Childhood Acute Lymphoblastic Leukemia: High Genomic Stability from Initial Diagnosis to Early Relapse.
Authors: Meissner Barbara , Eckert Cornelia , Moericke Anja , von Stackelberg Arend , Kirschner-Schwabe Renate , Cario Gunnar , Schrauder André , Zimmermann Martin , Welte Karl , Schrappe Martin , Stanulla Martin 
Published: April 2020

Abstract
Despite considerable improvements regarding treatment outcome about 20% of children with acute lymphoblastic leukemia (ALL) still suffer from recurrent disease. Especially patients with an early relapse occurring before 6 months of treatment cessation have a poor prognosis and, therefore, urgently need therapy optimization. As an initial step, detection of genetic aberrations that are associated with resistant disease and/or early relapse might be of great value as they could serve as prognostic markers to predict disease recurrence and, in addition, may increase our understanding of mechanisms underlying treatment resistance and early relapse. This knowledge may also help to identify new therapeutic strategies including targeted approaches. Surprisingly, almost no information is available on the genetic evolution from initial diagnosis to early relapse. As a first aim in the process of uncovering the pathomechanism of early relapse we wanted to find out if early relapse of childhood ALL reflects primarily resistant disease with little or no additional aberrations at relapse or represents evolution and selection of a new and more resistant clone possibly triggered through chemotherapy. Recently, high throughput technologies (single nucleotide polymorphism [SNP]–Arrays) have been developed to screen the whole genome with high resolution for submicroscopic, genetic alterations by simultaneously analyzing the SNP genotype and determining the copy number state. This prompted us to perform SNP-array analysis encompassing more than 100.000 SNPs in 20 childhood ALL samples collected at initial diagnosis and to compare them to their counterparts obtained at relapse. The analyzed patients belonged to the intermediate or high risk treatment group; 16 exhibited B-precursor and 4 T-precursor ALL. Exclusion criteria were translocations t(12;21), t(9;22) and (4;11) as well as pre-existing conditions (e.g. Down syndrome). At initial diagnosis, the leukemic sample of all patients already displayed a complex karyotype with multiple genetic lesions (average numbers per patient: 5.15 deletions, 1.35 amplifications, and 0.65 copy number neutral LOH (CNN-LOH)). Most alterations remained stable from initial diagnosis to relapse (99 of 103 (96%) initially observed deletions as well as 24 of 27 (89%) amplifications). Four deletions occurring in 3 different patients at initial diagnosis disappeared at relapse. Nevertheless, these patients had additional stable copy number alterations. Newly occurring aberrations at relapse were less frequent (average numbers per patient: 1.8 new deletions, 0.75 new amplifications, and 0.15 new CNN-LOH). In 3 patients genetic alterations at diagnosis and relapse were entirely identical. The most commonly affected chromosome was 9p (75% of samples). Fourteen patients had either heterozygous or homozygous deletions of CDKN2A at initial diagnosis and relapse with 2 patients progressing from heterozygous to homozygous deletions. PAX5 deletions (mainly heterozygous) were detectable in 9 patients at initial diagnosis and 10 patients at relapse. Other sides of recurrent deletions – mainly detected at relapse – included multiple areas of chromosome 7p (p21.3, p15.3, p14.3, p14.3-14.1, p14.1-p13) as well as chromosome 1q (deletion: q42.12-q44, amplification: q25.2-q31.1), chromosome 17p (deletion: p13.3-p11.2) and 17q (amplification: q21.2-q25.1). Potential pathogenetic implications of specific recurrent genetic lesions will be discussed. In conclusion, our results demonstrate a high degree of genomic stability from initial diagnosis to early relapse of childhood ALL. These results suggest that – at least in some patients – early relapse might already be predetermined by a resistant leukemic clone at the time of initial diagnosis.