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1.
Cell ; 184(14): 3812-3828.e30, 2021 07 08.
Artículo en Inglés | MEDLINE | ID: mdl-34214472

RESUMEN

We study a patient with the human papilloma virus (HPV)-2-driven "tree-man" phenotype and two relatives with unusually severe HPV4-driven warts. The giant horns form an HPV-2-driven multifocal benign epithelial tumor overexpressing viral oncogenes in the epidermis basal layer. The patients are unexpectedly homozygous for a private CD28 variant. They have no detectable CD28 on their T cells, with the exception of a small contingent of revertant memory CD4+ T cells. T cell development is barely affected, and T cells respond to CD3 and CD2, but not CD28, costimulation. Although the patients do not display HPV-2- and HPV-4-reactive CD4+ T cells in vitro, they make antibodies specific for both viruses in vivo. CD28-deficient mice are susceptible to cutaneous infections with the mouse papillomavirus MmuPV1. The control of HPV-2 and HPV-4 in keratinocytes is dependent on the T cell CD28 co-activation pathway. Surprisingly, human CD28-dependent T cell responses are largely redundant for protective immunity.


Asunto(s)
Antígenos CD28/deficiencia , Patrón de Herencia/genética , Papillomaviridae/fisiología , Piel/virología , Linfocitos T/inmunología , Adulto , Secuencia de Aminoácidos , Animales , Secuencia de Bases , Antígenos CD28/genética , Antígenos CD28/metabolismo , Linfocitos T CD4-Positivos/inmunología , Niño , Endopeptidasas/metabolismo , Femenino , Genes Recesivos , Células HEK293 , Homocigoto , Humanos , Inmunidad Humoral , Memoria Inmunológica , Células Jurkat , Queratinocitos/patología , Masculino , Ratones Endogámicos C57BL , Oncogenes , Papiloma/patología , Papiloma/virología , Linaje , Señales de Clasificación de Proteína , ARN Mensajero/genética , ARN Mensajero/metabolismo
2.
Nature ; 613(7944): 519-525, 2023 01.
Artículo en Inglés | MEDLINE | ID: mdl-36653560

RESUMEN

Identifying causal factors for Mendelian and common diseases is an ongoing challenge in medical genetics1. Population bottleneck events, such as those that occurred in the history of the Finnish population, enrich some homozygous variants to higher frequencies, which facilitates the identification of variants that cause diseases with recessive inheritance2,3. Here we examine the homozygous and heterozygous effects of 44,370 coding variants on 2,444 disease phenotypes using data from the nationwide electronic health records of 176,899 Finnish individuals. We find associations for homozygous genotypes across a broad spectrum of phenotypes, including known associations with retinal dystrophy and novel associations with adult-onset cataract and female infertility. Of the recessive disease associations that we identify, 13 out of 20 would have been missed by the additive model that is typically used in genome-wide association studies. We use these results to find many known Mendelian variants whose inheritance cannot be adequately described by a conventional definition of dominant or recessive. In particular, we find variants that are known to cause diseases with recessive inheritance with significant heterozygous phenotypic effects. Similarly, we find presumed benign variants with disease effects. Our results show how biobanks, particularly in founder populations, can broaden our understanding of complex dosage effects of Mendelian variants on disease.


Asunto(s)
Alelos , Bancos de Muestras Biológicas , Enfermedad , Animales , Femenino , Estudio de Asociación del Genoma Completo , Fenotipo , Enfermedad/genética , Finlandia , Distrofias Retinianas , Catarata , Infertilidad Femenina , Genes Recesivos , Heterocigoto , Efecto Fundador , Dosificación de Gen , Registros Electrónicos de Salud
3.
Annu Rev Cell Dev Biol ; 30: 705-22, 2014.
Artículo en Inglés | MEDLINE | ID: mdl-25288120

RESUMEN

Most animal genomes are diploid, and mammalian development depends on specific adaptations that have evolved secondary to diploidy. Genomic imprinting and dosage compensation restrict haploid development to early embryos. Recently, haploid mammalian development has been reinvestigated since the establishment of haploid embryonic stem cells (ESCs) from mouse embryos. Haploid cells possess one copy of each gene, facilitating the generation of loss-of-function mutations in a single step. Recessive mutations can then be assessed in forward genetic screens. Applications of haploid mammalian cell systems in screens have been illustrated in several recent publications. Haploid ESCs are characterized by a wide developmental potential and can contribute to chimeric embryos and mice. Different strategies for introducing genetic modifications from haploid ESCs into the mouse germline have been further developed. Haploid ESCs therefore introduce new possibilities in mammalian genetics and could offer an unprecedented tool for genome exploration in the future.


