Profiling telomere content and composition at single-cell resolution incancer and immune cells

Abstract

Biological processes such as aging, carcinogenesis, and immune responses depend on the ability of cells to maintain or rapidly expand populations. This capacity is constrained by a cells replicative potential, which is reflected in its telomere content. Despite the central role of telomeres in cancer and immunity, their analysis at single-cell resolution across diverse cell types remains challenging. Here we show that scATAC-seq data enables quantitative telomeromics when key technical and biological confounders are accounted for. We present a computational framework that addresses read sparsity, telomere representation, and chromatin-state-dependent competition for sequencing signal, enabling robust estimation of telomere content and telomeric variant repeat composition from scATAC-seq data. By inferring global chromatin condensation directly from scATAC-seq profiles, our approach corrects for cell-cycle-associated biases while simultaneously capturing chromatin-state dysregulation in cancer. Applied to a large cancer atlas, this framework reveals patient-specific telomere maintenance phenotypes, including telomerase-associated and alternative lengthening of telomeres (ALT)-like profiles preserved across subclonal populations. Extending beyond cancer cells, we observe that telomere content in exhausted T cell subpopulations prior to immunotherapy is predictive for effective response to PD-1 checkpoint blockade. Together, these results establish scATAC-seq as a robust platform for single-cell telomeromics in cancer and immunity. Graphical Abstract O_FIG O_LINKSMALLFIG WIDTH=200 HEIGHT=78 SRC="FIGDIR/small/609339v2_ufig1.gif" ALT="Figure 1"> View larger version (26K): org.highwire.dtl.DTLVardef@4f9498org.highwire.dtl.DTLVardef@a4b787org.highwire.dtl.DTLVardef@d1e25org.highwire.dtl.DTLVardef@136196b_HPS_FORMAT_FIGEXP M_FIG C_FIG Created in BioRender. Popp, F. (2026) https://BioRender.com/mi2jove