Telomeres protect the ends of chromosomes from damage. This image shows telomeres (green) and DNA (blue) during DNA repair activities. [Salk Institute]

Two leading groups have developed new techniques to study telomeres using long-read sequencing that could be major advances for the study of these key chromosome parts and their effects on aging, cancer, and other diseases. Their studies are already shedding light on these.

One technique was developed by researchers at the Salk Institute for Biological Studies, the other is from work at Stanford Cancer Institute, Stanford University School of Medicine. Both studies were published in Nature Communications today, June 18, 2024. The lead author on the Salk Institute paper is Tobias T. Schmidt, while the lead author on the Stanford Cancer Institute paper is Santiago E. Sanchez.

Telomere length shortens with age, which leads to cellular senescence, apoptosis, and oncogenic transformation, affecting the health and lifespan of an individual. Shortened telomeres are also linked to increased incidence of disease and poor survival. However, current telomere length measurement methods suffer limits in resolution and accuracy. These methods include: terminal restriction fragment (TRF) analysis, STELA, TeSLA, quantitative PCR, Q-FISH, flow FISH, DNA combing, and telomere length estimates based on next-generation sequencing data. These methods all use either telomere enrichment, staining of telomeres with specific probes, or a combination of both. 

These traditional methods, the Salk researchers point out, fail to resolve chromosome arm and allele-specific composition of individual telomeres due to their repetitive nature and length. With the advent of DNA long-read sequencing, researchers are aiming to sequence entire telomeres and harvest subtelomeric information to annotate individual telomeric reads to specific chromosome arms. 

Recent studies have shown that long-read sequencing technologies such as PacBio HiFi and Oxford Nanopore (ONT) can sequence and measure telomeres at enhanced resolution

The Salk Institute researchers developed “Telo-seq” to sequence whole human telomeres using nanopore sequencing. They then applied the tool to explore bulk, chromosome arm, and allele-specific human telomere length and composition in aging and cancer. 

One key advantage they point out is that “Telo-seq can reliably discriminate between telomerase- and ALT-positive cancer cell lines. Thus, Telo-seq is a tool to study telomere biology during development, aging, and cancer at unprecedented resolution.”

Meanwhile, the Stanford Cancer Center group developed sequencing preparation and bioinformatic pipeline “Telometer” to reproducibly measure telomeres from either whole-genome or telomere-enriched long reads. 

The Stanford team’s Telometer method measures telomere attrition and de novo elongation with up to 30 bp resolution in genetically defined populations of human cells, in blood cells from healthy donors and in blood cells from patients with genetic defects. 

They have already generated lab findings, and write, “We find that human aging is accompanied by a progressive loss of long telomeres and an accumulation of shorter telomeres. In patients with defects in telomere maintenance, the accumulation of short telomeres is more pronounced and correlates with phenotypic severity.”

The Stanford group also applied machine learning to train a binary classification model that distinguishes healthy individuals from those with telomere biology disorders. 

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