Understanding resistance to targeted cancer drugs through loss of function genetic screens

Comprehensive analysis of cancer genomes has provided important insights in the critical alterations that confer proliferation and survival advantage to the tumor, so-called driver mutations. Tumors harboring these genetic changes frequently exhibit striking sensitivities to inhibition of these oncogenic driver pathways, a principle referred to as oncogene addiction. Substantial progress has been made in the development of drugs that specifically target components of the pathways that are associated with these driver mutations. This has enabled the first steps in a shift from the use of cytotoxic drugs to highly selective targeted therapeutic agents for the treatment of cancer. Unfortunately, despite the expanding development of targeted anti-cancer strategies, treatment failure due to primary or acquired resistance is still an almost inevitable outcome in most advanced human cancers. Understanding drug resistance mechanisms will help design more efficient combination treatment strategies that help block resistance mechanisms before they become clinically manifest. In this review, we discuss how RNA interference functional genetic screens can be used to identify clinically relevant mechanisms of drug resistance and how this technology can be used to develop effective combination therapies.     

Epigenetic impact of dietary polyphenols in cancer chemoprevention: lifelong remodeling of our epigenomes

Cancer, as one of the non-communicable diseases, remains one of the leading causes of death around the world. Recently, epigenetic changes in DNA methylation patterns at CpG sites (epimutations) or deregulated chromatin states of tumor promoting genes and noncoding RNAs emerged as major governing factors in tumor progression and cancer drug sensitivity. Furthermore, various environmental factors such as nutrition, behavior, stress, and toxins remodel our epigenomes lifelong in a beneficial or detrimental way. Since epigenetic marks (epimutations) are reversible in contrast to genetic defects, chemopreventive nutritional polyphenols (soy, genistein, resveratrol, catechin, curcumin) are currently evaluated for their ability to reverse adverse epigenetic marks in cancer (stem) cells to attenuate tumorigenesis-progression, prevent metastasis or sensitize for drug sensitivity. Although polyphenols in fruit and vegetables may help to reduce the risk of cancer, few protective effects have been firmly established, presumably because of inappropriate timing or dosing of diet exposure or due to confounding factors such as smoking and alcohol. In this review will discuss the possible epigenetic contributions of dietary polyphenols in cancer chemoprevention.     

Epigenetics of drug abuse: predisposition or response

Drug addiction continues to be a serious medical and social problem. Vulnerability to develop an addiction to drugs is dependent on genetic, environmental, social and biological factors. In particular, the interactions of environmental and genetic factors indicate the significance of epigenetic mechanisms, which have been found to occur in response to illicit drug use or as underlying factors in chronic substance abuse and relapse. Epigenetics is defined as the heritable and possibly reversible modifications in gene expression that do not involve alterations in the DNA sequence. This review discusses the various types of epigenetic modifications and their relevance to drug addiction to elucidate whether epigenetics is a predisposing factor, or a response to, developing an addiction to drugs of abuse.     

Epigenetics and chemoresistance in colorectal cancer: An opportunity for treatment tailoring and novel therapeutic strategies

Colorectal cancer is the second leading cause of cancer-related deaths in the world. Despite many therapeutic opportunities, prognosis remains dismal for patients with metastatic disease, and a significant portion of early-stage patients develop recurrence after chemotherapy. Epigenetic gene regulation is a major mechanism of cancer initiation and progression, through the inactivation of several tumor suppressor genes. Emerging evidence indicates that epigenetics may also play a key role in the development of chemoresistance. In the present review, we summarize epigenetic mechanisms triggering resistance to three commonly used agents in colorectal cancer: 5-fluorouracil, irinotecan and oxaliplatin. Those epigenetic biomarkers may help stratify colorectal cancer patients and develop a tailored therapeutic approach. In addition, epigenetic modifications are reversible through specific drugs: histone-deacetylase and DNA-methyl-transferase inhibitors. Preclinical studies suggest that these drugs may reverse chemoresistance in colorectal tumors. In conclusion, an epigenetic approach to colorectal cancer chemoresistance may pave the way to personalized treatment and to innovative therapeutic strategies.     