Asunto(s)
Células Madre Embrionarias/citología , Haploidia , Animales , Blastocisto/citología , Quimera , Transferencia de Embrión , Desarrollo Embrionario , Genes Recesivos , Genes Reporteros , Pruebas Genéticas/métodos , Impresión Genómica , Mutación de Línea Germinal , Humanos , Ratones , Ratones Transgénicos , Neoplasias/genética , Partenogénesis , Especificidad de la Especie , Transgenes
4.
Am J Hum Genet ; 111(10): 2299-2306, 2024 Oct 03.
Artículo en Inglés | MEDLINE | ID: mdl-39226897

RESUMEN

Retinitis pigmentosa (RP) is a Mendelian disease characterized by gradual loss of vision, due to the progressive degeneration of retinal cells. Genetically, it is highly heterogeneous, with pathogenic variants identified in more than 100 genes so far. Following a large-scale sequencing screening, we identified five individuals (four families) with recessive and non-syndromic RP, carrying as well bi-allelic DNA changes in COQ8B, a gene involved in the biosynthesis of coenzyme Q10. Specifically, we detected compound heterozygous assortments of five disease-causing variants (c.187C>T [p.Arg63Trp], c.566G>A [p.Trp189Ter], c.1156G>A [p.Asp386Asn], c.1324G>A [p.Val442Met], and c.1560G>A [p.Trp520Ter]), all segregating with disease according to a recessive pattern of inheritance. Cell-based analysis of recombinant proteins deriving from these genotypes, performed by target engagement assays, showed in all cases a significant decrease in ligand-protein interaction compared to the wild type. Our results indicate that variants in COQ8B lead to recessive non-syndromic RP, possibly by impairing the biosynthesis of coenzyme Q10, a key component of oxidative phosphorylation in the mitochondria.


Asunto(s)
Alelos , Linaje , Retinitis Pigmentosa , Ubiquinona , Adulto , Femenino , Humanos , Masculino , Persona de Mediana Edad , Genes Recesivos , Heterocigoto , Mutación , Retinitis Pigmentosa/genética , Ubiquinona/biosíntesis , Ubiquinona/genética , Ubiquinona/análogos & derivados
5.
Cell ; 150(3): 533-48, 2012 Aug 03.
Artículo en Inglés | MEDLINE | ID: mdl-22863007

RESUMEN

Nephronophthisis-related ciliopathies (NPHP-RC) are degenerative recessive diseases that affect kidney, retina, and brain. Genetic defects in NPHP gene products that localize to cilia and centrosomes defined them as "ciliopathies." However, disease mechanisms remain poorly understood. Here, we identify by whole-exome resequencing, mutations of MRE11, ZNF423, and CEP164 as causing NPHP-RC. All three genes function within the DNA damage response (DDR) pathway. We demonstrate that, upon induced DNA damage, the NPHP-RC proteins ZNF423, CEP164, and NPHP10 colocalize to nuclear foci positive for TIP60, known to activate ATM at sites of DNA damage. We show that knockdown of CEP164 or ZNF423 causes sensitivity to DNA damaging agents and that cep164 knockdown in zebrafish results in dysregulated DDR and an NPHP-RC phenotype. Our findings link degenerative diseases of the kidney and retina, disorders of increasing prevalence, to mechanisms of DDR.


Asunto(s)
Daño del ADN , Proteínas de Unión al ADN/metabolismo , Exoma , Enfermedades Renales Quísticas/genética , Proteínas de Microtúbulos/metabolismo , Animales , Cilios/metabolismo , Técnicas de Silenciamiento del Gen , Genes Recesivos , Humanos , Proteína Homóloga de MRE11 , Ratones , Proteínas , Transducción de Señal , Pez Cebra/embriología , Pez Cebra/metabolismo
6.
Hum Mol Genet ; 32(5): 825-834, 2023 02 19.
Artículo en Inglés | MEDLINE | ID: mdl-36173926

