[HTML][HTML] Genomic landscape characterization of large granular lymphocyte leukemia with a systems genetics approach

A Coppe, EI Andersson, A Binatti, VR Gasparini… - Leukemia, 2017 - nature.com
A Coppe, EI Andersson, A Binatti, VR Gasparini, S Bortoluzzi, M Clemente, M Herling
Leukemia, 2017nature.com
Large granular lymphocyte (LGL) leukemia is a rare clonal disease characterized by a
persistent increase in the number of CD8+ cytotoxic T cells or CD16/56+ natural killer (NK)
cells. It is associated with recurrent infections, severe cytopenias and autoimmune diseases.
JAK/STAT pathway activation, deregulation of proapoptotic pathways (sphingolipid and
FAS/FAS ligand) and activation of pro-survival signaling pathways (PI3K/AKT and RAS) are
known hallmarks of LGL leukemia. Activating somatic STAT3 mutations have been reported …
Large granular lymphocyte (LGL) leukemia is a rare clonal disease characterized by a persistent increase in the number of CD8+ cytotoxic T cells or CD16/56+ natural killer (NK) cells. It is associated with recurrent infections, severe cytopenias and autoimmune diseases. JAK/STAT pathway activation, deregulation of proapoptotic pathways (sphingolipid and FAS/FAS ligand) and activation of pro-survival signaling pathways (PI3K/AKT and RAS) are known hallmarks of LGL leukemia. Activating somatic STAT3 mutations have been reported in the SH2 domain (30–70% of cases), 1–3 and in the DNA-binding or coiled-coil domain (2%). 4 STAT5B mutations are more rare, but typical of CD4+ T-LGL leukemia cases. 5–7 The JAK/STAT pathway can also be activated by non-mutational mechanisms such as increased interleukin-6 (IL-6) secretion and epigenetic inactivation of JAK-STAT pathway inhibitors. 8 Indeed, aberrant STAT signaling is observed in almost all LGL leukemia patients irrespective of the presence of JAK/STAT mutations. 9 To characterize the genomic landscape of LGL leukemia, we performed whole-exome sequencing (Supplementary Methods and Supplementary Figure 1) from 19 paired tumor-control samples derived from untreated LGL leukemia patients including conventional CD8+(n= 13) T-cell cases, and more rare CD4+ or CD4+ CD8+ T-cell cases (n= 3), and NK LGL leukemias (n= 3; Supplementary Table 1). Eleven STAT-mutation-negative patients were included for identification of new driver mutations. All sequenced samples were highly purified sorted cell populations (either CD8+ or CD4+ T cells or NK cells), and T-cell receptor Vbeta analysis confirmed monoclonal expansions in the tumor fractions of T-cell cases (see Supplementary Methods and Supplementary Table 1). The average sequencing coverage in the tumor samples was 32x (Supplementary Figure 2). Both the coverage and the number of raw called variants were similar in tumor and control samples. After selecting high confidence variants (see Supplementary Methods), and filtering out variants already described in human populations single nucleotide polymorphism database and/or with allele frequency higher than 5% in exome aggregation consortium exomes, 28508 somatic variants in 16518 genes were identified in the whole cohort with a high prevalence of C> T and G> A transversions (Supplementary Figure 3A). Next, among high confidence and rare variants, we selected 370 variants in 347 genes with a strong predicted functional impact (Supplementary Methods and Supplementary Table 2). The observed differences in numbers of somatic mutations (range 5–40, average 20) and genes involved (range 4–41, 19) per patient were not because of coverage differences (Supplementary Figure 3B). A slight tendency toward more mutated genes per patient in STAT-mutation-positive (22.9 in average) versus negative patients (18.4 in average) was noticed. Sanger sequencing validations of somatic variants were obtained in 14 genes (Supplementary Table 3 and Supplementary Figure 4) being recurrent or prioritized according to functional criteria and/or connections emerged by integrated pathway-derived networks. The positions of the mutations in protein domains of selected genes are shown in Supplementary Figure 5. In addition to STAT3 (all in CD8+ T-LGL) and STAT5B (CD4+ and CD8+ cases) mutations (in 8/19 patients, 42%), 14 other genes had recurrent mutations including transcriptional/epigenetic regulator, tumor suppressor and cell proliferation genes (Figure 1a and 2a). KMT2D has been linked to lymphomagenesis10 and found to be frequently …
nature.com