Eugenia Rosalinda Zanella

The genomic landscape of response to EGFR blockade in colorectal cancer

Colorectal cancer is the third most common cancer worldwide, with 1.2 million patients diagnosed annually. In late-stage colorectal cancer, the most commonly used targeted therapies are the monoclonal antibodies cetuximab and panitumumab, which prevent epidermal growth factor receptor (EGFR) activation. Recent studies have identified alterations in KRAS and other genes as likely mechanisms of primary and secondary resistance to anti-EGFR antibody therapy. Despite these efforts, additional mechanisms of resistance to EGFR blockade are thought to be present in colorectal cancer and little is known about determinants of sensitivity to this therapy. To examine the effect of somatic genetic changes in colorectal cancer on response to anti-EGFR antibody therapy, here we perform complete exome sequence and copy number analyses of 129 patient-derived tumour grafts and targeted genomic analyses of 55 patient tumours, all of which were KRAS wild-type. We analysed the response of tumours to anti-EGFR antibody blockade in tumour graft models and in clinical settings and functionally linked therapeutic responses to mutational data. In addition to previously identified genes, we detected mutations in ERBB2, EGFR, FGFR1, PDGFRA, and MAP2K1 as potential mechanisms of primary resistance to this therapy. Novel alterations in the ectodomain of EGFR were identified in patients with acquired resistance to EGFR blockade. Amplifications and sequence changes in the tyrosine kinase receptor adaptor gene IRS2 were identified in tumours with increased sensitivity to anti-EGFR therapy. Therapeutic resistance to EGFR blockade could be overcome in tumour graft models through combinatorial therapies targeting actionable genes. These analyses provide a systematic approach to evaluating response to targeted therapies in human cancer, highlight new mechanisms of responsiveness to anti-EGFR therapies, and delineate new avenues for intervention in managing colorectal cancer.

Inhibition of MEK and PI3K/mTOR Suppresses Tumor Growth but Does Not Cause Tumor Regression in Patient-Derived Xenografts of RAS-Mutant Colorectal Carcinomas

Purpose: Gene mutations along the Ras pathway (KRAS, NRAS, BRAF, PIK3CA) occur in approximately 50% of colorectal cancers (CRC) and correlate with poor response to anti–EGF receptor (EGFR) therapies. We assessed the effects of mitogen-activated protein (MAP)/extracellular signal-regulated kinase (ERK) kinase (MEK) and phosphoinositide 3-kinase (PI3K)/mTOR inhibitors, which neutralize the major Ras effectors, in patient-derived xenografts from RAS/RAF/PIK3CA-mutant metastatic CRCs (mCRC). Experimental Design: Forty mCRC specimens harboring KRAS, NRAS, BRAF, and/or PIK3CA mutations were implanted in nonobese diabetic/severe combined immunodeficient (NOD/SCID) mice. Each xenograft was expanded into four treatment arms: placebo, the MEK inhibitor AZD6244, the PI3K/mTOR inhibitor, BEZ235, or AZD6244 + BEZ235. Cases initially treated with placebo crossed over to AZD6244, BEZ235, and the anti-EGFR monoclonal antibody cetuximab. Results: At the 3-week evaluation time point, cotreatment of established tumors with AZD6244 + BEZ235 induced disease stabilization in the majority of cases (70%) but did not lead to overt tumor regression. Monotherapy was less effective, with BEZ235 displaying higher activity than AZD6244 (disease control rates, DCRs: AZD6244, 27.5%; BEZ235, 42.5%). Triple therapy with cetuximab provided further advantage (DCR, 88%). The extent of disease control declined at the 6-week evaluation time point (DCRs: AZD6244, 13.9%; BEZ235, 16.2%; AZD6244 + BEZ235, 34%). Cross-analysis of mice harboring xenografts from the same original tumor and treated with each of the different modalities revealed subgroups with preferential sensitivity to AZD6244 (12.5%), BEZ235 (35%), or AZD6244 + BEZ235 (42.5%); another subgroup (10%) showed equivalent response to any treatment. Conclusions: The prevalent growth-suppressive effects produced by MEK and PI3K/mTOR inhibition suggest that this strategy may retard disease progression in patients. However, data offer cautionary evidence against the occurrence of durable responses. Clin Cancer Res; 18(9); 2515–25. ©2012 AACR.

