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Sensitivity and specificity evaluation of multiple neurodegenerative proteins for Creutzfeldt-Jakob disease diagnosis using a deep-learning approach. 使用深度学习方法评估多种神经退行性蛋白对克雅氏病诊断的敏感性和特异性
IF 2.3 3区 生物学 Q4 BIOCHEMISTRY & MOLECULAR BIOLOGY Pub Date : 2019-01-01 DOI: 10.1080/19336896.2019.1639482
Sol Moe Lee, Jae Wook Hyeon, Soo-Jin Kim, Heebal Kim, Ran Noh, Seonghan Kim, Yeong Seon Lee, Su Yeon Kim

The diagnosis of sporadic Creutzfeldt-Jakob disease (sCJD) can only be confirmed by abnormal protease-resistant prion protein accumulation in post-mortem brain tissue. The relationships between sCJD and cerebrospinal fluid (CSF) proteins such as 14-3-3, tau, and α-synuclein (a-syn) have been investigated for their potential value in pre-mortem diagnosis. Recently, deep-learning (DL) methods have attracted attention in neurodegenerative disease research. We established DL-aided pre-mortem diagnostic methods for CJD using multiple CSF biomarkers to improve their discriminatory sensitivity and specificity. Enzyme-linked immunosorbent assays were performed on phospho-tau (p-tau), total-tau (t-tau), a-syn, and β-amyloid (1-42), and western blot analysis was performed for 14-3-3 protein from CSF samples of 49 sCJD and 256 non-CJD Korean patients, respectively. The deep neural network structure comprised one input, five hidden, and one output layers, with 20, 40, 30, 20 and 12 hidden unit numbers per hidden layer, respectively. The best performing DL model demonstrated 90.38% accuracy, 83.33% sensitivity, and 92.5% specificity for the three-protein combination of t-tau, p-tau, and a-syn, and all other patients in a separate CSF set (n = 15) with other neuronal diseases were correctly predicted to not have CJD. Thus, DL-aided pre-mortem diagnosis may provide a suitable tool for discriminating CJD patients from non-CJD patients.

散发性克雅氏病(sCJD)的诊断只能通过死后脑组织中蛋白酶抗性朊蛋白的异常积累来证实。sCJD与脑脊液蛋白(CSF)之间的关系,如14-3-3,tau和α-突触核蛋白(a-syn),已被研究其在死前诊断中的潜在价值。近年来,深度学习方法在神经退行性疾病的研究中受到了广泛的关注。我们建立了使用多种脑脊液生物标志物的dl辅助克雅氏病死前诊断方法,以提高其区分敏感性和特异性。采用酶联免疫吸附法检测磷酸化tau蛋白(p-tau)、总tau蛋白(t-tau)、a-syn蛋白和β-淀粉样蛋白(1-42),并对49例sCJD和256例非cjd韩国患者脑脊液样本中的14-3-3蛋白进行western blot分析。深度神经网络结构由1个输入层、5个隐藏层和1个输出层组成,每个隐藏层分别有20、40、30、20和12个隐藏单元号。表现最好的DL模型对t-tau、p-tau和a-syn三种蛋白组合的准确性为90.38%,敏感性为83.33%,特异性为92.5%,而在单独的CSF组中(n = 15)患有其他神经元疾病的所有其他患者都能正确预测没有CJD。因此,dl辅助的死前诊断可能为区分CJD患者和非CJD患者提供一种合适的工具。
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引用次数: 3
Clinicopathological findings of an MM2-cortical-type sporadic Creutzfeldt-Jakob disease patient with cortical blindness during a course of glaucoma and age-related macular degeneration. 1例伴有青光眼和老年性黄斑变性过程中皮层性失明的mm2皮质型散发性克雅氏病患者的临床病理结果
IF 2.3 3区 生物学 Q4 BIOCHEMISTRY & MOLECULAR BIOLOGY Pub Date : 2019-01-01 DOI: 10.1080/19336896.2019.1631680
Yuichi Hayashi, Yasushi Iwasaki, Masahiro Waza, Hideaki Shibata, Akio Akagi, Akio Kimura, Takashi Inuzuka, Katsuya Satoh, Tetsuyuki Kitamoto, Mari Yoshida, Takayoshi Shimohata

