HCK Promotes High-Grade Serous Ovarian Cancer Tumorigenesis through CD44 and NOTCH3 Signaling

High-grade serous ovarian cancer (HGSOC) is a highly aggressive and lethal subtype of ovarian cancer. While most patients initially respond to standard-of-care treatment, the majority will eventually relapse and succumb to their disease. Despite significant advances in our understanding of this disease, the mechanisms that govern the distinctions between HGSOC with good and poor prognosis remain unclear. In this study, we implemented a proteogenomic approach to analyze gene expression, proteomic and phosphoproteomic profiles of HGSOC tumor samples to identify molecular pathways that distinguish HGSOC tumors relative to clinical outcome. Our analyses identify significant upregulation of hematopoietic cell kinase (HCK) expression and signaling in poor prognostic HGSOC patient samples. Analyses of independent gene expression datasets and IHC of patient samples confirmed increased HCK signaling in tumors relative to normal fallopian or ovarian samples and demonstrated aberrant expression in tumor epithelial cells. Consistent with the association between HCK expression and tumor aggressiveness in patient samples, in vitro phenotypic studies showed that HCK can, in part, promote cell proliferation, colony formation, and invasive capacity of cell lines. Mechanistically, HCK mediates these phenotypes, partly through CD44 and NOTCH3-dependent signaling, and inhibiting CD44 or NOTCH3 activity, either genetically or through gamma-secretase inhibitors, can revert HCK-driven phenotypes.

IMPLICATIONS

Collectively, these studies establish that HCK acts as an oncogenic driver of HGSOC through aberrant activation of CD44 and NOTCH3 signaling and identifies this network as a potential therapeutic opportunity in a subset of patients with aggressive and recurrent HGSOC.

SOX4-SMARCA4 complex promotes glycolysis-dependent TNBC cell growth through transcriptional regulation of Hexokinase 2

Tumor cells rely on increased glycolytic capacity to promote cell growth and progression. While glycolysis is known to be upregulated in the majority of triple negative (TNBC) or basal-like subtype breast cancers, the mechanism remains unclear. Here, we used integrative genomic analyses to identify a subset of basal-like tumors characterized by increased expression of the oncogenic transcription factor SOX4 and its co-factor the SWI/SNF ATPase SMARCA4. These tumors are defined by unique gene expression programs that correspond with increased tumor proliferation and activation of key metabolic pathways, including glycolysis. Mechanistically, we demonstrate that the SOX4-SMARCA4 complex mediates glycolysis through direct transcriptional regulation of Hexokinase 2 (HK2) and that aberrant HK2 expression and altered glycolytic capacity are required to mediate SOX4-SMARCA4-dependent cell growth. Collectively, we have defined the SOX4-SMARCA4-HK2 signaling axis in basal-like breast tumors and established that this axis promotes metabolic reprogramming which is required to maintain tumor cell growth.

Abstract P6-11-05: Carnitine palmitoyltransferase 1A (CPT1A) mediates therapeutic response to endocrine therapy in estrogen receptor positive breast cancer

Breast cancer (BC) is the most commonly diagnosed cancer and second leading cause of cancer-related deaths in women in the United States, with more than 70% of the cases are hormone receptor positive (HR+) disease. Endocrine based therapies (ET) are successfully used, however, 30-50% will acquire ET resistance leading to tumor progression. Since the mechanism of acquired resistance remains unknown for ~60% of patients, identifying novel mechanisms of resistance is essential. We recently reported that carnitine palmitoyltransferase 1A (CPT1A), the rate limiting enzyme in fatty acid oxidation, is overexpressed in aggressive HR+ tumors, including ET resistant patients. We propose that CPT1A level and activity changes the tumor microenvironment to enhance tumorigenesis and contribute to ET resistance. To determine the mechanism by which CPT1A is promoting cell proliferation, tumor microenvironment, cellular signaling and ET resistance, we used a series of in vitro studies incorporating a panel of either endogenously or experimentally derived CPT1A-low and CPT1A-high controls, HR+ breast cancer cell lines as well as their ET resistant counterparts. We determined that CPT1A is upregulated in cell lines that acquire ET resistance. Our analyses demonstrated that levels of CPT1A can affect tumor formation ability in both CPT1A-high and adjacent CPT1A-low tumor cells with concurrent changes in both intra- and inter-cellular signaling which may be essential to promote tumor progression and mediate therapeutic response. This represents a promising step in understanding the mechanisms that promote tumorigenesis and ET resistance in HR+ breast cancer.

Citation Format: Shaimaa Hussein, Michael L. Gatza, Shridar Ganesan. Carnitine palmitoyltransferase 1A (CPT1A) mediates therapeutic response to endocrine therapy in estrogen receptor positive breast cancer [abstract]. In: Proceedings of the 2022 San Antonio Breast Cancer Symposium; 2022 Dec 6-10; San Antonio, TX. Philadelphia (PA): AACR; Cancer Res 2023;83(5 Suppl):Abstract nr P6-11-05.

SMAD4 is critical in suppression of BRAF-V600E serrated tumorigenesis

BRAF-driven colorectal cancer is among the poorest prognosis subtypes of colon cancer. Previous studies suggest that BRAF-mutant serrated cancers frequently exhibit Microsatellite Instability (MSI) and elevated levels of WNT signaling. The loss of tumor-suppressor Smad4 in oncogenic BRAF-V600E mouse models promotes rapid serrated tumor development and progression, and SMAD4 mutations co-occur in human patient tumors with BRAF-V600E mutations. This study assesses the role of SMAD4 in early-stage serrated tumorigenesis. SMAD4 loss promotes microsatellite stable (MSS) serrated tumors in an oncogenic BRAF-V600E context, providing a model for MSS serrated cancers. Inactivation of Msh2 in these mice accelerated tumor formation, and whole-exome sequencing of both MSS and MSI serrated tumors derived from these mouse models revealed that all serrated tumors developed oncogenic WNT mutations, predominantly in the WNT-effector gene Ctnnb1 (β-catenin). Mouse models mimicking the oncogenic β-catenin mutation show that the combination of three oncogenic mutations (Ctnnb1, Braf, and Smad4) are critical to drive rapid serrated dysplasia formation. Re-analysis of human tumor data reveals BRAF-V600E mutations co-occur with oncogenic mutations in both WNT and SMAD4/TGFβ pathways. These findings identify SMAD4 as a critical factor in early-stage serrated cancers and helps broaden the knowledge of this rare but aggressive subset of colorectal cancer.

Nuclear Receptor-Mediated Metabolic Reprogramming and the Impact on HR+ Breast Cancer

Simple Summary

Breast cancer is the most commonly diagnosed and second leading cause of cancer-related deaths in women in the United States, with hormone receptor positive (HR+) tumors representing more than two-thirds of new cases. Recent evidence has indicated that dysregulation of multiple metabolic programs, which can be driven through nuclear receptor activity, is essential for tumor genesis, progression, therapeutic resistance and metastasis. This study will review the current advances in our understanding of the impact and implication of altered metabolic processes driven by nuclear receptors, including hormone-dependent signaling, on HR+ breast cancer.

Abstract

Metabolic reprogramming enables cancer cells to adapt to the changing microenvironment in order to maintain metabolic energy and to provide the necessary biological macromolecules required for cell growth and tumor progression. While changes in tumor metabolism have been long recognized as a hallmark of cancer, recent advances have begun to delineate the mechanisms that modulate metabolic pathways and the consequence of altered signaling on tumorigenesis. This is particularly evident in hormone receptor positive (HR+) breast cancers which account for approximately 70% of breast cancer cases. Emerging evidence indicates that HR+ breast tumors are dependent on multiple metabolic processes for tumor progression, metastasis, and therapeutic resistance and that changes in metabolic programs are driven, in part, by a number of key nuclear receptors including hormone-dependent signaling. In this review, we discuss the mechanisms and impact of hormone receptor mediated metabolic reprogramming on HR+ breast cancer genesis and progression as well as the therapeutic implications of these metabolic processes in this disease.

CPT1A and fatty acid β-oxidation are essential for tumor cell growth and survival in hormone receptor-positive breast cancer

Chromosome 11q13-14 amplification is a defining feature of high-risk hormone receptor-positive (HR+) breast cancer; however, the mechanism(s) by which this amplicon contributes to breast tumorigenesis remains unclear. In the current study, proteogenomic analyses of >3000 breast tumors from the TCGA, METABRIC and CPTAC studies demonstrated that carnitine palmitoyltransferase 1A (CPT1A), which is localized to this amplicon, is overexpressed at the mRNA and protein level in aggressive luminal tumors, strongly associated with indicators of tumor proliferation and a predictor of poor prognosis. In vitro genetic studies demonstrated that CPT1A is required for and can promote luminal breast cancer proliferation, survival, as well as colony and mammosphere formation. Since CPT1A is the rate-limiting enzyme during fatty acid oxidation (FAO), our data indicate that FAO may be essential for these tumors. Pharmacologic inhibition of FAO prevented in vitro and in vivo tumor growth and cell proliferation as well as promoted apoptosis in luminal breast cancer cells and orthotopic xenograft tumor models. Collectively, our data establish an oncogenic role for CPT1A and FAO in HR+ luminal tumors and provide preclinical evidence and rationale supporting further investigation of FAO as a potential therapeutic opportunity for the treatment of HR+ breast cancer.

