DNA甲基化与癌症

DNA甲基化是重要的表观遗传修饰,主要发生在DNA的CpG岛. DNA的甲基化通过DNA甲基转移酶（DNA methyltransferases, DNMTs）完成. DNA甲基化参与了细胞分化、基因组稳定性、X染色体失活、基因印记等多种细胞生物学过程.单基因水平及基因组范围内的DNA甲基化改变在肿瘤发生发展中亦发挥重要作用. 抑癌基因的异常甲基化引起的表达抑制,可导致肿瘤细胞的增殖失控和侵袭转移,并参与肿瘤组织的血管生成过程.在许多肿瘤的研究中都发现了基因组整体DNA低甲基化所导致的染色体不稳定性. 本文从DNA的异常高甲基化和低甲基化两方面论述了DNA甲基化在细胞恶变发生发展过程中的改变及其影响,并阐述了DNA甲基化改变在肿瘤诊断和治疗中的作用.     

线虫染色体研究揭示肿瘤基因组发生机制

近日一项针对线虫染色体DNA重排的研究揭示了肿瘤发生中大规模的基因组重复的机制.这一重要发现发表在4月22日在线刊出的Science杂志上.来自美国北卡罗莱纳大学教堂山分校医学院的科学家研究了线虫的端粒,也就是位于染色体末端的一     

DNA损伤检验点与损伤修复及基因组稳定性

生物有机体基因组DNA经常会受到内源或外源因素的影响而导致结构发生变化,产生损伤;在长期进化过程中,有机体也相应形成了一系列应对与修复损伤DNA,并维持染色体基因组正常结构功能的机制。其中DNA损伤检验点（DNA damage checkpoint）就是在感应DNA损伤的基础上,对损伤感应信号进行转导,或引起细胞周期的暂停,从而使细胞有足够的时间对损伤DNA进行修复,或最终导致细胞发生凋亡。DNA损伤检验点信号转导途径是一个高度保守的信号感应过程,整个途径大致可以分为损伤感应、信号传递及信号效应3个组成部分。其中3-磷脂酰肌醇激酶家族类成员ATM（ataxia-telangiectasia mutated）和ATR（ataxia-telangiectasia and Rad3-related）活性的增加构成整个途径活化的第一步。它们通过激活下游的效应激酶,Chk2／Chk1,通过协同作用许多其他调控细胞周期、DNA复制、DNA损伤修复及细胞凋亡等过程的蛋白质因子来实现细胞对DNA损伤的高度协调反应。近十几年,随着此领域研究的不断深入,人们逐步揭示了DNA损伤检验点途径发生过程中,各种核心组分通过与不同调节因子、效应因子及DNA损伤修复蛋白间的复杂相互作用,以实现监测感应异常DNA结构并实施相应反应的机制;其中,检验点衔接因子（mediators）及染色质结构,尤其是核小体组蛋白的共价修饰在调控ATM／ATR活性,促进ATM／ATR与底物间的相互作用以及介导DNA损伤位点周围染色质区域上多蛋白复合物在时间与空间上的动态形成发挥着重要的作用。同时,人们也开始发现DNA损伤检验点途径与DNA损伤修复、基因组稳定性以及肿瘤发生等过程之间某些内在的联系。该反应途径在通过协调细胞针对DNA损伤做出各种反应的基础上,直接或间接地参与或调控DNA损伤修复过程,并与DNA损伤修复途径协同作用最终保证染色体基凶组结构的完整性,而检验点途径的改变,则会引起基因组不稳定的发生,包括从突变频率的提高到大范围的染色体重排,以及染色体数量的畸变。如：突变发生在肿瘤形成早期,会大大增加肿瘤发生的几率。文章将对DNA损伤检验点途径机制及其对DNA损伤修复、基因组稳定性影响的最新进展进行综述。     