Here, we report an autopsy-verified patient with MM2-coritical-type sporadic Creutzfeldt-Jakob disease (MM2C-type sCJD) presenting cortical blindness during a course of glaucoma and age-related macular degeneration, and focus on the difficulties involved in early clinical diagnosis. An 83-year-old man was admitted to our hospital 15 months after the onset of cortical blindness, and 9 months after the onset of progressive dementia. Neurological examination revealed dementia, frontal signs, visual disturbance, dysphagia, myoclonus and exaggerated tendon reflexes in the four extremities. Diffusion-weighted MRI (DW-MRI) showed cortical hyperintensities predominantly in the bilateral occipital lobes. PRNP gene analysis showed no mutations with methionine homozygosity at codon 129. Cerebrospinal fluid (CSF) examination revealed elevation of 14-3-3 and total tau protein. The symptoms progressed gradually, and the patient died of aspiration pneumonia, 30 months after the onset. Neuropathological examination revealed extensive large confluent vacuole-type spongiform changes in the cerebral cortices. Prion protein (PrP) immunostaining showed perivascular and plaque-type PrP deposits. We diagnosed our patient as MM2C-type sCJD. There are two difficulties in the early clinical diagnosis of MM2C-type sCJD with ocular disease in the elderly; delayed utilization of DW-MRI, and accompaniment of ocular disease. For early diagnosis of MM2C-type sCJD, we conclude that clinician should perform DW-MRI for patients with isolated dementia or cortical visual disturbance.

在这里,我们报告了一名尸检证实的mm2 -皮质型散发性克雅氏病(mm2c -型sCJD)患者,在青光眼和年龄相关性黄斑变性过程中表现为皮质失明,并重点讨论了早期临床诊断的困难。一位83岁男性患者在皮质性失明15个月后、进行性痴呆9个月后入住我院。神经学检查显示痴呆、额叶征、视觉障碍、吞咽困难、肌阵挛和四肢肌腱反射过度。弥散加权MRI (DW-MRI)显示双侧枕叶皮层高信号为主。PRNP基因分析显示,密码子129处无甲硫氨酸纯合突变。脑脊液(CSF)检查显示14-3-3和总tau蛋白升高。症状逐渐加重,患者在发病30个月后死于吸入性肺炎。神经病理学检查显示大脑皮层广泛的大融合空泡型海绵状改变。朊蛋白(PrP)免疫染色显示血管周围和斑块型PrP沉积。我们诊断患者为mm2c型sCJD。老年人mm2c型sCJD伴眼部疾病的早期临床诊断存在两个难点;延迟使用DW-MRI,并伴有眼部疾病。对于mm2c型sCJD的早期诊断,我们认为临床医生应该对孤立性痴呆或皮质性视觉障碍患者进行DW-MRI检查。
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引用次数: 5
THERPA v2: an update of a small molecule database related to prion protein regulation and prion disease progression THERPA v2:与朊病毒蛋白调节和朊病毒疾病进展相关的小分子数据库的更新
IF 2.3 3区 生物学 Q4 BIOCHEMISTRY & MOLECULAR BIOLOGY Pub Date : 2019-01-01 DOI: 10.1080/19336896.2019.1689789
Sol Moe Lee, S. S. Kim, Heebal Kim, Su Yeon Kim
Prion diseases are rare, rapidly progressive neurodegenerative disorders that affect mammalian species [1,2]. Abnormal accumulation of infectious form of the prion protein in the brain causes prion disease. Various small molecules have been used to inhibit and treat this disease [3,4]. We built a repository of therapeutic molecules associated with prion protein and prion diseases (THERPA) to allow users to easily browse information describing various small molecules in publicly available articles [5]. THERPA is an open-access database containing data regarding small molecules related to prion protein and prion diseases, which is aimed at allowing researchers to easily explore and analyse data of interest. Here, we describe the relocation of the webpage and THERPA database updates. The THERPA repository has been relocated to the Korea National Institute of Health website for stable maintenance (www.nih.go.kr/ therpa). The e-Government Standard Framework (www.egovframe.go.kr) was used to create the
朊病毒疾病是一种罕见的、快速进展的神经退行性疾病,影响哺乳动物[1,2]。感染性朊病毒蛋白在大脑中的异常积累会导致朊病毒疾病。各种小分子已被用于抑制和治疗这种疾病[3,4]。我们建立了一个与朊病毒蛋白和朊病毒疾病相关的治疗分子库(THERPA),允许用户轻松浏览公开文章中描述各种小分子的信息[5]。THERPA是一个开放式数据库,包含与朊病毒蛋白和朊病毒疾病相关的小分子数据,旨在让研究人员轻松探索和分析感兴趣的数据。在这里,我们描述了网页的重新定位和THERPA数据库的更新。THERPA储存库已移至韩国国立卫生研究所网站进行稳定维护(www.nih.go.kr/THERPA)。电子政府标准框架(www.egovrame.go.kr)用于创建
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引用次数: 4
The prion 2018 round tables (I): the structure of PrPSc. 朊病毒2018圆桌会议(I):PrPSc的结构。
IF 1.9 3区 生物学 Q4 BIOCHEMISTRY & MOLECULAR BIOLOGY Pub Date : 2019-01-01 DOI: 10.1080/19336896.2019.1569450
Ilia V Baskakov, Byron Caughey, Jesús R Requena, Alejandro M Sevillano, Witold K Surewicz, Holger Wille

