Systematic Approach Identifies Multiple Transcription Factor Perturbations That Rejuvenate Replicatively Aged Human Skin Fibroblasts

Abstract

Rejuvenation, long a quixotic dream, recently became a possibility through exciting new approaches to counteract aging. For example, parabiosis and partial reprogramming through overexpressing four stem cell transcription factors (Yamanaka factors) both rejuvenate organisms and cells. We hypothesize there are many other genetic solutions to human cell rejuvenation, and some solutions may be safer and more potent than current gene targets. We set out to develop a systematic approach to identify novel genes that, when overexpressed or repressed, reprogram the global gene expression of a cell back to a younger state. Using the Hayflick model of human cell replicative aging, we performed a Perturb-seq screen of 200 transcription factors (TFs) selected through a combination of bioinformatic analysis and literature search. We identified dozens of potentially rejuvenating TFs, those that when overexpressed or repressed in late passage cells reprogrammed global gene expression patterns back to an earlier passage state. We further validated four top TF perturbations through molecular phenotyping of various aging hallmarks. Late passage cells either overexpressing EZH2 or E2F3 or repressing STAT3 or ZFX had more cell division, less senescence, improved proteostasis, and enhanced mitochondrial function. These TF perturbations led to similar downstream gene expression programs. In addition, the rejuvenating effects of these TFs were independent of telomeres. We believe our general approach for identifying rejuvenating factors can be applied to other model systems, and some of the top TF perturbations we discovered will lead to future research in novel, safer rejuvenation therapies.

Transcriptional changes are tightly coupled to chromatin reorganization during cellular aging

“…These findings highlight the importance of systematically evaluating paired time course transcriptional and chromatin conformation data to advance our fundamental understanding of aging. Similar to recent work identifying rejuvenating TFs (Sengstack et al., 2022 ), we anticipate that some of the TFs we identified in this work could serve as potential therapeutic targets to attenuate, prevent, or even reverse age‐related declines, offering life‐changing benefits to the growing global geriatric population.…”