Abstract 2456: SOX4 and SMARCA4 upregulate glycolysis-driven tumor proliferation through Hexokinase 2 in triple negative breast cancer

Triple-negative breast cancer (TNBC) accounts for nearly 1-in-4 breast cancer related deaths in the United States yearly despite representing 10-12% of newly diagnosed cases. This aggressive disease, which is largely synonymous with the basal-like molecular subtype, predominantly affects younger and African American women. Despite recent advances, overall survival has not drastically improved, highlighting the need to identify novel therapeutic opportunities. We determined that the oncogenic transcription factor SOX4 is overexpressed in ~88.1% of basal-like tumors relative to adjacent normal tissue. Immunoprecipitation follow by MS was identified the SWI/SNF ATPase SMARCA4 as an essential SOX4 cofactor that is concurrently overexpressed in basal-like tumors. Mechanistic studies showed that this complex is required to maintain an active open chromatin conformation at regulatory regions upstream of SOX4-regulated genes. To identify the functional impact of overexpression in TNBC, RNAseq and ChIPseq analyses were used to identify SMARCA4-dependent and -independent SOX4 gene expression programs. Analyses of 3,000+ tumor samples from the METABRIC and TCGA cohorts was used to investigate the functional and clinical implications of these gene expression programs in human tumors. Investigation of SOX4 and SMARCA4 binding to promoters and subsequent gene transcription identified SMARCA4-dependent down-stream signaling programs associated with overall worse prognosis and key metabolomic processes. This correlation was confirmed in vitro by demonstrating that both SOX4 and SMARCA4 could mediate changes in intracellular glucose consumption. Metabolomic profiling of breast cancer cell lines demonstrated that SOX4 overexpression resulted in increased glycolysis. Mechanistic studies have determined that SOX4/SMARCA4 transcriptionally regulate expression of Hexokinase 2 (HK2) which catalyzes the first step in glucose metabolism, and HK2 activity is essential for SOX4/SMARCA4-regulation of glycolysis. Given that our data demonstrate that SOX4 or SMARCA4 can regulate cell proliferation/survival and that glycolysis has been shown to modulate cell proliferation, we hypothesized that SOX4-SMARCA4 cooperatively regulate the proliferative capacity of TNBC cells through altered glucose consumption. Consistent with this premise, in vitro studies showed that SOX4 and SMARCA4 are essential for breast tumor cell proliferation, survival and colony formation. Importantly, genetic or pharmacological inhibition of HK2 results in reduced TNBC cell proliferation and growth. Collectively these data demonstrate that the SOX4/SMARCA4 complex mediates the proliferative capacity of TNBC cells by modulating metabolic processes. Given the drug-ability of the glycolysis pathway, these results may have important clinical implications for TNBC patient treatment.

Citation Format: Pooja Khanna, Gaurav Mehta, Vrushank Bhatt, Jessie Y. Guo, Michael L. Gatza. SOX4 and SMARCA4 upregulate glycolysis-driven tumor proliferation through Hexokinase 2 in triple negative breast cancer [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2021; 2021 Apr 10-15 and May 17-21. Philadelphia (PA): AACR; Cancer Res 2021;81(13_Suppl):Abstract nr 2456.

FOXA1 and adaptive response determinants to HER2 targeted therapy in TBCRC 036

Inhibition of the HER2/ERBB2 receptor is a keystone to treating HER2-positive malignancies, particularly breast cancer, but a significant fraction of HER2-positive (HER2+) breast cancers recur or fail to respond. Anti-HER2 monoclonal antibodies, like trastuzumab or pertuzumab, and ATP active site inhibitors like lapatinib, commonly lack durability because of adaptive changes in the tumor leading to resistance. HER2+ cell line responses to inhibition with lapatinib were analyzed by RNAseq and ChIPseq to characterize transcriptional and epigenetic changes. Motif analysis of lapatinib-responsive genomic regions implicated the pioneer transcription factor FOXA1 as a mediator of adaptive responses. Lapatinib in combination with FOXA1 depletion led to dysregulation of enhancers, impaired adaptive upregulation of HER3, and decreased proliferation. HER2-directed therapy using clinically relevant drugs (trastuzumab with or without lapatinib or pertuzumab) in a 7-day clinical trial designed to examine early pharmacodynamic response to antibody-based anti-HER2 therapy showed reduced FOXA1 expression was coincident with decreased HER2 and HER3 levels, decreased proliferation gene signatures, and increased immune gene signatures. This highlights the importance of the immune response to anti-HER2 antibodies and suggests that inhibiting FOXA1-mediated adaptive responses in combination with HER2 targeting is a potential therapeutic strategy.

SOX4 and SMARCA4 cooperatively regulate PI3k signaling through transcriptional activation of TGFBR2

Dysregulation of PI3K/Akt signaling is a dominant feature in basal-like or triple-negative breast cancers (TNBC). However, the mechanisms regulating this pathway are largely unknown in this subset of aggressive tumors. Here we demonstrate that the transcription factor SOX4 is a key regulator of PI3K signaling in TNBC. Genomic and proteomic analyses coupled with mechanistic studies identified TGFBR2 as a direct transcriptional target of SOX4 and demonstrated that TGFBR2 is required to mediate SOX4-dependent PI3K signaling. We further report that SOX4 and the SWI/SNF ATPase SMARCA4, which are uniformly overexpressed in basal-like tumors, form a previously unreported complex that is required to maintain an open chromatin conformation at the TGFBR2 regulatory regions in order to mediate TGFBR2 expression and PI3K signaling. Collectively, our findings delineate the mechanism by which SOX4 and SMARCA4 cooperatively regulate PI3K/Akt signaling and suggest that this complex may play an essential role in TNBC genesis and/or progression.

Recent Advances in Integrative Multi-Omics Research in Breast and Ovarian Cancer

The underlying molecular heterogeneity of cancer is responsible for the dynamic clinical landscape of this disease. The combination of genomic and proteomic alterations, including both inherited and acquired mutations, promotes tumor diversity and accounts for variable disease progression, therapeutic response, and clinical outcome. Recent advances in high-throughput proteogenomic profiling of tumor samples have resulted in the identification of novel oncogenic drivers, tumor suppressors, and signaling networks; biomarkers for the prediction of drug sensitivity and disease progression; and have contributed to the development of novel and more effective treatment strategies. In this review, we will focus on the impact of historical and recent advances in single platform and integrative proteogenomic studies in breast and ovarian cancer, which constitute two of the most lethal forms of cancer for women, and discuss the molecular similarities of these diseases, the impact of these findings on our understanding of tumor biology as well as the clinical applicability of these discoveries.

Abstract PD15-09: Sox4 and smarca4 upregulate glycolysis-driven tumor proliferation through hexokinase 2 in tnbc

Background Triple-negative breast cancer (TNBC) accounts for nearly 1-in-4 breast cancer related deaths in the United States each year despite representing 10-12% of newly diagnosed cases. This aggressive disease, which is largely synonymous with the basal-like molecular subtype, predominantly affects younger women and women of African American decent. Despite a number of recent advances, overall survival has not drastically improved, highlighting the need to better understand mechanisms regulating tumor growth and progression as a means to identify novel therapeutic opportunities in these patients.

Methods In order to identify the functional impact of overexpression of the oncogenic transcription factor SOX4 and its co-factor SMARCA4 in TNBC, RNAseq and ChIPseq analyses were used to identify SMARCA4-dependent and -independent SOX4 gene expression programs. Analyses of more than 3,000 tumor samples from the METABRIC and TCGA cohorts was used to investigate the functional implications and clinical association of these gene expression programs in human tumors. Mass spectrometry (MS)-based metabolomic profiling in conjunction with genetic and pharmacological-based in vitro studies were used to demonstrate the impact of these programs on tumor cell metabolism, cell viability and proliferation.

Results We, and others, have previously demonstrated that the oncogenic transcription factor SOX4 is overexpressed in basal-like tumors. In order to identify mechanisms by which this protein mediates breast cancer tumorigenesis, we first identified SOX4 co-factors. Immunoprecipitation follow by MS was used to identify the SWI/SNF ATPase SMARCA4 as a prominent SOX4 cofactor that is concurrently overexpressed in basal-like tumors. Mechanistic studies showed that this complex is required to maintain an active open chromatin conformation at regulatory regions upstream of SOX4-regulated genes. ChIPseq and RNAseq-based analyses were next used to investigate the role of this complex in TNBC signaling and tumorigenesis. Our analyses identified SMARCA4-dependent and -independent SOX4 gene expression programs and demonstrated that SMARCA4-dependent SOX4 signaling is associated with poor clinical outcome. Further in silico analyses of human tumors indicate that each program mediates distinct down-stream signaling; SMARCA4-dependent signaling is associated with altered tumor metabolism and increased proliferative signaling. Consistent with this premise, in vitro studies showed that SOX4 and SMARCA4 are essential for breast tumor cell proliferation, survival and colony formation. Metabolomic profiling of breast cancer cell lines demonstrated that SOX4 overexpression resulted in increased glycolysis. The effect of SOX4 and SMARCA4 on cell metabolism was validated by demonstrating that this complex can mediate intracellular glucose consumption. Finally, we determined that SOX4 and SMARCA4 cooperatively regulate mRNA expression of hexokinase 2 (HK2), which catalyzes for the first step in glucose metabolism, and demonstrated that HK2 activity is essential for SOX4/SMARCA4-regulation of glycolysis. Importantly, in vitro genetic and pharmacological studies identified a link between HK2 activity, glycolysis and SOX4/SMARCA4-mediated cell proliferation and viability in TNBC.

Conclusions Our studies have identified SOX4 and its transcriptional cofactor SMARCA4 as being uniformly overexpressed in basal-like or TNBC tumors. These analyses demonstrate that SOX4 and SMARCA4 cooperatively promote tumorigenesis in TNBC cells, in part, by modulating glycolysis and cell proliferation through transcriptional regulation of HK2. Given the drug-ability of the glycolysis pathway, these results have potential clinical implications for treatment of TNBC patients.

Citation Format: Pooja Khanna, Gaurav Mehta, Michael L Gatza. Sox4 and smarca4 upregulate glycolysis-driven tumor proliferation through hexokinase 2 in tnbc [abstract]. In: Proceedings of the 2020 San Antonio Breast Cancer Virtual Symposium; 2020 Dec 8-11; San Antonio, TX. Philadelphia (PA): AACR; Cancer Res 2021;81(4 Suppl):Abstract nr PD15-09.

