表观遗传学——耳聋研究的新视野

耳聋是一种常见的人类感觉系统缺陷,新生儿发病率可达1/1000～3/1000。耳蜗感觉神经上皮毛细胞的结构或功能异常可导致耳聋,遗传因素在其中起重要作用。虽然一些与遗传性耳聋相关的基因及染色体位点已经被定位或克隆,仍有很多耳聋的病因尚不清楚。人们发现,除了常见的热点基因突变(GJB2、SLC26A4、线粒体DNA C1494T和A1555G等)外,一些表观遗传学的改变也在耳聋的发生中起重要作用。例如,miR-96突变会导致人和小鼠的渐进性失聪,异常的CpG岛甲基化与一些耳聋综合征的发生有关等。文章着重对表观遗传学在耳聋领域的研究现状和进展进行了综述。     

肿瘤表观基因组学研究进展

多年来遗传学改变一直是肿瘤研究的焦点,近来人们越来越认识到异常表观遗传修饰在肿瘤形成中所起的重要作用。表观遗传修饰包括DNA甲基化、组蛋白修饰等,其变异会导致基因转录异常。表观基因组学是在基因组水平上对表观遗传学改变的研究。文章主要介绍目前已知的肿瘤表观基因组学相关内容,阐述表观遗传修饰与肿瘤的紧密关系及异常表观遗传修饰作为生物标记在肿瘤诊断、预后及治疗方面的最新研究进展。     

血液系统肿瘤性疾病的骨髓微环境

既往研究表明,造血细胞的细胞遗传学、分子遗传学或表观遗传学异常导致血液系统恶性肿瘤发生.然而,近期的研究表明骨髓微环境在血液系统肿瘤性疾病的发生、疾病进展和对化疗药物耐受中发挥着重要的作用.该文总结了稳态条件下骨髓微环境的组成以及对正常造血的调控,异常的骨髓微环境如何驱动血液系统肿瘤性疾病发生,以及血液系统肿瘤性疾病如...     

表观遗传学研究进展

表观遗传学是在基因组DNA序列不发生变化的条件下,基因表达发生的改变也是可以遗传的,导致可遗传的表现型变化。表观遗传学主要包括DNA甲基化作用、组蛋白修饰作用、染色质重塑、遗传印记、随机染色体(X)失活及RNA世界等。与表观遗传学相关的疾病主要有肿瘤、心血管病、精神病和自身免疫系统性病等。现就表观遗传学与疾病进行综述。     

DNA甲基化与食管腺癌关系研究进展

癌症本质上是一种多种因素导致的基因疾病。作为肿瘤形成假说中的重要补充内容,表观遗传学已经成为新的研究中心。DNA甲基化是人类基因组发生最为常见的一种表观遗传学事件,因而研究甲基化与肿瘤的关系成为当前分子生物学的热点之一。这篇综述是关于DNA甲基化与食管腺癌的研究进展,包括DNA高甲基化异常与食管腺癌的发生,以及针对甲基化的检测手段,诊断,治疗以及预后。     

肝癌表观遗传学研究进展

肝细胞癌是原发性肝癌的主要类型,也是恶性程度最高的肿瘤之一．目前人们对肝癌的发病机制并不十分清楚．研究表明,由遗传学和表观遗传学改变弓『起的原癌基因的活化和抑癌基因的灭活而引起细胞恶性改变是肿瘤发生的核心生物学过程．过去人们普遍认为遗传学上的基因突变是肿瘤发病机制中的关键事件,尤其是抑癌基因的体细胞突变与肿瘤的发生有着密切的关系．但是,近年来随着对肿瘤认识的深入,人们发现DNA序列以外的调控机制（即表观遗传学）异常在肿瘤的发生、发展过程中也起到非常重要的作用．表观遗传学机制包括：DNA甲基化修饰,组蛋白修饰,非编码RNAs（包括microRNA）,染色质重塑等．其中,DNA甲基化和microRNA与肝癌发生的关系是得到最为深入研究的表观遗传学机制．本文将结合本课题组的研究重点,综述DNA甲基化和microRNA在肝癌研究中的进展．     

