Medical Biology - Research Publications

Permanent URI for this collection

Search Results

Now showing 1 - 10 of 25
  • Item
    Thumbnail Image
    Cutting edge approaches to detecting brain mosaicism associated with common focal epilepsies: implications for diagnosis and potential therapies
    Ye, Z ; Bennett, MF ; Bahlo, M ; Scheffer, IE ; Berkovic, SF ; Perucca, P ; Hildebrand, MS (TAYLOR & FRANCIS LTD, 2021-11-02)
    INTRODUCTION: Mosaic variants arising in brain tissue are increasingly being recognized as a hidden cause of focal epilepsy. This knowledge gain has been driven by new, highly sensitive genetic technologies and genome-wide analysis of brain tissue from surgical resection or autopsy in a small proportion of patients with focal epilepsy. Recently reported novel strategies to detect mosaic variants limited to brain have exploited trace brain DNA obtained from cerebrospinal fluid liquid biopsies or stereo-electroencephalography electrodes. AREAS COVERED: The authors review the data on these innovative approaches published in PubMed before 12 June 2021, discuss the challenges associated with their application, and describe how they are likely to improve detection of mosaic variants to provide new molecular diagnoses and therapeutic targets for focal epilepsy, with potential utility in other nonmalignant neurological disorders. EXPERT OPINION: These cutting-edge approaches may reveal the hidden genetic etiology of focal epilepsies and provide guidance for precision medicine.
  • Item
    No Preview Available
    Genome-wide genetic screen identifies host ubiquitination as important for Legionella pneumophila Dot/Icm effector translocation
    Ong, SY ; Schuelein, R ; Wibawa, RR ; Thomas, DW ; Handoko, Y ; Freytag, S ; Bahlo, M ; Simpson, KJ ; Hartland, EL (WILEY, 2021-10)
    The Dot/Icm system of Legionella pneumophila is essential for virulence and delivers a large repertoire of effectors into infected host cells to create the Legionella containing vacuole. Since the secretion of effectors via the Dot/Icm system does not occur in the absence of host cells, we hypothesised that host factors actively participate in Dot/Icm effector translocation. Here we employed a high-throughput, genome-wide siRNA screen to systematically test the effect of silencing 18,120 human genes on translocation of the Dot/Icm effector, RalF, into HeLa cells. For the primary screen, we found that silencing of 119 genes led to increased translocation of RalF, while silencing of 321 genes resulted in decreased translocation. Following secondary screening, 70 genes were successfully validated as 'high confidence' targets. Gene set enrichment analysis of siRNAs leading to decreased RalF translocation, showed that ubiquitination was the most highly overrepresented category in the pathway analysis. We further showed that two host factors, the E2 ubiquitin-conjugating enzyme, UBE2E1, and the E3 ubiquitin ligase, CUL7, were important for supporting Dot/Icm translocation and L. pneumophila intracellular replication. In summary, we identified host ubiquitin pathways as important for the efficiency of Dot/Icm effector translocation by L. pneumophila, suggesting that host-derived ubiquitin-conjugating enzymes and ubiquitin ligases participate in the translocation of Legionella effector proteins and influence intracellular persistence and survival.
  • Item
    Thumbnail Image
    Deletions in VANGL1 are a risk factor for antibody-mediated kidney disease
    Jiang, SH ; Mercan, S ; Papa, I ; Moldovan, M ; Walters, GD ; Koina, M ; Fadia, M ; Stanley, M ; Lea-Henry, T ; Cook, A ; Ellyard, J ; McMorran, B ; Sundaram, M ; Thomson, R ; Canete, PF ; Hoy, W ; Hutton, H ; Srivastava, M ; McKeon, K ; de la Rua Figueroa, I ; Cervera, R ; Faria, R ; D'Alfonso, S ; Gatto, M ; Athanasopoulos, V ; Field, M ; Mathews, J ; Cho, E ; Andrews, TD ; Kitching, AR ; Cook, MC ; Alarcon Riquelme, M ; Bahlo, M ; Vinuesa, CG (CELL PRESS, 2021-12-21)
    We identify an intronic deletion in VANGL1 that predisposes to renal injury in high risk populations through a kidney-intrinsic process. Half of all SLE patients develop nephritis, yet the predisposing mechanisms to kidney damage remain poorly understood. There is limited evidence of genetic contribution to specific organ involvement in SLE.1,2 We identify a large deletion in intron 7 of Van Gogh Like 1 (VANGL1), which associates with nephritis in SLE patients. The same deletion occurs at increased frequency in an indigenous population (Tiwi Islanders) with 10-fold higher rates of kidney disease compared with non-indigenous populations. Vangl1 hemizygosity in mice results in spontaneous IgA and IgG deposition within the glomerular mesangium in the absence of autoimmune nephritis. Serum transfer into B cell-deficient Vangl1+/- mice results in mesangial IgG deposition indicating that Ig deposits occur in a kidney-intrinsic fashion in the absence of Vangl1. These results suggest that Vangl1 acts in the kidney to prevent Ig deposits and its deficiency may trigger nephritis in individuals with SLE.
