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Supplemental data on additional models to support the role of EZH2 in RTKi resistance

Objectives We aimed to identify transcriptional gene signatures predictive of clinical response, for pharmacodynamic evaluation, and to provide mechanistic insight into JNJ-55920839, a human IgG1κ neutralizing mAb targeting IFN-α/IFN-ω, in participants with systemic lupus erythematosus (SLE). Methods Blood samples were obtained from SLE participants at baseline and up to Day 130, who received six 10 mg/kg IV doses of JNJ-55920839/placebo every 2 weeks. Participants with mild-to-moderate SLE who achieved clinical responses using SLE Disease Activity Index 2000 Responder Index 4-point change were considered responders. Transcriptional signatures from longitudinally collected blood were generated by RNA-Seq; signatures were generated by microarray from baseline blood samples exposed in vitro to JNJ-55920839 versus untreated. Results Two gene signatures (IFN-I Signaling and Immunoglobulin Immune Response) exhibited pharmacodynamic changes among JNJ-55920839 responders. The Immunoglobulin signature, but not the IFN-I signature, was elevated at baseline in JNJ-55920839 responders. A gene cluster associated with neutrophil-mediated immunity was reduced at baseline in JNJ-55920839 responders, substantiated by lower neutrophil counts in responders. An IFN-I signature was suppressed by JNJ-55920839 in vitro treatment versus untreated blood to a greater extent in responders before in vivo dosing. Conclusions These signatures may enable enrichment for treatment responders when using IFN-I-suppressing treatments in SLE.

Receptor tyrosine kinase inhibitors have shown clinical benefit in clear cell renal cell carcinoma (ccRCC), but novel therapeutic strategies are needed. The angiopoietin/Tie2 and MET pathways have been implicated in tumor angiogenesis, metastases, and macrophage infiltration. In our study, we used trebananib, an angiopoietin 1/2 inhibitor, and a novel small-molecule MET kinase inhibitor in patient-derived xenograft (PDX) models of ccRCC. Our goal was to assess the ability of these compounds to alter the status of tumor-infiltrating macrophages, inhibit tumor growth and metastases, and prolong survival. Seven-week-old SCID mice were implanted subcutaneously or orthotopically with human ccRCC models. One month postimplantation, mice were treated with angiopoietin 1/2 inhibitor trebananib (AMG 386), MET kinase inhibitor, or combination. In our metastatic ccRCC PDX model, RP-R-02LM, trebananib alone, and in combination with a MET kinase inhibitor, significantly reduced lung metastases and M2 macrophage infiltration (P = 0.0075 and P = 0.0205, respectively). Survival studies revealed that treatment of the orthotopically implanted RP-R-02LM tumors yielded a significant increase in survival in both trebananib and combination groups. In addition, resection of the subcutaneously implanted primary tumor allowed for a significant survival advantage to the combination group compared with vehicle and both single-agent groups. Our results show that the combination of trebananib with a MET kinase inhibitor significantly inhibits the spread of metastases, reduces infiltrating M2-type macrophages, and prolongs survival in our highly metastatic ccRCC PDX model, suggesting a potential use for this combination therapy in treating patients with ccRCC.

Purpose: Translocation renal cell carcinoma (tRCC) represents a rare subtype of kidney cancer associated with various TFE3, TFEB, or MITF gene fusions that are not responsive to standard treatments for RCC. Therefore, the identification of new therapeutic targets represents an unmet need for this disease. Experimental Design: We have established and characterized a tRCC patient-derived xenograft, RP-R07, as a novel preclinical model for drug development by using next-generation sequencing and bioinformatics analysis. We then assessed the therapeutic potential of inhibiting the identified pathway using in vitro and in vivo models. Results: The presence of a SFPQ-TFE3 fusion [t(X;1) (p11.2; p34)] with chromosomal break-points was identified by RNA-seq and validated by RT-PCR. TFE3 chromatin immunoprecipitation followed by deep sequencing analysis indicated a strong enrichment for the PI3K/AKT/mTOR pathway. Consistently, miRNA microarray analysis also identified PI3K/AKT/mTOR as a highly enriched pathway in RP-R07. Upregulation of PI3/AKT/mTOR pathway in additional TFE3–tRCC models was confirmed by significantly higher expression of phospho-S6 (P < 0.0001) and phospho-4EBP1 (P < 0.0001) in established tRCC cell lines compared with clear cell RCC cells. Simultaneous vertical targeting of both PI3K/AKT and mTOR axis provided a greater antiproliferative effect both in vitro (P < 0.0001) and in vivo (P < 0.01) compared with single-node inhibition. Knockdown of TFE3 in RP-R07 resulted in decreased expression of IRS-1 and inhibited cell proliferation. Conclusions: These results identify TFE3/IRS-1/PI3K/AKT/mTOR as a potential dysregulated pathway in TFE3–tRCC, and suggest a therapeutic potential of vertical inhibition of this axis by using a dual PI3K/mTOR inhibitor for patients with TFE3–tRCC.

Objective: In a previously reported phase II randomized, placebo-controlled, interventional trial, we demonstrated that treatment with ustekinumab, an anti–interleukin-12 (IL-12)/IL-23 p40 neutralizing monoclonal antibody, improved global and organ-specific measures of disease activity in patients with active systemic lupus erythematosus (SLE). Utilizing the biomarker data from this phase II clinical study, we sought to determine whether modulation of the expression of IL-12, IL-23, or both cytokines by ustekinumab is associated with clinical efficacy in patients with SLE. Methods: This phase II randomized, placebo-controlled study enrolled 102 patients with autoantibody-positive SLE whose disease remained active despite standard-of-care therapy. Patients were randomized at a 3:2 ratio to receive ~6 mg/kg ustekinumab intravenously or placebo at week 0, followed by subcutaneous injections of 90 mg ustekinumab or placebo every 8 weeks, with placebo crossover to 90 mg ustekinumab every 8 weeks. The SLE Responder Index 4 (SRI-4) at week 24 was used to determine which patients could be classified as ustekinumab responders and which could be classified as nonresponders. In addition to measurements of p40 and IL-23, serum levels of interferon-γ (IFNγ), IL-17A, IL-17F, and IL-22, as a proxy for the IL-12 and IL-23 pathways, were quantified by immunoassay. Results: Changes in the serum levels of IL-17A, IL-17F, and IL-22 at different time points after treatment were not consistently significantly associated with an SRI-4 clinical response to ustekinumab in patients with SLE. In contrast, an SRI-4 response to ustekinumab was significantly associated (P < 0.01) with durable reductions in the serum IFNγ protein levels at several time points relative to baseline, which was not observed in ustekinumab nonresponders or patients who received placebo. Conclusion: While not diminishing a potential role of IL-23, these serum biomarker assessments indicate that IL-12 blockade has an important role in the mechanism of action of ustekinumab treatment in patients with SLE.