IGF2 is an actionable target that identifies a distinct subpopulation of colorectal cancer patients with marginal response to anti-EGFR therapies

Colorectal cancers that display reduced sensitivity to EGFR inhibition and strong IGF2 overexpression can be effectively treated by dual EGFR/IGF2 blockade. Better together Inhibitors of the epidermal growth factor receptor (EGFR) are already used to treat colorectal cancer. Unfortunately, although many patients’ tumors respond to these drugs, most of these responses are only partial and result in a slowing of tumor growth rather than a regression of the cancer. Now, Zanella et al. used a combination of patient samples and mouse xenografts to determine the reasons for the incomplete response to treatment and how it can be overcome. In some cases, more effective treatment just required a more complete inhibition of EGFR. Many of the other cancers overexpressed insulin-like growth factor 2 (IGF2), and the authors discovered that combining inhibitors of EGFR and IGF was an effective way to overcome resistance in these tumors. Among patients with colorectal cancer who benefit from therapy targeted to the epidermal growth factor receptor (EGFR), stable disease (SD) occurs more frequently than massive regressions. Exploring the mechanisms of this incomplete sensitivity to devise more efficacious treatments will likely improve patients’ outcomes. We tested therapies tailored around hypothesis-generating molecular features in patient-derived xenografts (“xenopatients”), which originated from 125 independent samples that did not harbor established resistance-conferring mutations. Samples from xenopatients that responded to cetuximab, an anti-EGFR agent, with disease stabilization displayed high levels of EGFR family ligands and receptors, indicating high EGFR pathway activity. Five of 21 SD models (23.8%) characterized by particularly high expression of EGFR and EGFR family members regressed after intensified EGFR blockade by cetuximab and a small-molecule inhibitor. In addition, a subset of cases in which enhanced EGFR inhibition was unproductive (6 of 16, 37.5%) exhibited marked overexpression of insulin-like growth factor 2 (IGF2). Enrichment of IGF2 overexpressors among cases with SD was demonstrated in the entire xenopatient collection and was confirmed in patients by mining clinical gene expression data sets. In functional studies, IGF2 overproduction attenuated the efficacy of cetuximab. Conversely, interception of IGF2-dependent signaling in IGF2-overexpressing xenopatients potentiated the effects of cetuximab. The clinical implementation of IGF inhibitors awaits reliable predictors of response, but the results of this study suggest rational combination therapies for colorectal cancer and provide evidence for IGF2 as a biomarker of reduced tumor sensitivity to anti-EGFR therapy and a determinant of response to combined IGF2/EGFR targeting.

Sustained inhibition of HER3 and EGFR is necessary to induce regression of HER2-amplified gastrointestinal carcinomas

Purpose: Preclinical studies in HER2-amplified gastrointestinal cancer models have shown that cotargeting HER2 with a monoclonal antibody and a small molecule is superior to monotherapy with either inhibitor, but the underlying cooperative mechanisms remain unexplored. We investigated the molecular underpinnings of this synergy to identify key vulnerabilities susceptible to alternative therapeutic opportunities. Experimental Design: The phosphorylation/activation of HER2, HER3, EGFR (HER receptors), and downstream transducers was evaluated in HER2-overexpressing colorectal and gastric cancer cell lines by Western blotting and/or multiplex phosphoproteomics. The in vivo outcome of antibody-mediated HER2 blockade by trastuzumab, reversible HER2 inhibition by lapatinib, and irreversible HER2 inhibition by afatinib was assessed in patient-derived tumorgrafts and cell-line xenografts by monitoring tumor growth curves and by using antibody-based proximity assays. Results: Trastuzumab monotherapy reduced HER3 phosphorylation, with minor consequences on downstream transducers. Lapatinib alone acutely inhibited all HER receptors and effectors but led to delayed rephosphorylation of HER3 and EGFR and partial restoration of ERK and AKT activity. When combined with lapatinib, trastuzumab prevented HER3/EGFR reactivation and caused prolonged inhibition of ERK/AKT. Afatinib alone was also very effective in counteracting the reinstatement of HER3, EGFR, and downstream signaling activation. In vivo, the combination of trastuzumab and lapatinib—or, importantly, monotherapy with afatinib—resulted in overt tumor shrinkage. Conclusions: Only prolonged inhibition of HER3 and EGFR, achievable by dual blockade with trastuzumab and lapatinib or irreversible HER2 inhibition by single-agent afatinib, led to regression of HER2-amplified gastrointestinal carcinomas. Clin Cancer Res; 21(24); 5519–31. ©2015 AACR.

