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Supplementary Figure 1 a. Doxorubicin resistance of DOXO-R C8 cells was further validated using the cell viability assay (SRB) following 48 hrs treatment with DOXO, n=4 independent experiment, 3 replicates/experiment. **p0.6 and pval

Table S18: Two-way ANOVA

Table S1: List of regions of genes with increased CNV (>= 0.5) and gene expression (>= 0.5) in DOXO-R cells compared to parental cells Table S2: List of all fold change and pvalue of DOXO-R C1 and C8 (vs parental cells) from gene expression analysis. Table S3. GSEA using the C5 module for the 1852 genes with gene expression fold change > 1.5 (pval < 0.05) in DOXO-R C1 and C8 Table S4. GSEA using the C5 module for the 407 genes with gene expression fold change > 1.5 (pval < 0.05) and CNV change > 0.5 Table S5: Mean LOG2FC of genes commonly up-regulated in C1 and C8 Table S6: Proteins that are significantly upregulated according to the following criteria. (i) only present in one or two of the Dox resistant cell lines (**) with at least 3 and 2 unique peptides, respectively. (ii) At least 1.5-fold upregulated in both cell lines with a maximum relative standard deviation (RSD) of 31% across control replicates and 25% RSD across resistant cell line replicates. Table S7: GSEA using the C5 module for the 98 overexpressed proteins in DOXO-R vs parental cells Table S8: mRNA fold change (POST vs PRE NAC) for 9 chemoresistant TNBC patients. Table S9: GSEA using the C5 module for NEO2 up regulated genes > 2.5 FC. The complete list of genes are listed below the GSEA analysis. Table S10: GSEA using the C5 module for NEO24 up regulated genes > 2.5 FC. The complete list of genes are listed below the GSEA analysis. Table S11: GSEA using the C5 module for NEO25 up regulated genes > 2.5 FC. The complete list of genes are listed below the GSEA analysis. Table S12: GSEA using the C5 module for NEO27 up regulated genes > 2.5 FC. The complete list of genes are listed below the GSEA analysis. Table S13: GSEA using the C5 module for NEO28 up regulated genes > 2.5 FC. The complete list of genes are listed below the GSEA analysis. Table S14: GSEA using the C5 module for NEO30 up regulated genes > 2.5 FC. The complete list of genes are listed below the GSEA analysis. Table S15: GSEA using the C5 module for NEO31 up regulated genes > 2.5 FC. The complete list of genes are listed below the GSEA analysis. Table S16: GSEA using the C5 module for NEO35 up regulated genes > 2.5 FC. The complete list of genes are listed below the GSEA analysis. Table S17: GSEA using the C5 module for NEO44 up regulated genes > 2.5 FC. The complete list of genes are listed below the GSEA analysis.

The major obstacle in successfully treating triple-negative breast cancer (TNBC) is resistance to cytotoxic chemotherapy, the mainstay of treatment in this disease. Previous preclinical models of chemoresistance in TNBC have suffered from a lack of clinical relevance. Using a single high dose chemotherapy treatment, we developed a novel MDA-MB-436 cell-based model of chemoresistance characterized by a unique and complex morphologic phenotype, which consists of polyploid giant cancer cells giving rise to neuron-like mononuclear daughter cells filled with smaller but functional mitochondria and numerous lipid droplets. This resistant phenotype is associated with metabolic reprogramming with a shift to a greater dependence on fatty acids and oxidative phosphorylation. We validated both the molecular and histologic features of this model in a clinical cohort of primary chemoresistant TNBCs and identified several metabolic vulnerabilities including a dependence on PLIN4, a perilipin coating the observed lipid droplets, expressed both in the TNBC-resistant cells and clinical chemoresistant tumors treated with neoadjuvant doxorubicin-based chemotherapy. These findings thus reveal a novel mechanism of chemotherapy resistance that has therapeutic implications in the treatment of drug-resistant cancer.Implications:These findings underlie the importance of a novel morphologic–metabolic phenotype associated with chemotherapy resistance in TNBC, and bring to light novel therapeutic targets resulting from vulnerabilities in this phenotype, including the expression of PLIN4 essential for stabilizing lipid droplets in resistant cells.

SPEN is mutated in T47D cells (S1); SPEN is down-regulated and mutated in breast cancer (S2); SPEN regulates cell growth and survival (S3); SPEN knockdown in triple negative breast cancer cell lines limits proliferation (S4); SPEN regulates cell death and survival (S5); SPEN regulates transcriptional activity of the Estrogen Receptor (S6); SPEN regulates response of ERα-positive breast cancer cells to tamoxifen (S7); SPEN does not affect ERα-positive breast cancer cells response to fulvestrant (S8).

Legends for Supplemental Figures S1-S8.

Clinical data (S1); Expression levels of SPEN and PGR as evaluated with DNA microarrays (S2); IC50 values of SPEN-overexpressing T47D clones, SPEN-silenced MCF-7 clones and their respective controls (S3); Loss of heterozysity assessment using polymorphic microsatellite repeat markers (S4); Primers sequence for the sequencing of SPEN (S5).

Bioenergetic perturbations driving neoplastic growth increase the production of reactive oxygen species (ROS), requiring a compensatory increase in ROS scavengers to limit oxidative stress. Intervention strategies that simultaneously induce energetic and oxidative stress therefore have therapeutic potential. Phenformin is a mitochondrial complex I inhibitor that induces bioenergetic stress. We now demonstrate that inflammatory mediators, including IFNγ and polyIC, potentiate the cytotoxicity of phenformin by inducing a parallel increase in oxidative stress through STAT1-dependent mechanisms. Indeed, STAT1 signaling downregulates NQO1, a key ROS scavenger, in many breast cancer models. Moreover, genetic ablation or pharmacological inhibition of NQO1 using β-lapachone (an NQO1 bioactivatable drug) increases oxidative stress to selectively sensitize breast cancer models, including patient derived xenografts of HER2+ and triple negative disease, to the tumoricidal effects of phenformin. We provide evidence that therapies targeting ROS scavengers increase the anti-neoplastic efficacy of mitochondrial complex I inhibitors in breast cancer., Complex I inhibition induces oxidative stress leading to cancer cell cytotoxicity. Here, the authors show, in breast cancer models, that inflammatory mediators can potentiate complex I inhibitor phenformin cytotoxicity through STAT1-mediated downregulation of the reactive oxygen species scavenger NQO1.

