Heterozygous Protein-truncating Variants Research Articles

Human genetic analyses of organelles highlight the nucleus in age-related trait heritability.

Most age-related human diseases are accompanied by a decline in cellular organelle integrity, including impaired lysosomal proteostasis and defective mitochondrial oxidative phosphorylation. An open question, however, is the degree to which inherited variation in or near genes encoding each organelle contributes to age-related disease pathogenesis. Here, we evaluate if genetic loci encoding organelle proteomes confer greater-than-expected age-related disease risk. As mitochondrial dysfunction is a 'hallmark' of aging, we begin by assessing nuclear and mitochondrial DNA loci near genes encoding the mitochondrial proteome and surprisingly observe a lack of enrichment across 24 age-related traits. Within nine other organelles, we find no enrichment with one exception: the nucleus, where enrichment emanates from nuclear transcription factors. In agreement, we find that genes encoding several organelles tend to be 'haplosufficient,' while we observe strong purifying selection against heterozygous protein-truncating variants impacting the nucleus. Our work identifies common variation near transcription factors as having outsize influence on age-related trait risk, motivating future efforts to determine if and how this inherited variation then contributes to observed age-related organelle deterioration.

Functional and clinical implications of genetic structure in 1686 Italian exomes.

To reconstruct the phenotypical and clinical implications of the Italian genetic structure, we thoroughly analyzed a whole-exome sequencing data set comprised of 1686 healthy Italian individuals. We found six previously unreported variants with remarkable frequency differences between Northern and Southern Italy in the HERC2, OR52R1, ADH1B, and THBS4 genes. We reported 36 clinically relevant variants (submitted as pathogenic, risk factors, or drug response in ClinVar) with significant frequency differences between Italy and Europe. We then explored putatively pathogenic variants in the Italian exome. On average, our Italian individuals carried 16.6 protein-truncating variants (PTVs), with 2.5% of the population having a PTV in one of the 59 American College of Medical Genetics (ACMG) actionable genes. Lastly, we looked for PTVs that are likely to cause Mendelian diseases. We found four heterozygous PTVs in haploinsufficient genes (KAT6A, PTCH1, and STXBP1) and three homozygous PTVs in genes causing recessive diseases (DPYD, FLG, and PYGM). Comparing frequencies from our data set to other public databases, like gnomAD, we showed the importance of population-specific databases for a more accurate assessment of variant pathogenicity. For this reason, we made aggregated frequencies from our data set publicly available as a tool for both clinicians and researchers (http://nigdb.cineca.it; NIG-ExIT).

Exome Sequencing and Congenital Heart Disease in Sub-Saharan Africa.

Congenital heart disease (CHD) is the most common birth defect and affects roughly 1% of the global population. There have been many large CHD sequencing projects in developing countries but none in sub-Saharan Africa. In this exome sequencing study, we recruited families from Lagos, Nigeria, affected by structural heart disease. Ninety-eight participants with CHD and an average age of 3.6 years were recruited from Lagos, Nigeria. Exome sequencing was performed on probands and parents when available. For genes of high interest, we conducted functional studies in Drosophila using a cardiac-specific RNA interference-based gene silencing system. The 3 most common CHDs were tetralogy of Fallot (20%), isolated ventricular septal defect (14%), and transposition of the great arteries (8%). Ten percent of the cohort had pathogenic or likely pathogenic variants in genes known to cause CHD. In 64 complete trios, we found 34 de novo variants that were not present in the African population in the Genome Aggregation Database (v3). Nineteen loss of function variants were identified using the genome-wide distribution of selection effects for heterozygous protein-truncating variants (shet). Nine genes caused a significant mortality when silenced in the Drosophila heart, including 4 novel disease genes not previously associated with CHD (UBB, EIF4G3, SREBF1, and METTL23). This study identifies novel candidate genes and variants for CHD and facilitates comparisons with previous CHD sequencing studies in predominantly European cohorts. The study represents an important first step in genomic studies of CHD in understudied populations. Registration: URL: https://www.clinicaltrials.gov; Unique identifier: NCT01952171.