Acquired resistance to drugs targeting receptor tyrosine kinases

Development of resistance to chemotherapeutic drugs represents a significant hindrance to the effective treatment of cancer patients. The molecular mechanisms responsible have been investigated for over half a century and have revealed the lack of a single cause. Rather, a multitude of mechanisms have been delineated ranging from induction and expression of membrane transporters that pump drugs out of cells (multidrug resistance (MDR) phenotype), changes in the glutathione system and altered metabolism to name a few. Treatment of cancer patients/cancer cells with chemotherapeutic agents and/or molecularly targeted drugs is accompanied by acquisition of resistance to the treatment administered. Chemotherapeutic agent resistance was initially assumed to be due to induction of mutations leading to a resistant phenotype. This has also been true for molecularly targeted drugs. Considerable experience has been gained from the study of agents targeting the Bcr-Abl tyrosine kinase including imatinib, dasatinib and sunitinib. It is clear that mutations alone are not responsible for the many resistance mechanisms in play. Rather, additional mechanisms are involved, ranging from epigenetic changes, alternative splicing and the induction of alternative/compensatory signaling pathways. In this review, resistance to receptor tyrosine kinase inhibitors (RTKIs), RTK-directed antibodies and antibodies that inactivate ligands for RTKs are discussed. New approaches and concepts aimed at avoiding the generation of drug resistance will be examined. The recent observation that many RTKs, including the IGF-1R, are dependence receptors that induce apoptosis in a ligand-independent manner will be discussed and the implications this signaling paradigm has on therapeutic strategies will be considered.     

Current clinical trials for epigenetic targets and therapeutic inhibitors for pancreatic cancer therapy

Pancreatic cancer (PC) is an aggressive disease characterized by high mortality. Diagnosis at advanced stage, resistance, and recurrence are major hurdles for PC therapy and contribute to poor survival rate. Mutations in tumor-promoting kinases and epigenetic dysregulation in tumor suppressor genes are hallmarks of PC and can be used for diagnosis and therapy. In this review, we highlight dysregulated genes associated with epigenetic mechanisms, including DNA methylation and histone acetylation, involved in PC progression and resistance. We also explore epigenetic drugs currently in clinical trials. Combining epigenetic drugs and targeted therapies might represent a promising approach for PC.     

Learning from the failures of drug discovery in B-cell non-Hodgkin lymphomas and perspectives for the future: chronic lymphocytic leukemia and diffuse large B-cell lymphoma as two ends of a spectrum in drug development

Introduction: Despite substantial recent advances, there is still an unmet need for better therapies in B-cell non Hodgkin lymphomas (B-NHL), especially in relapsed or refractory disease. Many novel targeted drugs have been developed based on a better molecular understanding of B-NHL.

Areas covered: This article focuses on chronic lymphocytic leukemia (CLL) as a representative for indolent lymphomas and paradigmatic for the tremendous progress in treating B-NHL on the one hand and diffuse large B-cell lymphoma (DLBCL) as a representative for aggressive lymphomas and paradigmatic for many unsolved problems in lymphoma treatment or the other hand. We highlight salient points in current therapies targeting genetic, epigenetic, immunological and microenvironmental alterations. Possible reasons for drug failure in clinical trials like tumor heterogeneity, clonal evolution and drug resistance mechanisms are discussed. Based thereon, some perspectives for further drug discovery are given.

Expert opinion: In view of the pathogenetic complexity of lymphomas, therapies targeting exclusively a single alteration may fail because resistance mechanisms are present either initially or evolve during treatment. Therefore, future therapies in B-NHL may have to target the greatest possible number of genetic, immunological or epigenetic alterations still allowing tolerability and to monitor these alterations during therapy.     