The tumor suppressor PTEN is the main negative regulator of PI3K/AKT/mTOR signaling and is commonly found downregulated in breast cancer (BC). Conflicting data from conventional immunoassays such as immunohistochemistry (IHC) has sparked controversy about PTEN's role as a prognostic and predictive biomarker in BC, which can be largely attributed to the lack of specificity, sensitivity, and interlaboratory standardization. Here, we present a fully standardized, highly sensitive, robust microflow immuno-MRM (iMRM) assay that enables precise quantitation of PTEN concentrations in cells and fresh frozen (FF) and formalin-fixed paraffin-embedded (FFPE) tissues, down to 0.1 fmol/10 μg of extracted protein, with high interday and intraday precision (CV 6.3%). PTEN protein levels in BC PDX samples that were determined by iMRM correlate well with semiquantitative IHC and WB data. iMRM, however, allowed the precise quantitation of PTEN-even in samples that were deemed to be PTEN negative by IHC or western blot (WB)-while requiring substantially less tumor tissue than WB. This is particularly relevant because the extent of PTEN downregulation in tumors has been shown to correlate with severity. Our standardized and robust workflow includes an 11 min microflow LC-MRM analysis on a triple-quadrupole MS and thus provides a much needed tool for the study of PTEN as a potential biomarker for BC.

IntroductionEfforts to bridge the know–do gap have paved the way for development of the field of knowledge translation (KT). KT aims to understand how evidence use can best be promoted and supported through different activities. For dissemination activities, infographics are gaining in popularity as a promising KT tool to reach multiple health research users (eg, health practitioners, patients and families, decision-makers). However, to our knowledge, no study has yet mapped the available evidence on this tool using a systematic method. This scoping review will explore the depth and breadth of evidence on infographics use and its effectiveness in improving research uptake (eg, raising awareness, influencing attitudes, increasing knowledge, informing practice and changing behaviour).Methods and analysisWe will use the scoping review methodological framework first proposed by Arksey and O’Malley (2005), improved by Levac et al, and further refined by the Joanna Briggs Institute (2020). The search will be conducted in MEDLINE, Cumulative Index to Nursing and Allied Health Literature, PsycINFO, Social Science Abstracts, Library and Information Science Abstracts, Education Resources Information Center, Cairn and Google Scholar. We will also search for relevant literature from the reference lists of the included publications. Two independent reviewers will select the studies. All study designs will be eligible for inclusion, with no date or publication status restrictions. The included studies will have evaluated infographics that disseminate health research evidence and target a non-scientific audience. A data extraction form will be developed and used to extract and chart the data, which will then be synthesised to present a descriptive summary of the results.Ethics and disseminationEthics approval is not required. To inform the research and KT communities, various dissemination activities will be developed, including user-friendly KT tools (eg, webinars, fact sheets and infographics), open-access publication and presentations at KT events and conferences.

Trastuzumab is integral to HER2+ cancer treatment, but its therapeutic index is narrowed by the development of resistance. Phosphorylation of the translation initiation factor eIF2α (eIF2α-P) is the nodal point of the integrated stress response, which promotes survival or death in a context-dependent manner. Here, we show an anti-tumor function of the protein kinase PKR and its substrate eIF2α in a mouse HER2+ breast cancer model. The anti-tumor function depends on the transcription factor ATF4, which upregulates the CDK inhibitor P21CIP1 and activates JNK1/2. The PKR/eIF2α-P arm is induced by Trastuzumab in sensitive but not resistant HER2+ breast tumors. Also, eIF2α-P stimulation by the phosphatase inhibitor SAL003 substantially increases Trastuzumab potency in resistant HER2+ breast and gastric tumors. Increased eIF2α-P prognosticates a better response of HER2+ metastatic breast cancer patients to Trastuzumab therapy. Hence, the PKR/eIF2α-P arm antagonizes HER2 tumorigenesis whereas its pharmacological stimulation improves the efficacy of Trastuzumab therapy., The HER2 monoclonal antibody, Trastuzumab, is the current standard treatment for HER2+ cancers but resistance to therapy occurs. Here, the authors show that activation of the PKR/eIF2α-P pathway exhibits anti-tumor effects in HER2+ cancer and is required for the response to Trastuzumab.

The major obstacle in successfully treating triple-negative breast cancer (TNBC) is resistance to cytotoxic chemotherapy, the mainstay of treatment in this disease. Previous preclinical models of chemoresistance in TNBC have suffered from a lack of clinical relevance. Using a single high dose chemotherapy treatment, we developed a novel MDA-MB-436 cell-based model of chemoresistance characterized by a unique and complex morphologic phenotype, which consists of polyploid giant cancer cells giving rise to neuron-like mononuclear daughter cells filled with smaller but functional mitochondria and numerous lipid droplets. This resistant phenotype is associated with metabolic reprogramming with a shift to a greater dependence on fatty acids and oxidative phosphorylation. We validated both the molecular and histologic features of this model in a clinical cohort of primary chemoresistant TNBCs and identified several metabolic vulnerabilities including a dependence on PLIN4, a perilipin coating the observed lipid droplets, expressed both in the TNBC-resistant cells and clinical chemoresistant tumors treated with neoadjuvant doxorubicin-based chemotherapy. These findings thus reveal a novel mechanism of chemotherapy resistance that has therapeutic implications in the treatment of drug-resistant cancer. Implications: These findings underlie the importance of a novel morphologic–metabolic phenotype associated with chemotherapy resistance in TNBC, and bring to light novel therapeutic targets resulting from vulnerabilities in this phenotype, including the expression of PLIN4 essential for stabilizing lipid droplets in resistant cells.

