A Comprehensive Cytogenetic and Molecular Genetic Characterization of Patients with T-PLL Revealed Two Distinct Genetic Subgroups and JAK3 Mutations As an Important Prognostic Marker
Authors: Stengel Anna , Kern Wolfgang , Zenger Melanie , Perglerová Karolina , Schnittger Susanne , Haferlach Torsten , Haferlach Claudia 
Published: October 2019

Abstract
Background: T-cell prolymphocytic leukemia (T-PLL) is a rare, mature T-cell neoplasm with poor prognosis. Only few T-PLL cases have been analyzed with regard to cytogenetic and molecular genetic aberrations so far. Therefore, we performed a comprehensive characterization of patients with T-PLL, including the identification of potential correlations between the respective markers and their impact on prognosis.
Methods: The cohort comprised 47 T-PLL cases (32 male, 15 female). Median age was 69.8 years (range: 32.7-86.6 years). Diagnosis of T-PLL was assigned by immunophenotyping and cytomorphology. All 47 patients were further investigated using (i) chromosome banding analysis (CBA), (ii) interphase FISH to determine the copy number state for TP53 and ATM and chromosomal rearrangements of TCRA/D and TCL1 and (iii) array CGH. Next-generation amplicon deep-sequencing was performed to analyze mutations in ATM,BCOR, TP53 (n=47, respectively); JAK1 (n=44) and JAK3 (n=45) were analyzed by Sanger sequencing. Clinical follow-up data was available for 43 patients.
Results: In all 47 cases, chromosomal abnormalities and/or molecular mutations were detected. Combining CBA and FISH data, an inv(14)(q11q32)/t(14;14)(q11;q32) was observed in 37/47 (78.7%) cases, a t(X;14)(q27;q11) in 3 cases (6.4%) and an i(8)(q10) in 17/47 (36.2%) cases. ATM deletions were detected in 27/47 (57.5%), TP53 deletions in 11/47 (23.4%) patients. Array CGH analyses revealed additional gains and losses of specific chromosomal regions, mainly affecting 7q (deletions in region 7q34-7q36; n=16), 12p (deletions in 12p12-12p13; n=11) and 22q (deletions in 22q11-q12 with a concomitant gain of 22q12-q13; n=8). Regarding molecular analyses, the most frequently mutated gene was ATM (34/47; 72.3%). Mutations in TP53 were found in 7/47 (14.9%) and in BCOR in 4/47 (8.5%) patients. Mutations of JAK1 were found in 3/44 (6.8%), and of JAK3 in 8/45 (17.8%) cases.
ATM and TP53 frequently carried a mutation of one allele and a deletion of the other: 23/34 (67.6%) cases with ATM mutation also showed an ATM deletion and in 5/7 (71.4%) cases with TP53 mutation also a TP53 deletion was detected. Regarding chromosomal aberrations, all cases with i(8)(q10) harbored a TCRA/D rearrangement and an ATM mutation, whereas TP53 mutations were not present in any case with i(8)(q10). ATM mutations were found to be correlated to TCRA/D rearrangements (33/40 TCRA/D+ cases, 82.5%; 1/7 TCRA/D- cases, 14.3%; p<0.001). In contrast, TP53 mutations were predominantly observed in patients without TCRA/D rearrangement (4/7 TCRA/D- cases, 57.1%; 3/40 TCRA/D+ cases, 7.5%; p=0.008). Additionally, all three JAK1 mutations were detected in cases with a TCRA/D rearrangement. When splitting the cohort into patients ≤60 years (n=13) and >60 years (n=34), JAK1 mutations (0/12 vs. 3/32) and mutations/deletions in the TP53 gene were detected exclusively in patients >60 years (TP53mut: 0/13 vs. 7/34; TP53del: 0/13 vs. 11/34). JAK3 mutations were also found predominantly in older patients (1/12; 8.3% vs. 7/33; 21.2%).
Median overall survival (OS) was 27.4 months. No influence on OS was found for mutations and/or deletions of ATM, TP53, BCOR orJAK1 or aberrations of chromosomes 8 or 14. The age of patients was found to impact OS (median OS, ≤60 years: 29.0 months vs. >60 years: 15.9 months), although this was not significant (p=0.077). However, OS was found to be significantly shorter in patients with JAK3 mutation compared to patients without JAK3 mutation (median OS, 5.1 months vs. 29.1 months; p=0.009).
Conclusions: Genetic abnormalities were revealed in all 47 cases with T-PLL. Two distinct genetic subgroups of T-PLL were identified: A large subset, comprising 81% of patients, showed abnormalities involving the TCRA/D locus activating the proto-oncogenes TCL1 (14q32) or MTCP1 (Xq28). This subgroup had higher frequencies of i(8)(q10) and of ATM mutations, while the second group was characterized by a higher frequency of TP53 mutations (figure). Further, JAK3 mutations were identified as an important prognostic marker, showing a significant negative impact on OS.
Figure 1: Genetic abnormalities in T-PLL Figure 1:. Genetic abnormalities in T-PLL
mut=mutation, del=deletion, TCRA/D=rearrangements involving TCRA/D, TCL1=rearrangements involving TCL1, MTCP1= rearrangements involving MTCP1

Disclosures
Stengel: MLL Munich Leukemia Laboratory: Employment. Kern:MLL Munich Leukemia Laboratory: Employment, Equity Ownership. Zenger:MLL Munich Leukemia Laboratory: Employment. Perglerová:MLL2 s.r.o.: Employment. Schnittger:MLL Munich Leukemia Laboratory: Employment, Equity Ownership. Haferlach:MLL Munich Leukemia Laboratory: Employment, Equity Ownership. Haferlach:MLL Munich Leukemia Laboratory: Employment, Equity Ownership.