Epigenetic reprogramming in breast cancer: From new targets to new therapies

Abstract

Breast cancer is the most commonly diagnosed cancer and the second leading cause of cancer death among women in the United States. Recently, interest has grown in the role of epigenetics in breast cancer development and progression. Epigenetic changes such as DNA methylation, histone modifications, and abnormal expression of non-coding RNAs emerged as novel biomarkers in breast cancer diagnosis, therapy, and prevention. This review focuses on the most recent mechanistic findings underlying epigenetic changes in breast cancer development and their role as predictors of breast cancer risk. The rapid progress in our understanding of epigenetic findings in breast cancer has opened new avenues for potential therapeutic approaches via identification of epigenetic targets. We highlight the development of novel epigenetically targeted drugs, relevant clinical trials in breast cancer patients, and recent approaches combining epigenetic agents with chemotherapy and/or endocrine therapy that may incrementally improve long-term outcomes in appropriately selected breast cancer patients. Biomarkers of response are needed, however, to identify patient subsets that are most likely to benefit from epigenetic treatment strategies.     

DNA methylation detection methods used in colorectal cancer

Colorectal cancer (CRC) remains a major contributor to the number of cancer-related deaths that occur annually worldwide. With the development of molecular biology methods, an increasing number of molecular biomarkers have been identified and investigated. CRC is believed to result from an accumulation of epigenetic changes, and detecting aberrant DNA methylation patterns is useful for both the early diagnosis and prognosis of CRC. Numerous studies are focusing on the development of DNA methylation detection methods or DNA methylation panels. Thus, this review will discuss the commonly used techniques and technologies to evaluate DNA methylation, their merits and deficiencies as well as the prospects for new methods.     

Molecular biomarkers in esophageal,gastric, and colorectal adenocarcinoma

Cancers of the esophagus, stomach and colon contribute to a major health burden worldwide and over 20% of all cancer deaths. Biomarkers that should indicate pathogenic process and are measureable in an objective manner for these tumors are rare and not established in the clinical setting. In general biomarkers can be very useful for cancer management as they can improve clinical decision-making regarding diagnosis, surveillance, and therapy. Biomarkers can be different types of molecular entities (such as DNA, RNA or proteins), which can be detected, in different tissues or body fluids. However, more important is the type of biomarker itself, which allows diagnostic, prognostic or predictive analyses for different clinical problems. This review aims to systematically summarize the recent findings of genetic and epigenetic markers for gastrointestinal tumors within the last decade. While many biomarkers seem to be very promising, especially if used as panels, further development is urgently needed to address practical considerations of biomarkers in cancer treatment.     

Epigenetics and cancer

Both genetics and epigenetics regulate gene expression in cancer. Regulation by genetics involves a change in the DNA sequence, whereas epigenetic regulation involves alteration in chromatin structure and methylation of the promoter region. During the initiation, development, and progression of cancer, a number of genes undergo epigenetic changes. Some of these changes can be used as biomarkers for early detection of cancer as well as to follow treatment. A panel of epigenetic biomarkers is preferred to a single biomarker in clinical assays. Changes in gene expression due to epigenetic regulation can be reversed by chemicals, and this approach opens up a novel approach in cancer prevention and treatment.     

Epigenetic biomarkers in colorectal cancer diagnostics

Colorectal cancer (CRC) is a significant health burden worldwide. Despite advancements in treatment options, improvements in CRC patient survival have been limited owing to lack of early detection and limited capacity for optimal therapeutic decision-making. Biomarkers to improve CRC diagnosis, prognosis and prediction of treatment response therefore represent opportunities to improve patient outcome. In addition to genetic alterations and genomic instability, it is now clear that epigenetic alterations play dramatic roles in driving tumor onset and progression in CRC. A recent surge in investigation of epigenetic biomarkers including DNA methylation, miRNA expression and histone modifications has demonstrated that these alterations may be enticing translational biomarker candidates in CRC. In particular, methylation kits have already been incorporated into clinical practice for a handful of cancers, including CRC. This review will aim to summarize the established and emerging roles of epigenetic modifications in CRC detection, prognostication and prediction of treatment response.     

