growth during iron limitation. (ii) Response variation: Some aspects of the iron limitation response vary among strains, notably the activation of hypha-associated genes. As this gene set is tied to tissue damage and virulence, variation may impact the progression of infection. (iii) Genotype-phenotype variation: The impact of a sef1Δ/Δ mutation on cell wall integrity varies, and for the two strains examined the phenotype correlated with sef1Δ/Δ impact on several cell wall integrity genes. (iv) Phenotype discovery: DNA repair genes were induced modestly by iron limitation in sef1Δ/Δ mutants, with fold changes we would usually ignore. However, the response occurred in both strains tested and was reminiscent of a much stronger response described in Cryptococcus neoformans, a suggestion that it may have biological meaning. In fact, we observed that the iron limitation of a sef1Δ/Δ mutant caused recessive phenotypes to emerge at two heterozygous loci. Overall, our results show that a network that is critical for pathogen proliferation presents variation outside of its core functions.IMPORTANCEA key virulence factor of Candida albicans is the ability to maintain iron homeostasis in the host where iron is scarce. We focused on a central iron regulator, SEF1. We found that iron regulator Sef1 is required for growth, cell wall integrity, and genome integrity during iron limitation. The novel aspect of this work is the characterization of strain variation in a circuit that is required for survival in the host and the connection of iron acquisition to genome integrity in C. albicans.

A model organism pipeline provides insight into the clinical heterogeneity of TARS1 loss-of-function variants

Aminoacyl-tRNA synthetases (ARSs) are ubiquitously expressed, essential enzymes that complete the first step of protein translation: ligation of amino acids to cognate tRNAs. Genes encoding ARSs have been implicated in myriad dominant and recessive phenotypes, the latter often affecting multiple tissues but with frequent involvement of the central and peripheral nervous systems, liver, and lungs. Threonyl-tRNA synthetase (TARS1) encodes the enzyme that ligates threonine to tRNATHR in the cytoplasm. To date, TARS1 variants have been implicated in a recessive brittle hair phenotype. To better understand TARS1-related recessive phenotypes, we engineered three TARS1 missense variants at conserved residues and studied these variants in Saccharomyces cerevisiae and Caenorhabditis elegans models. This revealed two loss-of-function variants, including one hypomorphic allele (R433H). We next used R433H to studythe effects of partial loss of TARS1 function in a compound heterozygous mouse model (R432H/null). This model presents with phenotypes reminiscent of patients with TARS1 variants and with distinct lung and skin defects. This study expands the potential clinical heterogeneity of TARS1-related recessive disease, which should guide future clinical and genetic evaluations of patient populations.

Molecular and Biological Characteristics of a Peach Latent Mosaic Viroid PC Isolate in Peach from China: Base Mutations in Hairpin Stems and Implications for Symptomatology.

Peach latent mosaic viroid (PLMVd) infects peach trees in China and induces a conspicuous albino phenotype (peach calico, PC) that is closely associated with variants containing a 12-to-14 nucleotide hairpin insertion capped by a U-rich loop. Initially, PC disease distribution was limited to parts of Italy, and it was first detected in the field in China in 2019. To explore the molecular and biological characteristics of PLMVd PC isolates in peach in China, we conducted a comprehensive analysis of disease phenotype development and investigated the data-associated pathogenicity and in vivo dynamics of the Chinese isolate PC-A2 using slash-inoculation into GF-305 peach seedlings. Inoculated seedlings displayed PC symptoms much earlier following topping treatment, and PLMVd infectivity was further assessed using bioassay and semiquantitative RT-PCR experiments. Evolutionary analysis showed that the PC isolate and its progeny variants clustered into a single phylogroup distinct from reference PC-C40 isolates from Italy and PC-K1 and PC-K2 from South Korea. Some PC-A2 progeny variants from green leaves of PC-expressing seedlings showed unbalanced point mutations in hairpin stems compared with the PC-C40 reference sequence and constituted a new stem insertion type. The results reveal associations between the recessive phenotypes of peach albino symptoms and base variation in hairpin stem insertions relative to the PC-C40/chloroplastic heat shock protein 90 reference sequence.