Targeting epigenetic modifiers in cancer

The chromatin structure of a gene plays an important role in regulating its expression. This structure is established through the action of various protein complexes that remodel nucleosomes, catalyse post-translational modifications, deposit histone variants and methylate DNA. Together these complexes establish epigenetic marks that influence expression of the gene. Some of these epigenetic marks are transient while others, such as those involved in silencing genes are more stable and can require several cell divisions to be fully implemented or reversed. Deregulated gene expression programs are a feature of cancer biology and it is now apparent that epigenetic changes, as well as genetic changes, are important in establishing these aberrant expression patterns. However, unlike genetic alterations, epigenetic changes are reversible. The complexes that catalyse these modifications therefore represent valuable targets for therapeutic intervention. Here we will review the most recent literature describing the protein complexes that catalyse epigenetic modifications and the inhibitors of these complexes that are being pursued as cancer drugs. In addition we will highlight those epigenetic modifiers that provide promise as therapeutic targets but for which inhibitors are not currently available.     

Reversing epigenetic mechanisms of drug resistance in solid tumors using targeted microRNA delivery

ABSTRACT

Introduction: Tumor cells utilize many different mechanisms to desensitize themselves to the cytotoxic effects of drugs, but it has recently been recognized that alterations in epigenetic control of gene expression underly many of them. As master regulators of gene expression, microRNAs (miRNAs) present a promising therapeutic strategy for the reversal of epigenetic changes that lead to drug resistance phenotypes in tumor cells.

Areas covered: Effects of epigenetic changes on drug resistance in a variety of solid tumors are discussed. Specific miRNAs that are involved with the regulation of epigenetic machinery are highlighted. Further, we consider how delivery of miRNA or antagomirs may be utilized to resensitize drug-resistant tumor cells.

Expert opinion: Reversal of epigenetically controlled tumor drug resistance mechanisms via miRNA delivery presents a novel strategy for enhancing the efficacy of chemotherapeutics. Further, the ability to target delivery of miRNAs may provide the opportunity to go beyond reversal of resistance to hyper-sensitization of tumor cells to the cytotoxic effects of drugs. However, understanding of the role of miRNA in epigenetic regulation is still in its early stages and further research is critical for potential utility in improving therapeutic efficacy in cancer patients.     

Epigenetics and cancer: implications for drug discovery and safety assessment

It is necessary to determine whether chemicals or drugs have the potential to pose a threat to human health. Research conducted over the last two decades has led to the paradigm that chemicals can cause cancer either by damaging DNA or by altering cellular growth, probably via receptor-mediated changes in gene expression. However, recent evidence suggests that gene expression can be altered markedly via several diverse epigenetic mechanisms that can lead to permanent or reversible changes in cellular behavior. Key molecular events underlying these mechanisms include the alteration of DNA methylation and chromatin, and changes in the function of cell surface molecules. Thus, for example, DNA methyltransferase enzymes together with chromatin-associated proteins such as histone modifying enzymes and remodelling factors can modify the genetic code and contribute to the establishment and maintenance of altered epigenetic states. This is relevant to many types of toxicity including but not limited to cancer. In this paper, we describe the potential for interplay between genetic alteration and epigenetic changes in cell growth regulation and discuss the implications for drug discovery and safety assessment.     

Liposome-based approaches to overcome anticancer drug resistance.

Drug resistance remains an important obstacle towards better outcomes in the treatment of cancer. One general approach to overcome this problem has been to inhibit specific resistance mechanisms, such as P-glycoprotein (PGP)-mediated drug efflux, using small molecule agents or other therapeutic strategies. Alternatively, drug delivery approaches using liposomes or other carriers can in principle target drugs to tumor tissue, tumor cells, or even compartments within tumor cells. By increasing bioavailability of drugs at sites of action, these approaches may provide therapeutic advantages, including enhanced efficacy against resistant tumors. Current liposomal anthracyclines have achieved clinical use in cancer treatment by providing efficient encapsulation of drug in stable and non-reactive carriers, and there is evidence indicating potential benefit in some clinical settings involving resistant tumors. Other liposome-based strategies include constructs designed to be taken up by tumor cells, as well as further modifications to allow triggered drug release. These approaches seek to overcome drug resistance by more efficient delivery to tumor cells, and in some cases by concomitant avoidance or inhibition of drug efflux mechanisms. Newer agents employ molecular targeting, such as immunoliposomes using antibody-directed binding and internalization. These agents selectively deliver drug to tumor cells, can efficiently internalize for intracellular drug release, and can potentially enhance both efficacy and safety.     