Supplemental material, sj-pdf-1-lup-10.1177_0961203321995576 for Novel signatures associated with systemic lupus erythematosus clinical response to IFN-α/-ω inhibition by Loqmane Seridi, Matteo Cesaroni, Ashley Orillion, Jessica Schreiter, Marc Chevrier, Stanley Marciniak, Thi-Sau Migone, William Stohl, Walter Winn Chatham, Richard Alan Furie, Jacqueline Benson and Jarrat Jordan in Lupus

Acquired and intrinsic resistance to receptor tyrosine kinase inhibitors (RTKi) represents a major hurdle in improving the management of clear cell renal cell carcinoma (ccRCC). Recent reports suggest that drug resistance is driven by tumor adaptation via epigenetic mechanisms that activate alternative survival pathways. The histone methyl transferase EZH2 is frequently altered in many cancers, including ccRCC. To evaluate its role in ccRCC resistance to RTKi, we established and characterized a spontaneously metastatic, patient-derived xenograft model that is intrinsically resistant to the RTKi sunitinib, but not to the VEGF therapeutic antibody bevacizumab. Sunitinib maintained its antiangiogenic and antimetastatic activity but lost its direct antitumor effects due to kinome reprogramming, which resulted in suppression of proapoptotic and cell-cycle–regulatory target genes. Modulating EZH2 expression or activity suppressed phosphorylation of certain RTKs, restoring the antitumor effects of sunitinib in models of acquired or intrinsically resistant ccRCC. Overall, our results highlight EZH2 as a rational target for therapeutic intervention in sunitinib-resistant ccRCC as well as a predictive marker for RTKi response in this disease. Cancer Res; 77(23); 6651–66. ©2017 AACR.

Purpose: Recent advances in immunotherapy highlight the antitumor effects of immune checkpoint inhibition despite a relatively limited subset of patients receiving clinical benefit. The selective class I histone deacetylase inhibitor entinostat has been reported to have immunomodulatory activity including targeting of immune suppressor cells in the tumor microenvironment. Thus, we decided to assess whether entinostat could enhance anti–PD-1 treatment and investigate those alterations in the immunosuppressive tumor microenvironment that contribute to the combined antitumor activity. Experimental Design: We utilized syngeneic mouse models of lung (LLC) and renal cell (RENCA) carcinoma and assessed immune correlates, tumor growth, and survival following treatment with entinostat (5 or 10 mg/kg, p.o.) and a PD-1 inhibitor (10 and 20 mg/kg, s.c.). Results: Entinostat enhanced the antitumor effect of PD-1 inhibition in two syngeneic mouse tumor models by reducing tumor growth and increasing survival. Entinostat inhibited the immunosuppressive function of both polymorphonuclear (PMN)- and monocytic-myeloid derived suppressor cell (M-MDSC) populations. Analysis of MDSC response to entinostat revealed significantly reduced arginase-1, iNOS, and COX-2 levels, suggesting potential mechanisms for the altered function. We also observed significant alterations in cytokine/chemokine release in vivo with a shift toward a tumor-suppressive microenvironment. Conclusions: Our results demonstrate that entinostat enhances the antitumor effect of PD-1 targeting through functional inhibition of MDSCs and a transition away from an immune-suppressive tumor microenvironment. These data provide a mechanistic rationale for the clinical testing and potential markers of response of this novel combination in solid tumor patients. Clin Cancer Res; 23(17); 5187–201. ©2017 AACR.