Understanding the structure of PrPSc is without doubt a sine qua non to understand not only PrPSc propagation, but also critical features of that process such as the strain phenomenon and transmission barriers. While elucidation of the PrPSc structure has been full of difficulties, we now have a large amount of structural information that allows us to begin to understand it. This commentary article summarizes a round table that took place within the Prion 2018 meeting held in Santiago de Compostela to discuss the state of the art in this matter. Two alternative models of PrPSc exist: the PIRIBS and the 4-rung β-solenoid models. Both of them have relevant features. The 4-rung β-solenoid model agrees with experimental constraints of brain derived PrPSc obtained from cryo-EM and X-ray fiber diffraction studies. Furthermore, it allows facile accommodation of the bulky glycans that decorate brain-derived PrPSc. On the other hand, the infectious PrP23-144 amyloid exhibits a PIRIBS architecture. Perhaps, both types of structure co-exist.

毫无疑问,了解 PrPSc 的结构不仅是了解 PrPSc 传播的必要条件,也是了解该过程的关键特征(如应变现象和传播障碍)的必要条件。虽然对 PrPSc 结构的阐明充满困难,但我们现在已经掌握了大量结构信息,可以开始理解它。这篇评论文章总结了在圣地亚哥-德孔波斯特拉举行的2018年朊病毒会议期间召开的圆桌会议,会议讨论了这一问题的最新进展。PrPSc存在两种替代模型:PIRIBS模型和4环β-solenoid模型。这两种模型都具有相关特征。4环β-solenoid模型与低温电子显微镜和X射线纤维衍射研究获得的大脑衍生PrPSc的实验约束相吻合。此外,它还能方便地容纳装饰脑源性 PrPSc 的大体积聚糖。另一方面,传染性 PrP23-144 淀粉样蛋白呈现出 PIRIBS 结构。也许,这两种类型的结构同时存在。
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引用次数: 0
Sodium hydroxide treatment effectively inhibits PrPCWD replication in farm soil. 氢氧化钠处理能有效抑制PrPCWD在农田土壤中的复制。
IF 2.3 3区 生物学 Q4 BIOCHEMISTRY & MOLECULAR BIOLOGY Pub Date : 2019-01-01 DOI: 10.1080/19336896.2019.1617623
Hyun-Joo Sohn, Kyung-Je Park, In-Soon Roh, Hyo-Jin Kim, Hoo-Chang Park, Hae-Eun Kang

