Common genetic variance at the SMAD9 colorectal cancer risk locus influences tumour mutational phenotype

I set out to investigate whether common germline variance associated with colorectal cancer (CRC) risk can influence the somatic mutational landscapes of CRC. Some Mendelian cancer syndromes, such as Lynch syndrome (LS) and MUTYH associated polyposis, associate with defined mutational landscapes and this association can be functionally informative. In this thesis I investigated instead the influence of common risk variants such as those identified by GWAS approaches, the functional impacts of which are currently imperfectly understood. I identified 8 CRC risk loci for investigation that also exhibited eQTL effects in normal colorectal mucosa. Comparisons of tumour mutational loads at each of these showed a significant relationship with the SMAD9 (rs493248) locus and this locus was selected for further investigations. These revealed a relative depletion of highly mutated microsatellite instable (MSI) tumours on the risk allele background. This was verified in a meta-analysis of 5 independent cohorts (OR=0.73, 95%CI 0.63-0.86, p=1x10-4). Separate case-control studies for MSI and microsatellite stable (MSS) CRC risk at the SMAD9 risk locus indicated that the risk allele associated specifically with MSS CRC risk. A corresponding lower risk was demonstrated for MSI CRC (LS excluded) and suggested instead a protective association for this subtype. The latter was not significant, however this comparison lacked statistical power. I further explored two mechanistic hypotheses for these observations. SMAD9 forms part of the Transforming Growth Factor Beta (TGFb) signalling pathway, with tumour suppressive functions in early CRC. I suggested that the eQTL may selectively favour tumours with or without further mutations of TGFb signalling dependent on SMAD9 expression. The correlation with MSS and MSI CRC would come about since these tumours tend to regulate this pathway differently. Comparison of mutations in CRC driver genes demonstrated a correlation of TGFb signalling mutations with the SMAD9 locus but lacked causal support. Subsequent knock-down of SMAD9 in MSI and MSS cell lines did however not indicate a proliferative advantage for MSS CRC. Secondly, I suggested a possible alternate role for SMAD9 risk variance in increasing DNA mismatch repair activity. Comparison of single base substitution signatures showed a depletion of DNA mismatch repair signatures among MSS tumours from risk allele carriers. This appeared to support my second hypothesis although results require replication. In conclusion, I discovered a robust correlation between CRC microsatellite instability and variance at the SMAD9 CRC risk locus and eQTL. This contributes to our functional understanding of this locus and the genetic basis of CRC susceptibility

Down-regulation of mechanisms involved in cell transport and maintenance of mucosal integrity in pigs infected with Lawsonia intracellularis

Lawsonia intracellularis is an obligate intracellular bacterium, responsible for the disease complex known as proliferative enteropathy (PE). L. intracellularis is associated with intestinal crypt epithelial cell proliferation but the mechanisms responsible are yet to be defined. Microarray analysis was used to investigate the host-pathogen interaction in experimentally infected pigs to identify pathways that may be involved. Ileal samples originating from twenty-eight weaner pigs experimentally challenged with a pure culture of L. intracellularis (strain LR189/5/83) were subjected to microarray analysis. Microarray transcriptional signatures were validated using immunohistochemistry and quantitative real time PCR of selected genes at various time points post challenge. At peak of infection (14 days post challenge) 86% of altered transcripts were down regulated, particularly those involved in maintenance of mucosal integrity and regulation of cell transport. Among the up-regulated transcripts, CD163 and CDK1 were novel findings and considered to be important, due to their respective roles in innate immunity and cellular proliferation. Overall, targeted cellular mechanisms included those that are important in epithelial restitution, migration and protection; maintenance of stable inter-epithelial cell relationships; cell transport of nutrients and electrolytes; innate immunity; and cell cycle

Neuroanatomical Correlates of Psychotic-Like Experiences Assessed in 2,695 Individuals via the ENIGMA Consortium