Une couverture universelle des soins de sante en 2030 pour tous les etres humains, du Nord au Sud? Realiser cet objectif de developpement durable aussi ambitieux que necessaire exigera une exceptionnelle volonte politique, mais aussi de solides donnees probantes sur les moyens d’y arriver, notamment sur les interventions de sante mondiale les plus efficaces. Savoir les evaluer est donc un enjeu majeur. On ne peut plus se contenter de mesurer leur efficacite : il nous faut comprendre pourquoi elles l’ont ete (ou pas), comment et dans quelles conditions. Cet ouvrage collectif reunissant 27 auteurs et 12 autrices de differents pays et de disciplines variees a pour but de presenter de maniere claire et accessible, en francais, un florilege d’approches et de methodes avancees en evaluation d’interventions : quantitatives, qualitatives, mixtes, permettant d’etudier l’evaluabilite, la perennite, les processus, la fidelite, l’efficience, l’equite et l’efficacite d’interventions complexes. Chaque methode est presentee dans un chapitre a travers un cas reel pour faciliter la transmission de ces savoirs precieux.

Optimization of pyridine-based noncatalytic site integrase inhibitors (NCINIs) based on compound 2 has led to the discovery of molecules capable of inhibiting virus harboring N124 variants of HIV integrase (IN) while maintaining minimal contribution of enterohepatic recirculation to clearance in rat. Structure-activity relationships at the C6 position established chemical space where the extent of enterohepatic recirculation in the rat is minimized. Desymmetrization of the C4 substituent allowed for potency optimization against virus having the N124 variant of integrase. Combination of these lessons led to the discovery of compound 20, having balanced serum-shifted antiviral potency and minimized excretion in to the biliary tract in rat, potentially representing a clinically viable starting point for a new treatment option for individuals infected with HIV.

Triple negative breast cancer (TNBC) is the most aggressive form of breast cancer, with prognosis tightly dependent on its responsiveness to cytotoxic chemotherapy. Indeed, overcoming chemoresistance is a major unmet need in this disease. Patient derived xenografts (PDXs) are now widely used in research since they faithfully represent the patient's tumor. However, testing novel drug combinations is a challenge in these models since it is time consuming and quite expensive to test each novel combination. The development of conditionally reprogrammed cells (CRCs) offers the opportunity to perform high throughput screens on clinically relevant models in a more timely and less expensive manner. To this end, we developed a 7 CRCs from PDXs of drug-resistant TNBC tumors. We characterized these CRCs at the molecular level and validated drug resistance to confirm they matched treatment response in both clinical and PDX tumors from which they were derived. These CRCs underwent high-throughput screens of both compound and shRNA libraries of genes targeted by FDA-approved drugs to identify novel drug combinations as well as genetic vulnerabilities that could re-sensitize these cells to carboplatin or paclitaxel chemotherapy. We found that drugs such as mitomycin C and oxfendazole were putative chemo-sensitizers while genes such as ATR and CDK2 were identified as novel genetic vulnerabilities. Treatment of these drug-resistant cells with combinations of carboplatin with mitomycin C or with an ATR inhibitor resulted in synergistic growth inhibition in proliferation and colony formation assays. We are further validating these combinations in organoid models derived from PDXs. These results have the potential to lead to novel therapeutic strategies against chemoresistant TNBCs. Citation Format: Adriana Aguilar-Mahecha, Catherine Chabot, Nancy Santos-Martinez, Cedric Darini, Midhet Hajira, Tim Kong, Genevieve Morin, Sidong Huang, Morag Park, Mark Basik. The use of conditionally reprogrammed cells for high throughput screening for novel drug combinations to treat drug resistant triple negative breast cancers [abstract]. In: Proceedings of the Annual Meeting of the American Association for Cancer Research 2020; 2020 Apr 27-28 and Jun 22-24. Philadelphia (PA): AACR; Cancer Res 2020;80(16 Suppl):Abstract nr 4108.

The treatment of breast cancer has benefitted tremendously from the generation of estrogen receptor-α (ERα)–targeted therapies, but disease relapse continues to pose a challenge due to intrinsic or acquired drug resistance. In an effort to delineate potential predictive biomarkers of therapy responsiveness, multiple groups have identified several uncharacterized cofactors and interacting partners of ERα, including Split Ends (SPEN), a transcriptional corepressor. Here, we demonstrate a role for SPEN in ERα-expressing breast cancers. SPEN nonsense mutations were detectable in the ERα-expressing breast cancer cell line T47D and corresponded to undetectable protein levels. Further analysis of 101 primary breast tumors revealed that 23% displayed loss of heterozygosity at the SPEN locus and that 3% to 4% harbored somatically acquired mutations. A combination of in vitro and in vivo functional assays with microarray-based pathway analyses showed that SPEN functions as a tumor suppressor to regulate cell proliferation, tumor growth, and survival. We also found that SPEN binds ERα in a ligand-independent manner and negatively regulates the transcription of ERα targets. Moreover, we demonstrate that SPEN overexpression sensitizes hormone receptor–positive breast cancer cells to the apoptotic effects of tamoxifen, but has no effect on responsiveness to fulvestrant. Consistent with these findings, two independent datasets revealed that high SPEN protein and RNA expression in ERα-positive breast tumors predicted favorable outcome in patients treated with tamoxifen alone. Together, our data suggest that SPEN is a novel tumor-suppressor gene that may be clinically useful as a predictive biomarker of tamoxifen response in ERα-positive breast cancers. Cancer Res; 75(20); 4351–63. ©2015 AACR.

