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Supplementary Table S1. List of genes and exons analyzed by targeted next-generation sequencing. Supplementary Table S2. Summary of molecular data from the ISH and sequencing analyses conducted on both the pre-treatment primary tumor and the liver biopsy obtained after progression on panitumumab plus vemurafenib treatment. List of abbreviations: IHC, immunohistochemistry; ND, not done; SISH, dual-color silver in-situ hybridization; FISH, fluorescence in-situ hybridization.

Supplementary Figure S1. Copy number increase of MDM2 gene at progression after vemurafenib+panitumumab. Supplementary Figure S2. Representative examples of colorectal carcinomas bearing BRAF mutations and MET gene copy number gain. Supplementary Figure S3. Untreated WiDr parental cells exhibit similar levels of activated RAS-GTP protein compared to their MET-amplified resistant derivatives treated with encorafenib+cetuximab+alpelisib (E+C+A).

Supplementary Figure Legends

Supplementary Figure 4_Revised

Supplementary Figure legends (S1-S4)

Next generation sequencing Immunohistochemistry for HER-2 and MET Dual color silver in situ hybridization (SISH) for HER-2 and MET

Definition of trastuzumab resistant (A) and trastuzumab sensitive (B) patients according to combined assessment of RECIST response and time to progression to trastuzumab plus cisplatin/fluoropyrimidine induction treatment given for up to 6 cycles and followed by maintenance treatment with trastuzumab alone until disease progression.

Supplementary Figure 3

Supplementary Table 1

Purpose:Gastric and gastroesophageal adenocarcinomas represent the third leading cause of cancer mortality worldwide. Despite significant therapeutic improvement, the outcome of patients with advanced gastroesophageal adenocarcinoma is poor. Randomized clinical trials failed to show a significant survival benefit in molecularly unselected patients with advanced gastroesophageal adenocarcinoma treated with anti-EGFR agents.Experimental Design:We performed analyses on four cohorts: IRCC (570 patients), Foundation Medicine, Inc. (9,397 patients), COG (214 patients), and the Fondazione IRCCS Istituto Nazionale dei Tumori (206 patients). Preclinical trials were conducted in patient-derived xenografts (PDX).Results:The analysis of different gastroesophageal adenocarcinoma patient cohorts suggests that EGFR amplification drives aggressive behavior and poor prognosis. We also observed that EGFR inhibitors are active in patients with EGFR copy-number gain and that coamplification of other receptor tyrosine kinases or KRAS is associated with worse response. Preclinical trials performed on EGFR-amplified gastroesophageal adenocarcinoma PDX models revealed that the combination of an EGFR mAb and an EGFR tyrosine kinase inhibitor (TKI) was more effective than each monotherapy and resulted in a deeper and durable response. In a highly EGFR-amplified nonresponding PDX, where resistance to EGFR drugs was due to inactivation of the TSC2 tumor suppressor, cotreatment with the mTOR inhibitor everolimus restored sensitivity to EGFR inhibition.Conclusions:This study underscores EGFR as a potential therapeutic target in gastric cancer and identifies the combination of an EGFR TKI and a mAb as an effective therapeutic approach. Finally, it recognizes mTOR pathway activation as a novel mechanism of primary resistance that can be overcome by the combination of EGFR and mTOR inhibitors.See related commentary by Openshaw et al., p. 2964

