Multiomic analysis of downstream molecular effect of teloemre length in individual chromosome arms

PROJECT SUMMARY Healthy human cells contain 92 telomeres (2 arms per 46 chromosomes), each with unique lengths that shorten during cell division, and that protect the genome from enzymatic degradation. Average telomere length (TL) of all 92 telomeric alleles has clinical relevance as a biomarker for cellular aging and a broad variety of health-related conditions, including telomere biology disorders (TBD): inherited disorders that exhibiting idiopathic pulmonary and liver fibrosis, bone marrow failure and cancer predisposition. Telomeres also play an important regulatory role in gene expression through the telomere position effect (TPE). However, the clinical relevance of these individual 92 chromosome arm-specific TLs and their connection with TPE is still unclear. None of the existing methods to measure TL are at the same time accurate, scalable, suited for any tissue source, or able to provide length of individual telomeres. This includes Flow-cytometry Fluorescence In-Situ Hybridization (flowFISH), the only CAP/CLIA-approved test to measure TL. Recent advances in long-read sequencing technologies have allowed our group to develop Telogator, a novel bioinformatics approach that estimates TL for all 92 alleles, individually, from this data. We propose to use this approach in combination with multiomics analyses to test the main hypothesis that individual chromosome arm-specific TL are clinically relevant in the diagnosis and understanding of TBD, and that individual shortened telomeres can trigger transcriptomic and epigenomic changes involved in the pathogenesis of the disease. Through the Mayo Clinic TBD Specialty Clinic, we have managed over 150 patients with manifestations of TBD including flowFISH and genetic germline testing. These individuals are clinically and molecularly annotated, they have already given consent for research through our IRB-approved protocol and PBMC samples are readily available. We will use this unique resource to test our hypothesis by completing the following aims: In Aim 1 we will define the reference TL values at the chromosome arm level across the lifespan of healthy individuals using our novel sequencing-based bioinformatic tool (Telogator) on 30 individuals distributed in age decades from their 20s to their 70s. We will then compare these reference values with the length of individual telomeres from TBD patients (n=30) calculated using the same approach. In Aim 2 we will characterize the transcriptomic (RNAseq) and epigenomic (ChIP-seq) changes in correlation to the TL of each individual chromosome arm to describe genes regulation through TPE in the context of TBD. This project will explore the conceptually innovative idea that TL of individual chromosome arms has clinical significance and can exert characteristic epigenomic and transcriptomic changes in human cells. Our research will translate into better diagnostic tools for TBD and pave the way for future research in the pathogenesis of the disease. Understanding the gene regulation related to chromosome-specific TL will facilitate the study of other telomere-related processes like aging and cancer.