PF362 A FIRST HIGH-DEFINITION LANDSCAPE OF SOMATIC MUTATIONS IN CHRONIC LYMPHOPROLIFERATIVE DISORDER OF NK CELLS
Authors: V.R. Gasparini, A. Binatti, A. Teramo, A. Coppe, C. Vicenzetto, G. Calabretto, G. Barilà, G. Semenzato, R. Zambello, S. Bortoluzzi
Journal: HemaSphere (2019)

Background: Chronic Lymphoproliferative Disorder of NK cells (CLPD-NK) is included in the 2017 WHO classification of mature T- and NK-cell neoplasms as provisional entity. Similarly to T-cell large granular lymphocytes leukemia (T-LGLL), CLPD-NK is characterized by an indolent clinical course and is clearly distinguished from the aggressive NK cell leukemia (ANKL), this latter behaving as an acute severe disease. CLPD-NK and T-LGLL patients mostly present cytopenias when symptomatic. Accumulating evidence on the genomic landscape of T-LGLL pointed to a key role of somatic mutations within JAK-STAT (mostly in STAT3 and STAT5B genes) and RAS-MAPK pathways (Coppe et al. Leukemia 2017) in this form. Recent data highlighted more heterogeneous molecular features in ANKL, involving JAK2 and STAT3 mutations, lesions of epigenetic modifiers, tumour suppressors and a putative role of Epstein Barr Virus (Dufva et al. Nat Comm. 2018). Aims: In our cohort of 57 CLPD-NK patients the frequency of STAT mutations has been found significantly lower (<10% of all cases) compared to literature data (Barilà et al. Blood Cancer J. 2018). The genomic landscape of CLPD-NK patients negative for STAT mutations was thus investigated to better elucidate the molecular basis of the disease. Methods: Ten CLPD-NK patients were recruited according to negativity for STAT mutations and typical immunophenotype (CD16+/CD57±/CD56±). WES profiling (Agilent SureSelect 60 Mbp, Illumina sequencing, paired end reads) of immunomagnetically purified leukemic clone (>95% purity) and of normal granulocytes, as control, was obtained for each patient. Sequencing data were analyzed by an in-house bioinformatic pipeline encompassing data cleaning, read mapping against the reference genome and somatic variant calling with complementary approaches (MuTect, MuTect2 and Strelka2). Variants were next filtered according to population allele frequency (gnomAD <5%), clinical significance (COSMIC and ClinVar) and predicted functional impact on proteins (SnpEff, MetaSVM and MetaLR). Results: High sequencing depth was obtained with a mean coverage of 150 reads. From over 6,000 somatic variants detected in the cohort, 869 SNPs and 14 indels, rare and of high predicted impact were prioritized. Number of variants (88 per patient in average) and mutation spectra were very homogeneous in the cohort. Of note, the high discovery power of our settings disclosed an extensive subclonality of somatic variants, with over 78% with an allele variant frequency (VAF) lower than 5% in the leukemic clone (Figure 1A). Nevertheless, 20 deleterious and high VAF somatic variants occurred in each patient in average (Figure 1B). Very low recurrence of mutated genes in CLPD-NK patients was found. Pathway-derived mutation network analysis (Lovisa et al. Haematologica 2019) revealed functional connections among genes mutated in different patients. A major involvement of JAK-STAT pathway is likely to be ruled out, but all cases presented deleterious high VAF mutations of genes and pathways potentially impacting on cell survival, proliferation and chromatin-remodelling. In addition, somatic lesions in proteins involved in innate immunity and NK-cells activation seem particularly interesting.Summary/Conclusion: Ongoing comparison of genes and pathways mutated in CLPD-NK with available data for T-LGLL and ANKL is providing new clues on biological similarities and differences of these clinical entities. This study contributes to a better definition of the molecular mechanisms accounting for CLPD-NK, thus opening new areas of investigation.