Genetic and Genomic Characterisation of Older Adults with Acute Lymphoblastic Leukemia Treated on the UKALL14 and UKALL60+ Clinical Trials
Authors: Creasey Thomas , Barretta Emilio , Kirkwood Amy A. , Schwab Claire , Patrick Pip , Clifton-Hadley Laura , Wrench Bela , Menne Tobias F , McMillan Andrew K , Morley Nicholas J. , Snowden John A , Harrison Christine J. , Leongamornlert Daniel A. , Papaemmanuil Elli , Rowntree Clare J , Marks David I , Fielding Adele K. , Moorman Anthony V. 
Published: November 2019

Acute lymphoblastic leukemia (ALL) is characterised by recurrent chromosomal abnormalities and genomic microdeletions. Although the incidence of adult ALL increases with age, very few studies have specifically examined the genetic aberrations in adults aged ≥60 years.

The objectives of the study were to define the frequency of recurrent chromosomal abnormalities and characterise the copy number profile of ALL in older adults.

All patients from UKALL14 and UKALL60+ clinical trials aged ≥60 years at diagnosis of ALL were considered in the study. Cytogenetic and fluorescence in situ hybridisation (FISH) results at diagnosis were used to classify patients in 1 of 5 genetic subgroups - BCR-ABL1, TCF3-PBX1, MLL/KMT2A rearranged (KMT2Ar), low hypodiploidy/near triploidy (HoTr) and high hyperdiploidy (HeH). T-ALL patients were considered separately. B-cell precursor (BCP) ALL patients lacking a primary chromosomal abnormality (B-other ALL - including normal, failed and complex karyotypes, and other non-recurrent chromosomal abnormalities), were selected for extended FISH screening to identify ABL-class fusions, JAK-STAT activating rearrangements and other primary translocations using dual colour break apart probes for ABL1, ABL2, PDGFRB/CSF1R, CRLF2, JAK2, IGH@, ZNF384 and MEF2D.

Separately, single nucleotide polymorphism (SNP) arrays were performed to identify copy number abnormalities (CNAs). Multiplex ligation-dependent probe amplification (MLPA) was used to confirm CNAs in 9 specific genes/regions (EBF1, IKZF1, CDKN2A/B, JAK2, PAX5, ETV6, BTG1, RB1, and PAR1).

207 patients aged ≥60 years at diagnosis were identified from UKALL14 (n=91) and UKALL60+ (n=116). Median age was 64 years (range 60-83) and 50% were male. Cytogenetic data at diagnosis were available for 86% (n=178) of patients. Frequencies of individual genetic subgroups are shown in figure (A). Extended FISH screening of B-other ALL cases identified rearrangements in CRLF2 in 5% (8/146), ZNF384 in 2% (3/137) and MEF2D in <1% (1/136) of the cohort. IGH@ translocations were found in 9% (13/148, including 6 IGH-CRLF2). No variant ABL1 (0/168), ABL2 (0/148), PDGFRB/CSF1R (0/151) or JAK2 (0/149) rearrangements were detected.

SNP arrays were performed on 83 patient samples using Illumina CytoSNP 850k (n=52) or Affymetrix Cytoscan HD (n=31) arrays. Recurrent whole chromosome and whole arm abnormalities seen in >3 cases are shown in figure (B) (HeH and HoTr cases (n=10) excluded). Recurrent deletions were identified affecting IKZF1 in 52% (n=43), CDKN2A/B in 45% (n=37), PAX5 in 39% (n=32), RB1 in 22% (n=18), ETV6 in 21% (n=17), EBF1 in 19% (n=16), BTG1 in 12% (n=10), CD200/BTLA in 16% (n=13) and ATP10A in 13% (n=11). The frequency of individual deletions varied by genetic subtypes (Figure (C)). Recurrent novel and less-well described intragenic microdeletions were also seen in COL11A1 (n=11, 13%), MEF2C (n=8, 10%), MBNL1 (n=7, 8%), PTEN (n=6, 7%), NF1 (n=4, 5%), LEMD3 (n=5, 6%), and KDM6A (n=4, 5%). These deletions will need to be validated by a second technique.

