Investigation Of Seven Genes Commonly Deleted In 271 Adult ALL Patients: Association With Cytogenetics and Clinical Features

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.

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

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).

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-ABL1^pos 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.

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.

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.