Circulating tumor cells: Advances in isolation and analysis,and challenges for clinical applications

Circulating tumor cells (CTCs) are rare cancer cells released from tumors into the bloodstream that are thought to have a key role in cancer metastasis. The presence of CTCs has been associated with worse prognosis in several major cancer types, including breast, prostate and colorectal cancer. There is considerable interest in CTC research and technologies for their potential use as cancer biomarkers that may enhance cancer diagnosis and prognosis, facilitate drug development, and improve the treatment of cancer patients. This review provides an update on recent progress in CTC isolation and molecular characterization technologies. Furthermore, the review covers significant advances and limitations in the clinical applications of CTC-based assays for cancer prognosis, response to anti-cancer therapies, and exploratory studies in biomarkers predictive of sensitivity and resistance to cancer therapies.     

New perspectives and strategy research biomarkers for hepatocellular carcinoma.

Hepatocellular carcinoma (HCC) is the fifth most common cancer worldwide. Cirrhosis caused by hepatitis B virus, hepatitis C virus or chronic alcohol intake is associated with major risk. Systematic screening for HCC of asymptomatic patients with cirrhosis is needed for earlier detection of small tumors requiring treatment (liver transplantation, surgical resection, percutaneous techniques). The recommended screening strategy among cirrhotic patients is based on regular liver ultrasonography associated with serum alpha-fetoprotein (AFP) assay. As the performance of AFP is not satisfactory, additional tumoral markers are proposed (des-gamma-carboxyprothrombin, glycosylated AFP-L3 fraction). Currently, diagnosis of HCC in cirrhotic patients includes non-invasive tests (imaging after contrast administration, AFP assay); diagnostic biopsy is performed when imaging is limited. After treatment, tumor recurrence is assessed by regular follow-up (AFP assay and imaging). Despite the lack of accurate markers, recent developments in genomic and proteomic approaches will allow the discovery of new biomarkers for primary tumors, as well as for recurrence. This review summarizes the current state of biomarkers for screening, diagnosis and follow-up of HCC, and highlights new perspectives in the field.     

Translational Research: Precision Medicine,Personalized Medicine,Targeted Therapies: Marketing or Science?

Personalized medicine is based on: 1) improved clinical or non-clinical methods (including biomarkers) for a more discriminating and precise diagnosis of diseases; 2) targeted therapies of the choice or the best drug for each patient among those available; 3) dose adjustment methods to optimize the benefit-risk ratio of the drugs chosen; 4) biomarkers of efficacy, toxicity, treatment discontinuation, relapse, etc. Unfortunately, it is still too often a theoretical concept because of the lack of convenient diagnostic methods or treatments, particularly of drugs corresponding to each subtype of pathology, hence to each patient. Stratified medicine is a component of personalized medicine employing biomarkers and companion diagnostics to target the patients likely to present the best benefit-risk balance for a given active compound. The concept of targeted therapy, mostly used in cancer treatment, relies on the existence of a defined molecular target, involved or not in the pathological process, and/or on the existence of a biomarker able to identify the target population, which should logically be small as compared to the population presenting the disease considered. Targeted therapies and biomarkers represent important stakes for the pharmaceutical industry, in terms of market access, of return on investment and of image among the prescribers. At the same time, they probably represent only the first generation of products resulting from the combination of clinical, pathophysiological and molecular research, i.e. of translational research.     