Chronic wasting disease (CWD) agents are shed into biological samples, facilitating their horizontal transmission between cervid species. Once prions enter the environment, binding of PrPCWD by soil particles may maintain them near the soil surface, posing a challenge for decontamination. A 2 N sodium hydroxide (NaOH) or 2% sodium hypochlorite (NaClO) solution is traditionally recommended for prion decontamination of equipment and surfaces. Using protein misfolding cyclic amplification with beads and a bioassay with TgElk mice, we compared the effects of these disinfectants in CWD-contaminated soil for 1 or 16 h to those of controls of known infectious titres. Our results suggest that 2 N NaOH in a 1/5 farm soil volume provides a large decrease (>102-fold) in prion infectivity.

慢性消耗性疾病(CWD)病原体进入生物样本,促进它们在子宫颈物种之间的水平传播。一旦朊病毒进入环境,PrPCWD与土壤颗粒的结合可能会使它们保持在土壤表面附近,给去污带来挑战。传统上建议使用2n氢氧化钠(NaOH)或2%次氯酸钠(NaClO)溶液对设备和表面进行朊病毒净化。利用蛋白错误折叠循环扩增和TgElk小鼠的生物测定,我们比较了这些消毒剂在ccd污染土壤中1或16小时的效果与已知感染滴度的对照。我们的研究结果表明,在1/5的农田土壤体积中加入2 N NaOH可使朊病毒的传染性大幅降低(>102倍)。
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引用次数: 5
Michael Ter-Avanesyan (1949-2018) - life in science. Michael Ter-Avanesyan(1949-2018)——科学生命。
IF 2.3 3区 生物学 Q4 BIOCHEMISTRY & MOLECULAR BIOLOGY Pub Date : 2019-01-01 DOI: 10.1080/19336896.2019.1567201
Vitaly V Kushnirov

This commentary describes scientific path and accomplishments of our late colleague, Prof. Michael D. Ter-Avanesyan, who made several seminal contributions into prion research.

这篇评论描述了我们已故同事Michael D. Ter-Avanesyan教授的科学路径和成就,他为朊病毒研究做出了几项开创性贡献。
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引用次数: 1
Proteolysis: a double-edged sword for the development of amyloidoses. 蛋白水解:淀粉样变性发展的双刃剑。
IF 2.3 3区 生物学 Q4 BIOCHEMISTRY & MOLECULAR BIOLOGY Pub Date : 2018-09-09 DOI: 10.1080/19336896.2018.1521234
Atsushi Okamoto, Nao Hosoda, Shin-Ichi Hoshino

The yeast Saccharomyces cerevisiae has proven to be a useful model system to investigate the mechanism of prion generation and inheritance, to which studies in Sup35 made a great contribution. Recent studies demonstrated that 'protein misfolding and aggregation' (i.e. amyloidogenesis) is a common principle underlying the pathogenesis of neurodegenerative diseases including prion, amyotrophic lateral sclerosis (ALS), Perkinson's (PD), Alzheimer's (AD) diseases and polyglutamine (polyQ) diseases such as spinocerebellar ataxia (SCA) and Hantington's disease (HD). By these findings, the yeast has again been drawing increased attention as a useful system for studying neurodegenerative proteinopathies. So far, it has been reported that proteolytic cleavage of causative amyloidogenic proteins might affect the pathogenesis of the respective neurodegenerative diseases. Although those reports provide a clear phenomenological description, in the majority of cases, it has remained elusive if proteolysis is directly involved in the pathogenesis of the diseases. Recently, we have demonstrated in yeast that proteolysis suppresses prion generation. The yeast-based strategy might make a breakthrough to the unsolved issues.

