9 research outputs found
Climate change impacts on seagrass meadows and macroalgal forests: an integrative perspective on acclimation and adaptation potential
Marine macrophytes are the foundation of algal forests and seagrass meadows-some of the most productive and diverse coastal marine ecosystems on the planet. These ecosystems provide nursery grounds and food for fish and invertebrates, coastline protection from erosion, carbon sequestration, and nutrient fixation. For marine macrophytes, temperature is generally the most important range limiting factor, and ocean warming is considered the most severe threat among global climate change factors. Ocean warming induced losses of dominant macrophytes along their equatorial range edges, as well as range extensions into polar regions, are predicted and already documented. While adaptive evolution based on genetic change is considered too slow to keep pace with the increasing rate of anthropogenic environmental changes, rapid adaptation may come about through a set of non-genetic mechanisms involving the functional composition of the associated microbiome, as well as epigenetic modification of the genome and its regulatory effect on gene expression and the activity of transposable elements. While research in terrestrial plants demonstrates that the integration of non-genetic mechanisms provide a more holistic picture of a species' evolutionary potential, research in marine systems is lagging behind. Here, we aim to review the potential of marine macrophytes to acclimatize and adapt to major climate change effects via intraspecific variation at the genetic, epigenetic, and microbiome levels. All three levels create phenotypic variation that may either enhance fitness within individuals (plasticity) or be subject to selection and ultimately, adaptation. We review three of the most important phenotypic variations in a climate change context, including physiological variation, variation in propagation success, and in herbivore resistance. Integrating different levels of plasticity, and adaptability into ecological models will allow to obtain a more holistic understanding of trait variation and a realistic assessment of the future performance and distribution of marine macrophytes. Such multi-disciplinary approach that integrates various levels of intraspecific variation, and their effect on phenotypic and physiological variation, is of crucial importance for the effective management and conservation of seagrasses and macroalgae under climate change.FCT
SFRH/BPD/115162/2016
Portuguese FCT through MARFOR
Biodiversa/0004/2015
Norwegian Research Council (Havkyst project)
243916
European Regional Development Fund (ERDF)
Mar 2020 program through the VALPRAD project
16-01-04-FMP-0007
SFRH/PBD/107878/2015info:eu-repo/semantics/publishedVersio
Profiling Genome-Wide DNA Methylation Patterns in Human Aortic and Mitral Valves
Cardiac valve structure and function are complex and include dynamic interactions between cells, extracellular matrix (ECM) and their hemodynamic environment. Valvular gene expression is tightly regulated by a variety of mechanisms including epigenetic factors such as histone modifications, RNA-based mechanisms and DNA methylation. To date, methylation fingerprints of non-diseased human aortic and mitral valves have not been studied. In this work I analyzed the differential methylation profiles of 12 non-diseased aortic and mitral valve tissue samples (in matched pairs). Methylation data were acquired via reduced representation bisulfite sequencing (RRBS). Of 1601 promoters analyzed genome-wide, my analysis revealed 584 differentially methylated (DM) promoters, of which 13 were reported in endothelial mesenchymal trans-differentiation (EMT), 37 in aortic and mitral valve disease and 7 in ECM remodeling. Both functional classification and network analysis showed that genes associated with the differentially methylated promoters were enriched for WNT-, Cadherin-, Endothelin-, PDGF- and VEGF- signaling implicated in valvular physiology and pathophysiology. Additional enrichment was detected for TGFB-, NOTCH- and Integrin- signaling involved in EMT as well as ECM remodeling. These data provide the first insight into differential regulation of human aortic and mitral valve tissue and identify candidate genes linked to differentially methylated promoters. This work will improve the understanding of valve biology, valve tissue engineering approaches and contributes to the identification of relevant drug targets
Comprehensive Sequencing with Surface Tagmentation Based Technology
Next-generation sequencing technologies (NGS) have undergone extensive improvements since the invention of the 454 sequencing system in 2005. With tremendous progress in throughput, speed and a dramatic reduction in per-base cost, DNA sequencing is widely used in basic science as well as translational research. However, it is still a challenge to acquire a complete human genome. The long-range information is often missing due to the short length of NGS reads, which leaves many gaps in between scaffolds rather than an entire piece for each chromosome. Moreover, without the long-range information, haplotype-resolved genome sequencing and structural variant detection can be difficult, however, it is critical to understand the genetic basis of complex phenotypes with haplotype information. These complex structural genomic variations are often involved in numerous diseases, such as cancer. Here we developed a novel method to provide a more complete human genome sequence and allow genome studies to accurately identify all variants and phase them to the appropriate homologous chromosome. Ultimately, our approach can decrease the cost of whole genome sequencing while dramatically increasing the accuracy and completeness of the sequencing.
