Adaptation without natural selection

Document is itself an extended abstract

The impact of the environment on DNA methylation in humans and zebrafish

DNA methylation is a chemical modification to the DNA strand, which can control gene expression. DNA methylation can be modified by the environment. For example, tobacco use substantially alters DNA methylation, and hence DNA methylation therefore provides a route through which the environment can lead to alterations in gene expression. Consequently, alterations to DNA methylation patterns have been associated with disease phenotypes in humans and other mammals. However, the precise role of environmentally-induced DNA methylation changes in the onset of pathological phenotypes is not often clearly defined. Here, we investigate the response of DNA methylation to two different environmental exposures – adulthood cannabis and in utero tobacco exposure. These environmental exposures are important because they are associated with adverse phenotypes – long-term cannabis use, particularly through adolescence, is associated with adverse psychosocial wellbeing. The development of conduct problem (CP, including autism and antisocial behaviour disorder) in childhood and adolescence is associated with exposure to tobacco during development (in utero). However, as yet, no studies have explored the role of DNA methylation in the link between these exposures and their associated phenotypic effects. Therefore, here we first asked whether DNA methylation in a longitudinal human cohort, the Christchurch Health and Development Study (CHDS), was altered in response to long term cannabis exposure, with and without tobacco. Using the Illumina EPIC array, we detected nominal differential DNA methylation in response to cannabis specifically, in genes associated with the following pathways; Cholinergic synapse, glutamatergic synapse and dopaminergic synapse. These observations show a potential mediation between DNA methylation in the observed phenotypic effects of cannabis use. In order to develop a tool to investigate this association further, we assessed the efficacy of a targeted, high throughput amplicon-based approach, bisulfite - based amplicon sequencing (BSAS), to replicate differential methylation at loci identified via EPIC array. We found that the ability of BSAS to detect equivalent differential methylation was locus-specific, meaning that it has value as a validation and replication tool, but that each locus for validation must be tested before being applied to a large study. Cannabis use is a contentious issue, mainly because of the debate around its therapeutic but also its psychoactive properties. In order to quantify the impact of both of its main cannabinoids, (-)-trans-∆9-tetrahydrocannabinol (THC) and cannabidiol (CBD) were exposed to zebrafish embryos. Following exposure reduced representation bisulfite sequencing (RRBS) was used to quantify their impact of each cannabinoid on DNA methylation. Differential methylation was found in each of the exposure groups, findings demonstrated the greatest number of methylation differences was in the CBD exposure group. CBD DNA methylation differences were found in genes that have roles in neurodevelopment, neurotransmission and behaviour. THC DNA methylati on differences on the other hand were found to alter genes with roles in the axon guidance and retinal ganglion pathways, supporting the role of DNA methylati on in the biological response to THC. Furthermore, our data revealed a role for both THC and CBD in brain related pathways, indicating that further research is needed to understand the full biological impacts of the two compounds. Next, to determine if tobacco-induced DNA methylation alterations are important in the link between in utero tobacco exposure and the development of CP, here, we applied BSAS to a subset of CHDS participants to assess DNA methylation in in utero-exposed individuals compared to non-exposed individuals, with and without CP. We selected a panel of genes with known roles in in utero neurodevelopment, and identified differential methylation that was specific to individuals exposed to tobacco during development, who had high CP scores. We imply that developmentally-induced DNA methylati on alterations may be playing a role in the development of CP in exposed individuals. To investigate this further, we applied a genome-wide approach (EPIC array) to a larger cohort and identified nominal significance at genes involved in global developmental delay and neurological disorders, indicating that, in addition to CP, visual impairment may be a phenotypic response to in utero tobacco exposure. Lastly, we discuss whether DNA methylation analysis in whole blood samples is able to predict DNA methylation changes in brain tissue. To answer this question, we used publicly available data of the top lists of differentially methylated CpG sites in blood and brain tissue from individuals with schizophrenia. We found that, the methylation of individual CpG sites did not replicate between tissues, the genes and pathways that have biological relevance to schizophrenia (e.g. mTOR signalling pathway and the mRNA surveillance pathway) were identified in both tissue types, demonstrating the value and applicability of whole blood as a proxy tissue. Overall, here we demonstrate a role for DNA methylation in the biological response to cannabis, and a link between in utero tobacco exposure and development of CP. Further research is required to understand the mechanism through which these changes can contribute to disease

Child-mediated health communication: A conceptual framework for increasing stroke literacy in hard to reach populations

Effectively engaging economically-disadvantaged ethnic minority communities for promoting health has proved to be challenging for a variety of reasons, including factors related to healthcare access, literacy, inadequate or ineffective cultural appropriateness of materials, and the relatively low priority for health due to competing demands related to economic hardship. We have developed a framework of Child-Mediated Health Communication (CMHC), which focuses on children as channels for carrying out health promotion interventions to parents and other caregivers. CMHC is an innovative, alternative strategy for engaging this underserved population, where traditional methods of health promotion have not been successful. We discuss the theoretical foundation, development, and effectiveness of a CMHC framework in our stroke preparedness communication intervention, Hip Hop Stroke