Abstract PO-035: SOX4 and SMARCA4 upregulate glycolysis-driven tumor proliferation through Hexokinase 2 in Triple Negative Breast Cancer

SOX4 is a well-established oncogenic transcription factor and has been shown to be associated with malignant transformation and metastasis in several cancer types including breast, prostate, acute lymphoblastic leukemia, and melanoma. While SOX4 is overexpressed in ~85% of TNBCs (Triple Negative Breast Cancers), the mechanisms by which it contributes to activation of pro-proliferative or pro-survival signaling in these tumors remains unclear. We determined that SOX4 forms a novel and essential complex with the SWI/SNF ATPase SMARCA4 and demonstrated that this complex is required to maintain an open and active chromatin conformation at the promoter and enhancer regions of SOX4-regulated genes. An integrated analysis of ChIPseq and RNAseq data was used to identify SMARCA4-dependent and SMARCA4-independent SOX4 gene expression programs and enrichment analyses indicated that these programs are responsible for unique down-stream signaling networks. SMARCA4-dependent SOX4 signaling was found to be correlate with a poor prognosis in TNBC tumors and was associated with increased cell proliferation and activation of pro-oncogenic processes, including glycolysis. Consistent with these data, in vitro studies showed that SOX4 and SMARCA4 are essential for TNBC breast tumor cell proliferation, survival and colony formation. Mass spectrometry-based metabolomic profiling was used to demonstrate that SOX4 can induce glycolysis as evident by increased glucose-6-phosphate, glyceralehyde-3-phosphate, dihydroxyacetone phosphate, 2-phosphoglycerate, pyruvate and lactate following SOX4 overexpression and the effect of SOX4 and SMARCA4 on glucose consumption was confirmed in vitro. Mechanistically, we determined that SOX4 and SMARCA4 cooperate to transcriptionally regulate expression of Hexokinase 2 (HK2), which catalyzes the first step in glucose metabolism, and that increased expression of HK2 is required to mediate SOX4-dependent glycolysis. Finally we demonstrate that genetic or pharmacological inhibition of HK2 results in reduced TNBC cell proliferation and growth. Collectively, our data suggest that SOX4 and SMARCA4 cooperate to regulate glycolysis and cell proliferation in TNBC in part through activation of HK2 expression. Given the noted association between SOX4 expression and increased tumor proliferation and aggressiveness in multiple forms of cancer, as well as evidence that SOX4 can regulate SMARCA4 expression, these data suggest that aberrant SOX4 activity may have a similar effect on metabolic and cell signaling across multiple tumor types.

Citation Format: Pooja Khanna, Gaurav Mehta, Vrushank Bhatt, Jessie Y. Guo, Michael L. Gatza. SOX4 and SMARCA4 upregulate glycolysis-driven tumor proliferation through Hexokinase 2 in Triple Negative Breast Cancer [abstract]. In: Abstracts: AACR Special Virtual Conference on Epigenetics and Metabolism; October 15-16, 2020; 2020 Oct 15-16. Philadelphia (PA): AACR; Cancer Res 2020;80(23 Suppl):Abstract nr PO-035.

Abstract 5858: Multiplatform analyses identify upregulated hematopoietic cell kinase activity in poorly prognostic high-grade serous ovarian cancer and its role in regulating tumor aggressiveness

High-grade serous ovarian cancer (HGSOC) is the most predominant and lethal subtype of ovarian cancer. While most patients initially respond to standard-of-care treatment, the majority will eventually relapse. Despite improved treatment strategies, the prognosis has not improved significantly and the overall 5-year survival rate remains ~31%. To understand the underlying mechanisms that govern the distinctions between tumors with good and poor prognoses, we implemented a proteogenomic approach to analyze gene expression, proteomic and phosphoproteomic profiles of HGSOC tumors available in the TCGA and the CPTAC studies. Our analyses identified upregulated hematopoietic cell kinase (HCK) signaling along with innate immunity related and ERBB activity in poor prognostic tumors. These results were confirmed using independent datasets to demonstrate HCK up-regulation in tumor samples compared to borderline tumors and/or normal samples. Further analyses of micro-dissected HGSOC tumor tissue determined that HCK was specifically upregulated in tumor epithelial cells. Importantly, differential analysis of CPTAC phospho-proteomic data identified significant enrichment of phosphorylated HCK in the primary tumors of patients with tumor recurrence within 1 year compared to tumor-free patients. Interestingly, in-silico analyses suggest that HCK may play a dichotomous tumorigenic role as HCK was strongly associated with pro-survival signaling pathways as well as enrichment of pro-tumorigenic immune signaling. Consistent with these results, in vitro studies in NIH-OVCAR3 and CAOV3 cell lines with high endogenous HCK expression demonstrated that HCK silencing decreased cell proliferation, invasion, and colony formation. Conversely, HCK overexpression significantly induced proliferation and clonogenic capacity in OVSAHO cells (low HCK). These results suggest that HCK is essential for HGSOC proliferation and survival. Reverse phase protein array (RPPA) analysis was next used to identify potential mechanisms by which HCK modulates HGSOC tumorigenesis. Our analyses identified a number of candidate proteins that are significantly downregulated following shRNA-mediated silencing of HCK including PD-L1, CD44, and NOTCH3. Further in silico analyses demonstrated significant enrichment of PD-L1 protein expression in HGSOC tumors with high HCK activity suggesting a potential role for HCK in regulating the tumor microenvironment. These latter analyses also identified a significant correlation between HCK and CD44 mRNA and protein expression in human tumors. Importantly, experimental studies in CAOV3 cells confirmed that shRNA silencing of HCK inhibited PD-L1, CD44 and NOTCH3 protein expression; these results were confirmed by lentiviral overexpression of HCK which resulted in increased CD44 and NOTCH3 expression in OVSAHO cells. Given that CD44 and NOTCH3 signaling have been shown to mediate tumor cell proliferation and survival, our data, which indicate that CD44 and NOTCH3 expression are regulated by HCK activity, suggest that these genes may contribute to HCK mediated HGSOC tumorigenesis. Our data collectively implicate HCK as a novel driver of HGSOC development and progression and may represent a novel therapeutic opportunity in this subset of patients.

Citation Format: Christen A. Khella, Michael L. Gatza. Multiplatform analyses identify upregulated hematopoietic cell kinase activity in poorly prognostic high-grade serous ovarian cancer and its role in regulating tumor aggressiveness [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 5858.

Abstract P3-03-02: Integrative proteogenomic analyses identifies CPT1A and fatty acid oxidation as a potential therapeutic strategy in hormone receptor positive breast cancer

Background: Clinically, approximately two-thirds of the nearly 250,000 breast cancer cases diagnosed each year in the United States are hormone receptor positive (HR+), luminal breast tumors. Slower growing luminal breast tumors are often successfully treated using endocrine based therapies resulting in a relatively good prognosis for these patients. However more highly proliferative luminal tumors are often resistant, or become resistant, to current therapies leading to a worse outcome for these patients. As such, there is a critical need to identify genomic alterations and dysregulated signaling pathway in this subset of tumors that may represent novel therapeutic opportunities. Methods: In order to identify genetic events responsible for tumorigenesis and to identify potential drug-able genetic alterations and/or pathways associated with high levels of proliferation in HR+ tumors, we used an integrative genomics-based strategy to interrogate orthogonal genome-wide data from more than 2,500 patients from the TCGA, METABRIC, CPTAC studies. Data from a genome-wide RNAi screen was used to delineate essential from non-essential genes in HR+ breast cancer cell lines. Genetic and pharmacological-based in vitro and in vivo studies were used to demonstrate the impact identified candidate genes on cell viability, proliferation, colony formation, spheroid formation and tumor growth rate. Results: Integrative genomic analyses of human breast tumors identified DNA amplification as well as mRNA and protein over-expression of carnitine palmitoyltransferase 1A (CPT1A) in highly proliferative luminal tumors. Further in silico analyses demonstrated that high CPT1A expression corresponded with protein markers of proliferation in human tumors and is prognostic in HR+ tumors in both the TCGA and METABRIC cohorts. Since CPT1A is the rate limiting enzyme responsible for fatty acid import into the mitochondria during Fatty Acid β Oxidation (FAO), these data indicate that highly proliferative luminal tumors may utilize FAO as a prominent energy source. As such, we hypothesized that inhibiting CPT1A and/or FAO in this subset of tumors or cell lines may represent a potential therapeutic opportunity. Consistent with our hypothesis, analyses of data from a genome-wide RNAi screen in 27 breast cancer cell lines suggested that HR+ cells lines are dependent on CPT1A expression. Importantly, we experimentally demonstrated that in vitro genetic silencing of CPT1A or pharmacological inhibition of FAO in ER+ breast cancer cell lines results in reduced cell viability and increased cell death as well as decreased spheroid formation. Importantly, our data indicated that in vivo inhibition of CPT1A resulted in decreased tumor volume and growth rate in orthotopic xenograft tumor models. Conclusions: In this study, integrative proteogenomic analyses identified amplification and over-expression of CPT1A in highly proliferative ER+ breast tumors. In vitro and in vivo studies demonstrated that CPT1A is an essential oncogenic driver in HR+/luminal breast cancer and establish CTP1A/FAO inhibition as a putative therapeutic strategy for treatment of these tumors.

Citation Format: Michael L Gatza, Vrushank Bhatt, Kimberly Parker, Guarav Mehta, Christen Khella, Yanxiang Guo, Nidhi Jariwala. Integrative proteogenomic analyses identifies CPT1A and fatty acid oxidation as a potential therapeutic strategy in hormone receptor positive breast cancer [abstract]. In: Proceedings of the 2019 San Antonio Breast Cancer Symposium; 2019 Dec 10-14; San Antonio, TX. Philadelphia (PA): AACR; Cancer Res 2020;80(4 Suppl):Abstract nr P3-03-02.

