Investigation Of Seven Genes Commonly Deleted In 271 Adult ALL Patients: Association With Cytogenetics and Clinical Features
Authors: Fasan Annette , Haferlach Claudia , Ulke Madlen , Kern Wolfgang , Haferlach Torsten , Schnittger Susanne 
Published: October 2019

Abstract

Introduction
Recent genomic studies have shown that copy number abnormalities (CNA) of genes involved in B-lymphocyte development and differentiation, cell cycle control and in hematopoiesis are common in B-precursor-ALL (B-ALL). Partial or complete deletions of the IKZF1 gene are frequently detected, especially in patients harboring the BCR-ABL1 fusion gene. Furthermore, several other gene deletions, such as in PAX5, ETV6, RB1, BTG1 and CDKN2A/B have also been described in B- and T-ALL patients. To date, characterization of CNA mainly has focused on pediatric ALL and data on adult ALL are scarce.

Aim
To evaluate the pattern of CNA in a large cohort of 271 adult ALL cases and their correlation to cytogenetics and clinical features.

Patients and Methods
We analyzed blood or bone marrow samples of 271 adult ALL cases (B-ALL: n=215; T-ALL: n=56). The B-ALL subgroup comprised 109 females and 106 males, median age was 58.4 years (range: 18.1-89.5 years). The T-ALL group comprised 16 females and 40 males, median age was 38.0 years (range: 18.8-87.7 years). ALL was diagnosed by immunophenotyping. B-ALL cases were classified into seven subgroups according to the following cytogenetics: 1) t(9;22)(q34;q11) (n=63), 2) 11q23/MLL rearrangements (n=21), 3) MYC rearrangements (n=8), 4) hypodiploidy (n=16), 5) hyperdiploidy (n=24), 6) normal karyotype (CN) (n=31), 7) other cytogenetic aberrations (n=35). In 17 cases no cytogenetic data was available. CNA of seven genes were analyzed by multiplex ligation-dependent probe amplification (MLPA) using the SALSA MLPA P335 ALL-KZF1 kit (MCR Holland, The Netherlands).

Results
Overall, 126/215 (58.6%) of B-ALL patients and 32/56 (57.1%) of T-ALL cases showed deletions (DEL) of at least one of the genes analyzed. In nine cases, amplifications were detected due to chromosomal gains. In the B-ALL cohort the overall occurrence of DEL was as follows: IKZF1: n=85 (39.5%), CDKN2A/B: n=60 (27.9%), PAX5: n=30 (13.9%), RB1: n=13 (6.0%), ETV6: n=7 (3.3%), BTG1: n=5 (2.3%) and EBF1: n=3 (1.4%). 53 (24.5%) patients had one, 33 (15.3%) had two, 23 (10.6%) had three and 17 (7.4%) had four or five deletions. Most DEL were detected in the c-ALL subgroup (n=103/155; 66.5% vs. 23/60, 38.3% of non c-ALL cases). Patients harboring CDKN2A/B or PAX5 DEL were significantly younger compared to patients without these DEL (medain age: 51.8 years vs. 57.2 years; p=0.048 and 47.4 years vs. 57.0 years; p=0.006, respectively). There was no significant association of any DEL with gender, WBC count, hemoglobin levels or platelet count. Patients with BCR-ABL1 rearrangements showed the highest number of DEL (47/63; 74.6%), followed by patients with hyperdiploidy (16/25, 64.0%). The most common DEL in these subgroups were IKZF1 and CDKN2A/B. Fewer DEL were detected in CN cases (9/31, 29.0%) and cases with MLL rearrangements (5/21, 23.8%). Regarding individual abnormalities, of 60 cases with CDKN2A/B DEL, 21 cases showed visible cytogenetic abnormalities of the short arm of chromosome 9 (9p) while 39 cases showed no 9p abnormality. 30/60 cases with CDKN2A/B deletions had additional PAX5 deletions, nine of these showing 9p abnormality. IKZF1 deletions (n=85) were heterogeneous with either the whole gene (n=22) or intrageneic with different exons involved (n=63). RB1 deletions comprised two types: 1) loss of the entire gene (n=5); 2) focal deletions including exons 19-26 (n=8). 11 cases with RB1 deletions harbored concurrent IKZF1 deletions. A negative prognostic impact was shown only for IKZF1 deletions in the cohort of 63 BCR-ABL1pos cases (p=0.07). In the T-ALL cohort, eight patients (14.5%) had one, 18 patients (32.7%) had two, six patients (10.9%) had three and two patients (3.6%) had four deletions. CDKN2A/B (26/55; 47.3%) comprised the most frequent DEL, with 15 of these cases showing visible abnormalities of 9p. Other DEL occurred with low frequencies. T-ALL patients with gene deletions were significantly younger (median 40.6 years vs. 52.2 years; p=0.045). There was no difference in WBC, hemoglobin, platelet counts or survival.

Conclusions
1) MLPA is a useful tool to further genetically characterize adult ALL. 2) The pattern of DEL in ALL cases is heterogenous with IKZF1, CDKN2A/B and PAX5 comprising the most frequent aberrations. 3) We were able to confirm the association between distinct DEL and specific cytogenetic subgroups. 4) In both B- and T-ALL DEL were associated with younger age.

Disclosures:
Fasan: MLL Munich Leukemia Laboratory: Employment. Haferlach:MLL Munich Leukemia Laboratory: Employment, Equity Ownership. Ulke:MLL Munich Leukemia Laboratory: Employment. Kern:MLL Munich Leukemia Laboratory: Employment, Equity Ownership. Haferlach:MLL Munich Leukemia Laboratory: Employment, Equity Ownership. Schnittger:MLL Munich Leukemia Laboratory: Employment, Equity Ownership.