Background:Systemic Lupus Erythematous (SLE) is a clinically and biologically diverse disease, for which only one new therapy has been approved in the past 60 years. In a phase 2 trial on patients with mild-to-moderate SLE, ustekinumab (UST) improved clinical and laboratory measures of disease activity compared with placebo (PBO).1Objectives:We previously reported an association of IFN-γ reduction with response to UST,2suggesting an impact on the IL12/Th1 axis. To extend these findings, we performed unbiased transcriptomic analysis from baseline whole blood samples to identify genes that discriminate UST responders (UST-R) from non-responders (UST-NR) using the primary endpoint of Systemic Lupus Erythematosus Responder Index (SRI)-4 at week 24 to define response.Methods:UST was studied in a Ph2 PBO-controlled study of 102 patients with seropositive SLE and active disease despite standard therapy. Patients were randomized 3:2 to receive IV UST 6 mg/kg or placebo followed by subcutaneous injections of UST 90 mg or PBO every 8 weeks. Whole blood gene expression at baseline was measured via microarray using RNA samples from 100 patients, as samples from 2 patients failed quality control. An unbiased approach was used to identify gene signatures present at baseline that associate with UST response. Recombinant IL-12 or IL-23 was incubatedin vitrowith whole blood from 6 healthy donors for 24h and RNA-Seq was performed to determine the effect of these treatments on representative genes comprising the UST response signature.Results:A non-biased machine learning algorithm identified a 9-gene whole blood signature composed primarily of cytotoxic cell-associated transcripts (PRF1, KLRD1, GZMH, NKG7, GNLY, FGFBP2, TRGC2, TARP, TRGV2) that was enriched at baseline in UST-R vs UST-NR. By Gene Set Variation Analysis, the cytotoxic signature enrichment in UST-NR was less at baseline than both UST-R and a healthy control cohort (P=0.0087, P=0.056, respectively), whereas UST-R cytotoxic gene enrichment was similar to healthy controls (P=0.31). No significant difference in cytotoxic signature enrichment was observed at baseline between PBO responders and PBO non-responders or healthy controls (Figure). Enrichment levels of the cytotoxic gene signature remained stable over time in PBO and UST-NR groups while a trend of decreased cytotoxic signature was observed in UST-R, although never reaching levels seen in UST-NR. To begin to understand the relationship between IL-12 and IL-23, the targets of UST, and the cytotoxic signature, whole blood was stimulated with these cytokinesin vitro. Recombinant IL-12, but not IL-23, resulted in increased expression of representative members of this cytotoxic gene signature.Conclusion:We identified a novel cytotoxic signature in baseline blood samples that associated with UST response in SLE. The observation that IL-12 can increase this signaturein vitroand that IL-12 is a robust inducer of cytotoxic cell activity3as well as IFN-γ3suggests an important role of IL-12 blockade in the mechanism of action of UST in SLE.References:[1]van Vollenhoven RF. Lancet. 2018;392:1330-39[2]Jordan. ACR 2018 Abstract # 2951[3]G. Trinchieri. Nat Rev Immunol. 2003;3:133-46Figure.Disclosure of Interests:Loqmane Seridi Employee of: Janssen Research & Development, LLC, Matteo Cesaroni Employee of: Janssen Research & Development, LLC, Matthew J Loza Employee of: Janssen Research & Development, LLC, Jessica Schreiter Employee of: Janssen Research & Development, LLC, Kristen Sweet Employee of: Janssen Research & Development, LLC, Yevgeniya Orlovsky Employee of: Janssen Research & Development, LLC, Spring House, PA, United States of America, Isabelle Baribaud Employee of: Janssen Research & Development, LLC, Ashley Orillion Employee of: Janssen Research & Development, LLC, Peter Lipsky Consultant of: Horizon Therapeutics, Ronald van Vollenhoven Grant/research support from: AbbVie, Amgen, Arthrogen, Bristol-Myers Squibb, GlaxoSmithKline (GSK), Janssen Research & Development, LLC, Lilly, Pfizer, Roche, and UCB, Consultant of: AbbVie, AstraZeneca, Biotest, Bristol-Myers Squibb, Celgene, Crescendo Bioscience, GSK, Janssen, Lilly, Medac, Merck, Novartis, Pfizer, Roche, UCB and Vertex, Speakers bureau: AbbVie, AstraZeneca, Biotest, Bristol-Myers Squibb, Celgene, Crescendo Bioscience, GlaxoSmithKline, Janssen, Lilly, Merck, Novartis, Pfizer, Roche, UCB, Vertex, Bevra H. Hahn Grant/research support from: Janssen Research & Development, LLC, George Tsokos Grant/research support from: Janssen Research & Development, LLC, Marc Chevrier Employee of: Janssen Research & Development, LLC, Shawn Rose Employee of: Janssen Research & Development, LLC, Frederic Baribaud Shareholder of: Janssen Research & Development, LLC, Employee of: Janssen Research & Development, LLC, Jarrat Jordan Employee of: Janssen Research & Development, LLC

HDAC inhibitors (HDACIs) are anticancer agents being developed in preclinical and clinical settings due to their capacity to modulate gene expression involved in cell growth, differentiation and apoptosis, through modification of both chromatin histone and nonhistone proteins. Most HDACIs in clinical development have cytotoxic or cytostatic properties and their direct inhibitory effects on tumor cells are well documented. Numerous studies have revealed that HDACIs have potent immunomodulatory activity in tumor-bearing animals and cancer patients, providing guidance to apply these agents in cancer immunotherapies. Here, we summarize recent reports addressing the effects of HDACIs on tumor cell immunogenicity, and on different components of the host immune system. In addition, we discuss the complexity of the immunomodulatory activity of these agents, which depends on the class specificity of the HDACIs, different experimental settings and the target immune cell populations.

Purpose: Diet and healthy weight are established means of reducing cancer incidence and mortality. However, the impact of diet modifications on the tumor microenvironment and antitumor immunity is not well defined. Immunosuppressive tumor-associated macrophages (TAMs) are associated with poor clinical outcomes and are potentially modifiable through dietary interventions. We tested the hypothesis that dietary protein restriction modifies macrophage function toward antitumor phenotypes. Experimental Design: Macrophage functional status under different tissue culture conditions and in vivo was assessed by Western blot, immunofluorescence, qRT-PCR, and cytokine array analyses. Tumor growth in the context of protein or amino acid (AA) restriction and immunotherapy, namely, a survivin peptide–based vaccine or a PD-1 inhibitor, was examined in animal models of prostate (RP-B6Myc) and renal (RENCA) cell carcinoma. All tests were two-sided. Results: Protein or AA-restricted macrophages exhibited enhanced tumoricidal, proinflammatory phenotypes, and in two syngeneic tumor models, protein or AA-restricted diets elicited reduced TAM infiltration, tumor growth, and increased response to immunotherapies. Further, we identified a distinct molecular mechanism by which AA-restriction reprograms macrophage function via a ROS/mTOR-centric cascade. Conclusions: Dietary protein restriction alters TAM activity and enhances the tumoricidal capacity of this critical innate immune cell type, providing the rationale for clinical testing of this supportive tool in patients receiving cancer immunotherapies.