RESUMEN

In human autosomal recessive woolly hair/hypotrichosis (ARWH/HT), many mutations have been identified in a gene encoding LPA6, a G protein-coupled receptor (GPCR) for lysophosphatidic acid (LPA). However, information regarding the effects of such mutations on receptor function is limited. In this study, we examined functional impacts of selected amino acid changes in LPA6 identified in ARWH/HT patients. In our exogenous expression experiments, all mutants except S3T failed to respond to LPA, indicating that they are loss-of-function mutants. Among the nine mutants, five (D63V, G146R, N246D, L277P and C278Y) displayed impaired expression at the cell surface because of endoplasmic reticulum (ER) retention, indicating that these mutants are trafficking-defective, as reported in other disease-associated GPCRs. Notably, alkyl-OMPT, a potent synthetic agonist for LPA6 restored the defective cell surface expression of two of the ER-retained mutants, D63V and N246D, possibly by its chaperoning function that allows them to escape intracellular retention as well as proteasomal degradation. Furthermore, the alkyl-OMPT-rescued N246D mutant was shown be functional. Our findings encourage future application of pharmacoperone therapy for ARWH/HT patients with specific LPA6 mutations.


Asunto(s)
Enfermedades del Cabello , Hipotricosis , Humanos , Hipotricosis/genética , Cabello , Enfermedades del Cabello/genética , Mutación , Genes Recesivos
7.
Am J Hum Genet ; 109(1): 33-49, 2022 01 06.
Artículo en Inglés | MEDLINE | ID: mdl-34951958

RESUMEN

The identification of genes that evolve under recessive natural selection is a long-standing goal of population genetics research that has important applications to the discovery of genes associated with disease. We found that commonly used methods to evaluate selective constraint at the gene level are highly sensitive to genes under heterozygous selection but ubiquitously fail to detect recessively evolving genes. Additionally, more sophisticated likelihood-based methods designed to detect recessivity similarly lack power for a human gene of realistic length from current population sample sizes. However, extensive simulations suggested that recessive genes may be detectable in aggregate. Here, we offer a method informed by population genetics simulations designed to detect recessive purifying selection in gene sets. Applying this to empirical gene sets produced significant enrichments for strong recessive selection in genes previously inferred to be under recessive selection in a consanguineous cohort and in genes involved in autosomal recessive monogenic disorders.


Asunto(s)
Frecuencia de los Genes , Genes Recesivos , Genética de Población , Selección Genética , Algoritmos , Alelos , Genes Dominantes , Predisposición Genética a la Enfermedad , Variación Genética , Genética de Población/métodos , Genómica/métodos , Genotipo , Humanos , Patrón de Herencia , Funciones de Verosimilitud , Modelos Genéticos , Mutación , Reino Unido
8.
Hum Genomics ; 18(1): 35, 2024 Apr 03.
Artículo en Inglés | MEDLINE | ID: mdl-38570878

RESUMEN

BACKGROUND: To investigate the genetics of early-onset progressive cerebellar ataxia in Iran, we conducted a study at the Children's Medical Center (CMC), the primary referral center for pediatric disorders in the country, over a three-year period from 2019 to 2022. In this report, we provide the initial findings from the national registry. METHODS: We selected all early-onset patients with an autosomal recessive mode of inheritance to assess their phenotype, paraclinical tests, and genotypes. The clinical data encompassed clinical features, the Scale for the Assessment and Rating of Ataxia (SARA) scores, Magnetic Resonance Imaging (MRI) results, Electrodiagnostic exams (EDX), and biomarker features. Our genetic investigations included single-gene testing, Whole Exome Sequencing (WES), and Whole Genome Sequencing (WGS). RESULTS: Our study enrolled 162 patients from various geographic regions of our country. Among our subpopulations, we identified known and novel pathogenic variants in 42 genes in 97 families. The overall genetic diagnostic rate was 59.9%. Notably, we observed PLA2G6, ATM, SACS, and SCA variants in 19, 14, 12, and 10 families, respectively. Remarkably, more than 59% of the cases were attributed to pathogenic variants in these genes. CONCLUSIONS: Iran, being at the crossroad of the Middle East, exhibits a highly diverse genetic etiology for autosomal recessive hereditary ataxia. In light of this heterogeneity, the development of preventive strategies and targeted molecular therapeutics becomes crucial. A national guideline for the diagnosis and management of patients with these conditions could significantly aid in advancing healthcare approaches and improving patient outcomes.


