Transcription Factor-Binding Site Identification and Enrichment Analysis

Transcription factors orchestrate complex regulatory networks of gene expression. A better understanding of the common transcription factors, and their shared interactions, among a set of coregulated or differentially expressed genes can provide powerful insights into the key pathways governing such expression patterns. Critically, such information must also be considered in the context of the frequency in which a transcription factor is present in a properly selected background, and in the context of existing evidence of gene and transcription factor interaction. Given the vast amount of publicly available gene expression data that can be further scrutinized by the user-friendly analysis tools described here, many useful insights are assuredly to be revealed. The proceeding methods for application of the analysis tool CiiiDER for transcription factor-binding site identification, enrichment analysis, and coregulatory factor identification should be applicable to any dataset comparing differential gene expression in response to various stimuli and gene coexpression datasets. These methods should assist the researcher in identifying the most relevant regulators within a gene set, and refining the list of targets for future study to those which may share biologically important regulatory networks.

Subcellular Fractionation to Demonstrate Activation of Intrinsic Apoptotic Pathway

Within the cell, proteins are segregated into different organelles depending on their function and activation status. In response to stimulus, posttranslational modifications or loss of organelle membrane integrity lead to the movement of proteins from one compartment to another. This movement of proteins or protein translocation, exerts a significant effect on protein function. This is clearly demonstrated in the context of apoptosis wherein the cytoplasmic translocation of the mitochondrial resident protein, cytochrome C, initiates the activation of the intrinsic arm of the apoptotic pathway. Experimentally, protein translocation can be demonstrated by subcellular fractionation and subsequent western blot analysis of the isolated fractions. This chapter describes the step-by-step procedure in obtaining mitochondrial and cytoplasmic fractions from cell pellets and determining their purity and integrity.

Determination of Caspase Activation by Western Blot

Apoptosis is a type of programmed cell death induced by a cascade of biochemical events, which leads to distinct morphological changes characterized by cell shrinkage, membrane blebbing, chromatin condensation, and DNA fragmentation. Apoptosis is executed by a class of cysteine proteases called caspases. Caspases are synthesized as inactive pro-caspases and activated by a series of cleavage reactions. Active caspases cleave cellular substrates and are thus the main effectors of the apoptotic cell death pathway. Detection of caspase cleavage by western blot analysis is a conventional method to demonstrate the induction of apoptosis. In the context of apoptosis, the proper analysis of western blot results depends on the understanding of the mechanisms and outcomes of caspase processing during the course of its activation. In this chapter, we describe the step-by-step methodology in the western blot analysis of caspase cleavage during apoptosis. We detail protocols for protein extraction, quantitation, casting, and running gel electrophoresis and western blot analysis of caspase -8 and caspase -9 activation. The described methods can be applied to any particular protein of interest.

Covid-19 pandemic and pregnancy

At the end of 2019, a new coronavirus disease, COVID-19, emerged and quickly spread around the world. Severe acute respiratory syndrome Coronavirus 2 (SARS-CoV-2), the causative virus of this disease, belongs to the β-coronavirus family, together with SARS and middle east respiratory syndrome, and has similar biological characteristics to these viruses. For obstetricians, the susceptibility and prognoses of pregnant women and the effects of the infection on the fetus have been the focus of attention; however, at present, the seriousness of the disease in pregnant women is not apparent, and COVID-19 does not increase the rate of miscarriage, stillbirth, preterm labor or teratogenicity. Even so, carriers might transmit SARS-CoV-2 to pregnant women. Thus, we must keep in mind that all medical personnel must understand and maintain standard precautions in their clinical and laboratory practices.

Abstract A01: Specific targeting of adipose tissue-associated metastasis using bile salt nanoparticles

Purpose: Mortality in ovarian cancer occurs in the setting of recurrent disease. Recurrent disease is known to arise from residual disease, which persists after the conclusion of standard of care, consequently rebuilding the tumor. Adipose tissue provides cancer cells with a unique microenvironment that can enhance survival by upregulating antiapoptosis genes or by decreasing drug bioavailability. Indeed, adipose-rich organs such as the omentum are not only preferential sites for metastasis but also main sites of residual disease in ovarian cancer. We hypothesized that targeting adipose-rich tissues could limit residual disease and prevent recurrence. Thus, the objective of this study was to develop effective drug delivery platforms that can specifically target residual disease in adipose-rich tissues.