Aggressive Mammary Cancers Lacking Lymphocytic Infiltration Arise in Irradiated Mice and Can Be Prevented by Dietary Intervention

Because the incidence of breast cancer increases decades after ionizing radiation exposure, aging has been implicated in the evolution of the tumor microenvironment and tumor progression. Here, we investigated radiation-induced carcinogenesis using a model in which the mammary glands of 10-month-old BALB/c mice were transplanted with Trp53-null mammary tissue 3 days after exposure to low doses of sparsely ionizing γ-radiation or densely ionizing particle radiation. Mammary transplants in aged, irradiated hosts gave rise to significantly more tumors that grew more rapidly than those in sham-irradiated mice, with the most pronounced effects seen in mice irradiated with densely ionizing particle radiation. Tumor transcriptomes identified a characteristic immune signature of these aggressive cancers. Consistent with this, fast-growing tumors exhibited an immunosuppressive tumor microenvironment with few infiltrating lymphocytes, abundant immunosuppressive myeloid cells, and high COX-2 and TGFβ. Only irradiated hosts gave rise to tumors lacking cytotoxic CD8⁺ lymphocytes (defined here as immune desert), which also occurred in younger irradiated hosts. These data suggest that host irradiation may promote immunosuppression. To test this, young chimera mice were fed chow containing a honeybee-derived compound with anti-inflammatory and immunomodulatory properties, caffeic acid phenethyl ester (CAPE). CAPE prevented the detrimental effects of host irradiation on tumor growth rate, immune signature, and immunosuppression. These data indicated that low-dose radiation, particularly densely ionizing exposure of aged mice, promoted more aggressive cancers by suppressing antitumor immunity. Dietary intervention with a nontoxic immunomodulatory agent could prevent systemic effects of radiation that fuel carcinogenesis, supporting the potential of this strategy for cancer prevention.

Integrative proteogenomic analyses of human tumours identifies ADNP as a novel oncogenic mediator of cell cycle progression in high-grade serous ovarian cancer with poor prognosis

Background

Despite toxic side effects and limited durable response, the current standard-of-care treatment for high grade serous ovarian cancer (HGSOC) remains platinum/taxane-based chemotherapy. Given that the overall prognosis has not improved drastically over the past several decades, there is a critical need to understand the underlying mechanisms that lead to tumour development and progression.

Methods

We utilized an integrative proteogenomic analysis of HGSOC tumours applying a poor prognosis gene expression signature (PPS) as a conceptual framework to analyse orthogonal genomic and proteomic data from the TCGA (n = 488) and CPTAC (n = 169) studies. Genes identified through in silico analyses were assessed in vitro studies to demonstrate their impact on proliferation and cell cycle progression.

Findings

These analyses identified DNA amplification and overexpression of the transcription factor ADNP (Activity Dependent Neuroprotector Homeobox) in poorly prognostic tumours. Validation studies confirmed the prognostic capacity of ADNP and suggested an oncogenic role for this protein given the association between ADNP expression and pro-proliferative signalling. In vitro studies confirmed ADNP as a novel and essential mediator of cell proliferation through dysregulation of cell cycle checkpoints.

Interpretation

We identified ADNP as being amplified and overexpressed in poor prognosis HGSOC in silico analyses and demonstrated that ADNP is a novel and essential oncogene in HGSOC which mediates proliferation through dysregulation of cell cycle checkpoints in vitro.

Funding

The National Cancer Institute of the National Institutes of Health, the V Foundation for Cancer Research and the New Jersey Commission for Cancer Research.

Emerging Role of SOX Proteins in Breast Cancer Development and Maintenance

The SOX genes encode a family of more than 20 transcription factors that are critical regulators of embryogenesis and developmental processes and, when aberrantly expressed, have been shown to contribute to tumor development and progression in both an oncogenic and tumor suppressive role. Increasing evidence demonstrates that the SOX proteins play essential roles in multiple cellular processes that mediate or contribute to oncogenic transformation and tumor progression. In the context of breast cancer, SOX proteins function both as oncogenes and tumor suppressors and have been shown to be associated with tumor stage and grade and poor prognosis. Experimental evidence demonstrates that a subset of SOX proteins regulate critical aspects of breast cancer biology including cancer stemness and multiple signaling pathways leading to altered cell proliferation, survival, and tumor development; EMT, cell migration and metastasis; as well as other tumor associated characteristics. This review will summarize the role of SOX family members as important mediators of tumorigenesis in breast cancer, with an emphasis on the triple negative or basal-like subtype of breast cancer, as well as examine the therapeutic potential of these genes and their downstream targets.

Multi-omic Dissection of Oncogenically Active Epiproteomes Identifies Drivers of Proliferative and Invasive Breast Tumors

Proliferative and invasive breast tumors evolve heterogeneously in individual patients, posing significant challenges in identifying new druggable targets for precision, effective therapy. Here we present a functional multi-omics method, interaction-Correlated Multi-omic Aberration Patterning (iC-MAP), which dissects intra-tumor heterogeneity and identifies in situ the oncogenic consequences of multi-omics aberrations that drive proliferative and invasive tumors. First, we perform chromatin activity-based chemoproteomics (ChaC) experiments on breast cancer (BC) patient tissues to identify genetic/transcriptomic alterations that manifest as oncogenically active proteins. ChaC employs a biotinylated small molecule probe that specifically binds to the oncogenically active histone methyltransferase G9a, enabling sorting/enrichment of a G9a-interacting protein complex that represents the predominant BC subtype in a tissue. Second, using patient transcriptomic/genomic data, we retrospectively identified some G9a interactor-encoding genes that showed individualized iC-MAP. Our iC-MAP findings represent both new diagnostic/prognostic markers to identify patient subsets with incurable metastatic disease and targets to create individualized therapeutic strategies.

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ChaC dissects tumor heterogeneity for identifying oncogenic-active proteins

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An oncogenic-active G9a-interactome represents the invasive tumor in a tissue

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iC-MAP identifies multi-omics aberrations that drive invasive tumors

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Patient-specific iC-MAP of select interactor genes are of prognostic value

Multi-Omic Data Interpretation to Repurpose Subtype Specific Drug Candidates for Breast Cancer

Triple-negative breast cancer (TNBC), which is largely synonymous with the basal-like molecular subtype, is the 5th leading cause of cancer deaths for women in the United States. The overall prognosis for TNBC patients remains poor given that few treatment options exist; including targeted therapies (not FDA approved), and multi-agent chemotherapy as standard-of-care treatment. TNBC like other complex diseases is governed by the perturbations of the complex interaction networks thereby elucidating the underlying molecular mechanisms of this disease in the context of network principles, which have the potential to identify targets for drug development. Here, we present an integrated "omics" approach based on the use of transcriptome and interactome data to identify dynamic/active protein-protein interaction networks (PPINs) in TNBC patients. We have identified three highly connected modules, EED, DHX9, and AURKA, which are extremely activated in TNBC tumors compared to both normal tissues and other breast cancer subtypes. Based on the functional analyses, we propose that these modules are potential drivers of proliferation and, as such, should be considered candidate molecular targets for drug development or drug repositioning in TNBC. Consistent with this argument, we repurposed steroids, anti-inflammatory agents, anti-infective agents, cardiovascular agents for patients with basal-like breast cancer. Finally, we have performed essential metabolite analysis on personalized genome-scale metabolic models and found that metabolites such as sphingosine-1-phosphate and cholesterol-sulfate have utmost importance in TNBC tumor growth.

Abstract P2-03-03: BRG1-SOX4 mediates a novel and essential signaling network that activates PI3K/Akt signaling in TNBC

Background:

Triple negative (TNBC) breast cancer, which is largely synonymous with the basal-like molecular subtype, is an aggressive malignancy that accounts for nearly 1 in 4 breast cancer related deaths and disproportionately affects younger women and women of African American decent. Given the lack of drug-able targets expressed by TNBC tumors, few therapeutic options exist beyond currently utilized cytotoxic therapies, and the overall prognosis for these patients remains poor. While TNBC tumors are characterized by high PI3K signaling, clinical trials targeting this pathway have had limited success. Therefore, identifying mechanisms driving key oncogenic pathways, including PI3K, is paramount to understanding the transformation process and enabling the development of rational, personalized therapeutic regimens.

Methods:

We utilized a PI3K gene expression signature as a conceptual framework to analyze genome-wide mRNA expression and DNA copy number data from human breast tumors to identify genetic drivers of PI3K/Akt signaling. Kinome profiling was used to identify changes in the drug-able kinome regulated by these genes and in vitro studies were used to delineate mechanisms by which identified genes mediate oncogenic PI3K signaling in TNBC.

Results:

Integrative proteogenomic analyses of orthogonal genome-wide data from ˜3,000 human tumors from the TCGA and METABRIC studies identified amplification and overexpression of the oncogenic transcription factor SOX4 as well as the SWI/SNF ATPase BRG1 in tumors with high PI3K activity. These alterations were predominantly expressed in TNBC or basal-like breast tumors. Chromatin immunoprecipitation followed by DNA sequencing (ChIPseq) as well as shRNA-based studies confirmed that BRG1 regulates SOX4 expression in TNBC cell lines. Analyses of data from a genome-wide RNA interference (RNAi) screen in 27 breast cancer cell lines further indicated that SOX4 is essential in cell lines with high PI3K activity and this was confirmed by colony formation and cell proliferation assays. Importantly, in vitro analyses confirmed that both BRG1 and SOX4 regulate Akt phosphorylation and down-stream signaling. Profiling of the drug-able kinome in SOX4 depleted cell lines compared to control cells using Multiplexed kinase Inhibitor Beads couple with quantitative Mass Spectrometry (MIB/MS) identified 21 drug-able kinases regulated by SOX4 activity including TGFBR2 which has been previously shown to regulate PI3K activity. RNA sequencing (RNAseq) and RT-PCR analyses confirmed that SOX4 mediates TGFBR2 mRNA levels and co-immunoprecipitation experiments in conjunction with ChIP assays demonstrated that BRG1 and SOX4 form a complex at the TGFBR2 promoter and enhancer region to regulate TGFBR2 expression.

Abstract P4-07-03: Immunomodulation of triple negative breast cancer by caffeic acid phenethyl ester (CAPE)

Background: CAPE is the major active component of propolis, a widely available, safe, honeybee natural product with anti-inflammatory, antioxidant, and antitumor properties. We have previously shown diverse effects of CAPE in breast cancer. We postulated that CAPE may be useful in primary or secondary prevention for triple-negative breast cancers (TNBC) and evaluated this in a Trp53 null mammary chimera model in which the tumor spectrum is shifted to TNBC when the host is irradiated (Nguyen, 2011). Bioinformatics species comparisons show that TNBC from this model exhibits a spectrum of tumors that is molecularly similar to that seen in human TNBC (Nguyen, 2013).

