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Genome-wide DNA methylation profiling in mixed ancestry South Africans with diabetes or prediabetes
Author(s)
Solomon, Wendy Lynn
Date Issued
2021
Type
Thesis
Publisher
Cape Peninsula University of Technology
Abstract
Type 2 diabetes mellitus (T2DM) is a global health concern and has shown to be a rising
public health crisis in Africa. South Africa, in particular, has shown the highest prevalence of
the disease with a large percentage of undiagnosed individuals. There is a need for
intervention strategies that include early detection of at-risk individuals and the prevention of
disease progression. Although studies have shown a relationship between the occurrence of
T2DM and genetic and lifestyle factors, it has been suggested that epigenetic mechanisms
such as DNA methylation contribute to the pathogenesis of T2DM through its association with
the transcriptional activity of genes. There are however limited studies focussing on the
genome-wide DNA methylation profiling of diabetic and prediabetic subjects from Africa and
in particular, South Africa. The aim of the current study therefore was to conduct genome-wide
DNA methylation in South African subjects with varying glucose tolerance and investigate the
relationship between the observed DMRs and cardiometabolic risk factors.
A cross-sectional case-control study design was used to conduct genome-wide DNA
methylation profiling and lncRNA analysis on the peripheral blood of 48 South African
individuals from the Bellville South community in the Western Cape. The participants were
classified according to their glucose tolerance status and comprised 12 participants with
known diabetes on metformin treatment, 12 screen-detected (newly diagnosed) diabetics, 12
prediabetics and 12 participants with normal glucose tolerance (NGT). After DNA extraction,
DNA immunoprecipitation sequencing was used to identify statistically significant differentially
methylated regions (DMRs) and lncRNA-associated DMRs, followed by gene ontology and
KEGG pathway analysis. Lastly, the significant DMRs identified were validated by performing
pyrosequencing of bisulphite converted DNA.
The study identified several DMRs and functional pathways affected in subjects with
diabetes and prediabetes. A total of 366 DMRs and 641 lncRNA-associated DMRs were
observed, of which 63% were hypermethylated and 37% hypomethylated. Gene ontology and
KEGG pathway analyses identified hypermethylation in cardiovascular processes in screendetected
diabetic subjects indicating that a decrease in the expression of the associated genes
may be associated with these functions in diabetes. Furthermore, hypomethylation was
evident in purine metabolism in the screen-detected diabetic subjects highlighting the risk of
increased reactive oxygen species production, inflammation and cell damage associated with
excess uric acid in diabetic individuals. The study also identified DMRs and their functional
pathways which showed a possible progression from prediabetes to diabetes.
Hypomethylation of LBP (Lipopolysaccharide Binding Protein) in prediabetic subjects
suggested that increased expression of this DMR could potentially be used as a biomarker for
the progression to diabetes due to its association with increased inflammatory cytokines,
insulin resistance and beta-cell dysfunction. Furthermore, hypomethylation of the regulation
of wound healing and blood coagulation and their associated DMRs, SERPINF2 and DMTN,
was observed in prediabetic subjects. Elevated levels of SERPINF2 (alpha 2-antiplasmin) and
DMNT (dematin) expression in hyperglycaemic subjects could be used as an indicator of the
increased risk for cardiovascular disease and red blood cell stability.
Metformin, which is used as the first line of treatment for T2DM, has been shown to be
affected by DNA methylation patterns. Hypermethylation of the cytokine-cytokine receptor
interaction and oxidative phosphorylation pathways in known diabetics on metformin treatment
suggested that metformin may have an inhibitory effect on complement-mediated
inflammation and mitochondrial oxidative phosphorylation in diabetic individuals. The cAMP
signalling pathway was also found to be hypermethylated in metformin-treated subjects which
suggest the use of DNA methylation as a potential marker to monitor the effects of metformin
on glucose homeostasis. Furthermore, hypermethylation of the functional pathways and
DMRs identified in metformin-treated subjects when compared to the untreated screendetected
subjects were associated with Diabetic Peripheral Neuropathy (DPN).
Several novel lncRNAs were observed when comparing the lncRNA-associated DMRs
identified amongst individuals with varying degrees of glucose tolerance. Hypomethylation of
the complement component C4 was observed in hyperglycaemic subjects suggesting a
possible association with the cardiometabolic risk factors and complement-mediated
inflammation associated with T2DM. The lncRNA-associated DMRs observed in metformintreated
subjects included the mitochondrial ATP synthase-coupling factor 6 (ATP5J) enzyme
thought to be involved in the oxidative phosphorylation pathway with associations to T2DM
and hypertension.