MiR-9 regulates PDGFRbeta expression in TNBC cell lines

Supplementary Table 3

Supplementary Figure 6_Revised

Organization of cancer cells into endothelial-like cell-lined structures to support neovascularization and to fuel solid tumors is a hallmark of progression and poor outcome. In triple-negative breast cancer (TNBC), PDGFRβ has been identified as a key player of this process and is considered a promising target for breast cancer therapy. Thus, we aimed at investigating the role of miRNAs as a therapeutic approach to inhibit PDGFRβ-mediated vasculogenic properties of TNBC, focusing on miR-9 and miR-200. In MDA-MB-231 and MDA-MB-157 TNBC cell lines, miR-9 and miR-200 promoted and inhibited, respectively, the formation of vascular-like structures in vitro. Induction of endogenous miR-9 expression, upon ligand-dependent stimulation of PDGFRβ signaling, promoted significant vascular sprouting of TNBC cells, in part, by direct repression of STARD13. Conversely, ectopic expression of miR-200 inhibited this sprouting by indirectly reducing the protein levels of PDGFRβ through the direct suppression of ZEB1. Notably, in vivo miR-9 inhibition or miR-200c restoration, through either the generation of MDA-MB-231–stable clones or peritumoral delivery in MDA-MB-231 xenografted mice, strongly decreased the number of vascular lacunae. Finally, IHC and immunofluorescence analyses in TNBC specimens indicated that PDGFRβ expression marked tumor cells engaged in vascular lacunae. In conclusion, our results demonstrate that miR-9 and miR-200 play opposite roles in the regulation of the vasculogenic ability of TNBC, acting as facilitator and suppressor of PDGFRβ, respectively. Moreover, our data support the possibility to therapeutically exploit miR-9 and miR-200 to inhibit the process of vascular lacunae formation in TNBC. Cancer Res; 76(18); 5562–72. ©2016 AACR.

Supplementary Figure 1: Patients with acquired MET amplification have shorter PFS as compared to those with MET-negative tumors. PFS duration expressed as month time units is shown for individual patients with acquired MET amplification (blue histograms) and MET-negative (red histograms) tumors (panel A). Kaplan Meier curves show shorter median PFS of MET-amplified (blue) as compared with MET-negative (red) patients; moreover, around 40% and 15% patients MET-negative (but none of MET-amplified subjects) were still progression-free at 10 and even 20 months, respectively (panel B).

Online Methods

Supplementary Table 2

MiR-200 family inhibits tube formation ability through PDGFRbeta repression

Supplementary Figure 5

Supplementary Figure 1

Purpose: Refining the selection of HER2-positive metastatic gastric cancer patient candidates for trastuzumab is a challenge of precision oncology. Preclinical studies have suggested several genomic mechanisms of primary resistance, leading to activation of tyrosine kinase receptors other than HER2 or downstream signaling pathways.Experimental Design: We carried out this multicenter, prospective, case-control study to demonstrate the negative predictive impact of a panel of candidate genomic alterations (AMNESIA panel), including EGFR/MET/KRAS/PI3K/PTEN mutations and EGFR/MET/KRAS amplifications. Hypothesizing a prevalence of candidate alterations of 30% and 0% in resistant and sensitive HER2-positive patients, respectively, 20 patients per group were needed.Results: AMNESIA panel alterations were significantly more frequent in resistant (11 of 20, 55%) as compared with sensitive (0% of 17) patients (P < 0.001), and in HER2 IHC 2+ (7 of 13, 53.8%) than 3+ (4 of 24, 16.7%) tumors (P = 0.028). Patients with tumors bearing no candidate alterations had a significantly longer median progression-free [5.2 vs. 2.6 months; HR, 0.34; 95% confidence interval (CI), 0.07–0.48; P = 0.001] and overall survival (16.1 vs. 7.6 months; HR, 0.38; 95% CI, 0.09–0.75; P = 0.015). The predictive accuracy of the AMNESIA panel and HER2 IHC was 76% and 65%, respectively. The predictive accuracy of the combined evaluation of the AMNESIA panel and HER2 IHC was 84%.Conclusions: Our panel of candidate genomic alterations may be clinically useful to predict primary resistance to trastuzumab in patients with HER2-positive metastatic gastric cancer and should be further validated with the aim of molecularly stratifying HER2-addicted cancers for the development of novel treatment strategies. Clin Cancer Res; 24(5); 1082–9. ©2017 AACR.

Kaplan Meier estimates of PFS according to HER2 IHC expression (2+ versus 3+) in patients molecularly selected by the AMNESIA panel, i.e. in absence of EGFR/MET/KRAS/PI3K mutations and EGFR/MET/KRAS amplifications.