The evolving landscape of therapeutic drug development for hepatocellular carcinoma

Currently, only one drug, sorafenib, is FDA approved for the treatment of advanced hepatocellular carcinoma (HCC), achieving modest objective response rates while still conferring an overall survival benefit. Unlike other solid tumors, no oncogenic addiction loops have been validated as clinically actionable targets in HCC. Outcomes of HCC could potentially be improved if critical molecular subclasses with distinct therapeutic vulnerabilities can be identified, biomarkers that predict recurrence or progression early can be determined and key epigenetic, genetic or microenvironment drivers that determine best response to a specific targeting treatment can be uncovered.Our group and others have examined the molecular heterogeneity of hepatocellular carcinoma. We have developed a panel of patient derived xenograft models to enable focused pre-clinical drug development of rationally designed therapies in specific molecular subgroups. We observed unique patterns, including synergies, of drug activity across our molecularly diverse HCC xenografts, pointing to specific therapeutic vulnerabilities for individual tumors. These efforts inform clinical trial designs and catalyze therapeutic development. It also argues for efficient strategic allocation of patients into appropriate enriched clinical trials. Here, we will discuss some of the recent important therapeutic studies in advanced HCC and also some of the potential strategies to optimize clinical therapeutic development moving forward.     

The molecular diagnosis of hepatitis B virus-associated hepatocellular carcinoma

Hepatitis B virus (HBV) infection is the major cause of hepatocellular carcinoma (HCC) worldwide. The pathogenesis of HBV-associated HCC has been studied extensively, and molecular changes during malignant transformation have been identified. It has been proposed that the insertion of HBV DNA into the human genome results in chromosomal instability and inactivation of tumor suppressor genes. Transactivation of oncogenes, inactivation of tumor suppressor genes, and alteration of the cell cycle by HBV proteins are also involved in the progression of hepatocellular carcinogenesis. Traditional clinical examinations of HCC, such as biopsy, computer tomography, ultrasonic imaging, and detection of such biomarkers as a-fetoprotein, are currently the "gold standard" in diagnosis.These tests diagnose HCC only in the late stages of disease. This limitation has greatly reduced the chance of survival of HCC patients. To resolve this problem, new biomarkers that can diagnose HCC in earlier stages are necessary. Based on recent molecular studies of the effects of HBV on cellular transformation, differentially expressed biomarkers of HBV infection have been elucidated. With the analyses of the HBV replication profile, the viral load (HBV DNA levels) of patients, and the viral protein expression, the severity of hepatitis in the preneoplastic stages can be assessed. In the future, with the molecular profiles identified by genomic and proteomic approaches, stage-specific biomarkers should be identified to monitor the progression and prognosis of HCC.     

Molecular analysis of cell-free circulating DNA for the diagnosis of somatic mutations associated with resistance to tyrosine kinase inhibitors in non-small-cell lung cancer

In non-small-cell lung cancer, the molecular diagnosis of somatic mutations is instrumental for the choice of the most appropriate treatment. However, despite an initial response, resistance to tyrosine kinase inhibitors occurs and thereafter tumors progress. For this reason, next generation inhibitors able to overcome acquired resistances are currently in development. Therefore, the identification of the molecular determinants of resistance is needed to adapt treatment accordingly. The analysis of circulating cell-free tumor DNA represents a powerful tool to monitor the somatic changes induced by treatment. This review focuses on the most recent advantages in the diagnosis of acquired resistance in circulating cell-free tumor DNA and underlines the strategies ready to be translated in the clinical practice.     

急性髓细胞白血病的表观遗传学异常改变及其靶向治疗的研究进展

目前,由于传统化疗的局限性,急性髓细胞白血病(AML)的治疗一直未能取得突破性的进展,特别是如何提高复发/难治性患者的疗效已成为AML临床治疗中一个亟待解决的难题.近年来,随着对AML分子生物学研究的不断深入,一些具有预后意义的分子遗传学改变有望作为AML危险度分层的指标以及治疗靶点,而引起学术界的广泛关注.有关AML分子靶向药物治疗的研究层出不穷,其中针对AML表观遗传学异常改变的治疗研究已经取得了较大的进展.表观遗传学改变与基因突变有重要的区别,即表观遗传学改变是可逆的,通过使用针对相应的表观遗传学异常改变的药物可使沉默的抑癌基因重新表达.目前,应用于AML临床治疗的针对表观遗传学异常改变的药物主要包括DNA去甲基化药物与组蛋白去乙酰化酶抑制剂,以及二者的联合应用.针对AML表观遗传学异常改变的治疗方案有望成为中、高危AML患者,尤其是不能耐受化疗的老年患者的治疗选择之一.笔者拟就AML的表观遗传学改变,以及其靶向治疗的研究进展进行综述.     

