Comprehensive sequencing of the myocilin gene in a selected cohort of severe primary open-angle glaucoma patients.

Primary open-angle glaucoma (POAG) is the most common form of glaucoma, prevalent in approximately 1-2% of Caucasians in the UK over the age of 40. It is characterised by an open anterior chamber angle, raised intraocular pressure (IOP) and optic nerve damage leading to loss of sight. The myocilin gene (MYOC) is the most common glaucoma-causing gene, accounting for ~2% of British POAG cases. 358 patients were selected for next generation sequencing (NGS) with the following selection criteria: Caucasian ethnicity, intraocular pressure (IOP) 21-40 mm Hg, cup:disc ratio ≥0.6 and visual field mean deviation ≤-3. The entire MYOC gene (17,321 bp) was captured including the promoter, introns, UTRs and coding exons. We identify 12 exonic variants (one stop-gain, five missense and six synonymous variants), two promoter variants, 133 intronic variants, two 3' UTR variants and 23 intergenic variants. Four known or predicted pathogenic exonic variants (p.R126W, p.K216K, p.Q368* and p.T419A) were identified across 11 patients, which accounts for 3.07% of this POAG cohort. This is the first time that the entire region of MYOC has been sequenced and variants reported for a cohort of POAG patients

A small gene sequencing panel realises a high diagnostic rate in patients with congenital nystagmus following basic phenotyping

Nystagmus is a disorder of uncontrolled eye movement and can occur as an isolated trait (idiopathic INS, IINS) or as part of multisystem disorders such as albinism, significant visual disorders or neurological disease. Eighty-one unrelated patients with nystagmus underwent routine ocular phenotyping using commonly available phenotyping methods and were grouped into four sub-cohorts according to the level of phenotyping information gained and their findings. DNA was extracted and sequenced using a broad utility next generation sequencing (NGS) gene panel. A clinical subpanel of genes for nystagmus/albinism was utilised and likely causal variants were prioritised according to methods currently employed by clinical diagnostic laboratories. We determine the likely underlying genetic cause for 43.2% of participants with similar yields regardless of prior phenotyping. This study demonstrates that a diagnostic workflow combining basic ocular phenotyping and a clinically available targeted NGS panel, can provide a high diagnostic yield for patients with infantile nystagmus, enabling access to disease specific management at a young age and reducing the need for multiple costly, often invasive tests. By describing diagnostic yield for groups of patients with incomplete phenotyping data, it also permits the subsequent design of 'real-world' diagnostic workflows and illustrates the changing role of genetic testing in modern diagnostic workflows for heterogeneous ophthalmic disorders.This article is freely available via Open Access. Click on the Publisher URL to access the full-text

Targeting Proteotoxic Stress in Cancer: A Review of the Role that Protein Quality Control Pathways Play in Oncogenesis.

Despite significant advances in cancer diagnostics and therapeutics the majority of cancer unfortunately remains incurable, which has led to continued research to better understand its exceptionally diverse biology. As a result of genomic instability, cancer cells typically have elevated proteotoxic stress. Recent appreciation of this functional link between the two secondary hallmarks of cancer: aneuploidy (oxidative stress) and proteotoxic stress, has therefore led to the development of new anticancer therapies targeting this emerging “Achilles heel” of malignancy. This review highlights the importance of managing proteotoxic stress for cancer cell survival and provides an overview of the integral role proteostasis pathways play in the maintenance of protein homeostasis. We further review the efforts undertaken to exploit proteotoxic stress in multiple myeloma (as an example of a hematologic malignancy) and triple negative breast cancer (as an example of a solid tumor), and give examples of: (1) FDA-approved therapies in routine clinical use; and (2) promising therapies currently in clinical trials. Finally, we provide new insights gleaned from the use of emerging technologies to disrupt the protein secretory pathway and repurpose E3 ligases to achieve targeted protein degradation

Mutations in TYR and OCA2 associated with oculocutaneous albinism in Pakistani families