Methods: The model consists of Trp53 null mammary epithelium transplanted to cleared mammary glands of wildtype mice. Mice irradiated with 1 Gy received transplants 3 days later and were placed on a CAPE or a control diet at 1month post transplantation that was maintained throughout the experiment. Tumor development was monitored by palpation for up to 18 months. Tumors were immunostained for estrogen receptor (ER) status and ER negative tumors were selected from all the groups for RNA sequencing. TNBC molecular subtypes were determined for control (n=5) and CAPE treated (n=9) samples using methods described by Lehman, 2011. Gene expression signatures consisting of 270 genes was analyzed for functional enrichment to identify patterns of signaling, as well as additional tumor characteristics, in each cohort of tumors.

Results: Host irradiation significantly accelerated tumor growth rate compared to the control sham irradiated mice. CAPE treatment blocked this effect, but did not affect the control tumor growth rate. Resected tumors in CAPE treated mice recurred at significantly longer intervals (40 days in control group versus 90 days with CAPE) and much less frequently than tumors from mice on a control diet. Mean expression analysis showed that CAPE induces a distinct gene expression pattern in ER negative tumors from irradiated mice. As previously described (Illa-Bochaca, 2014), ER negative tumors from sham irradiated mice on a control diet were enriched in immune response genes. These genes were suppressed in tumors arising in irradiated host, but this effect of host irradiation was abrogated in mice on the CAPE diet. While untreated tumors were classified into the Basal-like 2 (BL2) or Mesenchymal TNBC molecular subtypes, we observed an increase in subtype diversity after CAPE treatment with tumors being classified as Immunomodulatory and Luminal Androgen Receptor (LAR) in addition to BL2 and Mesenchymal subtypes. Consistent with these data, functional enrichment analyses of RNA sequencing data identified increased immune signaling as well as upregulation of a number of signaling pathways including TGFβ, HGF, and EGFR in treated samples.

Conclusion: These findings support the potential use of CAPE to modify the aggressive behavior of TNBC, which may be due to effects on the immune system in which CAPE acts to re-establish anti-tumor immunity. The finding that CAPE treatment shifts the tumor spectrum to Immunomodulatory subtypes suggests that it may be useful both for women at high risk for TNBC and to prevent or delay TNBC breast cancer recurrence, perhaps in combination with immunotherapy.

Citation Format: Omene C, Patel M, Karagoz K, Gatza ML, Barcellos-Hoff MH. Immunomodulation of triple negative breast cancer by caffeic acid phenethyl ester (CAPE) [abstract]. In: Proceedings of the 2018 San Antonio Breast Cancer Symposium; 2018 Dec 4-8; San Antonio, TX. Philadelphia (PA): AACR; Cancer Res 2019;79(4 Suppl):Abstract nr P4-07-03.

Exosomal miRNA confers chemo resistance via targeting Cav1/p-gp/M2-type macrophage axis in ovarian cancer

Background

Circulating miRNAs are known to play important roles in intercellular communication. However, the effects of exosomal miRNAs on cells are not fully understood.

Methods

To investigate the role of exosomal miR-1246 in ovarian cancer (OC) microenvironment, we performed RPPA as well as many other in vitro functional assays in ovarian cancer cells (sensitive; HeyA8, Skov3ip1, A2780 and chemoresistant; HeyA8-MDR, Skov3-TR, A2780-CP20). Therapeutic effect of miR-1246 inhibitor treatment was tested in OC animal model. We showed the effect of OC exosomal miR-1246 uptake on macrophages by co-culture experiments.

Findings

Substantial expression of oncogenic miR-1246 OC exosomes was found. We showed that Cav1 gene, which is the direct target of miR-1246, is involved in the process of exosomal transfer. A significantly worse overall prognosis were found for OC patients with high miR-1246 and low Cav1 expression based on TCGA data. miR-1246 expression were significantly higher in paclitaxel-resistant OC exosomes than in their sensitive counterparts. Overexpression of Cav1 and anti-miR-1246 treatment significantly sensitized OC cells to paclitaxel. We showed that Cav1 and multi drug resistance (MDR) gene is involved in the process of exosomal transfer. Our proteomic approach also revealed that miR-1246 inhibits Cav1 and acts through PDGFβ receptor at the recipient cells to inhibit cell proliferation. miR-1246 inhibitor treatment in combination with chemotherapy led to reduced tumor burden in vivo. Finally, we demonstrated that when OC cells are co-cultured with macrophages, they are capable of transferring their oncogenic miR-1246 to M2-type macrophages, but not M0-type macrophages.

Interpretation

Our results suggest that cancer exosomes may contribute to oncogenesis by manipulating neighboring infiltrating immune cells. This study provide a new mechanistic therapeutic approach to overcome chemoresistance and tumor progression through exosomal miR-1246 in OC patients.

Recurrence analysis on prostate cancer patients with Gleason score 7 using integrated histopathology whole-slide images and genomic data through deep neural networks

Prostate cancer is the most common nonskin-related cancer, affecting one in seven men in the United States. Gleason score, a sum of the primary and secondary Gleason patterns, is one of the best predictors of prostate cancer outcomes. Recently, significant progress has been made in molecular subtyping prostate cancer through the use of genomic sequencing. It has been established that prostate cancer patients presented with a Gleason score 7 show heterogeneity in both disease recurrence and survival. We built a unified system using publicly available whole-slide images and genomic data of histopathology specimens through deep neural networks to identify a set of computational biomarkers. Using a survival model, the experimental results on the public prostate dataset showed that the computational biomarkers extracted by our approach had hazard ratio as 5.73 and C -index as 0.74, which were higher than standard clinical prognostic factors and other engineered image texture features. Collectively, the results of this study highlight the important role of neural network analysis of prostate cancer and the potential of such approaches in other precision medicine applications.

Abstract B45: Amplification of ADNP and CEP250 promotes poor prognosis in high-grade serous ovarian cancer

High-grade serous ovarian cancer (HGSOC) is the most commonly diagnosed and most lethal subtype of gynecologic cancer. The poor prognosis associated with this disease stems from two major problems: diagnosis at later stages when ovarian cancer cells have metastasized to distant organs and intrinsic or developed resistance to primary platinum-taxane based therapies. Therefore, understanding the driver mechanisms of HGSOC is required to discover more effective therapeutic agents and identify potential drug targets.

In this study, we applied an integrative multi-omics approach based on the use of a poor-prognostic gene expression signature as a conceptual framework to analyze orthogonal genomic and proteomic data from human ovarian tumors derived from the TCGA (n=489) and CPTAC (n=169) projects, including RNA expression, DNA copy number alterations, protein and phosphoprotein expression. In combination with data from a genome-wide RNA-mediated interference screen in human ovarian cancer cell lines, we also identified essential genetic drivers of poor prognosis.

We identified genes in amplified regions that were positively correlated with poor-prognostic signature and showed an increased amplification frequency (q < 0.05). Then, we applied the poor-prognostic gene expression signatures to a panel of 29 ovarian cancer cell lines that had mRNA expression data and were also part of an RNAi proliferation screen in which a genome-wide shRNA library (~9,000 genes) had been used to identify essential genes. We used a negative Spearman rank correlation to identify essential genes in context of poor-prognosis signature. To prioritize these candidate genes, we next compared the results of these analyses and identified 128 genes that were uniquely essential for cell viability in ovarian cancer cell lines and that were amplified in the context of the poor-prognosis signature.

In order to uncover underlying mechanisms in HGSOC, we examined relationships between the poor-prognostic gene expression signature score and proteins and phosphoprotein expression. We used a Spearman correlation comparing poor-prognostic signature score to protein expression level. The proteomic data obtained from different platforms that are analyses of reverse phase protein array (RPPA) (n=412) data including 141 proteins and 31 phosphoproteins and mass-spectrometry (MS)-based (n=169) data including 3330 proteins (n=169) and 2533 (n=69) phosphoproteins. Significant proteins derived from TCGA data enriched with biologic processes including cell cycle control (p=6.8E-11), cell proliferation and differentiation (P=1.9E-7) and inhibition of apoptosis (P=1.4E-5) and signaling pathways including ERBB signaling (P=3.0E-10), mTOR signaling (P=5.9E-9) and insulin signaling (P=2.9E-7) pathways. Significant proteins derived from CPTAC data played role in splicesome (P=2.4E-24), chromatin packaging and remodeling (P=3.7E-4), and cell cycle (P=1.2E-3).

Next, we integrated all these analyses and determined that amplified essential genes including ADNP (Activity-Dependent Neuroprotective Protein), CEP250 (Centrosomal Nek2-Associated Protein 1), and MED1 (Mediator Complex Subunit 1) are also involved in significant phosphorylated proteins (P<0.05) correlated with poor-prognostic signature. We determined that amplification of ADNP (P = 0.0228; hazard ratio (HR), 0.84), CEP250 (P = 0.0346; HR, 0.82) predicted a significantly worse outcome in HGSOC patients, whereas MED1 amplification had no effect on patient survival (P = 0.0803).

In conclusion, these analyses suggest that ADNP and CEP250 amplification are novel modulators of poor prognosis in ovarian cancer, and that these alterations are not only potential drivers of oncogenesis but also their associated pathways may represent novel therapeutic targets in HGSOC.

Citation Format: Kubra Karagoz, Christen Khella, Michael L. Gatza. Amplification of ADNP and CEP250 promotes poor prognosis in high-grade serous ovarian cancer. [abstract]. In: Proceedings of the AACR Conference: Addressing Critical Questions in Ovarian Cancer Research and Treatment; Oct 1-4, 2017; Pittsburgh, PA. Philadelphia (PA): AACR; Clin Cancer Res 2018;24(15_Suppl):Abstract nr B45.