In the first chapter, I overviewed the current DNA sequencing technologies, compared short-read sequencing and long-read sequencing and illustrated their advantages and drawbacks. In chapter 2, I summarized the major haplotype-resolved DNA sequencing approaches, which include Hi-C, synthetic long reads and CPT-Seq. In chapter 3, I provided a detailed description of our novel methods to construct NGS library directly on a solid surface, which simplified NGS pipeline significantly and can contribute to the goal of sequencing a genome for $100. In chapter 4, an approach to generate megabase long linked reads is described. With DNA combing, surface tagmentation and barcode-enabled DNA chip, the method would allow us to assemble and phase the variants across entire chromosomes. In the last chapter, I discussed the potential application of our technologies in epigenomics, RNA sequencing and genomic medicine. The technologies described in this dissertation will transform genomics and have impacts in the biological sciences, from personalized medicine to de novo sequencing of human genome
Using genomic approaches to characterise the immune response to biologicals
Biologic therapies are effective treatments for inflammatory bowel disease (IBD). Successful treatment leads to reduced hospitalisation and surgeries, and an improvement in quality of life for patients. Unfortunately, the use of these treatments are associated with challenges such as treatment failure, an increased risk of infections, and suboptimal vaccine responses. An understanding of the molecular mechanisms underlying the challenges of existing IBD therapies, such as anti-tumour necrosis factor (anti-TNF), will allow strategies to be developed to overcome these challenges and aid drug sequencing. Technological advances in genomics has enabled a deeper understanding of these molecular mechanisms.
The primary aim of this thesis was to utilise genomic approaches to understand the molecular mechanisms underlying the effects of anti-TNF therapies in the setting of treatment failure and attenuated vaccine response. In this thesis, I demonstrated that DNA methylation profiles might potentially be used as a predictor for anti-TNF drug concentration at week 14, which is the only modifiable factor associated with primary non-response to anti-TNF at week 14. In the setting of the COVID-19 pandemic, I demonstrated that antibody response following SARS-CoV-2 vaccine was attenuated in patients treated with infliximab compared to vedolizumab. Using genomic approaches including DNA methylation and single-cell RNA profiling, I identified acute but non-persistent changes in immune cell proportions following a third dose of SARS-CoV-2 vaccine, and identified baseline DNA methylation signatures that were associated with vaccine antibody response. Further, I optimised a pipeline for profiling single cell gene expression in human PBMC samples from an observational cohort study.
The findings from my thesis have improved understanding of the molecular mechanisms underlying the challenges of IBD therapies using genomic approaches. Overall, it has changed clinical practice, influenced government policies, and brings us one step closer to implementing personalised treatments for patients with IBD.Wellcome GW4-CAT Doctoral Fellowship, grant number 222850/Z/21/
The role of microRNAs, DNA methylation and translational control in regulation of sex specific gene expression in mouse liver
Sex differences are widespread in both mouse and human liver, and are associated with sex differences in drug metabolism and liver pathophysiology. The secretory patterns of growth hormone (GH) is one of the major drivers of liver sex specificity, where intermittent and continuous secretion in male and female respectively lead to sex bias in the expression of more than 1000 genes in mouse liver, via a complex interplay of GH-responsive transcription factors and epigenetic mechanisms. This thesis explores three themes of molecular control in the regulation of liver sex differences: microRNAs, DNA methylation, and translational control. Studies herein identified two microRNAs, miR-1948-5p and miR-802-5p, whose expression is sex biased and regulated by GH and the
transcription factor STAT5b. Small RNA sequencing confirmed the sex specificity of these two microRNAs and identified an additional 18 sex-biased microRNAs. Computational and experimental characterization of miR-1948-5p and miR-802-5p confirmed their authenticity. In vivo inhibition of these microRNAs by locked nucleic acids indicated that miR-1948-5p and miR-802-5p played a functional role in repressing female-biased genes and male-biased genes, respectively. This thesis also investigated the impact of GH and STAT5b on liver DNA methylation profiles. Reduced representation bisulfite sequencing was performed on liver tissues from four mouse models that perturbed the GH and STAT5b axis. In the wildtype liver, sex biased demethylation was positively associated with sex biased chromatin opening and gene expression. Global hypermethylation was observed in livers of mice with lit/lit mutation resulting in GH deficiency or with hepatocyte-specific deletion of the STAT5ab locus. Strikingly, these hypermethylated loci were enriched for enhancer elements and STAT5b binding sites found in wild-type mouse liver. Hypophysectomy followed by GH replacement mouse models identified differentially methylated regions that were sex-biased and rapidly methylated and demethylated in response to GH stimulation. Finally, we used ribosome profiling to validate sex-biased protein translation and identify mechanisms of translational control. In sum, this body of work provides novel insights and broadens our understanding of the diverse molecular mechanisms underlying sexual dimorphism in the liver.2020-10-08T00:00:00
Multi-omics approach to understand the role of plasma proteins in cognitive ageing and dementia
The global burden of age-related cognitive decline and dementia will continue to
rise in tandem with our ageing population. This necessitates the discovery of novel
biomarkers and candidate drug targets to combat cognitive dysfunction. Blood
proteins are important drug targets, and blood samples can be acquired routinely
in clinical settings and epidemiological studies. Whereas hundreds of blood
proteins are associated with cognitive ability and dementia, we do not understand
whether these associations represent correlation or causation. Genome-wide
association studies (GWAS) are required to define variants that are associated
with blood protein levels. These variants can proxy for candidate disease-markers
and assess their causal associations with health outcomes in analysis methods
such as Mendelian randomisation. DNA methylation is an epigenetic mechanism
that regulates gene expression and is influenced by genetic and environmental
factors. Studying the relationship between DNA methylation and protein levels
could reveal whether genetic variation or environmental factors likely mediate
associations between blood proteins and disease states. The first aim of this
thesis is to conduct GWAS and epigenome-wide association studies (EWAS,
using DNA methylation) on plasma levels of 422 unique proteins. Using these
data, I apply causal inference approaches to determine whether blood proteins
are causally associated with Alzheimer’s disease risk.