Neuron-derived neurotrophic factor is mutated in congenital hypogonadotropic hypogonadism

Congenital hypogonadotropic hypogonadism (CHH) is a rare genetic disorder characterized by infertility and the absence of puberty. Defects in GnRH neuron migration or altered GnRH secretion and/or action lead to a severe gonadotropin-releasing hormone (GnRH) deficiency. Given the close developmental association of GnRH neurons with the olfactory primary axons, CHH is often associated with anosmia or hyposmia, in which case it is defined as Kallmann syndrome (KS). The genetics of CHH are heterogeneous, and >40 genes are involved either alone or in combination. Several CHH-related genes controlling GnRH ontogeny encode proteins containing fibronectin-3 (FN3) domains, which are important for brain and neural development. Therefore, we hypothesized that defects in other FN3-superfamily genes would underlie CHH. Next-generation sequencing was performed for 240 CHH unrelated probands and filtered for rare, protein-truncating variants (PTVs) in FN3-superfamily genes. Compared to gnomAD controls the CHH cohort was statistically enriched for PTVs in neuron-derived neurotrophic factor (NDNF) (p = 1.40 × 10−6). Three heterozygous PTVs (p.Lys62∗, p.Tyr128Thrfs∗55, and p.Trp469∗, all absent from the gnomAD database) and an additional heterozygous missense mutation (p.Thr201Ser) were found in four KS probands. Notably, NDNF is expressed along the GnRH neuron migratory route in both mouse embryos and human fetuses and enhances GnRH neuron migration. Further, knock down of the zebrafish ortholog of NDNF resulted in altered GnRH migration. Finally, mice lacking Ndnf showed delayed GnRH neuron migration and altered olfactory axonal projections to the olfactory bulb; both results are consistent with a role of NDNF in GnRH neuron development. Altogether, our results highlight NDNF as a gene involved in the GnRH neuron migration implicated in KS.

1550-P: Whole-Exome Sequencing in Children with Suspected Maturity-Onset Diabetes of the Young (MODY)

The yield of commercial gene panels for MODY has been reported as low as 27% suggesting the role of un-identified gene variants in MODY. We aimed to study novel genetic factors of MODY. We identified 10 probands who had clinical characteristics suggestive of MODY (i.e., positive family history of diabetes, negative islet autoantibodies, and diagnosis of diabetes at <25 y/o) but negative genetic test results on a commercial MODY gene panel. We performed whole-exome sequencing (WES) in probands and their parents. In each trio, we prioritized rare protein-altering variants (stop-gain, frameshift indels, splicing and missense variants) in 70 neonatal diabetes and MODY candidate genes. Mean age at diabetes diagnosis was 10 (± 3.8) years. Six were females; 4 were non-Hispanic white, 5 Hispanic, and 1 Asian. Previously assigned diabetes types were type 1 diabetes (T1D) (n=7), unknown (n=2) and ketosis-prone diabetes (n=1). We found a likely pathogenic, de novo variant in INS gene (c.94G>A, p.Gly32Ser), confirmed by Sanger sequencing, in a proband who was previously diagnosed with T1D at 3 y/o. This very rare variant, absent in the general population (gnomAD database), has been reported previously in multiple individuals with neonatal diabetes. We also identified a frameshift deletion (c.2650delC, p.Gln884AsnfsTer57) in RFX6 gene in a child with a previous diagnosis of T1D at 12 y/o. The variant was inherited from the mother, who was diagnosed with diabetes of unknown etiology at 25 y/o. Heterozygous protein-truncating variants in RFX6 gene have been recently reported in individuals with MODY. In conclusion, we identified two new MODY cases, with a novel variant not previously associated with MODY in one of them, using WES in children who were initially diagnosed with T1D. Our study demonstrates clinical utility of exome sequencing in atypical cases of diabetes suspected of MODY. Disclosure M. Tosur: None. A. Sabo: None. M.M. Khayat: None. S.N. Jhangiani: None. A.K. Refaey: None. D. Muzny: None. R.A. Gibbs: None. A. Balasubramanyam: None. M.J. Redondo: None. Funding Mike Hogg Fund

Neuron-Derived Neurotrophic Factor Is Mutated in Congenital Hypogonadotropic Hypogonadism