Tumor mutational burden is a determinant of immune-mediated survival in breast cancer

Mounting evidence supports a role for the immune system in breast cancer outcomes. The ability to distinguish highly immunogenic tumors susceptible to anti-tumor immunity from weakly immunogenic or inherently immune-resistant tumors would guide development of therapeutic strategies in breast cancer. Genomic, transcriptomic and clinical data from The Cancer Genome Atlas (TCGA) and Molecular Taxonomy of Breast Cancer International Consortium (METABRIC) breast cancer cohorts were used to examine statistical associations between tumor mutational burden (TMB) and the survival of patients whose tumors were assigned to previously-described prognostic immune subclasses reflecting favorable, weak or poor immune-infiltrate dispositions (FID, WID or PID, respectively). Tumor immune subclasses were associated with survival in patients with high TMB (TMB-Hi, P < 0.001) but not in those with low TMB (TMB-Lo, P = 0.44). This statistical relationship was confirmed in the METABRIC cohort (TMB-Hi, P = 0.047; TMB-Lo, P = 0.39), and also found to hold true in the more-indolent Luminal A tumor subtype (TMB-Hi, P = 0.011; TMB-Lo, P = 0.91). In TMB-Hi tumors, the FID subclass was associated with prolonged survival independent of tumor stage, molecular subtype, age and treatment. Copy number analysis revealed the reproducible, preferential amplification of chromosome 1q immune-regulatory genes in the PID immune subclass. These findings demonstrate a previously unappreciated role for TMB as a determinant of immune-mediated survival of breast cancer patients and identify candidate immune-regulatory mechanisms associated with immunologically cold tumors. Immune subtyping of breast cancers may offer opportunities for therapeutic stratification.

SMAD4 Suppresses WNT-Driven Dedifferentiation and Oncogenesis in the Differentiated Gut Epithelium

The cell of origin of colon cancer is typically thought to be the resident somatic stem cells, which are immortal and escape the continual cellular turnover characteristic of the intestinal epithelium. However, recent studies have identified certain conditions in which differentiated cells can acquire stem-like properties and give rise to tumors. Defining the origins of tumors will inform cancer prevention efforts as well as cancer therapies, as cancers with distinct origins often respond differently to treatments. We report here a new condition in which tumors arise from the differentiated intestinal epithelium. Inactivation of the differentiation-promoting transcription factor SMAD4 in the intestinal epithelium was surprisingly well tolerated in the short term. However, after several months, adenomas developed with characteristics of activated WNT signaling. Simultaneous loss of SMAD4 and activation of the WNT pathway led to dedifferentiation and rapid adenoma formation in differentiated tissue. Transcriptional profiling revealed acquisition of stem cell characteristics, and colabeling indicated that cells expressing differentiated enterocyte markers entered the cell cycle and reexpressed stem cell genes upon simultaneous loss of SMAD4 and activation of the WNT pathway. These results indicate that SMAD4 functions to maintain differentiated enterocytes in the presence of oncogenic WNT signaling, thus preventing dedifferentiation and tumor formation in the differentiated intestinal epithelium.Significance: This work identifies a mechanism through which differentiated cells prevent tumor formation by suppressing oncogenic plasticity. Cancer Res; 78(17); 4878-90. ©2018 AACR.

New Mechanisms of Resistance to MEK Inhibitors in Melanoma Revealed by Intravital Imaging

Targeted therapeutics that are initially effective in cancer patients nearly invariably engender resistance at some stage, an inherent challenge in the use of any molecular-targeted drug in cancer settings. In this study, we evaluated resistance mechanisms arising in metastatic melanoma to MAPK pathway kinase inhibitors as a strategy to identify candidate strategies to limit risks of resistance. To investigate longitudinal responses, we developed an intravital serial imaging approach that can directly visualize drug response in an inducible RAF-driven, autochthonous murine model of melanoma incorporating a fluorescent reporter allele (tdTomatoLSL). Using this system, we visualized formation and progression of tumors in situ, starting from the single-cell level longitudinally over time. Reliable reporting of the status of primary murine tumors treated with the selective MEK1/2 inhibitor (MEKi) trametinib illustrated a time-course of initial drug response and persistence, followed by the development of drug resistance. We found that tumor cells adjacent to bundled collagen had a preferential persistence in response to MEKi. Unbiased transcriptional and kinome reprogramming analyses from selected treatment time points suggested increased c-Kit and PI3K/AKT pathway activation in resistant tumors, along with enhanced expression of epithelial genes and epithelial-mesenchymal transition downregulation signatures with development of MEKi resistance. Similar trends were observed following simultaneous treatment with BRAF and MEK inhibitors aligned to standard-of-care combination therapy, suggesting these reprogramming events were not specific to MEKi alone. Overall, our results illuminate the integration of tumor-stroma dynamics with tissue plasticity in melanoma progression and provide new insights into the basis for drug response, persistence, and resistance.Significance: A longitudinal study tracks the course of MEKi treatment in an autochthonous imageable murine model of melanoma from initial response to therapeutic resistance, offering new insights into the basis for drug response, persistence, and resistance. Cancer Res; 78(2); 542-57. ©2017 AACR.

NRF2 Induction Supporting Breast Cancer Cell Survival Is Enabled by Oxidative Stress-Induced DPP3-KEAP1 Interaction

NRF2 is a transcription factor serving as a master regulator of the expression of many genes involved in cellular responses to oxidative and other stresses. In the absence of stress, NRF2 is constantly synthesized but maintained at low levels as it is targeted by KEAP1 for ubiquitination and proteasome-mediated degradation. NRF2 binds KEAP1 mainly through a conserved "ETGE" motif that has also been found in several other proteins, such as DPP3, which has been shown to bind KEAP1 and enhance NRF2 function upon overexpression. Here we demonstrate the interaction between endogenous DPP3 and endogenous KEAP1. We further show that the DPP3-KEAP1 interaction is strongly induced by hydrogen peroxide and that DPP3 is required for timely NRF2 induction and nuclear accumulation in the estrogen receptor (ER)-positive MCF7 breast cancer cells. Moreover, we present evidence that the binding of DPP3 to KEAP1 stabilizes the latter. Finally, we show that DPP3 is overexpressed in breast cancer and that elevated levels of DPP3 mRNA correlate with increased NRF2 downstream gene expression and poor prognosis, particularly for ER-positive breast cancer. Our studies reveal novel insights into the regulation of NRF2 and identify DPP3 and an NRF2 transcriptional signature as potential biomarkers for breast cancer prognosis and treatment. Cancer Res; 77(11); 2881-92. ©2017 AACR.

Proteogenomics connects somatic mutations to signalling in breast cancer

Somatic mutations have been extensively characterized in breast cancer, but the effects of these genetic alterations on the proteomic landscape remain poorly understood. We describe quantitative mass spectrometry-based proteomic and phosphoproteomic analyses of 105 genomically annotated breast cancers of which 77 provided high-quality data. Integrated analyses allowed insights into the somatic cancer genome including the consequences of chromosomal loss, such as the 5q deletion characteristic of basal-like breast cancer. The 5q trans effects were interrogated against the Library of Integrated Network-based Cellular Signatures, thereby connecting CETN3 and SKP1 loss to elevated expression of EGFR, and SKP1 loss also to increased SRC. Global proteomic data confirmed a stromal-enriched group in addition to basal and luminal clusters and pathway analysis of the phosphoproteome identified a G Protein-coupled receptor cluster that was not readily identified at the mRNA level. Besides ERBB2, other amplicon-associated, highly phosphorylated kinases were identified, including CDK12, PAK1, PTK2, RIPK2 and TLK2. We demonstrate that proteogenomic analysis of breast cancer elucidates functional consequences of somatic mutations, narrows candidate nominations for driver genes within large deletions and amplified regions, and identifies therapeutic targets.

Comprehensive Molecular Portraits of Invasive Lobular Breast Cancer

Invasive lobular carcinoma (ILC) is the second most prevalent histologic subtype of invasive breast cancer. Here, we comprehensively profiled 817 breast tumors, including 127 ILC, 490 ductal (IDC), and 88 mixed IDC/ILC. Besides E-cadherin loss, the best known ILC genetic hallmark, we identified mutations targeting PTEN, TBX3, and FOXA1 as ILC enriched features. PTEN loss associated with increased AKT phosphorylation, which was highest in ILC among all breast cancer subtypes. Spatially clustered FOXA1 mutations correlated with increased FOXA1 expression and activity. Conversely, GATA3 mutations and high expression characterized luminal A IDC, suggesting differential modulation of ER activity in ILC and IDC. Proliferation and immune-related signatures determined three ILC transcriptional subtypes associated with survival differences. Mixed IDC/ILC cases were molecularly classified as ILC-like and IDC-like revealing no true hybrid features. This multidimensional molecular atlas sheds new light on the genetic bases of ILC and provides potential clinical options.

Activating PIK3CA Mutations Induce an Epidermal Growth Factor Receptor (EGFR)/Extracellular Signal-regulated Kinase (ERK) Paracrine Signaling Axis in Basal-like Breast Cancer

Mutations in PIK3CA, the gene encoding the p110α catalytic subunit of phosphoinositide 3-kinase (PI3K) have been shown to transform human mammary epithelial cells (MECs). These mutations are present in all breast cancer subtypes, including basal-like breast cancer (BLBC). Using liquid chromatography-tandem mass spectrometry (LC-MS/MS), we identified 72 protein expression changes in human basal-like MECs with knock-in E545K or H1047R PIK3CA mutations versus isogenic MECs with wild-type PIK3CA. Several of these were secreted proteins, cell surface receptors or ECM interacting molecules and were required for growth of PIK3CA mutant cells as well as adjacent cells with wild-type PIK3CA. The proteins identified by MS were enriched among human BLBC cell lines and pointed to a PI3K-dependent amphiregulin/EGFR/ERK signaling axis that is activated in BLBC. Proteins induced by PIK3CA mutations correlated with EGFR signaling and reduced relapse-free survival in BLBC. Treatment with EGFR inhibitors reduced growth of PIK3CA mutant BLBC cell lines and murine mammary tumors driven by a PIK3CA mutant transgene, all together suggesting that PIK3CA mutations promote tumor growth in part by inducing protein changes that activate EGFR.