A major barrier for cancer immunotherapy is the presence of suppressive cell populations in patients with cancer, such as myeloid-derived suppressor cells (MDSC) and tumor-associated macrophages (TAM), which contribute to the immunosuppressive microenvironment that promotes tumor growth and metastasis. Tasquinimod is a novel antitumor agent that is currently at an advanced stage of clinical development for treatment of castration-resistant prostate cancer. A target of tasquinimod is the inflammatory protein S100A9, which has been demonstrated to affect the accumulation and function of tumor-suppressive myeloid cells. Here, we report that tasquinimod provided a significant enhancement to the antitumor effects of two different immunotherapeutics in mouse models of cancer: a tumor vaccine (SurVaxM) for prostate cancer and a tumor-targeted superantigen (TTS) for melanoma. In the combination strategies, tasquinimod inhibited distinct MDSC populations and TAMs of the M2-polarized phenotype (CD206+). CD11b+ myeloid cells isolated from tumors of treated mice expressed lower levels of arginase-1 and higher levels of inducible nitric oxide synthase (iNOS), and were less immunosuppressive ex vivo, which translated into a significantly reduced tumor-promoting capacity in vivo when these cells were coinjected with tumor cells. Tumor-specific CD8+ T cells were increased markedly in the circulation and in tumors. Furthermore, T-cell effector functions, including cell-mediated cytotoxicity and IFNγ production, were potentiated. Taken together, these data suggest that pharmacologic targeting of suppressive myeloid cells by tasquinimod induces therapeutic benefit and provide the rationale for clinical testing of tasquinimod in combination with cancer immunotherapies. Cancer Immunol Res; 3(2); 136–48. ©2014 AACR.

Androgen receptor (AR) plays a crucial role in the development and progression of prostate cancer. AR expression has also been reported in other solid tumors, including renal cell carcinoma (RCC), but its biological role here remains unclear. Through integrative analysis of a reverse phase protein array, we discovered increased expression of AR in an RCC patient–derived xenograft model of acquired resistance to the receptor tyrosine kinase inhibitor (RTKi) sunitinib. AR expression was increased in RCC cell lines with either acquired or intrinsic sunitinib resistance in vitro. An AR signaling gene array profiler indicated elevated levels of AR target genes in sunitinib-resistant cells. Sunitinib-induced AR transcriptional activity was associated with increased phosphorylation of serine 81 (pS81) on AR. Additionally, AR overexpression resulted in acquired sunitinib resistance and the AR antagonist enzalutamide-induced AR degradation and attenuated AR downstream activity in sunitinib-resistant cells, also indicated by decreased secretion of human kallikrein 2. Enzalutamide-induced AR degradation was rescued by either proteasome inhibition or by knockdown of the AR ubiquitin ligase speckle-type POZ protein (SPOP). In vivo treatment with enzalutamide and sunitinib demonstrated that this combination efficiently induced tumor regression in a RCC model following acquired sunitinib resistance. Overall, our results suggest the potential role of AR as a target for therapeutic interventions, in combination with RTKi, to overcome drug resistance in RCC. Significance: These findings highlight the therapeutic potential of targeting the androgen receptor to overcome RCC resistance to receptor tyrosine kinase inhibitors. Cancer Res; 78(11); 2886–96. ©2018 AACR.

The Hippo signaling pathway regulates cellular proliferation and survival, thus exerting profound effects on normal cell fate and tumorigenesis. Pivotal effectors of this pathway are YAP/TAZ, transcriptional co-activators whose dysfunction contributes to epithelial-to-mesenchymal transition and malignant transformation. Therefore, it is of great importance to decipher the mechanisms underlying the regulations of YAP/TAZ at various levels. Here we report that non-receptor tyrosine phosphatase 14 (PTPN14) interacts with the Kibra protein. The interaction between PTPN14 and Kibra is through the PPXY domain of PTPN14 and WW domain of Kibra. PTPN14 and Kibra can induce the LATS1 activation independently and cooperatively. Interestingly, activation of LATS1 by PTPN14 is dependent on the C terminus of PTPN14 and independent of the upstream mammalian STE20-like kinase (MST) proteins. Furthermore, we demonstrate that PTPN14 increases the LAST1 protein stability. Last, overexpression of Kibra rescues the increased cell migration and aberrant three-dimensional morphogenesis induced by knockdown of PTPN14, and this rescue is mediated through the activation of the upstream LATS1 kinase and subsequent cytoplasmic sequestration of YAP. In summary, our results indicate a potential regulatory role of PTPN14 in the Hippo pathway and demonstrate another layer of regulation in the YAP oncogenic function.

Background: Data from epidemiological studies have linked dietary intake to the development of prostate cancer (CaP). We have previously shown that dietary protein restriction inhibits tumor growth by modulating PI3K/mTOR signaling in vivo. Additionally we have shown that dietary methionine restriction influence macrophage polarization which enhances the ability of the immune system to fight cancer. In this study we hypothesize that caloric restriction is capable of restricting tumor growth and potentiating the antitumor effect of androgen deprivation therapy (ADT) and PD1 inhibition. Methods: We utilized two prostate cancer models for our in vivo studies; castrate resistant LuCaP 23.1 AI prostate cancer model and MYC-Driven prostate cancer model in C57BL/6 mice. Caloric restriction was carried out by exposing mice to alternating fasting either as a single intervention (in LuCaP 23.1 model) or in combination with ADT (enzalutamide or surgical castration) or PD-1 inhibition in Myc-CaP model. Tumor sizes and weights were blindly assessed during the study and upon study termination respectively. IHC staining for both Ki-67 and mTOR phosphorylation was done to assess the impact of fasting+/- ADT on tumor growth and mTOR signaling. Macrophage polarization/distribution in tumors was assessed using immunofluorescence. Blood was collected at the end of the study for future comprehensive analysis of PBMCS. Results: In both models, alternating fasting was associated with significant decrease in tumor weight at the end of study in comparison to control group (*p Conclusions: Caloric restriction can hinder prostate cancer growth and potentiate the therapeutic effect of ADT. Our results provide basis for the translational use of dietary modification both as preventive measure as well as a therapeutic intervention that can improve the benefit of current standard treatments. Citation Format: May Elbanna, Justin Budka, Paige Dausinas, Remi Adelaiye-Ogala, Nur Damayanti, Ashley Orillion, Eri Banno, Luigi Fontana, Roberto Pili. Caloric restriction potentiates the therapeutic benefit of androgen deprivation therapy and alters macrophage polarization when combined with PD1 inhibition in murine models of prostate cancer [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2019; 2019 Mar 29-Apr 3; Atlanta, GA. Philadelphia (PA): AACR; Cancer Res 2019;79(13 Suppl):Abstract nr 1611.

