Characterization of mature T-cell leukemias by next-generation sequencing and drug sensitivity testing

Research output: ThesisDoctoral Thesis

Abstract

Mature T-cell malignancies comprise a heterogeneous group of diseases with widely variable clinical courses, ranging from indolent, slowly progressing to rapidly progressing disease, leading to death. While some compounds have been found to be active in these diseases, much work remains to be done to characterize the disease entities genetically and molecularly and develop effective therapeutic options. Recent studies have found recurrent genetic mutations in the JAK/STAT pathway that contribute to the pathogenesis of T-LGL leukemia and PLL leukemia. The aim of this PhD project was to reveal new somatic mutations underlying different mature T-cell malignancies and further elucidate their functional impact on the pathogenesis of the disease. Furthermore, ex vivo drug screening of selected patient samples was applied in an effort to find clinically relevant drugs for the individual patient. In the first study, exome sequencing was applied to three STAT-mutation negative T-LGL leukemia patients to elucidate the molecular background of this subset of patients. Mutations in genes associated with either the STAT-pathway directly (such as PTPRT) or T-cell activation were observed in all patients. These novel mutations are potentially biologically relevant and are associated with a similar disease phenotype as that of patients with mutations in the STAT3 gene. In the second study, the exome sequencing of additional LGL leukemia patients revealed recurrent STAT3 mutations outside the hotspot SH2-domain. Further targeted amplicon sequencing of the entire STAT3 gene in a larger T-LGL cohort revealed mutations in the coiled-coil and DNA-binding domain present in 4% of patients. Similarly, in the third study, STAT5B mutations previously found to be rare in CD8+ LGL leukemia (2%) were discovered to be significantly over-represented in CD4+ cases (55%). For both studies, the activation and phosphorylation patterns of the new mutations were confirmed with functional assays. In the fourth study, T-PLL leukemia patient samples were screened with a drug sensitivity and resistance testing platform to elucidate drug sensitivity patterns. The patients were divided by selective sensitivities to HDAC, PI3K/AKT/mTOR, HSP90, and JAK inhibitors. Intriguingly, all T-PLL samples were sensitive to the CDK inhibitor SNS-032, which was shown to inhibit distal TCR signaling and points to a centrally disturbed cell cycle regulation. Furthermore, different classes of p53 activators showed T-PLL specific responses, indicating a previously unexplored targeted treatment for these patients. In combination with the drug responses, a targeted sequencing of known JAK/STAT mutations was applied together with gene expression profiling to molecularly characterize this rare disease. Strikingly, drug responses did not link to the presence of JAK/STAT mutations, TCL1A-activating translocations, or ATM deletion status, suggesting that screening for recurrent genetic biomarkers does not readily translate into applicable deductions on effective therapeutic strategies in T-PLL. However, the ex vivo drug response data enabled the discovery of new drug classes with potential efficacy in T-PLL.
Original languageEnglish
Place of PublicationHelsinki
Publisher
Print ISBNs978-951-51-2891-1
Electronic ISBNs978-951-51-2892-8
Publication statusPublished - 2017
MoE publication typeG5 Doctoral dissertation (article)

Fields of Science

  • 3111 Biomedicine
  • 3122 Cancers

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