Several strategies have been proposed to estimate biological age by leveraging
inter-individual variation in DNA methylation profiles. Epigenetic measures of
ageing correlate strongly with chronological age. Recently, a novel epigenetic
measure of ageing termed ‘DNAm GrimAge’ was developed to predict one’s risk
of mortality. DNAm GrimAge is a composite biomarker that incorporates
methylation-based predictors of seven blood protein levels and smoking. The
relationship between this biomarker of ageing and cognitive decline or dementia
is not known. Therefore, the second aim of this thesis is to examine whether
DNAm GrimAge associates with measures of brain health and Alzheimer’s
disease. To conduct these aims, I utilise data from two cohort studies: the Lothian
Birth Cohort 1936 (n ≤ 906, LBC1936) and Generation Scotland (n ≤ 9,537, GS).
In Chapters 1-3, I provide an overview of cognitive ageing and dementia. I
describe GWAS and EWAS on blood protein levels and the development of DNAm
GrimAge. In Chapter 4, I detail the population cohorts and main methodologies
that are used in this thesis.
In Chapter 5, I conduct GWAS and EWAS on plasma levels of 92 neurology-related proteins (n ≤ 750, LBC1936). I identified 41 independent genetic and 26
epigenetic loci that associate with 33 and 9 proteins, respectively. I showed that
an immune-related protein, poliovirus receptor (PVR), is causally associated with
Alzheimer’s disease risk. In Chapter 6, I use a novel Bayesian framework termed
BayesR+ to perform an integrated GWAS/EWAS on plasma levels of 70
inflammation-associated proteins (n = 876, LBC1936). Many GWAS and EWAS
use linear models, which examine every measured genetic or epigenetic site in
isolation. BayesR+ accounts for intercorrelations among genetic and epigenetic
sites and the reciprocal influences of these data types. I estimated the contribution
of genetic and epigenetic variation towards inter-individual differences in
inflammatory protein levels, considered alone and together. There was no
evidence for causal associations between blood inflammatory proteins and the
risk of Alzheimer’s disease. In Chapter 7, I perform a systematic literature review
to identify known blood protein correlates of Alzheimer’s disease. I then use
BayesR+ to conduct an integrated GWAS and EWAS on plasma levels of 282
Alzheimer’s disease-associated proteins (n ≤ 1,064, GS). I observed strong
evidence for causal associations between two proteins, TBCA and TREM2, and
Alzheimer’s disease risk.
In Chapter 8, I examine associations between DNAm GrimAge and measures of
brain health (n ≤ 709, LBC1936). A higher-than-expected DNAm GrimAge
associated with poorer performance on cognitive tasks and neurostructural
correlates of dementia at age 73. I observed weak evidence to suggest that DNAm
GrimAge assessed at age 70 predicts cognitive decline up to age 79. In Chapter
9, I assess whether DNAm GrimAge and other measures of epigenetic ageing
predict the prevalence and incidence of common disease states, including
Alzheimer’s disease (n ≤ 9,537, GS). Epigenetic ageing measures did not predict
the prevalence or incidence of Alzheimer’s disease. In Chapter 10, I discuss the
major findings from this thesis in light of their limitations.
The work presented in this thesis helps to detail the molecular regulation of 422
plasma protein levels and their causal associations with Alzheimer’s disease. This
work also highlights the performance of DNAm GrimAge in predicting indices of
cognitive performance and common disease states. By incorporating genetic,
epigenetic and protein data in two large-scale epidemiological studies, my findings
inform our understanding of relationships between blood proteins and cognitive
ageing and dementia