Background: Immune checkpoint inhibitors targeting the PD-1/PD-L1 axis have shown clinical benefit in solid tumor patients, including renal cell carcinoma (RCC). However, the rate of clinical response remains modest. Growing evidence suggests that epigenetic modifying agents may have an immunomodulatory role. Our group has previously demonstrated that the selective class I histone deacetylase (HDAC) inhibitor entinostat decreases the function of regulatory T-cells (Treg) and myeloid-derived suppressor cells (MDSC), and synergizes with PD-1 blockade. In this study, we assessed the immunomodulatory activity and efficacy of combining PD-1 blockade with the pan-HDAC inhibitor vorinostat in a RCC model. Methods: To test the efficacy of a combination therapy with a PD-1 inhibitor, mDX-400 (10 and 20 mg/kg I.P) (Merck & Co., Inc.) and a pan-HDAC inhibitor, vorinostat (100 and 150 mg/kg I.P) (Merck & Co., Inc.), we utilized a syngeneic mouse model of metastatic RCC following orthotopic implantation of luciferase expressing RENCA cells in immunocompetent BALB/c mice. Antitumor activity was assessed by bioluminescence technique as well as end point measurements of tumor weights. Immune landscape profiling of tumor infiltrating lymphocytes (TILs) was performed by flow cytometry, immunohistochemistry, and immunofluorescence. Survival analysis was performed by Kaplan–Meier estimates and log-rank statistic. Differences in chromatin accessibility in peripheral blood mononuclear cells (PBMC) were assessed by Assay for Transposase-Accessible Chromatin with high-throughput sequencing (ATAC-seq). Results: Statistically significant reductions in end point tumor weights, as well as lung metastases nodules, were observed in mice treated with the combination of vorinostat (100 mg/kg P=0.0391; 150 mg/kg P=0.0165) and mDX-400 (20 mg/kg) compared to vehicle, while no statistical significant reduction was observed in those treated with single-agent mDX-400. Combination therapy also significantly lengthened the survival of the mice (median survival = 60 days; P=0.009) compared to treatment with the single agent mDX-400 (median survival=42 days). Immune landscape profiling did not demonstrate a significant increase in CD8+ tumor infiltration (P=0.479), but a statistically significant increase in natural killer cell infiltration (P=0.048) was observed. Though the CD8+ tumor infiltration was unchanged, a significant reduction (P=0.049) of exhausted CD8+ T-cells (CD8+PD1+) was observed in the combination treatment compared to mDX400 alone. Furthermore, a decrease was observed in the immunosuppressive Tregs (CD4+FOXP4+) and MDSC (CD11b+Gr1+) in the combination group compared to mDX400 alone. Bioinformatic analyses of ATAC-seq data from the PBMC cells of mice in the combination treatment and mDX400 alone showed increased chromatin accessibility between the two conditions. Pathway analysis of genes associated with more accessible chromatin in the combination treatment than mDX400 treatment identified enrichment of cell cycle control and immune cell activation pathways. Conclusions: Our results demonstrate that the pan-HDAC inhibitor vorinostat augments the antitumor effect of immune checkpoint inhibitor mDX-400 and prolongs survival in the RENCA model. This combination advantage was achieved by changing the immune landscape in TILs, especially by decreasing the exhausted subset of T-cells. The combination of these drugs is associated with higher chromatin accessibility near genes involved in cell cycle progression and immune cell activation. Taken together, our results support the clinical testing of pan-HDAC inhibitors in combination of PD-1 inhibitors and provide a novel potential immunomodulatory effect of epigenetic drugs. Citation Format: Nur P. Damayanti, Justin A. Budka, Josue D. Ordaz, Ashley Orillion, Khunsha Ahmed, Xioana Chu, Yue Wang, Yunlong Liu, Roberto Pili. T-cell rejuvenation is associated with vorinostat-induced immune response in combination with immune checkpoint blockade [abstract]. In: Proceedings of the Fourth CRI-CIMT-EATI-AACR International Cancer Immunotherapy Conference: Translating Science into Survival; Sept 30-Oct 3, 2018; New York, NY. Philadelphia (PA): AACR; Cancer Immunol Res 2019;7(2 Suppl):Abstract nr A184.

Background Class I histone deacetylases (HDACs) have been reported to be overexpressed in clear cell renal cell carcinoma (ccRCC), whereas the expression of class II HDACs is unknown. Methods Four isogenic cell lines C2/C2VHL and 786-O/786-OVHL with differential VHL expression are used in our studies. Cobalt chloride is used to mimic hypoxia in vitro. HIF-2α knockdowns in C2 and 786-O cells is used to evaluate the effect on HDAC 1 expression and activity. Invasion and migration assays are used to investigate the role of HDAC 1 and HDAC 6 expression in ccRCC cells. Comparisons are made between experimental groups using the paired T-test, the two-sample Student’s T-test or one-way ANOVA, as appropriate. ccRCC and the TCGA dataset are used to observe the clinical correlation between HDAC 1 and HDAC 6 overexpression and overall and progression free survival. Results Our analysis of tumor and matched non-tumor tissues from radical nephrectomies showed overexpression of class I and II HDACs (HDAC6 only in a subset of patients). In vitro, both HDAC1 and HDAC6 over-expression increased cell invasion and motility, respectively, in ccRCC cells. HDAC1 regulated invasiveness by increasing matrix metalloproteinase (MMP) expression. Furthermore, hypoxia stimulation in VHL-reconstituted cell lines increased HIF isoforms and HDAC1 expression. Presence of hypoxia response elements in the HDAC1 promoter along with chromatin immunoprecipitation data suggests that HIF-2α is a transcriptional regulator of HDAC1 gene. Conversely, HDAC6 and estrogen receptor alpha (ERα) were co-localized in cytoplasm of ccRCC cells and HDAC6 enhanced cell motility by decreasing acetylated α-tubulin expression, and this biological effect was attenuated by either biochemical or pharmacological inhibition. Finally, analysis of human ccRCC specimens revealed positive correlation between HIF isoforms and HDAC. HDAC1 mRNA upregulation was associated with worse overall survival in the TCGA dataset. Conclusions Taking together, these results suggest that HDAC1 and HDAC6 may play a role in ccRCC biology and could represent rational therapeutic targets. Electronic supplementary material The online version of this article (doi:10.1186/s12885-016-2604-7) contains supplementary material, which is available to authorized users.