Inferring Diploid 3D Chromatin Structures from Hi-C Data

The 3D organization of the genome plays a key role in many cellular processes, such as gene regulation, differentiation, and replication. Assays like Hi-C measure DNA-DNA contacts in a high-throughput fashion, and inferring accurate 3D models of chromosomes can yield insights hidden in the raw data. For example, structural inference can account for noise in the data, disambiguate the distinct structures of homologous chromosomes, orient genomic regions relative to nuclear landmarks, and serve as a framework for integrating other data types. Although many methods exist to infer the 3D structure of haploid genomes, inferring a diploid structure from Hi-C data is still an open problem. Indeed, the diploid case is very challenging, because Hi-C data typically does not distinguish between homologous chromosomes. We propose a method to infer 3D diploid genomes from Hi-C data. We demonstrate the accuracy of the method on simulated data, and we also use the method to infer 3D structures for mouse chromosome X, confirming that the active homolog exhibits a bipartite structure, whereas the active homolog does not

Dual production of polyhydroxyalkanoates and antibacterial/antiviral gold nanoparticles

Gold nanoparticles (AuNPs) have been explored for their use in medicine. Here, we report a sustainable, and cost-effective method to produce AuNPs using a bacterial strain such as Pseudomonas mendocina CH50 which is also known to be a polyhydroxyalkanoate (PHA) producer. A cell-free bacterial supernatant, which is typically discarded after PHA extraction, was used to produce spherical AuNPs of 3.5 ± 1.5 nm in size as determined by Transmission Electron Microscopy (TEM) analysis. The AuNPs/PHA composite coating demonstrated antibacterial activity against Staphylococcus aureus 6538P, and antiviral activity, with a 75% reduction in viral infectivity against SARS-CoV-2 pseudotype virus

Genome-Wide Methylation Profiling in 229 Patients With Crohn's Disease Requiring Intestinal Resection: Epigenetic Analysis of the Trial of Prevention of Post-operative Crohn's Disease (TOPPIC).

Background &amp; Aims: DNA methylation alterations may provide important insights into gene-environment interaction in cancer, aging, and complex diseases, such as inflammatory bowel disease (IBD). We aim first to determine whether the circulating DNA methylome in patients requiring surgery may predict Crohn's disease (CD) recurrence following intestinal resection; and second to compare the circulating methylome seen in patients with established CD with that we had reported in a series of inception cohorts. Methods: TOPPIC was a placebo-controlled, randomized controlled trial of 6-mercaptopurine at 29 UK centers in patients with CD undergoing ileocolic resection between 2008 and 2012. Genomic DNA was extracted from whole blood samples from 229 of the 240 patients taken before intestinal surgery and analyzed using 450KHumanMethylation and Infinium Omni Express Exome arrays (Illumina, San Diego, CA). Coprimary objectives were to determine whether methylation alterations may predict clinical disease recurrence; and to assess whether the epigenetic alterations previously reported in newly diagnosed IBD were present in the patients with CD recruited into the TOPPIC study. Differential methylation and variance analysis was performed comparing patients with and without clinical evidence of recurrence. Secondary analyses included investigation of methylation associations with smoking, genotype (MeQTLs), and chronologic age. Validation of our previously published case-control observation of the methylome was performed using historical control data (CD, n = 123; Control, n = 198). Results: CD recurrence in patients following surgery is associated with 5 differentially methylated positions (Holm P &lt;.05), including probes mapping to WHSC1 (P = 4.1 × 10 -9, Holm P =.002) and EFNA3 (P = 4.9 × 10 -8, Holm P =.02). Five differentially variable positions are demonstrated in the group of patients with evidence of disease recurrence including a probe mapping to MAD1L1 (P = 6.4 × 10 -5). DNA methylation clock analyses demonstrated significant age acceleration in CD compared with control subjects (GrimAge + 2 years; 95% confidence interval, 1.2–2.7 years), with some evidence for accelerated aging in patients with CD with disease recurrence following surgery (GrimAge +1.04 years; 95% confidence interval, -0.04 to 2.22). Significant methylation differences between CD cases and control subjects were seen by comparing this cohort in conjunction with previously published control data, including validation of our previously described differentially methylated positions (RPS6KA2 P = 1.2 × 10 -19, SBNO2 = 1.2 × 10 -11) and regions (TXK [false discovery rate, P = 3.6 × 10 -14], WRAP73 [false discovery rate, P = 1.9 × 10 -9], VMP1 [false discovery rate, P = 1.7 × 10 -7], and ITGB2 [false discovery rate, P = 1.4 × 10 -7]). Conclusions: We demonstrate differential methylation and differentially variable methylation in patients developing clinical recurrence within 3 years of surgery. Moreover, we report replication of the CD-associated methylome, previously characterized only in adult and pediatric inception cohorts, in patients with medically refractory disease needing surgery.</p