基因组“巨变”诱导癌症发生

一项引人瞩目的新研究颠覆了癌症的发展是缓慢而有序的传统观点.研究发现在细胞的某次大灾难中,基因组会被打断成几百个碎片,从而引发大规模的突变.在所有常见的肿瘤类型中,这些染色体断裂后重接的现象时有发生,这个理论解释了至少1/40的肿瘤发生的原因.这个现象在骨癌中尤其常见,在1/4的样     

中心体:洞悉肿瘤的发生(英文)

动物细胞中主要作为微管组织中心的中心体在细胞分裂时确保了染色体平均分配到两个子细胞的过程,从而保证了基因组的稳定性。中心体的结构或功能异常都将不可避免的引起基因组不稳定,从而导致肿瘤的发生。鉴于主要由中心体异常引起的染色体不稳定是肿瘤细胞的一个典型特征,而染色体不稳定又与肿瘤细胞的耐药性有着密切联系,因而不难想象以中心体为靶点的肿瘤治疗的合理性。因此,本文将着重阐述中心体在细胞调控,特别是与肿瘤发生密切相关的细胞活动及药物耐受中的重要作用,以期为更好阐明药物耐受机制,并为与中心体相关的抗肿瘤药物研发提供新思路。     

端粒酶(Telomerase)PCR ELISA——用于检测端粒酶活性的快速方法

宝灵曼公司最近推出了一种端粒酶PCR ELISA,它能对培养细胞或其他生物样品的细胞提取物中的端粒酶活性作高度灵敏的定性检测。 端粒是真核细胞染色体末端的特殊DNA-蛋白质结构,端粒DNA的特点是含有大量串连重复并富含G的重复序列,这些序列在进化中是高度保守的。端粒被认为可以阻止基因组DNA被降解或发生有害的重组,如:末端融合、重排、染色体易位和染色体缺失。由于     

致瘤性DNA病毒的整合机制及致瘤效应

恶性肿瘤是一种严重危害人类生命和健康的疾病,而致瘤性DNA病毒是多种恶性肿瘤的主要致病因子.致瘤性DNA病毒的整合可以使宿主细胞正常组织逐步向炎症组织转变,并可导致癌变.病毒整合可引起宿主细胞基因组不稳定和重排,产生新的融合基因,并导致宿主基因表达异常,也是病毒本身得以复制,逃避宿主免疫识别并长期维系自我生存的机制之一.本文综述了目前对致瘤性DNA病毒整合规律以及致瘤性DNA病毒整合致瘤效应的研究和进展,并展望致瘤性DNA病毒整合的研究方向以及在肿瘤发生、发展、诊断和治疗上的应用前景.     

细胞周期检验点与肿瘤发生之间关系的研究进展

DNA损伤反应引起的基因组不稳定性并不足以导致肿瘤发生,还需要一些协同突变促进肿瘤的生长或存活,因此,基因组结构不稳定和周期检验点突变失活是肿瘤发生的重要因素。与正常细胞不同,肿瘤细胞中细胞周期检验点反应缺陷,当肿瘤细胞遭受基因毒药物损伤时,可通过激活周期检验点反应阻滞细胞周期进程,加强损伤修复,导致耐药表型的产生。因此,寻找特异性的检验点抑制剂来加强化疗药物或辐射对肿瘤细胞的杀伤效应,已成为肿瘤治疗的一个研究方向。     

原子力显微镜观测紫外线诱导的K562肿瘤细胞DNA损伤

利用彗星电泳检测出UVB、UVC短时间照射会使肿瘤细胞的DNA发生断裂,而长时间照射之后彗星电泳无法检测到碎片,推测可能是由于DNA分子交联的原因[1],国内外尚无定论.为了更直观的研究这种现象,提取了UVB,UVA照射后K562细胞的DNA,并调节到合适的浓度在原子力显微镜下观测.实验结果表明UVB对K562肿瘤细胞DNA损伤的影响呈现时间/剂量效应,较短时间照射主要产生DNA的链断裂,较长时间辐射则主要产生DNA链的交联.UVC对K562肿瘤细胞DNA的损伤大于UVB.UVC短时照射即可引起DNA的断裂和交联,较长时间辐射主要产生交联和一些断裂;长时间照射不但产生大量交联,同时有大量断裂产生,并发生凝缩和缠绕等结构破坏.     

