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Clarifying the effect of gut microbiota on allergic conjunctivitis risk is instrumental for predictive, preventive, and personalized medicine: a Mendelian randomization analysis. 澄清肠道微生物群对过敏性结膜炎风险的影响有助于预测、预防和个性化医疗:一项孟德尔随机分析。
IF 6.5 2区 医学 Q1 Medicine Pub Date : 2023-06-01 DOI: 10.1007/s13167-023-00321-9
Kangcheng Liu, Yingjun Cai, Kun Song, Ruolan Yuan, Jing Zou
<p><strong>Background: </strong>Allergic conjunctivitis is an ocular immune disease which affects the conjunctiva, eyelids, and cornea. Growing evidence implicates the gut microbiota in balancing and modulating immunity response, and in the pathogenesis of allergic disease. As a result, gut microbial imbalance could be a useful indicator for allergic conjunctivitis. From the perspective of predictive, preventive, and personalized medicine (PPPM), clarifying the role of gut microbial imbalance in the development of allergic conjunctivitis could provide a window of opportunity for primary prediction, targeted prevention, and personalized treatment of the disease.</p><p><strong>Working hypothesis and methodology: </strong>In our study, we hypothesized that individuals with microbial dysbiosis may be more susceptible to allergic conjunctivitis due to an increased inflammatory response. To verify the working hypothesis, our analysis selected genetic variants linked with gut microbiota features (<i>N</i> = 18,340) and allergic conjunctivitis (4513 cases, 649,376 controls) from genome-wide association studies. The inverse-variance weighted (IVW) estimate, Mendelian randomization (MR)-Egger, weighted median estimator, maximum likelihood estimator (MLE), and MR robust adjusted profile score (MR.RAPS) were employed to analyze the impact of gut microbiota on the risk of allergic conjunctivitis and identify allergic conjunctivitis-related gut microbes. Ultimately, these findings may enable the identification of individuals at risk of allergic conjunctivitis through screening of gut microbial imbalances, and allow for new targeted prevention and personalized treatment strategies.</p><p><strong>Results: </strong>Genetic liability to <i>Ruminococcaceae_UCG_002</i> (OR, 0.83; 95% CI, 0.70-0.99; <i>P</i> = 4.04×10<sup>-2</sup>), <i>Holdemanella</i> (OR, 0.78; 95% CI, 0.64-0.96; <i>P</i> = 2.04×10<sup>-2</sup>), <i>Catenibacterium</i> (OR, 0.69; 95% CI, 0.56-0.86; <i>P</i> = 1.09×10<sup>-3</sup>), <i>Senegalimassilia</i> (OR, 0.71; 95% CI, 0.55-0.93; <i>P</i> = 1.23×10<sup>-2</sup>) genus were associated with a low risk of allergic conjunctivitis with IVW. Besides, we found suggestive associations of a genetic-driven increase in the <i>Oscillospira</i> (OR, 1.41; 95% CI, 1.00-2.00; <i>P</i> = 4.63×10<sup>-2</sup>) genus with a higher risk of allergic conjunctivitis. Moreover, MLE and MR.RAPS show consistent results with IVW after further validation and strengthened confidence in the true causal associations. No heterogeneity and pleiotropy was detected.</p><p><strong>Conclusions: </strong>Our study suggests that gut microbiota may play a causal role in the development of allergic conjunctivitis and provides new insights into the microbiota-mediated mechanism of the disease. Gut microbiota may serve as a target for future predictive diagnostics, targeted prevention, and individualized therapy in allergic conjunctivitis, facilitating the transition from reactive med
