扩增子测序技术应用于乳腺癌循环游离DNA无创性检测的研究

目的:应用扩增子测序方法检测乳腺癌循环游离DNA肿瘤相关突变。方法:军事医学科学院附属医院的10例HER2阳性晚期乳腺癌患者血样入组,应用扩增子测序技术检测血细胞和血浆中的循环游离DNA(cfDNA),筛选出肿瘤相关基因突变,即循环肿瘤DNA(ctDNA)。结果:检测10例晚期乳腺癌患者外周循环血50个基因,共检出11个突变基因,其中PIK3CA、ERBB4的阳性检出率均达到100%,AKT、TP53的阳性检出率为90%。结论:检测覆盖度及深度均良好,结果提示11个基因的热点突变区域出现单核苷酸的多态性基因突变,突变基因与PI3K-AKT-m TOR通路、Ras-Raf-MEK-ERK通路明显相关。扩增子测序技术和筛选方法可以用于乳腺癌ctDNA的无创性检测。     

外周血循环RNA、微小RNA与肿瘤诊断*

循环核酸(circulating nucleic acid, CNA)是指存在于血液(血清或血浆)等体液中的细胞外游离DNA和RNA,与生理和病理状态下的细胞代谢密切相关,循环DNA和RNA水平的检测及其在基因诊断等方面的应用对于恶性肿瘤等疾病的诊断和监测具有十分重要的意义。近期人们在进行循环DNA、RNA分子检测的同时,在循环微小RNA(microRNA, miRNA)方面也做了许多的工作,研究结果使得与肿瘤相关的核酸分子检测这一领域变的更加让人振奋。在血液中检出肿瘤特异性的miRNA并将其作为肿瘤的生物学标志对于早期诊断肿瘤具有至关重要的意义。     

母体外周血游离RNA分子特性及其在无创产前检测中的潜在应用

胎儿游离DNA在母体外周血血浆中的发现颠覆性地改变现有的无创产前检测方法,例如基于孕妇外周血血浆DNA对胎儿染色体异常的无创检测在全球范围内快速得到了认可和广泛应用。受到胎儿游离DNA研究成果的鼓舞,科学家也陆续展开了关于孕妇外周血中胎儿游离RNA的研究。现将集中讨论血浆RNA的特性及其潜在的应用。     

循环血液中游离DNA与胃肠道肿瘤的关系

胃肠道肿瘤是一类严重威胁人类健康的疾病.治疗上早期诊断是一个重要环节.人们一直在寻找一种简便无创的检测方法,对胃肠道肿瘤进行有效检测,并评价与肿瘤进展、分期、治疗效果几预后的关系.而临床上传统的肿瘤标志物在特异性上和敏感性上均不十分令人满意.血液中游离DNA的检测作为分子生物学研究的一个新兴领域,在肿瘤标志物检测方面给我们提供了新的手段.该文主要探讨了循环血液中游离DNA与胃肠道肿瘤的关系.     

晚期胃肠道肿瘤患者血浆游离DNA片段的检测、定量

目的探讨肿瘤患者循环血液中DNA改变,及对提高肿瘤患者治愈率和生存率的临床实际意义。方法随机采集了2004年10月~12月大连医科大学附属二院经病理确诊的初治晚期胃、大肠癌患者的血标本18份,门诊健康体检者血标本16份,通过酚/氯仿提取法定量检测两组的血浆DNA片段,进行对照比较,分析健康人与晚期胃肠道肿瘤患者血浆游离DNA片段水平的差异、晚期胃肠道肿瘤患者血浆游离DNA片段水平与预后相关指标的相关性。结果晚期胃肠道肿瘤组血浆游离DNA片段水平高于正常健康对照组,其血浆游离DNA片段的均值分别为(346.3±81.62)μg/m l与(27.6±6.91)μg/m l,差异有显著性;胃癌、大肠癌患者两组间的血浆游离DNA片段差异无显著性,均值分别为:(350.8±110.92)μg/m l与(357.1±126.26)μg/m l;在预后相关指标的各因素中,晚期胃肠道肿瘤患者的血浆游离DNA片段水平与免疫状态、是否存在远处转移有明显相关性,其中与免疫状态呈负相关,与远处转移呈正相关。结论晚期胃肠道肿瘤患者血中的游离DNA片段水平较健康人高,可能与患者自身状态、病理分型、疾病状态有关;游离DNA片段可以作为检测晚期胃肠道肿瘤的特异性指标,还可以替代免疫状态及是否存在远处转移等指标评价远期预后,并有取材方便、检测时间短、可以定量分析的优点,对临床有一定的指导意义和应用价值。     