Methods: The delivery system is a nanoparticle platform composed of polymerized ursodeoxycholic acid (PUDCA) synthesized by esterification of UDCA monomer. Paclitaxel (PTX) or deep-infrared FL dye (DIR) was encapsulated to a final concentration of 24 ug or 5 mg per mg PUDCA, respectively. In vitro dose response studies were performed using mCherry+ human OCSC1-F2 ovarian cancer cells for 72 h. DMSO-resuspended PTX (DMSO-PTX) was used as control. In vivo studies were performed in athymic nude mice bearing i.p. tumors from mCherry+ OCSC1-F2 cells. For biodistribution studies, DIR-PUDCA was administered as one-time i.p. injection of 1.3 mg of DIR-PUDCA followed by ex vivo measurement of FL intensity after 14 days. DMSO-resuspended DIR (DMSO-DIR) was used as control. For efficacy studies, the groups were: (1) vehicle control; (2) taxol (PTX in Cremaphor; 12mg/kg) + DMSO-PTX (31.2 ug PTX); and (3) taxol + PUDCA-PTX. Treatment was administered i.p. twice a week for a total of 4 doses. Tumor burden and residual disease were determined by quantification of mCherry ROI FL area.

Results: PUDCA-PTX demonstrated significantly improved efficacy both in vitro and in vivo. PUDCA-PTX demonstrated a six-fold reduction in in vitro GI50 compared to DMSO-PTX (23.04 nM PUDCA-PTX vs. 137.2 nM DMSO-PTX). Biodistribution studies showed delivery of DIR specifically to adipose-rich tissues (DIR mean FL intensity (MFI) for greater and lesser omentum = 76570±17808 vs. mesentery MFI = 22326±2956; p = 0.0297). Efficacy studies showed that PUDCA-PTX was significantly more effective in inhibiting tumor progression (p = 0.0191) and, more importantly, in preventing recurrent disease compared to DMSO-PTX. Finally, PUDCA-PTX was able to significantly reduce omental-residual disease compared to DMSO-PTX (p=0.049).

Conclusion: We demonstrate for the first time that PUDCA is able to target residual disease localized in adipocyte-rich tissues and that this significantly delays tumor progression and prevents recurrence. These results underscore the value of i.p.-delivered PUDCA as a drug delivery platform for enhanced targeting of cancer cells within adipose-rich tissues and its value in the management of ovarian cancer patients.

Citation Format: Roslyn Tedja, Ayesha B. Alvero, Jung Seok Lee, Mary Pitruzzello, Tarek Fahmy, Gil G. Mor. Specific targeting of adipose tissue-associated metastasis using bile salt nanoparticles [abstract]. In: Proceedings of the AACR Special Conference on Advances in Ovarian Cancer Research; 2019 Sep 13-16, 2019; Atlanta, GA. Philadelphia (PA): AACR; Clin Cancer Res 2020;26(13_Suppl):Abstract nr A01.

Abstract TMIM-084: PKCα INDUCES TWIST1 PHOSPHORYLATION AT SERINE 144 AND PROMOTES EMT IN OVARIAN CANCER CELLS

PURPOSE: Metastasis and carcinomatosis remains a major problem in ovarian cancer. Metastasis requires a process known as Epithelial-to-Mesenchymal Transition (EMT), where by epithelial cancer cells undergo dynamic changes to acquire a mesenchymal and invasive phenotype. Twist1 is a transcription factor with a central role in EMT. We previously showed that in epithelial ovarian cancer (EOC), Twist1 is constitutively ubiquitinated and targeted for proteasomal degradation and inhibition of Twist degradation is associated with mesenchymal phenotype and chemoresistance. Accordingly, identification of mechanisms that promote EMT by inhibiting the active degradation of Twist1 is critical for prevention of carcinomatosis. In this study, we report the identification of PKCα as a central regulator of Twist1. We identified 11 possible PKCα phosphorylation sites on Twist1. We show that Twist1 is a novel substrate of the kinase PKCα and that PKCα-induced Twist1 phosphorylation abrogates Twist1 ubiquitination leading to its stabilization and consequently EMT.

