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Purpose: Response to a complex trastuzumab-based regimen is affected by multiple features of the tumor and its microenvironment. Developing a predictive algorithm is key to optimizing HER2-targeting therapy.Experimental Design: We analyzed 137 pretreatment tumors with mRNA-seq and DNA exome sequencing from CALGB 40601, a neoadjuvant phase III trial of paclitaxel plus trastuzumab with or without lapatinib in stage II to III HER2-positive breast cancer. We adopted an Elastic Net regularized regression approach that controls for covarying features within high-dimensional data. First, we applied 517 known gene expression signatures to develop an Elastic Net model to predict pCR, which we validated on 143 samples from four independent trials. Next, we performed integrative analyses incorporating clinicopathologic information with somatic mutation status, DNA copy number alterations (CNA), and gene signatures.Results: The Elastic Net model using only gene signatures predicted pCR in the validation sets (AUC = 0.76). Integrative analyses showed that models containing gene signatures, clinical features, and DNA information were better pCR predictors than models containing a single data type. Frequently selected variables from the multiplatform models included amplifications of chromosome 6p, TP53 mutation, HER2-enriched subtype, and immune signatures. Variables predicting resistance included Luminal/ER+ features.Conclusions: Models using RNA only, as well as integrated RNA and DNA models, can predict pCR with improved accuracy over clinical variables. Somatic DNA alterations (mutation, CNAs), tumor molecular subtype (HER2E, Luminal), and the microenvironment (immune cells) were independent predictors of response to trastuzumab and paclitaxel-based regimens. This highlights the complexity of predicting response in HER2-positive breast cancer. Clin Cancer Res; 24(21); 5292–304. ©2018 AACR.

High doses of ionizing radiation induce acute damage to epithelial cells of the gastrointestinal (GI) tract, mediating toxicities restricting the therapeutic efficacy of radiation in cancer and morbidity and mortality in nuclear disasters. No approved prophylaxis or therapy exists for these toxicities, in part reflecting an incomplete understanding of mechanisms contributing to the acute radiation-induced GI syndrome (RIGS). Guanylate cyclase C (GUCY2C) and its hormones guanylin and uroguanylin have recently emerged as one paracrine axis defending intestinal mucosal integrity against mutational, chemical, and inflammatory injury. Here, we reveal a role for the GUCY2C paracrine axis in compensatory mechanisms opposing RIGS. Eliminating GUCY2C signaling exacerbated RIGS, amplifying radiation-induced mortality, weight loss, mucosal bleeding, debilitation, and intestinal dysfunction. Durable expression of GUCY2C, guanylin, and uroguanylin mRNA and protein by intestinal epithelial cells was preserved following lethal irradiation inducing RIGS. Oral delivery of the heat-stable enterotoxin (ST), an exogenous GUCY2C ligand, opposed RIGS, a process requiring p53 activation mediated by dissociation from MDM2. In turn, p53 activation prevented cell death by selectively limiting mitotic catastrophe, but not apoptosis. These studies reveal a role for the GUCY2C paracrine hormone axis as a novel compensatory mechanism opposing RIGS, and they highlight the potential of oral GUCY2C agonists (Linzess; Trulance) to prevent and treat RIGS in cancer therapy and nuclear disasters. Cancer Res; 77(18); 5095–106. ©2017 AACR.

Supplementary Figure 1. Silencing p53 expression in intestine of p53int-/- mice eliminates phospho-p53 responses to DNA damage induced by radiation. Supplementary Figure 2. Silencing p53 expression in intestine of p53int-/- mice amplifies RIGS-related toxicity. Supplementary Figure 3. Littermates are utilized to minimize the effect of genetic backgrounds in transgenic mice. Supplementary Figure 4. HCT116 cells do not exhibit GUCY2C ligand binding. Supplementary Figure 5. Total body irradiation induces gastrointestinal injury. Supplementary Figure 6. Hormone expression is preserved in RIGS in Gucy2c-/- mice. Supplementary Figure 7. Oral ST fails to oppose RIGS in the absence of GUCY2C. Supplementary Figure 8. Silencing p53 expression in intestine of p53int-/- mice does not affect apoptosis in RIGS.

Supplementary Figure Legends

Supplementary eTables 1-12

Supplementary Figures 1-5

Body weights and guanylin expression in C57BL/6 mice on a lean or high fat (HF) diet, or switched from a high fat to a lean diet (HF-Lean).

Mouse diet calorie and nutrient content.

Daily calorie intake, body weights, and guanylin expression in Balb/c mice on lean or high fat (HF) diets.

Daily calorie intake, body weights, and guanylin expression in wild type and obesity-resistant (HF-R) C57BL/6 mice on lean or high fat (HF) diets.

Relative GUCY2C expression in proximal (PC) and distal (DC) colons of mice on lean or high fat (HF) diets.

Relative guanylin expression in proximal (PC) and distal (DC) colons of mice on lean or high fat (HF) diets.

Legend for Supplementary Figures S1-S7.

Daily calorie intake and body weights in mice on lean, high carbohydrate (HC), or high fat (HF) diets.

Daily calorie intake, body weights, and guanylin expression in Ob/Ob mice on ad libitum or calorie-restricted diets.