背景:过敏性结膜炎是一种影响结膜、眼睑和角膜的眼部免疫性疾病。越来越多的证据表明,肠道微生物群在平衡和调节免疫反应以及过敏性疾病的发病机制中起着重要作用。因此,肠道微生物失衡可能是过敏性结膜炎的一个有用指标。从预测、预防和个性化医学(PPPM)的角度来看,明确肠道微生物失衡在变应性结膜炎发展中的作用,可以为疾病的初步预测、针对性预防和个性化治疗提供机会。工作假设和方法:在我们的研究中,我们假设微生物生态失调的个体可能由于炎症反应增加而更容易患过敏性结膜炎。为了验证工作假设,我们的分析从全基因组关联研究中选择了与肠道微生物群特征(N = 18,340)和过敏性结膜炎(4513例,649,376例对照)相关的遗传变异。采用反方差加权(IVW)估计、孟德尔随机化(MR)-Egger、加权中位数估计、最大似然估计(MLE)和MR稳健调整谱评分(MR. raps)来分析肠道微生物群对过敏性结膜炎风险的影响,并识别过敏性结膜炎相关肠道微生物。最终,这些发现可以通过筛选肠道微生物失衡来识别过敏性结膜炎的风险个体,并允许新的有针对性的预防和个性化治疗策略。结果:Ruminococcaceae_UCG_002遗传倾向(OR, 0.83;95% ci, 0.70-0.99;P = 4.04×10-2), Holdemanella (OR, 0.78;95% ci, 0.64-0.96;P = 2.04×10-2), Catenibacterium (OR, 0.69;95% ci, 0.56-0.86;P = 1.09×10-3),塞内加尔(OR, 0.71;95% ci, 0.55-0.93;P = 1.23×10-2)属与IVW变应性结膜炎的低风险相关。此外,我们还发现了基因驱动的示波器螺旋体增加的暗示关联(OR, 1.41;95% ci, 1.00-2.00;P = 4.63×10-2)属,过敏性结膜炎风险较高。此外,MLE和MR.RAPS在进一步验证后显示出与IVW一致的结果,并增强了对真实因果关系的信心。未发现异质性和多效性。结论:我们的研究提示肠道菌群可能在过敏性结膜炎的发生发展中发挥因果作用,并为微生物介导的疾病机制提供了新的见解。肠道微生物群可以作为未来变应性结膜炎预测性诊断、针对性预防和个体化治疗的目标,促进疾病管理从反应性医疗服务向PPPM的转变。补充信息:在线版本包含补充资料,下载地址:10.1007/s13167-023-00321-9。
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引用次数: 1
Multi-omics identification of an immunogenic cell death-related signature for clear cell renal cell carcinoma in the context of 3P medicine and based on a 101-combination machine learning computational framework. 在3P医学背景下,基于101组合机器学习计算框架的透明细胞肾细胞癌免疫原性细胞死亡相关特征的多组学鉴定。
IF 6.5 2区 医学 Q1 Medicine Pub Date : 2023-05-31 eCollection Date: 2023-06-01 DOI: 10.1007/s13167-023-00327-3
Jinsong Liu, Yanjia Shi, Yuxin Zhang
<p><strong>Background: </strong>Clear cell renal cell carcinoma (ccRCC) is a prevalent urological malignancy associated with a high mortality rate. The lack of a reliable prognostic biomarker undermines the efficacy of its predictive, preventive, and personalized medicine (PPPM/3PM) approach. Immunogenic cell death (ICD) is a specific type of programmed cell death that is tightly associated with anti-cancer immunity. However, the role of ICD in ccRCC remains unclear.</p><p><strong>Methods: </strong>Based on AddModuleScore, single-sample gene set enrichment analysis (ssGSEA), and weighted gene co-expression network (WGCNA) analyses, ICD-related genes were screened at both the single-cell and bulk transcriptome levels. We developed a novel machine learning framework that incorporated 10 machine learning algorithms and their 101 combinations to construct a consensus immunogenic cell death-related signature (ICDRS). ICDRS was evaluated in the training, internal validation, and external validation sets. An ICDRS-integrated nomogram was constructed to provide a quantitative tool for predicting prognosis in clinical practice. Multi-omics analysis was performed, including genome, single-cell transcriptome, and bulk transcriptome, to gain a more comprehensive understanding of the prognosis signature. We evaluated the response of risk subgroups to immunotherapy and screened drugs that target specific risk subgroups for personalized medicine. Finally, the expression of ICD-related genes was validated by qRT-PCR.</p><p><strong>Results: </strong>We identified 131 ICD-related genes at both the single-cell and bulk transcriptome levels, of which 39 were associated with overall survival (OS). A consensus ICDRS was constructed based on a 101-combination machine learning computational framework, demonstrating outstanding performance in predicting prognosis and clinical translation. ICDRS can also be used to predict the occurrence, development, and metastasis of ccRCC. Multivariate analysis verified it as an independent prognostic factor for OS, progression-free survival (PFS), and disease-specific survival (DSS) of ccRCC. The ICDRS-integrated nomogram provided a quantitative tool in clinical practice. Moreover, we observed distinct biological functions, mutation landscapes, and immune cell infiltration in the tumor microenvironment between the high- and low-risk groups. Notably, the immunophenoscore (IPS) score showed a significant difference between risk subgroups, suggesting a better response to immunotherapy in the high-risk group. Potential drugs targeting specific risk subgroups were also identified.</p><p><strong>Conclusion: </strong>Our study constructed an immunogenic cell death-related signature that can serve as a promising tool for prognosis prediction, targeted prevention, and personalized medicine in ccRCC. Incorporating ICD into the PPPM framework will provide a unique opportunity for clinical intelligence and new management approaches.</p><p><strong