Figure S1. VHL, HIF, HDAC1 and related gene expression in renal tumor cell lines. Gene expression analysis of renal tumor cell lines using the Broad-Novartis cancer cell line encyclopedia show the levels of players in the VHL-HIF axis. The top row indicates the gene analyzed in different renal tumor cell lines (in the left most column). Red color indicates gene upregulation and blue color indicates downregulation of genes in the renal tumor cell lines. Figure S2. Hypoxia induces HDAC 1 expression in clear cell renal tumor cell line. a) Parental VHL null cells C2 and 786–0 were compared to cells with wt-VHL introduced for HIF-1α, HIF-2α and HDAC 1 protein expression. The left panel measures protein expression in C2 isogeneic cell lines and the right panel measures protein expression in 786–0 isogenic cell lines. The numbers below the bands represent densitometry performed by Image J analysis on representative immunoblots relative to their respective isogeneic VHL null cells with GAPDH serving as a loading control. b) HDAC 1 expression was compared between 786–0 and 786-0VHL cells under normoxic and hypoxic conditions (mimicked by the use of 100 μM cobalt chloride) after overnight serum starvation. The numbers below the bands represent densitometry performed by Image J analysis on representative immunoblots relative to 786–0 bands in normoxic conditions with total GAPDH serving as loading control. c-d) HDAC 1 protein expression was quantitatively measured by flow cytometry under normoxic and hypoxic conditions. *p

Interdisciplinary courses have become a standard component in general education programs. The assumption is that they improve student outcomes. This article is an ethnographic case study of an interdisciplinary course at a research university. It examines the relationship among interdisciplinary curriculum, institutional context, and student outcomes.

Sunitinib is considered a first-line therapeutic option for patients with advanced clear cell renal cell carcinoma (ccRCC). Despite sunitinib's clinical efficacy, patients eventually develop drug resistance and disease progression. Herein, we tested the hypothesis whether initial sunitinib resistance may be transient and could be overcome by dose increase. In selected patients initially treated with 50 mg sunitinib and presenting with minimal toxicities, sunitinib dose was escalated to 62.5 mg and/or 75 mg at the time of tumor progression. Mice bearing two different patient-derived ccRCC xenografts (PDX) were treated 5 days per week with a dose-escalation schema (40–60–80 mg/kg sunitinib). Tumor tissues were collected before dose increments for immunohistochemistry analyses and drug levels. Selected intrapatient sunitinib dose escalation was safe and several patients had added progression-free survival. In parallel, our preclinical results showed that PDXs, although initially responsive to sunitinib at 40 mg/kg, eventually developed resistance. When the dose was incrementally increased, again we observed tumor response to sunitinib. A resistant phenotype was associated with transient increase of tumor vasculature despite intratumor sunitinib accumulation at higher dose. In addition, we observed associated changes in the expression of the methyltransferase EZH2 and histone marks at the time of resistance. Furthermore, specific EZH2 inhibition resulted in increased in vitro antitumor effect of sunitinib. Overall, our results suggest that initial sunitinib-induced resistance may be overcome, in part, by increasing the dose, and highlight the potential role of epigenetic changes associated with sunitinib resistance that can represent new targets for therapeutic intervention. Mol Cancer Ther; 14(2); 513–22. ©2014 AACR.

In 1998-1999, the University of California added a new dimension to its K-12 outreach: partnerships between the university and educationally low-performing high schools. The program aimed to improve the academic performance of targeted high schools and their feeder middle and elementary schools. This paper examines the processes that led to the four-pronged outreach plan, the various political and organization processes that shaped outreach, and the institutional significance and impact of UC's foray into school reform.

Background: Cystine/glutamate exchanger xCT is a catalytic component of system xc- involved in transport of ‘conditionally indispensable’ amino acid cystine. Cystine transport is a rate limiting step for the synthesis of glutathione, a major intracellular redox regulator. Recently, we and other groups reported the overexpression of xCT and its association with drug resistance in several human cancers including bladder, glioma, breast, and colon. There are no studies to show the xCT expression in clear cell renal cell carcinoma (ccRCC) and its association with tyrosine kinase inhibitors resistance and metastasis. In the current study we have evaluated xCT expression in human ccRCC tumors arranged in tissue microarray (TMA) and determined its role in receptor tyrosine kinase inhibitor (RTKI) resistance and metastases using the patient derived tumor xenografts (PDX) models and TKI resistance ccRCC cells. Methods: Human Renal cell carcinoma tumor nephrectomy specimens arranged in tissue microarray (TMA) were used to determine xCT expression by immunohistochemistry. Patient derived tumor xenografts (PDX) of primary, metastasis, and sunitinib resistance were used to determine the role of xCT in RCC. To understand the molecular alterations associated with RTKI resistance, we have generated sunitinib resistance 786 OR ccRCC cells and performed RNAseq analysis. To determine the xCT inhibition effect on ccRCC tumor metastases, sulfasalazine, an inhibitor of xCT was used to treat metastatic ccRCC tumor xenografts transplanted in SCID mice. Results: Immunohistochemical evaluation of xCT in RCC TMA revealed that 70 % (19 out of 27) of the tumors express different levels of xCT. Association with tumor response to RTKI will be presented. RTKI less responsive PDX RP-R-02 was developed using the dose escalation treatment strategy and was found to have an upregulation of xCT when the tumors become less responsive to sunitinib. RNAseq analysis revealed differential gene expression of various pathway genes including lysosome biogenesis and function such as SLC7A11, HPS4, HPS5, CTSB, IFI30, PPT1, SCPEP1, TPP1, ATP6AP1L, MCOLN1, PRKAG2, and VPS18 in sunitinib resistant 786 OR cells compared to parental cells supports the role of lysosomes function in RTKI drug resistance. Furthermore, xCT inhibitor sulfasalazine treatment significantly decreased the metastasis lung nodules of RP-R-02LM in SCID mice demonstrated the xCT role in RCC tumor metastasis. Conclusions: We found preliminary evidence that overexpression of xCT may be associated with RTKI resistance in ccRCC. These results suggest that targeting the xCT in ccRCC may reverse the resistance and enhance the efficacy of RTKI. Additional studies using larger numbers of ccRCC tumors are required to identify xCT as a potential predictive biomarker for response/resistance to RTKI in ccRCC patients. Citation Format: Sreenivasulu Chintala, Remi Adelaiye-Ogala, Ashley Orillion, Sreevani Arisa, May Elbanna, Nur P. Damayanti, Roberto Pili. Association of xCT overexpression with RTKI resistance and metastases in clear cell renal cell carcinoma [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 94. doi:10.1158/1538-7445.AM2017-94

