Bioinformatic Analysis for the Validation of Novel Biomarkers for Cancer Diagnosis and Drug Sensitivity

Background: The genetic control of tumour progression presents the opportunity for bioinformatics and gene expression data to be used as a basis for tumour grading. The development of a genetic signature based on microarray data allows for the development of personalised chemotherapeutic regimes. Method: ONCOMINE was utilised to create a genetic signature for ovarian serous adenocarcinoma and to compare the expression of genes between normal ovarian and cancerous cells. Ingenuity Pathways Analysis was also utilised to develop molecular pathways and observe interactions with exogenous molecules. Results: The gene signature demonstrated 98.6% predictive capability for the differentiation between borderline ovarian serous neoplasm and ovarian serous adenocarcinoma. The data demonstrated that many genes were related to angiogenesis. Thymidylate synthase, GLUT-3 and HSP90AA1 were related to tanespimycin sensitivity (p=0.005). Conclusions: Genetic profiling with the gene signature demonstrated potential for clinical use. The use of tanespimycin alongside overexpression of thymidylate synthase, GLUT-3 and HSP90AA1 is a novel consideration for ovarian cancer treatment

Emerging role of nuclear factor erythroid 2-related factor 2 in the mechanism of action and resistance to anticancer therapies

Nuclear factor E2-related factor 2 (NRF2), a transcription factor, is a master regulator of an array of genes related to oxidative and electrophilic stress that promote and maintain redox homeostasis. NRF2 function is well studied in in vitro, animal and general physiology models. However, emerging data has uncovered novel functionality of this transcription factor in human diseases such as cancer, autism, anxiety disorders and diabetes. A key finding in these emerging roles has been its constitutive upregulation in multiple cancers promoting pro-survival phenotypes. The survivability pathways in these studies were mostly explained by classical NRF2 activation involving KEAP-1 relief and transcriptional induction of reactive oxygen species (ROS) neutralizing and cytoprotective drug-metabolizing enzymes (phase I, II, III and 0). Further, NRF2 status and activation is associated with lowered cancer therapeutic efficacy and the eventual emergence of therapeutic resistance. Interestingly, we and others have provided further evidence of direct NRF2 regulation of anticancer drug targets like receptor tyrosine kinases and DNA damage and repair proteins and kinases with implications for therapy outcome. This novel finding demonstrates a renewed role of NRF2 as a key modulatory factor informing anticancer therapeutic outcomes, which extends beyond its described classical role as a ROS regulator. This review will provide a knowledge base for these emerging roles of NRF2 in anticancer therapies involving feedback and feed forward models and will consolidate and present such findings in a systematic manner. This places NRF2 as a key determinant of action, effectiveness and resistance to anticancer therapy

Redox control of multidrug resistance and Its possible modulation by antioxidants

Clinical efficacy of anticancer chemotherapies is dramatically hampered by multidrug resistance (MDR) dependent on inherited traits, acquired defence against toxins, and adaptive mechanisms mounting in tumours. There is overwhelming evidence that molecular events leading to MDR are regulated by redox mechanisms. For example, chemotherapeutics which overrun the first obstacle of redox-regulated cellular uptake channels (MDR1, MDR2, and MDR3) induce a concerted action of phase I/II metabolic enzymes with a temporal redox-regulated axis. This results in rapid metabolic transformation and elimination of a toxin. This metabolic axis is tightly interconnected with the inducible Nrf2-linked pathway, a key switch-on mechanism for upregulation of endogenous antioxidant enzymes and detoxifying systems. As a result, chemotherapeutics and cytotoxic by-products of their metabolism (ROS, hydroperoxides, and aldehydes) are inactivated and MDR occurs. On the other hand, tumour cells are capable of mounting an adaptive antioxidant response against ROS produced by chemotherapeutics and host immune cells. The multiple redox-dependent mechanisms involved in MDR prompted suggesting redox-active drugs (antioxidants and prooxidants) or inhibitors of inducible antioxidant defence as a novel approach to diminish MDR. Pitfalls and progress in this direction are discussed

