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PDF file - 51KB, Supplementary Table S4a lists gene sets enriched in TBK1-II treated HER2+ breast cancer cells.

PDF file - 753KB, Supplementary Figure S5 shows representative images of HCC1954 and SKBR3 HER2+ BC cells transduced with indicated lenti-shRNA against human Tbk1 or lenti-GFP.

PDF file - 47KB, Supplementary Table S2a and S2b list hits on Her2/Neu spheres and monolayer cells.

PDF file - 48KB, Supplementary Table S3 lists hits on Her2/Neu monolayer cells only.

PDF file - 131KB, Supplementary Figure S4 shows the effect of autophagy inhibitors CQ and 5-MA on proliferation and survival of HER2+ mouse and human breast cancer cell lines.

PDF file - 55KB, Supplementary Figure S3 shows expression of kinase hits in primary and secondary Her2/Neu tumor cells from RNA profiling analysis.

PDF file - 67KB, Supplementary Figure S2 shows results from the primary and validation screens with hits on sphere only or both sphere and monolayer, as well as sensitivity of HC11 cells.

PDF file - 93KB

HER2+ breast cancer is currently treated with chemotherapy plus anti-HER2 inhibitors. Many patients do not respond or relapse with aggressive metastatic disease. Therefore, there is an urgent need for new therapeutics that can target HER2+ breast cancer and potentiate the effect of anti-HER2 inhibitors, in particular those that can target tumor-initiating cells (TIC). Here, we show that MMTV-Her2/Neu mammary tumor cells cultured as nonadherent spheres or as adherent monolayer cells select for stabilizing mutations in p53 that “immortalize” the cultures and that, after serial passages, sphere conditions maintain TICs, whereas monolayer cells gradually lose these tumorigenic cells. Using tumorsphere formation as surrogate for TICs, we screened p53-mutant Her2/Neu+ tumorsphere versus monolayer cells with a lentivirus short hairpin RNA kinome library. We identified kinases such as the mitogen-activated protein kinase and the TGFβR protein family, previously implicated in HER2+ breast cancer, as well as autophagy factor ATG1/ULK1 and the noncanonical IκB kinase (IKK), TANK-binding kinase 1 (TBK1), which have not been previously linked to HER2+ breast cancer. Knockdown of TBK1 or pharmacologic inhibition of TBK1 and the related protein, IKKϵ, suppressed growth of both mouse and human HER2+ breast cancer cells. TBK1/IKKϵ inhibition promoted cellular senescence by suppressing p65–NF-κB and inducing p16Ink4a. In addition, TBK1/IKKϵ inhibition cooperated with lapatinib, a HER2/EGFR1–targeted drug, to accelerate apoptosis and kill HER2+ breast cancer cells both in culture and in xenografts. Our results suggest that patients with HER2+ breast cancer may benefit from anti-TBK1/IKKϵ plus anti-HER2 combination therapies and establish conditions that can be used to screen for additional TIC-specific inhibitors of HER2+ breast cancer. Cancer Res; 74(7); 2119–30. ©2014 AACR.

PDF file - 43KB, Supplementary Table S1 lists hits on Her2/Neu spheres only.

PDF file - 51KB, Supplementary Figure S1 summarizes the primary screens including number of shRNAs/kinases tested, and number of hits on Her2+ tumorspheres only, tumorsphere plus monolayer or monolayer only.

PDF file - 45KB, Supplementary Figure S7 shows the molecular structure and pharmacokinetic of TBK1-II In NOD/SCID mice.

PDF file - 66KB, Supplementary Figure S6 shows IC50 values of indicated drugs on Her2/Neu-monolayer, SKBR3, HCC1954 or JIMT1 cells.

Pineoblastoma is a rare pediatric cancer induced by germline mutations in the tumor suppressors RB1 or DICER1. Presence of leptomeningeal metastases is indicative of poor prognosis. Here we report that inactivation of Rb plus p53 via a WAP-Cre transgene, commonly used to target the mammary gland during pregnancy, induces metastatic pineoblastoma resembling the human disease with 100% penetrance. A stabilizing mutation rather than deletion of p53 accelerates metastatic dissemination. Deletion of Dicer1 plus p53 via WAP-Cre also predisposes to pineoblastoma, albeit with lower penetrance. In silico analysis predicts tricyclic antidepressants such as nortriptyline as potential therapeutics for both pineoblastoma models. Nortriptyline disrupts the lysosome, leading to accumulation of non-functional autophagosome, cathepsin B release and pineoblastoma cell death. Nortriptyline further synergizes with the antineoplastic drug gemcitabine to effectively suppress pineoblastoma in our preclinical models, offering new modality for this lethal childhood malignancy., Pineoblastoma is a rare pediatric cancer. Here, the authors present inactivation of Rb plus p53 via a WAP-Cre transgene induces metastatic pineoblastoma resembling human disease, and using this model, predict tricyclic antidepressants as a potential therapy for pineoblastoma, supported by their pre-clinical model.