Background The primary cilium is a microtubule-based and nonmotile organelle functioning as a cellular antenna that is involved in the regulation of cell proliferation, differentiation, and migration. In breast cancer cells, the primary cilium is a structure that decreases in incidence with increasing degrees of transformation and may be biologically more important in estrogen receptor (ERα)-negative breast cancer cells. Split ends (SPEN) is an ERα corepressor that we have identified as a tumor suppressor protein in ERα-positive breast cancer cells whose hormone-independent roles in breast cancer have never been explored. Methods We determined the hormone-independent transcriptional program regulated by the ERα cofactor SPEN in breast cancer using DNA microarrays. The biological functions regulated by SPEN independently of hormones were studied in vitro in ERα-positive and ERα-negative breast cancer cells. Finally, we examined the clinical relevance of SPEN expression in cohorts of breast cancer samples with outcome data. Results We found that SPEN is coexpressed with a number of genes involved in ciliary biology, including the ciliogenic transcription factor RFX3, in a hormone-independent manner. SPEN reexpression in T47D cells containing a nonsense mutation in SPEN restored the primary cilium, whereas its knockdown in MCF10A and Hs578T cells considerably decreased primary cilia levels. We also report that SPEN regulates migration in breast cells, but only in those harboring primary cilia, and that KIF3A silencing, a critical factor in primary cilia, partially reverses SPEN’s effects, suggesting that SPEN may coordinate cellular movement through primary cilia-dependent mechanisms. Finally, we found that high SPEN RNA levels were predictive of early metastasis in two independent cohorts of 77 (HR 2.25, P = 0.03) and 170 (HR = 2.23, P = 0.004) patients with ERα-negative breast cancer. Conclusions Together, our data demonstrate a role for SPEN in the regulation of primary cilia formation and cell migration in breast cancer cells, which may collectively explain why its expression is associated with time to metastasis in cohorts of patients with ERα-negative breast cancers. Electronic supplementary material The online version of this article (doi:10.1186/s13058-017-0897-3) contains supplementary material, which is available to authorized users.

A scaffold replacement approach was used to identifying the pyridine series of noncatalytic site integrase inhibitors. These molecules bind with higher affinity to a tetrameric form compared to a dimeric form of integrase. Optimization of the C6 and C4 positions revealed that viruses harboring T124 or A124 amino acid substitutions are highly susceptible to these inhibitors, but viruses having the N124 amino acid substitution are about 100-fold less susceptible. Compound 20 had EC50 values10 nM against viruses having T124 or A124 substitutions in IN and800 nM in viruses having N124 substitions. Compound 20 had an excellent in vitro ADME profile and demonstrated reduced contribution of biliary excretion to in vivo clearance compared to BI 224436, the lead compound from the quinoline series of NCINIs.

An assay recapitulating the 3' processing activity of HIV-1 integrase (IN) was used to screen the Boehringer Ingelheim compound collection. Hit-to-lead and lead optimization beginning with compound 1 established the importance of the C3 and C4 substituent to antiviral potency against viruses with different aa124/aa125 variants of IN. The importance of the C7 position on the serum shifted potency was established. Introduction of a quinoline substituent at the C4 position provided a balance of potency and metabolic stability. Combination of these findings ultimately led to the discovery of compound 26 (BI 224436), the first NCINI to advance into a phase Ia clinical trial.

Great advances in analytical technology coupled with accelerated new drug development and growing understanding of biological challenges, such as tumor heterogeneity, have required a change in the focus for biobanking. Most current banks contain samples of primary tumors, but linking molecular signatures to therapeutic questions requires serial biopsies in the setting of metastatic disease, next-generation of biobanking. Furthermore, an integration of multidimensional analysis of various molecular components, that is, RNA, DNA, methylome, microRNAome and post-translational modifications of the proteome, is necessary for a comprehensive view of a tumor's biology. While data using such biopsies are now regularly presented, the preanalytical variables in tissue procurement and processing in multicenter studies are seldom detailed and therefore are difficult to duplicate or standardize across sites and across studies. In the context of a biopsy-driven clinical trial, we generated a detailed protocol that includes morphological evaluation and isolation of high-quality nucleic acids from small needle core biopsies obtained from liver metastases. The protocol supports stable shipping of samples to a central laboratory, where biopsies are subsequently embedded in support media. Designated pathologists must evaluate all biopsies for tumor content and macrodissection can be performed if necessary to meet our criteria of >60% neoplastic cells and

DEP-1/CD148 is a receptor-like protein tyrosine phosphatase with antiproliferative and tumor-suppressive functions. Interestingly, it also positively regulates Src family kinases in hematopoietic and endothelial cells, where we showed it promotes VE-cadherin–associated Src activation and endothelial cell survival upon VEGF stimulation. However, the molecular mechanism involved and its biologic functions in endothelial cells remain ill-defined. We demonstrate here that DEP-1 is phosphorylated in a Src- and Fyn-dependent manner on Y1311 and Y1320, which bind the Src SH2 domain. This allows DEP-1–catalyzed dephosphorylation of Src inhibitory Y529 and favors the VEGF-induced phosphorylation of Src substrates VE-cadherin and Cortactin. Accordingly, RNA interference (RNAi)–mediated knockdown of DEP-1 or expression of DEP-1 Y1311F/Y1320F impairs Src-dependent biologic responses mediated by VEGF including permeability, invasion, and branching capillary formation. In addition, our work further reveals that above a threshold expression level, DEP-1 can also dephosphorylate Src Y418 and attenuate downstream signaling and biologic responses, consistent with the quiescent behavior of confluent endothelial cells that express the highest levels of endogenous DEP-1. Collectively, our findings identify the VEGF-dependent phosphorylation of DEP-1 as a novel mechanism controlling Src activation, and show this is essential for the proper regulation of permeability and the promotion of the angiogenic response.

Tumor-suppressor genes (TSGs) have been classically defined as genes whose loss of function in tumor cells contributes to the formation and/or maintenance of the tumor phenotype. TSGs containing nonsense mutations may not be expressed because of nonsense-mediated RNA decay (NMD). We combined inhibition of the NMD process, which clears transcripts that contain nonsense mutations, with the application of high-density single-nucleotide polymorphism arrays analysis to discriminate allelic content in order to identify candidate TSGs in five breast cancer cell lines. We identified ARID1A as a target of NMD in the T47D breast cancer cell line, likely as a consequence of a mutation in exon-9, which introduces a premature stop codon at position Q944. ARID1A encodes a human homolog of yeast SWI1, which is an integral member of the hSWI/SNF complex, an ATP-dependent, chromatin-remodeling, multiple-subunit enzyme. Although we did not find any somatic mutations in 11 breast tumors, which show DNA copy-number loss at the 1p36 locus adjacent to ARID1A, we show that low ARID1A RNA or nuclear protein expression is associated with more aggressive breast cancer phenotypes, such as high tumor grade, in two independent cohorts of over 200 human breast cancer cases each. We also found that low ARID1A nuclear expression becomes more prevalent during the later stages of breast tumor progression. Finally, we found that ARID1A re-expression in the T47D cell line results in significant inhibition of colony formation in soft agar. These results suggest that ARID1A may be a candidate TSG in breast cancer.