范可尼贫血症与DNA交联损伤修复

范可尼贫血症(FA)又称范可尼综合征,是一种常染色体或X染色体连锁的隐性遗传病.范可尼贫血症患者具有先天性发育异常、骨髓衰竭、高度癌症易感性等特征.尽管范可尼贫血症是一种在人群中发生比例仅为1:1000000～5:1000000的罕见遗传病,但它却是一个可以用来研究DNA损伤修复和肿瘤发生的重要模型.迄今为止,已经确定了15个范可尼贫血症基因(FA基因)以及一些范可尼贫血症相关基因.当15个FA基因中的任何一个发生突变,都会导致范可尼贫血症的发生.从这些基因发生突变的病人身上所分离得到的细胞则具有对DNA交联损伤试剂(如丝裂霉素C等)高度敏感,以及基因组不稳定的表型.在此,对目前所了解的FA基因所编码的FA蛋白参与DNA交联损伤修复的具体分子机制进行了回顾与阐述.     

Genomic organization and evolution of double minutes/homogeneously staining regions with MYC amplification in human cancer

The mechanism for generating double minutes chromosomes (dmin) and homogeneously staining regions (hsr) in cancer is still poorly understood. Through an integrated approach combining next-generation sequencing, single nucleotide polymorphism array, fluorescent in situ hybridization and polymerase chain reaction-based techniques, we inferred the fine structure of MYC-containing dmin/hsr amplicons harboring sequences from several different chromosomes in seven tumor cell lines, and characterized an unprecedented number of hsr insertion sites. Local chromosome shattering involving a single-step catastrophic event (chromothripsis) was recently proposed to explain clustered chromosomal rearrangements and genomic amplifications in cancer. Our bioinformatics analyses based on the listed criteria to define chromothripsis led us to exclude it as the driving force underlying amplicon genesis in our samples. Instead, the finding of coexisting heterogeneous amplicons, differing in their complexity and chromosome content, in cell lines derived from the same tumor indicated the occurrence of a multi-step evolutionary process in the genesis of dmin/hsr. Our integrated approach allowed us to gather a complete view of the complex chromosome rearrangements occurring within MYC amplicons, suggesting that more than one model may be invoked to explain the origin of dmin/hsr in cancer. Finally, we identified PVT1 as a target of fusion events, confirming its role as breakpoint hotspot in MYC amplification.     

Chromothripsis: Breakage-fusion-bridge over and over again

The acquisition of massive but localized chromosome translocations, a phenomenon termed chromothripsis, has received widespread attention since its discovery over a year ago. Until recently, chromothripsis was believed to originate from a single catastrophic event, but the molecular mechanisms leading to this event are yet to be uncovered. Because a thorough interpretation of the data are missing, the phenomenon itself has wrongly acquired the status of a mechanism used to justify many kinds of complex rearrangements. Although the assumption that all translocations in chromothripsis originate from a single event has met with criticism, satisfactory explanations for the intense but localized nature of this phenomenon are still missing. Here, we show why the data used to describe massive catastrophic rearrangements are incompatible with a model comprising a single event only and propose a molecular mechanism in which a combination of known cellular pathways accounts for chromothripsis. Instead of a single traumatic event, the protection of undamaged chromosomes by telomeres can limit repetitive breakage-fusion-bridge events to a single chromosome arm. Ultimately, common properties of chromosomal instability, such as aneuploidy and centromere fission, might establish the complex genetic pattern observed in this genomic state.     