Asunto(s)
Degeneraciones Espinocerebelosas , Niño , Humanos , Irán/epidemiología , Degeneraciones Espinocerebelosas/genética , Pruebas Genéticas , Fenotipo , Genes Recesivos
9.
Nature ; 568(7753): 541-545, 2019 04.
Artículo en Inglés | MEDLINE | ID: mdl-30971820

RESUMEN

Osteoclasts are multinucleated giant cells that resorb bone, ensuring development and continuous remodelling of the skeleton and the bone marrow haematopoietic niche. Defective osteoclast activity leads to osteopetrosis and bone marrow failure1-9, whereas excess activity can contribute to bone loss and osteoporosis10. Osteopetrosis can be partially treated by bone marrow transplantation in humans and mice11-18, consistent with a haematopoietic origin of osteoclasts13,16,19 and studies that suggest that they develop by fusion of monocytic precursors derived from haematopoietic stem cells in the presence of CSF1 and RANK ligand1,20. However, the developmental origin and lifespan of osteoclasts, and the mechanisms that ensure maintenance of osteoclast function throughout life in vivo remain largely unexplored. Here we report that osteoclasts that colonize fetal ossification centres originate from embryonic erythro-myeloid progenitors21,22. These erythro-myeloid progenitor-derived osteoclasts are required for normal bone development and tooth eruption. Yet, timely transfusion of haematopoietic-stem-cell-derived monocytic cells in newborn mice is sufficient to rescue bone development in early-onset autosomal recessive osteopetrosis. We also found that the postnatal maintenance of osteoclasts, bone mass and the bone marrow cavity involve iterative fusion of circulating blood monocytic cells with long-lived osteoclast syncytia. As a consequence, parabiosis or transfusion of monocytic cells results in long-term gene transfer in osteoclasts in the absence of haematopoietic-stem-cell chimerism, and can rescue an adult-onset osteopetrotic phenotype caused by cathepsin K deficiency23,24. In sum, our results identify the developmental origin of osteoclasts and a mechanism that controls their maintenance in bones after birth. These data suggest strategies to rescue osteoclast deficiency in osteopetrosis and to modulate osteoclast activity in vivo.


Asunto(s)
Células Madre Hematopoyéticas/citología , Osteoclastos/citología , Osteoclastos/metabolismo , Osteopetrosis/genética , Animales , Animales Recién Nacidos , Desarrollo Óseo , Femenino , Genes Recesivos , Masculino , Ratones , Osteopetrosis/patología , Erupción Dental
10.
J Med Genet ; 61(8): 783-787, 2024 Jul 19.
Artículo en Inglés | MEDLINE | ID: mdl-38719349

RESUMEN

BACKGROUND: We aimed to analyse the efficacy and added value of a targeted Israeli expanded carrier screening panel (IL-ECSP), beyond the first-tier test covered by the Israeli Ministry of Health (IMOH) and the second-tier covered by the Health Maintenance Organisations (HMOs). METHODS: A curated variant-based IL-ECSP, tailored to the uniquely diverse Israeli population, was offered at two tertiary hospitals and a major genetics laboratory. The panel includes 1487 variants in 357 autosomal recessive and X-linked genes. RESULTS: We analysed 10 115 Israeli samples during an 18-month period. Of these, 6036 (59.7%) were tested as couples and 4079 (40.3%) were singles. Carriers were most frequently identified with mutations in the following genes: GJB2/GJB6 (1:22 allele frequency), CFTR (1:28), GBA (1:34), TYR (1:39), PAH (1:50), SMN1 (1:52) and HEXA (1:56). Of 3018 couples tested, 753 (25%) had no findings, in 1464 (48.5%) only one partner was a carrier, and in 733 (24.3%) both were carriers of different diseases. We identified 79 (2.6%) at-risk couples, where both partners are carriers of the same autosomal recessive condition, or the female carries an X-linked disease. Importantly, 48.1% of these would not have been detected by ethnically-based screening tests currently provided by the IMOH and HMOs, for example, variants in GBA, TYR, PAH and GJB2/GJB6. CONCLUSION: This is the largest cohort of targeted ECSP testing, tailored to the diverse Israeli population. The IL-ECSP expands the identification of couples at risk and empowers their reproductive choices. We recommend endorsing an expanded targeted panel to the National Genetic Carrier Screening programme.