  • Item
    Thumbnail Image
    Progressive Myoclonus Epilepsies Diagnostic Yield With Next-Generation Sequencing in Previously Unsolved Cases
    Canafoglia, L ; Franceschetti, S ; Gambardella, A ; Striano, P ; Giallonardo, AT ; Tinuper, P ; Di Bonaventura, C ; Michelucci, R ; Ferlazzo, E ; Granata, T ; Magaudda, A ; Licchetta, L ; Filla, A ; La Neve, A ; Riguzzi, P ; Cantisani, TA ; Fanella, M ; Castellotti, B ; Gellera, C ; Bahlo, M ; Zara, F ; Courage, C ; Lehesjoki, A-E ; Oliver, KL ; Berkovic, SF (LIPPINCOTT WILLIAMS & WILKINS, 2021-12)
    BACKGROUND AND OBJECTIVES: To assess the current diagnostic yield of genetic testing for the progressive myoclonus epilepsies (PMEs) of an Italian series described in 2014 where Unverricht-Lundborg and Lafora diseases accounted for ∼50% of the cohort. METHODS: Of 47/165 unrelated patients with PME of indeterminate genetic origin, 38 underwent new molecular evaluations. Various next-generation sequencing (NGS) techniques were applied including gene panel analysis (n = 7) and/or whole-exome sequencing (WES) (WES singleton n = 29, WES trio n = 7, and WES sibling n = 4). In 1 family, homozygosity mapping was followed by targeted NGS. Clinically, the patients were grouped in 4 phenotypic categories: "Unverricht-Lundborg disease-like PME," "late-onset PME," "PME plus developmental delay," and "PME plus dementia." RESULTS: Sixteen of 38 (42%) unrelated patients reached a positive diagnosis, increasing the overall proportion of solved families in the total series from 72% to 82%. Likely pathogenic variants were identified in NEU1 (2 families), CERS1 (1 family), and in 13 nonfamilial patients in KCNC1 (3), DHDDS (3), SACS, CACNA2D2, STUB1, AFG3L2, CLN6, NAXE, and CHD2. Across the different phenotypic categories, the diagnostic rate was similar, and the same gene could be found in different phenotypic categories. DISCUSSION: The application of NGS technology to unsolved patients with PME has revealed a collection of very rare genetic causes. Pathogenic variants were detected in both established PME genes and in genes not previously associated with PME, but with progressive ataxia or with developmental encephalopathies. With a diagnostic yield >80%, PME is one of the best genetically defined epilepsy syndromes.