Supplementary Figure 2

Supplementary Figure S4. PDGFRbeta identifies vascular lacunae in TNBC tissues

Purpose: Even if RAS-BRAF wild-type and HER2/MET–negative metastatic colorectal cancer (mCRC) patients frequently respond to anti-EGFR mAbs, acquired resistance almost invariably occurs. Mechanisms of resistance to EGFR blockade include the emergence of KRAS, NRAS, and EGFR extracellular domain mutations as well as HER2/MET alterations. However, these findings derive from retrospective studies that analyzed one single resistance mechanism at a time; moreover, it is still unclear how molecular heterogeneity affects clonal evolution in patients. In this work, we aimed at extensively characterizing and correlating the molecular characteristics of tissue- and blood-based data in a prospective cohort of patients with mCRC who received anti-EGFR antibodies.Experimental design: Twenty-two RAS-BRAF wild-type, HER2/MET–negative mCRC patients progressing on anti-EGFR therapy after initial response underwent rebiopsy. Next-generation sequencing and silver in situ hybridization (SISH)/IHC analyses were performed both on archival tumors and postprogression samples. Circulating tumor (ctDNA) molecular profiles were obtained in matched tissue–plasma samples.Results: RAS mutations and HER2/MET amplification were the most frequently detected resistance mechanisms in both tissue and blood sample analysis. On the other hand, BRAF and EGFR ectodomain mutations were much rarer. Patients with acquired MET amplification showed worse PFS on anti-EGFRs. We detected both intralesion heterogeneity, as suggested by co-occurrence of different resistance mechanisms in the same sample, and interlesion heterogeneity. The combined analysis of tissue and blood (ctDNA) results highlights the complexity of clonal evolution triggered by EGFR blockade.Conclusions: Our results indicate that it may be extremely challenging to target the complex landscape of molecular heterogeneity associated with emergence of resistance to targeted therapies in patients with mCRC. Clin Cancer Res; 23(10); 2414–22. ©2016 AACR.

Prevalence of alterations not included in the AMNESIA panel, reported by means of NGS from resistant (cases) versus sensitive (controls) patients.

Supplementary Figure 7

The file contains all the supplementary tables (S1-S4): - Supplementary Table S1. Clinicopathologic features of 78 breast cancer patients (set 1) and 85 TNBC (set 2). - Supplementary Table S2. Relation between miR-9 expression and clinicopathologic characteristics in human breast cancer. - Supplementary Table S3. Top 40 genes predicted as miR-9 target and statistically significant down-modulated in basal versus luminal breast cancer. - Supplementary Table S4. Relation between clinicopathologic characteristics and miR-9 and miR-200c in TNBC human tissues.

Angioimmunoblastic lymphoma (AILT) is the second most common subtype of peripheral T-cell lymphoma (PTCL) and is characterized by dismal prognosis. Thus far, only a few studies have dealt with its molecular pathogenesis. We performed gene expression profile (GEP) analysis of six AILT, six anaplastic large cell lymphomas (ALCL), 28 PTCL-unspecified (PTCL/U), and 20 samples of normal T lymphocytes (including CD4+, CD8+, and activated and resting subpopulations), aiming to (a) assess the relationship of AILT with other PTCLs, (b) establish the relationship between AILT and normal T-cell subsets, and (c) recognize the cellular programs deregulated in AILT possibly looking for novel potential therapeutic targets. First, we found that AILT and other PTCLs have rather similar GEP, possibly sharing common oncogenic pathways. Second, we found that AILTs are closer to activated CD4+, rather than to resting or CD8+ lymphocytes. Furthermore, we found that the molecular signature of follicular T helper cells was significantly overexpressed in AILT, reinforcing the idea that AILT may arise from such cellular counterpart. Finally, we identified several genes deregulated in AILT, including PDGFRA, REL, and VEGF. The expression of several molecules was then studied by immunohistochemistry on tissue microarrays containing 45 independent AILT cases. Notably, we found that the vascular endothelial growth factor (VEGF) was expressed not only by reactive cells, but also by neoplastic cells, and that nuclear factor-κB (NF-κB) activation is uncommon in AILT, as suggested by frequent exclusively cytoplasmic c-REL localization. Our study provides new relevant information on AILT biology and new candidates for possible therapeutic targets such as PDGFRA (platelet-derived growth factor α) and VEGF. [Cancer Res 2007;67(22):10703–10]

Supplementary File 1 from Gene Expression Analysis of Angioimmunoblastic Lymphoma Indicates Derivation from T Follicular Helper Cells and Vascular Endothelial Growth Factor Deregulation