事实证明,酵母是研究朊病毒产生和遗传机制的有用模型系统,Sup35 的研究对此做出了巨大贡献。最近的研究表明,"蛋白质错误折叠和聚集"(即淀粉样蛋白生成)是神经退行性疾病(包括朊病毒、肌萎缩性脊髓侧索硬化症(ALS)、帕金森氏症(PD)、阿尔茨海默氏症(AD)以及脊髓小脑共济失调(SCA)和汉丁顿氏病(HD)等多谷氨酰胺(polyQ)疾病)发病机制的共同原理。通过这些发现,酵母作为研究神经退行性蛋白病的有用系统再次引起了越来越多的关注。迄今为止,已有报道称致病性淀粉样蛋白的蛋白水解裂解可能会影响相关神经退行性疾病的发病机制。尽管这些报道提供了清晰的现象描述,但在大多数情况下,蛋白水解是否直接参与了疾病的发病机制仍然难以捉摸。最近,我们在酵母中证明了蛋白水解抑制朊病毒的产生。基于酵母的策略可能会对未解决的问题有所突破。
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引用次数: 0
Unexpected prion phenotypes in experimentally transfused animals: predictive models for humans? 实验性输血动物的意外朊病毒表型:人类的预测模型?
IF 2.3 3区 生物学 Q4 BIOCHEMISTRY & MOLECULAR BIOLOGY Pub Date : 2018-08-16 DOI: 10.1080/19336896.2018.1505399
Emmanuel E Comoy, Jacqueline Mikol, Jean-Philippe Deslys

The recently reevaluated high prevalence of healthy carriers (1/2,000 in UK) of variant Creutzfeldt-Jakob Disease (v-CJD), whose blood might be infectious, suggests that the evolution of this prion disease might not be under full control as expected. After experimental transfusion of macaques and conventional mice with blood derived from v-CJD exposed (human and animal) individuals, we confirmed in these both models the transmissibility of v-CJD, but we also observed unexpected neurological syndromes transmissible by transfusion: despite their prion etiology confirmed through transmission experiments, these original cases would escape classical prion diagnosis, notably in the absence of detectable abnormal PrP with current techniques. It is noteworthy that macaques developed an original, yet undescribed myelopathic syndrome associating demyelination and pseudo-necrotic lesions of spinal cord, brainstem and optical tract without affecting encephalon, which is rather evocative of spinal cord disease than prion disease in human medicine. These observations strongly suggest that the spectrum of human prion diseases may extend the current field restricted to the phenotypes associated to protease-resistant PrP, and may notably include spinal cord diseases.

最近重新评估发现,变异型克雅氏症(v-CJD)的健康携带者(英国为1/2,000)的发病率很高,他们的血液可能具有传染性,这表明这种朊病毒疾病的演变可能并不像预期的那样受到完全控制。在实验性地给猕猴和传统小鼠输注来自暴露于 v-CJD(人类和动物)的个体的血液后,我们在这两种模型中都证实了 v-CJD 的传播性,但我们也观察到了通过输血传播的意想不到的神经综合征:尽管通过传播实验证实了它们的朊病毒病因,但这些原始病例却逃脱了经典朊病毒诊断,尤其是在当前技术无法检测到异常 PrP 的情况下。值得注意的是,猕猴出现了一种原始的、尚未被描述的脊髓病综合征,这种综合征与脊髓、脑干和光束的脱髓鞘和假性坏死病变有关,但不影响大脑,这让人联想到脊髓病,而不是人类医学中的朊病毒病。这些观察结果有力地表明,人类朊病毒疾病的范围可能会扩展到目前仅限于与蛋白酶抗性 PrP 相关的表型的领域,尤其可能包括脊髓疾病。
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引用次数: 0
Microbial specialization by prions. 朊病毒的微生物特化
IF 2.3 3区 生物学 Q4 BIOCHEMISTRY & MOLECULAR BIOLOGY Pub Date : 2018-07-24 DOI: 10.1080/19336896.2018.1469945
Gregory A Newby, Can Kayatekin