DNA甲基化修饰对血管疾病稳态失衡的影响

自稳态平衡是机体生命活动的重要基础,在维持机体的正常生理功能中发挥重要作用。血管疾病中的稳态失衡受物理、化学、生物等内外环境改变及致病因素的影响,其中氧稳态、血流稳态、糖脂代谢稳态在内环境的影响中较为突出,由此引起的一系列表观遗传修饰将导致血管结构和功能的异常。表观遗传学中的DNA甲基化与血管疾病的发生发展密不可分。此外,5-羟甲基胞嘧啶(5-hydroxymethylcytosine, 5hmC)及N6-甲基腺嘌呤(N⁶-methyladenine, m⁶A)作为新的修饰碱基,将为表观遗传学研究提供新的思路。文章主要对DNA甲基化修饰变异在血管疾病稳态失衡方面的研究进展进行了阐述。     

阿尔兹海默病中DNA甲基化对β-淀粉样蛋白的影响

DNA甲基化是最常见也是目前研究得最成熟的表观遗传机制,近年来其在阿尔兹海默病(Alzheimer’s disease,AD)等神经系统退行性疾病中的作用逐渐受到研究者的关注。β-淀粉样蛋白(Beta-amyloid,Aβ)变性聚集与AD的主要病理特征——老年斑(Senile plaques,SP)的形成密切相关。同时,它还能诱导细胞凋亡、激发炎症级联反应、产生氧化应激、导致线粒体功能障碍等,从而加剧AD的病理过程。研究表明,DNA甲基化在Aβ生成、清除及毒性相关基因的调控中发挥着重要作用。由于DNA甲基化的可逆性,深入探究DNA甲基化在AD发生、发展中的作用,可能为AD的治疗带来曙光。文章综述了AD中DNA甲基化对Aβ的影响,进一步阐释了AD发病的表观遗传学机制,为AD的表观遗传学治疗提供了理论基础。     

上皮细胞转分化及其表观遗传学调控

上皮细胞转分化现象及其与疾病发生发展的关系,近年已成为细胞生物学、免疫学等多学科关注的聚焦点。转分化作为细胞分化发育的基本生物学现象,存在于机体诸多生理病理过程,也受表观遗传学的调控。相对于经典遗传学而言,表观遗传学作为一门新兴学科,其为生物体的基因表达调控及遗传现象提供了新的理论阐释。现知,DNA甲基化、组蛋白修饰及非编码RNA等均可导致上皮细胞基因发生表观遗传改变,与上皮细胞转分化的发生发展密切相关,并在该过程中发挥重要的调控作用。进一步阐明细胞转分化的分子基础及其表观遗传学调控机制,将有助于认识生命现象基本过程,并可为炎症性疾病、自身免疫病、器官纤维化,以及肿瘤发生与转移等机制的研究与防治,提供新的思路和应对策略。对上皮细胞转分化与表观遗传学调控关系作一简述。     

DNA羟甲基化调控动脉粥样硬化的研究进展

DNA羟甲基化作为一种表观遗传学修饰,对基因的表达调控起到了重要作用。近年来,越来越多的研究发现在心血管疾病中可见5-羟甲基胞嘧啶(5-hydroxymethylcytosine, 5hmC)和染色体10/11易位(ten-eleven translocation,TET)家族蛋白的异常改变,提示这些心血管疾病与DNA羟甲基化的调控密切相关。DNA羟甲基化水平与动脉粥样硬化常见的危险因素如衰老、性别、高血压和吸烟存在一定关联,并且和动脉粥样硬化发生过程中所涉及的免疫炎症反应以及内皮细胞和血管平滑肌细胞的功能相关。本文综述了DNA羟甲基化和TET家族蛋白对于动脉粥样硬化的作用机制及研究现状,以期为动脉粥样硬化的发生发展及诊断治疗提供表观遗传学方面的研究思路。     

MicroRNAs and epigenetic regulation in the mammalian inner ear: implications for deafness

Sensorineural hearing loss is the most common sensory disorder in humans and derives, in most cases, from inner-ear defects or degeneration of the cochlear sensory neuroepithelial hair cells. Genetic factors make a significant contribution to hearing impairment. While mutations in 51 genes have been associated with hereditary sensorineural nonsyndromic hearing loss (NSHL) in humans, the responsible mutations in many other chromosomal loci linked with NSHL have not been identified yet. Recently, mutations in a noncoding microRNA (miRNA) gene, MIR96, which is expressed specifically in the inner-ear hair cells, were linked with progressive hearing loss in humans and mice. Furthermore, additional miRNAs were found to have essential roles in the development and survival of inner-ear hair cells. Epigenetic mechanisms, in particular, DNA methylation and histone modifications, have also been implicated in human deafness, suggesting that several layers of noncoding genes that have never been studied systematically in the inner-ear sensory epithelia are required for normal hearing. This review aims to summarize the current knowledge about the roles of miRNAs and epigenetic regulatory mechanisms in the development, survival, and function of the inner ear, specifically in the sensory epithelia, tectorial membrane, and innervation, and their contribution to hearing.     

