The Human Pancreatic Islet Methylome and Its Role in Type 2 Diabetes

Abstract

Islet dysfunction is central to the development and progression of type 2 diabetes (T2D). Epigenetic modifications are essential for establishing and maintaining cell identity and function in normal circumstances. Exposure to adverse environmental factors may alter the epigenome, and result in changes of gene expression and the resulting phenotype. The aim of this thesis was to analyze DNA methylation levels of specific genes, as well as genome-wide DNA methylation, in order to determine whether epigenetic dysregulation of pancreatic islets contributes to islet dysfunction in subjects with T2D. We also assessed the relationship between genetic variation and DNA methylation. We further examined the potential use of DNA methylation in blood DNA to predict future T2D.

At the specific gene level, we found that DNA methylation of INS and PDX-1 was increased in pancreatic islets from subjects with T2D (Studies I and II). Conversely, their mRNA expression, insulin content and glucose-stimulated insulin secretion (GSIS) were decreased in the same islets. We next analyzed genome-wide DNA methylation in human pancreatic islets from both T2D and non-diabetic donors (Study III). Nearly 1,500 CpG sites (853 genes) were differentially methylated in T2D islets, with the majority showing decreased DNA methylation. 102 genes showed both altered DNA methylation and mRNA expression in T2D islets, including CDKN1A, PDE7B, SEPT9 and EXOC3L2. Our functional experiments provided further evidence that altering the expression of these genes, by modeling the situation in T2D, results in impaired insulin and glucagon secretion in cell line models.

Furthermore, we showed that nearly half of the single nucleotide polymorphisms (SNPs) associated with T2D are CpG-SNPs, which can introduce or remove a CpG site (Study IV). Accordingly, we found that the degree of DNA methylation at CpG-SNP sites varied between individuals with different genotypes, and that some of the CpG-SNPs were associated with differential gene expression, alternative splicing and hormonal secretion.

In Study V, we showed that altered DNA methylation at two CpG sites in the ABCG1 and PHOSPHO1 genes in blood from non-diabetic individuals was associated with a higher risk of future T2D. Subsequently, we found that CpG sites annotated to these genes were differentially methylated in T2D target tissues.

Taken together, our findings suggest that epigenetic dysregulation of pancreatic islets play a role in islet dysfunction in subjects with T2D, and can be influenced by genetic variation and the environment.

Abstract (Swedish)

Popular Abstract in English

Sugar is the main source of energy in our bodies. If your blood sugar drops below a certain level, it can cause serious damage to your brain. On the other hand, having a very high blood sugar level for a long time can cause diabetes. For this reason, blood sugar levels in our bodies are maintained within a certain range by a group of hormones that work together. These hormones are produced by the pancreatic islets that consist of five cell types. Each cell type produces a special hormone that plays a role in the fine-tuning of sugar levels in our bodies. When you have a meal, your blood sugar will rise, and the pancreatic beta-cells will sense this and release insulin. Insulin is a hormone that sends a signal to certain cells in your body to store excess sugar and remove it from blood. When you haven’t eaten for some time, your blood sugar goes down and pancreatic alpha-cells produce glucagon. Glucagon does the opposite of insulin and sends a signal to certain cells in your body to release some sugar from their stores. Patients with type 2 diabetes have problems producing enough insulin, and produce more glucagon than is needed. To make things worse, the cells that are supposed to receive signals from insulin to store sugar are not very responsive. As a result, sugar is not cleared from your blood. Having high blood sugar for a long time is one of the main reasons for heart attacks, kidney failure, blindness and lower limb amputation.

Why do certain people get type 2 diabetes? Many factors can increase your risk of getting type 2 diabetes. Some are genetic (determined by the genes you inherit from your parents), and others are environmental. People that have diabetes running in their family are more likely to become diabetic themselves. The main reasons why the number of people with type 2 diabetes is increasing worldwide are probably: being overweight, eating unhealthy food, and not exercising. Other factors include: smoking, ethnicity, aging, high blood pressure, and poor nutrition during pregnancy. One way in which these different environmental factors can affect the way your body works is via epigenetic modifications.