Selective analysis of cancer-cell intrinsic transcriptional traits defines novel clinically relevant subtypes of colorectal cancer

Stromal content heavily impacts the transcriptional classification of colorectal cancer (CRC), with clinical and biological implications. Lineage-dependent stromal transcriptional components could therefore dominate over more subtle expression traits inherent to cancer cells. Since in patient-derived xenografts (PDXs) stromal cells of the human tumour are substituted by murine counterparts, here we deploy human-specific expression profiling of CRC PDXs to assess cancer-cell intrinsic transcriptional features. Through this approach, we identify five CRC intrinsic subtypes (CRIS) endowed with distinctive molecular, functional and phenotypic peculiarities: (i) CRIS-A: mucinous, glycolytic, enriched for microsatellite instability or KRAS mutations; (ii) CRIS-B: TGF-β pathway activity, epithelial–mesenchymal transition, poor prognosis; (iii) CRIS-C: elevated EGFR signalling, sensitivity to EGFR inhibitors; (iv) CRIS-D: WNT activation, IGF2 gene overexpression and amplification; and (v) CRIS-E: Paneth cell-like phenotype, TP53 mutations. CRIS subtypes successfully categorize independent sets of primary and metastatic CRCs, with limited overlap on existing transcriptional classes and unprecedented predictive and prognostic performances.

Abstract LB-293: Targeting the PI3K pathway to intercept cetuximab tolerance in metastatic colorectal cancer

In the precision medicine era, multi-parametric interrogation of tumors in cancer patients has enabled rationally refined clinical trials and considerably improved response rates. Nevertheless, incomplete mass obliteration and late relapse invariably emerge. This also relates to metastatic colorectal cancer (mCRC), as massive tumor regression upon anti-EGFR therapy with cetuximab is relatively infrequent. Clinical evidence suggests that tumor recurrence may be endorsed by a population of lingering cancer cells that survive therapy and fuel residual disease through reversible, non-mutational cues, thus installing a “poised” state of drug tolerance that anticipates tumor relapse. The mechanisms underlying this resilience, and the strategies to tackle it, remain to be explored. In this study, we capitalized on different exploratory resources, including a proprietary collection of patient-derived xenografts, as well as CRC cell lines and primary cultures, to explore the mechanisms of cetuximab tolerance. Biochemical characterization of cetuximab persisters evidenced a dichotomous output, with full MAPK neutralization but persistent PI3K/AKT activity, suggesting that PI3K is engaged as a competitor route. Consistently, concomitant EGFR/PI3K blockade specifically unleashed apoptosis in cell lines, as opposed to the cytostatic activity of cetuximab alone, and prevented colosphere growth recovery after drug washout. In vivo, evaluation of residual cellularity confirmed the superior efficacy of dual EGFR/PI3K deactivation. Hence, both the number and fitness of tolerant cells were thwarted by EGFR/PI3K interception. Integrative morphologic analysis, immunohistochemistry, gene-expression profiling and reporter assays in vitro put forward increased beta-catenin activity and Paneth cell-like reprogramming as distinctive traits of residual cells surviving cetuximab treatment. These features are likely related to cetuximab-induced biochemical rewiring, as relieve of ERK-mediated beta-catenin repression in conjunction with persistent PI3K-AKT activity may converge on Wnt-dependent Paneth cell-like differentiation. Importantly, PI3K inhibition dampened cetuximab-triggered Paneth cell specification, thus intercepting a putative mechanism of drug-tolerance. Future studies will extricate the relative contribution of PI3K, MAPK, and Wnt-dependent networks to sustaining the reservoir of persisters, and how Paneth-like traits may foster residual disease. Citation Format: Barbara Lupo, Paolo Gagliardi, Francesco Sassi, Eugenia Rosalinda Zanella, Francesca Cottino, Andrea Bertotti, Livio Trusolino. Targeting the PI3K pathway to intercept cetuximab tolerance in metastatic colorectal cancer [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2017; 2017 Apr 1-5; Washington, DC. Philadelphia (PA): AACR; Cancer Res 2017;77(13 Suppl):Abstract nr LB-293. doi:10.1158/1538-7445.AM2017-LB-293