The use of patient derived models for pre-clinical drug testing provides a unique opportunity for testing non-conventional therapies and novel drug combinations to overcome drug resistance in cancer. We have established 22 models from breast cancer, 20 PDXs were engrafted in house and two were generated from live tissue obtained from PDXs established in a partner lab. The overall engraftment rate in house was of 24%. Engraftment varied according to BC subtype: 38% (3/8) for ER-HER2+ and 33% (17/51) for TNBC. No PDXs could be generated from ER+PR+Her2- tumors (0/13) or ER+HER2+ breast cancers (0/11). Post-chemotherapy drug resistant tumors engrafted with better success (18/55) compared to non-treated tumors (2/28). In 3 patients, we established PDX models with tissues collected at different anatomical sites, enabling the study of tumor heterogeneity. For one patient, 2 PDX models were established from serial samples after different lines of chemotherapy. Molecular profiling at the copy number and mutation level has confirmed the molecular stability of our models over engraftment passages. Drug studies were performed to validate clinical drug response and models were also treated with unconventional drugs and drug combinations to overcome drug resistance. Drugs that resulted in significant tumor regression in drug resistant TNBC models included irinotecan as well as olaparib in combination with an angiogenesis inhibitor. We successfully established one PDX model from a recurrent Her2+ gastric tumor resistant to trastuzumab. In this model, treatment with T-DM1 alone as well as with pertuzumab/trastuzumab resulted in complete tumor regression, while everolimus significantly inhibited tumor growth. This PDX study provided an alternative clinical management for the patient who subsequently received T-DM1 and showed clinical response, validating the results obtained in the PDX model. To develop a more agile model, we also established conditionally reprogrammed cell lines directly from patient tumors or from PDX models. Drug resistant conditionally reprogrammed cells from Her2+ breast cancers harboring a FGFR1 amplification were found to be sensitive to FGFR inhibitors, chloroquine, and a CDK4/6 inhibitor. Correlation of drug responses between conditionally reprogrammed cells and matched PDX models will be presented. These live tumor models enable timely and clinically pertinent drug testing, which has the potential to expand the known therapeutic arsenal as well as provide truly personalized therapy to cancer patients. Citation Format: Marguerite Buchanan, Catherine Chabot, Josiane Lafleur, Urszula Krzemien, Cathy Lan, Olga Savichtcheva, Jean-François Boileau, Cristiano Ferrario, Paul Savage, Morag Park, Gerald Batist, Adriana Aguilar-Mahecha, Mark Basik. Use of PDXs and patient-derived cell lines to uncover unconventional drug therapies and combinations for the treatment of drug-resistant cancers [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2018; 2018 Apr 14-18; Chicago, IL. Philadelphia (PA): AACR; Cancer Res 2018;78(13 Suppl):Abstract nr 2149.

The dynamic organization of the human genome in the nucleus is gaining recognition as a determining factor in its functional regulation. In order to be expressed, replicated or repaired, a genomic locus has to be present at the right place at the right time. In the present study, we have investigated the choice of a double-strand break (DSB) repair partner for a given genomic loci in an ATM-deficient human fibroblast cell line. We found that partner choice is restricted such that a given genomic locus preferentially uses certain sites in the genome to repair itself. These preferential sites can be in the vicinity of the damage site or megabases away or on other chromosomes entirely, while potential sites closer to the break along the length of the chromosome can be ignored. Moreover, there can be more than a 10-fold difference in usage between repair sites located only 10 kb apart. Interestingly, arms of a given chromosome are less accessible to one another than to other chromosomes. Altogether, these results indicate that the accessibility between genomic sites in the human genome during DSB repair is specific and conserved in a cell population.

DEP-1/PTPRJ is a receptor-like protein tyrosine phosphatase mainly known for its antiproliferative and tumor-suppressive functions. Many identified substrates are growth factor receptors, and DEP-1 is deleted and/or mutated in human cancers including that of the breast. However, DEP-1 was also identified as a promoter of Src activation and proinvasive functions in the endothelium, suggesting it could perhaps mediate breast cancer invasiveness that is likewise driven by Src family kinases. We show here that DEP-1 expression was greater in highly invasive breast cancer cells (MDA-MB-231, Hs578T, BT-549) than in the less invasive or untransformed cell lines tested (MCF-7, T47D, SK-BR3 and MCF10A). DEP-1 silencing experiments in invasive cells demonstrated that moderately expressed and catalytically active DEP-1 was required, in collaboration with basal epidermal growth factor receptor activity, for Src activation and the phosphorylation of its substrate Cortactin, and for their colocalization at the cell’s leading edge. This correlated with an increased number of cell protrusions, and an enhanced capacity of the cells to migrate and invade. Similarly, moderate overexpression of DEP-1 in the low-invasive cells resulted in the promotion of their invasiveness in an Src-dependent manner. Consistent with these data, the expression of endogenous DEP-1 was elevated in a bone metastatic cell line derived from MDA-MB-231 cells, and promoted increased Src Y418 and Cortactin Y421 phosphorylation, as well as pro-MMP9 secretion and Matrigel invasion. Importantly, the silencing of DEP-1 in MDA-MB-231 cells greatly decreased their ability to metastasize, despite having no effect on tumor growth or angiogenesis. Hence, we found that moderate expression of DEP-1 was associated with the increased relapse and decreased survival of breast cancer patients. These results therefore identify a new and unsuspected role for DEP-1 as a mediator of an invasive cell program implicating Src activation and the promotion of breast cancer progression.

The NS3 serine protease enzyme of the hepatitis C virus (HCV) is essential for viral replication. Short peptides mimicking the N-terminal substrate cleavage products of the NS3 protease are known to act as weak inhibitors of the enzyme and have been used as templates for the design of peptidomimetic inhibitors. Automated solid-phase synthesis of a small library of compounds based on such a peptidomimetic scaffold has led to the identification of potent and highly selective inhibitors of the NS3 protease enzyme.

