Why mediation analysis trumps Mendelian randomization in population epigenomics studies of the Dutch Famine

Our recent analysis of genome-wide DNA methylation data in men and women exposed to the Dutch Famine met passionate criticism by several researchers active on Twitter. It also prompted a more reasoned letter by Richmond and colleagues. At the core of the debate is the proper interpretation of findings from a mediation analysis. We used this method to identify specific DNA methylation changes that statistically provide a link between prenatal exposure to famine and adult metabolic traits. Our critics first argue that our results do not suggest mediation but reverse-causation, where famine-induced metabolic traits drive changes in DNA methylation. We rebut this scenario in a simulation study showing that our test of mediation was unlikely to become statistically significant in the case of reverse-causation. Some critics then argue that Mendelian randomization provides the sole path to correct inference. This belief misses a crucial point: DNA methylation, especially when measured in peripheral blood, is not likely to be a causal mediator from a biological point of view. It could however be a proxy of epigenetic regulation changes in specific tissues, for example at the level of transcription factor binding. If so, a Mendelian randomization approach using genetic variants affecting local DNA methylation in blood will be disconnected from the underlying biological mechanism and is bound to yield false-negative results. Our new simulation studies strengthen the original reasoning that the relationship between prenatal famine and metabolic traits is statistically mediated by specific DNA methylation changes while the specific molecular mechanism awaits elucidation.