Background: Our previous work showed a significant reduction of tumor growth, macrophage infiltration, circulating IGF-1, and mTOR activation with low protein diet in a patient derived xenograft model of prostate cancer. The evolutionarily conserved, nutrient sensing, mTOR pathway plays a central role in both development of advanced stage prostate cancer and immune responsiveness. This study presents novel data on the impact of dietary protein modification on the function of the host immune system in response to prostate cancer and immunotherapy. Methods: Our In vitro studies utilized bone marrow or tumor derived (RP-B6 Myc) macrophages. In vivo studies utilized the recently characterized RP-B6 Myc model. Mice were fed ad libitum control or methionine restricted diets for four weeks prior to S.C. implantation with ~1mm2 tumor pieces. Treatment of survivin peptide vaccine (1mg/ml S.C. 1 X week) and anti-PD-1 (20mg/kg I.P. 2 X week) began at ~50mm2 tumor size. Tumor volumes were blindly recorded 2 X week. End point analyses include: tumor weight, flow cytometric analysis, proteomic profiler analyses, and microbiome analyses from each diet and treatment group. Results: We show here that while methionine restriction (MR) has little impact on our RP-B6 Myc prostate cancer cell line, it does yield a significant alteration in both the polarization and function of M1 and M2 macrophages. In the in vitro MR conditions, we observed significantly enhanced polarization of M1 macrophages and reduced polarization of M2 macrophages. Functional analysis revealed increased tumoricidal activity of both M1, ‘antitumor’, and M2, ‘pro-tumor,’ macrophages suggesting a flip in M2 function from tumor-promoting to tumoricidal. Further analysis of the released cytokines in MR media conditions yielded significant increase of antitumor cytokines & chemokines, such as IL-12, IL-27, CXCL9, CXCL10, CXCL11, CCL2, CCL4, and TNF-alpha, a double-edged sword which in our system correlates with decreased cancer cell viability upon co-culture with amino acid restricted M1 and M2 macrophages. Our preliminary results show dietary MR yielding a significant inhibition of prostate cancer growth in the RP-B6-Myc model and our ongoing study with survivin peptide vaccine and anti-PD-1 immunotherapies will be available to present in the conference. Conclusions: Our data suggest that restricting methionine is sufficient to alter both the polarization and tumoricidal function of macrophages. Our preliminarily results show that restricted dietary methionine is able to inhibit prostate cancer growth, modify the host immune response and better inhibit prostate cancer growth alone or in combination with immunotherapy. These results provide a strong basis to consider diet restriction as a means to limit cancer growth targeting tumor immune system and potentially to enhance cancer patient responses to immunotherapy. Citation Format: Ashley R. Orillion, Sreenivasulu Chintala, Remi Adelaiye-Ogala, Li Shen, Nur Damayanti, May Elbanna, Sreevani Arisa, Bennett Elzey, Chinghai Kao, Luigi Fontana, Roberto Pili. Methionine restriction increases macrophage tumoricidal activity and significantly inhibits prostate cancer growth [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 250. doi:10.1158/1538-7445.AM2017-250

Background: Translocation Renal Cell Carcinoma (tRCC) represents an aggressive subtype of kidney cancer associated with various gene fusions involving translocation of one of two members of micropthalmia transcription factor (MiT) family, TFE3 or TFEB. Despite identification of multiple TFE3 gene fusions in tRCC, heterogeneous phenotype and various dysregulated signaling pathway resulting from variety of gene fusion partners pose a challenge to establish effective treatments for these patients. In this work, we sought to study the biology underlying oncogenesis in tRCC involving TFE3 fusion with genes associated with pre-mRNA splicing factor machinery; NONO, SFPQ and PRCC. Methods: To investigate the biology of different TFE3 fusion proteins, oncogenic phenotypes and oncogenic signaling were compared among cells with distinct endogenous expression of TFE3 fusions such as SFPQ-TFE3, NONO-TFE3, PRCC-TFE3. Endogenous SFPQ-TFE3 expressing cells, RP-RO7, were generated from patient derived xenograft. UOK-109 and UOK-146 (kindly provided by Dr. Marston Lenehan, NCI) were used as endogenous NONO-TFE3 and PRCC-TFE3 expressing cells, respectively. TFE3 fusion transcripts were identified with RT-PCR. TFE3 fusion preferential DNA binding was assessed with ChIP-sequencing. Oncogenic phenotype assessment was done in 2D culture and two different 3D models; 1) Solid tumor model, in which cancer cell interaction with extracellular matrix and stromal cells, were represented in multiculture-spheroid system, 2) Invasion model, in which cell ability to invade basement membrane barrier was modeled with matrix restricted spheroid. Results: Dissimilar oncogenic phenotypes were seen among RP-R07, UOK-109 and UOK-146 in 2D and 3D culture. The presence of nuclear E-Cadherin was observed in all three cells model, with increasing level of nuclear expression in fusion partner dependent manner (P Conclusions: Our results indicate a distinct biology underlying tRCC oncogenesis in different TFE3 fusion models involving kinase reprograming and nucleocytoplasmic shuttling regulation. These differences also suggest the possibility of generating personalized treatments targeting specific TFE3 fusion genes associated with the spliceosome machinery. Citation Format: Nur P. Damayanti, Sreenivasulu Chintala, Ashley Orillion, Remi Adelaiye-Ogala, May F. Elbanna, Pete Hollenhorst, Roberto Pili. Delineating translocation renal cell carcinoma oncogenesis in cells harboring TFE3 fusion with spliceosome machinery associated genes [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 4475. doi:10.1158/1538-7445.AM2017-4475