The Role of Mitochondrial DNA Mutations in Hearing Loss

Mutations in mitochondrial DNA (mtDNA) are one of the most important causes of hearing loss. Of these, the homoplasmic A1555G and C1494T mutations at the highly conserved decoding site of the 12S rRNA gene are well documented as being associated with either aminoglycoside-induced or nonsyndromic hearing loss in many families worldwide. Moreover, five mutations associated with nonsyndromic hearing loss have been identified in the tRNA^Ser(UCN) gene: A7445G, 7472insC, T7505C, T7510C, and T7511C. Other mtDNA mutations associated with deafness are mainly located in tRNA and protein-coding genes. Failures in mitochondrial tRNA metabolism or protein synthesis were observed from cybrid cells harboring these primary mutations, thereby causing the mitochondrial dysfunctions responsible for deafness. This review article provides a detailed summary of mtDNA mutations that have been reported in deafness and further discusses the molecular mechanisms of these mtDNA mutations in deafness expression.     

Homozygosity mapping identifies a novel GIPC3 mutation causing congenital nonsyndromic hearing loss in a Saudi family

Hearing loss is one of the most common sensory disorders in humans and has a genetic cause in 50% of the cases. Our recent studies indicate that nonsyndromic hearing loss (NSHL) in the Saudi Arabian population is genetically heterogeneous and is not caused by mutations in GJB2 and GJB6, the most common genes for deafness in various populations worldwide. Identification of the causative gene/mutation in affected families is difficult due to extreme genetic heterogeneity and lack of phenotypic variability. We utilized an SNP array-based whole-genome homozygosity mapping approach in search of the causative gene, for the phenotype in a consanguineous Saudi family, with five affected individuals presenting severe to profound congenital NSHL. A single shared block of homozygosity was identified on chromosome 19p13.3 encompassing GIPC3, a recently identified hearing loss gene. Subsequently, a novel mutation c.122 C>A (p.T41K) in GIPC3 was found. This is the first report of GIPC3 mutation in a Saudi family. The presence of the GIPC3 mutations in only one of 100 Saudi families with congenital NSHL suggests that it appears to be a rare cause of familial or sporadic deafness in this population.     

Genes and deafness

Many different genes appear to be involved in the development and function of the mammalian inner ear. Some of the genes involved during early inner ear morphogenesis have been identified using mutations or targetted transgenic interruption, while a handful of genes involved in pigmentation anomalies associated with hearing impairement have been cloned. Several genes involved in syndromic late-onset hearing loss have also been isentified. However, the lajority of cases of hereditary hearing impairement from childhood probably involve genes expressed in the sensory neuroepithelia of the inner ear, and none of the genes or mutations causing this type of deafness have yet been identified. Here, we review the progress that has been made in finding genes for deafness and in using mouse mutants to elucidate the biological basis of the hearing deficit.     

Inherited connexin mutations associated with hearing loss

One of the most dramatic discoveries in the field of hereditary hearing loss is the association of this sensory defect with connexin mutations. Most significant is the large proportion, 30-50%, of inherited hearing loss that is due to mutations in connexin 26. The proteins these genes encode are expressed in the cochlear duct, in regions containing gap junctions. Together, these findings suggest a crucial role for gap junction proteins in the mammalian inner ear. Mouse models with specific connexin mutations leading to deafness will help resolve the many questions regarding the role of these gap junction proteins in the inner ear.     

Mutations in a novel gene,TMIE, are associated with hearing loss linked to the DFNB6 locus

We have identified five different homozygous recessive mutations in a novel gene, TMIE (transmembrane inner ear expressed gene), in affected members of consanguineous families segregating severe-to-profound prelingual deafness, consistent with linkage to DFNB6. The mutations include an insertion, a deletion, and three missense mutations, and they indicate that loss of function of TMIE causes hearing loss in humans. TMIE encodes a protein with 156 amino acids and exhibits no significant nucleotide or deduced amino acid sequence similarity to any other gene.     

