PO-142 RNAi-mediated therapeutic knockdown of the neuropilin axis and GIPC1 in pancreatic carcinoma

Abstract

IntroductionB-cell acute lymphoblastic leukaemia (B-ALL) is caused by malignant transformation of B-cell progenitors and has multiple genetic subtypes, each characterised by specific genetic abnormalities, including MLL-rearranged and TCF3/PBX1 t(1;19). Survival for B-ALL is favourable compared to many other cancers, however, there is a need for novel therapeutic approaches that are less toxic and lead to better long term outcome for patients compared to current treatment options. These could potentially be found by identifying subtype-specific synthetic lethal (SL) genes. We have developed a novel bioinformatic approach which uses genome-wide methylation and expression data to identify candidate SL genes in specific genetic subtypes of disease. We aimed toidentify candidate SL genes in MLL-rearranged B-ALL, utilising our novel bioinformatics approach.Material and methodsGenome-wide methylation and expression data from patient samples were used to identify candidate genes. Candidate SL genes were knocked down with siRNA in cell lines with/without the corresponding subtype defining genetic abnormality. Apoptosis was measured by Annexin-V staining, and proliferation by cell counts using a specialised flow cytometer. Gene re-expression was performed using a lentiviral construct, co-expressing eGFP.Results and discussionsSurprisingly, in addition to a single candidate SL gene specific for MLL-fusion related B-ALL, our novel bioinformatic analysis also identified two classes of gene not generally seen in our analysis of other subtypes; a candidate subtype-specific tumour suppressor (KLF11) and a candidate shared SL gene (LAMP5, shared with t(1;19). LAMP5 knockdown significantly increased apoptosis (12.7%, p=0.0012) and decreased proliferation (23.3%, p=0.0006) in a t(1;19) cell line but not in MLL cell lines. As predicted, KLF11 re-expression in the MLL-rearranged SEM cell line caused significantly reduced cell growth/survival compared with the KLF11-negative parental cell line. However, high level re-expression in three cell lines expressing endogenous KLF11 resulted in similar effects on cell growth, implying that high level KLF11 expression was universally toxic in leukaemia cell lines.ConclusionLAMP5 may be a SL gene, however only specifically in t(1;19) B-ALL. This is the first time this gene has been linked to leukaemia and if confirmed to have a role in this subtype of B-ALL it would represent a novel therapeutic target.