Background: Recent meta-analytical evidence indicates that cortical thickness abnormalities in schizophrenia are influenced by illness severity and antipsychotic medication exposure. Schizotypy research allows investigating the neuroanatomical correlates of psychotic-like experiences without illness- and treatment-related confounders. Here we present the first large-scale meta-analysis of cortical thickness in schizotypy across 23 datasets worldwide. Methods: The study involved structural MRI scans from 2,695 healthy individuals (mean [range] age, 29.1 [17-55.8], 46.3% male) who also completed self-report schizotypy questionnaires. Each site used FreeSurfer to extract cortical thickness for 70 Desikan-Killiany atlas regions (34 regions per hemisphere + left and right hemisphere mean thickness), and performed partial correlation analyses with total schizotypy scores in R to predict left, right and mean cortical thickness by region, adjusting by sex and age. Random-effects meta-analyses of partial correlation effect sizes for each region were performed using R’s metafor package. Results: Schizotypy scores were positively associated with mean cortical thickness of the medial orbitofrontal cortex (r=0.077; pFDR=0.006) and the frontal pole (r=0.073; pFDR=0.006). By hemisphere, schizotypy was associated with cortical thickness of the left medial orbitofrontal cortex (r=0.066; pFDR=0.044), and at trend-level with the right medial orbitofrontal cortex and left frontal pole (both r=0.062; pFDR=0.053). Conclusions: Worldwide cooperative analyses of neuroimaging data shows that subclinical psychotic-like experiences are associated with greater prefrontal cortical thickness. The directionality of the effects is opposite to that of thinner cortex in schizophrenia. Given that accelerated prefrontal thinning has been associated with progression to psychosis in at-risk individuals, our findings may reflect mechanisms of resilience in schizotypy.Supported By GM is supported by a Sir Henry Dale Fellowship, jointly funded by The Wellcome Trust and The Royal Society. Keyword, ENIGMA Consortium

Cortical and subcortical neuroanatomical signatures of schizotypy in 3004 individuals assessed in a worldwide ENIGMA study

Neuroanatomical abnormalities have been reported along a continuum from at-risk stages, including high schizotypy, to early and chronic psychosis. However, a comprehensive neuroanatomical mapping of schizotypy remains to be established. The authors conducted the first large-scale meta-analyses of cortical and subcortical morphometric patterns of schizotypy in healthy individuals, and compared these patterns with neuroanatomical abnormalities observed in major psychiatric disorders. The sample comprised 3004 unmedicated healthy individuals (12–68 years, 46.5% male) from 29 cohorts of the worldwide ENIGMA Schizotypy working group. Cortical and subcortical effect size maps with schizotypy scores were generated using standardized methods. Pattern similarities were assessed between the schizotypy-related cortical and subcortical maps and effect size maps from comparisons of schizophrenia (SZ), bipolar disorder (BD) and major depression (MDD) patients with controls. Thicker right medial orbitofrontal/ventromedial prefrontal cortex (mOFC/vmPFC) was associated with higher schizotypy scores (r = 0.067, pFDR = 0.02). The cortical thickness profile in schizotypy was positively correlated with cortical abnormalities in SZ (r = 0.285, pspin = 0.024), but not BD (r = 0.166, pspin = 0.205) or MDD (r = −0.274, pspin = 0.073). The schizotypy-related subcortical volume pattern was negatively correlated with subcortical abnormalities in SZ (rho = −0.690, pspin = 0.006), BD (rho = −0.672, pspin = 0.009), and MDD (rho = −0.692, pspin = 0.004). Comprehensive mapping of schizotypy-related brain morphometry in the general population revealed a significant relationship between higher schizotypy and thicker mOFC/vmPFC, in the absence of confounding effects due to antipsychotic medication or disease chronicity. The cortical pattern similarity between schizotypy and schizophrenia yields new insights into a dimensional neurobiological continuity across the extended psychosis phenotype