PS921 INACTIVATION OF SH2B3 THROUGH CN‐LOH 12Q IS UNIQUELY ASSOCIATED WITH B‐CELL PRECURSOR ALL WITH IAMP21 OR OTHER CHROMOSOME 21 GAIN
Authors: Sinclair P. , Ryan S. , Bashton M. , Hollern S. , Hanna R. , Case M. , Schwalbe E. , Schwab C. , Cranston R. , Hawking Z. , Young B. , Irving J. , Vora A. , Moorman A. , Harrison C. 
Published: June 2019

Background:

In more than 30% of childhood B‐cell precursor acute lymphoblastic leukaemia (B‐ALL), chromosome 21 sequence is overrepresented through constitutional or acquired aneuploidy or structural rearrangements, exemplified by intrachromosomal amplification of chromosome 21 (iAMP21). How these abnormalities promote B‐ALL remains obscure but a mechanistic link is suggested by the existence of shared co‐occurring abnormalities.

Aims:

We aimed to identify and characterise acquired genetic abnormalities that cooperate with amplification or aneuploidy of chromosome 21 to promote B‐ALL.

Methods:

Regions of copy neutral loss of heterozygosity and deletion were defined by analysis of SNP6.0 arrays, methylation arrays were used to assess loss of imprinting. The mutational status of SH2B3 was determined by amplicon sequencing and a homology model based on the resolved structure of the Sh2 domain of Sh2b1 was used to assess the impact of an acquired in‐frame substitution. STAT activation status was determined by flow cytometric immunophenotyping.

Results:

Analysis of B‐ALL patients with iAMP21, other structural amplifications of chromosome 21 or constitutional or acquired additional whole copies of chromosome 21 (n = 99), revealed recurrent CN‐LOH of 6p, 9p and 12q. In patients without overrepresentation of chromosome 21, CN‐LOH 6p and 9p were also recurrent but intriguingly, CN‐LOH 12q was absent, among our own (n = 203) or published cases (n = 974). Further analysis demonstrated CN‐LOH 12q was not associated with loss of imprinting but with homozygous mutations or deletions of the adaptor protein, SH2B3. In patients without CN‐LOH 12q, bi‐allelic abnormalities of SH2B3 occurred, but only in iAMP21‐ALL, giving an overall incidence of 18% in this sub‐type. Taking into account our own cohort, analysis of archival array data and review of published cases, we conclude that in B‐ALL, SH2B3 abnormalities are invariably bi‐allelic, frequent in iAMP21‐ALL, recurrent but less common in association with acquired aneuploidy 21 but extremely rare in the absence of overrepresentation of chromosome 21. Importantly, as iAMP21 patients are now uniformly treated as high risk, preliminary analysis of 26 patients treated on UKALL97/99 (n = 5) or UKALL2003 (n = 21), linked 12q abnormalities to poor outcome in iAMP21‐ALL (p = 0.03). Homology modelling of an iAMP21‐ALL associated R392W mutation in the SH2 domain of SH2B3 demonstrated loss of critical interactions required for binding and suppression of activated JAK. Further implicating the JAK/STAT pathway as one target for SH2B3 tumour suppressor activity, stimulation with IL7 of iAMP21‐ALL patient derived xenograft cells, with but not without SH2B3 inactivation, resulted in activation of STAT5 though not other STATs.

Summary/Conclusion:

Although chromosome 21 copy number profiles are highly heterogeneous in iAMP21‐ALL a limited number of candidate oncogenes are consistently amplified, overexpressed and spared from disruption by structural rearrangements. From our data we infer that in iAMP21‐ALL, high expression of one or more of these candidate genes creates strong pressure for loss of SH2B3 function while lower but still elevated expression of the same gene/s, resulting from gain of one or two copies of whole chromosome 21, produces a similar though weaker selective environment. Since JAK/STAT activation is common in B‐ALL without gain of chromosome 21 and given the near‐exclusive association we observed, we are currently exploring the possibility that SH2B3 also interacts with other pathways specifically activated by increased doses of chromosome 21 genes.