Supplementary Tables 1-5 from Gene Expression Analysis of Angioimmunoblastic Lymphoma Indicates Derivation from T Follicular Helper Cells and Vascular Endothelial Growth Factor Deregulation

Purpose: Gastric and gastroesophageal adenocarcinomas represent the third leading cause of cancer mortality worldwide. Despite significant therapeutic improvement, the outcome of patients with advanced gastroesophageal adenocarcinoma is poor. Randomized clinical trials failed to show a significant survival benefit in molecularly unselected patients with advanced gastroesophageal adenocarcinoma treated with anti-EGFR agents. Experimental Design: We performed analyses on four cohorts: IRCC (570 patients), Foundation Medicine, Inc. (9,397 patients), COG (214 patients), and the Fondazione IRCCS Istituto Nazionale dei Tumori (206 patients). Preclinical trials were conducted in patient-derived xenografts (PDX). Results: The analysis of different gastroesophageal adenocarcinoma patient cohorts suggests that EGFR amplification drives aggressive behavior and poor prognosis. We also observed that EGFR inhibitors are active in patients with EGFR copy-number gain and that coamplification of other receptor tyrosine kinases or KRAS is associated with worse response. Preclinical trials performed on EGFR-amplified gastroesophageal adenocarcinoma PDX models revealed that the combination of an EGFR mAb and an EGFR tyrosine kinase inhibitor (TKI) was more effective than each monotherapy and resulted in a deeper and durable response. In a highly EGFR-amplified nonresponding PDX, where resistance to EGFR drugs was due to inactivation of the TSC2 tumor suppressor, cotreatment with the mTOR inhibitor everolimus restored sensitivity to EGFR inhibition. Conclusions: This study underscores EGFR as a potential therapeutic target in gastric cancer and identifies the combination of an EGFR TKI and a mAb as an effective therapeutic approach. Finally, it recognizes mTOR pathway activation as a novel mechanism of primary resistance that can be overcome by the combination of EGFR and mTOR inhibitors. See related commentary by Openshaw et al., p. 2964

Purpose: Total loss of surface presentation of human leukocyte antigen (HLA) class I molecules, protecting tumor cells from the recognition by cytotoxic host CD8+ T cells, is known to be caused by mutations in the β2-microglobulin (β2m) gene. We asked whether abnormalities of chromosome 15, harboring the β2m gene on 15q21, in addition to β2m gene mutations, are causative for the HLA class I–negative phenotype of melanoma cells.Experimental Design: To answer this, we established primary cell lines from the β2m-negative metastatic melanoma tissues of four different patients and analyzed them for β2m gene mutations and chromosome 15 aberrations, the latter by loss of heterozygosity analysis, fluorescence in situ hybridization (FISH), and multicolor FISH.Results: Mutations at the β2m gene level were detected in all cell lines. The loss of heterozygosity analysis of microsatellite markers located on chromosome 15 in three of the four cell lines pointed to an extensive loss of chromosome 15 material. Subsequent molecular cytogenetic analysis revealed the coexistence of apparently normal and rearranged versions of chromosome 15 in three cell lines whereas the fourth cell line solely showed rearranged versions. Two of the four cell lines exhibited a special type of intrachromosomal rearrangement characterized by FISH signals specific for the subtelomeric region of 15q at both ends of the chromosome and one centromeric signal in between.Conclusions: Our data indicate that the complete loss of HLA class I expression in melanoma cells is due to the coincidence of the following mutational events: (a) chromosome 15 instability associated with an extensive loss of genetic material and (b) β2m gene mutations.