A series of novel monobactam inhibitors of human cytomegalovirus (HCMV) protease has been described that possess a heterocyclic thiomethyl side chain at C-4. Changes to the heterocycle did not significantly change the inhibitory activity of these compounds in an enzymatic assay, although improvements in solubility and cell culture activity were noted. A number of permutations between C-4 substitutions and N-1 derivatives led to the identification of several β-lactams with antiviral activity in a plaque reduction assay. N-methyl thiotetrazole-containing compounds were found to be the most potent inhibitors in the enzymatic assay.

The primary cilium (PC) is a microtubule-based and non-motile organelle that functions as animal cells’ antennae, regulating a number of signalling pathways, including the mTOR, PDGFR and Wnt pathways, in addition to being essential for activation of the canonical Hedgehog (Hh) pathway. In breast cancer, the PC is a structure that is frequently lost due to transcription- and mutation-driven alterations in cilium-related genes. In a study aiming to delineate the hormone-independent transcriptional program regulated by SPEN, a gene that we have identified as a tumour suppressor gene in estrogen receptor (ER)-positive breast cancers, we found that SPEN was co-expressed (R>0.95) with a number of genes involved in ciliary biology (P = 1.64E-19), including the ciliogenic transcription factors RFX2, RFX3 and FOXJ1. Interestingly, the overexpression of SPEN resulted in the restoration of the PC in T47D cells, which have previously been shown to lack this structure. Consistent with the re-establishment of a PC in T47D cells, SPEN-overexpressing T47D cells had decreased mTOR signalling, hyperactivation of PC-dependent pathways, including the Hh and PDGFR pathways, and increased migration. Silencing SPEN expression in the non-tumorigenic MCF10A cells, which express high endogenous levels of SPEN and show a high prevalence of PC (36%), considerably decreased PC levels in MCF10A cells and was accompanied with increased mTORC1 activity as well as attenuated cell migration. We also found that SPEN silencing in MCF10A cells decreased the expression of the ciliogenic transcription factor RFX3 and that SPEN interacts with DNA upstream of RFX3 gene transcription start site in chromatin immunoprecipitation experiments. Collectively, these observations indicate that SPEN may mediate its effects, at least in part, through the transcriptional regulation of RFX3. Accordingly, RFX3 expression levels were strongly positively correlated (R = 0.55, P Citation Format: Stéphanie Légaré, Catherine Chabot, Mark Basik. SPEN stimulates primary cilia formation, cell migration and is associated with metastasis in breast cancer. [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 5055.

In this part 2, new indole 5-carboxamide Thumb Pocket 1 inhibitors of HCV NS5B polymerase are described. Structure-activity relationships (SAR) were explored at the central amino acid linker position and the right-hand-side of the molecule in an attempt to identify molecules with a balanced overall profile of potency (EC(50)100 nM), physicochemical properties and ADME characteristics.

Gab1 was previously described as a positive modulator of Akt, Src, ERK1/2, endothelial cell migration, and capillary formation in response to vascular endothelial growth factor (VEGF). However, its involvement in endothelial cell survival, as well as the potential contribution of the other family member Gab2 to signalling and biological responses remained unknown. Here, we show that Gab2 is tyrosine phosphorylated in a Grb2-dependent manner downstream of activated VEGF receptor-2 (VEGFR2), and that it associates with signalling proteins including PI3K and SHP2, but apparently not with the receptor. Similarly to Gab1, over-expression of Gab2 induces endothelial cell migration in response to VEGF, whereas its depletion using siRNAs results in its reduction. Importantly, depletion of both Gab1 and Gab2 leads to an even greater inhibition of VEGF-induced cell migration. However, contrary to what has been reported for Gab1, the silencing of Gab2 results in increased Src, Akt and ERK1/2 activation, slightly reduced p38 phosphorylation, and up-regulation of Gab1 protein levels. Accordingly, re-expression of Gab2 in Gab2-/- fibroblasts leads to opposite results, suggesting that the modulation of both Gab2 and Gab1 expression in these conditions might contribute to the impaired signalling observed. Consistent with their opposite roles on Akt, the depletion of Gab1, but not of Gab2, results in reduced FOXO1 phosphorylation and VEGF-mediated endothelial cell survival. Mutation of VEGFR2 Y801 and Y1214, which abrogates the phosphorylation of Gab1, also correlates with inhibition of Akt. Altogether, these results underscore the non-redundant and essential roles of Gab1 and Gab2 in endothelial cells, and suggest major contributions of these proteins during in vivo angiogenesis.

Vascular endothelial growth factor (VEGF) is involved in the promotion of endothelial cell proliferation, migration, and capillary formation. These activities are mainly mediated by the VEGFR2 receptor tyrosine kinase that upon stimulation, promotes the activation of numerous proteins including phospholipase Cgamma (PLCgamma), phosphatidylinositol 3-kinase (PI3K), Akt, Src, and ERK1/2. However, the VEGFR2-proximal signaling events leading to the activation of these targets remain ill defined. We have identified the Gab1 adapter as a novel tyrosine-phosphorylated protein in VEGF-stimulated cells. In bovine aortic endothelial cells, Gab1 associates with VEGFR2, Grb2, PI3K, SHP2, Shc, and PLCgamma, and its overexpression enhances VEGF-dependent cell migration. Importantly, silencing of Gab1 using small interfering RNAs leads to the impaired activation of PLCgamma, ERK1/2, Src, and Akt; blocks VEGF-induced endothelial cell migration; and perturbs actin reorganization and capillary formation. In addition, co-expression of VEGFR2 with Gab1 mutants unable to bind SHP2 or PI3K in human embryonic kidney 293 cells and bovine aortic endothelial cells mimics the defects observed in Gab1-depleted cells. Our work thus identifies Gab1 as a novel critical regulatory component of endothelial cell migration and capillary formation and reveals its key role in the activation of VEGF-evoked signaling pathways required for angiogenesis.