An integrated genomics approach identifies drivers of proliferation in luminal-subtype human breast cancer

Elucidating the molecular drivers of human breast cancers requires a strategy capable of integrating multiple forms of data and an ability to interpret the functional consequences of a given genetic aberration. Here we present an integrated genomic strategy based on the use of gene expression signatures of oncogenic pathway activity (n=52) as a framework to analyze DNA copy number alterations in combination with data from a genome-wide RNAi screen. We identify specific DNA amplifications, and importantly, essential genes within these amplicons representing key genetic drivers, including known and novel regulators of oncogenesis. The genes identified include eight that are essential for cell proliferation (FGD5, METTL6, CPT1A, DTX3, MRPS23, EIF2S2, EIF6 and SLC2A10) and are uniquely amplified in patients with highly proliferative luminal breast tumors, a clinical subset of patients for which few therapeutic options are effective. Our results demonstrate that this general strategy has the potential to identify putative therapeutic targets within amplicons through an integrated use of genetic, genomic, and genome-wide RNAi data sets.

FOXO transcription factors control E2F1 transcriptional specificity and apoptotic function

The transcription factor E2F1 is a key regulator of proliferation and apoptosis but the molecular mechanisms that mediate these cell fate decisions remain unclear. Here, we identify FOXO transcription factors as E2F1 target genes that act in a feed-forward regulatory loop to reinforce gene induction of multiple apoptotic genes. We found that E2F1 forms a complex with FOXO1 and FOXO3. RNAi-mediated silencing of FOXO impaired E2F1 binding to the promoters of cooperative target genes. A FOXO3 mutant insensitive to inactivation by survival kinases rescued the inhibitory effect of growth factor signaling on E2F1-mediated transcription and apoptosis. The E2F1/FOXO axis is frequently blocked in cancer, as evidenced by the specific downregulation of the FOXO-dependent E2F1 transcriptional program in multiple cancer types and by the association of a reduced E2F1/FOXO transcriptional program with poor prognosis. HDAC and phosphoinositide 3-kinase (PI3K) inhibitors were identified as specific activators of E2F1/FOXO transcription, acting to enhance E2F1-induced apoptosis in a FOXO3-dependent manner. Notably, combining the histone deacetylase inhibitor vorinostat with a PI3K inhibitor led to enhanced FOXO-dependent apoptosis. Collectively, our results identify E2F1/FOXO cooperation as a regulatory mechanism that places E2F1 apoptotic activity under the control of survival signaling. Therapeutic reactivation of this tumor suppressive mechanism may offer a novel broad-acting therapy for cancer.

Interaction of E2F7 transcription factor with E2F1 and C-terminal-binding protein (CtBP) provides a mechanism for E2F7-dependent transcription repression

Previous work has identified distinct functions for E2F proteins during a cellular proliferative response including a role for E2F1-3 in the activation of transcription at G1/S and a role for E2F4-8 in repressing the same group of E2F1-3 target genes as cells progress through S phase. We now find that E2F7 and E2F8, which are induced by E2F1-3 at G1/S, can form a heterodimer with E2F1 through interactions involving the DNA-binding domains of the two proteins. In vitro DNA interaction assays demonstrate the formation of an E2F1-E2F7 complex, as well as an E2F7-E2F7 complex on adjacent E2F-binding sites. We also show that E2F7 recruits the co-repressor C-terminal-binding protein (CtBP) and that CtBP2 is essential for E2F7 to repress E2F1 transcription. Taken together, these findings suggest a mechanism for the repression of transcription by E2F7.

TβRIII/β-arrestin2 regulates integrin α5β1 trafficking, function, and localization in epithelial cells

The type III TGF-β receptor (TβRIII) is a ubiquitous co-receptor for TGF-β superfamily ligands with roles in suppressing cancer progression, in part through suppressing cell motility. Here we demonstrate that TβRIII promotes epithelial cell adhesion to fibronectin in a β-arrestin2 dependent and TGF-β/BMP independent manner by complexing with active integrin α5β1, and mediating β-arrestin2-dependent α5β1 internalization and trafficking to nascent focal adhesions. TβRIII-mediated integrin α5β1 trafficking regulates cell adhesion and fibronectin fibrillogenesis in epithelial cells, as well as α5 localization in breast cancer patients. We further demonstrate that increased TβRIII expression correlates with increased α5 localization at sites of cell-cell adhesion in breast cancer patients, while higher TβRIII expression is a strong predictor of overall survival in breast cancer patients. These data support a novel, clinically relevant role for TβRIII in regulating integrin α5 localization, reveal a novel crosstalk mechanism between the integrin and TGF-β superfamily signaling pathways and identify β-arrestin2 as a regulator of α5β1 trafficking.

Abstract 5123: An integrated genomics approach to identify novel drivers of oncogenic pathway activity in human cancer

Human cancers are defined by molecular and clinical heterogeneity. The molecular diversity of human tumors is a significant contributing factor to the inefficiency of current therapeutic regimens and the high failure rate of developing new anti-cancer therapies. One of the major contributing factors to this variability is the enormous diversity and complexity of genome alterations. In order to understand the molecular complexity driving tumor development and to identify novel therapeutic targets to enhance treatment efficacy and overcome therapeutic resistance, we have developed an integrative genomics approach to identify novel drivers of oncogenic pathway activity and applied this strategy to investigate serous ovarian cancer. Since it has been demonstrated that mutations in many different genes can result in the activation of an oncogenic signaling pathway resulting in enhanced cell proliferation and transformation, our analysis focused on regulation of pathway activity rather than the mutation of a single gene. As such, we utilized 18 previously developed and validated gene expression signatures of oncogenic pathway activity as a framework to integrate multiple, disparate forms of genomic data. We first identified 1,020 high-grade, late stage serous ovarian tumors with Affymetrix U133 expression data from multiple published studies and the predicted oncogenic pathway activity was determined for each tumor. Of these tumors, &gt;500 had matched aCGH data which were used to identify statistically significant chromosomal alterations directly and indirectly associated with each pathway. This strategy was validated by identifying associations between pathway activity and copy number alterations of known pathway drivers. We next compiled a dataset of ovarian cancer cell lines with U133 expression data and for which genome-wide shRNA proliferation data was available. These data were used to identify essential genes required for cell viability in pathway-dependent manner. The resulting genes were analyzed by DAVID and GATHER to validate that this strategy identified key pathway components. Finally, by integrating results obtained from the aCGH and shRNA analyses, we identified known and candidate genes associated with oncogenic pathway activity that are required for cell viability and are amplified in human tumors. These analyses have identified alterations of putative and known regulators of pathway activity that often exist independent of each other in human tumors suggesting that examining the mutational status of a single gene is an incomplete measure of pathway activity and that this strategy is able to identify novel regulators, and therefore potential therapeutic targets, of oncogenic signaling pathways required for tumor proliferation. Additional studies are underway to investigate the role identified candidate genes play in pathway activity and tumor proliferation.

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 5123. doi:1538-7445.AM2012-5123

Predictive and prognostic markers of recurrence after resection of primary or metastatic colorectal cancer

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Background: Current biomarkers for colorectal cancer sub-classify tumors based on single mutations, such as KRAS; however, studies of single mutations belie the molecular complexity of colorectal cancer in which an average of 14 key genes per tumor is dysregulated. We hypothesize that colorectal cancer may be molecularly sub-classified based on an oncogenic pathway prediction model in which tumors are grouped based on patterns of oncogenic pathway dysregulation/expression.

Methods: Affymetrix microarray data from 850 patients with primary colorectal cancer from publically available datasets were combined using Bayesian factor regression modeling normalization. The activity of 19 separate oncogenic pathways was predicted among tumors to generate patterns of pathway activity for each sample. Mixture modeling was applied to these samples to identify subgroups of tumors with unique patterns of pathway dysregulation. Validation of subclasses was performed on a dataset of 133 primary and metastatic colorectal cancer samples of patients undergoing curative surgical resection at our institution. Tumors were subgrouped according to our previous model and recurrence free survival was calculated. In vivo validation was performed by treating NOD/SCID mice bearing patient derived tumors with everolimus with changes in tumor size calculated between day 0 and day 21.

Results: Mixture modeling resulted in 6 individual subgroups of colorectal cancer based on pathway dysregulation. Kaplan Meier curves revealed that patients in subclass 4 had the poorest prognosis while patients in subclass 6 had the best prognosis (p=0.05). Further, tumors in subclass 4 were generally enriched for high mTOR pathway activation and patient derived explants from subclass 4 with high predicted mTOR activity were found to be sensitive to the MTOR pathway inhibitor everolimus.

Conclusions: Prediction of oncogenic signaling pathway activity is a powerful tool that may be used to molecularly sub-classify colorectal cancer into biologically relevant subgroups. These subgroups have prognostic and predictive implications for recurrence following surgical resection and responsiveness to targeted therapy.

SIGNATURE: a workbench for gene expression signature analysis

Background

The biological phenotype of a cell, such as a characteristic visual image or behavior, reflects activities derived from the expression of collections of genes. As such, an ability to measure the expression of these genes provides an opportunity to develop more precise and varied sets of phenotypes. However, to use this approach requires computational methods that are difficult to implement and apply, and thus there is a critical need for intelligent software tools that can reduce the technical burden of the analysis. Tools for gene expression analyses are unusually difficult to implement in a user-friendly way because their application requires a combination of biological data curation, statistical computational methods, and database expertise.

Results

We have developed SIGNATURE, a web-based resource that simplifies gene expression signature analysis by providing software, data, and protocols to perform the analysis successfully. This resource uses Bayesian methods for processing gene expression data coupled with a curated database of gene expression signatures, all carried out within a GenePattern web interface for easy use and access.

Conclusions

SIGNATURE is available for public use at http://genepattern.genome.duke.edu/signature/.