Patients with RAS and BRAF wt mCRC are regarded as the best candidates to receive anti-EGFRs. Nevertheless, almost half of these patients do not achieve response, so that a deeper refinement of candidates’ selection would be highly desirable. Different molecular alterations, supported by a strong and sound biologic rationale, have been suggested as predictors of primary resistance to anti-EGFRs, but up today their potential impact has been suggested only in preclinical experiences and retrospective series, and their low frequency makes difficult the validation of each single marker. The present case-control study was conducted to prospectively demonstrate the negative predictive impact of HER-2 amplification or mutations, MET amplification, NTRK/ROS1/ALK/RET rearrangements, and mutations activating MAPKs or PI3K/Akt axis. Patients with RAS and BRAF wt mCRC clearly resistant (cases) vs. clearly sensitive (controls) to single-agent anti-EGFRs were selected, their archival tissue samples were collected and the prevalence of above-mentioned alterations was prospectively assessed. HER-2 status was evaluated by immunohistochemistry (IHC) and silver in-situ hybridization (SISH); MET amplification was studied by SISH; gene rearrangements were screened by IHC followed by RNA-based NGS confirmation. Other candidate mutations were investigated by NGS (Hotspot Cancer Panel v2, Ion Torrent Personal Genome platform (Life Technologies®). Hypothesizing a prevalence of candidate alterations of 0% and 15% among controls and cases, respectively, we needed to include 47 cases and 47 controls to be able to reject the null hypothesis that the prevalence of alterations is equal, with α-error 0.05 and β-error 0.20. Moreover, we evaluated the predictive impact of microsatellite instability, since hypermutated tumors may hardly rely on a single pathway (i.e. EGFR) for their growth. Forty-six cases and 47 controls were included. The primary endpoint was met: above-mentioned alterations were reported in 19 (41.3%) cases and 1 (2.1%) control (p This is the first prospective demonstration that the combined assessment of these rare alterations allows to better select patients for treatment with anti-EGFRs, while opening the way to properly tailored therapies. Molecular alterationCases (Resistant patients)Controls (Sensitive patients)N=46N=47HER-2 amplification7*0HER-2 mutations1 (G776V, exon 20)0MET amplification5*0NTRK rearrangements2 (SCYL3-NTRK1 and TPM3-NTRK1)0ALK rearrangements00ROS1 rearrangements00RET rearrangements1 (CCDC6-RET)0PIK3CA mutations (exon 20)1 (A1035V, exon 20)1 (H1047R, exon 20)PTEN mutations3 (L247S, R233stop and del P248, exon 7)0Total n. of patients with candidate alterations191Microsatellite instability (MSI-high)60RAS mutations at low allele fraction **2 (KRAS G12V, exon 2, 6%; NRAS Q61R, exon 3, 10%)0New RAS mutations3 (2 KRAS L19F, exon 2; KRAS T50I, exon 3)0* in 1 case HER-2 and MET co-amplification was found** previously defined as wt by pyrosequencing Citation Format: Chiara Cremolini, Rosa Berenato, Federica Morano, Roberto Moretto, Federica Perrone, Elena Tamborini, Daniele Rossini, Annunziata Gloghini, Adele Busico, Giovanni Fucà, Chiara Baratelli, Emiliano Tamburini, Iolanda Capone, Chiara Costanza Volpi, Massimo Milione, Massimo Di Maio, Gabriella Fontanini, Filippo De Braud, Alfredo Falcone, Filippo Pietrantonio. Dissecting primary resistance to anti-EGFR monoclonal antibodies (anti-EGFRs) in RAS and BRAF wild-type (wt) metastatic colorectal cancer (mCRC) [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-238. doi:10.1158/1538-7445.AM2017-LB-238