Intraperitoneal chemotherapy for peritoneal metastases : an expert opinion

Introduction: The rationale for intraperitoneal (IP) drug delivery for patients with peritoneal metastases (PM) is based on the pharmacokinetic advantage resulting from the peritoneal-plasma barrier, and on the potential to adequately treat small, poorly vascularized PM. Despite a history of more than three decades, many aspects of IP drug delivery remain poorly studied. Areas covered: We outline the anatomy and physiology of the peritoneal cavity, including the pharmacokinetics of IP drug delivery. We discuss transport mechanisms governing tissue penetration of IP chemotherapy, and how these are affected by the biomechanical properties of the tumor stroma. We provide an overview of the current clinical evidence on IP chemotherapy in ovarian, colorectal, and gastric cancer. We discuss the current limitations of IP drug delivery and propose several potential areas of progress. Expert opinion: The potential of IP drug delivery is hampered by off-label use of drugs developed for systemic therapy. The efficacy of IP chemotherapy for PM depends on cancer type, disease extent, and mode of drug delivery. Results from ongoing randomized trials will allow to better delineate the potential of IP chemotherapy. Promising approaches include IP aerosol therapy, prolonged delivery platforms such as gels or biomaterials, and the use of nanomedicine

Aerosolization of nanotherapeutics as a newly emerging treatment regimen for peritoneal carcinomatosis

Recent advances in locoregional chemotherapy have opened the door to new approaches for the clinical management of peritoneal carcinomatosis (PC) by facilitating the delivery of anti-neoplastic agents directly to the tumor site, while mitigating adverse effects typically associated with systemic administration. In particular, an innovative intra-abdominal chemotherapeutic approach, known as Pressurized Intraperitoneal Aerosol Chemotherapy (PIPAC), was recently introduced to the intraperitoneal (IP) therapy regimens as a palliative therapeutic option in patients with PC, presumably providing a better drug distribution pattern together with deeper drug penetration into tumor nodules within the peritoneal space. Furthermore, the progress of nanotechnology in the past few decades has prompted the application of different nanomaterials in IP cancer therapy, offering new possibilities in this field ranging from an extended retention time to sustained drug release in the peritoneal cavity. This review highlights the progress, challenges, and opportunities in utilizing cancer nanotherapeutics for locoregional drug delivery, with a special emphasis on the aerosolization approach for intraperitoneal therapies

Organometallic iridium(III) anticancer complexes with new mechanisms of action: NCI-60 screening, mitochondrial targeting, and apoptosis

Platinum complexes related to cisplatin, cis-[PtCl2(NH3)2], are successful anticancer drugs; however, other transition metal complexes offer potential for combating cisplatin resistance, decreasing side effects, and widening the spectrum of activity. Organometallic half-sandwich iridium (IrIII) complexes [Ir(Cpx)(XY)Cl]+/0 (Cpx = biphenyltetramethylcyclopentadienyl and XY = phenanthroline (1), bipyridine (2), or phenylpyridine (3)) all hydrolyze rapidly, forming monofunctional G adducts on DNA with additional intercalation of the phenyl substituents on the Cpx ring. In comparison, highly potent complex 4 (Cpx = phenyltetramethylcyclopentadienyl and XY = N,N-dimethylphenylazopyridine) does not hydrolyze. All show higher potency toward A2780 human ovarian cancer cells compared to cisplatin, with 1, 3, and 4 also demonstrating higher potency in the National Cancer Institute (NCI) NCI-60 cell-line screen. Use of the NCI COMPARE algorithm (which predicts mechanisms of action (MoAs) for emerging anticancer compounds by correlating NCI-60 patterns of sensitivity) shows that the MoA of these IrIII complexes has no correlation to cisplatin (or oxaliplatin), with 3 and 4 emerging as particularly novel compounds. Those findings by COMPARE were experimentally probed by transmission electron microscopy (TEM) of A2780 cells exposed to 1, showing mitochondrial swelling and activation of apoptosis after 24 h. Significant changes in mitochondrial membrane polarization were detected by flow cytometry, and the potency of the complexes was enhanced ca. 5× by co-administration with a low concentration (5 μM) of the γ-glutamyl cysteine synthetase inhibitor L-buthionine sulfoximine (L-BSO). These studies reveal potential polypharmacology of organometallic IrIII complexes, with MoA and cell selectivity governed by structural changes in the chelating ligands