Asunto(s)
Conexina 26 , Pruebas Genéticas , Humanos , Israel/epidemiología , Femenino , Pruebas Genéticas/métodos , Masculino , Conexina 26/genética , Conexinas/genética , Tamización de Portadores Genéticos/métodos , Mutación , Atención Preconceptiva/métodos , Frecuencia de los Genes , Asesoramiento Genético , Heterocigoto , Genes Recesivos , Adulto
11.
Hum Hered ; 89(1): 1-7, 2024.
Artículo en Inglés | MEDLINE | ID: mdl-38342085

RESUMEN

INTRODUCTION: Previous studies have demonstrated effects of rare coding variants on common, clinically relevant phenotypes although the additive burden of these variants makes only a small contribution to overall trait variance. Although recessive effects of individual homozygous variants have been studied, little work has been done to elucidate the impact of rare coding variants occurring together as compound heterozygotes. METHODS: In this study, attempts were made to identify pairs of variants likely to be occurring as compound heterozygotes using 200,000 exome-sequenced subjects from the UK Biobank. Pairs of variants, which were seen together in the same subject more often than would be expected by chance, were excluded as it was assumed that these might be present in the same haplotype. Attention was restricted to variants with minor allele frequency ≤0.05 and to those predicted to alter amino acid sequence or prevent normal gene expression. For each gene, compound heterozygotes were assigned scores based on the rarity and predicted functional consequences of the constituent variants and the scores were used in a logistic regression analysis to test for association with hypertension, hyperlipidaemia, and type 2 diabetes. RESULTS: No statistically significant associations were observed and the results conformed to the distribution, which would be expected under the null hypothesis. The average number of apparently compound heterozygous subjects for each gene was only 282.2. CONCLUSION: It seems difficult to detect an effect of compound heterozygotes on the risk of these phenotypes. Even if recessive effects from compound heterozygotes do occur, they would only affect a small number of people and overall would not make a substantial contribution to phenotypic variance. This research has been conducted using the UK Biobank Resource.


Asunto(s)
Exoma , Fenotipo , Femenino , Humanos , Masculino , Diabetes Mellitus Tipo 2/genética , Exoma/genética , Secuenciación del Exoma/métodos , Frecuencia de los Genes/genética , Genes Recesivos , Predisposición Genética a la Enfermedad , Variación Genética , Heterocigoto , Biobanco del Reino Unido , Reino Unido
12.
J Cell Mol Med ; 28(8): e18119, 2024 Apr.
Artículo en Inglés | MEDLINE | ID: mdl-38534090

RESUMEN

Hearing loss is a clinically and genetically heterogeneous disorder, with over 148 genes and 170 loci associated with its pathogenesis. The spectrum and frequency of causal variants vary across different genetic ancestries and are more prevalent in populations that practice consanguineous marriages. Pakistan has a rich history of autosomal recessive gene discovery related to non-syndromic hearing loss. Since the first linkage analysis with a Pakistani family that led to the mapping of the DFNB1 locus on chromosome 13, 51 genes associated with this disorder have been identified in this population. Among these, 13 of the most prevalent genes, namely CDH23, CIB2, CLDN14, GJB2, HGF, MARVELD2, MYO7A, MYO15A, MSRB3, OTOF, SLC26A4, TMC1 and TMPRSS3, account for more than half of all cases of profound hearing loss, while the prevalence of other genes is less than 2% individually. In this review, we discuss the most common autosomal recessive non-syndromic hearing loss genes in Pakistani individuals as well as the genetic mapping and sequencing approaches used to discover them. Furthermore, we identified enriched gene ontology terms and common pathways involved in these 51 autosomal recessive non-syndromic hearing loss genes to gain a better understanding of the underlying mechanisms. Establishing a molecular understanding of the disorder may aid in reducing its future prevalence by enabling timely diagnostics and genetic counselling, leading to more effective clinical management and treatments of hearing loss.


Asunto(s)
Sordera , Pérdida Auditiva , Humanos , Genes Recesivos , Pakistán , Mutación , Pérdida Auditiva/genética , Linaje , Proteínas de la Membrana/genética , Proteínas de Neoplasias/genética , Serina Endopeptidasas/genética , Proteína 2 con Dominio MARVEL/genética
13.
BMC Genomics ; 25(1): 417, 2024 Apr 27.
Artículo en Inglés | MEDLINE | ID: mdl-38678201

