Gain of the Short Arm of Chromosome 2 Is a New Recurring Chromosome Aberration in CLL Which Is Significantly Associated with an Unmutated IgGVH Status and a Complex Aberrant Karyotype and Leads to a Higher Expression of Genes Located on 2P.
Authors: Haferlach Claudia , Rauhut Sonja , Merk Sylvia , Dicker Frank , Schnittger Susanne , Kern Wolfgang , Dugas Martin , Haferlach Torsten 
Published: April 2020

Abstract
CLL is a genetically heterogeneous disease. Genetic aberrations allow to distinguish different biological subgroups within CLL. Based on chromosome banding analysis we identified complete and partial gain of the short arm of chromosome 2 always including 2p23 to 2p25 in 28/1051 CLL cases (2.7%) as a new recurring chromosome aberration. Recurring aberrations accompanying gain of 2p were: loss of 1p (n=3), 1q (n=3), 2q (n=3), 6q (n=3), 8p (n=7), 11q (n=10), 12q (n=4), 13q (n=21), 17p (n=7), 17q (n=3), 18p (n=5), and gain of 2q (n=3), 3q (n=3), 13q (n=3), 21q (n=3). In 24/28 cases the mutational status of the immunoglobulin variable heavy chain gene (IgVH) was available. 20 cases showed an unmutated and only 4 a mutated IgVH status. Thus, 2p gain is significantly associated with an unmutated IgVH status as compared to the non 2p group (83% vs 51%, p=0.002). In 8 cases an ATM deletion (29%) and in 5 cases a TP53 deletion (18%) (1 case showed both) were observed (frequency in non 2p+ cohort: 12%; p=0.036 and 7%; p=0.031). A median number of 4 chromosome aberrations per case was observed in 2p+ CLL (range: 1–16, mean=5.2) as compared to only 1 abnormality per case in the non 2p+ cohort (range: 0–10, mean 1.7) (p&lt;0.0001). In 4 cases the rearrangement leading to 2p+ was the sole abnormality. In 6 cases 2p gain was found in a subclone only. Gene expression analysis (Affymetrix, HG U133 Plus 2.0) was performed in 25 cases with gain of 2p and compared to 11 cases with CLL and normal karyotype. Using 10fold cross validation (10f CV) resulted in an assignment of all 25 cases with 2p into the correct class, however 4 cases with normal karyotype were misclassified into the 2p group (accuracy (a) 89%, sensitivity (s) 100%, specificity (sp) 64% for 2p+). Classification based on an independent test set led to comparable results (median a: 83%, s: 100%, sp: 50% for 2p+). In addition cases with gain of 2p were compared to 48 CLL cases comprising various chromosome aberrations excluding gain of 2p. Using 10f CV resulted in an assignment of only 13 of 25 cases with 2p into the correct class (a: 75%, s: 52%, sp: 88%). Classification based on an independent test set led to comparable results (median a: 79%, s: 50%, sp: 94%). However, focussing on the top 100 differentially expressed probe sets comprising 88 genes revealed that 10 of 28 genes with a higher expression in the 2p+ group as compared to the non 2p+ group were located on 2p (LOC56902, PPP3R1, MSH6, RTN4, COX7A2L, HADHA, TTC32, ACP1, CPSF3, PDIA6). These are involved in mismatch repair and in negative regulation of anti-apoptosis. In contrast only one of the top 60 genes showing a lower expression in the 2p+ group was located on 2p. Interestingly, ATM showed a significantly lower expression in the 2p+ group. In conclusion:
Gain of 2p is a new recurrent chromosome abnormality in CLL. It occurs both as the sole abnormality and as a secondary event during clonal evolution. Gain of 2p is associated with an unmutated IgVH status, a complex aberrant karyotype, and a high frequency of ATM- and TP53-deletion. Comparable to other unbalanced chromosome abnormalities gain of 2p is not associated with a distinct gene expression profile sufficient for classification but leads to a higher expression of genes located on 2p.