Broad targeting of resistance to apoptosis in cancer

Apoptosis or programmed cell death is natural way of removing aged cells from the body. Most of the anti-cancer therapies trigger apoptosis induction and related cell death networks to eliminate malignant cells. However, in cancer, de-regulated apoptotic signaling, particularly the activation of an anti-apoptotic systems, allows cancer cells to escape this program leading to uncontrolled proliferation resulting in tumor survival, therapeutic resistance and recurrence of cancer. This resistance is a complicated phenomenon that emanates from the interactions of various molecules and signaling pathways. In this comprehensive review we discuss the various factors contributing to apoptosis resistance in cancers. The key resistance targets that are discussed include (1) Bcl-2 and Mcl-1 proteins; (2) autophagy processes; (3) necrosis and necroptosis; (4) heat shock protein signaling; (5) the proteasome pathway; (6) epigenetic mechanisms; and (7) aberrant nuclear export signaling. The shortcomings of current therapeutic modalities are highlighted and a broad spectrum strategy using approaches including (a) gossypol; (b) epigallocatechin-3-gallate; (c) UMI-77 (d) triptolide and (e) selinexor that can be used to overcome cell death resistance is presented. This review provides a roadmap for the design of successful anti-cancer strategies that overcome resistance to apoptosis for better therapeutic outcome in patients with cancer

Current applications and future potential for bioinorganic chemistry in the development of anticancer drugs

This review illustrates notable recent progress in the field of medicinal bioinorganic chemistry as many new approaches to the design of innovative metal-based anticancer drugs are emerging. Current research addressing the problems associated with platinum drugs has focused on other metal-based therapeutics that have different modes of action and on prodrug and targeting strategies in an effort to diminish the side-effects of cisplatin chemotherapy

The Role Of Oxidative Stress In The Establishment Of Resistance To Cisplatin In Epithelial Ovarian Cancer Cells

Epithelial ovarian cancer is the deadliest of all gynecologic cancers with an estimated 22,280 new cases and 14,240 deaths expected in 2016 in the US alone. This high mortality rate can be partially attributed to a lack of universal screening and the development of resistance to the recommended chemotherapeutics. Typically, the treatment of ovarian cancer requires both cytoreductive surgery (CRS) and platinum/taxane combination chemotherapy. Initially, 50–80% of patients with advanced disease will achieve complete clinical response. Unfortunately, most will relapse within 18 months with chemoresistant disease. Thus, understanding the mechanisms of platinum resistance is critical in order to improve the care of ovarian cancer patients. Several theories to explain cisplatin resistance have been proposed but failed to translate into clinical practice. Typically drug resistance mechanisms are multifactorial but can be broadly categorized as follows: 1) pharmacokinetic, resulting in inadequate intratumor cisplatin concentration, 2) tumor micro-environment, involving membrane transporters by reducing cisplatin uptake or increasing efflux, 3) increased inactivation and sequestration of cisplatin, 4) activation of DNA repair and antiapoptotic mechanisms, 5) decreased autophagy and, 6) cancer-cell specific mechanisms such as: acquired somatic mutations and epigenetic changes and persistence of slow growing cancer stem cells that maintain the cancer phenotype. We have recently characterized EOC tissues and cells to manifest a persistent pro-oxidant state with the upregulation of several key oxidant enzymes including: myeloperoxidase (MPO), inducible nitric oxide synthase (iNOS), and nicotinamide adenine dinucleotide phosphate (NAD(P)H) oxidase with concurrent decrease in apoptosis compared to normal human ovarian tissues and cells. More importantly, shutting down the expression of one or more of these key oxidant enzymes reduced the pro-oxidant state, and significantly induced apoptosis. Single-nucleotide polymorphisms (SNPs) are point mutations that are selectively maintained in populations and are distributed throughout the human genome at an estimated overall frequency of at least one in every 1000 base pairs. Several SNPs in key oxidants and antioxidants enzymes have been associated with various cancers including ovarian. Therefore, we are proposing the following hypothesis: cisplatin treatment induces mutations in key oxidant and antioxidant enzymes resulting in further enhancement of oxidative stress and the acquisition of resistance in EOC cells. To test this hypothesis, we are proposing then following specific aims: Specific Aim 1: To determine the association of specific single nucleotide polymorphisms (SNPs) in key oxidant and antioxidant enzymes with EOC risk and survival in patients. The rationale of this aim is based on the fact that oxidative stress is strongly associated with several cancers, including ovarian. Known specific SNPs in oxidant and antioxidant genes may alter their expression profile and enzymatic functions. These SNPs have been reported to be associated not only with cancer risks, but also patient response to treatment and survival. The hypothesis of this aim is that specific SNPs in key oxidant and antioxidant enzymes are associated with overall patient survival. To achieve this aim, we will perform a case-control study using stored blood samples of research participants from the Karmanos Cancer Center. Individuals (n=143) recruited were divided into controls (n=94),) and ovarian cancer cases (n=49). Samples will undergo DNA extraction followed by TaqMan® SNP genotype analysis for rs4880 manganese superoxide dismutase (MnSOD), rs4673 (NAD(P)H oxidase (CYBA), rs3448 glutathione peroxidase (GPX1), rs2297518 inducible nitric oxide synthase (iNOS), rs1002149 glutathione reductase (GSR), and rs1001179 catalase (CAT). We will perform a multivariate analysis for identification of confounding variables and potential predictors of risk. Additionally, to study the impact of the SNPs on overall survival, Cox regression and Kaplan-Meier survival analyses will be used. Specific Aim 2: To determine the association of key oxidant and antioxidant enzymes as well as specific SNPs in these enzymes with the development of cisplatin resistance in EOC cells. The rationale of this aim is based on previous findings showing an association between the altered redox enzymes and EOC, in both patients and human cell lines. The hypothesis of this aim is that the acquisition of resistance to cisplatin in EOC cells is associated with enhanced pro-oxidant profile, as well as specific SNPs in key oxidant and antioxidant enzymes. To achieve this aim, we will utilize two human EOC cell lines, MDAH-2774 and SKOV-3 and their cisplatin resistant counterparts. We will perform TaqMan PCR genotyping, real-time RT-PCR, ELISA, and Griess assay to study the expression profile of the following genes: CYBA/NOX4, iNOS, CAT, SOD3, GSR and GPX1. To analyze the difference in the expression profiles of these genes for sensitive compared to resistant cells, we will use a Student’s t-test. Specific Aim 3: To determine whether specific SNP(s) in key oxidant and antioxidant enzymes cause the acquisition of cisplatin resistance in EOC cells. The rationale of this aim is based on the established fact that cisplatin treatment causes DNA damage, and the observation that specific SNPs in the redox enzymes were found to be associated with poor survival in patients. The hypothesis of this aim is: specific SNPs in key oxidant and antioxidant enzymes cause cisplatin resistance. To achieve this aim, we will utilize the CRISPR/Cas9 system to generate point mutations in sensitive EOC cells corresponding to the SNP genotype of the chemoresistant MDAH-2774 and SKOV-3 EOC cells. The cells will then be tested for cisplatin resistance using the MTT viability assay using the IC50 method. Results will be analyzed with regression analysis and student t-tests