Breast cancer is the most common malignancy among women worldwide. As conventional therapies are only partially successful in eradicating breast cancer, the development of novel strategies is a top priority. We previously showed that C25, a new racemosin B derivative, exerts its anti-cancer activity through inhibition of autophagy, but the underlying mechanism remained unknown. Here we show that C25 inhibits the growth of diverse breast cancer cell subtypes and effectively suppresses tumor progression in a xenotransplantation model of triple negative breast cancer. C25 acts as a lysosomotropic agent to induce lysosomal membrane permeabilization and inhibit autophagic flux, resulting in cathepsin release and cell death. In accordance, RNA sequencing and gene set enrichment analysis revealed that C25 induces pathways consistent with autophagy inhibition, cell cycle arrest and senescence. Interestingly, knockdown of TFEB or SQSTM1 reduced cell death induced by C25 treatment. Finally, we show that C25 synergizes with the chemo-therapeutics etoposide and paclitaxel to further limit breast cancer cell growth. Thus, C25 alone or in combination with other anti-neoplastic agents offers a novel therapeutic strategy for aggressive forms of breast cancer and possibly other malignancies.

SUMMARY CDH1 and PIK3CA are the two most frequently mutated genes in invasive lobular carcinoma (ILC) of the breast. Transcription profiling has identified molecular subtypes for ILC, one of which, immune-related (IR), is associated with gene expression linked to lymphocyte and macrophage infiltration. Here, we report that deletion of Cdh1, together with activation of Pik3ca in mammary epithelium of genetically modified mice, leads to formation of IR-ILC-like tumors with immune cell infiltration, as well as gene expression linked to T-regulatory (Treg) cell signaling and activation of targetable immune checkpoint pathways. Interestingly, these tumors show enhanced Rac1-and Yap-dependent transcription and signaling, as well as sensitivity to PI3K, Rac1, and Yap inhibitors in culture. Finally, high-dimensional immunophenotyping in control mouse mammary gland and IR-ILC tumors by mass cytometry shows dramatic alterations in myeloid and lymphoid populations associated with immune suppression and exhaustion, highlighting the potential for therapeutic intervention via immune checkpoint regulators., Graphical Abstract, In Brief An et al. describe the development and characterization of a mouse model for invasive lobular carcinoma (ILC) of the breast based on the two most mutated genes in human ILC. This model is analogous to immune-related ILC, shows myeloid and T cell alterations consistent with immune suppression and exhaustion, and represents a platform for therapeutics.

Carbazole derivatives show anti-cancer activity and are of great interest for drug development. In this study, we synthesized and analyzed several new alkylamide derivatives of racemocin B, a natural indolo[3,2-a]carbazole molecule originally isolated from the green alga Caulerpa racemose. Several alkylamide derivatives were found to exhibit moderate to strong growth inhibition against human breast cancer cell lines. They induced G2/M cell cycle arrest and apoptosis in the aggressive triple-negative breast cancer cell line MDA-MB-231. Among these derivatives, compound 25 with the lowest IC50 induced cell death by suppressing autophagy. This was accompanied by inhibition of autophagic flux and accumulation of autophagy protein 1 light chain 3, LC3II, and p62. The novel alkylamide derivative offers a potential new treatment for human breast cancer.

A switch from catabolic to anabolic metabolism, a major hallmark of cancer, enables rapid cell duplication, and is driven by multiple oncogenic alterations, including PIK3CA mutation, MYC amplification, and TP53 loss. However, tumor growth requires active mitochondrial function and oxidative phosphorylation (OXPHOS). Recently, loss of the retinoblastoma (RB1) tumor suppressor in breast cancer was shown to induce mitochondrial protein translation (MPT) and OXPHOS. Here, we discuss how increased OXPHOS can enhance anabolic metabolism and cell proliferation, as well as cancer stemness and metastasis. Mitochondrial STAT3, FER/FER-T, and CHCHD2 are also implicated in OXPHOS. We propose that RB1 loss represents a prototypic oncogenic alteration that promotes OXPHOS, that aggressive tumors acquire lethal combinations of oncogenes and tumor suppressors that stimulate anabolism versus OXPHOS, and that targeting both metabolic pathways would be therapeutic.