Epigenetic and genetic alterations-based molecular classification of head and neck cancer

The long-term survival rates for patients diagnosed with advanced head and neck cancer (HNC) remain poor. Many perplexing factors, including etiology and comorbidity, lead to different molecular malfunctions of HNC cells and determine the prognosis of the disease. Traditional diagnostic methods are limited in that they fail to provide an effective classification diagnosis, such as a more precise prediction of prognosis and decisions for personalized treatment regimens. Recently, molecular biology techniques, especially epigenetic and genetic techniques, have been developed that have enabled us to gain a greater insight into the molecular pathways underlying the cancers. Translating the research into a format that will facilitate effective molecular classification, support personalized treatment and determine prognosis remains a challenge. In this review, the authors provide an overview of cancer epigenetic and genetic alterations, tissue banks, and several promising biomarkers or candidates that may ultimately prove to be beneficial in a clinical setting for patients with HNC.     

抑癌基因CST6及其异常甲基化后在肿瘤发生中的意义

人类半胱氨酸蛋白酶抑制剂基因（cystatinE／MorCST6），又称胱抑C，最初是从转移性乳腺癌细胞中分离出来的一种具有抑制半胱氨酸蛋白酶作用的新基因。有研究发现CST6基因在浸润性乳腺癌、宫颈癌、转移性前列腺癌以及神经胶质脑瘤中表达均有下调，具有抑癌基因的潜能，并且还发现造成该基因表达下调的原因除了基因突变、基因缺失以外，表观遗传修饰的作用更为普遍，而且后者导致的基因沉默可以通过药物逆转。现今有一些关于CST6与癌症发生发展的研究取得了一定的成果。本文综述了CST6基因的功能研究以及其异常甲基化与癌症发生发展关系的研究进展，有望为揭示肿瘤的发生机制提供新的思路，为肿瘤的预防、诊断、治疗提供新的靶点。     

Current approaches in the transcriptional-guided gene therapy of human hepatocellular carcinoma

Hepatocellular carcinoma (HCC), the predominant histological subtype of primary human liver cancer, is one of the most prevalent cancer types worldwide, accounting for an estimated 500,000 deaths annually. The clinical management of HCC is challenging on many counts. HCC is a phenotypically and genetically heterogeneous polyclonal disease and is resistant to most conventional chemotherapy. Early manifestation of HCC is characteristically silent and slow growing with few symptoms, and HCC is therefore often diagnosed at an advanced stage, when potentially curative surgical or local ablative therapy is not feasible. Therefore, clinically validated biomarkers that could confer pathological and functional changes associated with the formation and progression of HCC are urgently needed to provide important molecular basis for the development of novel treatments. Recently, comprehensive molecular gene profiling of primary liver cancer tissues has been employed to identify specific genes that are linked to hepatocarcinogenesis. Current attempts to translate molecular knowledge to design strategies for the experimental gene therapy of HCC are reviewed.     

Metabolomics analysis of multidrug-resistant breast cancer cells in vitro using methyl-tert-butyl ether method