What are epigenetic modifications, and how do they work? Epigenetic modifications are molecules that are attached to your DNA and can change the way your genes behave without changing the gene itself. The DNA that you inherit from your parents is made up of a sequence of four letters (A, T, C and G); this sequence provides your cells with an instruction manual that tells them what to do. Although all the cells in your body carry exactly the same instruction manual (DNA), they look and behave very differently. This is because a group of proteins and small molecules that are attached to your DNA make every cell-type use different parts of the instruction manual (express different genes). In other words, each cell has a different epigenome on top of the DNA that tells it to express a group of genes, and prevents it from expressing others. The epigenome can help your genome remember certain experiences that it was exposed to. They could be good experiences (for example, healthy diet and exercise) that help your body adapt, or they could be bad experiences (for example, unhealthy diet, pollutants, starvation and poor nutrition as a fetus) that make you sick. There are different types of epigenetic modifications that give different signals, and can be located in different parts of the DNA sequence. DNA methylation is one of these epigenetic modifications; it is made by the attachment of a molecule, known as a methyl group, to the letter C in your DNA sequence (mainly those followed by the letter G). These methyl groups can block certain proteins from reaching the switch button that turns your genes on.

DNA methylation of pancreatic islets is different in patients with type 2 diabetes. Pancreatic islets from patients with type 2 diabetes have either more or fewer of these methyl groups in different parts of their DNA sequence than healthy people. In general, patients with type 2 diabetes have fewer methyl groups attached to their DNA, especially in certain parts of the DNA sequence. In some cases, the genes that are located in these regions behave differently in patients with type 2 diabetes, including genes that are important for the normal function of pancreatic islets and their ability to produce insulin and glucagon. For example, pancreatic islets from patients with type 2 diabetes have more methyl groups attached to the gene that produces insulin and another gene that regulates it. It is possible that these epigenetic changes are one of the reasons that make patients with type 2 diabetes produce less insulin.

The sequence of letters that makes up your DNA is predetermined by your parents. Because the methyl group is mainly added to the letter C, followed by a G, people that don’t have CG cannot have a methyl group attached to their DNA. That means that many of the changes caused by the addition or removal of these methyl groups will be different for different people based on the sequence of letters that make up their DNA. If this happens in a region that plays a role in diabetes, people with a certain sequence of letters will be more affected than others.

Almost 50 percent of people are unaware that they have diabetes. By the time they are diagnosed, a lot of the damage has already been done to their bodies. Researchers have been trying to find a ‘fingerprint’ that can help them identify individuals that are likely to get type 2 diabetes, so that they can get help, and control their blood sugar level before it gets worse. A number of DNA ‘fingerprints’ have been found, but researchers are still trying to find even more reliable ones. Epigenetic ‘fingerprints’ are an interesting tool that is already being used in cancer research. We and other researchers are trying to find an epigenetic ‘fingerprint’ in blood DNA that could predict if an individual will get diabetes in the future.

How can I avoid becoming diabetic? You can avoid getting type 2 diabetes by exercising, eating healthy food, and avoiding many of the other risk factors. Although you can’t change your genes, having a healthy lifestyle can protect you from getting diabetes, or at least delay its onset. We believe that sometimes an unhealthy lifestyle can make certain epigenetic changes to the pancreatic islets, and that these changes can cause diabetes. The good news is that some of these changes can be reversed by a healthy lifestyle, and thus protect you from getting diabetes.

• author: Dayeh, Tasnim
• supervisor: Charlotte Ling; Marloes Dekker Nitert
• opponent: Professor Simmons, Rebecca, University of Pennsylvania
• organization: Diabetes - Epigenetics (research group); LUDC (Lund University Diabetes Centre)-lup-obsolete (research group); EXODIAB: Excellence of Diabetes Research in Sweden
• publishing date: 2016
• type: Thesis
• publication status: published
• subject: Endocrinology and Diabetes
• keywords: CpG-SNP, glucagon secretion, insulin secretion, human pancreatic islets, DNA methylation, Epigenetics
• in: Lund University Faculty of Medicine Doctoral Dissertation Series
• volume: 2016:9
• pages: 170 pages
• defense location: Jubileumsaulan, MFC, Jan Waldenströms gata 5, Skånes Universitetssjukhus i Malmö.
• defense date: 2016-02-03 09:00:00
• ISSN: 1652-8220
• ISBN: 978-91-7619-234-4
• language: English
• LU publication?: yes
• id: f3e79233-0ca8-41ec-b00f-7835f8c61f98 (old id 8515603)
• date added to LUP: 2016-04-01 13:49:53
• date last changed: 2019-05-22 01:34:40