Novel epigenetic clock for fetal brain development predicts prenatal age for cellular stem cell models and derived neurons

Abstract

Induced pluripotent stem cells (iPSCs) and their differentiated neurons (iPSC-neurons) are a widely used cellular model in the research of the central nervous system. However, it is unknown how well they capture age-associated processes, particularly given that pluripotent cells are only present during the earliest stages of mammalian development. Epigenetic clocks utilize coordinated age-associated changes in DNA methylation to make predictions that correlate strongly with chronological age. It has been shown that the induction of pluripotency rejuvenates predicted epigenetic age. As existing clocks are not optimized for the study of brain development, we developed the fetal brain clock (FBC), a bespoke epigenetic clock trained in human prenatal brain samples in order to investigate more precisely the epigenetic age of iPSCs and iPSC-neurons. The FBC was tested in two independent validation cohorts across a total of 194 samples, confirming that the FBC outperforms other established epigenetic clocks in fetal brain cohorts. We applied the FBC to DNA methylation data from iPSCs and embryonic stem cells and their derived neuronal precursor cells and neurons, finding that these cell types are epigenetically characterized as having an early fetal age. Furthermore, while differentiation from iPSCs to neurons significantly increases epigenetic age, iPSC-neurons are still predicted as being fetal. Together our findings reiterate the need to better understand the limitations of existing epigenetic clocks for answering biological research questions and highlight a limitation of iPSC-neurons as a cellular model of age-related diseases.

Single-cell transcriptomics identifies master regulators of neurodegeneration in SOD1 ALS iPSC-derived motor neurons

“…ALS patient-derived iPSCs have provided unprecedented access to human diseased MNs, enabling researchers to follow the course of degeneration in a dish. Our ipMNs have a developmental age corresponding to 75–90 days post conception, similar to previous observations ( Ho et al., 2016 ; Steg et al., 2021 ). However, iPSC-derived neurons display disease-related phenotypes and dysregulated molecular pathways induced by the underlying mutations ( Dafinca et al., 2020 ; Fujimori et al., 2018 ; Hall et al., 2017 ; Mehta et al., 2021 ; Selvaraj et al., 2018 ).…”

Fetal origin of sex‐bias brain aging

“…They are commonly referred to as epigenetic clock (epiclock) and serve as reliable predictors of the biological age of organs. [18][19][20][21] Several studies have profiled methylation changes in the brain during aging 17,22,23 and in the developing brain at fetal stages and found that aberrant methylation in the fetal brain can influence the risk of brain diseases later in life. 24,25 Commonalities in morphometric changes have also been observed in the brain during development and aging.…”

“…Methylation, the majority of which occurs in CpGs (5’‐Cytosine‐phosphate‐Guanine‐3′) sites, changes in correlation with age. They are commonly referred to as epigenetic clock (epiclock) and serve as reliable predictors of the biological age of organs 18–21 . Several studies have profiled methylation changes in the brain during aging 17,22,23 and in the developing brain at fetal stages and found that aberrant methylation in the fetal brain can influence the risk of brain diseases later in life 24,25 .…”

Mapping cis-regulatory elements in human neurons links psychiatric disease heritability and activity-regulated transcriptional programs

“…Notably, the maturation of PV neurons is protracted and exquisitely regulated by experience and cell-extrinsic factors ( Donato et al, 2015 ). Most currently available differentiation methods render immature or fetal cells ( Steg et al, 2021 ; Studer et al, 2015 ). This sets the stage for optimized methods, in which distinct cell types can be generated for mechanistic investigation.…”