Comprehensive assessment of recessive, pathogenic AARS1 alleles in a humanized yeast model reveals loss-of-function and dominant-negative effects.

Alanyl-tRNA synthetase 1 (AARS1) encodes the enzyme that ligates tRNA molecules to alanine in the cytoplasm, which is required for protein translation. Variants in AARS1 have been implicated in early-onset, multi-system recessive phenotypes and in later-onset dominant peripheral neuropathy; to date, no single variant has been associated with both dominant and recessive diseases raising questions about shared mechanisms between the two inheritance patterns. AARS1 variants associated with recessive disease are predicted to result in null or hypomorphic alleles and this has been demonstrated, in part, via yeast complementation assays. However, pathogenic alleles have not been assessed in a side-by-side manner to carefully scrutinize the strengths and limitations of this model system. To address this, we employed a humanized yeast model to evaluate the functional consequences of all AARS1 missense variants reported in recessive disease. The majority of variants showed variable loss-of-function effects, ranging from no growth to significantly reduced growth. These data deem yeast a reliable model to test the functional consequences of human AARS1 variants; however, our data indicate that this model is prone to false-negative results and is not informative for genotype-phenotype studies. We next tested missense variants associated with no growth for dominant-negative effects. Interestingly, K81T AARS1, a variant implicated in recessive disease, demonstrated loss-of-function and dominant-negative effects, indicating that certain AARS1 variants may be capable of causing both dominant and recessive disease phenotypes.

#2695 A Polycystin-1-Bicaudal C1 complex regulates focal adhesion function through integrin beta-1, F-actin organisation and local translation in HKE cells

Abstract Background and Aims Variants in Bicc1, result in a recessive murine PKD phenotype (bpk, jcpk) by uncertain mechanisms. In a recent study, we reported genetic and biochemical evidence of novel interactions between PKD1, PKD2 and BICC1 in Xenopus, mouse and man suggesting that BICC1 is a modifier of the ADPKD phenotype (submitted). In this study, our major aim was to investigate the molecular mechanisms underlying cystogenesis that result from loss of the normal interaction between the PKD1 protein, Polycystin-1 (PC1), a cell surface receptor and Bicaudal C1 (BICC1), an RNA-binding protein. Methods Isogenic PKD1 and BICC1 CRISP-Cas9 KO cells were generated from a conditionally-immortalised wild-type human proximal tubular line (UCL93); RNA-seq was performed in PKD1 and BICC1 KO cells to identify commonly altered genes and pathways; MS pull-down was conducted in HEK293 cells with BICC1-HA to identify BICC1 interacting proteins; cellular phenotypes in normal and KO cells were assessed through adhesion and migration assays, alongside Traction Force Microscopy (TFM); proximal ligation assays (PLA) to confirm protein-protein interactions; single-molecule FISH (smFISH) to localize mRNA transcripts; puromycin labeling with a proximity ligation assay (Puro-PLA) to detect sites of translation of specific mRNAs. Results Consistent with a functional interaction, loss of PC1 resulted in lower BICC1 levels and vice-versa in single KO (SKO) cells. In migrating cells, BICC1 was expressed at the leading edge where it co-localised with β1-integrin (ITGB1) by PLA, suggesting enrichment at focal adhesion sites (FA). BICC1 KO cells had no cilia phenotype but instead displayed striking disorganization of stress fibres and aster-like structures, features which could be completely rescued by lentiviral Bicc1-HA re-expression. Gene set enrichment and pathway analysis confirmed that F-actin organization and actin-associated proteins (AAP) were commonly dysregulated in SKO cells. BICC1 was also found to interact ITGB1, several components of an integrin-associated complex and proteins involved in actin turnover by MS pull-down. Both SKO cells showed major abnormalities of cell attachment, detachment and directional migration indicative of functional alterations in cell-matrix and cell-cell adhesion. We confirmed that FA structure and function were altered by reduced co-localisation of several AAPs (including TNS1 and FBLIM1) and by TFM. BICC1 directly interacted with F-actin and FBLIM1 in pull-down assays and with FBLIM1 by RNA-IP. Finally, we found evidence of FBLIM1 mRNA by smFISH and of local FBLIM1 translation (Puro-PLA) at FA sites in wild-type cells, both of which were markedly reduced in SKO cells. Conclusion Our data reveal the key roles for actin dynamics and local translation as novel mechanisms regulated by PC1 and BICC1 in the pathogenesis of ADPKD. We demonstrate that BICC1 and PC1 are co-regulated, forming a PC1-BICC1 complex critical for maintaining the structural integrity and function of FAs in normal kidney epithelial cells. Loss of this interaction results in major alterations in cell adhesion, migration and stress fibre organisation, features typical of the ADPKD cellular phenotype. BICC1 plays a dual role in this process via protein-protein interactions with ITGB1, F-actin and other AAPs, and through protein-RNA interactions regulating the local translation of key AAPs (FBLIM1) at FA sites.

