Discovery Of A “Gene Factory” For Human Longevity

Our genetic makeup is an important factor in lifespan determination. Lifespan is a polygenic trait, but few of the genes responsible have been discovered. FOXO3 was shown by Brad Willcox’s group in Hawaii a decade ago to be a longevity gene. Their findings were then replicated in multiple studies of long-lived populations worldwide. FOXO3 encodes the transcription factor forkhead/winged helix box gene, group O, type 3 (Foxo3). Foxo3, by binding to the promoter of various genes across the genome, regulates a wide array of processes that confer cell resilience and healthy aging.

Recently, the Willcox team reported in Aging Cell that FOXO3 operates by interacting directly with 46 genes either side of its genomic location on chromosome 6q21. They found that FOXO3 is located at the hub of this early-replicating, highly conserved region. Importantly, like FOXO3, its 46 neighboring genes are also involved in various processes that contribute to cell resilience, such as autophagy, stress response, energy/nutrient sensing, cell proliferation, apoptosis and stem cell maintenance. By working together the genes, when co-expressed, make cells and their associated organs healthier with age, thus potentially increasing the probability of having a longer, healthier lifespan.

The first author of the study, Tim Donlon, further discovered that the interaction of FOXO3 with its neighboring genes involved CCCTC-binding factor zinc finger protein (CTCF), a transcription factor that binds promoters, so attracting tissue-specific transcriptional activators, repressors, cohesion, and RNA polymerase II. CTCF is pivotal to chromatin architecture. It makes contact with tens of thousands of sites across the genome by using different combinations of its 11 zinc finger domains to bind different DNA target sequences and proteins. CTCF brings cis-regulatory elements together into co-regulated islands several hundred kb in size. Multiple islands are then brought together into a functional neighborhood, or “archipelago”, of 3–5 Mb. The action of CTCF causes the looping of chromatin between the CTCF binding sites on DNA.

The researchers had in effect discovered what they referred to as the first “gene factory” for healthy aging and longevity.

They then used fluorescent in situ hybridization (FISH) of lymphoblastoid cell lines to confirm their findings. By examining nuclei in which different genes were labelled with different colored fluorescent dyes they were able to visualize the movement of FOXO3 and some of these 46 neighboring genes into close proximity with the expression machinery (i.e., the transcription apparatus) when the cell moves from a “quiescent” state to an “activated” state. The illustration above shows these findings.

FOXO3 May Function To Help Regulate Neighboring Genes

In a case-control genetic study of 110 single nucleotide polymorphisms (SNPs) in FOXO3 and 5 kb of its flanking DNA, they found 41 SNPs that were associated with longevity, defined as living to 95 years of age or older. The subjects for the study were American men of Japanese ancestry living on Oahu, the most populated island of Hawaii. Amongst the SNPs, they found that the nucleotide changes in 13 disrupted binding sites for 18 transcription factors.

By modeling with the use of the WashU Genome Browser they found that these SNPs were connected to the FOXO3 promoter via RNA II polymerase binding and likely formed a longevity-associated haplotype or cis-regulatory unit. They confirmed that these SNPs are functional by semi-quantitative PCR of FOXO3 mRNA in genotypically different lymphoblastoid cell lines. They also showed that two of the genes, HACE1 and AMD1, which are furthest from FOXO3, are also activated by stress. But they are yet to test the response of all of the other genes. Measurements in their FISH experiments further showed that neighboring genes coalesced together around FOXO3 following stress and that the movement of the FOXO3 longevity haplotype was greater than the movement of the common haplotype in lymphoblastoid cell lines. These findings are interesting in that genotype-phenotype correlations common in the study of complex traits often focus on single protein-coding genes but ignore gene neighborhoods.

Recently, Boyle and co-workers at Stanford proposed an “omnigenic” model, which suggests that complex polygenic traits are caused by minuscule contributions from a vast number of sufficiently interconnected peripheral DNA variants that affect core disease-related genes in relevant tissues. Brian Morris, the author for correspondence on the FOXO3 article, has suggested that physical interactions between genes themselves might be an additional contributory factor in the omnigenic model. Whether gene-gene interactions might help explain some of the missing heritability inherent in complex polygenic traits generally will require further research.

It may be that modulation of FOXO3 activity could have an amplifier effect on genes in its neighborhood, so adding to the effects that its own gene product, FoxO3, has on expression of specific genes across the genome.

The new FOXO3 findings will hopefully inspire others to try to discover additional longevity gene neighborhoods elsewhere and to see whether these also show similar kinds of gene-gene interactions.

These novel findings provide considerable food for thought in unraveling the intricate mechanisms responsible for longevity and other complex polygenic conditions.

References

• Donlon TA, Morris BJ, Chen R, Masaki KH, Allsopp RC, Willcox DC, Elliott A Willcox BJ. FOXO3 longevity interactome on chromosome 6. Aging Cell 2017;16:1016-1025. PMID: 28722347  PMCID: PMC5595686 DOI: 10.1111/acel.12625
• Boyle EA, Li YI Pritchard JK. An expanded view of complex traits: From polygenic to omnigenic. Cell 2017;169:1177-1186.  PMID: 28622505   PMCID: PMC5536862 [Available on 2018-06-15]   DOI: 10.1016/j.cell.2017.05.038
• Morris BJ. Blood pressure genome-wide association studies, missing heritability, and omnigenics. Circ Cardiovasc Genet 2017;10: pii: e001943. PMID: 29030405  doi: 10.1161/CIRCGENETICS.117.001943

This study, FOXO3 longevity interactome on chromosome 6, was recently published by Timothy A. Donlon, Brian J. Morris, Randi Chen, Bradley J. Willcox and co-workers in the journal Aging Cell (see first Reference above).