Identifying substrate proteins for GAN1 and Keap1

Abstract only availableGAN1 and Keap1 are proteins characterized by a N-terminal BTB domain and a C-terminal Kelch repeat domain. Both of these domains are protein-protein interaction domains, suggesting that these BTB-Kelch proteins form signaling complexes in cells. Previous work has suggested that BTB-Kelch proteins function as substrate adaptor proteins for Cul3-dependent E3 ubiquitin ligase complexes. The goal of this project was to identify substrate proteins of GAN1 and Keap1. This information will be particularly useful when for understanding Giant Axonal Neuropathy, a sensorimotor disease characterized by excessive accumulation of neurofilaments in neurons that contain mutated GAN1 genes. We used an affinity purification approach to identify candidate substrate proteins for GAN1 and Keap1. Recombinant GAN1 and Keap1 genes containing a C-terminal chitin binding domain (CBD) were inserted into pBabe puro vectors. These vectors were used to generate virus stocks, which were used to infect a microglial cell line, BV-2. Stable cell lines were generated using puromycin selection. A mock-infected cell line was generated in parallel. When the cell lines were confluent, the cells were lysed using a 0.1% SDS RIPA solution and chitin beads were used to precipitate the CBD-tagged proteins. Western blot analyses were performed to determine if the purification of the CBD-tagged proteins was successful. No CBD-tagged proteins were identified in our first pull-down experiment. We are currently reexamining the precipitation protocol and preparing to lysate the same set of cells.Life Sciences Undergraduate Research Opportunity Progra

Construction of shRNA vectors against BTB-Kelch substrate adaptor proteins [abstract]

Abstract only availableFaculty Mentor: Mark Hannink, BiochemistryThe BTB-Kelch substrate adaptor proteins are proteins that contain an N-terminal BTB and a C-terminal Kelch domain. These proteins function as substrate adaptors for protein ubiquination. BTB-Kelch substrate adaptor proteins may influence the differentiation of C2C12 myoblasts into myotubules. To better understand the role of BTB-Kelch proteins for the differentiation of myoblasts cells, we designed short hairpin RNA (shRNA) molecules to inhibit mRNA expression of five BTB-Kelch proteins found in Mus musculus (mouse). These proteins are: klhl9, klhl24, kbtbd8, klhdc8b, and Enc1. Expression vectors for the shRNAs were constructed using pSico and pSicoR, which are lentiviral vectors that contain an internal U6 promoter for expression of a shRNA molecule and a CMV-GFP cassette. Positive clones were identified by restriction mapping. Positive clones were purified and sequenced. The plasmid DNAs were transfected into 293T cells to generate virus. The viruses were used to infect C2C12 myoblasts. Two days after infection, the cells will be examined for GFP expression, which will show a green fluorescent marker in the infected cells verifying successful uptake of the virus. Further analysis will identify any differences in the differentiation of C2C12 myoblasts into myotubules following shRNA-mediated knockdown of these BTB-Kelch proteins

Whole genome sequencing for the diagnosis of neurological repeat expansion disorders in the UK: a retrospective diagnostic accuracy and prospective clinical validation study

Background: repeat expansion disorders affect about 1 in 3000 individuals and are clinically heterogeneous diseases caused by expansions of short tandem DNA repeats. Genetic testing is often locus-specific, resulting in underdiagnosis of people who have atypical clinical presentations, especially in paediatric patients without a previous positive family history. Whole genome sequencing is increasingly used as a first-line test for other rare genetic disorders, and we aimed to assess its performance in the diagnosis of patients with neurological repeat expansion disorders. Methods: we retrospectively assessed the diagnostic accuracy of whole genome sequencing to detect the most common repeat expansion loci associated with neurological outcomes (AR, ATN1, ATXN1, ATXN2, ATXN3, ATXN7, C9orf72, CACNA1A, DMPK, FMR1, FXN, HTT, and TBP) using samples obtained within the National Health Service in England from patients who were suspected of having neurological disorders; previous PCR test results were used as the reference standard. The clinical accuracy of whole genome sequencing to detect repeat expansions was prospectively examined in previously genetically tested and undiagnosed patients recruited in 2013–17 to the 100 000 Genomes Project in the UK, who were suspected of having a genetic neurological disorder (familial or early-onset forms of ataxia, neuropathy, spastic paraplegia, dementia, motor neuron disease, parkinsonian movement disorders, intellectual disability, or neuromuscular disorders). If a repeat expansion call was made using whole genome sequencing, PCR was used to confirm the result. Findings: the diagnostic accuracy of whole genome sequencing to detect repeat expansions was evaluated against 793 PCR tests previously performed within the NHS from 404 patients. Whole genome sequencing correctly classified 215 of 221 expanded alleles and 1316 of 1321 non-expanded alleles, showing 97·3% sensitivity (95% CI 94·2–99·0) and 99·6% specificity (99·1–99·9) across the 13 disease-associated loci when compared with PCR test results. In samples from 11 631 patients in the 100 000 Genomes Project, whole genome sequencing identified 81 repeat expansions, which were also tested by PCR: 68 were confirmed as repeat expansions in the full pathogenic range, 11 were non-pathogenic intermediate expansions or premutations, and two were non-expanded repeats (16% false discovery rate). Interpretation: In our study, whole genome sequencing for the detection of repeat expansions showed high sensitivity and specificity, and it led to identification of neurological repeat expansion disorders in previously undiagnosed patients. These findings support implementation of whole genome sequencing in clinical laboratories for diagnosis of patients who have a neurological presentation consistent with a repeat expansion disorder. Funding: Medical Research Council, Department of Health and Social Care, National Health Service England, National Institute for Health Research, and Illumina.</p