血浆游离DNA全基因组甲基化测序的实用稳定性评估

随着液体活检技术的发展,血浆游离DNA成为当前的研究热点之一。血浆游离DNA的全基因组甲基化测序被认为在癌症检测等医学应用拥有巨大潜力,但目前尚缺乏针对该实验流程的实用稳定性评估。文中利用两名志愿者在不同时间采样的血浆游离DNA,在不同实验平台分别进行DNA甲基化的重亚硫酸盐转化前建库(Pre-BS)、转化后建库(Post-BS)和常规DNA建库,获取多因素影响下的测序数据样本。在此基础上,建立了一套血浆游离DNA测序数据分析的质量控制参考流程,综合评估了血液采集提取、游离DNA建库测序过程的实用稳定性,为血浆游离DNA全基因组甲基化测序应用于临床液体活检提供实用性的基础参考。     

无创产前DNA检测可有效筛查唐氏综合症降低出生缺陷

为了探究无创产前DNA检测筛查唐氏综合症降低出生缺陷的效果,本研究选择2012年4月至2017年12月我院收治的孕期产检6 192例孕妇作为研究对象,应用DNA测序方法对孕妇血浆中胎儿游离DNA进行染色体非整倍体检测,并检测其灵敏度和特异性,同时采用羊水核型分析两种结果。研究显示,阳性共73例,69例做了进一步检查,显示40例胎儿染色体检查核型正常继续妊娠,29例染色体异常。比较不同年龄组的孕妇血清学筛查唐氏综合征高风险情况,研究表明随着孕妇年龄的增加,DS阳性率逐渐降低(p0.05);血清学筛查后胎儿游离DNA (cffDNA)检测与染色体核型分析的阳性例数基本一致(p0.05)。本研究表明,采用产前无创检测胎儿游离DNA操作方便,检测灵敏度和特异性高,不会对胎儿的正常发育造成不良影响,且阳性检测率与羊水核染色体核型结果基本相同,是无创产前诊断唐氏综合征的重要方法,值得在临床上推广使用。     

脑卒中血清游离DNA及脑源性神经营养因子水平变化及临床意义

为评估血清游离DNA及脑源性神经营养因子(brain-derived neurotrophic factor,BDNF)在脑卒中患者诊断中的临床价值,本研究收集131例脑卒中患者及50例健康体检者的外周血标本,提取血浆游离DNA,用SYBR Green染料实时荧光PCR方法检测血清游离DNA含量;采用酶联免疫吸附法检测血清BDNF含量,并检测血清同型半胱氨酸(Hcy)及超敏C反应蛋白(hs-CRP)。结果显示血清游离DNA、BDNF、Hcy、hs-CRP在脑梗死、脑出血患者及健康对照组三组间比较差异均有统计学意义(H分别为77.939,49.443,13.724,30.943;p0.001)。脑梗死患者游离DNA、Hcy、hs-CRP含量均高于健康对照组,差异均具有统计学意义(U分别为7.892,3.576,5.204;p0.05);脑出血患者DNA、Hcy、hs-CRP含量均高于健康对照组,差异均具有统计学意义(U分别为7.446,2.664,4.357;p0.001)。脑梗死及脑出血患者血清BDNF含量均低于健康对照组,差异具有统计学意义(U分别为-6.393,-5.794;p0.001)。脑梗死及脑出血患者两组间血清游离DNA、BDNF、Hcy、hs-CRP含量差异均无统计学意义(U分别为-1.483,0.936,0.119,-0.362;p0.05)。血清BDNF与脑卒中患者的年龄有关,其含量随患者年龄的增加而降低。血清游离DNA及BDNF在脑卒中患者的诊断中具有潜在的临床应用价值,其或可成为脑卒中诊断的有用指标。     