Dual production of polyhydroxyalkanoates and antibacterial/antiviral gold nanoparticles

Gold nanoparticles (AuNPs) have been explored for their use in medicine. Here, we report a sustainable, and cost-effective method to produce AuNPs using a bacterial strain such as Pseudomonas mendocina CH50 which is also known to be a polyhydroxyalkanoate (PHA) producer. A cell-free bacterial supernatant, which is typically discarded after PHA extraction, was used to produce spherical AuNPs of 3.5 ± 1.5 nm in size as determined by Transmission Electron Microscopy (TEM) analysis. The AuNPs/PHA composite coating demonstrated antibacterial activity against Staphylococcus aureus 6538P, and antiviral activity, with a 75% reduction in viral infectivity against SARS-CoV-2 pseudotype virus

Altered DNA methylation within DNMT3A, AHRR, LTA/TNF loci mediates the effect of smoking on inflammatory bowel disease

This work aims to investigate how smoking exerts effect on the development of inflammatory bowel disease (IBD). A prospective cohort study and a Mendelian randomization study are first conducted to evaluate the association between smoking behaviors, smoking-related DNA methylation and the risks of Crohn’s disease (CD) and ulcerative colitis (UC). We then perform both genome-wide methylation analysis and co-localization analysis to validate the observed associations. Compared to never smoking, current and previous smoking habits are associated with increased CD (P = 7.09 × 10−10) and UC (P &lt; 2 × 10−16) risk, respectively. DNA methylation alteration at cg17742416 [DNMT3A] is linked to both CD (P = 7.30 × 10−8) and UC (P = 1.04 × 10−4) risk, while cg03599224 [LTA/TNF] is associated with CD risk (P = 1.91 × 10−6), and cg14647125 [AHRR] and cg23916896 [AHRR] are linked to UC risk (P = 0.001 and 0.002, respectively). Our study identifies biological mechanisms and pathways involved in the effects of smoking on the pathogenesis of IBD

Altered DNA methylation within DNMT3A, AHRR, LTA/TNF loci mediates the effect of smoking on inflammatory bowel disease

This work aims to investigate how smoking exerts effect on the development of inflammatory bowel disease (IBD). A prospective cohort study and a Mendelian randomization study are first conducted to evaluate the association between smoking behaviors, smoking-related DNA methylation and the risks of Crohn's disease (CD) and ulcerative colitis (UC). We then perform both genome-wide methylation analysis and co-localization analysis to validate the observed associations. Compared to never smoking, current and previous smoking habits are associated with increased CD (P = 7.09 × 10-10) and UC (P -16) risk, respectively. DNA methylation alteration at cg17742416 [DNMT3A] is linked to both CD (P = 7.30 × 10-8) and UC (P = 1.04 × 10-4) risk, while cg03599224 [LTA/TNF] is associated with CD risk (P = 1.91 × 10-6), and cg14647125 [AHRR] and cg23916896 [AHRR] are linked to UC risk (P = 0.001 and 0.002, respectively). Our study identifies biological mechanisms and pathways involved in the effects of smoking on the pathogenesis of IBD

A booster dose enhances immunogenicity of the COVID-19 vaccine candidate ChAdOx1 nCoV-19 in aged mice.

BACKGROUND: The spread of SARS-CoV-2 has caused a worldwide pandemic that has affected almost every aspect of human life. The development of an effective COVID-19 vaccine could limit the morbidity and mortality caused by infection and may enable the relaxation of social-distancing measures. Age is one of the most significant risk factors for poor health outcomes after SARS-CoV-2 infection; therefore, it is desirable that any new vaccine candidates elicit a robust immune response in older adults. METHODS: Here, we use in-depth immunophenotyping to characterize the innate and adaptive immune response induced upon intramuscular administration of the adenoviral vectored ChAdOx1 nCoV-19 (AZD-1222) COVID-19 vaccine candidate in mice. FINDINGS: A single vaccination generates spike-specific Th1 cells, Th1-like Foxp3+ regulatory T cells, polyfunctional spike-specific CD8+ T cells. and granzyme-B-producing CD8 effectors. Spike-specific IgG and IgM are generated from both the early extrafollicular antibody response and the T follicular helper cell-supported germinal center reaction, which is associated with the production of virus-neutralizing antibodies. A single dose of this vaccine generated a similar type of immune response in aged mice but of a reduced magnitude than in younger mice. We report that a second dose enhances the immune response to this vaccine in aged mice. CONCLUSIONS: This study shows that ChAdOx1 nCoV-19 induces both cellular and humoral immunity in adult and aged mice and suggests a prime-boost strategy is a rational approach to enhance immunogenicity in older persons. FUNDING: This study was supported by BBSRC, Lister institute of Preventative Medicine, EPSRC VaxHub, and Innovate UK