Congenital hypogonadotropic hypogonadism (CHH) is a rare genetic disorder characterized by infertility and the absence of puberty. Defects in GnRH neuron migration or altered GnRH secretion and/or action lead to a severe gonadotropin-releasing hormone (GnRH) deficiency. Given the close developmental association of GnRH neurons with the olfactory primary axons, CHH is often associated with anosmia or hyposmia, in which case it is defined as Kallmann syndrome (KS). The genetics of CHH are heterogeneous, and >40 genes are involved either alone or in combination. Several CHH-related genes controlling GnRH ontogeny encode proteins containing fibronectin-3 (FN3) domains, which are important for brain and neural development. Therefore, we hypothesized that defects in other FN3-superfamily genes would underlie CHH. Next-generation sequencing was performed for 240 CHH unrelated probands and filtered for rare, protein-truncating variants (PTVs) in FN3-superfamily genes. Compared to gnomAD controls the CHH cohort was statistically enriched for PTVs in neuron-derived neurotrophic factor (NDNF) (p = 1.40× 10-6). Three heterozygous PTVs (p.Lys62∗, p.Tyr128Thrfs∗55, and p.Trp469∗, all absent from the gnomAD database) and an additional heterozygous missense mutation (p.Thr201Ser) were found in four KS probands. Notably, NDNF is expressed along the GnRH neuron migratory route in both mouse embryos and human fetuses and enhances GnRH neuron migration. Further, knock down of the zebrafish ortholog of NDNF resulted in altered GnRH migration. Finally, mice lacking Ndnf showed delayed GnRH neuron migration and altered olfactory axonal projections to the olfactory bulb; both results are consistent with a role of NDNF in GnRH neuron development. Altogether, our results highlight NDNF as a gene involved in the GnRH neuron migration implicated in KS.

HIST1H1E heterozygous protein-truncating variants cause a recognizable syndrome with intellectual disability and distinctive facial gestalt: A study to clarify the HIST1H1E syndrome phenotype in 30 individuals.

Histone Gene Cluster 1 Member E, HIST1H1E, encodes Histone H1.4, is one of a family of epigenetic regulator genes, acts as a linker histone protein, and is responsible for higher order chromatin structure. HIST1H1E syndrome (also known as Rahman syndrome, OMIM #617537) is a recently described intellectual disability (ID) syndrome. Since the initial description of five unrelated individuals with three different heterozygous protein-truncating variants (PTVs) in the HIST1H1E gene in 2017, we have recruited 30 patients, all with HIST1H1E PTVs that result in the same shift in frame and that cluster to a 94-base pair region in the HIST1H1E carboxy terminal domain. The identification of 30 patients with HIST1H1E variants has allowed the clarification of the HIST1H1E syndrome phenotype. Major findings include an ID and a recognizable facial appearance. ID was reported in all patients and is most frequently of moderate severity. The facial gestalt consists of a high frontal hairline and full lower cheeks in early childhood and, in later childhood and adulthood, affected individuals have a strikingly high frontal hairline, frontal bossing, and deep-set eyes. Other associated clinical features include hypothyroidism, abnormal dentition, behavioral issues, cryptorchidism, skeletal anomalies, and cardiac anomalies. Brain magnetic resonance imaging (MRI) is frequently abnormal with a slender corpus callosum a frequent finding.

Abstract 1734: Crispr/Cas9 screening of Brca1 and Brca2 susceptibility genes in breast and ovarian cancer precursor cells can identify phenotypically different mutants with variable penetrance