  • Item
    Thumbnail Image
    UKB.COVID19: an R package for UK Biobank COVID-19 data processing and analysis
    Wang, L ; Jackson, V ; Fearnley, L ; Bahlo, M (F1000 Research Ltd, 2021-08-19)
    COVID-19 caused by SARS-CoV-2 has resulted in a global pandemic with a rapidly developing global health and economic crisis. Variations in the disease have been observed and have been associated with the genomic sequence of either the human host or the pathogen. Worldwide scientists scrambled initially to recruit patient cohorts to try and identify risk factors. A resource that presented itself early on was the UK Biobank (UKBB), which is investigating the respective contributions of genetic predisposition and environmental exposure to the development of disease. To enable COVID-19 studies, UKBB is now receiving COVID-19 test data for their participants every two weeks. In addition, UKBB is delivering more frequent updates of death and hospital inpatient data (including critical care admissions) on the UKBB Data Portal. This frequently changing dataset requires a tool that can rapidly process and analyse up-to-date data. We developed an R package specifically for the UKBB COVID-19 data, which summarises COVID-19 test results, performs association tests between COVID-19 susceptibility/severity and potential risk factors such as age, sex, blood type, comorbidities and generates input files for genome-wide association studies (GWAS). By applying the R package to data released in April 2021, we found that age, body mass index, socioeconomic status and smoking are positively associated with COVID-19 susceptibility, severity, and mortality. Males are at a higher risk of COVID-19 infection than females. People staying in aged care homes have a higher chance of being exposed to SARS-CoV-2. By performing GWAS, we replicated the 3p21.31 genetic finding for COVID-19 susceptibility and severity. The ability to iteratively perform such analyses is highly relevant since the UKBB data is updated frequently. As a caveat, users must arrange their own access to the UKBB data to use the R package.
  • Item
    Thumbnail Image
    Loss-of-function variants in Kv11.1 cardiac channels as a biomarker for SUDEP
    Soh, MS ; Bagnall, RD ; Bennett, MF ; Bleakley, LE ; Mohamed Syazwan, ES ; Marie Phillips, A ; Chiam, MDF ; McKenzie, CE ; Hildebrand, M ; Crompton, D ; Bahlo, M ; Semsarian, C ; Scheffer, IE ; Berkovic, SF ; Reid, CA (WILEY, 2021-07)
    OBJECTIVE: To compare the frequency and impact on the channel function of KCNH2 variants in SUDEP patients with epilepsy controls comprising patients older than 50 years, a group with low SUDEP risk, and establish loss-of-function KCNH2 variants as predictive biomarkers of SUDEP risk. METHODS: We searched for KCNH2 variants with a minor allele frequency of <5%. Functional analysis in Xenopus laevis oocytes was performed for all KCNH2 variants identified. RESULTS: KCNH2 variants were found in 11.1% (10/90) of SUDEP individuals compared to 6.0% (20/332) of epilepsy controls (p = 0.11). Loss-of-function KCNH2 variants, defined as causing >20% reduction in maximal amplitude, were observed in 8.9% (8/90) SUDEP patients compared to 3.3% (11/332) epilepsy controls suggesting about threefold enrichment (nominal p = 0.04). KCNH2 variants that did not change channel function occurred at a similar frequency in SUDEP (2.2%; 2/90) and epilepsy control (2.7%; 9/332) cohorts (p > 0.99). Rare KCNH2 variants (<1% allele frequency) associated with greater loss of function and an ~11-fold enrichment in the SUDEP cohort (nominal p = 0.03). In silico tools were unable to predict the impact of a variant on function highlighting the need for electrophysiological analysis. INTERPRETATION: These data show that loss-of-function KCNH2 variants are enriched in SUDEP patients when compared to an epilepsy population older than 50 years, suggesting that cardiac mechanisms contribute to SUDEP risk. We propose that genetic screening in combination with functional analysis can identify loss-of-function KCNH2 variants that could act as biomarkers of an individual's SUDEP risk.