Background: Oculocutaneous albinism (OCA) is a genetically heterogeneous disorder of abnormal melanin synthesis, resulting in decreased or absent pigmentation of eyes, skin and hair. OCA has been classified based on genetic findings into seven subtypes (OCA 1–7). OCA1 is the most common subtype, accounting for 50% of cases worldwide (Hutton and Spritz, 2008; Rooryck et al., 2008), and is caused by mutations in the tyrosinase (TYR) gene. This study describes genetic investigations in 11 families from Pakistan with individuals with OCA. Methods: Whole genome SNP genotyping for autozygosity mapping was undertaken using the Illumina Human CytoSNP-12 array, and exome sequencing performed using the Illumina TruSight One sequencing panel. For individuals putatively linked to the TYR gene, dideoxy sequencing of TYR was performed using primers targeting all five coding exons and intron-exon splice sites to identify mutations in individuals diagnosed with OCA. Dideoxy sequencing was also performed to confirm the presence and cosegregation of TYR and OCA2 variants identified via exome sequencing. Results: We identified new and previously reported variations in TYR and OCA2 genes in 11 OCA families from Pakistan. One novel missense variant in TYR (NM_000372.4: c.240G&gt;C; p.Trp80Cys), and three novel variants in OCA2 (missense variants NM_000275.2: c.2458T&gt;C; p.Ser820Pro and c.1762C&gt;T; p.Arg588Trp, as well as a frameshift variant c.408_409delTT; p.Arg137Ilefs*83), were observed in five OCA families. In addition, four previously identified variants in TYR (c.649C&gt;T; p.Arg217Trp, c.1255G&gt;A; p.Gly419Arg, c.832C&gt;T; p.Arg278Ter, and c.132T&gt;A p.Ser44Arg) and three previously identified variants in OCA2 (c.1045-15T&gt;G, c.2020C&gt;G; p.Leu674Val and c.1327G&gt;A; p.Val443Ile) were identified in eight OCA families. All affected individuals displayed the cardinal features of OCA with white hair, pale skin, nystagmus and decreased vision. Conclusions: Our findings broaden the molecular spectrum associated with TYR and OCA2 mutations in Pakistani families, aiding the development and refinement of genetic diagnostic and counselling services in Pakistan.</p

Optical genome mapping identifies a germline retrotransposon insertion in SMARCB1 in two siblings with atypical teratoid rhabdoid tumors

Abstract In a subset of pediatric cancers, a germline cancer predisposition is highly suspected based on clinical and pathological findings, but genetic evidence is lacking, which hampers genetic counseling and predictive testing in the families involved. We describe a family with two siblings born from healthy parents who were both neonatally diagnosed with atypical teratoid rhabdoid tumor (ATRT). This rare and aggressive pediatric tumor is associated with biallelic inactivation of SMARCB1, and in 30% of the cases, a predisposing germline mutation is involved. Whereas the tumors of both siblings showed loss of expression of SMARCB1 and acquired homozygosity of the locus, whole exome and whole genome sequencing failed to identify germline or somatic SMARCB1 pathogenic mutations. We therefore hypothesized that the insertion of a pathogenic repeat-rich structure might hamper its detection, and we performed optical genome mapping (OGM) as an alternative strategy to identify structural variation in this locus. Using this approach, an insertion of ~2.8 kb within intron 2 of SMARCB1 was detected. Long-range PCR covering this region remained unsuccessful, but PacBio HiFi genome sequencing identified this insertion to be a SINE-VNTR-Alu, subfamily E (SVA-E) retrotransposon element, which was present in a mosaic state in the mother. This SVA-E insertion disrupts correct splicing of the gene, resulting in loss of a functional allele. This case demonstrates the power of OGM and long-read sequencing to identify genomic variations in high-risk cancer-predisposing genes that are refractory to detection with standard techniques, thereby completing the clinical and molecular diagnosis of such complex cases and greatly improving counseling and surveillance of the families involved

Nesprin 1 is critical for nuclear positioning and anchorage

Nesprin 1 is an outer nuclear membrane protein that is thought to link the nucleus to the actin cytoskeleton. Recent data suggest that mutations in Nesprin 1 may also be involved in the pathogenesis of Emery-Dreifuss muscular dystrophy. To investigate the function of Nesprin 1 in vivo, we generated a mouse model in which all isoforms of Nesprin 1 containing the C-terminal spectrin-repeat region with or without KASH domain were ablated. Nesprin 1 knockout mice are marked by decreased survival rates, growth retardation and increased variability in body weight. Additionally, nuclear positioning and anchorage are dysfunctional in skeletal muscle from knockout mice. Physiological testing demonstrated no significant reduction in stress production in Nesprin 1-deficient skeletal muscle in either neonatal or adult mice, but a significantly lower exercise capacity in knockout mice. Nuclear deformation testing revealed ineffective strain transmission to nuclei in muscle fibers lacking Nesprin 1. Overall, our data show that Nesprin 1 is essential for normal positioning and anchorage of nuclei in skeletal muscle

UQ Open Science Conference 2018

This is a collection of resources and presentations for the Open Science Conference held at the University of Queensland, 24-25 September 201