METHODS: The following cell lines were used: (1) ovarian cancer cells lines OVCAR3 and OVCA432; (2) in-house developed cultures of ovarian cancer cells, R182 and R2615; and (3) HEK293T cells. The effect of constitutively active (PKCαCAT), dominant negative (PKCαDN), and wild-type (wt-PKCα) PKCα on levels of Twist1 were determined by transient transfection using qRT-PCT and western blot analysis. Levels of phosphorylated Twist1 were measured in Twist1 immunoprecipitate-complex using anti-phospho-serine/threonine/tyrosine antibody. The phospho-deficient mutant Twist1 S144A was constructed using QuickChange Site-directed Mutagenesis Kit. PKCα was knocked-out in ovarian cancer cells using CRISPR/Cas9. EMT was induced by treatment with 10 ng/ml TGFβ1 and confirmed molecularly (i.e. loss of epithelial markers E-cadherin, Ck18, Claudin 3 and gain of mesenchymal markers Twist1, N-cadherin, and vimentin). Intra-peritoneal tumors were established by injecting 10 million ovarian cancer cells in athymic nude mice.

RESULTS: Transfection with PKCαCAT(active) resulted in a significant increase in Twist1 protein levels compared to PKCαDN(inactive) or empty vector control in EOC and HEK293T cells. This was not a transcriptional effect (no increase in Twist1 mRNA) but due to increase in the levels of phospho-serine/threonine/tyrosine on Twist1. We identified S144 as the putative PKCα phosphorylation site on Twist1 protein. Whereas wt-Twist1 was readily ubiquitinated when transfected in ovarian cancer cells and HEK293T, the phosphomimic S144D Twist1 demonstrated significantly less ubiquitination. Furthermore, we identified TGFβ1 as an activator of the endogenous PKCα-Twist1 axis in ovarian cancer cells. TGFβ1 is able to: (1) activate PKCα; (2) increase Twist1 protein levels; (3) and induce EMT (spheroid formation). Knock-out of PKCα in ovarian cancer cells abrogated TGFβ1-induced EMT in vitro and inhibit carcinomatosis in vivo in athymic nude mice model.

CONCLUSION: We demonstrate for the first time a TGFβ1-PKCα-Twist1 signaling pathway that specifically targets Twist1 protein for phosphorylation and stabilization. This is a non-classical pathway of TGFβ1 induced EMT. Moreover, we identify S144 on Twist1 as novel and direct PKCα-phosphorylation site that can control Twist1 stability. Given the pleiotropic nature of TGFβ1 signaling, the identification of PKCα as a novel target may aid in the development of better therapeutic modalities that can prevent EMT and curtail metastasis formation in ovarian cancer.

Citation Format: Roslyn Tedja, Cai Roberts, Carlos Cardenas, Ayesha B. Alvero, Mary Pitruzzello, Yang Yang-Hartwich, Carlotta Glackin and Gil G. Mor. PKCα INDUCES TWIST1 PHOSPHORYLATION AT SERINE 144 AND PROMOTES EMT IN OVARIAN CANCER CELLS [abstract]. In: Proceedings of the 12th Biennial Ovarian Cancer Research Symposium; Sep 13-15, 2018; Seattle, WA. Philadelphia (PA): AACR; Clin Cancer Res 2019;25(22 Suppl):Abstract nr TMIM-084.

Marijuana-derived cannabinoids inhibit uterine endometrial stromal cell decidualization and compromise trophoblast-endometrium cross-talk

Marijuana (cannabis) use by pregnant women in the United States is increasing and there is a dire need to understand the beneficial or harmful effects of cannabis during pregnancy. Uterine endometrial stromal cells are fibroblast-like cells that differentiate into secretory cells, a process called decidualization, to create a microenvironment conducive for placenta formation and early embryonic growth. In this study, using model human cell lines, we for the first time demonstrate that Δ9-tetrahydrocannabinol (THC), cannabidiol (CBD) and cannabinol (CBN) inhibit endometrial stromal cell decidualization and have adverse effects on trophoblast-endometrium cross-talk.

Abstract 1969: PKCα-induced Twist1 phosphorylation is a novel regulator of Twist1 stabilization

Background:

Epithelial - mesenchymal transition (EMT) is a pre-requisite for cancer metastasis. Twist-1 is a transcription factor with a central role in the process of EMT and therefore metastasis formation. Using ovarian cancer models, our group has previously shown that although the stationary epithelial phenotype express Twist1 mRNA, this phenotype is enforced by mechanisms that constitutively ubiquitinates and degrades the Twist1 protein. The objective of this study is to identify molecular mechanisms that promote Twist1 protein stabilization and therefore confer a mesenchymal and mobile phenotype.

