T-cell prolymphocytic leukemia (T-PLL) is a rare and poor-prognostic mature T-cell malignancy. To address its incomplete molecular concept, we integrated large-scale profiling data of alterations in gene expression, allelic copy number (CN), and nucleotide sequences in 111 well-characterized patients. Besides prominent signatures of T-cell activation and prevalent clonal variants, we also identified novel hot-spots for CN variability, fusion molecules, alternative transcripts, and progression-associated dynamics. The overall lesional spectrum of T-PLL is mainly annotated to axes of DNA damage responses, T-cell receptor / cytokine signaling, and histone modulation. We formulate a multi-dimensional model of T-PLL pathogenesis centered around a unique combination of TCL1 overexpression with damaging ATM aberrations as initiating core lesions. The effects imposed by TCL1 cooperate with compromised ATM towards a leukemogenic phenotype of impaired DNA damage processing. Dysfunctional ATM appears inefficient in alleviating elevated redox burdens and telomere attrition and in evoking a p53-dependent apoptotic response to genotoxic insults. As non-genotoxic strategies, synergistic combinations of p53 reactivators and deacetylase inhibitors reinstate such cell death execution.
Overall design
Purified T-cells from 98 T-PLL patients (Supplementary Data1 for additional information) were analyzed using various high-throughput profiling platforms (overlap indicated): Illumina HumanHT‑12 v4 BeadChip arrays (n=70 cases) for gene expression profiling (GEP). CD3+ pan T-cells isolated from peripheral blood (PB) of healthy donors with a similar age-median were used as “normal” controls for GEP (n=10). The isolation strategy of PB tumor cells and matched same-sample germline controls from PB mononuclear cells (PBMCs) of T-PLL patients employed a two-step magnetic separation (MACS columns) process: (1) Positive enrichment of T-PLL tumor cells: magnetic beads bound to anti-CD4 or anti-CD8 antibodies (Microbeads, Miltenyi Biotec) and LS Columns (Miltenyi Biotec) were used. The specificity of beads was selected according to the individual immunophenotype. (2) Depletion of residual T-PLL cells from the flow-through designated as normal control: Depletion Columns (LD, Miltenyi Biotec) were used to remove residual CD4 or CD8 positive cells from the flow-through obtained from step 1. For further details, see Methods section.
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