The elusive evidence for chromothripsis

The chromothripsis hypothesis suggests an extraordinary one-step catastrophic genomic event allowing a chromosome to ‘shatter into many pieces’ and reassemble into a functioning chromosome. Recent efforts have aimed to detect chromothripsis by looking for a genomic signature, characterized by a large number of breakpoints (50–250), but a limited number of oscillating copy number states (2–3) confined to a few chromosomes. The chromothripsis phenomenon has become widely reported in different cancers, but using inconsistent and sometimes relaxed criteria for determining rearrangements occur simultaneously rather than progressively. We revisit the original simulation approach and show that the signature is not clearly exceptional, and can be explained using only progressive rearrangements. For example, 3.9% of progressively simulated chromosomes with 50–55 breakpoints were dominated by two or three copy number states. In addition, by adjusting the parameters of the simulation, the proposed footprint appears more frequently. Lastly, we provide an algorithm to find a sequence of progressive rearrangements that explains all observed breakpoints from a proposed chromothripsis chromosome. Thus, the proposed signature cannot be considered a sufficient proof for this extraordinary hypothesis. Great caution should be exercised when labeling complex rearrangements as chromothripsis from genome hybridization and sequencing experiments.     

Chromosome-breakage genomic instability and chromothripsis in breast cancer

Background

Chromosomal breakage followed by faulty DNA repair leads to gene amplifications and deletions in cancers. However, the mere assessment of the extent of genomic changes, amplifications and deletions may reduce the complexity of genomic data observed by array comparative genomic hybridization (array CGH). We present here a novel approach to array CGH data analysis, which focuses on putative breakpoints responsible for rearrangements within the genome.

Results

We performed array comparative genomic hybridization in 29 primary tumors from high risk patients with breast cancer. The specimens were flow sorted according to ploidy to increase tumor cell purity prior to array CGH. We describe the number of chromosomal breaks as well as the patterns of breaks on individual chromosomes in each tumor. There were differences in chromosomal breakage patterns between the 3 clinical subtypes of breast cancers, although the highest density of breaks occurred at chromosome 17 in all subtypes, suggesting a particular proclivity of this chromosome for breaks. We also observed chromothripsis affecting various chromosomes in 41% of high risk breast cancers.

Conclusions

Our results provide a new insight into the genomic complexity of breast cancer. Genomic instability dependent on chromosomal breakage events is not stochastic, targeting some chromosomes clearly more than others. We report a much higher percentage of chromothripsis than described previously in other cancers and this suggests that massive genomic rearrangements occurring in a single catastrophic event may shape many breast cancer genomes.

Electronic supplementary material

The online version of this article (doi:10.1186/1471-2164-15-579) contains supplementary material, which is available to authorized users.     

Chromothripsis in Healthy Individuals Affects Multiple Protein-Coding Genes and Can Result in Severe Congenital Abnormalities in Offspring

Chromothripsis represents an extreme class of complex chromosome rearrangements (CCRs) with major effects on chromosomal architecture. Although recent studies have associated chromothripsis with congenital abnormalities, the incidence and pathogenic effects of this phenomenon require further investigation. Here, we analyzed the genomes of three families in which chromothripsis rearrangements were transmitted from a mother to her child. The chromothripsis in the mothers resulted in completely balanced rearrangements involving 8–23 breakpoint junctions across three to five chromosomes. Two mothers did not show any phenotypic abnormalities, although 3–13 protein-coding genes were affected by breakpoints. Unbalanced but stable transmission of a subset of the derivative chromosomes caused apparently de novo complex copy-number changes in two children. This resulted in gene-dosage changes, which are probably responsible for the severe congenital phenotypes of these two children. In contrast, the third child, who has a severe congenital disease, harbored all three chromothripsis chromosomes from his healthy mother, but one of the chromosomes acquired de novo rearrangements leading to copy-number changes. These results show that the human genome can tolerate extreme reshuffling of chromosomal architecture, including breakage of multiple protein-coding genes, without noticeable phenotypic effects. The presence of chromothripsis in healthy individuals affects reproduction and is expected to substantially increase the risk of miscarriages, abortions, and severe congenital disease.     

