E-Poster Presentation 34th Lorne Cancer Conference 2022

ZNF384-rearranged B-cell acute lymphoblastic leukaemia is potentiated by recurrent genomic lesions susceptible to therapeutic targeting (#341)

Barbara J McClure 1 2 , Susan L Heatley 1 2 3 , Jacqueline A Rehn 1 2 , James Breen 2 4 , David T Yeung 1 2 5 , Deborah L White 1 2 3 6 7
  1. Cancer Program, Precision Medicine Theme, SAHMRI, Adelaide, SA, Australia
  2. Faculty of Health and Medical Science, University of Adelaide, Adelaide, SA, Australia
  3. Australian and New Zealand Children’s Oncology Group, (ANZCHOG), Clayton, Victoria, Australia
  4. South Australian Genomics Centre (SAGC), SAHMRI, Adelaide, SA, Australia
  5. Haematology Department, Royal Adelaide Hospital and SA Pathology, Adelaide, SA, Australia
  6. School of Biological Sciences, University of Adelaide, Adelaide, SA, Australia
  7. Australian Genomics Health Alliance (AGHA), The Murdoch Children’s Research Institute, Parkville, Victoria, Australia

 

Aim: 

Characterising the genomic landscape of ZNF384-rearranged (ZNF384r) B-cell acute lymphoblastic leukaemia (B-ALL) will reveal subtype specific genomic alterations and define targetable pathways for assessment in precision therapeutic approaches.

 Method: 

Philadelphia chromosome-negative B-ALL samples (n=487) were transcriptionally sequenced to identify fusion genes and single nucleotide variants (SNV), and gene deletions were detected by multiplex ligation-dependent probe amplification. Signalling pathways were assessed on the EP300-ZNF384 driven human JIH-5 cell line by intracellular flow cytometry of STAT1/3/5 phosphorylation in the presence or absence of inhibitors.

Results: 

Transcriptomic sequencing identified ZNF384r in 3.7% (18/487) of Ph-neg B-ALL at diagnosis (comprising children 1.4% (3/210), adolescent young adults 6.1% (10/165), adults 4.5% (5/112)). The 5’-partners identified were EP300(72%, 13/18), TCF3 (17%, 3/18), ARID1B (5.6%, 1/18) and CREBBP (5.6%, 1/18). IKZF1, RB1, CDKN2A, and PAX5 deletions (7%  each, 1/14) occurred less frequently than deletions in ETV6 (35.6%, 5/14), BTG (21.4%, 3/14) and CDKN2B (21.4%, 3/14). SNVs were detected in RAS 27.8% (5/18), PTPN11 (5.6%, 1/18), JAK2 (5.6%, 1/18) and CREBBP (11.1%, 2/18). In relapse samples EP300 or TCF3 were the most common fusion partner, (37.5%, 3/8), in addition to 12.5% (1/8) TAF15 and 12.5% CREBBP. Upregulation of CLCF1, CXCL2, FLT3, STAT2, ICAM2, MMP11and SPKH1 gene expression was detected in ZNF384r B-ALL. An in vitro model of ZNF384r B-ALL demonstrated intrinsic phosphorylation of STAT3, (consistent with JAK/STAT signalling upregulation observed in ZNF384r B-ALL Gene-set enrichment analysis), but not STAT1 or STAT5. Dasatinib and ruxolitinib were unable to abrogate STAT3 phosphorylation, while dasatinib reduced JIH-5  total tyrosine-phosphorylation. Pathways involved in ZNF384-fusions are currently under investigation.

Conclusion: 

We have characterised the transcriptome of one of the largest ZNF384r B-ALL cohorts and have revealed subtype specific targets warranting investigation for future precision approaches to therapy.