High-Resolution Genome Wide Copy Number Alteration (CNA) and Loss of Heterozigosity (LOH) Analysis in Chronic Myeloid Leukemia (CML) Shows That High and Intermediate Sokal Risk Pts (Pts) Have Multiple Losses Targeting Genes Involved in DNA Repair.
Authors: Soverini Simona , Colarossi Sabrina , Gnani Alessandra , Astolfi Annalisa , Formica Serena , Castagnetti Fausto , Palandri Francesca , Gugliotta Gabriele , Poerio Angela , Iacobucci Ilaria , Amabile Marilina , Marzocchi Giulia , Luatti Simona , Terragna Carolina , Durante Sandra , Testoni Nicoletta , Rosti Gianantonio , Baccarani Michele , Martinelli Giovanni 
Published: October 2019

Abstract
Abstract 3262
Poster Board III-1
CML pts display a certain degree of clinical heterogeneity that is documented by the varying levels of response to tyrosine kinase inhibitor therapy and is best reflected by the Sokal risk score. Clinical differences must be a sign of some biological heterogeneity the basis of which, however, are still poorly understood. Today many high-throughput assays are available that allow to unravel the complexity of cancer cells in a genome-wide fashion. We have used Human 6.0 SNP Arrays (Affymetrix) to perform high-resolution (<1 kb) karyotyping of DNA samples from 73 newly diagnosed chronic phase CML pts. Median age was 55 years (range, 25–73 years); male to female ratio was 39/34; pts were almost equally distributed by Sokal risk score (low, n=23; intermediate, n= 23 high, n= 27). Of 189 genes known to be implicated in the cellular DNA repair pathways, 135 (71%) were found to map in regions affected by CNAs or copy-neutral LOH (uniparental disomy, UPD) in 44/73 (60%) pts. However, this was markedly more frequent in high and intermediate Sokal risk pts (20/27, 74% and 16/23, 69%, respectively) than in low Sokal risk pts (8/23, 33%), although neither the total number of detected regions of CNAs/UPD per sample nor the QC parameters differ significantly across different risk categories. Regions of CNA involving DNA repair genes ranged from 105 Kb to 1.1 Mb and were either focal lesions involving a part or the whole single gene (17% of cases), or more extensive losses/gains including 2 to 84 genes. Monoallelic deletions were much more frequent than amplifications. Regions of UPD involving DNA repair genes were much larger and ranged from 980 kb to 32 Mb.
The pathways and genes most frequently affected by CNAs or UPD are listed in the Table below:
Base Excision Repair (BER) MUTYH DNA glycosilase 1p34.1 loss/upd 10 pts PNKP Polynucleotide kinase 19q13.33 loss 10 pts NEIL1 DNA glycosilase 15q24.2 loss 7 pts POLB DNA polymerase beta 8p11.21 loss/upd 6 pts PCNA Sliding clamp for DNA polymerases 20p12.3 loss 6 pts Mismatch Repair (MMR) PMS2L5 Mut L homolog - mismatch and loop recognition 7q11.23 loss/upd 11 pts MSH2 Mut S homolog - mismatch and loop recognition 2p21 loss 8 pts POLD1 DNA polymerase delta 19q13.33 loss 8 pts POLA2 DNA polymerase alpha, subunit 2 2p16.3 loss/upd 6 pts POLE2 DNA polymerase epsilon, subunit 2 14q21–22 loss 5 pts Nucleotide Excision Repair (NER) ERCC1 5’ incision subunit of TFIIH complex 19q13.32 loss 11 pts ERCC2 5’ to 3’DNA helicase of TFIIH complex 19q13.32 loss 10 pts XAB2 Transcription-coupled NER factor 19p13.2 loss/upd 9 pts CDK7 Kinase subunit of TFIIH complex 5q13.2 loss 7 pts RPA4 Binds damaged DNA in preincision complexes Xp21.33 loss/upd 7 pts RPA2 Binds damaged DNA in preincision complexes 12q24.31 loss/upd 6 pts Homologous Recombination (HR) RAD51C Homologous pairing 17q23.2 loss/upd 7 pts RAD52 Accessory factor for recombination 12p13.33 loss 7 pts XRCC2 DNA break and crosslink repair 7q36.1 loss 5 pts Non-Homologous End Joining (NHEJ) PRKDC DNA-dependent protein kinase, catalytic subunit 8q11.21 loss/upd 5 pts DCLRE1C Artemis nuclease 10p13 loss 5 pts REV7 DNA polymerase zeta, subunit 1p36.22 gain 5 pts Other genes involved in DNA replication/repair/modification or chromatin remodeling CHAF1A Chromatin assembly factor 19p13.3 loss 15 pts RECQL5 DNA helicase 17q25.1 loss/upd 11 pts RAD9B PCNA-like DNA damage sensor 12q24.11 loss/upd 10 pts CHEK2 DNA-damage checkpoint 22q12.1 loss/upd 8 pts RAD17 RFC-like DNA damage sensor 5q13.2 loss 6 pts TREX1 DNAase III exonuclease 3p12.31 loss/upd 6 pts
For some genes (e.g., RAD52), the monoallelic deletion we detected was found to translate into reduced mRNA expression, observation that was also independently confirmed in an additional group of high/intermediate versus low Sokal risk pts. In all the 44 pts, multiple pathways and multiple genes within the same pathway were affected, supporting the hypothesis that the lesions we detected might actually have consequences on DNA integrity despite the known partial functional redundancy of pathways and effectors. For many of the genes identified in this screen, activating or inactivating mutations are known to occur, and together with overexpression or haploinsufficiency, have been linked to a mutator phenotype in several malignant conditions. We are currently investigating whether this may be the case also in CML. Supported by European LeukemiaNet, AIL, AIRC, PRIN, Fondazione del Monte di Bologna e Ravenna.

Disclosures:
Baccarani: Novartis: Honoraria, Research Funding, Speakers Bureau; Bristol-Myers Squibb: Honoraria, Research Funding, Speakers Bureau.