Microbial prions facilitate a variety of phenotypic switches. Recently-developed tools that can directly interrogate, in the living cell, the aggregation state of a protein have enabled a wider range of experiments for prion-mediated behaviors. With such tools, the roles of the yeast prion [SWI+] in migration and mating were studied. Although [SWI+] cells were consistently less fit than their [swi-] counterparts under traditional laboratory conditions, in these new phenotypic paradigms [SWI+] cells demonstrated a distinct advantage. [SWI+] cells dispersed over a larger area under conditions resembling rainfall and outcrossed more frequently. We postulate that many behaviors in microorganisms may be modulated by stochastic prion switching. In diverse and changing natural environments, prion switching at low frequency may promote greater fitness of the population by specializing a small number of individuals with altered responses to their environments.

微生物朊病毒可促进各种表型的转换。最近开发的工具可以在活细胞中直接检测蛋白质的聚集状态,从而可以对朊病毒介导的行为进行更广泛的实验。利用这些工具,我们研究了酵母朊病毒 [SWI+] 在迁移和交配中的作用。虽然在传统的实验室条件下,[SWI+] 细胞的适应性一直不如[swi] 细胞,但在这些新的表型范例中,[SWI+] 细胞表现出了明显的优势。在类似降雨的条件下,[SWI+]细胞的扩散面积更大,外交也更频繁。我们推测,微生物的许多行为可能受到随机朊病毒切换的调节。在多样化和不断变化的自然环境中,低频率的朊病毒切换可能会使少数个体对环境的反应发生改变,从而提高种群的适应性。
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引用次数: 0
Effects of peptidyl-prolyl isomerase 1 depletion in animal models of prion diseases. 肽基脯氨酸异构酶1耗竭对朊病毒疾病动物模型的影响。
IF 2.3 3区 生物学 Q4 BIOCHEMISTRY & MOLECULAR BIOLOGY Pub Date : 2018-03-04 Epub Date: 2018-05-18 DOI: 10.1080/19336896.2018.1464367
Giuseppe Legname, Tommaso Virgilio, Edoardo Bistaffa, Chiara Maria Giulia De Luca, Marcella Catania, Paola Zago, Elisa Isopi, Ilaria Campagnani, Fabrizio Tagliavini, Giorgio Giaccone, Fabio Moda

Pin1 is a peptidyl-prolyl isomerase that induces the cis-trans conversion of specific Ser/Thr-Pro peptide bonds in phosphorylated proteins, leading to conformational changes through which Pin1 regulates protein stability and activity. Since down-regulation of Pin1 has been described in several neurodegenerative disorders, including Alzheimer's Disease (AD), Parkinson's Disease (PD) and Huntington's Disease (HD), we investigated its potential role in prion diseases. Animals generated on wild-type (Pin1+/+), hemizygous (Pin1+/-) or knock-out (Pin1-/-) background for Pin1 were experimentally infected with RML prions. The study indicates that, neither the total depletion nor reduced levels of Pin1 significantly altered the clinical and neuropathological features of the disease.

Pin1是一种肽基脯氨酸异构酶,可诱导磷酸化蛋白中特定Ser/Thr-Pro肽键的顺反转换,导致构象变化,从而调节蛋白质的稳定性和活性。由于Pin1的下调已在几种神经退行性疾病中被描述,包括阿尔茨海默病(AD)、帕金森病(PD)和亨廷顿病(HD),我们研究了它在朊病毒疾病中的潜在作用。在Pin1野生型(Pin1+/+)、半合子(Pin1+/-)或敲除型(Pin1-/-)背景下产生的动物实验感染RML朊病毒。该研究表明,Pin1的总消耗和降低水平都不能显著改变该疾病的临床和神经病理特征。
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引用次数: 4
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Prion
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