  • Item
    Thumbnail Image
    Comparative genomics revealed adaptive admixture in Cryptosporidium hominis in Africa
    Tichkule, S ; Jex, AR ; van Oosterhout, C ; Sannella, AR ; Krumkamp, R ; Aldrich, C ; Maiga-Ascofare, O ; Dekker, D ; Lamshoeft, M ; Mbwana, J ; Rakotozandrindrainy, N ; Borrmann, S ; Thye, T ; Schuldt, K ; Winter, D ; Kremsner, PG ; Oppong, K ; Manouana, P ; Mbong, M ; Gesase, S ; Minja, DTR ; Mueller, I ; Bahlo, M ; Nader, J ; May, J ; Rakotozandrindrain, R ; Adegnika, AA ; Lusingu, JPA ; Amuasi, J ; Eibach, D ; Caccio, SM (MICROBIOLOGY SOC, 2021-01)
    Cryptosporidiosis is a major cause of diarrhoeal illness among African children, and is associated with childhood mortality, malnutrition, cognitive development and growth retardation. Cryptosporidium hominis is the dominant pathogen in Africa, and genotyping at the glycoprotein 60 (gp60) gene has revealed a complex distribution of different subtypes across this continent. However, a comprehensive exploration of the metapopulation structure and evolution based on whole-genome data has yet to be performed. Here, we sequenced and analysed the genomes of 26 C. hominis isolates, representing different gp60 subtypes, collected at rural sites in Gabon, Ghana, Madagascar and Tanzania. Phylogenetic and cluster analyses based on single-nucleotide polymorphisms showed that isolates predominantly clustered by their country of origin, irrespective of their gp60 subtype. We found a significant isolation-by-distance signature that shows the importance of local transmission, but we also detected evidence of hybridization between isolates of different geographical regions. We identified 37 outlier genes with exceptionally high nucleotide diversity, and this group is significantly enriched for genes encoding extracellular proteins and signal peptides. Furthermore, these genes are found more often than expected in recombinant regions, and they show a distinct signature of positive or balancing selection. We conclude that: (1) the metapopulation structure of C. hominis can only be accurately captured by whole-genome analyses; (2) local anthroponotic transmission underpins the spread of this pathogen in Africa; (3) hybridization occurs between distinct geographical lineages; and (4) genetic introgression provides novel substrate for positive or balancing selection in genes involved in host-parasite coevolution.
  • Item
    Thumbnail Image
    Identification of genetic factors influencing metabolic dysregulation and retinal support for MacTel, a retinal disorder (vol 4, 274, 2021)
    Bonelli, R ; Jackson, VE ; Prasad, A ; Munro, JE ; Farashi, S ; Heeren, TFC ; Pontikos, N ; Scheppke, L ; Friedlander, M ; Egan, CA ; Allikmets, R ; Ansell, BRE ; Bahlo, M (NATURE RESEARCH, 2021-04-09)
    A Correction to this paper has been published: https://doi.org/10.1038/s42003-021-01972-y
  • Item
    Thumbnail Image
    Transcriptome analysis of a ring chromosome 20 patient cohort
    Myers, KA ; Bennett, MF ; Hildebrand, MS ; Coleman, MJ ; Zhou, G ; Hollingsworth, G ; Cairns, A ; Riney, K ; Berkovic, SF ; Bahlo, M ; Scheffer, IE (WILEY, 2021-01)
    Ring chromosomes occur when the ends of normally rod-shaped chromosomes fuse. In ring chromosome 20 (ring 20), intellectual disability and epilepsy are usually present, even if there is no deleted coding material; the mechanism by which individuals with complete ring chromosomes develop seizures and other phenotypic abnormalities is not understood. We investigated altered gene transcription as a contributing factor by performing RNA-sequencing (RNA-seq) analysis on blood from seven patients with ring 20, and 11 first-degree relatives (all parents). Geographic analysis did not identify altered expression in peritelomeric or other specific chromosome 20 regions. RNA-seq analysis revealed 97 genes potentially differentially expressed in ring 20 patients. These included one epilepsy gene, NPRL3, but this finding was not confirmed on reverse transcription Droplet Digital polymerase chain reaction analysis. Molecular studies of structural chromosomal anomalies such as ring chromosome are challenging and often difficult to interpret because many patients are mosaic, and there may be genome-wide chromosomal instability affecting gene expression. Our findings nevertheless suggest that peritelomeric altered transcription is not the likely pathogenic mechanism in ring 20. Underlying genetic mechanisms are likely complex and may involve differential expression of many genes, the majority of which may not be located on chromosome 20.
  • Item
    Thumbnail Image
    Rapid Diagnosis of Spinocerebellar Ataxia 36 in a three-Generation Family Using Short-Read Whole-Genome Sequencing Data
    Rafehi, H ; Szmulewicz, DJ ; Pope, K ; Wallis, M ; Christodoulou, J ; White, SM ; Delatycki, MB ; Lockhart, PJ ; Bahlo, M (WILEY, 2020-09)