基于微滴式数字PCR检测肠癌病人游离环状DNA KRAS突变的新方法

基于微滴式数字聚合酶链式反应(Droplet digital polymerase chain reaction,dd PCR)设计一种检测肠癌游离循环DNA(Circulating cell free DNA,cf DNA)中KRAS(V-Ki-ras2 Kirsten ratsarcoma viral oncogene homolog)基因突变的新方法并评估其灵敏度和准确性。根据肠癌病人KRAS基因的突变类型设计并合成,采用dd PCR扩增并评估其灵敏度和准确性;根据AMRS-PCR引物设计原理设计KRAS基因的实时定量PCR扩增引物并评估其准确性,进而比较dd PCR和q PCR二者之间的优缺点;最后针对52例肠癌病人的cf DNA采用dd PCR进行检测,研究dd PCR在cf DNA KRAS基因突变检测的应用。成功使用dd PCR和q PCR两种方法对KRAS野生型及7种突变型建立检测方法,使用质粒标准品及实际样品验证该两种方法可行并对其假阳性率、线性范围及检测下限等性能进行了评价,最后成功对52例临床患者和20例正常人的血浆cf DNA样本进行检测,临床灵敏度为97.64%,临床特异性为81.43%。dd PCR的检测性能优于q PCR,LOD达到个位数DNA拷贝,最低可确认突变浓度达到0.01%–0.04%。样本提取效率在方法学建立中也十分重要,直接影响到灵敏度和Cut Off值的判定。临床患者检测结果显示其KRAS突变率接近报道水平。     

新的肿瘤分子标记物--肿瘤相关循环DNA

肿瘤患者外周血循环DNA的存在及相关改变为肿瘤的诊断和监测提供了新的靶分子,血浆／血清作为容易获得的检测对象比传统的癌组织活检具有更大的使用弹性和临床应用价值,循环DNA作为新的肿瘤标志物的研究在不久的未来将成为科学研究的热点。     

循环血游离Shope病毒DNA含量与兔VX2肿瘤18F-FDG PET/CT影像表现的相关性分析

目的:探讨循环血中Shope病毒DNA含量与兔VX2肿瘤18F-FDG PET/CT影像学特征间的关系及其临床意义。方法:采用组织块接种法建立兔VX2肿瘤模型,并行18F-FDG PET-CT观测肿瘤大小及糖代谢相关值,实时定量荧光探针PCR法检测肿瘤组织及血浆中Shope病毒特征性DNA片段含量。结果:移植前外周血中未检测出Shope病毒特异性DNA片段;移植后2周,VX2肿瘤组织和循环血中均可以检测到特征性Shope病毒DNA片段。瘤体内DNA含量明显高于循环血中含量。循环血Shope病毒DNA含量与FDG-PET的最大标准摄取值(SUVmax)明显呈正相关(r=0.943,p=0.005),但与肿瘤体积相关性尚不明确(r=0.657,p=0.156)。结论:循环血Shope病毒DNA有望作为一种潜在的VX2肿瘤标志物,其廉价、无创的特性,有望在肿瘤的早期诊断和预后随访中发挥优势。     

Angiogenic alterations associated with circulating neoplastic DNA in ovarian carcinoma

