Biology subjects

Ferguson, M.

Publications and source records attributed to Ferguson, M..

27 records · Page 2Linked to original sources

bioRxiv2020

Structural variants at the BRCA1/2 loci are a common source of homologous repair deficiency in high grade serous ovarian carcinoma

Around half of high grade serous ovarian carcinomas (HGSOC) show homologous recombination repair deficiency (HRD), often caused by germline or somatic single nucleotide variant (SNV) mutations or small indels disrupting BRCA1/2. We have uniformly processed the largest collection of whole genome sequencing (WGS) data from HGSOC samples to date (N=205), comprehensively characterising the somatic mutational landscape, and expression at the BRCA1/2 loci. We discover that large structural variants (SV) are a frequent but unappreciated source of BRCA1/2 disruption in these tumours. Somatic structural variation at these loci is dominated by multi-megabase deletions that span the entirety of BRCA1 (median = 4.9Mb) or BRCA2 (median = 6.2Mb), independently affecting a substantial proportion of patients (16%) in addition to those affected by damaging germline or somatic short variants, within the BRCA1/2 coding sequences (24%). In common with previous studies, we show that the presence of damaging somatic SNVs or short indels in BRCA1 (OR=10, 95% CI 1.8-103, p=0.002, adj p=0.027 and BRCA2 (OR=17, 95% CI 2.1-816), p=0.002, adj.p=0.021) was found to influence HRD. For the first time we also study the compound effect of SV and SNV or short indel mutations at both loci, demonstrating that SVs often contribute to compound deficiencies involving SNVs or indels, with large somatic deletions contributing to these compound deficiencies in 15/205 (7%) of samples. Notably the strongest risk of HRD (OR=19 (2.4-896), p=6.6x10-3, adj P=8.5x10-3) is generated by combined large deletions at BRCA1 and BRCA2 in the absence of SNVs or indels, affecting 3% of patients. Overall, we show that HRD is a complex phenotype in HGSOC tumours, affected by the patterns of shorter variants such as SNVs and indels, SVs, methylation and expression seen at multiple loci, and we construct a successful (ROC AUC = 0.75) predictive model of HRD using such variables. In addition, HRD impacts patient survival when conferred by mechanisms other than through the well-understood short variants at BRCA1/2, currently exploited in the clinic. These results alter our understanding of the mutational landscape at the BRCA1/2 loci in highly rearranged tumours, and increase the number of patients predicted to benefit from therapies exploiting HRD in tumours such as PARP inhibition.

cancer biology↗

bioRxiv2019

Symbiotic Lactobacillus brevis promote stem cell expansion and tumorigenesis in the Drosophila intestine.

Microbial factors influence homeostatic and oncogenic growth in the intestinal epithelium. However, we know little about immediate effects of commensal bacteria on stem cell division programs. In this study, we examined effects of commensal Lactobacillus species on homeostatic, and tumorigenic stem cell growth in the Drosophila intestine. We identified Lactobacillus brevis as a potent stimulator of stem cell growth. In a wildtype midgut, Lactobacillus brevis activates growth regulatory pathways that drive stem cell divisions. In a Notch-deficient background, Lactobacillus brevis-mediated growth causes rapid expansion of mutant progenitors, leading to accumulation of large, multi-layered tumors throughout the midgut. Mechanistically, we showed that Lactobacillus brevis disrupts expression and subcellular distribution of progenitor cell integrins, supporting symmetric divisions that expand intestinal stem cell populations. Collectively, our data emphasize the impact of commensal microbes on growth and maintenance of the intestinal progenitor compartment.

cell biology↗

bioRxiv2019

Multispectral Imaging Differentiates Unique Macrophage Profiles in Patients with Distinct Chronic Liver Diseases

Intrahepatic macrophages influence the composition of the microenvironment, host immune response to liver injury, and development of fibrosis. Compared to stellate cells, the role of intrahepatic macrophages in the development of fibrosis remains ill defined. Multispectral imaging allows detection of multiple markers in situ in human formalin-fixed, paraffin-embedded tissue. This cutting-edge technology is ideal for analyzing human liver tissues since it allows spectral unmixing of fluorophore signals, subtraction of auto-fluorescence, and preserves architecture and the in vivo hepatic milieu. We analyzed resident Kupffer cells (CD68+), monocyte-derived macrophages (Mac387+), pro-fibrogenic macrophages (CD163+), and co-expression of pro-inflammatory (CD14) and anti-inflammatory (CD16) markers in liver biopsies from patients with hepatitis C virus (HCV) and different stages of fibrosis. Liver biopsies with advanced fibrosis showed increased accumulation of CD163+, MAC387+ and CD68+ macrophages in the portal tracts when compared to those with minimal fibrosis. Imaging software generated t-distributed stochastic neighbor embedding (t-SNE) plots and phenotype matrices that facilitated comparison of macrophage profiles. These included monocyte-derived (CD68+/Mac387+) and pro-fibrotic/anti-inflammatory (CD163+/CD16+) phenotypes. We established that the utility of this platform could be extended to liver biopsies from patients with other chronic liver diseases including nonalcoholic steatohepatitis and autoimmune hepatitis. Each disease exhibited a unique profile after spectral imaging analysis and this platform holds the potential to identify patients predisposed to progressive liver disease based on the macrophage composition. In summary, spectral imaging is a powerful tool that enables analysis of macrophage profiles in different types of chronic liver diseases and has potential to change the manner in which we evaluate liver biopsies leading to more personalized treatment strategies.