Presentation of Rare Phenotypes Associated with the FKBP10 Gene.

Pathogenic variants in the FKBP10 gene lead to a spectrum of rare autosomal recessive phenotypes, including osteogenesis imperfecta (OI) Type XI, Bruck syndrome Type I (BS I), and the congenital arthrogryposis-like phenotype (AG), each with variable clinical manifestations that are crucial for diagnosis. This study analyzed the clinical-genetic characteristics of patients with these conditions, focusing on both known and newly identified FKBP10 variants. We examined data from 15 patients, presenting symptoms of OI and joint contractures. Diagnostic methods included genealogical analysis, clinical assessments, radiography, whole exome sequencing, and direct automated Sanger sequencing. We diagnosed 15 patients with phenotypes due to biallelic FKBP10 variants-4 with OI Type XI, 10 with BS I, and 1 with the AG-like phenotype-demonstrating polymorphism in disease severity. Ten pathogenic FKBP10 variants were identified, including three novel ones, c.1373C>T (p.Pro458Leu), c.21del (p.Pro7fs), and c.831_832insCG (p.Gly278Argfs), and a recurrent variant, c.831dup (p.Gly278Argfs). Variant c.1490G>A (p.Trp497Ter) was found in two unrelated patients, causing OI XI in one and BS I in the other. Additionally, two unrelated patients with BS I and epidermolysis bullosa shared identical homozygous FKBP10 and KRT14 variants. This observation illustrates the diversity of FKBP10-related pathology and the importance of considering the full spectrum of phenotypes in clinical diagnostics.

#760 Monogenic lupus with ANCA associated vasculitis-phenotype and ANCA positivity due to DNASE1L3 mutations: case report and review of the literature