OBJECTIVES: Forty percent of women with ovarian carcinoma have circulating free neoplastic DNA identified in plasma. Angiogenesis is critical in neoplastic growth and metastasis. We sought to determine whether circulating neoplastic DNA results from alterations in the balance of angiogenesis activators and inhibitors. METHODS: Sixty patients with invasive ovarian carcinomas with somatic TP53 mutations that had been characterized for circulating neoplastic DNA had carcinoma analyzed for microvessel density using immunohistochemistry with CD31 and for the expression of VEGF, ANGPT1, ANGPT2, PTGS2, PLAU, THBS1, CSF1, PIK3CA, HIF1A, IL8, MMP2, and MMP9 message by real-time quantitative polymerase chain reaction. The expression of each gene was calculated relative to GAPDH expression for each neoplasm. Patient plasma had been tested for circulating neoplastic DNA using a ligase detection reaction. RESULTS: MMP2 expression was significantly correlated with free plasma neoplastic DNA (P = .007). Microvessel density was not correlated with plasma neoplastic DNA or BRCA1/2 mutation status. The expression pattern of other angiogenic factors did not correlate with plasma neoplastic DNA but correlated with each other. BRCA1/2 mutated carcinomas had significantly different expression profiles of angiogenesis activators and inhibitors in comparison to sporadic carcinomas. CONCLUSIONS: MMP2 expression is associated with the presence of circulating neoplastic DNA in women with ovarian carcinoma. These data are consistent with the proinvasive properties of MMP2 and suggest that the presence of circulating neoplastic DNA indicates a more aggressive malignant phenotype. Carcinomas with germ line BRCA1/2 mutations had a lower angiogenic profile than those without mutations.     

循环肿瘤DNA的检测及研究现状

中国癌症发病率与世界水平相持平,死亡率要高于世界水平。虽然更多先进的技术已经运用到癌症治疗领域,但是癌症的死亡率依然居高不下。癌症之所以难克服,是因为肿瘤细胞具有异质性。“液体活检”技术的出现,使无创性治疗方法开始应用到肿瘤治疗领域,循环肿瘤DNA(circulating tumor DNA,ctDNA)则是“液体活检”中的一种重要素材。血液中游离的DNA被称为cfDNA(Cell free DNA),含有突变的cfDNA就被称作ctDNA。ctDNA所含有的突变一般是单个碱基替换所造成的,只有癌细胞才会有这种情况的发生,这使得ctDNA具有极高的特异性,可作为高灵敏的生物标记物。由于ctDNA存在于血液中,其无创性价值重大。     

Circulating Level of Neutrophil Extracellular Traps Is Not a Useful Biomarker for Assessing Disease Activity in Antineutrophil Cytoplasmic Antibody-Associated Vasculitis

Antineutrophil cytoplasmic antibody (ANCA)-associated vasculitis (AAV) is a group of life-threatening disorders, and frequently affects the kidneys. This study investigated whether the circulating neutrophil extracellular traps (NETs) levels were associated with disease activity of AAV. We collected serum samples from 34 patients with AAV in active stage and 62 patients with AAV in remission. Cell free DNA in serum was quantified using the Quant-iT PicoGreen assay. NETs associated MPO-DNA complexes, citrullinated-histone H3-DNA (cit-H3-DNA) complexes and the concentration of deoxyribonuclease I (DNase I) were quantified using ELISA. The activity of DNase I was quantified using radial enzyme-diffusion method. Associations between circulating levels of NETs with clinico-pathological parameters were analyzed. Serum levels of NETs in active AAV patients were significantly higher than those in healthy controls, and the level of cell free DNA correlated with C-reactive protein (CRP). However, no correlation was found between MPO-DNA complexes or cit-H3-DNA complexes level and CRP. Also there was no significant correlation between NETs level and initial serum creatinine, estimated glomerular filtration rate (eGFR), crescents formation or Birmingham Vasculitis Activity Score (BVAS). Furthermore, there was no significant difference of serum levels of cell free DNA or MPO-DNA complexes between active stage and remission of AAV. In conclusion, circulating levels of NETs cannot be used as a biomarker to assess disease activity in AAV patients.     