RESUMEN

BACKGROUND: Between 2020 and 2022, eight calves in a Nebraska herd (composite Simmental, Red Angus, Gelbvieh) displayed exercise intolerance during forced activity. In some cases, the calves collapsed and did not recover. Available sire pedigrees contained a paternal ancestor within 2-4 generations in all affected calves. Pedigrees of the calves' dams were unavailable, however, the cows were ranch-raised and retained from prior breeding seasons, where bulls used for breeding occasionally had a common ancestor. Therefore, it was hypothesized that a de novo autosomal recessive variant was causative of exercise intolerance in these calves. RESULTS: A genome-wide association analysis utilizing SNP data from 6 affected calves and 715 herd mates, followed by whole-genome sequencing of 2 affected calves led to the identification of a variant in the gene PYGM (BTA29:g.42989581G > A). The variant, confirmed to be present in the skeletal muscle transcriptome, was predicted to produce a premature stop codon (p.Arg650*). The protein product of PYGM, myophosphorylase, breaks down glycogen in skeletal muscle. Glycogen concentrations were fluorometrically assayed as glucose residues demonstrating significantly elevated glycogen concentrations in affected calves compared to cattle carrying the variant and to wild-type controls. The absence of the PYGM protein product in skeletal muscle was confirmed by immunohistochemistry and label-free quantitative proteomics analysis; muscle degeneration was confirmed in biopsy and necropsy samples. Elevated skeletal muscle glycogen persisted after harvest, resulting in a high pH and dark-cutting beef, which is negatively perceived by consumers and results in an economic loss to the industry. Carriers of the variant did not exhibit differences in meat quality or any measures of animal well-being. CONCLUSIONS: Myophosphorylase deficiency poses welfare concerns for affected animals and negatively impacts the final product. The association of the recessive genotype with dark-cutting beef further demonstrates the importance of genetics to not only animal health but to the quality of their product. Although cattle heterozygous for the variant may not immediately affect the beef industry, identifying carriers will enable selection and breeding strategies to prevent the production of affected calves.


Asunto(s)
Estudio de Asociación del Genoma Completo , Glucógeno Fosforilasa de Forma Muscular , Animales , Bovinos , Femenino , Masculino , Enfermedades de los Bovinos/genética , Genes Recesivos , Glucógeno Fosforilasa de Forma Muscular/genética , Glucógeno Fosforilasa de Forma Muscular/deficiencia , Músculo Esquelético/metabolismo , Músculo Esquelético/patología , Linaje , Polimorfismo de Nucleótido Simple , Secuenciación Completa del Genoma
14.
Neurogenetics ; 25(2): 79-83, 2024 Apr.
Artículo en Inglés | MEDLINE | ID: mdl-38240911

RESUMEN

Narcolepsy with cataplexy is a complex disease with both genetic and environmental risk factors. To gain further insight into the homozygous HCRT-related narcolepsy, we present a case series of five patients from two consanguineous families, each harboring a novel homozygous variant of HCRT c.17_18del. All affected individuals exhibited severe cataplexy accompanied by narcolepsy symptoms during infancy. Additionally, cataplexy symptoms improved or disappeared in the majority of patients over time. Pathogenic variants in HCRT cause autosomal recessive narcolepsy with cataplexy. Genetic testing of the HCRT gene should be conducted in specific subgroups of narcolepsy, particularly those with early onset, familial cases, and a predominantly cataplexy phenotype.


Asunto(s)
Narcolepsia , Linaje , Adolescente , Adulto , Niño , Femenino , Humanos , Masculino , Alelos , Cataplejía/genética , Consanguinidad , Genes Recesivos , Homocigoto , Mutación/genética , Narcolepsia/genética , Orexinas/genética , Fenotipo
15.
Hum Genet ; 143(3): 311-329, 2024 Mar.
Artículo en Inglés | MEDLINE | ID: mdl-38459354

RESUMEN

Identification of genes associated with nonsyndromic hearing loss is a crucial endeavor given the substantial number of individuals who remain without a diagnosis after even the most advanced genetic testing. PKHD1L1 was established as necessary for the formation of the cochlear hair-cell stereociliary coat and causes hearing loss in mice and zebrafish when mutated. We sought to determine if biallelic variants in PKHD1L1 also cause hearing loss in humans. Exome sequencing was performed on DNA of four families segregating autosomal recessive nonsyndromic sensorineural hearing loss. Compound heterozygous p.[(Gly129Ser)];p.[(Gly1314Val)] and p.[(Gly605Arg)];p[(Leu2818TyrfsTer5)], homozygous missense p.(His2479Gln) and nonsense p.(Arg3381Ter) variants were identified in PKHD1L1 that were predicted to be damaging using in silico pathogenicity prediction methods. In vitro functional analysis of two missense variants was performed using purified recombinant PKHD1L1 protein fragments. We then evaluated protein thermodynamic stability with and without the missense variants found in one of the families and performed a minigene splicing assay for another variant. In silico molecular modeling using AlphaFold2 and protein sequence alignment analysis were carried out to further explore potential variant effects on structure. In vitro functional assessment indicated that both engineered PKHD1L1 p.(Gly129Ser) and p.(Gly1314Val) mutant constructs significantly reduced the folding and structural stabilities of the expressed protein fragments, providing further evidence to support pathogenicity of these variants. Minigene assay of the c.1813G>A p.(Gly605Arg) variant, located at the boundary of exon 17, revealed exon skipping leading to an in-frame deletion of 48 amino acids. In silico molecular modeling exposed key structural features that might suggest PKHD1L1 protein destabilization. Multiple lines of evidence collectively associate PKHD1L1 with nonsyndromic mild-moderate to severe sensorineural hearing loss. PKHD1L1 testing in individuals with mild-moderate hearing loss may identify further affected families.