Background: Drug screening is a key component for drug development and optimizing anti-tumor therapies. Traditionally, in vitro drug testing has been conducted in monolayer systems that are not capable of recapitulating the tumor complexity. Recently, the field has witnessed the rise of interest in 3D culture systems which are capable of reproducing tumor complexity while circumventing the cost associated with in vivo drug testing. Our access to fresh patient samples has enabled us to establish a novel 3D culture system consisting of bladder cancer patient derived cell lines. Using a wide range of matrices and co-culture conditions with tumor associated stromal cells we were able to establish a unique high throughput drug testing tool. Methods: Matrigel and collagen based matrices were used to establish 3D culture systems of bladder cancer patient derived cells. Tumor cells were cultured in 3D conditions either alone or in coculture with tumor associated stromal cells. Response to Cisplatin and PI3K pathway targeted agents (i.e. LY LY3023414) was tested in both conditions. High throughput imaging via Thermo ArrayScan XTI was used to assess the biological behavior of spheroids as well as their response to therapies overtime. Confocal microscopy was used to validate the biological mimicry of tumor derived spheroids to the original patient tumors. Integration of RNA-seq data from the patient-derived tumor cells with the biological behavior and therapeutic response in 3D culture is ongoing for the purpose of characterizing the 3D model Results: In 3D culture conditions; bladder cancer derived cells were able to re-express E-cadherin that was suppressed upon propagation in monolayer. The re-expression of the epithelial marker (E-cadherin) observed in 3D accurately mirrors the original tumors; which are of epithelial origin. Phenotypic differences were observed across different matrix conditions and also among different tumor derived cells. Bladder 3D organoids of luminal origin were more sensitive to both cisplatin and PI3K pathway inhibitors as compared to those of basal origin. This drug response profile was reminiscent of what we observed in vivo using patient derived xenograft (PDX) models derived from the same tumors. The phenotypic as well as the drug response variations observed in our 3D culture correlated with variable gene expression profiles (luminal vs basal) that were detected in our RNA-seq data. Conclusion: As compared to monolayer, 3D culture is more capable of recapitulating tumor complexity and accurately reflects the drug resistance / sensitivity profiles that are observed in PDX models in vivo. Therefore, a 3D culture system provides an invaluable tool for high throughput screening of drugs in bladder cancer and providing a better understanding of tumor biology in the search of more effective treatments for bladder cancer patients. Citation Format: May Elbanna, Sreenivasulu Chintala, Eric Ciamporcero, Remi Adelayie, Ashley Orillion, Sreevani Arisa, Nur Damayanti, Michelle Grimard, TJ Puls, Sherry Harbin, Melissa Fishel, Roberto Pili. In vitro modeling of patient derived bladder cancer cell lines in 3D culture systems [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 5783. doi:10.1158/1538-7445.AM2017-5783

Background: Advanced renal cell carcinoma (RCC) responds initially to anti-angiogenic therapies but eventually develop resistance which may be driven by the expression of key intratumoral pro-survival protein and overall kinome reprogramming. Androgen receptor (AR) expression has been reported in clear cell renal cell carcinoma (ccRCC) but its biological role remains elusive and its association with resistance to tyrosine kinase inhibitors (TKIs) has not been studied. Here we report the role of AR and its association with resistance to TKIs in advanced RCC. Methods: Human RCC cell lines; 786-0, 786-0R (with induced sunitinib resistance), ACHN, URMC2 (with intrinsic sunitinib resistance) were used to assess the combination effect of sunitinib and the AR antagonist enzalutamide in vitro. In vivo studies utilizing 786-0 tumors assessed the combination effect of enzalutamide and sunitinib following acquired resistance to sunitinib. AR expression was detected by qRT-PCR and Western blot analysis, and AR localization by immunofluorescence in treated and non-treated cells. Gene array was used to assess 93 AR associated genes in sensitive and resistant cells. Results: Quantitative RT-PCR data revealed a significant increase in AR expression with sunitinib resistance (>100 folds; p>0.001). In vitro and in vivo studies indicated significant increase in nuclear and cytoplasmic expression of AR with sunitinib treatment in resistant cells which was abrogated with single agent enzalutamide and combination treatment. More interestingly, combination treatment of enzalutamide and sunitinib significantly decreased cell growth and induced tumor regression in vitro and in vivo, respectively. Conclusion: Our data suggest the role of AR both in intrinsic and acquired sunitinib resistance in ccRCC and provide a rationale for combination strategies to restore TKI sensitivity that can be tested in the clinical setting. Citation Format: Remi M. Adelaiye-Ogala, Sreenivasulu Chintala, Ashley Orillion, May Elbanna, Ben Elzey, Nur Damayanti, Kiersten M. Miles, Chinghai Kao, Piergiorgio Pettazzoni, Giulio F. Draetta, Roberto Pili. Targeting androgen receptor overcomes resistance to tyrosine kinase inhibitors in advanced clear cell renal cell carcinoma [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 4170. doi:10.1158/1538-7445.AM2017-4170