HER2+ breast cancer is currently treated with chemotherapy plus anti-HER2 inhibitors. Many patients do not respond or relapse with aggressive metastatic disease. Therefore, there is an urgent need for new therapeutics that can target HER2+ breast cancer and potentiate the effect of anti-HER2 inhibitors, in particular those that can target tumor-initiating cells (TIC). Here, we show that MMTV-Her2/Neu mammary tumor cells cultured as nonadherent spheres or as adherent monolayer cells select for stabilizing mutations in p53 that “immortalize” the cultures and that, after serial passages, sphere conditions maintain TICs, whereas monolayer cells gradually lose these tumorigenic cells. Using tumorsphere formation as surrogate for TICs, we screened p53-mutant Her2/Neu+ tumorsphere versus monolayer cells with a lentivirus short hairpin RNA kinome library. We identified kinases such as the mitogen-activated protein kinase and the TGFβR protein family, previously implicated in HER2+ breast cancer, as well as autophagy factor ATG1/ULK1 and the noncanonical IκB kinase (IKK), TANK-binding kinase 1 (TBK1), which have not been previously linked to HER2+ breast cancer. Knockdown of TBK1 or pharmacologic inhibition of TBK1 and the related protein, IKKϵ, suppressed growth of both mouse and human HER2+ breast cancer cells. TBK1/IKKϵ inhibition promoted cellular senescence by suppressing p65–NF-κB and inducing p16Ink4a. In addition, TBK1/IKKϵ inhibition cooperated with lapatinib, a HER2/EGFR1–targeted drug, to accelerate apoptosis and kill HER2+ breast cancer cells both in culture and in xenografts. Our results suggest that patients with HER2+ breast cancer may benefit from anti-TBK1/IKKϵ plus anti-HER2 combination therapies and establish conditions that can be used to screen for additional TIC-specific inhibitors of HER2+ breast cancer. Cancer Res; 74(7); 2119–30. ©2014 AACR.

Triple-negative breast cancer (TNBC) is a heterogeneous disease that includes Basal-like and Claudin-low tumors. The Claudin-low tumors are enriched for features associated with epithelial-to-mesenchymal transition (EMT) and possibly for tumor initiating cells. Primary TNBCs respond relatively well to conventional chemotherapy; however, metastatic disease is virtually incurable. Thus, there is a great interest in identifying specific therapeutic targets for TNBC. The tumor suppressor RB1 is frequently lost in Basal-like breast cancer. To test for a causative role of RB1 gene loss in BC and for its effect on specific subtypes, we deleted mouse Rb in mammary stem/bipotent progenitor cells. This led to diverse mammary tumors including TNBC, with a subset of the latter containing p53 mutations and exhibiting features of Basal-like BC or EMT. Combined mutation of Rb and p53 in mammary stem/bipotent progenitors induced EMT type tumors. Here, we review our findings and those of others, which connect Rb and p53 to EMT in TNBC. Furthermore, we discuss how by understanding this circuit and its vulnerabilities, we may identify novel therapy for TNBC.

Triple-negative breast cancer (TNBC) includes basal-like and claudin-low subtypes for which no specific treatment is currently available. Although the retinoblastoma tumor-suppressor gene (RB1) is frequently lost together with TP53 in TNBC, it is not directly targetable. There is thus great interest in identifying vulnerabilities downstream of RB1 that can be therapeutically exploited. Here, we determined that combined inactivation of murine Rb and p53 in diverse mammary epithelial cells induced claudin-low–like TNBC with Met, Birc2/3-Mmp13-Yap1, and Pvt1-Myc amplifications. Gene set enrichment analysis revealed that Rb/p53-deficient tumors showed elevated expression of the mitochondrial protein translation (MPT) gene pathway relative to tumors harboring p53 deletion alone. Accordingly, bioinformatic, functional, and biochemical analyses showed that RB1-E2F complexes bind to MPT gene promoters to regulate transcription and control MPT. Additionally, a screen of US Food and Drug Administration–approved (FDA-approved) drugs identified the MPT antagonist tigecycline (TIG) as a potent inhibitor of Rb/p53-deficient tumor cell proliferation. TIG preferentially suppressed RB1-deficient TNBC cell proliferation, targeted both the bulk and cancer stem cell fraction, and strongly attenuated xenograft growth. It also cooperated with sulfasalazine, an FDA-approved inhibitor of cystine xCT antiporter, in culture and xenograft assays. Our results suggest that RB1 deficiency promotes cancer cell proliferation in part by enhancing mitochondrial function and identify TIG as a clinically approved drug for RB1-deficient TNBC.