Chromatin supraorganization, DNA fragmentation, and cell death in erythrocytes of the rattlesnake, Crotalus durissus terrificus (Serpentes, Viperidae), infected with the protozoan, Hepatozoon spp. (Apicomplexa, Hepatozoidae)

Forms of the protozoan of the Hepatozoon genus are detected free in the circulation and also within some of the erythrocytes of infected snakes. In healthy snakes, DNA fragmentation and cell death usually affect a few circulating erythrocytes in agreement with the long life span expected for these cells. In the present study we investigated whether infection by Hepatozoon spp. affected the incidence of DNA fragmentation and cell death in erythrocytes from the rattlesnake, Crotalus durissus terrificus. Methods such as the kinetics of Feulgen-DNA hydrolysis, and the TUNEL and comet assays, previously used for the study of chromatin organization and DNA fragmentation in erythrocytes of healthy snakes, were used. The results indicated that Hepatozoon spp. increased the DNA fragmentation and chromatin condensation typical of cell death in circulating erythrocytes of C. d. terrificus, including cells that do not harbour the parasite. The Hepatozoon infection is thus suggested to accelerate destruction of erythrocytes in the rattlesnake, not only affecting cells harbouring the parasite, but also in those without it.     

Current status and future potential of somatic mutation testing from circulating free DNA in patients with solid tumours

Genetic alterations can determine the natural history of cancer and its treatment response. With further advances in DNA sequencing technology, multiple novel genetic alterations will be discovered which could be exploited as prognostic, predictive and pharmacodynamic biomarkers in the development and use of cancer therapeutics. As such, the importance in clinical practice of efficient and robust somatic mutation testing in solid tumours cannot be overemphasized in the current era of personalized medicine. However, significant challenges remain regarding the testing of genetic biomarkers in clinical practice. Reliance on archived formalin fixed, paraffin embedded tumour, obtained from diagnostic biopsies, for testing somatic genetic alterations could restrict the scientific community in asking relevant questions about a patient’s cancer biology. Problems inherent with using formalin fixed, archival tissue are well recognized and difficult to resolve. It could be argued that to achieve rapid and efficient incorporation of genetic biomarkers into clinical practice, somatic mutation testing in cancer patients should be simpler, less invasive using a readily available clinical sample, whilst maintaining robustness and reproducibility. In this regard, use of circulating free DNA (cfDNA) from plasma or serum as an alternative and/or additional source of DNA to test cancer specific genetic alterations is an attractive proposition. In light of encouraging results from recent studies, this mini review will discuss the current role and future potential of somatic mutation testing from circulating or cell free DNA derived from the blood of patients with solid tumours.     

Human anti-DNA autoantibodies and induced antibodies against ROS-modified-DNA show similar antigenic binding characteristics.

Alterations in DNA structure by hydroxyl radical modification was characterized by UV spectroscopy, Tm, nuclease S1 digestibility and base modification. In view of indicted role of oxygen free radicals in human diseases, an attempt has been made to precisely compare the antigen binding properties of induced antibodies against hydroxyl radical modified DNA with those of naturally occurring anti-DNA autoantibodies. Antibodies induced against ROS-DNA showed diverse antigen binding characteristics which were comparable with those derived from SLE patients. The immune IgG recognized native DNA, heat denatured DNA, and synthetic polynucleotides in B-/B-like conformations. IgG isolated from SLE sera showed preference for ROS-DNA in competition-inhibition assay. The antigenic diversity of induced antibodies and preference of circulating anti-DNA autoantibodies for ROS-DNA over that of native DNA demonstrates the possible role of modified DNA antigens in the pathogenesis of SLE.     

Fibrinolysis and liver regeneration.