DNA甲基化和组蛋白乙酰化介导的肿瘤抗凋亡机制与靶向治疗

肿瘤发生发展是复杂且多步骤的过程,是遗传和表观遗传异常共同作用的结果。遗传变异能引起细胞增殖、分化和凋亡通路异常而导致肿瘤发生,越来越多的研究表明,表观遗传改变可引起癌基因的扩增或肿瘤抑制基因的沉默,在癌症的发生发展中同样发挥着重要作用。常见的表观遗传修饰包括基因启动子区域CpG岛甲基化、组蛋白修饰（包括组蛋白乙酰化和甲基化）、非编码RNA调控以及RNA的修饰。这些表观遗传变化不仅影响基因功能,还通过影响肿瘤微环境促使癌症特征的形成（包括持续增殖、抵抗治疗、血管生成、局部侵袭和远处转移）。本综述将重点阐述DNA甲基化和组蛋白乙酰化在介导肿瘤抗凋亡机制中的作用,并将讨论靶向表观遗传因子的抗肿瘤药物的发展现状及前景。     

Recent trends in cancer drug resistance reversal strategies using nanoparticles

INTRODUCTION: Resistance to chemotherapy is a major obstacle in the successful amelioration of tumors in many cancer patients. Resistance is either intrinsic or acquired, involving mechanisms such as genetic aberrations, decreased influx and increased efflux of drugs. Strategies for the reversal of resistance involve the alteration of enzymes responsible for drug resistance, the modulation of proteins regulating apoptosis mechanisms and improving the uptake of drugs using nanotechnology. Novel strides in the reversal of drug resistance are emerging, involving the use of nanotechnology, targeting stem cells, etc. AREAS COVERED: This paper reviews the most recent cancer drug reversal strategies involving nanotechnology for targeting cancer cells and cancer stem cells (CSCs), for enhanced uptake of micro- and macromolecular inhibitors. EXPERT OPINION: Nanotechnology used in conjunction with existing therapies, such as gene therapy and P-glycoprotein inhibition, has been shown to improve the reversal of drug resistance; the mechanisms involved in this include specific targeting of drugs and nucleotide therapeutics, enhanced cellular uptake of drugs and improved bioavailability of drugs with poor physicochemical characteristics. Important strategies in the reversal of drug resistance include: a multifunctional nanoparticulate system housing a targeting moiety; therapeutics to kill resistant cancer cells and CSCs; cytotoxic drugs and a tumor microenvironment stimuli-responsive element, to release the encapsulated therapeutics.     

Epigenetic-dependent regulation of drug transport and metabolism: an update

The pharmacokinetics of a drug are subject to large interindividual variability, which can result in lack of response or adverse drug reactions. In addition to genetic polymorphisms and drug interactions, key genes involved in the metabolism and transport of drugs are demonstrated to have epigenetic influences that can potentially affect interindividual variability in drug response. Emerging studies have focused on the importance of DNA methylation for ADME gene expression and for drug action and resistance, particularly in cancer. However, the epigenetic and ncRNA-dependent regulation of these genes, as well as the pharmacological consequences, is in need of greater attention. In the current review we provide an update of epigenetic and ncRNA-dependent regulation of ADME genes.     

Drug resistance: challenges to effective therapy

The success of current treatment strategies is limited by the development of therapy resistance as evidenced by recurrence of the primary tumor or distant metastasis. Eradication of primary and metastatic disease requires interventions at both the cancer cell and tumor microenvironment levels. In this review, we will discuss mechanisms that are intrinsic to cancer cells, and those that are mediated by the tumor microenvironment as contributors to drug resistance. Mechanisms contributing to multidrug resistance phenotype and the challenges facing molecular targeted therapy are discussed. The DNA damage tolerance pathway confers tolerance to a variety of structurally and functionally unrelated drugs. A rationale for targeting the DNA damage tolerance pathway as a novel tool for overcoming drug resistance is discussed. We have also addressed the need for employing clinically relevant model systems for performing drug sensitivity evaluations. These model systems must take into account the three-dimensional organization and in vivo relationship of tumor with its microenvironment. Such integrative efforts would not only yield a more global understanding of the tumor- and microenvironment-derived mechanisms involved in emergence of drug resistance but would also provide novel therapeutic targets that will disrupt the interactions between the tumor cells and its microenvironment.     