Targeted Exon Sequencing Successfully Discovers Rare Causative Genes and Clarifies the Molecular Epidemiology of Japanese Deafness Patients

Target exon resequencing using Massively Parallel DNA Sequencing (MPS) is a new powerful strategy to discover causative genes in rare Mendelian disorders such as deafness. We attempted to identify genomic variations responsible for deafness by massive sequencing of the exons of 112 target candidate genes. By the analysis of 216randomly selected Japanese deafness patients (120 early-onset and 96 late-detected), who had already been evaluated for common genes/mutations by Invader assay and of which 48 had already been diagnosed, we efficiently identified causative mutations and/or mutation candidates in 57 genes. Approximately 86.6% (187/216) of the patients had at least one mutation. Of the 187 patients, in 69 the etiology of the hearing loss was completely explained. To determine which genes have the greatest impact on deafness etiology, the number of mutations was counted, showing that those in GJB2 were exceptionally higher, followed by mutations in SLC26A4, USH2A, GPR98, MYO15A, COL4A5 and CDH23. The present data suggested that targeted exon sequencing of selected genes using the MPS technology followed by the appropriate filtering algorithm will be able to identify rare responsible genes including new candidate genes for individual patients with deafness, and improve molecular diagnosis. In addition, using a large number of patients, the present study clarified the molecular epidemiology of deafness in Japanese. GJB2 is the most prevalent causative gene, and the major (commonly found) gene mutations cause 30–40% of deafness while the remainder of hearing loss is the result of various rare genes/mutations that have been difficult to diagnose by the conventional one-by-one approach. In conclusion, target exon resequencing using MPS technology is a suitable method to discover common and rare causative genes for a highly heterogeneous monogenic disease like hearing loss.     

Forty-six genes causing nonsyndromic hearing impairment: which ones should be analyzed in DNA diagnostics?

Hearing impairment is the most common sensory disorder, present in 1 of every 500 newborns. With 46 genes implicated in nonsyndromic hearing loss, it is also an extremely heterogeneous trait. Here, we categorize for the first time all mutations reported in nonsyndromic deafness genes, both worldwide and more specifically in Caucasians. The most frequent genes implicated in autosomal recessive nonsyndromic hearing loss are GJB2, which is responsible for more than half of cases, followed by SLC26A4, MYO15A, OTOF, CDH23 and TMC1. None of the genes associated with autosomal dominant nonsyndromic hearing loss accounts for a preponderance of cases, although mutations are somewhat more frequently reported in WFS1, KCNQ4, COCH and GJB2. Only a minority of these genes is currently included in genetic diagnostics, the selection criteria typically reflecting: (1) high frequency as a cause of deafness (i.e. GJB2); (2) association with another recognisable feature (i.e. SLC26A4 and enlarged vestibular aqueduct); or (3) a recognisable audioprofile (i.e. WFS1). New and powerful DNA sequencing technologies have been developed over the past few years, but have not yet found their way into DNA diagnostics. Implementing these technologies is likely to happen within the next 5 years, and will cause a breakthrough in terms of power and cost efficiency. It will become possible to analyze most - if not all - deafness genes, as opposed to one or a few genes currently. This ability will greatly improve DNA diagnostics, provide epidemiological data on gene-based mutation frequencies, and reveal novel genotype-phenotype correlations.     

SLC26A4 Mutations in Patients with Moderate to Severe Hearing Loss

Mutations in SLC26A4 cause either syndromic or nonsyndromic hearing loss. We identified a link between hearing loss and DFNB4 in 3 of the 50 families participating in this study. Sequencing analysis revealed two SLC26A4 mutations, p.V239D and p.S57X, in affected members of the 3 families. These mutations have been previously reported in deaf individuals from the subcontinent, all of whom manifested profound deafness. The patients investigated in our study exhibited moderate to severe hearing loss. Our results show that inactivating SLC26A4 mutations that cause profound deafness can also be involved in the etiology of moderate to severe hearing loss. The type of mutation cannot predict the severity of the hearing loss in all cases, and there may be additional epistatic interactions that could modify the phenotype.