Comprehensive Analysis of p16INK4a in Childhood Acute Lymphoblastic Leukemia Reveals Homozygous Deletion, Haploinsufficiency and Acquired Isodisomy at the 9p Locus with Intact p16INK4a.
Authors: Sulong Sarina , Irving Julie , Case Marian , Minto Lynne , Bown Nick , Bailey Simon , Harrison Christine , Hall Andrew 
Published: April 2020

Abstract
Genetic alterations including chromosomal translocation, promoter hypermethylation, somatic mutation and gene deletion are believed to play a key role in the leukemogenic process in childhood acute lymphoblastic leukemia (ALL). The p16INK4a (CDKN2A/MTS1/p16/INK4a) gene located on chromosome 9p21 is a tumor suppressor gene whose product can block cell division during the G1/S phase of the cell cycle. Inactivation of p16INK4a in ALL can occur by deletion, promoter hypermethylation or somatic mutation. However, published reports are inconsistent in terms of both incidence and route of p16INK4a inactivation suggesting that a detailed analysis of all possible modes of inactivation in a large cohort is essential to clarify the status of this gene in leukemogenesis. In this study, we report the findings of a comprehensive analysis of p16INK4a in 115 DNA samples with childhood ALL (86 cases at presentation and 29 cases at relapse) in which a combination of techniques including, fluorescence in situ hybridization (FISH), mapping arrays, denaturing high performance liquid chromatography (dHPLC) and methylation specific-PCR (MSP) were used to assess the mode of inactivation of this gene. Data from a genome-wide screening in 86 presentation cases and 20 of 29 relapse cases using Affymetrix Mapping 10K and/or 50K single nucleotide polymorphism (SNP) microarray technique showed loss of heterozygosity (LOH) at the p16INK4a locus in 21% (22/106) of cases (14 at presentation and 8 at relapse), 14 (8 at presentation and 6 at relapse) with an associated loss of copy number and 8 (6 at presentation and 2 at relapse) with a normal copy number, indicative of acquired isodisomy (AID). FISH analysis on 19 of the 22 confirmed that those cases with LOH and copy number loss had either p16INK4a homozygous (n=6) or hemizygous (n=6) deletion and those with LOH associated with AID (n=7) retained 2 copies. Mutation and methylation analyses were performed on those cases identified to have one p16INK4a allele or retention of both alleles. Partial methylation of p16INK4a was found in only 1 case. Mutational screening by dHPLC of the coding region revealed a somatic mutation, H83Y, in a subpopulation of leukemic blasts in one patient at relapse. Three common SNPs were identified including A148T in exon 2 and 500C&gt;G and 540 C&gt;T in the 3′ UTR. These data show that mutation and hypermethylation of p16INK4a are rare events in childhood ALL but that homozygous and hemizygous deletion is relatively common. The loss of only one p16INK4a allele in this latter group, without evidence for mutation or hypermethylation of the remaining one suggests that p16INK4a may be haploinsufficient in ALL. The finding that LOH on 9p locus is common but in nearly 40% of these cases is associated with AID with intact p16INK4a, suggests the existence of another tumor suppressor gene or oncogene in this region, which may have importance in leukemogenesis.