In conclusion, these findings show that DNA methylation patterns differ amongst individuals
with varying degrees of glucose tolerance within a South African population. Furthermore, the
study showed that DNA methylation patterns are associated with certain cardiometabolic traits
and diabetic complications, and could be used as potential biomarkers for the occurrence and
progression of T2DM. The expression of several DMRs and lncRNA-associated DNA
methylation regions observed in metformin-treated T2DM may also be potential targets for
therapeutic monitoring in patients with diabetes.
public health crisis in Africa. South Africa, in particular, has shown the highest prevalence of
the disease with a large percentage of undiagnosed individuals. There is a need for
intervention strategies that include early detection of at-risk individuals and the prevention of
disease progression. Although studies have shown a relationship between the occurrence of
T2DM and genetic and lifestyle factors, it has been suggested that epigenetic mechanisms
such as DNA methylation contribute to the pathogenesis of T2DM through its association with
the transcriptional activity of genes. There are however limited studies focussing on the
genome-wide DNA methylation profiling of diabetic and prediabetic subjects from Africa and
in particular, South Africa. The aim of the current study therefore was to conduct genome-wide
DNA methylation in South African subjects with varying glucose tolerance and investigate the
relationship between the observed DMRs and cardiometabolic risk factors.
A cross-sectional case-control study design was used to conduct genome-wide DNA
methylation profiling and lncRNA analysis on the peripheral blood of 48 South African
individuals from the Bellville South community in the Western Cape. The participants were
classified according to their glucose tolerance status and comprised 12 participants with
known diabetes on metformin treatment, 12 screen-detected (newly diagnosed) diabetics, 12
prediabetics and 12 participants with normal glucose tolerance (NGT). After DNA extraction,
DNA immunoprecipitation sequencing was used to identify statistically significant differentially
methylated regions (DMRs) and lncRNA-associated DMRs, followed by gene ontology and
KEGG pathway analysis. Lastly, the significant DMRs identified were validated by performing
pyrosequencing of bisulphite converted DNA.
The study identified several DMRs and functional pathways affected in subjects with
diabetes and prediabetes. A total of 366 DMRs and 641 lncRNA-associated DMRs were
observed, of which 63% were hypermethylated and 37% hypomethylated. Gene ontology and
KEGG pathway analyses identified hypermethylation in cardiovascular processes in screendetected
diabetic subjects indicating that a decrease in the expression of the associated genes
may be associated with these functions in diabetes. Furthermore, hypomethylation was
evident in purine metabolism in the screen-detected diabetic subjects highlighting the risk of
increased reactive oxygen species production, inflammation and cell damage associated with
excess uric acid in diabetic individuals. The study also identified DMRs and their functional
pathways which showed a possible progression from prediabetes to diabetes.
Hypomethylation of LBP (Lipopolysaccharide Binding Protein) in prediabetic subjects
suggested that increased expression of this DMR could potentially be used as a biomarker for
the progression to diabetes due to its association with increased inflammatory cytokines,
insulin resistance and beta-cell dysfunction. Furthermore, hypomethylation of the regulation
of wound healing and blood coagulation and their associated DMRs, SERPINF2 and DMTN,
was observed in prediabetic subjects. Elevated levels of SERPINF2 (alpha 2-antiplasmin) and
DMNT (dematin) expression in hyperglycaemic subjects could be used as an indicator of the
increased risk for cardiovascular disease and red blood cell stability.
Metformin, which is used as the first line of treatment for T2DM, has been shown to be
affected by DNA methylation patterns. Hypermethylation of the cytokine-cytokine receptor
interaction and oxidative phosphorylation pathways in known diabetics on metformin treatment
suggested that metformin may have an inhibitory effect on complement-mediated
inflammation and mitochondrial oxidative phosphorylation in diabetic individuals. The cAMP
signalling pathway was also found to be hypermethylated in metformin-treated subjects which
suggest the use of DNA methylation as a potential marker to monitor the effects of metformin
on glucose homeostasis. Furthermore, hypermethylation of the functional pathways and
DMRs identified in metformin-treated subjects when compared to the untreated screendetected
subjects were associated with Diabetic Peripheral Neuropathy (DPN).
Several novel lncRNAs were observed when comparing the lncRNA-associated DMRs
identified amongst individuals with varying degrees of glucose tolerance. Hypomethylation of
the complement component C4 was observed in hyperglycaemic subjects suggesting a
possible association with the cardiometabolic risk factors and complement-mediated
inflammation associated with T2DM. The lncRNA-associated DMRs observed in metformintreated
subjects included the mitochondrial ATP synthase-coupling factor 6 (ATP5J) enzyme
thought to be involved in the oxidative phosphorylation pathway with associations to T2DM
and hypertension.
In conclusion, these findings show that DNA methylation patterns differ amongst individuals
with varying degrees of glucose tolerance within a South African population. Furthermore, the
study showed that DNA methylation patterns are associated with certain cardiometabolic traits
and diabetic complications, and could be used as potential biomarkers for the occurrence and
progression of T2DM. The expression of several DMRs and lncRNA-associated DNA
methylation regions observed in metformin-treated T2DM may also be potential targets for
therapeutic monitoring in patients with diabetes.
Additional information
Thesis (DPhil (Biomedical Sciences))--Cape Peninsula University of Technology, 2021
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