674. Insertional Mutagenesis to Identify Mechanisms of Cetuximab Resistance in Colorectal Cancer

Anti-cancer drugs designed to target specific molecular pathways have shown an excellent therapeutic potential but also very poor long-term durability of tumor responses, mainly due to the outbreak of resistant clones among the residual neoplastic cell population. For that reason, understanding the molecular mechanisms underlying the onset of anti-cancer drug resistance (ACDR) is one of the major goals of clinical research. ACDR has been widely studied by DNA/RNA sequencing of primary human samples and several culprits identified. We have previously developed an approach based on lentiviral vector (LV)-induced insertional mutagenesis that allowed to identify the genes involved in lapatinib and erlotinib resistance on HER2+ human breast cancer cell lines and EGFR+ pancreatic cell line respectively. Here we took advantage of this platform to investigate ACDR genes in colorectal cancer (CRC). Cetuximab, anti-EGFR monoclonal antibody, is used as first line therapy in metastatic CRC, which results in prolonged survival of treated patients. However, nearly all patients relapse due to ACDR. We thus selected CRC cells sensitive to cetuximab deriving either from five microsatellite stable cell lines or from eight Patient Derived Xenografts (PDX), primary human CRC cells implanted subcutaneously into immunodeficient mice (NSG). To induce insertional mutagenesis we generated a luciferase-expressing LV harboring the SFFV enhancer/promoter in the long terminal repeats able to perturb the expression of genes nearby the integration site. As control, we used a non-genotoxic SIN-LV. We set up a collagenase IV-based disaggregation protocol that allows single-cell suspension and a serum-free culture condition to maintain the stemness of in vitro cultured cells. This protocol allowed to efficiently disaggregate and expand CRC cells in vitro as well as reach a LV copy number per cell ranging from 0.25 to 5.6. Luciferase gene expression was stable and allowed live-animal monitoring for up to 30 weeks after transplant. CRC-0069 and -0077 PDXs and NCI-H508 and HDC82 cell lines were transduced ex vivo and kept in vitro and/or transplanted in NSG mice. After in vitro or in vivo expansion of the transduced CRCs cetuximab treatment was applied. After an initial shrinking of the tumor mass in mice we observed ACDR in 3 out of 10 mice transplanted with NCI-H508 cells transduced with SFFV-LV and in none of the controls. Genomic DNA from resistant cells is being used for insertion site (IS) analysis to identify common IS, ACDR gene candidates. IS obtained from SIN-LV groups will be used to filter LV integration biases, whereas IS from SFFV-LV transduced cells but not treated with cetuximab will be used to filter mutations that provide a proliferative advantage unrelated to cetuximab treatment. We will validate the most promising candidates by LV-mediated overexpression and knockdown techniques. This approach could pave the way to perform insertional mutagenesis-based forward genetics studies on primary human samples.

Abstract LB-354: Investigating potential molecular biomarkers for cetuximab response in metastatic colorectal cancer tissue using reverse phase protein array