Massive genomic rearrangement acquired in a single catastrophic event during cancer development

Cancer is driven by somatically acquired point mutations and chromosomal rearrangements, conventionally thought to accumulate gradually over time. Using next-generation sequencing, we characterize a phenomenon, which we term chromothripsis, whereby tens to hundreds of genomic rearrangements occur in a one-off cellular crisis. Rearrangements involving one or a few chromosomes crisscross back and forth across involved regions, generating frequent oscillations between two copy number states. These genomic hallmarks are highly improbable if rearrangements accumulate over time and instead imply that nearly all occur during a single cellular catastrophe. The stamp of chromothripsis can be seen in at least 2%-3% of all cancers, across many subtypes, and is present in ～25% of bone cancers. We find that one, or indeed more than one, cancer-causing lesion can emerge out of the genomic crisis. This phenomenon has important implications for the origins of genomic remodeling and temporal emergence of cancer.     

Chromothripsis in Hepatocarcinogenesis: The Role of a Micronuclear Aberration and Polyploidy

In this study, we used the mouse model of chemically induced hepatocarcinogenesis to investigate the chromosomal aberrations in hepatic cells. The model was obtained by combined treatment of mice with Dipin (radiomimetic drug) followed by partial hepatectomy. Cytological analysis of isolated liver cells treated with Dipin has demonstrated a number of hepatocytes with structural nuclear abnormalities and multiple micronuclei. Karyotype analysis of polyploid hepatocytes has shown numerous chromosomal aberrations including alleged morphological manifestations of chromothripsis, a special type of genomic reorganization characterized by the local disintegration of chromosomes. Micronuclei with chromosomal fragments have developed as a result of double-strand DNA breaks and might serve as the initial substrate for chromothripsis. The emergence of micronuclei containing chromosomal fragments is the most important result of the treatment employed. Therefore, the presented model of liver cancer (hepatocarcinogenesis) can be used to study the process of chromothripsis in the future.     

Pathways to chromothripsis

Chromothripsis is a recently recognized mode of genetic instability that generates chromosomes with strikingly large numbers of segmental re-arrangements. While the characterization of these derivative chromosomes has provided new insights into the processes by which cancer genomes can evolve, the underlying signaling events and molecular mechanisms remain unknown. In medulloblastomas, chromothripsis has been observed to occur in the context of mutational inactivation of p53 and activation of the canonical Hedgehog (Hh) pathway. Recent studies have illuminated mechanistic links between these 2 signaling pathways, including a novel PTCH1 homolog that is regulated by p53. Here, we integrate this new pathway into a hypothetical model for the catastrophic DNA breakage that appears to trigger profound chromosomal rearrangements.     

Chromothripsis is a common mechanism driving genomic rearrangements in primary and metastatic colorectal cancer

Background

Structural rearrangements form a major class of somatic variation in cancer genomes. Local chromosome shattering, termed chromothripsis, is a mechanism proposed to be the cause of clustered chromosomal rearrangements and was recently described to occur in a small percentage of tumors. The significance of these clusters for tumor development or metastatic spread is largely unclear.

Results

We used genome-wide long mate-pair sequencing and SNP array profiling to reveal that chromothripsis is a widespread phenomenon in primary colorectal cancer and metastases. We find large and small chromothripsis events in nearly every colorectal tumor sample and show that several breakpoints of chromothripsis clusters and isolated rearrangements affect cancer genes, including NOTCH2, EXO1 and MLL3. We complemented the structural variation studies by sequencing the coding regions of a cancer exome in all colorectal tumor samples and found somatic mutations in 24 genes, including APC, KRAS, SMAD4 and PIK3CA. A pairwise comparison of somatic variations in primary and metastatic samples indicated that many chromothripsis clusters, isolated rearrangements and point mutations are exclusively present in either the primary tumor or the metastasis and may affect cancer genes in a lesion-specific manner.

Conclusions

We conclude that chromothripsis is a prevalent mechanism driving structural rearrangements in colorectal cancer and show that a complex interplay between point mutations, simple copy number changes and chromothripsis events drive colorectal tumor development and metastasis.