Abstract Background and Aims Monogenic systemic lupus erythematosus (SLE) accounts for 7-10% of cases of early-onset SLE. DNASE1L3 is an extracellular nuclease that digests chromatin released from apoptotic cells and its deficiency, enhance autoantibody production and type I interferon responses and cause different autosomal recessive phenotypes including SLE and hypocomplementemic urticarial vasculitis syndrome (HUVS) [1]. In some cases patients can have a mixed SLE-AAV phenotype. Kidney involvement in patients with DNASE1L3 mutations is poorly characterised. Method We present the case report of a 7-years-old boy with monogenic SLE due to DNASE1L3 mutations who developed severe glomerulonephritis leading to kidney failure. Results The patient had a history of urticaria and arthralgia and presented with fever, haemolytic anaemia, lymphadenopathy, hepato-splenomegaly, erythematous- macular and necrotic skin lesions, and interstitial lung disease. He also had acute kidney injury (serum creatinine 5.4 mg/dL), nephrotic- range proteinuria (3.9 g/24 h) and microhaematuria. Immunological tests revealed low C3 and C4, positive anti-nuclear antibody (ANA) and myeloperoxidase-antineutrophil cytoplasmic antibodies (MPO-ANCA), with negativity of anti-extractable nuclear antigen antibodies (anti-ENA) and anti-double stranded DNA (anti-dsDNA). Kidney biopsy showed pauci-immune (mesangial C3+ and IgG+) necrotising crescentic glomerulonephritis. The patient proved refractory to standard immunosuppression with cyclophosphamide and steroids. Two years later, due to renal function decline, a new kidney biopsy was performed and showed diffuse necrotising glomerulonephritis with endo- and extra-capillary proliferation; intense mesangial and subendothelial full-house deposits were evident on immunofluorescence. The patient did not respond to other lines of immunosuppression (mycophenolate mofetil, tacrolimus, azathioprine, rituximab), including the JAK inhibitor ruxolitinib. Kidney failure progressed to end stage at the age of 15 years, when the patient began haemodialysis. The kidney presentation, immunological profile and the first kidney biopsy led to diagnosis of AAV. However, the diagnosis was questioned due to the refractory course, the systemic clinical presentation and the second kidney histology (consistent with lupus nephritis). High interferon signature was detected and in the suspicion of a monogenic lupus nephritis Whole Exome Sequencing was performed and revealed homozygous DNASE1L3 variants (c.290_291delCA p.T97Ifs*2); thus, a final diagnosis of DNASE1L3 monogenic SLE was made. DNASE1L3 serum levels were normal but the DNAse enzymatic activity was low. Conclusion Renal involvement is one of the most frequent manifestations of DNASE1L3-related lupus; in the literature 32 cases of DNASE1L3-associated lupus nephritis are described. ANCA are positive in about 55% of these cases and are associated with a mixed lupus-AAV phenotype. All cases are characterized by resistance to common immunosuppressors and poor renal prognosis [2]. DNASE1L3 regulates neutrophil extracellular trap (NET) clearance and when this function is reduced the permanence of NETs induces endothelial damage and autoantibody formation. This pathogenic pathway is shared both by SLE and by AAV. There is no association between specific mutations and antibody positivity or clinical manifestations.

Autosomal Dominant Spastic Paraplegia With Dysregulation of Bowel Function Associated With Heterozygous AP4S1 Gene Mutation: Case Report.

The aim of our study was to examine the genetic variants already described in hereditary spastic paraplegia in a family where 2 members had spasticity, dysregulation of sphincter function, and dyspraxia in the proband. The study included 2 members of a non-consanguineous family with spastic gait, sphincter abnormalities, and neuropsychological characteristics. Whole-exome sequencing was used in the proband and his mother, both diagnosed with hereditary spastic paraplegia, to identify the underlying genetic cause. We identified a heterozygous variant already known in AP4S1 NM_007077.3: c.289C>T p. (Arg97*) in both patients. The AP4S1 gene on the 14q12 chromosome is responsible for directing proteins from the trans-Golgi network to the endosomal-lysosomal system. Homozygous AP4S1 mutations can cause a severe autosomal recessive phenotype with spasticity and intellectual disability in infants (SPG52). Interpretation: For the first time, a heterozygous pathogenic variant of the AP4S1 gene was observed in symptomatic individuals with hereditary spastic paraplegia. The clinical features of this heterozygous variant of the AP4S1 gene have little overlap with the severe clinical recessive features of SPG52. In this study, we delineated a heterozygous AP4S1 phenotype characterized by spasticity, dysregulation of sphincter functions, and developmental coordination disorder characteristics. Our results provided arguments for heterozygous variant associations in AP4S1 with hereditary spastic paraplegia and expanded the clinical spectrum of A4-related diseases.

