Single cell sequencing reveals shared clonal signatures in non-malignant B- and tumor cells in T-prolymphocytic leukemia

Shared clonal signatures in non-malignant B-cells and T-PLL cells indicate a common clonal ancestry.

The role of germline ATM mutations in the leukemogensis of T-PLL should be explored

The aim of this study was to elucidate the clonal origin and evolutionary dynamics of T-prolymphocytic leukemia (T-PLL) using targeted next generation sequencing (NGS) of paired samples from diagnosis and relapse. DNA from both non-malignant and tumor cells was extracted from sorted cell fractions obtained from 16 patients with T-PLL. NGS was performed using a customized Haloplex gene Panel comprising 19 genes recurrently mutated in T-PLL (ATM and JAK/STAT pathway). Droplet digital polymerase chain reaction (ddPCR) was performed to confirm mutations detected by NGS with low variant allele frequencies (VAF). Single-cell analysis of genomic DNA combined with cell surface protein markers was performed using the Mission Bio Tapestri Platform. The most frequently mutated gene was ATM (n=10) followed by STAT5B (n=7), JAK3 (n=3), EZH2 (n=3), BCOR (n=1) and STAT6 (n=1). Relapse samples were available for 9/16. Varying patterns of clonal shifts were observed between diagnosis and relapse (increase, decrease, both increase/decrease and no change). The presence of pathogenic variants in ATM, EZH2, STAT5B and JAK3 in both normal sorted B-cells and clonal T-cells was confirmed. Single-cell analysis revealed shared mutations in both non-malignant B and clonal T-cells in one case. A pathogenic variant within the ATM gene of potential germline origin was observed in one case. T-PLL exhibits variable patterns of clonal evolution between diagnosis and relapse. Single cells multiomics analysis reveals shared mutational signatures in both non-malignant B-cells and clonal T-cells. The role of germline ATM mutations in the pathogenesis of T-PLL should be further explored.