Asunto(s)
Sordera , Mutación Missense , Linaje , Receptores de Superficie Celular , Estereocilios , Animales , Femenino , Humanos , Masculino , Sordera/genética , Secuenciación del Exoma , Genes Recesivos , Pérdida Auditiva Sensorineural/genética , Pérdida Auditiva Sensorineural/patología , Modelos Moleculares , Receptores de Superficie Celular/genética , Estereocilios/metabolismo , Estereocilios/patología , Estereocilios/genética
16.
Am J Hum Genet ; 108(5): 764-785, 2021 05 06.
Artículo en Inglés | MEDLINE | ID: mdl-33811808

RESUMEN

Tandem repeats represent one of the most abundant class of variations in human genomes, which are polymorphic by nature and become highly unstable in a length-dependent manner. The expansion of repeat length across generations is a well-established process that results in human disorders mainly affecting the central nervous system. At least 50 disorders associated with expansion loci have been described to date, with half recognized only in the last ten years, as prior methodological difficulties limited their identification. These limitations still apply to the current widely used molecular diagnostic methods (exome or gene panels) and thus result in missed diagnosis detrimental to affected individuals and their families, especially for disorders that are very rare and/or clinically not recognizable. Most of these disorders have been identified through family-driven approaches and many others likely remain to be identified. The recent development of long-read technologies provides a unique opportunity to systematically investigate the contribution of tandem repeats and repeat expansions to the genetic architecture of human disorders. In this review, we summarize the current and most recent knowledge about the genetics of repeat expansion disorders and the diversity of their pathophysiological mechanisms and outline the perspectives of developing personalized treatments in the future.


Asunto(s)
Investigación Biomédica/tendencias , Expansión de Repetición de Trinucleótido , Anticipación Genética , Efecto Fundador , Genes Dominantes , Genes Recesivos , Genoma Humano/genética , Humanos , Factores de Tiempo , Expansión de Repetición de Trinucleótido/genética
17.
Am J Hum Genet ; 108(7): 1318-1329, 2021 07 01.
Artículo en Inglés | MEDLINE | ID: mdl-34077761

RESUMEN

TP73 belongs to the TP53 family of transcription factors and has therefore been well studied in cancer research. Studies in mice, however, have revealed non-oncogenic activities related to multiciliogenesis. Utilizing whole-exome sequencing analysis in a cohort of individuals with a mucociliary clearance disorder and cortical malformation, we identified homozygous loss-of-function variants in TP73 in seven individuals from five unrelated families. All affected individuals exhibit a chronic airway disease as well as a brain malformation consistent with lissencephaly. We performed high-speed video microscopy, immunofluorescence analyses, and transmission electron microscopy in respiratory epithelial cells after spheroid or air liquid interface culture to analyze ciliary function, ciliary length, and number of multiciliated cells (MCCs). The respiratory epithelial cells studied display reduced ciliary length and basal bodies mislocalized within the cytoplasm. The number of MCCs is severely reduced, consistent with a reduced number of cells expressing the transcription factors crucial for multiciliogenesis (FOXJ1, RFX2). Our data demonstrate that autosomal-recessive deleterious variants in the TP53 family member TP73 cause a mucociliary clearance disorder due to a defect in MCC differentiation.