The comprehensive characterization of metabolome and lipidome to reveal unknown pathological conditions, are being used to investigate the molecular mechanisms of cancer, especially in the field of early diagnosis, treatment, and prognosis. The multidrug resistance (MDR) of tumor cells limits the therapeutic effect of anti-cancer drugs and is the main obstacle for chemotherapy. Here, we adopted a methyl-tert-butyl ether (MTBE)-based extraction method to simultaneously extract small polar molecules and lipophilic metabolites for nontargeted metabolomics of multidrug-resistant breast cancer cell line MCF-7/ADR and its parental cell line MCF-7/S by ultra-performance liquid chromatography coupled with quadrupole time-of-flight mass spectrometry. Distinctly different metabolic features were shown between MCF-7/ADR cells and MCF-7/S on the basis of multivariate analyses. 17 potential biomarkers were identified. And these potential biomarkers were mainly correlated with cell membrane lipids composition, cell signaling regulated by lipids, and anti-oxidation ability. The studies of cellular ultrastructure and morphology by in situ atomic force microscopy (AFM) also demonstrated the cellular membrane changed along with the MDR. We expect that this study could provide a new method for monitoring drug resistance during clinical chemotherapy and be useful for the development of drugs to overcome the MDR.

MTBE-based cellular lipidomics to investigate the mechanisms of multidrug resistance of breast cancer.     

Emerging role of long noncoding RNAs in recurrent hepatocellular carcinoma

Hepatocellular carcinoma (HCC) remains one of the most frequent types of liver cancer and is characterized by a high recurrence rate. Recent studies have proposed that long non-coding RNAs (lncRNAs) are potential biomarkers in several recurrent tumor types. It is now well understood that invasion, migration, and metastasis are important factors for tumor recurrence. Moreover, some of the known risk factors for HCC may affect the expression levels of several types of lncRNAs and thus affect the recurrence of liver cancer through lncRNA regulation. In this paper, we review the biological functions, molecular mechanisms, and roles of lncRNAs in HCC and summarize current knowledge about lncRNAs as potential biomarkers in recurrent HCC.     

“Hepatocellular carcinoma: A life-threatening disease”

An estimated rise in liver cancer incidence will increase to 95374 new cases by 2020. Hepatocellular Carcinoma (HCC), the most common primary malignant tumour of the liver, is considered to be the third leading cause of all cancer-related deaths and fifth common cancer worldwide. The reported data shows that the rate of HCC incidence in male population is three to four times higher compared with the female population. In the United States, HCV-induced liver cancer is increasing very fast because of the lack of proper treatment option. There are various treatment strategies available for HCC like liver transplantation, resection, ablation, embolization and chemotherapy still the prognosis is destitute. If the patient is eligible, liver transplantation is the only therapeutic option that may give around 90% survival rate, but the scarcity of liver donor limits its broad applicability. A sudden address is necessary to develop specific drugs, personalized medicine, for HCC.     

Repurposing drugs as pro-oxidant redox modifiers to eliminate cancer stem cells and improve the treatment of advanced stage cancers

Over the last decade, three major advances have contributed in improving the response rates against cancer including, immunotherapy; greater understanding of the molecular, biochemical, and cellular mechanisms in carcinogenesis thereby providing drug targets; and identification of reliable biomarkers for early detection to facilitate the earlier stage treatment of disease. However, no single universal cancer cure has yet been found, although combinations from the above areas have steadily improved survival outcomes. Hence, chemotherapy remains a key component in the oncologist's arsenal for cancer therapy, despite frequent development of drug resistance and more aggressive cancers with onset of advanced stage metastases. The focus here is to explore the repurposing of old drugs that cause pro-oxidative overload to overcome onset of resistance to chemotherapy and enhance chemotherapeutic responses, particularly against metastatic cancer. Excellent examples of US Food and Drug Administration approved drugs suitable for repurposing are the potent and specific thioreductase inhibitor auranofin and the nonsteroidal anti-inflammatory drug, celecoxib. Recently, both drugs were shown to selectively target and kill metastatic cancer cells and cancer stem cells (CSCs), predominantly by promoting excessive mitochondrial reactive oxygen species. Thus, targeting intracellular redox systems of advanced stage metastatic cancer cells and CSCs can promote an overload of pro-oxidative stress to activate the intrinsic pathway for programmed cell death. It is envisaged that more clinical studies will incorporate longer term use of repurposed drugs, such as auranofin or celecoxib, to target redox systems in cancer cells as part of common practice postcancer diagnosis, providing enhanced chemotherapeutic responses and increased cancer survival.