Combinations of direct acting antivirals (DAAs) that have the potential to suppress emergence of resistant virus and that can be used in interferon-sparing regimens represent a preferred option for the treatment of chronic HCV infection. We have discovered allosteric (thumb pocket 1) non-nucleoside inhibitors of HCV NS5B polymerase that inhibit replication in replicon systems. Herein, we report the late-stage optimization of indole-based inhibitors, which began with the identification of a metabolic liability common to many previously reported inhibitors in this series. By use of parallel synthesis techniques, a sparse matrix of inhibitors was generated that provided a collection of inhibitors satisfying potency criteria and displaying improved in vitro ADME profiles. "Cassette" screening for oral absorption in rat provided a short list of potential development candidates. Further evaluation led to the discovery of the first thumb pocket 1 NS5B inhibitor (BILB 1941) that demonstrated antiviral activity in patients chronically infected with genotype 1 HCV.

The crystallization and subsequent crystal treatment of both free human cytomegalovirus (hCMV) protease and its inhibitor complexes are reported. For free-enzyme crystals, diffraction was greatly improved by optimizing the crystallization conditions, raising the precipitant concentration in the reservoir and soaking the crystals in artificial mother liquors. Each of the six components in the final crystallization formula (16% PEG 4000, 0.1 M MES pH 6.0, 0.4 M LiCl, 10% glycerol, 5% t-butanol and 5 mM Na(2)S(2)O(3)) plays a distinctive role and is indispensable. A synergistic effect of Na(2)SO(4) and t--butanol on diffraction was observed and studied. A 2.0 A multiwavelength anomalous diffraction (MAD) data set was collected using a synchrotron-radiation source, leading to the elucidation of the three-dimensional structure of the enzyme. For the inhibitor-complex crystals, initial attempts with co-crystallization and soaking experiments at pH 6.0 did not produce conclusive results. Subsequently, experiments were designed to co-crystallize the complex at pH 8.0, the optimal pH for the enzyme and the inhibitor activity. Using 20-50 mM spermine in the crystallization buffer, crystals of two peptidomimetic inhibitor complexes were obtained at pH 7.5 and 8.0. Spermine was required for the inhibitor complexes to be crystallized at pH 8.0, possibly neutralizing net negative charges of hCMV protease owing to its acidic pI of 5.5. A 2.7 A data set was collected from one of the inhibitor complexes and the structure was determined using the molecular-replacement method.

The development of novel monobactam inhibitors of HCMV protease incorporating a carbon side chain at C-4 and a urea function at N-1 is described. Substitution with small groups at the C-3 position of the beta-lactam ring gave an increase in enzymatic activity and in stability; however, a lack of selectivity against other serine proteases was noted. The use of both tri- and tetrasubstituted urea functionalities gave effective inhibitors of HCMV protease. Benzyl substitution of the urea moiety was beneficial, especially when strong electron-withdrawing groups where attached at the para position. Modest antiviral activity was found in a plaque reduction assay.

The development of peptidomimetic inhibitors of the human cytomegalovirus (HCMV) protease showing sub-micromolar potency in an enzymatic assay is described. Selective substitution of the amino acid residues of these inhibitors led to the identification of tripeptide inhibitors showing improvements in inhibitor potency of 27-fold relative to inhibitor 39 based upon the natural tetrapeptide sequence. Small side chains at P1 were well tolerated by this enzyme, a fact consistent with previous observations. The S2 binding pocket of HCMV protease was very permissive, tolerating lipophilic and basic residues. The substitutions tried at P3 indicated that a small increase in inhibitor potency could be realized by the substitution of a tert-leucine residue for valine. Substitutions of the N-terminal capping group did not significantly affect inhibitor potency. Pentafluoroethyl ketones, alpha,alpha-difluoro-beta-keto amides, phosphonates and alpha-keto amides were all effective substitutions for the activated carbonyl component and gave inhibitors which were selective for HCMV protease. A slight increase in potency was observed by lengthening the P1' residue of the alpha-keto amide series of inhibitors. This position also tolerated a variety of groups making this a potential site for future modifications which could modulate the physicochemical properties of these molecules.

The majority of breast cancers are hormone-responsive and are treated with anti-estrogens, such as tamoxifen. However, most of the 30 and 50% of estrogen receptor positive (ER+) patients that initially respond to tamoxifen eventually become resistant to the drug. Although there are several mechanisms responsible for resistance of breast cancers to tamoxifen, no predictive biomarkers for tamoxifen resistance are in clinical use besides the estrogen receptor (ER) and the progesterone receptors (PR). Using a novel integrative genomic method based on the discovery of nonsense mutations in deleted chromosomal fragments, we identified a nonsense mutation in the SPEN gene in the T47D breast cancer cell line. SPEN is a transcriptional repressor of the estrogen-signaling pathway, which is recruited to estrogen-responsive elements upon activation of the ER. We found 4 somatic mutations (2 nonsense and 2 missense) in 23 breast tumors showing loss of heterozygosity at the SPEN locus. Moreover, tissue microarrays showed that SPEN was frequently over-expressed in the nucleus of normal breast epithelial cells, but in only 10% of breast tumor cells, suggesting that inactivation of SPEN in breast cancer contributes to disease progression. In vitro, overexpression of SPEN in the T47D breast cancer cell line, in which SPEN is mutated and endogenous levels of the protein are very low, resulted in significantly decreased cell proliferation and anchorage-independent growth, decreased PR expression as well as increased sensitivity to tamoxifen. Remarkably, tamoxifen treatment induced 5-fold higher levels of apoptosis in SPEN-overexpressing compared to control T47D cells. In addition, using a tissue microarray of 100 tumor samples from ER+ breast cancer patients treated with tamoxifen only, we found that patients whose tumors express high levels of SPEN had a much better prognosis than patients whose tumors express low or no levels of the protein. To identify transcriptional targets of SPEN besides the PR, we performed gene expression profiling on a panel of breast cancer cell lines in which SPEN was either overexpressed or knocked-down. We found an inverse relationship between SPEN and Apolipoprotein D (APOD) expression, suggesting that SPEN potently repressed transcription of the APOD gene. APOD encodes a glycoprotein from the lipocalin family, which can chelate multiple molecules including progesterone, arachidonic acid as well as tamoxifen itself. Hence, our analysis shows that the loss or mutation of SPEN in ER+ breast cancers has the potential to affect tumor growth as well as sensitivity to tamoxifen, in part through upregulation of APOD expression. Together, our results highlight the role of SPEN as a novel putative tumor suppressor gene in breast cancer and suggest that SPEN is a candidate predictive biomarker of tamoxifen resistance in ER+ breast cancer patients. Citation Format: Stéphanie Légaré, Luca Cavallone, Aline Mamo, Catherine Chabot, Dana Keilty, Anthony Magliocco, Alexander Klimowicz, Patricia Tonin, Mark Basik. SPEN is a novel candidate tumor suppressor gene that regulates response to tamoxifen in estrogen receptor positive breast cancers. [abstract]. In: Proceedings of the 104th Annual Meeting of the American Association for Cancer Research; 2013 Apr 6-10; Washington, DC. Philadelphia (PA): AACR; Cancer Res 2013;73(8 Suppl):Abstract nr LB-47. doi:10.1158/1538-7445.AM2013-LB-47

