Quantitative assessment of response to epigenetic-targeted therapy

PROJECT SUMMARYAlterations in chromatin regulators that target histone post translational modificationsPTMsare associated with diverse human pathologiesmost notably cancerThe ability to quantitatively assess diseaseassociated histone PTMs and their response to therapeutic intervention could have broad clinical applicationsincluding drug discoveryclinical trial designand personalized treatment regimensChromatin ImmunoprecipitationChIPthe current leading approach to map epigenetic marks in vivoyields only semiquantitative datalimiting its clinical useEpiCypher has recently developed the first quantitative ChIP platformtermed CAP ChIPCalibration and Antibody Profilingwhich uses PTM defined recombinant designer nucleosomesdNucsat a range of concentrations as DNA barcodedspike incalibration standardsHoweverthe potential application of CAP ChIP in pre clinicalclinical settings remains unexploredHereEpiCypher is applying CAP ChIP to quantitatively monitor histone PTM changes in response to epigenetic targeted therapy in tumor and healthy peripheral blood mononuclear cellsPBMCsin a preclinical modelThe innovation of this project stems from the application of defined calibration standards to enable quantitative ChIP seq with sufficient sensitivityprecisionand specificity to resolve biologically relevant changes induced by epigenetic inhibitor treatmentThe development of quantitative response measurements for epigenetically targeted therapies could accelerate their preand postclinical evaluationFor these studies we will focus on histone methyltransferase EZHthe catalytic subunit of the PRCcomplexand its enzymatic productH KmeEZHmutation and dysregulation have been linked to a wide array of cancersand its inhibition slows cancer cell proliferation in vitro and in vivoAs suchEZHhas been a major focus of therapeutic developmentwith several inhibitors already in Phase I II clinical trialsmaking it an excellent target for this proof of concept studyWe will specifically focus on diffuse large B cell lymphomaDLBCLwhich is responsive to EZHinhibitionand a disease in which EZHinhibitorse gTazemetostatare in clinical trialsCAP ChIP Seq will first be applied to explore the H Kmelandscape in cultured DLBCL cellstreatment with an EZHspecific inhibitorTazemetostat from EpizymeAimWe will then quantitatively evaluate the H Kmelandscape in xenograft DLBCL tumors from mice treated with EZHinhibitorAimSince many cancers cannot be easily biopsied to assess treatment responsewe will also test the application of CAP ChIP to PBMCs to determine to how PBMC chromatin changes correlate with those in the lymphomaIn Phase IIwe will scale up manufacturing and commercialize CAP ChIP kits to selected high value drug targets for preclinical drug developmente gLSDH K meand H K meand SETDH KmeIn additionEpiCypher will partner with pharmaceutical companies with active EZHdrug development programs to develop pharmacodynamic assays and possible response based biomarkers PROJECT NARRATIVEChromatin regulatory enzymes that add or remove histone post translational modificationsPTMsare emerging high value therapeutic targets for a wide array of human diseasesHoweverno clinically applicable strategies exist to quantify PTM changes at select genomic regions preand post treatmentmaking it difficult to measure the relative success of proposed therapiesHereEpiCypher is developing our Calibration and Antibody ProfilingChromatin ImmunoPrecipitationCAP ChIPplatform to directly monitor the response to epigenetictargeted therapyThis breakout technology has the potential to accelerate epigenetic drug development and enable next generation companion diagnostics for personalized cancer therapies