Integrated analysis of DNA methylation and gene expression reveals specific signaling pathways associated with platinum resistance in ovarian cancer

<p>Abstract</p> <p>Background</p> <p>Cisplatin and carboplatin are the primary first-line therapies for the treatment of ovarian cancer. However, resistance to these platinum-based drugs occurs in the large majority of initially responsive tumors, resulting in fully chemoresistant, fatal disease. Although the precise mechanism(s) underlying the development of platinum resistance in late-stage ovarian cancer patients currently remains unknown, CpG-island (CGI) methylation, a phenomenon strongly associated with aberrant gene silencing and ovarian tumorigenesis, may contribute to this devastating condition.</p> <p>Methods</p> <p>To model the onset of drug resistance, and investigate DNA methylation and gene expression alterations associated with platinum resistance, we treated clonally derived, drug-sensitive A2780 epithelial ovarian cancer cells with increasing concentrations of cisplatin. After several cycles of drug selection, the isogenic drug-sensitive and -resistant pairs were subjected to global CGI methylation and mRNA expression microarray analyses. To identify chemoresistance-associated, biological pathways likely impacted by DNA methylation, promoter CGI methylation and mRNA expression profiles were integrated and subjected to pathway enrichment analysis.</p> <p>Results</p> <p>Promoter CGI methylation revealed a positive association (Spearman correlation of 0.99) between the total number of hypermethylated CGIs and GI₅₀values (<it>i.e</it>., increased drug resistance) following successive cisplatin treatment cycles. In accord with that result, chemoresistance was reversible by DNA methylation inhibitors. Pathway enrichment analysis revealed hypermethylation-mediated repression of cell adhesion and tight junction pathways and hypomethylation-mediated activation of the cell growth-promoting pathways PI3K/Akt, TGF-beta, and cell cycle progression, which may contribute to the onset of chemoresistance in ovarian cancer cells.</p> <p>Conclusion</p> <p>Selective epigenetic disruption of distinct biological pathways was observed during development of platinum resistance in ovarian cancer. Integrated analysis of DNA methylation and gene expression may allow for the identification of new therapeutic targets and/or biomarkers prognostic of disease response. Finally, our results suggest that epigenetic therapies may facilitate the prevention or reversal of transcriptional repression responsible for chemoresistance and the restoration of sensitivity to platinum-based chemotherapeutics.</p