Approximately 15-20% of all invasive breast carcinomas overexpress the HER-2 receptor, a membrane surface-bound receptor tyrosine kinase upstream of critical proliferation and cell survival pathways. Trastuzumab, a humanized monoclonal antibody to the extracellular domain of HER-2, has proven to be a beneficial treatment for patients diagnosed as HER-2+, but does have its limitations. A majority of advanced HER-2 positive breast cancer patients will develop resistance to the therapy within the first year while many others do not respond to the drug when used alone. The purpose of this study was to determine whether AZD8931, a reversible pan-ERBB inhibitor that equipotently inhibits the tyrosine kinase-activity of EGFR, HER-2, and HER-3, could reverse this resistance in established trastuzumab-resistant BT474 and SKBR3 cell lines. To account for tumor heterogeneity in HER-2+ tumors, response to AZD8931 was examined in both ER-positive (BT474) and ER-negative (SKBR3) cell lines. Proliferation assays were used to assess the efficacy of AZD8931 alone and in combination with trastuzumab. Results showed significantly diminished cell growth in all tested cell lines, including those resistant to trastuzumab, at clinically relevant concentrations of AZD8931 ( Citation Format: {Authors}. {Abstract title} [abstract]. In: Proceedings of the 103rd Annual Meeting of the American Association for Cancer Research; 2012 Mar 31-Apr 4; Chicago, IL. Philadelphia (PA): AACR; Cancer Res 2012;72(8 Suppl):Abstract nr 770. doi:1538-7445.AM2012-770

Tumor suppressor genes (TSGs) have been classically defined as genes whose loss of function in tumor cells contributes to the formation and/or maintenance of the tumor phenotype. Typically but not always, tumors neutralize both alleles of TSGs by deleting one copy and mutating the other. One molecular strategy to discover potential tumor suppressor gene candidates involves the “re-expression” of RNA transcripts containing nonsense mutations by inhibition of the nonsense-mediated RNA decay (NMD) process. Combining NMD inhibition with array CGH has lead to the genome-wide identification of genes with biallelic inactivation (involving nonsense mutations on one allele and loss of the second allele) in prostate cancer cell lines and identified EphB2 as a novel candidate TSG in prostate cancer. Using such a strategy in 5 breast cancer cell lines, we identified ARID1A as a NMD target in the T47D breast cancer cell line. ARID1A encodes a human homologue of yeast SWI1, which contains a DNA-binding motif (AT-rich interactive domain, ARID) and is an integral member of the hSWI/SNF complex, an ATP-dependent chromatin-remodeling multiple-subunit enzyme. Mutations in the ARID1A gene were recently reported to be present in 50% of clear cell tumors of the ovary. We found the ARID1A gene contains a nonsense mutation in exon 9, which introduces a premature stop codon, changing Q944 to a stop codon in the T47D breast cancer cell line. Although we did not find any somatic mutations in breast tumors, we show that low ARID1A RNA expression or low ARID1A nuclear protein expression is associated with more aggressive breast cancer phenotypes in 2 independent cohorts of over 200 breast cancers each. We also found that low or absent ARID1A nuclear expression becomes more prevalent during the later stages of breast tumor progression. Finally, we found that ARID1A re-expression in the breast cancer cell line in which it is mutated results in significant inhibition of colony formation in soft agar. These results suggest that the ARID1A gene may be a candidate tumor suppressor gene in breast cancer, and that it warrants further investigation as potential diagnostic and therapeutic marker in breast cancer. Citation Format: {Authors}. {Abstract title} [abstract]. In: Proceedings of the 102nd Annual Meeting of the American Association for Cancer Research; 2011 Apr 2-6; Orlando, FL. Philadelphia (PA): AACR; Cancer Res 2011;71(8 Suppl):Abstract nr 4023. doi:10.1158/1538-7445.AM2011-4023

The radical reductions and allylations of a series of a-halo-P-alkoxy esters under bidentate chelation-controlled conditions are reported and compared with the analogous reactions under non-chelating conditions. The addition of Lewis acids is shown to give excellent selectivity for the syn products in the case of reduction, and the anti products in the case of allylation. In some cases, ratios greater than 1OO:l are obtained. The reactions require initiation with EbB and can be inhibited by m- and p-dinitrobenzene, which imply a radical-based mechanism. Iodides, bromides and phenyl selenides are all suitable substrates. Investigations also provide a rationale for the large excess of MgBr2.OEt2 which is apparently required in these reactions. Competition experiments provide a more detailed explanation of substrate reactivity. Traditionally radicals derived from acyclic precursors have seldom been considered as intermediates for the generation of asymmetric centers. Recently however, it has been discovered that radicals can indeed react with high levels of diastereoselectivity (1). This has been achieved mainly through the use of chiral auxiliaries (2) or by the influence of a stereogenic center adjacent to a carbonyl (1,2-asymmetric induction) (3,4, 5). The scope of these reactions has also been expanded by the use of Lewis acids (6, 7), solvent complexation (8) and intramolecular hydrogen bonding (9) to enhance and even reverse the facial bias. In this paper, we describe results we have obtained in chelation-controlled reductions, allylations and atom transfer reactions of a-halo-P-alkoxy esters, and present evidence for radical-based processes. Preliminary experiments designed to elucidate further mechanistic details will also be discussed. Scheme 1 X Ph -. *Et