Background: The prognosis of patients (pts) with PSCC is primarily depending on the involvement of regional lymph nodes. Owing to the limited efficacy of chemotherapy, new drugs are warranted. Dacomitinib (Daco) is a potent, irreversible TKI of human EGFR/HER1, HER2 and HER4. Methods: In a phase 2 study (NCT01728233), pts received Daco 45 mg/d, orally, continuously. Inclusion criteria were SCC histology, and clinical stage N2-3 or M1; no prior chemotherapy was allowed. Computed tomography (CT) and PET/CT scans were repeated q8 weeks. Responding (R) pts with locally-advanced (LA) PSCC were offered radical surgery. The primary endpoint was the objective response-rate (ORR=CR+PR according to RECIST v1.1). Stopping rules based on the Bayesian posterior probability (PP) were set; the target was to demonstrate that the ORR exceeded 20%. Translational analyses on pre-Daco tumor samples included: EGFR and HER2 amplification, in-situ hybridization for HPV, and next generation sequencing. Results: From 06/13 to 010/16, 28 patients were treated. 8 (28.6%) had visceral metastases. 50% had pelvic and 60.7% clinically-involved bilateral LN. 1 CR + 8 PR were obtained (ORR=32.1%, 80% credibility interval 21.0-43.0%). The median follow up was 19.8 months (IQR: 6.3-25.7); 12-m PFS was 26.2% (95%CI: 13.2-51.9); 12-m OS was 54.9% (95%CI: 36.4-82.8). The median OS of LA pts was 20 months (IQR: 11.1-NR). The current Bayesian PP of exceeding the 20% ORR target is 92.3%. Grade 3 adverse events (skin rash) were seen in 3 pts (10.7%). The median drug exposure was 2.2 months. Tissue samples from 25 pts were analyzed. Only 2 pts were HPV+ (1SD, 1PD). EGFR ampl was found in 4 pts (1 CR, 1 PR, 2 SD) and it was confirmed in all post-Daco samples. TERT mutations (60%) were found in responders only, PI3K/mTOR pathway gene mutations in 42.9% R vs 8.3% non responders, IGF2R in 40% and 20%, respectively. Mutations were largely consistent between matched pre- and post-therapy samples in 7 evaluated pts. Conclusions: Daco was active in advanced PSCC and provided the best ORR with a single agent in PSCC. The biology underlying response to Daco seems to be independent from HER-pathway alterations. The frontline therapy can provide a suitable window of opportunity to test new drugs in PSCC. Note: This abstract was not presented at the meeting. Citation Format: Andrea Necchi, Salvatore Lo Vullo, Daniele Raggi, Patrizia Giannatempo, Nicola Nicolai, Giuseppina Calareso, Elena Togliardi, Maurizio Colecchia, Federica Perrone, Annunziata Gloghini, Luigi Mariani, Roberto Salvioni. First-line therapy with dacomitinib, an orally available pan-her tyrosine kinase inhibitor, for locally-advanced or metastatic penile squamous cell carcinoma: Results of an open label, single-arm, single-center, phase 2 study [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 CT139. doi:10.1158/1538-7445.AM2017-CT139

Strategies aimed at obtaining a complete cytoreduction are needed to improve long-term survival for patients with colorectal cancer peritoneal carcinomatosis (CRC-pc). We established organoid models that presented cancer stem cell characteristics from naïve CRC-pc surgical samples of two patients (C1 and C2). The organoids recapitulated their corresponding clinical samples in terms of 3D structure and immmunoistochemical profile and were enriched in LGR5 positive cancer stem cells. Proteomic analyses of organoids highlighted their strong dependence on energy producing pathways, suggesting that their targeting may be an effective therapeutic approach for the ablation of cancer cell malignancies. To test this hypothesis we treated organoids with an inhibitor of MIF/CD74 signaling axis, 4-iodo-6-phenylpyrimidine (4-IPP), and metformin, which inhibits mitochondrial oxidation. Both the drugs target metabolism acting on AMP-activated protein kinase (AMPK), the main regulator of cellular energy homeostasis. AMPK inhibits the major anabolic processes sustaining cancer cell proliferation and growth and confers cell plasticity to survive under conditions of metabolic stress, such as hypoxia and glucose deprivation, which is commonly observed in tumors with rapid growth. As a new finding we observed that treatment of organoids with 4-IPP resulted in decreased AMPK signaling activity, inducing a stress-signaling response and death of cultured organoids. Conversely, metformin treatment enhanced AMPK activation under energy stress, decreasing the activity of the anabolic factors ribosomal protein S6 and p4EBP-1 and inhibiting the mitochondrial activity, hindering cell proliferation. Furthermore, metformin treated organoids exhibited a Warburg-like metabolic profile. Our results show that organoid metabolism can be disrupted by metformin-induced AMPK activation but also through a strong reduction in AMPK functions caused by the removal of MIF/CD74 signaling axis that induces an irreversible disruption of energy homeostasis and ultimately causes cell death. Overall, we suggest that AMPK functions are crucial for energy metabolism of colorectal cancer peritoneal carcinomatosis, and regulation of AMPK activity could be a potential molecular target for the treatment of CRC-pc. Citation Format: Fabio Bozzi, Angela Mogavero, Luca Varinelli, Annunziata Gloghini, Valerio Leoni, Galina V. Beznoussenko, Alexandre A. Mironov, Ermanno Leo, Marco A. Pierotti, Italia Bongarzone, Manuela Gariboldi. Disruption of energy homeostasis as an approach to block the proliferation of colon carcinomatosis. [abstract]. In: Proceedings of the AACR Special Conference on Colorectal Cancer: From Initiation to Outcomes; 2016 Sep 17-20; Tampa, FL. Philadelphia (PA): AACR; Cancer Res 2017;77(3 Suppl):Abstract nr B19.