Materials and methods:

Novel phosphorylation sites on Twist1 protein, which are adjacent to ubiquitination sites, were identified using NetPhosK and Ubpred. Further analysis demonstrates that most of these sites contain the consensus sequence for PKCα. Constitutively active PKCα (PKCαcat) was ectopically expressed in HEK293T cells and patient-derived epithelial ovarian cancer cell lines. Protein expression and phosphorylation status were determined using western blot analysis using either whole cell lysates or cellular fractions. Protein-protein interaction was determined by immunoprecipiation. The specific Twist1 domain required for PKCα interaction was determined by co-transfection with Twist1 deletion mutants.

Results:

Ectopic expression of PKCαcat in HEK293T cells and ovarian cancer cells resulted in increased levels of Twist1 protein compared to empty vector control. In ovarian cancer cells, PKCcat-induced upregulation of Twist1 protein is not associated with an increase in Twist1 mRNA but instead is associated with Twist1 phosphorylation, decreased ubiquitination, and enhanced stabilization. We identify the twist box (WR) domain of Twist1 as a pre-requisite for PKCα binding and PKCαcat-induced Twist1 stabilization. Moreover, we identify TGFβ1 as a potent activator of endogenous PKCα in epithelial ovarian cancer cells. TGFβ1 (1 ng/ml) is able to: promote the activation and membranal translocation of PKCα; increase Twist1 protein levels; and induce spheroid formation and EMT in epithelial ovarian cancer cells. Interestingly, TGFβ1 had no effect on Twist1 mRNA suggesting that this mechanism is independent of the classical TGFβ-Smad pathway.

Conclusions:

We demonstrate for the first time a novel TGFβ-PKCα signaling pathway that specifically targets Twist1 protein for phosphorylation and stabilization resulting in EMT. This mechanism is independent of the classical TGFβ-Smad pathway that controls EMT via transcriptional regulation. Since TGFβ is a pleiotropic cytokine that can affect multiple cell types, the identification of PKCα as a novel target in ovarian cancer cells may aid in the development of better therapeutic modalities that can prevent EMT and curtail metastasis formation.

Citation Format: Roslyn Tedja, Ayesha B. Alvero, Carlos Cardenas, Mary Pitruzzello, Gang Yin, Yang Yang-Hartwich, Cai Roberts, Carlotta Glackin, Gil G. Mor. PKCα-induced Twist1 phosphorylation is a novel regulator of Twist1 stabilization [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2017; 2017 Apr 1-5; Washington, DC. Philadelphia (PA): AACR; Cancer Res 2017;77(13 Suppl):Abstract nr 1969. doi:10.1158/1538-7445.AM2017-1969

Abstract 1995: The omentum promotes ovarian cancer cell survival by increasing cell cycle duration and chemoresistance

Background:

Ovarian cancer is the most lethal of all gynecologic cancers. It is characterized by the presence of carcinomatosis at time of presentation and chemoresistant micrometastatic seedings at the time of recurrence. The omentum, an adipocyte-rich organ, is a frequent site of ovarian cancer metastasis in patients and the most common site of post-chemotherapy residual disease in animal models. Whereas previous studies have shown how the adipocyte microenvironment can induce metabolic re-programming in cancer cells, it is not clear if it can regulate pathways that affect chemoresponse. The objective of this study is to determine the effect of the adipocyte microenvironment on pathways that control cell cycle and apoptosis.

Methods:

In vitro: Patient-derived epithelial ovarian cancer cell lines were cultured in the presence of absence of omentum conditioned-media. Cell growth was determined by measuring culture confluence using IncucyteTM. Protein expression was determined by western blot analysis, and flow cytometry. In vivo: Human ovarian cancer xenografts were established intra-peritoneally in nude mice. Tumor implants from adipocyte-rich organs such as the omentum, pelvic fat, and mesentery and tumor implants from non-adipocyte-rich organs such as liver, ovaries, and GI tract were collected and analyzed independently.

Results:

Compared to cells cultured in growth media, epithelial ovarian cancer cells cultured in omentum CM demonstrated a more fibroblastic morphology characterized by elongated shape and bipolarity, significantly slower growth kinetics (p < 0.0001) accompanied by upregulation of the cell cycle inhibitor, p27, and enhanced secretion of the pro-angiogenic factor, VEGF. More importantly, these cells express higher levels of the anti-apoptotic proteins Bclxl and Mcl-1. Consequently, ovarian cancer cells in growth media treated with Carboplatin had a IC50 of 14.5 μg/ml. In contrast, cells cultured in omentum CM demonstrated enhanced resistance to carboplatin with IC50 of > 50 μg/ml.