Colorectal cancer (CRC) is the third and second most commonly diagnosed cancer in males and females, and the second most common cause of cancer-related deaths in the developed world. Identifying the importance of epidermal growth factor (EGF) signalling pathways for the survival of CRC cells (Van Cutsem, Kohne et al. 2011) resulted in development of therapies that target EGF-receptors (EGFR). Late stage CRC patients are mainly treated with monoclonal anti-EGFR antibodies such as cetuximab. Although anti-EGFR therapies have significantly improved survival in CRC patients (Van Cutsem, Kohne et al. 2009), they are not effective in patients with activating KRAS, BRAF, NRAS and PI3KCA mutations (De Roock, Claes et al. 2010). Nevertheless, between 50-60% of patients will not benefit from the additional anti-EGFR treatment, even when these have a quadruple wild-type status (De Roock, De Vriendt et al. 2011), suggesting that novel biomarkers and targeted therapies are required. In this study, we investigate potential biomarkers for cetuximab response in a panel of 93 quadruple wild-type, liver metastatic CRC samples from patient derived xenografts (PDX) with known responses to cetuximab. Matching PDXs were used to measure changes in tumour volumes post cetuximab treatment (Bertotti, Papp et al. 2015) and were later categorised as regressing, progressing or stabilised. Protein expression levels were measured in matched PDXs, using a reverse phase protein array (RPPA) with a panel of 72 antibodies targeting key cancer related proteins as previously described). Statistical analysis of measured values showed significant correlation between high protein expression levels, such as Chk-1, PARP, HIAP-2 (cIAP-1), and PDX progression post cetuximab treatment. These proteins were significantly expressed lower in both regressing and stable PDXs. Interestingly, we found a high cross correlation between expression levels of these proteins across all the samples, giving them a great potential to act as predictive biomarkers for cetuximab response. Bioinformatics pathway enrichment of these proteins showed a significant enrichment of intrinsic apoptotic and cell cycle signalling pathways. These results have also been investigated in publically available patient data with cetuximab response and together will be used to construct a deterministic mathematical cell cycle model that will help to predict the outcome of cetuximab therapy in future. Citation Format: Naser Monsefi, Robert O’Byrne, Steven Carberry, Eugenia R. Zanella, Ana Barat, Mattia Cremona, Clare Morgan, Bryan T. Hennessy, Andrea Bertotti, Livio Trusolino, Jochen H.M. Prehn. Investigating potential molecular biomarkers for cetuximab response in metastatic colorectal cancer tissue using reverse phase protein array. [abstract]. In: Proceedings of the 107th Annual Meeting of the American Association for Cancer Research; 2016 Apr 16-20; New Orleans, LA. Philadelphia (PA): AACR; Cancer Res 2016;76(14 Suppl):Abstract nr LB-354.

Abstract B43: HER2-amplified gastric and colorectal cancers: Mechanistic insights into HER2 targeting approaches

Only 10% of genetically unselected patients with chemorefractory metastatic colorectal cancer (mCRC) receive clinical benefit from therapy with the anti-EGFR antibodies cetuximab and panitumumab. Among non-responsive patients, 70% bear tumors harboring at least one alteration in KRAS , NRAS , BRAF and PIK3CA genes; therefore, the remaining 30% of “quadruple negative” cases display still-unidentified features that sustain primary resistance to EGFR-targeted therapies. By performing genotype-response correlations in a preclinical platform of patient-derived mCRC xenografts (xenopatients), our group has recently identified HER2 amplification as a new biomarker of resistance to cetuximab within a quadruple negative population. We found that the anti-HER2 monoclonal antibody trastuzumab, despite its demonstrated efficacy in patients with HER2-positive breast and gastric cancers, was completely ineffective in HER2 -amplified mCRC xenopatients. Importantly, while the dual EGFR/HER2 small molecule inhibitor lapatinib induced disease stabilization, the combination of lapatinib with trastuzumab was synergistic, achieving rapid and long lasting tumor regressions. When the same regimens where applied to HER2-positive gastric cancer cells in vivo, trastuzumab and lapatinib as monotherapies induced disease stabilization, while the combination of both – similar to CRC – had stronger therapeutic effect. The aim of this study was to better characterize the molecular mechanisms underlying the synergistic effect of the combination therapy in HER2-positive gastric and colorectal cancers. We first generated three CRC cell lines (NCI-H508, DiFi and HDC-142) stably transfected with the HER2 oncogene and provided proof-of-concept of the causative role of HER2 in installing cetuximab resistance in mCRC. Indeed, while parental controls proved to be extremely sensitive to cetuximab, HER2 overexpressors displayed overt resistance, both in viability assays in vitro and in xenografts experiments in vivo. Moreover, NCI-H508-HER2 cells in vivo were poorly responsive to trastuzumab, while lapatinib induced disease stabilization and the combination of both achieved the strongest therapeutic effect. Overall, these responses were very similar to those observed for HER2-positive mCRC xenopatients, attesting to the reliability of this artificial cellular model for further mechanistic studies. We next analyzed the activation status of EGFR, HER2 and HER3 upon treatment with trastuzumab, lapatinib and combo and explored the signaling consequences of receptor blockade. Dose-response curves revealed that trastuzumab did not affect activation of EGFR and HER2, but was able to reduce HER3 phosphorylation; at variance, lapatinib and combo potently inhibited phosphorylation of all HERs in a similar manner, with no additive effect by combo. Interestingly, time-course experiments highlighted that treatment with lapatinib resulted in a paradoxical increase of HER3 expression and phosphorylation both in HER2-positive gastric cancer cells and in colorectal cancer cells. Importantly, adding trastuzumab to lapatinib completely neutralized lapatinib-induced HER3 hyper-phosphorylation, without affecting HER3 levels. Possibly, up-regulated HER3 could provide an alternate route to activate a “bypass track” signaling, attenuating the antitumor effects of lapatinib as monotherapy in these tumor settings. Full inhibition of a residual HER2 activity and consequent abolishment of HER3 phosphorylation achieved by the addition of trastuzumab could provide a mechanistic explanation of the synergic effect obtained with the combination therapy. Overall, these results provide new mechanistic insights into resistance and response to EGFR and HER2 targeted therapies and deserve further investigations to explore the key pathways involved in HER3 feedback up-regulation in the context of HER2-positive cancers. Citation Format: Simonetta Maria Leto, Francesco Sassi, Giorgia Migliardi, Eugenia Zanella, Irene Catalano, Andrea Bertotti, Livio Trusolino. HER2-amplified gastric and colorectal cancers: Mechanistic insights into HER2 targeting approaches. [abstract]. In: Proceedings of the AACR Precision Medicine Series: Drug Sensitivity and Resistance: Improving Cancer Therapy; Jun 18-21, 2014; Orlando, FL. Philadelphia (PA): AACR; Clin Cancer Res 2015;21(4 Suppl): Abstract nr B43.