Hardy-Weinberg Equilibrium Study of Some Morphogenetic Traits in a Nigerian Population

Background: The Hardy-Weinberg (HW) equilibrium studies the distribution of allelic and genotypic frequencies within a population. It provides a mathematical benchmark for a population that is evolving and not evolving. Aim: This study investigated six morphogenetic traits among families in a Nigerian population using the Hardy-Weinberg principle with the aim of evaluating if the population was in HW equilibrium. Methodology: A total of 45 families comprising a father, mother and at least one offspring were conveniently sampled in Ogbe- Ijoh district in Delta State, Nigeria. Earlobe attachment, Hand clasping, Hitchhiker’s thumb, Leg folding, Morton's toe and Widow's peak were studied for their allelic and genotypic frequencies. The Chi-square test was used to analyse the association between these traits and sex, and conformance to the Mendelian inheritance pattern was evaluated with a Mendelian Chi-square. The Hardy-Weinberg equilibrium compared the allelic frequencies of parents with those of offspring. Results: Males had higher frequencies for attached earlobes, Morton’s toe and widow's peak (35.1, 51.9, 49.4%), while the females showed a predominance for hitchhiker's thumb, right hand clasping and leg folding (50,72.4,70.7%). There was no association between the traits and gender (p>0.05). From the Mendelian Chi-square, free earlobe, right-hand clasping, right leg folding, Morton's toe (SBt), the recessive phenotype of hitchhiker's thumb as well as widow's peak were the dominant traits in the studied population (X2 < 3.841 ). The H-W equation revealed a deviation of the offspring’s genotype from those of the parents for earlobe, hand clasping, leg folding, Morton’s toe and widow's peak (1:1:2 [1:1; 4]; 2: 1: 3 [1:1:2]; 3:1:3 [1:1:2]; 5: 1: 4 [6:1:5}; 5:1:4 [7: 1:5]). However, parental and offspring alleles were identical for hitchhiker's thumb (5:1:5 [5:1: 5]). The homozygotes for both parents and offspring outnumbered the heterozygotes for all traits (295: 245; 156: 119). Conclusion: The study showed that only the hitchhiker's thumb was in HW equilibrium, suggesting that evolution may not occur at that locus. KEYWORDS: Hardy-Weinberg equilibrium, Mendel, Traits, Nigeria, Population.

Clinical application of next generation sequencing for Mendelian disease diagnosis in the Iranian population

Next-generation sequencing (NGS) has been proven to be one of the most powerful diagnostic tools for rare Mendelian disorders. Several studies on the clinical application of NGS in unselected cohorts of Middle Eastern patients have reported a high diagnostic yield of up to 48%, correlated with a high level of consanguinity in these populations. We evaluated the diagnostic utility of NGS-based testing across different clinical indications in 1436 patients from Iran, representing the first study of its kind in this highly consanguineous population. A total of 1075 exome sequencing and 361 targeted gene panel sequencing were performed over 8 years at a single clinical genetics laboratory, with the majority of cases tested as proband-only (91.6%). The overall diagnostic rate was 46.7%, ranging from 24% in patients with an abnormality of prenatal development to over 67% in patients with an abnormality of the skin. We identified 660 pathogenic or likely pathogenic variants, including 241 novel variants, associated with over 342 known genetic conditions. The highly consanguineous nature of this cohort led to the diagnosis of autosomal recessive disorders in the majority of patients (79.1%) and allowed us to determine the shared carrier status of couples for suspected recessive phenotypes in their deceased child(ren) when direct testing was not possible. We also highlight the observations of recessive inheritance of genes previously associated only with dominant disorders and provide an expanded genotype–phenotype spectrum for multiple less-characterized genes. We present the largest mutational spectrum of known Mendelian disease, including possible founder variants, throughout the Iranian population, which can serve as a unique resource for clinical genomic studies locally and beyond.