Type III TGF-β receptor enhances colon cancer cell migration and anchorage-independent growth

The type III TGF-β receptor (TβRIII or betagylcan) is a TGF-β superfamily coreceptor with emerging roles in regulating TGF-β superfamily signaling and cancer progression. Alterations in TGF-β superfamily signaling are common in colon cancer; however, the role of TβRIII has not been examined. Although TβRIII expression is frequently lost at the message and protein level in human cancers and suppresses cancer progression in these contexts, here we demonstrate that, in colon cancer, TβRIII messenger RNA expression is not significantly altered and TβRIII expression is more frequently increased at the protein level, suggesting a distinct role for TβRIII in colon cancer. Increasing TβRIII expression in colon cancer model systems enhanced ligand-mediated phosphorylation of p38 and the Smad proteins, while switching TGF-β and BMP-2 from inhibitors to stimulators of colon cancer cell proliferation, inhibiting ligand-induced p21 and p27 expression. In addition, increasing TβRIII expression increased ligand-stimulated anchorage-independent growth, a resistance to ligand- and chemotherapy-induced apoptosis, cell migration and modestly increased tumorigenicity in vivo. In a reciprocal manner, silencing endogenous TβRIII expression decreased colon cancer cell migration. These data support a model whereby TβRIII mediates TGF-β superfamily ligand-induced colon cancer progression and support a context-dependent role for TβRIII in regulating cancer progression.

Analysis of tumor environmental response and oncogenic pathway activation identifies distinct basal and luminal features in HER2-related breast tumor subtypes

Introduction

Breast cancer heterogeneity occurs as a consequence of the dysregulation of numerous oncogenic pathways as well as many non-genetic factors, including tumor microenvironmental stresses such as hypoxia, lactic acidosis, and glucose deprivation. Although the importance of these non-genetic factors is well recognized, it is not clear how to integrate these factors within the genetic framework of cancer as the next logical step in understanding tumor heterogeneity.

Methods

We report here the development of a series of gene expression signatures to measure the influences of microenvironmental stresses. The pathway activities of hypoxia, lactic acidosis, acidosis and glucose deprivation were investigated in a collection of 1,143 breast tumors, which have been separated into 17 breast tumor subgroups defined by their distinct patterns of oncogenic pathways. A validation dataset comprised of 547 breast tumors was also used to confirm the major findings, and representative breast cancer cell lines were utilized to validate in silico results and mechanistic studies.

Results

Through the integrative pathway analysis of microenvironmental stresses and oncogenic events in breast tumors, we identified many known and novel correlations between these two sources of tumor heterogeneity. Focusing on differences between two human epidermal growth factor receptor 2 (HER2)-related subgroups, previously identified based on patterns of oncogenic pathway activity, we determined that these subgroups differ with regards to tumor microenvironmental signatures, including hypoxia. We further demonstrate that each of these subgroups have features consistent with basal and luminal breast tumors including patterns of oncogenic signaling pathways, expression of subtype specific genes, and cellular mechanisms that regulate the hypoxia response. Importantly, we also demonstrate that the correlated pattern of hypoxia-related gene expression and basal-associated gene expression are consistent across HER2-related tumors whether we analyze the tumors as a function of our pathway-based classification scheme, using the intrinsic gene list (ERBB2+), or based on HER2 IHC status. Our results demonstrate a cell lineage-specific phenomenon in which basal-like tumors, HER2-related tumors with high hypoxia, as well as normal basal epithelial cells express increased mRNA levels of HIF-1α compared to luminal types and silencing of HIF-1α results in decreased expression of hypoxia-induced genes.

Conclusions

This study demonstrates differences in microenvironmental conditions in HER2-related subgroups defined by distinct oncogenic pathway activities, and provides a mechanistic explanation for differences in the observed hypoxia response between these subgroups. Collectively, these data demonstrate the potential of a pathway-based classification strategy as a framework to integrate genetic and non-genetic factors to investigate the basis of tumor heterogeneity.

Using a stem cell-based signature to guide therapeutic selection in cancer

Given the very substantial heterogeneity of most human cancers, it is likely that most cancer therapeutics will be active in only a small fraction of any population of patients. As such, the development of new therapeutics, coupled with methods to match a therapy with the individual patient, will be critical to achieving significant gains in disease outcome. One such opportunity is the use of expression signatures to identify key oncogenic phenotypes that can serve not only as biomarkers but also as a means of identifying therapeutic compounds that might specifically target these phenotypes. Given the potential importance of targeting tumors exhibiting a stem-like phenotype, we have developed an expression signature that reflects common biological aspects of various stem-like characteristics. The consensus stemness ranking (CSR) signature is upregulated in cancer stem cell-enriched samples at advanced tumor stages and is associated with poor prognosis in multiple cancer types. Using two independent computational approaches we utilized the CSR signature to identify clinically useful compounds that could target the CSR phenotype. In vitro assays confirmed selectivity of several predicted compounds including topoisomerase inhibitors and resveratrol towards breast cancer cell lines that exhibit a high-CSR phenotype. Importantly, the CSR signature could predict clinical response of breast cancer patients to a neoadjuvant regimen that included a CSR-specific agent. Collectively, these results suggest therapeutic opportunities to target the CSR phenotype in a relevant cohort of cancer patients.

A genomic strategy to elucidate modules of oncogenic pathway signaling networks

Recent studies have emphasized the importance of pathway-specific interpretations for understanding the functional relevance of gene alterations in human cancers. Although signaling activities are often conceptualized as linear events, in reality, they reflect the activity of complex functional networks assembled from modules that each respond to input signals. To acquire a deeper understanding of this network structure, we developed an approach to deconstruct pathways into modules represented by gene expression signatures. Our studies confirm that they represent units of underlying biological activity linked to known biochemical pathway structures. Importantly, we show that these signaling modules provide tools to dissect the complexity of oncogenic states that define disease outcomes as well as response to pathway-specific therapeutics. We propose that this model of pathway structure constitutes a framework to study the processes by which information propogates through cellular networks and to elucidate the relationships of fundamental modules to cellular and clinical phenotypes.

Ubiquitination of HTLV-I Tax in response to DNA damage regulates nuclear complex formation and nuclear export

Background

The HTLV-I oncoprotein, Tax, is a pleiotropic protein whose activity is partially regulated by its ability to interact with, and perturb the functions of, numerous cellular proteins. Tax is predominantly a nuclear protein that localizes to nuclear foci known as Tax Speckled Structures (TSS). We recently reported that the localization of Tax and its interactions with cellular proteins are altered in response to various forms of genotoxic and cellular stress. The level of cytoplasmic Tax increases in response to stress and this relocalization depends upon the interaction of Tax with CRM1. Cellular pathways and signals that regulate the subcellular localization of Tax remain to be determined. However, post-translational modifications including sumoylation and ubiquitination are known to influence the subcellular localization of Tax and its interactions with cellular proteins. The sumoylated form of Tax exists predominantly in the nucleus while ubiquitinated Tax exists predominantly in the cytoplasm. Therefore, we hypothesized that post-translational modifications of Tax that occur in response to DNA damage regulate the localization of Tax and its interactions with cellular proteins.

Results

We found a significant increase in mono-ubiquitination of Tax in response to UV irradiation. Mutation of specific lysine residues (K280 and K284) within Tax inhibited DNA damage-induced ubiquitination. In contrast to wild-type Tax, which undergoes transient nucleocytoplasmic shuttling in response to DNA damage, the K280 and K284 mutants were retained in nuclear foci following UV irradiation and remained co-localized with the cellular TSS protein, sc35.

Conclusion

This study demonstrates that the localization of Tax, and its interactions with cellular proteins, are dynamic following DNA damage and depend on the post-translational modification status of Tax. Specifically, DNA damage induces the ubiquitination of Tax at K280 and K284. Ubiquitination of these residues facilitates the dissociation of Tax from sc35-containing nuclear foci, and stimulates nuclear export of Tax through the CRM1 pathway.

Genotoxic stress and cellular stress alter the subcellular distribution of human T-cell leukemia virus type 1 tax through a CRM1-dependent mechanism

Human T-cell leukemia virus type 1 Tax is a predominantly nuclear viral oncoprotein that colocalizes with cellular proteins in nuclear foci known as Tax speckled structures (TSS). Tax is also diffusely distributed throughout the cytoplasm, where it interacts with and affects the functions of cytoplasmic cellular proteins. Mechanisms that regulate the distribution of Tax between the cytoplasm and nucleus remain to be identified. Since Tax has been shown to promote genome instability by perturbing cell cycle progression and DNA repair mechanisms following DNA damage, we examined the effect of genotoxic stress on the subcellular distribution and interacting partners of Tax. Tax localization was altered in response to various forms of cellular stress, resulting in an increase in cytoplasmic Tax and a decrease in Tax speckled structures. Concomitantly, colocalization of Tax with sc35 (a TSS protein) decreased following stress. Tax translocation required the CRM1 nuclear export pathway, and a transient interaction between Tax and CRM1 was observed following stress. These results suggest that the subcellular distribution of Tax and the interactions between Tax and cellular proteins respond dynamically to cellular stress. Changes in Tax distribution and interacting partners are likely to affect cellular processes that regulate cellular transformation.

Impact of transforming viruses on cellular mutagenesis, genome stability, and cellular transformation

It is estimated that 15% of all cancers are etiologically linked to viral infection. Specific cancers including adult T-cell leukemia, hepatocellular carcinoma, and uterine cervical cancer are associated with infection by human T-cell leukemia virus type I, hepatitis B virus, and high-risk human papilloma virus, respectively. In these cancers, genomic instability, a hallmark of multistep cancers, has been explicitly linked to the expression of oncoproteins encoded by these viruses. This review discusses mechanisms utilized by these viral oncoproteins, Tax, HBx, and E6/E7, to mediate genomic instability and cellular transformation.

Cellular transformation by the HTLV-I Tax protein, a jack-of-all-trades

The human T-cell leukemia virus type I (HTLV-I) is an oncogenic retrovirus that is responsible for adult T-cell leukemia and a neurological disease, HTLV-I-associated myelopathy/tropical spastic paraparesis. HTLV-I encodes an oncogenic protein, Tax, which affects a variety of cellular functions prompting it to be referred to as a jack-of-all trades. The ability of Tax to both transcriptionally regulate cellular gene expression and to functionally inactivate proteins involved in cell-cycle progression and DNA repair provide the basis for Tax-mediated transformation and leukemogenesis. This review will concentrate on the effects of Tax on the dysregulation of the G(1)/S and G(2)/M checkpoints as well as the suppression of DNA damage repair leading to cellular transformation.