The Clinical and Prognostic Influence Of Mutations In The Cohesin Complex In Acute Myeloid Leukemia
Authors: Thol Felicitas , Bollin Robin , Gehlhaar Marten , Walter Carolin , Dugas Martin , Suchanek Karl , Kirchner Aylin , Huang Liu , Chaturvedi Anuhar , Wichmann Martin , Wiehlmann Lutz , Damm Frederik , Goehring Gudrun , Schlegelberger Brigitte , Schlenk Richard F. , Döhner Konstanze , Döhner Hartmut , Krauter Jürgen , Ganser Arnold , Heuser Michael 
Published: October 2019

Abstract

Background
The cohesin complex presents a ring structure that regulates chromosome segregation during meiosis and mitosis and is thus essential for cell division. Genes that belong to the cohesin complex in somatic vertebrate cells are SMC1A, SMC3, RAD21 (SCC1), STAG2 (SA-2) and STAG1 (SA-1). Recently, mutations in the cohesin complex have been reported to occur in AML. The aim of this study was to evaluate the clinical and prognostic implications of cohesin mutations in 389 uniformly treated younger AML patients.

Patients and Methods
Diagnostic bone marrow or peripheral blood samples were analyzed from 389 younger adult patients with de novo (n=348) or secondary AML (n=41) with French-American-British (FAB) classification M0-M2 or M4-M7, who were entered into the multicenter treatment trials AML SHG 0199 (n=276) or AML SHG 0295 (n=113). Patient samples were assessed for frequently occurring mutations including FLT3-ITD, NPM1, DNMT3A, IDH1, IDH2. In the subgroup of cytogenetically normal AML (CN-AML), additional mutation analyses were performed for CEBPA, MLL-PTD, WT1 and WT1 SNP rs16754, NRAS, and expression levels of BAALC, ERG, EVI1, MN1, MLL and WT1. Sequencing of all coding exons of the cohesin genes was performed with the SOLiDTM system (Life Technologie, Darmstadt, Germany). Sequences were analyzed twice separately using the DNAnexus software and a separate pipeline of bioinformatics software. Identified mutations were validated by Sanger sequencing.

Results
27 patients (7%) were identified to carry a mutation in one of the cohesin genes. 10 patients harboured a mutation in STAG1. The second most frequently mutated gene in the cohesin complex was SMC3 with 7 patients showing this mutation. 5 patients harboured a mutation in RAD21, 3 patients in STAG2 and 2 patients in SMC1A. All mutations were mutually exclusive. The majority of mutations were missense mutations, apart from 2 frameshift mutations and 3 nonsense mutations. All evaluable patients lost their cohesin mutation during remission and with the exception of one patient regained their mutation during relapse.
Patients with mutations in the cohesin genes were older (47 vs 44 years, P=.04), had a higher white blood cell count (WBC) (P=.046) and a higher peripheral blast count (P=.048). We observed a strong correlation between cohesin gene and NPM1 mutations (P=.007). BAALC expression was lower in patients with a mutation compared to patients without a mutation in the cohesin genes (P=.026).
In order to get a better understanding of when mutations in the cohesin complex occur during clonal evolution we evaluated the allelic burden of mutations in the cohesin complex. Because of the strong association between NPM1 and cohesin mutations, the allelic ratio of mutated and wildtype NPM1 was compared to the allelic ratio of mutated and wildtype cohesin genes. Interestingly, we found a similar mutation burden between NPM1 and genes of the cohesin complex (Pearson correlation coefficient R=0.67), suggesting that cohesin gene mutations occurred in the same clone as NPM1 mutations.
When considering all mutations in the cohesin complex as one group, overall survival (OS), relapse free survival (RFS) and complete remission rate (CR) were not influenced by the presence of cohesin mutations (OS: HR 1.23; 95%CI 0.77-1.99; P=.4; RFS: HR 0.92; 95%CI 0.51-1.65; P=.77; CR: mutated 77% vs wildtype 76%, P=.83). We next evaluated the prognostic influence of each gene in the cohesin complex separately in all patients. STAG1, SMC3 and RAD21 mutations had no influence on OS and RFS. A trend for a reduced OS was observed for STAG2 mutated patients (OS: HR 3.02; 95%CI 0.97-9.46; P=.057), although the analysis is limited by the small number of mutated patients. In the subgroup of patients with cytogenetically normal AML we did not identify a difference in OS, RFS or CR rates for patients with (n=18) or without mutations (283) in the cohesin complex (OS: HR 1.00; 95%CI 0.52-1.92; P=.99; RFS: HR 0.64; 95%CI 0.30-1.39; P=.26; CR rates: mutated 80% vs wildtype 73%, P=.64).

Conclusion
Mutations in the cohesin genes represent novel, recurrent mutations in AML. We found a strong association between these mutations and mutations in NPM1. Cohesin complex mutations as a group had no prognostic impact in all and in cytogenetically normal AML patients.

Disclosures:
Schlenk: Amgen: Research Funding; Pfizer: Research Funding; Novartis: Research Funding; Chugai: Research Funding; Ambit: Honoraria.