pathology↗

bioRxiv2019

Complex symbiont-pathogen interactions inhibit intestinal repair

Pathogen-mediated damage to the intestinal epithelium activates compensatory growth and differentiation repair programs in progenitor cells. Accelerated progenitor growth replenishes damaged tissue and maintains barrier integrity. Despite the importance of epithelial renewal to intestinal homeostasis, we know little about the effects of pathogen-commensal interactions on progenitor growth. We found that the enteric pathogen Vibrio cholerae, blocks critical growth and differentiation pathways in Drosophila progenitors despite extensive damage to the epithelial tissue. We showed that inhibition of epithelial repair requires interactions of the Vibrio cholerae type six secretion system with a complex community of symbiotic bacteria, and that elimination of the gut microbiome is sufficient to restore homeostatic growth in infected intestines. Together, this work highlights the importance of pathogen-symbiont interactions on intestinal immune responses and outlines a previously undescribed impact of the type six secretion system on pathogenesis.

immunology↗

bioRxiv2019

Minimal and mild hearing loss in children: Association with auditory perception, cognition, and communication problems

Objectives Minimal and mild hearing loss are the most common but least understood forms of hearing loss in children. Children with better ear hearing level as low as 30 dB HL have a global language impairment and, according to the World Health Organization, a \"disabling level of hearing loss\". We examined in a population of 6 - 11 year olds how hearing level [≤] 40.0 dB HL (1 and 4 kHz pure tone average, PTA, threshold) related to auditory perception, cognition and communication.\n\nDesignSchool children (n=1638) were recruited in four centres across the UK. They completed a battery of hearing (audiometry, filter width, temporal envelope, speech-in-noise) and cognitive (IQ, attention, verbal memory, receptive language, reading) tests. Caregivers assessed their childrens communication and listening skills. Children included in this study (702 male; 752 female) had four reliable tone thresholds (1, 4 kHz each ear), and no caregiver reported medical or intellectual disorder. Normal hearing children (n=1124, 77.1%) had all four thresholds and PTA < 15 dB HL. Children with [≥] 15 dB HL for at least one threshold, and PTA < 20 dB (n=245, 16.8%) had Minimal hearing loss. Children with 20 [≤] PTA < 40 dB HL (n=88, 6.0%) had Mild hearing loss. Interaural Asymmetric hearing loss (|Left PTA - Right PTA| [≥] 10 dB) was found in 28.9% of those with Minimal and 39.8% of those with Mild hearing loss.\n\nResultsSpeech perception in noise, indexed by VCV pseudoword repetition in speech modulated noise, was impaired in children with Minimal and Mild hearing loss, relative to Normal hearing children. Effect size was largest (d=0.63) in Asymmetric Mild hearing loss and smallest (d=0.21) in Symmetric Minimal hearing loss. Spectral (filter width) and temporal (backward masking) perception were impaired in children with both forms of hearing loss, but supra-threshold perception generally related only weakly to PTA. Speech-in-noise (nonsense syllables) and language (pseudoword repetition) were also impaired in both forms of hearing loss and correlated more strongly with PTA. Children with Mild hearing loss were additionally impaired in working memory (digit span) and reading, and generally performed more poorly than those with Minimal loss. Asymmetric hearing loss produced as much impairment overall on both auditory and cognitive tasks as Symmetric hearing loss. Nonverbal IQ, attention and caregiver-rated listening and communication were not significantly impaired in children with hearing loss. Modelling suggested that 15 dB HL is objectively an appropriate lower audibility limit for diagnosis of hearing loss.\n\nConclusionsHearing loss between 15 - 30 dB PTA is, at ~20%, much more prevalent in 6-11 y.o. children than most current estimates. Key aspects of auditory and cognitive skills are impaired in both symmetric and asymmetric minimal and mild hearing loss. Hearing loss < 30 dB HL is most closely related to speech perception in noise, and to cognitive abilities underpinning language and reading. The results suggest wider use of speech-in-noise measures to diagnose and assess management of hearing loss and reduction of the clinical hearing loss threshold for children to 15 dB HL.

neuroscience↗

bioRxiv2018

The Immune Deficiency Pathway Attenuates Insulin Signaling to Protect Against Infection.

