Abstract 61P
Background
The PI3K inhibitor copanlisib is being evaluated as single agent and in combination for lymphoma and solid tumor patients. We and others reported synergism adding the BCL2 inhibitor venetoclax, and the combination is in its early clinical assessment. To explore genes affecting the response, we performed a genome wide CRISPR Cas9 screen in a marginal zone B cell lymphoma (MZL) cell line exposed to copanlisib/venetoclax (copa/vene).
Methods
Stable Cas9-expressing VL51 was infected with the genome-wide Brunello guide RNA library, interrogating 19114 genes. The sgRNAs statistical enrichment (P<0.05 FDR< 0.15) and gene set enrichment analysis were assessed between DNA extracted at T0 and at 2 weeks in cells exposed to DMSO, or copa (0.5nM) + vene (25nM).
Results
In control group, 160 genes had a positive β value (i.e., the sgRNAs knocking down the genes were positively enriched after 2 weeks), while 1152 had a negative β value (i.e., the sgRNAs knocking down the genes were negatively enriched), with 1152 differential enriched targets in total. In the copa/vene exposed cells, 207 genes had positive and 1324 negative β (total, 1531 differentially enriched targets). Genes defined as essential, according to DepMap, represented 768/1152 (67%) and 843/1531 (55%) in control and experimental arms, respectively. The experimental arm did not massively differ from the control arm: 815 genes (615, 74%, defined as essential by DepMap) overlapped between the 2 conditions and there was highly significant enrichments at GSEA. A few genes were relevant only in VL51 exposed to copa/vene and not to DMSO. Selected hits were individually validated. Knocking down VKORC1L1, XCL1, RFK, MAP2K6, POC1A, and WTN5A improved copa/vene activity. WTN5A was also validated using recombinant protein (10 ng/mL), which reduced copa/vene effect. SPARCL1, MAPK4, ID2, and MSTN silencing reduced copa/vene activity. MSTN, coding for myostatin, was also validated by adding the recombinant protein (10 ng/mL), which increased the drugs anti-tumor activity.
Conclusions
A genome wide genetic screen identified genes modulating the response to copa/vene and potential new therapeutic targets and biomarkers.
Clinical trial identification
Editorial acknowledgement
Legal entity responsible for the study
The authors.
Funding
Swiss Cancer Research foundation.
Disclosure
E. Zucca: Financial Interests, Personal, Advisory Board: BeigGene, Incyte, Merck, Roche, BMS, Miltenyi Biomedicine, Curis, Eli/Lilly, Ipsen; Financial Interests, Institutional, Other, Travel Grant: Roche, AbbVie; Financial Interests, Institutional, Other, Trial Sponsor: IELSG: AstraZeneca, Incyte, Janssen, Roche; Financial Interests, Institutional, Other, Trial Sponsor: IELSG: Celgene/BMS. A. Alimonti: Financial Interests, Personal, Other, Consulting fees: Relmada Therapeutics, Inc., IBSA Institute Biochimique SA, Debiopharm; Financial Interests, Personal, Stocks/Shares: Oncosence; Financial Interests, Personal, Ownership Interest: Bottega Organica; Financial Interests, Personal, Royalties, US9668961B2: ATRAHASIS Srl; Financial Interests, Personal, Royalties, US11235017B2: Altergon SA; Financial Interests, Institutional, Invited Speaker, US11168134B2: Fondazione Per L'istituto Oncologico Di Ricerca (IOR); Financial Interests, Institutional, Invited Speaker, US20200095314A1: Fondazione Per L'istituto Oncologico Di Ricerca (IOR); Financial Interests, Personal, Royalties, EP2762131B1: n/a; Financial Interests, Institutional, Research Grant: Dompé Farmaceutici, IBSA Institut Biochimique; Financial Interests, Institutional, Other, I have been the PI of a industry-sponsored clinical trial: Astellas Pharma Inc, AstraZeneca, Sun Pharma Global FZE. A. Stathis: Financial Interests, Institutional, Expert Testimony: Bayer, Eli Lilly; Financial Interests, Institutional, Advisory Board: Janssen, Roche; Financial Interests, Institutional, Other, Travel grant: AstraZeneca, Incyte; Financial Interests, Institutional, Invited Speaker: Pfizer, Merck MSD, Roche, Novartis, ADC Therapeutics, AbbVie, Bayer, Philogen, Cellestia, AstraZeneca, Incyte, Amgen, Loxo Oncology. F. Bertoni: Financial Interests, Institutional, Other, consultancy: Helsinn, Menarini; Financial Interests, Institutional, Other, member of the Advisory Board: Phi Pharma; Financial Interests, Personal, Other, co-inventor of patent WO2019185117A1: Fondazione per l'Istituto Oncologico di Ricerca (IOR); Financial Interests, Institutional Funding: ADC Therapeutics, Bayer AG, Cellestia, Helsinn, ImmunoGen, Menarini Ricerche, NEOMED Therapeutics 1, Nordic Nanovector ASA, PIQUR Therapeutics AG, Oncology Therapeutic Development; Financial Interests, Institutional, Research Grant: Spexis; Non-Financial Interests, Institutional, Product Samples: HTG; Other, Personal, Other, travel grant: Amgen, AstraZeneca, Jazz Pharmaceuticals; Other, Personal, Other, Travel grant: IOnctura SA, Geneva, Switzerland. All other authors have declared no conflicts of interest.