Abstract BRCA1 and BRCA2 mutations are the most significant risk factors for breast and ovarian cancer identified so far. A recent analysis of breast/ovarian cancer risks in approx. 12,000 BRCA1 carriers and 7,000 BRCA2 carriers found that PTVs (protein truncating variants) in the central region of both genes are more associated with ovarian cancer development (Ovarian Cancer Cluster Regions (OCCRs)), while PTVs in the 5’ and 3’ regions are more associated with breast cancer development (Breast Cancer Cluster Regions (BCCRs)). We aimed to identify the functional consequences of different BRCA1/2 mutants by creating various PTVs in BCCR and OCCR regions of both genes in precursor cell types for Basal-like Breast Cancer (BLBC) and High-Grade Serous Ovarian Cancer (HGSOC). To this end, we created partially transformed models of breast and fallopian tube epithelial cells (MCF12A and FT282, respectively) via an overexpression of a hot-spot p53 mutation (R175H), frequently observed in BLBC and HGSOC. We then generated PTVs in MCF12Ap53R175H and FT282p53R175H cells in two regions of BRCA1 (exon 11 (OCCR) and 16 (BCCR)) and two regions of BRCA2 (exon 9 (BCCR) and 13 (OCCR)) using CRISPR/Cas9 system. We targeted the olfactory receptor OR10A4 as a negative control. We clonally derived cell lines and genotyped PTVs via molecular cloning and Sanger sequencing. We established models of MCF12Ap53R175H and FT282p53R175H cells carrying PTVs for almost all regions. Mostly heterozygous PTVs survived; except of BRCA1 BCCR PTVs, which were lethal in FT282p53R175H, while MCF12Ap53R175H cells survived homozygous PTVs in this region. Typically, all PTVs led to diminished growth, although FT282p53R175H with BRCA2 OCCR PTVs showed similar proliferation rate as control. Heterozygous BRCA1/2 mutations were sufficient to induce nonsense mediated decay of BRCA1/2 mRNA transcripts. BRCA1 OCCR PTVs also specifically increased processing of delta11q splice isoform, known to decrease PARP inhibitor and Cisplatin sensitivity in BRCA1 mutant cell lines. Consistently, derived BRCA1/2 mutant clones showed increased Cisplatin resistance. Immunofluorescence and flow cytometry confirmed decreased BRCA1 protein levels upon introduction of BRCA1 PTVs. Our studies demonstrate that different BRCA1/2 mutations have different phenotypic effects in breast and ovarian cancer precursor cells. We found that BRCA1 and BRCA2 BCCR PTVs in FT282p53R175H had more severe effect on survival and proliferation than OCCR PTVs. This suggests that OCCR PTVs may have survival advantage in FT282p53R175H cells, compared to BCCR PTVs. Next, we will perform high-throughput CRISPR/Cas9 screen of hundreds of BRCA1 and BRCA2 PTVs to functionally validate the genetic epidemiology data indicating the different disease risks for different germline mutations in these susceptibility genes. Citation Format: Justyna Kanska, Kruttika Dabke, Zachary Schwartz, Norma Rodriquez-Malave, Nikoo Safi, Simon Gayther. Crispr/Cas9 screening of Brca1 and Brca2 susceptibility genes in breast and ovarian cancer precursor cells can identify phenotypically different mutants with variable penetrance [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2019; 2019 Mar 29-Apr 3; Atlanta, GA. Philadelphia (PA): AACR; Cancer Res 2019;79(13 Suppl):Abstract nr 1734.

Applicability of the Mutation-Selection Balance Model to Population Genetics of Heterozygous Protein-Truncating Variants in Humans.

The fate of alleles in the human population is believed to be highly affected by the stochastic force of genetic drift. Estimation of the strength of natural selection in humans generally necessitates a careful modeling of drift including complex effects of the population history and structure. Protein-truncating variants (PTVs) are expected to evolve under strong purifying selection and to have a relatively high per-gene mutation rate. Thus, it is appealing to model the population genetics of PTVs under a simple deterministic mutation-selection balance, as has been proposed earlier (Cassa etal. 2017). Here, we investigated the limits of this approximation using both computer simulations and data-driven approaches. Our simulations rely on a model of demographic history estimated from 33,370 individual exomes of the Non-Finnish European subset of the ExAC data set (Lek etal. 2016). Additionally, we compared the African and European subset of the ExAC study and analyzed de novo PTVs. We show that the mutation-selection balance model is applicable to the majority of human genes, but not to genes under the weakest selection.

Publisher Correction: Selective effects of heterozygous protein-truncating variants.

In the version of this article initially published, reference 10 incorrectly cited Seplyarskiy, V. B. et al. Weghorn, D. et al. is the correct reference. The error has been corrected in the HTML and PDF version of the article.

Estimating the selective effects of heterozygous protein-truncating variants from human exome data.

The dispensability of individual genes for viability has interested generations of geneticists. For some genes it is essential to maintain two functional chromosomal copies, while others may tolerate the loss of one or both copies. Exome sequence data from 60,706 individuals provide sufficient observations of rare protein truncating variants (PTVs) to make genome-wide estimates of selection against heterozygous loss of gene function. The cumulative frequency of rare deleterious PTVs is primarily determined by the balance between incoming mutations and purifying selection rather than genetic drift. This enables the estimation of the genome-wide distribution of selection coefficients for heterozygous PTVs and corresponding Bayesian estimates for individual genes. The strength of selection can discriminate the severity, age of onset, and mode of inheritance in Mendelian exome sequencing cases. We find that genes under the strongest selection are enriched in embryonic lethal mouse knockouts, putatively cell-essential genes, Mendelian disease genes, and regulators of transcription. Screening by essentiality, we find a large set of genes under strong selection that likely have critical function but have not yet been extensively annotated in published literature.