Spectrum of Genetic Variants in the Most Common Genes Causing Inherited Retinal Disease in a Large Molecularly Characterized United Kingdom Cohort

PurposeInherited retinal disease (IRD) is a leading cause of blindness. Recent advances in gene-directed therapies highlight the importance of understanding the genetic basis of these disorders. This study details the molecular spectrum in a large UK IRD patient cohort. DesignRetrospective study of electronic patient records. ParticipantsPatients with IRD who have attended the Genetics Service at Moorfields Eye Hospital between 2003 and July 2020, in whom a molecular diagnosis has been identified. MethodsGenetic testing was undertaken via a combination of single-gene testing, gene panel testing, whole exome sequencing, and more recently, whole genome sequencing. Likely disease-causing variants were identified from entries within the genetics module of the hospital electronic patient record (OpenEyes Electronic Medical Record, UK). Analysis was restricted to only genes listed in the Genomics England PanelApp R32 Retinal disorders panel (Version 3.24), which includes 412 genes associated with IRD. Manual curation ensured consistent variant annotation and included only plausible disease-associated variants. Main outcome measuresDetailed analysis was performed for variants in the five most frequent genes (ABCA4, USH2A, RPGR, PRPH2, BEST1), as well as for the commonest variants encountered in the IRD study cohort. ResultsWe identified 4415 individuals from 3953 families with molecularly diagnosed IRD (variants in 166 genes). 42.7% of families had variants in one of the five commonest IRD genes. Complex disease alleles contributed to disease in 16.9% of affected families with ABCA4-associated retinopathy. USH2A exon 13 variants were identified in 43% of affected individuals with USH2A-associated IRD. 71% of RPGR variants were clustered in the ORF15 region. PRPH2 and BEST1 variants were associated with a range of dominant and recessive IRD phenotypes. Of the 20 most prevalent variants identified, five were not in the commonest genes; these included founder variants in CNGB3, BBS1, TIMP3, EFEMP1 and RP1. ConclusionsWe describe the commonest pathogenic IRD alleles in a large single-center multi-ethnic UK cohort, and the burden of disease, in terms of families affected, attributable to these variants. Our findings will inform IRD diagnoses in future patients and helps delineate the cohort of patients eligible for gene-directed therapies under development.

Molecular underpinnings and environmental drivers of loss of heterozygosity in Drosophila intestinal stem cells

During development and aging, genome mutation leading to loss of heterozygosity (LOH) can uncover recessive phenotypes within tissue compartments. This phenomenon occurs in normal human tissues and is prevalent in pathological genetic conditions and cancers. While studies in yeast have defined DNA repair mechanisms that can promote LOH, the predominant pathways and environmental triggers in somatic tissues of multicellular organisms are not well understood. Here, we investigate mechanisms underlying LOH in intestinal stem cells in Drosophila. Infection with the pathogenic bacteria, Erwinia carotovora carotovora 15, but not Pseudomonas entomophila, increases LOH frequency. Using whole genome sequencing of somatic LOH events, we demonstrate that they arise primarily via mitotic recombination. Molecular features and genetic evidence argue against a break-induced replication mechanism and instead support cross-over via double Holliday junction-based repair. This study provides a mechanistic understanding of mitotic recombination, an important mediator of LOH, and its effects on stem cells invivo.

Genetic heterogeneity within a consanguineous family involving TTPA and SETX genes

Autosomal recessive cerebellar ataxias (ARCA) constitute a highly heterogeneous group of progressive neurodegenerative disorders that typically occur prior to adulthood. Despite some clinical resemblance between these disorders, different genes are involved. We report in this study four Tunisian patients belonging to the same large consanguineous family, sharing autosomal recessive cerebellar ataxia phenotypes but with clinical, biological, electrophysiological, and radiological differences leading to the diagnosis of two distinct ARCA caused by two distinct gene defects. Two of our patients presented ataxia with the vitamin E deficiency (AVED) phenotype, and the other two presented ataxia with oculo-motor apraxia 2 (AOA2). Genetic testing confirmed the clinical diagnosis by the detection of a frameshift c.744delA pathogenic variant in the TTPA gene, which is the most frequent in Tunisia, and a new variant c.1075dupT in the SETX gene. In Tunisia, data suggest that genetic disorders are common. The combined effects of the founder effect and inbreeding, added to genetic drift, may increase the frequency of detrimental rare disorders. The genetic heterogeneity observed in this family highlights the difficulty of genetic counseling in an inbred population. The examination and genetic testing of all affected patients, not just the index patient, is essential to not miss a treatable ataxia such as AVED, as in the case of this family.