Tumor vascularization is a fundamental step in solid tumor progression and is orchestrated by different pathways of vasculogenesis. In malignant tumors, neoplastic cells can differentiate into endothelial-like cells acquiring the expression of endothelial markers (i.e. CD31 and CD34) and participating in the formation of vascular-like structures that functionally deliver oxygen and nutrients to the tumor site. We recently identified PDGFRβ as an important player of this process in triple negative breast cancer (TNBC). Interestingly, increasing evidence supported a connection between PDGFRβ and epithelial to mesenchymal transition (EMT), important step for the endothelial trans-differentiation process. PDGFR signaling arose as a promising target for TNBC; thus a better understanding of this new role of PDGFRβ could be relevant in the biology and treatment of TNBC. We then aimed at investigating microRNAs able to regulate tumor vascularization via PDGFRβ-mediated endothelial differentiation in TNBC, focusing on miR-9 and miR-200 family in light of their known relation with PDGFRβ and EMT. Tube formation assay showed that in MDA-MB-231 and MDA-MB-157 TNBC cell lines transfection of miR-9 and miR-200 family members (miR-200b and miR-200c) promoted or inhibited, respectively, the ability of cells to form vascular-like structures when seeded on matrigel. Stimulation of PDGFRβ with PDGF-BB ligand induced miR-9 expression and enhanced the loop formation ability of treated cells. This advantage was, however, almost completely abrogated by the concomitant inhibition of miR-9, thus demonstrating that miR-9 contributed to PDGFRβ-mediated vasculogenic properties of TNBC. Moreover, we found that silencing of STARD13, direct target of miR-9 validated by luciferase reporter assay, improved the vasculogenic potential. Ectopic expression of miR-200 members, instead, suppressed PDGFRβ at protein level in both TNBC cell lines. Furthermore, the silencing of ZEB1, known target of miR-200 family, induced downregulation of PDGFRβ at protein and mRNA level; interestingly, the mRNA levels of ZEB1 and PDGFRβ strongly correlated in the TNBC subset of the TGCA dataset. The in vivo effect of miR-9 and miR-200 family on vasculogenic properties of TNBC was then validated first through the generation of MDA-MB-231 clones for stable inhibition of miR-9 and restoration of miR-200c; the resulting miR-9 sponge and miR-200c xenografted tumors showed lower number of vascular lacunae than controls, identified through immunohistochemical (IHC) staining for CD31. These results were validated in orthotopic MDA-MB-231 breast tumors treated with miR-9 inhibitors or miR-200c mimics by peritumoral injection. We finally evaluated PDGFRβ, by IHC, and miR-9 and miR-200c, by Real-time PCR, in a cohort of TNBC. IHC analysis demonstrated that PDGFRβ staining identified tumor cells participating in vascular lacunae, data further confirmed by immunofluorescence co-localization of PDGFRβ and CD31. Interestingly, unlike miR-9, the expression of miR-200c negatively associated with both the presence of vascular lacunae and tumor nests positive for PDGFRβ. Finally, in situ hybridization analysis revealed that miR-200c was mainly expressed by tumor cells. In conclusion, our results suggest that miR-9 and miR-200 family play an opposite role in the regulation of the vasculogenic aptitude of TNBC. MiR-9 is induced by PDGFRβ and enhances the vasculogenic properties of tumor cells in part through the negative regulation of STARD13. MiR-200, instead, inhibits this aggressive phenotype indirectly suppressing PDGFRβ through targeting of ZEB1. Citation Format: Elvira D'Ippolito, Ilaria Plantamura, Lucia Bongiovanni, Patrizia Casalini, Sara Baroni, Claudia Piovan, Rosaria Orlandi, Ambra V. Gualeni, Annunziata Gloghini, Anna Rossini, Filippo De Braud, Elda Tagliabue, Claudio Tripodo, Marilena V. Iorio. miR-9 and miR-200 regulate PDGFRβ-mediated endothelial differentiation of neoplastic cells in triple-negative breast cancer. [abstract]. In: Proceedings of the AACR Special Conference on Noncoding RNAs and Cancer: Mechanisms to Medicines ; 2015 Dec 4-7; Boston, MA. Philadelphia (PA): AACR; Cancer Res 2016;76(6 Suppl):Abstract nr A18.

