Session: 803. Emerging Tools, Techniques, and Artificial Intelligence in Hematology: Poster III
Hematology Disease Topics & Pathways:
Research, Acquired Marrow Failure Syndromes, Acute Myeloid Malignancies, Translational Research, Bone Marrow Failure Syndromes, Drug development, Diseases, Treatment Considerations, Myeloid Malignancies
We hypothesize that vulnerabilities to pharmacologic agents are imprinted in genomic features and that only rational stratification of patients according to their molecular make up (amino acid changes, mutations in functional domains, protein effect) might inform unsuspected sensitivities not otherwise recognized using a basket purely molecular approach.
Thus, we used a computational model to personalize drug response prediction by integrating genomic features stratified by functional effects on protein sequence. We curated a compendium of molecular data of 3,588 MN (22/58% MDS high/low risk; 20% secondary AML) and 452 primary AML. Data collected from The BEAT AML1 were also curated based on the scope of our analysis. Targeted NGS of 40 myeloid genes was uniformly applied. Variants were curated according to their functional impact due to their topology within the gene. For instance, TP53 mutations were divided based on the occurrence in the DNA binding domain and whether they were monoallelic vs biallelic, TET2 mutations were categorized based on their impact on the catalytic vs non catalytic domain, frameshift/stop codon/splice site vs missense, RUNX1 mutations based on whether or not they localized in the RUNT domain, SF3B1 mutations in K700E vs other common hotspots (R625, H662, K666), DNMT3A mutations in R882 vs non R882 vs frameshift/stop codon/splice site. Molecular and drug screening profile (79 FDA approved drugs) from The BEAT AML was used as discovery cohort to generate the model. Once modelling algorithm was assembled, an in-house in vitro drug/improved mutational dataset was generated for validation.
Given the success of deep representation learning approaches, we trained an encoder-decoder model to generate a low dimensional representation of genomic features. Using the pretrained encoder, we trained a downstream feed-forward neural network via the observations acquired from the discovery dataset. Given the trained model, we quantified genotype-drug response associations by Pearson correlation and compared the predictors with the in house generated dataset.
Out of 79 drugs, we found at least one drug showing sensitivity patterns against each unique protein configuration or mutational combination. The examples of specific observations illustrate the personalized approach. For instance, RUNX1 frameshifts shared a sensitivity profile with EZH2 frameshifts but not missense and SET domain. FLT3 missense, IDH1-R132H, TP53 splice sites, WT1 and CEBPA frameshifts exhibited divergent sensitivity patterns. Only RUNX1 frameshifts (but not others) showed sensitivity for MEK1/2 inhibitors except for cases with comutated TP53 splice site rendering them resistant. In contrast RUNX1 RUNT domain showed unique heightened response to CDK9 inhibitors. FLT3-TKD but not ITD showed higher sensitivity to cabozantinib while NRAS-Q61 to dactolisib (PI3K/mTOR dual inhibitor). Our trained algorithm integrated this seemingly unintelligible complexity of individual genotype/phenotype responses to overcome our inability to rationally predict sensitivity/resistance responses. This algorithm was then used in our ongoing confirmatory drug screen collection that mimics real life application in a clinical setting.
In summary, incorporation of protein configuration in drug response prediction might help unveiling unsuspected vulnerability profiles in MN addicted to specific gene mutations.
Disclosures: Scott: Vironexis Biotherapeutics, Inc.: Current equity holder in private company.