Molecular genetic diagnostics for inherited retinal dystrophies in the clinical setting

ObjectifÉvaluer le succès du dépistage génétique de la dystrophie rétinienne héréditaire (DRH) à des fins diagnostiques en milieu clinique. NatureAnalyse de cohorte rétrospective. ParticipantsUn total de 446 participants consécutifs de diverses origines ethniques vivant dans l'Ouest canadien. MéthodesLes données cliniques, notamment les antécédents familiaux, ont été recueillies auprès des participants qui ont fait l'objet d'un examen ophtalmique complet, suivi d'une analyse de leurs dossiers médicaux. On a offert un dépistage génétique réunissant un panel de 351 gènes aux patients chez lesquels on soupçonnait la présence d'une DRH entre le 1er mars 2019 et le 28 février 2022. Le principal paramètre de mesure était l'effet du dépistage génétique sur le diagnostic clinique. RésultatsLe dépistage génétique a donné lieu à un diagnostic moléculaire certain dans 249 cas sur 446 (55,8 %), à un résultat nettement négatif dans 90 cas sur 446 (20,1 %) et à un diagnostic incertain dans 108 cas sur 446 (24,2 %). On a identifié de manière concluante des variants pathogènes dans 69 gènes, les gènes le plus souvent touchés étant ABCA4 (31 variants), USH2A (25 variants) et RPGR (19 variants). Le groupe diagnostic incertain comprenait vraisemblablement des variants autosomiques dominants encore inconnus ou un variant pathogène comprenant un variant dans le même gène dont la signification est incertaine en ce qui touche le phénotype récessif. Fait à noter, on a obtenu un diagnostic moléculaire génétique incertain dans une proportion pouvant atteindre 47,3 % des participants est-asiatiques qui présentaient une dystrophie de la rétine externe. ConclusionsLa présente étude constitue la plus importante revue sur le dépistage moléculaire génétique des DRH au Canada. L'obtention de résultats négatifs ou incertains dans environ 45 % des cas témoigne du besoin criant en matière de recherche sur les causes moléculaires génétiques des DRH, particulièrement lorsqu'il s'agit d'interpréter un variant dont la signification est incertaine au sein de minorités ethniques.

Diagnostic implications of pitfalls in causal variant identification based on 4577 molecularly characterized families

Despite large sequencing and data sharing efforts, previously characterized pathogenic variants only account for a fraction of Mendelian disease patients, which highlights the need for accurate identification and interpretation of novel variants. In a large Mendelian cohort of 4577 molecularly characterized families, numerous scenarios in which variant identification and interpretation can be challenging are encountered. We describe categories of challenges that cover the phenotype (e.g. novel allelic disorders), pedigree structure (e.g. imprinting disorders masquerading as autosomal recessive phenotypes), positional mapping (e.g. double recombination events abrogating candidate autozygous intervals), gene (e.g. novel gene-disease assertion) and variant (e.g. complex compound inheritance). Overall, we estimate a probability of 34.3% for encountering at least one of these challenges. Importantly, our data show that by only addressing non-sequencing-based challenges, around 71% increase in the diagnostic yield can be expected. Indeed, by applying these lessons to a cohort of 314 cases with negative clinical exome or genome reports, we could identify the likely causal variant in 54.5%. Our work highlights the need to have a thorough approach to undiagnosed diseases by considering a wide range of challenges rather than a narrow focus on sequencing technologies. It is hoped that by sharing this experience, the yield of undiagnosed disease programs globally can be improved.

Hypomyelination, hypodontia and craniofacial abnormalities in a Polr3b mouse model of leukodystrophy.