Abstract 659: Sustained inhibition of HER3 and EGFR is necessary to induce regression of HER2-amplified gastrointestinal carcinomas

Proceedings: AACR 106th Annual Meeting 2015; April 18-22, 2015; Philadelphia, PA Purpose: Preclinical studies in HER2-amplified gastrointestinal cancer models have shown that co-targeting HER2 with a monoclonal antibody and a small molecule is superior to monotherapy with either inhibitor, but the underlying cooperative mechanisms remain unexplored. We investigated the molecular underpinnings of this synergy to identify key vulnerabilities susceptible to alternative therapeutic opportunities. Experimental Design: The signaling consequences of HER2, HER3 and EGFR (HERs) blockade were evaluated in HER2-overexpressing colorectal and gastric cancer cell lines by Western blotting. HERs’ canonical downstream transducers were quantitatively gauged by multiplex phospho-proteomics. The in vivo outcome of antibody-mediated HER2 blockade by trastuzumab, reversible HER2 inhibition by lapatinib, and irreversible HER2 inhibition by afatinib was assessed in patient-derived tumorgrafts and cell-line xenografts by monitoring tumor growth curves and by using antibody-based proximity assays for phosphoprotein analysis. Results: Trastuzumab monotherapy reduced HER3 phosphorylation, with minor consequences on downstream transducers. Lapatinib alone acutely inhibited all HER receptors and effectors but led to delayed rephosphorylation of HER3 and EGFR and partial restoration of ERK and AKT activity. When combined with lapatinib, trastuzumab prevented HER3/EGFR reactivation and caused prolonged inhibition of ERK/AKT. Afatinib alone was as effective as trastuzumab plus lapatinib in counteracting the reinstatement of HER3, EGFR, and downstream signaling activation. In vivo, the combination of trastuzumab and lapatinib - or monotherapy with afatinib - resulted in overt tumor shrinkage. Conclusions: Only prolonged inhibition of HER3 and EGFR, achievable by dual blockade with trastuzumab and lapatinib or irreversible HER2 inhibition by single-agent afatinib, led to regression of HER2-amplified gastrointestinal carcinomas. Citation Format: Simonetta Maria Leto, Francesco Sassi, Irene Catalano, Giorgia Migliardi, Eugenia Rosalinda Zanella, Andrea Bertotti, Livio Trusolino. Sustained inhibition of HER3 and EGFR is necessary to induce regression of HER2-amplified gastrointestinal carcinomas. [abstract]. In: Proceedings of the 106th Annual Meeting of the American Association for Cancer Research; 2015 Apr 18-22; Philadelphia, PA. Philadelphia (PA): AACR; Cancer Res 2015;75(15 Suppl):Abstract nr 659. doi:10.1158/1538-7445.AM2015-659