In this large cohort of older adults with ALL, we confirm that over a quarter of patients harbour BCR-ABL1. HoTr ALL is rare in younger patients but was the second most common specific chromosomal abnormality and good risk genetic subgroups were very uncommon. Additionally, we confirm the rarity of T-cell ALL in older adults (<5% of all cases). Within B-other ALL, CRLF2 rearrangements were the most common kinase activating abnormality, present in 5% of all patients, with IGH@ the translocation partner in 6/8 cases. ABL-class fusions were completely absent in this cohort of older patients, differing from published studies (Roberts et. al. JCO 2017). IKZF1 and CDKN2A/B deletions were seen in 52% and 45% of patients respectively. Importantly, these are frequently included in high risk copy number profiles such as IKZF1 plus (Stanulla et. al. JCO 2018), albeit not validated in older patients. A number of novel intragenic microdeletions, including tumour suppressor genes unreported in BCP-ALL, were identified and will require validation in a larger cohort. Collectively, these data further confirm the high risk of ALL in older adults. These patients appear genetically distinct to younger adults and the primary genetic abnormality remains unidentified in significant numbers, underlying the need for further genomic studies to elucidate the mutational landscape of ALL in older adults.

Disclosures

Menne: Takeda: Honoraria, Membership on an entity's Board of Directors or advisory committees, Research Funding, Speakers Bureau; Astra Zeneca: Honoraria, Membership on an entity's Board of Directors or advisory committees, Research Funding, Speakers Bureau; Kite/Gilead: Honoraria, Membership on an entity's Board of Directors or advisory committees, Other: Travel grant, Research Funding, Speakers Bureau; Bayer: Honoraria, Membership on an entity's Board of Directors or advisory committees, Other: Travel grant, Research Funding, Speakers Bureau; Celgene: Honoraria, Membership on an entity's Board of Directors or advisory committees, Other: Travel grant, Research Funding, Speakers Bureau; Pfizer: Honoraria, Membership on an entity's Board of Directors or advisory committees, Other: Travel grant; Novartis: Honoraria, Membership on an entity's Board of Directors or advisory committees, Research Funding, Speakers Bureau; Kyowa Kirin: Honoraria, Membership on an entity's Board of Directors or advisory committees, Other: Travel grant, Research Funding, Speakers Bureau; Jazz: Honoraria, Membership on an entity's Board of Directors or advisory committees, Other: Travel grant, Research Funding, Speakers Bureau; Amgen: Honoraria, Membership on an entity's Board of Directors or advisory committees, Other: Travel grant, Research Funding, Speakers Bureau; Daiichi Sankyo: Honoraria, Membership on an entity's Board of Directors or advisory committees; Janssen: Honoraria, Membership on an entity's Board of Directors or advisory committees, Research Funding, Speakers Bureau; Roche: Honoraria, Membership on an entity's Board of Directors or advisory committees, Research Funding, Speakers Bureau. McMillan:Sandoz: Honoraria; Gilead: Honoraria; F. Hoffmann-La Roche Ltd: Honoraria, Speakers Bureau; BMS: Honoraria; Pfizer: Honoraria, Research Funding; MSD: Honoraria; Novartis: Honoraria; Celgene: Honoraria, Speakers Bureau. Morley:Amgen: Membership on an entity's Board of Directors or advisory committees, Other: speaker fees, conference support ; TAKEDA: Other: conference support ; Janssen Pharmaceuticals: Other: speaker fees; ROCHE: Membership on an entity's Board of Directors or advisory committees, Other: conference support; ABBVIE: Other: speaker fees. Snowden:Kiadis: Membership on an entity's Board of Directors or advisory committees; Mallinckrodt: Honoraria; Janssen: Honoraria; IDMC: Honoraria; Jazz: Honoraria; Gilead: Honoraria. Papaemmanuil:Celgene: Research Funding. Rowntree:Novartis: Consultancy. Fielding:Amgen: Consultancy; Novartis: Consultancy; Pfizer: Consultancy; Incyte: Consultancy.