RNA polymerase III (Pol III)-related hypomyelinating leukodystrophy (POLR3-HLD), also known as 4H leukodystrophy, is a severe neurodegenerative disease characterized by the cardinal features of hypomyelination, hypodontia and hypogonadotropic hypogonadism. POLR3-HLD is caused by biallelic pathogenic variants in genes encoding Pol III subunits. While approximately half of all patients carry mutations in POLR3B encoding the RNA polymerase III subunit B, there is no in vivo model of leukodystrophy based on mutation of this Pol III subunit. Here, we determined the impact of POLR3BΔ10 (Δ10) on Pol III in human cells and developed and characterized an inducible/conditional mouse model of leukodystrophy using the orthologous Δ10 mutation in mice. The molecular mechanism of Pol III dysfunction was determined in human cells by affinity purification-mass spectrometry and western blot. Postnatal induction with tamoxifen induced expression of the orthologous Δ10 hypomorph in triple transgenic Pdgfrα-Cre/ERT; R26-Stopfl-EYFP; Polr3bfl mice. CNS and non-CNS features were characterized using a variety of techniques including microCT, ex vivo MRI, immunofluorescence, immunohistochemistry, spectral confocal reflectance microscopy and western blot. Lineage tracing and time series analysis of oligodendrocyte subpopulation dynamics based on co-labelling with lineage-specific and/or proliferation markers were performed. Proteomics suggested that Δ10 causes a Pol III assembly defect, while western blots demonstrated reduced POLR3BΔ10 expression in the cytoplasm and nucleus in human cells. In mice, postnatal Pdgfrα-dependent expression of the orthologous murine mutant protein resulted in recessive phenotypes including severe hypomyelination leading to ataxia, tremor, seizures and limited survival, as well as hypodontia and craniofacial abnormalities. Hypomyelination was confirmed and characterized using classic methods to quantify myelin components such as myelin basic protein and lipids, results which agreed with those produced using modern methods to quantify myelin based on the physical properties of myelin membranes. Lineage tracing uncovered the underlying mechanism for the hypomyelinating phenotype: defective oligodendrocyte precursor proliferation and differentiation resulted in a failure to produce an adequate number of mature oligodendrocytes during postnatal myelinogenesis. In summary, we characterized the Polr3bΔ10 mutation and developed an animal model that recapitulates features of POLR3-HLD caused by POLR3B mutations, shedding light on disease pathogenesis, and opening the door to the development of therapeutic interventions.

Lunapark deficiency leads to an autosomal recessive neurodevelopmental phenotype with a degenerative course, epilepsy and distinct brain anomalies.

LNPK encodes a conserved membrane protein that stabilizes the junctions of the tubular endoplasmic reticulum network playing crucial roles in diverse biological functions. Recently, homozygous variants in LNPK were shown to cause a neurodevelopmental disorder (OMIM#618090) in four patients displaying developmental delay, epilepsy and nonspecific brain malformations including corpus callosum hypoplasia and variable impairment of cerebellum. We sought to delineate the molecular and phenotypic spectrum of LNPK-related disorder. Exome or genome sequencing was carried out in 11 families. Thorough clinical and neuroradiological evaluation was performed for all the affected individuals, including review of previously reported patients. We identified 12 distinct homozygous loss-of-function variants in 16 individuals presenting with moderate to profound developmental delay, cognitive impairment, regression, refractory epilepsy and a recognizable neuroimaging pattern consisting of corpus callosum hypoplasia and signal alterations of the forceps minor ('ear-of-the-lynx' sign), variably associated with substantia nigra signal alterations, mild brain atrophy, short midbrain and cerebellar hypoplasia/atrophy. In summary, we define the core phenotype of LNPK-related disorder and expand the list of neurological disorders presenting with the 'ear-of-the-lynx' sign suggesting a possible common underlying mechanism related to endoplasmic reticulum-phagy dysfunction.