Developmental Time

understanding the molecular nature of developmental time.

The neural retina provides a convenient system to explore mechanisms that regulate developmental time, taking advantage of its highly regular sequence of development present in all vertebrates. This well-defined sequence of cell generation in the vertebrate retinas is analogous to that which occurs in other developing neural tissues, such as the Drosophila neuroblast lineage and the cerebral cortical laminar-specification. We recently investigated the link between developmental and chronological age using the human retina as a model and monitoring the status of an epigenetic clock, based on the status of DNA methylation. For these studies, we collaborate with Steve Horvath at UCLA. The Horvath clock is based on the weighted average of 353 CpGs, whereby methylation of 193 CpGs is positively correlated with age, while methylation of the other 160 CpGs is negatively correlated with age.

Our results show that (1) the epigenetic "aging" clock extends back to at least 8 weeks of gestational age, and possibly to conception. This graph shows the high degree of correlation between the chronological age and the methyl DNA age for human cerebral cortical samples from birth to over 80 years old. This is plotted with fetal retinal samples, showing that postconception chronological age is also correlated well with fetal methyl DNA age. Fetal samples show a much more rapidly changing methyl DNA clock.

(2) the epigenetic clock continues to tick in explant cultures, thus providing potential to explore the mechanisms underlying DNAm epigenetic age. For the experiment shown on the right, one of a pair of retinas was put into explant culture and the other was analyzed acutely, and in all cases the aging clock progressed in the 42 days in vitro.

(3) We derived organoids from human embryonic stem cells, and these make all the cell types normally present in the retina, but are much smaller than the normal retina (compare the normal retina in A,A' and the organoid at the same stage in B,B'.  Despite the difference in size, organoids derived from ESCs also show a good correlation between their DNAm age and their chronological age from the onset of the differentiation protocol. 

(4) The progeroid-like disorder, Down syndrome, leads to accelerated DNAm age and accelerated onset of age-related diseases, like macular degeneration and Alzheimer's disease.  We found that Down syndrome individuals already show an accelerated methyl DNA clock at fetal stages.

Overall, this study provides both an independent way to measure developmental time and establishes the human retina as a potential experimental model to study epigenetic aging in vitro. We are currently testing compounds known to modify the rate of aging to determine whether these affect the Horvath methyl DNA clock.  It may also be possible to determine the molecular pathways underlying this clock using this in vitro system and evidence of clock acceleration in Down syndrome tissues.