The plasmin and plasminogen activator proteases of the plasma fibrinolytic system were investigated as potential blood-borne mediators of the proliferative activation of hepatocytes by partial hepatectomy. Partial (68%) liver resection, as well as proliferatively activating the remaining hepatocytes, rapidly (by 30 minutes) doubled the level (or activity) of circulating plasminogen activator but later (2 hours) greatly depressed this level. This later depression of the activity of circulating plasminogen activator lasted for eight to ten hours before returning to the normal level two to four hours before the hepatocytes in the liver remnant began to synthesize DNA. This sequence of changes in the fibrinolytic potential was not abolished by prior thyroparathyroidectomy which is known to inhibit the initiation of hepatocyte DNA synthesis and to prevent the secretion of the calcium homeostatic hormones, another early systemic consequence of partial liver resection. Since the early rise in plasminogen activator activity did not cause the appearance of active (free) circulating plasmin, and since the injection of large doses of the fibrinolytic and protease inhibitors, EACA and Trasylol®, during this early, post-operative period of hyperfibrinolytic potential did not prevent hepatocytes from initiating DNA synthesis, it is unlikely that either plasmin or its activator protease are blood-borne initiators of hepatocyte proliferative development.     

Activation of poly(ADP-ribose) polymerase by myocardial ischemia and coronary reperfusion in human circulating leukocytes

Reactive free radical and oxidant production leads to DNA damage during myocardial ischemia/reperfusion. Consequent overactivation of poly(ADP-ribose) polymerase (PARP) promotes cellular energy deficit and necrosis. We hypothesized that PARP is activated in circulating leukocytes in patients with myocardial infarction and reperfusion during primary percutaneous coronary intervention (PCI). In 15 patients with ST segment elevation acute myocardial infarction, before and after primary PCI and 24 and 96 h later, we determined serum hydrogen peroxide concentrations, plasma levels of the oxidative DNA adduct 8-hydroxy-2'-deoxyguanosine (8OHdG), tyrosine nitration, PARP activation, and translocation of apoptosis-inducing factor (AIF) in circulating leukocytes. Plasma 8OHdG levels and leukocyte tyrosine nitration were rapidly increased by PCI. Similarly, poly(ADP-ribose) content of the leukocytes increased in cells isolated just after PCI, indicating immediate PARP activation triggered by reperfusion of the myocardium. In contrast, serum hydrogen peroxide concentrations and the translocation of AIF gradually increased over time and were most pronounced at 96 h. Reperfusion-related oxidative/nitrosative stress triggers DNA damage, which leads to PARP activation in circulating leukocytes. Translocation of AIF and lipid peroxidation occurs at a later stage. These results represent the first direct demonstration of PARP activation in human myocardial infarction. Future work is required to test whether pharmacological inhibition of PARP may offer myocardial protection during primary PCI.     

Rapid clearance of fetal DNA from maternal plasma.

Fetal DNA has been detected in maternal plasma during pregnancy. We investigated the clearance of circulating fetal DNA after delivery, using quantitative PCR analysis of the sex-determining region Y gene as a marker for male fetuses. We analyzed plasma samples from 12 women 1-42 d after delivery of male babies and found that circulating fetal DNA was undetectable by day 1 after delivery. To obtain a higher time-resolution picture of fetal DNA clearance, we performed serial sampling of eight women, which indicated that most women (seven) had undetectable levels of circulating fetal DNA by 2 h postpartum. The mean half-life for circulating fetal DNA was 16.3 min (range 4-30 min). Plasma nucleases were found to account for only part of the clearance of plasma fetal DNA. The rapid turnover of circulating DNA suggests that plasma DNA analysis may be less susceptible to false-positive results, which result from carryover from previous pregnancies, than is the detection of fetal cells in maternal blood; also, rapid turnover may be useful for the monitoring of feto-maternal events with rapid dynamics. These results also may have implications for the study of other types of nonhost DNA in plasma, such as circulating tumor-derived and graft-derived DNA in oncology and transplant patients, respectively.