Starvation,detoxification, and multidrug resistance in cancer therapy

The selection of chemotherapy drugs is based on the cytotoxicity to specific tumor cell types and the relatively low toxicity to normal cells and tissues. However, the toxicity to normal cells poses a major clinical challenge, particularly when malignant cells have acquired resistance to chemotherapy. This drug resistance of cancer cells results from multiple factors including individual variation, genetic heterogeneity within a tumor, and cellular evolution. Much progress in the understanding of tumor cell resistance has been made in the past 35 years, owing to milestone discoveries such as the identification and characterization of ABC transporters. Nonetheless, the complexity of the genetic and epigenetic rewiring of cancer cells makes drug resistance an equally complex phenomenon that is difficult to overcome. In this review, we discuss how the remarkable changes in the levels of glucose, IGF-I, IGFBP-1 and in other proteins caused by fasting have the potential to improve the efficacy of chemotherapy against tumors by protecting normal cells and tissues and possibly by diminishing multidrug resistance in malignant cells.     

Targeted inhibition of kinases in cancer therapy

With an understanding of the molecular changes that accompany cell transformation, cancer drug discovery has undergone a dramatic change in the past few years. Whereas most of the emphasis in the past has been placed on developing drugs that induce cell death based on mechanisms that do not discriminate between normal and tumor cells, recent strategies have emphasized targeting specific mechanisms that have gone awry in tumor cells. However, the identification of cancer-associated mutations in oncogenes and their amplification in tumors has suggested that inhibitors against such proteins might represent attractive substrates for targeted therapy. In the clinic, the success of imatinib (Gleevec?, STI571) and trastuzumab (Herceptin?), both firsts of their kind, spurred further development of new, second-generation drugs that target kinases in cancer. This review highlights a few important examples each of these types of therapies, along with some newer agents that are in various stages of development. Second-generation kinase inhibitors aimed at overriding emerging resistance to these therapies are also discussed.     

Genomics and cancer drug resistance

Cellular drug resistance is a major obstacle in cancer therapy. Mechanisms of resistance can be associated with altered expression of ATP-binding cassette (ABC) family of transporters on cell membrane transporters, the most common cause of multi-drug resistance (MDR), but can also include alterations of DNA repair pathways, resistance to apoptosis and target modifications. Anti-cancer treatments may be divided into different categories based on their purpose and action: chemotherapeutic agents damage and kill dividing cells; hormonal treatments prevent cancer cells from receiving signals essential for their growth; targeted drugs are a relatively new cancer treatment that targets specific proteins and pathways that are limited primarily to cancer cells or that are much more prevalent in cancer cells; and antibodies function by either depriving the cancer cells of necessary signals or by causing their direct death. In any case, resistance to anticancer therapies leads to poor prognosis of patients. Thus, identification of novel molecular targets is critical in development of new, efficient and specific cancer drugs. The aim of this review is to describe the impact of genomics in studying some of the most critical pathways involved in cancer drug resistance and in improving drug development. We shall also focus on the emerging role of microRNAs, as key gene expression regulators, in drug resistance. Finally, we shall address the specific mechanisms involved in resistance to tyrosine kinase inhibitors in chronic myeloid leukemia.     

Epigenetic therapy of cancer: past, present and future

The initiation and progression of cancer is controlled by both genetic and epigenetic events. Unlike genetic alterations, which are almost impossible to reverse, epigenetic aberrations are potentially reversible, allowing the malignant cell population to revert to a more normal state. With the advent of numerous drugs that target specific enzymes involved in the epigenetic regulation of gene expression, the utilization of epigenetic targets is emerging as an effective and valuable approach to chemotherapy as well as chemoprevention of cancer.