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The sum of target lesions is routinely used to evaluate patient objective responses to treatment in the RECIST criteria, but it fails to address response heterogeneity across metastases. This study argues that spatiotemporal heterogeneity across metastases and organ-specific response is informative for drug efficacy and patient survival. We analyzed the longitudinal data of 11,404 metastatic lesions in 2,802 colorectal cancer patients from five phase III clinical trials. Initially, a metric Gower distance was applied to quantify response heterogeneity across metastases. Next, the spatiotemporal response heterogeneity across anatomic sites, therapies, and KRAS mutation status was assessed and examined for its association with drug efficacy and long-term patient survival. The response of metastatic lesions broadly differed across anatomic sites and therapies. About 60% of patients had at least one lesion respond contrarily from total tumor size. High interlesion heterogeneity was associated with shorter progression-free survival and overall survival. Targeted therapies (bevacizumab or panitumumab) combined with standard chemotherapy reduced interlesion heterogeneity and elicited more favorable effects from liver lesions (P < 0.001) than chemotherapy alone. Moreover, the favorable responses in liver metastases (> 30% shrinkage) were associated with extended patient overall survival (P < 0.001), in contrast to lesions in the lungs and lymph nodes. Altogether, the spatiotemporal response heterogeneity across metastases informed drug efficacy and patient survival, which could improve the current methods for treatment evaluation and patient prognosis. Significance: These findings support the modification of RECIST criteria to include individual lesion response to improve assessments of drug efficacy.

Over 50% of colorectal cancer patients develop resistance after a transient response to therapy. Understanding tumor resistance from an evolutionary perspective leads to better predictions of treatment outcomes. The objectives of this study were to develop a computational framework to analyze tumor longitudinal measurements and recapitulate the individual evolutionary dynamics in metastatic colorectal cancer (mCRC) patients. A stochastic modeling framework was developed to depict the whole spectrum of tumor evolution prior to diagnosis and during and after therapy. The evolutionary model was optimized using a nonlinear mixed effect (NLME) method based on the longitudinal measurements of liver metastatic lesions from 599 mCRC patients. The deterministic limits in the NLME model were applied to optimize the stochastic model for each patient. Cox proportional hazards models coupled with the least absolute shrinkage and selection operator (LASSO) algorithm were applied to predict patients' progression-free survival (PFS) and overall survival (OS). The stochastic evolutionary model well described the longitudinal profiles of tumor sizes. The evolutionary parameters optimized for each patient indicated substantial interpatient variability. The number of resistant subclones at diagnosis was found to be a significant predictor to survival, and the hazard ratios with 95% CI were 1.09 (0.79–1.49) and 1.54 (1.01–2.34) for patients with three or more resistant subclones. Coupled with several patient characteristics, evolutionary parameters strongly predict patients' PFS and OS. A stochastic computational framework was successfully developed to recapitulate individual patient evolutionary dynamics, which could predict clinical survival outcomes in mCRC patients. Significance: A data analysis framework depicts the individual evolutionary dynamics of mCRC patients and can be generalized to project patient survival outcomes.

Considerable lesion-specific response heterogeneity exists in metastatic colorectal cancer patients, largely due to organ-specific ecological environments and evolutionary pressures. Metastatic lesions with poor response to therapy often become tumor sanctuary sites, leading to systemic resistance and tumor relapse. To map the lesion-specific response and relapse patterns, we investigated the longitudinal dynamics of individual lesions in metastatic colorectal cancer patients. Tumor longitudinal data in 4,308 colorectal cancer patients with 40,612 individual lesions were collected from eight Phase III trials in Project Data Sphere. First, tumor response dynamics (regression after treatment and progression upon resistance) were characterized using an empirical mathematical model. Next, tumor response time (when the lesion size decreases ≥20% from baseline) and relapse time (when the lesion size increases ≥30% from tumor nadir) were estimated for each individual lesion in patients being treated with bevacizumab, panitumumab, and/or chemotherapy. Random effect cox proportional models were applied to predict lesion-specific response and relapse probabilities and temporal sequence. We then took machine learning algorithm k-means to cluster patients based on their lesion relapse sequence. We found the response probabilities across organs are: Liver > Distal Lymph Nodes (LN) > Abdomen > Spleen > Lung > Regional LN > Adrenal > Muscle/Soft Tissue > Bone > Brain/CNS. Lesion relapse temporal sequence are: Brain/CNS > Liver > Adrenal > Muscle/Soft tissue > Abdomen > Bone > Spleen > Lung > Distal LN > Regional LN. Of note, lesions in the bone, brain, adrenal, and muscle/soft tissues often had low responses and high relapse probabilities, implying the greatest potential as tumor sanctuary sites. Liver, the most common metastatic organ in colorectal cancer, showed highest response rate but high relapse probabilities. Interestingly, the organ-specific response rate and relapse probabilities are respectively in line with drug distribution profiles and organ-specific immune landscape. Organ-specific relapse sequence in each patient is significantly correlated with patient long-term survival (p Citation Format: Jiawei Zhou, Quefeng Li, Amber Cipriani, Yanguang Cao. Mapping lesion specific response and relapse patterns in metastatic colorectal cancer patients [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2022; 2022 Apr 8-13. Philadelphia (PA): AACR; Cancer Res 2022;82(12_Suppl):Abstract nr 3789.

Neoantigen clonal architecture is known to influence the efficacy of immunotherapy. The immunodominance of clonal neoantigens over a canvas of heterogeneous subclonal neoantigens is particularly challenging to recapitulate in experimental models. We developed a computational model of neoantigen evolution that longitudinally tracks the “presentome” - that is, a cell’s aggregate neoantigen repertoire and HLA status - of simulated non-small cell lung cancer (NSCLC) prior to and during treatment with checkpoint blockade. Using neoantigen immunogenicity parameters from published reports, we first recapitulated the presentome of early-stage NSCLC. Upon simulating checkpoint blockade treatment of advanced NSCLC, we found salient correlates and consequences of response, including a profound clonal collapse among completely responding tumors. Our work could be adapted to longitudinally model the neoantigen architecture of other cancers and modalities of immunotherapy, ultimately informing cognizant strategies for future therapeutic development. Citation Format: Tim Qi, Benjamin Vincent, Yanguang Cao. Longitudinally modeling anti-neoantigen immunity under paradigms of immunodominance [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2022; 2022 Apr 8-13. Philadelphia (PA): AACR; Cancer Res 2022;82(12_Suppl):Abstract nr 2731.