Development of novel epigenetic biomarkers and detection reagents for aging

SUMMARY Aging, Alzheimer’s disease, and related dementias (AD/ADRD) are associated with a deterioration of chromatin structure. This deterioration is caused in part by dysregulation of histone post-translation modifications (hPTMs), which play driving roles in regulating chromatin structure and function. Restoration of healthy chromatin structure through manipulation of hPTMs can increase longevity and even reverse aging phenotypes. Therefore, a better understanding of chromatin regulation and aberrant hPTM patterns could lead to identification of novel therapeutic targets and biomarkers of aging and AD/ADRD. Notably, hPTMs do not function in isolation, and studying hPTM combinations provides essential information that cannot be gleaned from single hPTMs. Certain combinations have been well studied and considered canonical, whereas noncanonical combinations are rarer and generally associated with dysregulation. As such, further study of hPTM combinations is promising for clinical research to discern healthy vs. dysregulated noncanonical hPTM combinations. Discovery and study of coincident hPTMs has been limited because 1) most assays require a priori knowledge of a target, and 2) most reagents are specific to a single hPTM. These limitations hinder discovery of new hPTM combinations and cannot distinguish if co-occurring PTMs are on the same or separate histone tails. Thus, new approaches and tools are needed to discover and study pathogenic hPTM combinations to enable the next generation of research for aging and age-related diseases, including identification of novel biomarkers and accelerated therapeutic development. Here, EpiCypher is partnering with Dr. Nicolas Young (Baylor College of Medicine) to develop AgingPTMTM, a novel platform to study aging-associated combinatorial hPTMs (acPTMs) in tissue. This platform will enable the identification and study of new therapeutic targets and biomarkers for aging and AD/ADRD. There are three central innovations in this project: 1) the application of novel unbiased proteomic analysis to identify noncanonical hPTM combinations specific to aging and AD/ADRD, and 2) the development of new assays to further study acPTMs, 3) enabled by novel detection reagents composed of binding domain fusion proteins (i.e., acPTM Sensors). This platform will enable new studies into the mechanisms that drive aging pathology and identify new therapeutic targets and/or disease biomarkers. In Phase I feasibility studies, we identified aberrant hPTM combinations that increase with age in the brains of mice (acPTMs). We also showed that overexpression of an hPTM regulator is associated with a reduction in acPTMs and increased longevity, suggesting these acPTMs are therapeutic targets. In Phase II, we will develop a collection of three acPTM Sensors and complementary spike-in controls (Aim 1), and rigorously validate them for multiple applications, including genomics, in various tissues (Aim 2). In Aim 3, we will optimize commercial-scale manufacturing of the three Sensors and spike-in panels, assemble beta kits for genomic mapping, and apply our novel Sensors to validate these aging-associated hPTMs in human brain.