Immune and metabolic pathways collectively influence host responses to microbial invaders, and mutations in one pathway frequently disrupt activity in the other. We used the Drosophila model to characterize metabolic homeostasis in flies with modified Immune Deficiency (IMD) pathway activity. The IMD pathway is very similar to the mammalian Tumor Necrosis Factor-alpha pathway, a key regulator of vertebrate immunity and metabolism. We found that persistent activation of IMD resulted in hyperglycemia, depleted fat reserves, and developmental delays, implicating IMD in metabolic regulation. Consistent with this hypothesis, we found that imd mutants weigh more, are hyperlipidemic, and have impaired glucose tolerance. To test the importance of metabolic regulation for host responses to bacterial infection, we challenged insulin pathway mutants with lethal doses of several Drosophila pathogens. We found that loss-of-function mutations in the insulin pathway impacted host responses to infection in a manner that depends on the route of infection, and the identity of the infectious microbe. Combined, our results support a role for coordinated regulation of immune and metabolic pathways in host containment of microbial invaders.

immunology↗

bioRxiv2017

Leveraging Transcriptomics Data for Genomic Prediction Models in Cassava

BackgroundGenomic prediction models were, in principle, developed to include all the available marker information; with this approach, these models have shown in various crops moderate to high predictive accuracies. Previous studies in cassava have demonstrated that, even with relatively small training populations and low-density GBS markers, prediction models are feasible for genomic selection. In the present study, we prioritized SNPs in close proximity to genome regions with biological importance for a given trait. We used a number of strategies to select variants that were then included in single and multiple kernel GBLUP models. Specifically, our sources of information were transcriptomics, GWAS, and immunity-related genes, with the ultimate goal to increase predictive accuracies for Cassava Brown Streak Disease (CBSD) severity.\n\nResultsWe used single and multi-kernel GBLUP models with markers imputed to whole genome sequence level to accommodate various sources of biological information; fitting more than one kinship matrix allowed for differential weighting of the individual marker relationships. We applied these GBLUP approaches to CBSD phenotypes (i.e., root infection and leaf severity three and six months after planting) in a Ugandan Breeding Population (n = 955). Three means of exploiting an established RNAseq experiment of CBSD-infected cassava plants were used. Compared to the biology-agnostic GBLUP model, the accuracy of the informed multi-kernel models increased the prediction accuracy only marginally (1.78% to 2.52%).\n\nConclusionsOur results show that markers imputed to whole genome sequence level do not provide enhanced prediction accuracies compared to using standard GBS marker data in cassava. The use of transcriptomics data and other sources of biological information resulted in prediction accuracies that were nominally superior to those obtained from traditional prediction models.

genomics↗

bioRxiv2017

Genome-wide association mapping and genomic prediction unravels CBSD resistance in a Manihot esculenta breeding population

Cassava (Manihot esculenta Crantz), a key carbohydrate dietary source for millions of people in Africa, faces severe yield loses due to two viral diseases: cassava brown streak disease (CBSD) and cassava mosaic disease (CMD). The completion of the cassava genome sequence and the whole genome marker profiling of clones from African breeding programs (www.nextgencassava.org) provides cassava breeders the opportunity to deploy additional breeding strategies and develop superior varieties with both farmer and industry preferred traits. Here the identification of genomic segments associated with resistance to CBSD foliar symptoms and root necrosis as measured in two breeding panels at different growth stages and locations is reported. Using genome-wide association mapping and genomic prediction models we describe the genetic architecture for CBSD severity and identify loci strongly associated on chromosomes 4 and 11. Moreover, the significantly associated region on chromosome 4 colocalises with a Manihot glaziovii introgression segment and the significant SNP markers on chromosome 11 are situated within a cluster of nucleotide-binding site leucine-rich repeat (NBS-LRR) genes previously described in cassava. Overall, predictive accuracy values found in this study varied between CBSD severity traits and across GS models with Random Forest and RKHS showing the highest predictive accuracies for foliar and root CBSD severity scores.

genetics↗

bioRxiv2017

Integrated growth factor signaling promotes lung epithelial progenitor cell expansion and maintenance in mice and humans

The bud tip epithelium of the branching mouse and human lung contains multipotent progenitors that are able to self-renew and give rise to all mature lung epithelial cell types. The current study aimed to understand the developmental signaling cues that regulate bud tip progenitor cells in the human fetal lung, which are present during branching morphogenesis, and to use this information to induce a bud tip progenitor-like population from human pluripotent stem cells (hPSCs) in vitro. We identified that FGF7, CHIR-99021 and RA maintained isolated human fetal lung epithelial bud tip progenitor cells in an undifferentiated state in vitro, and led to the induction of a 3-dimensional lung-like epithelium from hPSCs. 3-dimensional hPSC-derived lung tissue was initially patterned, with airway-like interior domains and bud tip-like progenitor domains at the periphery. Epithelial bud tip-like domains could be isolated, expanded and maintained as a nearly homogeneous population by serial passaging. Comparisons between human fetal lung epithelial bud tip cells and hPSC-derived bud tip-like cells were carried out using immunostaining, in situ hybridization and transcriptome-wide analysis, and revealed that in vitro derived tissue was highly similar to native lung. hPSC-derived epithelial bud tip-like structures survived in vitro for over 16 weeks, could be easily frozen and thawed and maintained multi-lineage potential. Furthermore, hPSC-derived epithelial bud tip progenitors successfully engrafted in the proximal airways of injured immunocompromised NSG mouse lungs, where they persisted for up to 6 weeks and gave rise to several lung epithelial lineages.

developmental biology↗