Background: Acquired resistance to anti-EGFR MoAbs (cetuximab and panitumumab) represents a challenge in the treatment of mCRC, but its molecular mechanisms are not completely understood. Even in presence of RAS-BRAF-PI3KCA ”quadruple wt” and HER-2/MET negative status for protein expression and gene amplification, pts who primarily respond to anti-EGFR MoAbs will eventually develop secondary resistance. Prior retrospective and small series uniquely investigated a single biomarker, showing in some cases the emergence of KRAS mutations,HER-2 or MET amplifications. Our study aimed at comprehensively describing all known molecular alterations possibly associated with acquired resistance. Methods: Pts with mCRC were prospectively treated with cetuximab- or panitumumab-based therapy until progressive disease. All archival tumors were defined as RAS-BRAF-PI3KCA”quadruple wt” by Sanger sequencing, as well as HER-2/MET negative by both immunohistochemistry (IHC) and in-situ hybridization (ISH). At the time of disease progression, tumor re-biopsy was performed on the most accessible site of metastasis, as institutional procedure for a wide phase 1 screening program. On both archival tissue and re-biopsy, next generation sequencing of 50 genes' hotspot regions included in the Hotspot Cancer Panel v2 (Life Technologies) was performed by using the Ion Torrent Personal Genome Machine platform (Life Technologies). Moreover,HER-2/MET status were repeated on tumor re-biopsy by IHC and ISH. Results: Seventeen pts were recruited. All had prior objective response to anti-EGFRs. Next-generation sequencing confirmed RAS-BRAF-PI3KCA wt status on archival tumors. The results of our analyses on tumor re-biopsies are shown in the table: IDNGS: Acquired mutations (% mutant alleles)cellularity% mutant alleles normalized for cellularityHER2 ISHMET ISH#1KRAS Q61H (37%)80%46%--#2-Amplified-#3BRAF V600E (13%)90%14%--#4NRAS Q61R (13%)40%32%--#5--Amplified#6KRAS Q61K (4%)70%6% Acquired RAS or BRAF mutations were found in 4 (23%) and 1 (6%) cases, respectively. Acquired HER-2 or MET amplification were found in 4 (23%) and 2 (12%) cases, respectively. As shown for patient #6, some degree of intra-tumor heterogeneity may exist due to concomitant presence of low represented RAS-mutated and HER-2 amplified sub-clones. In some cases (35%), a detectable acquired mechanism of resistance remains unknown. Conclusions: Based on our results, currently known molecular alterations associated with acquired resistance were mainly mutually exclusive. In a relevant subset of cases additional molecular profiling is warranted. Citation Format: Filippo Pietrantonio, Rosa Berenato, Federica Perrone, Annunziata Gloghini, Elena Tamborini, Benedetta Picciani, Adele Busico, Giulio Settanni, Chiara Costanza Volpi, Ambra Vittoria Gualeni, Alessio Pellegrinelli, Massimo Milione, Marta Caporale, Monica Niger, Maria Di Bartolomeo, Filippo de Braud. Comprehensive molecular characterization of acquired resistance to anti-EGFR monoclonal antibodies (MoAbs) in patients with metastatic colorectal cancer (mCRC). [abstract]. In: Proceedings of the AACR-NCI-EORTC International Conference: Molecular Targets and Cancer Therapeutics; 2015 Nov 5-9; Boston, MA. Philadelphia (PA): AACR; Mol Cancer Ther 2015;14(12 Suppl 2):Abstract nr B57.