Asunto(s)
Lisencefalia/genética , Depuración Mucociliar/genética , Mucosa Respiratoria/metabolismo , Proteína Tumoral p73/genética , Diferenciación Celular/genética , Células Cultivadas , Ciliopatías/genética , Genes Recesivos , Homocigoto , Humanos , Mutación con Pérdida de Función , Microscopía por Video , Mucosa Respiratoria/citología , Mucosa Respiratoria/ultraestructura , Secuenciación del Exoma
18.
Am J Hum Genet ; 108(4): 608-619, 2021 04 01.
Artículo en Inglés | MEDLINE | ID: mdl-33740458

RESUMEN

The number and distribution of recessive alleles in the population for various diseases are not known at genome-wide-scale. Based on 6,447 exome sequences of healthy, genetically unrelated Europeans of two distinct ancestries, we estimate that every individual is a carrier of at least 2 pathogenic variants in currently known autosomal-recessive (AR) genes and that 0.8%-1% of European couples are at risk of having a child affected with a severe AR genetic disorder. This risk is 16.5-fold higher for first cousins but is significantly more increased for skeletal disorders and intellectual disabilities due to their distinct genetic architecture.


Asunto(s)
Consanguinidad , Composición Familiar , Genes Recesivos/genética , Variación Genética/genética , Fenotipo , Población Blanca/genética , Estudios de Cohortes , Europa (Continente)/etnología , Exoma/genética , Femenino , Pruebas Genéticas , Salud , Heterocigoto , Humanos , Discapacidad Intelectual/genética , Masculino
19.
Am J Hum Genet ; 108(1): 186-193, 2021 01 07.
Artículo en Inglés | MEDLINE | ID: mdl-33417887

RESUMEN

POLR3B encodes the second-largest catalytic subunit of RNA polymerase III, an enzyme involved in transcription. Bi-allelic pathogenic variants in POLR3B are a well-established cause of hypomyelinating leukodystrophy. We describe six unrelated individuals with de novo missense variants in POLR3B and a clinical presentation substantially different from POLR3-related leukodystrophy. These individuals had afferent ataxia, spasticity, variable intellectual disability and epilepsy, and predominantly demyelinating sensory motor peripheral neuropathy. Protein modeling and proteomic analysis revealed a distinct mechanism of pathogenicity; the de novo POLR3B variants caused aberrant association of individual enzyme subunits rather than affecting overall enzyme assembly or stability. We expand the spectrum of disorders associated with pathogenic variants in POLR3B to include a de novo heterozygous POLR3B-related disorder.


Asunto(s)
Ataxia/genética , Enfermedades Desmielinizantes del Sistema Nervioso Central Hereditarias/genética , ARN Polimerasa III/genética , Adolescente , Adulto , Ataxia Cerebelosa/genética , Niño , Preescolar , Femenino , Genes Recesivos/genética , Heterocigoto , Humanos , Masculino , Mutación Missense/genética , Proteómica/métodos , Adulto Joven
20.
Am J Hum Genet ; 108(7): 1301-1317, 2021 07 01.
Artículo en Inglés | MEDLINE | ID: mdl-34038740

RESUMEN

Human C2orf69 is an evolutionarily conserved gene whose function is unknown. Here, we report eight unrelated families from which 20 children presented with a fatal syndrome consisting of severe autoinflammation and progredient leukoencephalopathy with recurrent seizures; 12 of these subjects, whose DNA was available, segregated homozygous loss-of-function C2orf69 variants. C2ORF69 bears homology to esterase enzymes, and orthologs can be found in most eukaryotic genomes, including that of unicellular phytoplankton. We found that endogenous C2ORF69 (1) is loosely bound to mitochondria, (2) affects mitochondrial membrane potential and oxidative respiration in cultured neurons, and (3) controls the levels of the glycogen branching enzyme 1 (GBE1) consistent with a glycogen-storage-associated mitochondriopathy. We show that CRISPR-Cas9-mediated inactivation of zebrafish C2orf69 results in lethality by 8 months of age due to spontaneous epileptic seizures, which is preceded by persistent brain inflammation. Collectively, our results delineate an autoinflammatory Mendelian disorder of C2orf69 deficiency that disrupts the development/homeostasis of the immune and central nervous systems.


Asunto(s)
Encefalitis/genética , Enfermedades Mitocondriales/genética , Animales , Evolución Biológica , Sistemas CRISPR-Cas , Línea Celular , Encefalitis/mortalidad , Femenino , Genes Recesivos , Glucógeno/metabolismo , Humanos , Inflamación/genética , Masculino , Proteínas de la Membrana/genética , Enfermedades Mitocondriales/mortalidad , Linaje , Convulsiones/genética , Convulsiones/mortalidad , Pez Cebra/genética
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