Ten years and 1,000 studies later, epigeneticists discover problems in their arsenal

Twenty years ago, following the initial sequencing of the human genome, geneticists started carrying out extensive genome-wide association studies to find genomic regions connected to human disease.

Ten years and 1,000 studies later, epigeneticists discover problems in their arsenal

Image Credit: Baylor College of Medicine

In addition to the DNA sequence, another stable level of molecular data created during development called epigenetic modifications also plays a role in disease risk.

Researchers have been examining these epigenetic changes for more than ten years to look for links to disease. More than a thousand of these epigenome-wide association studies have been published as of late.

Now, a team led by scientists at Baylor College of Medicine confirms that the commercial tool that has been the workhorse for these studies is genuinely not suitable for population epigenetics in a study published in the journal Genome Biology.

Many people know that each person has a unique DNA sequence or genome. Less well known is that every cell in the body likewise has a unique level of molecular individuality called its epigenome.

Dr Robert A. Waterland, Study Co-Corresponding Author and Professor, Pediatrics and Nutrition, USDA/ARS Children’s Nutrition Research Center, Baylor College for Medicine

The epigenome, which is a system of molecular markings on DNA that instructs various cells in the body which genes to turn on or off in that cell type, is referred to as being “above” the genome.

Waterland added, “Epigenetic differences between people can affect their risk of disease.

Waterland is also a member of the Dan L Duncan Comprehensive Cancer Center at Baylor.

Epigeneticists examine DNA methylation, which takes place at specific locations known as CpG sites, to search for such variations. A commercial array that tests millions of CpG sites spread across the genome is the go-to tool for population studies of DNA methylation.

For the past 15 years, the Waterland lab and associates have concentrated on a distinct set of CpG sites: those at which DNA methylation varies significantly between individuals but is constant across all of the individual’s tissues.

They reasoned that since DNA from blood samples can be used to look into the epigenetic causes of disease in internal organs like the brain or heart, these sites would be most helpful for population studies.

Three years ago, we reported nearly 10,000 such regions in the human genome (named CoRSIVs for correlated regions of systemic interindividual variation) and proposed that studying them could be a novel way to uncover epigenetic causes of disease”, Waterland further added.

The current study looked into how genetics affects DNA methylation at CoRSIVs as a first step in this direction. Methylation quantitative trait loci (mQTL) are associations between a genetic variation and methylation at a particular CpG site.

Nearly all of the more than 200 studies of human mQTL that have been published make use of commercial methylation arrays.

The group created a method to target CoRSIVs and investigated their methylation in DNA samples from numerous tissues of close to 200 people. According to the first author, Dr Chathura J. Gunasekara, a data analyst in the Waterland lab, “what we found was somewhat of a shock” when they compared their findings with those of the largest prior study.

He continued, “Compared to the most powerful previous study including 33,000 people, our much smaller study focused on CoRSIVs discovered 72-times more mQTL.

The team looked for an explanation for this unexpected finding and found that approximately 95% of the CpG sites on the commercial methylation arrays do not exhibit noticeable methylation differences between individuals.

Statistical associations are built on interindividual variation or variance as is known to scientists. There is no chance of finding mQTL if there is no population variation.

The field of epigenetic epidemiology should also be shocked by this discovery.

Population variance is essential not only for mQTL detection, but also for detecting associations between DNA methylation and risk of disease. Compared to what the field has been doing, we anticipate that focusing on CoRSIVs will make epigenome-wide association studies about 70 times more powerful.

Dr Cristian Coarfa, Associate Professor, Molecular and Cellular Biology, Dan L Duncan Comprehensive Cancer Center, Baylor College for Medicine

In fact, CoRSIVs have already been linked to a wide range of health outcomes, such as thyroid function, cognitive function, cleft palate, schizophrenia, childhood obesity, and an autism spectrum disorder.

Waterland further added, “It is as if there has been this massive and very expensive fishing expedition for the last 10 years, but everyone has been fishing in the wrong place. We hope that the new tool we have developed will accelerate progress in understanding epigenetic causality of disease.

Source:
Journal reference:

Gunasekara, C. J., et al. (2022). Systemic interindividual epigenetic variation in humans is associated with transposable elements and under strong genetic control. Genome Biology. doi.org/10.1186/s13059-022-02827-3

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