Unraveling Genetic and Molecular Mechanisms of Trastuzumab Resistance in Cancer and Therapy-Associated Polyposis: Insights into Pathogenesis and Therapeutic Implications

Abstract

Background Intratumoral heterogeneity (ITH) of HER2 amplifications, and other oncogenic driver alterations are common in HER2+ GEA. However, their importance in predicting response to trastuzumab based therapy in these patients are not well studied. Methods Patients with advanced HER2+ GEA who were seen at DFCI between 2011-2023 were included in the study to evaluate response to Trastuzumab therapy. Next Generation Sequencing and single cell HER2 ISH assessment on pre-treatment tumor biopsies to analyze concomitant mutations and fraction of cells with HER2 high copy number, respectively. Outcomes OS and PFS were analyzed using Kaplan-Meier curves and Cox regression models to find association with concomitant genomic alterations. Responders and non-responders categorized based on PFS were analyzed multivariable using logistic regression to assess correlation with ITH. Results A total of 168 patients with HER2+ metastatic GEA treated with Trastuzumab based therapy were included. Most patients were males (85.7%) with a mean age of 60.6 years. HER2 IHC 3+ was observed in 86.3% of patients. Genomic analysis revealed ERBB2 amplification in 89% of patients. MET amplifications were associated with a significantly shorter PFS and OS, whereas CDK6 amplifications were significantly associated with shorter OS. HER2 was discordant between spatially disparate lesions in 44.7% of patients. Median HER2 copy number and HER2 IHC did not independently predict treatment response. However, HER2 intratumoral heterogeneity influenced response to trastuzumab therapy; higher fraction of cells with HER2 high copy number were significantly associated with long term response (OS >= 21.6 months) to Trastuzumab therapy independently as well as after adjusting for other covariates(coefficient estimate of 8.38, p.05). Conclusion Concomitant MET and CDK6 co-occurring with HER2 amplifications impacted clinical outcomes in patients treated with Trastuzumab. Patients with more homogenous HER2 CN ratio per cell (higher fraction of cells with HER2 high copy number ratio) responded for a longer duration to Trastuzumab based therapies and pave way for future studies to validate its use as a clinical assay to predict response to therapy. Abstract: Background The role of predisposing germline and acquired somatic genomic alterations to develop gastrointestinal polyposis post radiotherapy and chemotherapy exposure is unknown in childhood and young adult cancer survivors. Methods We investigated 29 cancer survivors with Therapy Associated Polyposis (TAP). Patients with more than 10 gastrointestinal polyps’ post-exposure to radiotherapy/chemotherapy were included. Baseline clinical data were collected, and genomic analysis involved DNA sequencing of polyp samples and blood/normal tissue for germline information. Earlier studies have established the role of GREM1 mutation in causing hereditary mixed polyposis syndrome in Ashkenazi Jews and hence GREM1 overexpression, using IHC, was explored in a subset of patients with family history of colonic polyposis. Organoids were generated from colon tissue collected prospectively. Candidate somatic single nucleotide variations, somatic small insertions and deletions, and mutational signatures were analyzed using methods such as Mutect2 and Bayesian non-negative matrix factorization to understand genomic alterations predisposing patients to TAP. Results A study of 29 TAP patients found a mean cancer diagnosis age of 13.79 years, mainly Hodgkin’s Lymphoma. Adenomatous polyposis turned out to be the most common type of histology seen in these patients and ascending colon was the most common site of occurrence of polyposis, irrespective of the therapies given, suggesting a genetic predisposition. A strong positive history of secondary cancers, family history of polyposis in 34.5% of the patients and mixed histology in almost all patients indicates towards the role of GREM1 alteration in pathophysiology of TAP. Mutational signature analysis of polyp tissue revealed ongoing mutational evolution, independent of germline mutations, and involvement of DNA mismatch repair genes in the disease pathophysiology. We anticipate more candidate mutations from our ongoing genomic analysis of patient samples. Like organoids from polyposis syndromes with known germline predisposition, TAP organoids displayed features of arrested differentiation compared to paired normal colon organoids. Conclusion In summary, we propose that therapy associated polyposis is associated with defective DNA damage repair pathways and future studies are warranted to validate the findings. We aim to propose other candidate genes to be tested for in germline genetic testing and suggest early surveillance in patients with harboring those alterations.