HER2(+) breast cancer (BC) is a highly aggressive subtype, affecting ~20% of BC patients. Current treatments include adjuvant or neoadjuvant chemotherapy plus anti-HER2 agents such as trastuzumab, a monoclonal antibody directed against HER2. Despite improvement in disease free survival, most patients eventually succumb to metastatic disease, which is largely incurable. Consequently, there is an urgent need to identify novel drugs that can efficiently kill HER2(+) BC and/or potentiate the effect of existing anti-HER2 therapies. We performed a lenti-viral shRNA kinome screen on non-adherent mouse Her2/Neu tumorspheres and identified TBK1, a non-canonical IκB kinase (IKK), as the most potent target [1]. TBK1 knock-down, or treatment with TBK1-II, a drug that efficiently inhibits TBK1 and its close relative IKKe (IKBKE), suppressed growth of human HER2(+) BC cells and induced cellular senescence. Senescence was associated with inhibition of phosphorylated/active p65-NFkB and induction of the cell cycle inhibitor, p16(ink4a). In addition, TBK1-II cooperated with lapatinib, a EGFR/HER2 inhibitor, to accelerate apoptosis in vitro and suppress tumor growth in a xenograft model of HER2(+) BC. Thus, TBK1/IKKe inhibitors may improve treatment of HER2(+) BC in cooperation with anti-HER2 therapy.

Triple-negative breast cancer (TNBCs) is an aggressive subtype with poor prognosis; drug-resistant metastases are common and highly lethal for which identification of therapeutic targets is of major medical interest. Previously we demonstrated that deletion of p53 and Rb in mouse mammary epithelium induced TNBC-like tumors but with limited capacity to metastasize. Therefore, we decided to employ sleeping beauty (SB) mutagenesis system that can identify oncogenic networks responsible to drive primary and metastatic tumors. In order to do this, we generated mice in which p53 (p53f/f) or p53 plus Rb (p53f/f:Rbf/f ) are deleted and the SB transposon is mobilized from chromosome 9 as well as controls in which both p53 and Rb are wild type. Forty primary tumors and forty metastases from each cohort will be harvested to identify common integration sites followed by deep sequencing. Then, the top 5-10 candidate oncogenes/tumor suppressors will be validated to determine whether their loss/activation would accelerate tumorigenesis/metastasis. H&E staining of mammary tumors collected so far from different genotypes revealed histologically diverse tumor types which includes but not limited to poorly differentiated tumors with areas of mesenchymal/spindle-like cells, acinar adenocarcinomas, and well differentiated tumors. All mice analyzed developed multiple mammary tumors in more than one mammary gland with average latency of 108, 158 and 170 days for p53/Rb deleted (N=7), p53 deleted (N=12), and wild type mice (N=2), respectively (p < 0.05). However, we did not always observe macro metastases in mice with primary mammary tumors and we decided to perform primary tumor survival surgery when tumors are oversized and let the mice live longer to develop metastases. With this technique, 3 out of 4 mice that underwent tumor removal surgery developed lung metastases when sacrificed. In total, lung metastases were observed in 5 out of 28 mice analyzed so far with/without surgery (18%) which histologically resemble their primary tumors. Since removing tumors from multiple glands is challenging, we decided to take a transplantation approach of the primary mammary epithelial cells of mid-pregnancy (13-16 dpc) p53f/f:Rbf/f:SB+ females and injecting them into the mammary glands of 3-4 week old NSG mice. So far, four NSG mice developed mammary tumors with average latency of 176 days. These tumors resemble spindle-shape histology. SB mutagenesis can promote metastasis in mouse models with limited dissemination potential such as the model proposed herein. The proposed experiments will identify novel oncogenic events that cooperate with p53-loss or combined p53/Rb-loss to induce primary and metastatic TNBCs which may serve as therapeutic targets for this aggressive disease. I have generated 3 sets of cohort of SB mutagenesis to identify these oncogenic events which are currently being analyzed in details. Citation Format: Ronak Ghanbari Azarnier, Agatha Zuchelkowski, Philip.E Chung, Zhe Jiang, Eldad Zacksenhaus. Identification of oncogenic/metastatic driver genes that cooperate with p53 or p53/Rb-loss to induce triple-negative breast 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 2801. doi:10.1158/1538-7445.AM2017-2801