Analysis of tumor implants in vivo showed similar results as observed in vitro. Thus, tumor implants isolated from adipocyte-rich organs express higher levels of p27, Bclxl, and Mcl-1.

Conclusion:

We demonstrate in this study that the adipocyte microenvironment induces major changes in the phenotype of ovarian cancer cells characterized by morphological changes chemoresistance and growth rate. These findings highlight the importance of the adipocyte microenvironment in the progression of ovarian cancer. Further studies that can identify specific therapeutic targets in the adipocyte-educated chemoresistant ovarian cancer cells may aid in the development of novel therapies and improve patient survival.

Citation Format: Carlos Cardenas, Ayesha B. Alvero, Mary Pitruzzello, Roslyn Tedja, Gil G. Mor. The omentum promotes ovarian cancer cell survival by increasing cell cycle duration and chemoresistance [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2017; 2017 Apr 1-5; Washington, DC. Philadelphia (PA): AACR; Cancer Res 2017;77(13 Suppl):Abstract nr 1995. doi:10.1158/1538-7445.AM2017-1995

Abstract 1519: Cantrixil targets ovarian cancer stem cells and prevents recurrence in a cisplatin-resistant animal model

Background: Chemoresistance is a major hurdle in the management of patients with epithelial ovarian cancer (EOC) and is associated with high mortality. Growing evidence suggests that chemoresistance is due to the presence of a subgroup of cancer cells with stemness properties and a high capacity for tumor repair. Current modalities are not able to target these cancer stem cells (CSC), thus there is a need to develop novel treatment approaches. We developed a library of super-benzopyran (SBP) analogues to generate potent compounds that can induce cell death in the chemoresistant CSC. We report the anti-tumoral in vivo efficacy of Cantrixil in a cisplatin-resistant animal model as monotherapy, and in combination with cisplatin. Furthermore, Cantrixil as salvage therapy prevents recurrence following paclitaxel treatment and significantly prolongs survival.

Materials and methods: A panel of SPB analogues were generated and activity was determined by testing against pure clones of CD44+/MyD88+ EOC stem cells. In vitro efficacy was screened using the IncucyteTM kinetic imaging platform complemented by CelltoxTM dye labelling. In vivo efficacy and toxicology was tested using an intra-peritoneal (i.p.) cisplatin-resistant ovarian cancer xenograft model 1.

Results: Cantrixil was the most potent analogue, inducing cell death in all EOC stem cell clones tested (IC50 of 136 nM). Cell death was associated with the activation of the JNK pathway, loss of mitochondrial membrane potential, and caspase activation. In vivo, Cantrixil, as mono-therapy, significantly decreased i.p. tumor burden compared to vehicle control (p = 0.0001 n = 10) while cisplatin had no effect(p = 0.8). Furthermore, the combination of Cantrixil and cisplatin significantly decreases tumor burden compared to ciplatin alone or control (p = 0.002 and p = 0.004) In addition, using an in vivo recurrent EOC model, maintenance treatment with Cantrixil given post a Paclitaxel regimen prevented recurrent disease and significantly decreased metastatic tumor burden compared to maintenance with Paclitaxel (p = 0.002).

Conclusion: We described the in vivo anti-tumoral effect of a novel compound, Cantrixil, which exhibits significant efficacy against chemoresistant EOC stem cells and is able to prevent recurrence in a cisplatin-resistant in vivo model. Recurrence characterized by chemoresistance is the main cause of mortality in ovarian cancer patients. Previous studies from our laboratory have shown that conventional chemotherapy is not effective on EOC stem cells and can not prevent recurrence. Our finding that Cantrixil, by targeting CSCs, can prevent recurrence in vivo as maintenance therapy or in combination with chemotherapy, provides a new opportunity for developing a new therapeutic strategy that can help ovarian cancer patients.

1. Craveiro V, et al. Cancer Medicine. 2013;2: 751-762.

Citation Format: Gil G. Mor, Eydis Lima, Natalia Sumi, Mary Pitruzzello, Yang Yang-Hartwich, David Brown, Andrew Heaton, Ayesha B. Alvero. Cantrixil targets ovarian cancer stem cells and prevents recurrence in a cisplatin-resistant animal model. [abstract]. In: Proceedings of the 106th Annual Meeting of the American Association for Cancer Research; 2015 Apr 18-22; Philadelphia, PA. Philadelphia (PA): AACR; Cancer Res 2015;75(15 Suppl):Abstract nr 1519. doi:10.1158/1538-7445.AM2015-1519