背景:肾透明细胞癌(ccRCC)是一种常见的泌尿系统恶性肿瘤,死亡率高。缺乏可靠的预后生物标志物破坏了其预测性、预防性和个性化药物(PPPM/3PM)方法的疗效。免疫原性细胞死亡(ICD)是一种特殊类型的程序性细胞死亡,与抗癌免疫密切相关。然而,ICD在ccRCC中的作用尚不清楚。方法:基于AddModuleScore、单样本基因集富集分析(ssGSEA)和加权基因共表达网络(WGCNA)分析,在单细胞和大量转录组水平上筛选ICD相关基因。我们开发了一种新的机器学习框架,该框架包含10种机器学习算法及其101种组合,以构建一致的免疫原性细胞死亡相关特征(ICDRS)。ICDRS在培训、内部验证和外部验证集中进行了评估。构建了ICDRS综合列线图,为临床实践中预测预后提供了定量工具。进行了多组学分析,包括基因组、单细胞转录组和大量转录组,以更全面地了解预后特征。我们评估了风险亚组对免疫疗法的反应,并筛选了针对特定风险亚组的个性化药物。最后,通过qRT-PCR验证ICD相关基因的表达。结果:我们在单细胞和大量转录组水平上鉴定了131个ICD相关基因,其中39个与总生存率(OS)相关。基于101组合机器学习计算框架构建了一致的ICDRS,在预测预后和临床翻译方面表现出色。ICDRS也可用于预测ccRCC的发生、发展和转移。多因素分析证实,它是ccRCC OS、无进展生存期(PFS)和疾病特异性生存期(DSS)的独立预后因素。ICDRS综合列线图为临床实践提供了定量工具。此外,我们在高风险组和低风险组的肿瘤微环境中观察到了不同的生物学功能、突变景观和免疫细胞浸润。值得注意的是,免疫表型评分(IPS)显示风险亚组之间存在显著差异,表明高危组对免疫疗法的反应更好。还确定了针对特定风险亚组的潜在药物。结论:我们的研究构建了一个免疫原性细胞死亡相关信号,该信号可作为ccRCC预后预测、靶向预防和个性化药物的一个有前途的工具。将ICD纳入PPPM框架将为临床智能和新的管理方法提供独特的机会。补充信息:在线版本包含补充材料,请访问10.1007/s13167-023-00327-3。
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引用次数: 0
Underexplored reciprocity between genome-wide methylation status and long non-coding RNA expression reflected in breast cancer research: potential impacts for the disease management in the framework of 3P medicine. 全基因组甲基化状态和长非编码RNA表达之间的相互作用未得到充分探讨,反映在乳腺癌症研究中:对3P医学框架下的疾病管理的潜在影响。
IF 6.5 2区 医学 Q1 Medicine Pub Date : 2023-05-22 eCollection Date: 2023-06-01 DOI: 10.1007/s13167-023-00323-7
Andrea Kapinova, Alena Mazurakova, Erika Halasova, Zuzana Dankova, Dietrich Büsselberg, Vincenzo Costigliola, Olga Golubnitschaja, Peter Kubatka

Breast cancer (BC) is the most common female malignancy reaching a pandemic scale worldwide. A comprehensive interplay between genetic alterations and shifted epigenetic regions synergistically leads to disease development and progression into metastatic BC. DNA and histones methylations, as the most studied epigenetic modifications, represent frequent and early events in the process of carcinogenesis. To this end, long non-coding RNAs (lncRNAs) are recognized as potent epigenetic modulators in pathomechanisms of BC by contributing to the regulation of DNA, RNA, and histones' methylation. In turn, the methylation status of DNA, RNA, and histones can affect the level of lncRNAs expression demonstrating the reciprocity of mechanisms involved. Furthermore, lncRNAs might undergo methylation in response to actual medical conditions such as tumor development and treated malignancies. The reciprocity between genome-wide methylation status and long non-coding RNA expression levels in BC remains largely unexplored. Since the bio/medical research in the area is, per evidence, strongly fragmented, the relevance of this reciprocity for BC development and progression has not yet been systematically analyzed. Contextually, the article aims at:consolidating the accumulated knowledge on both-the genome-wide methylation status and corresponding lncRNA expression patterns in BC andhighlighting the potential benefits of this consolidated multi-professional approach for advanced BC management. Based on a big data analysis and machine learning for individualized data interpretation, the proposed approach demonstrates a great potential to promote predictive diagnostics and targeted prevention in the cost-effective primary healthcare (sub-optimal health conditions and protection against the health-to-disease transition) as well as advanced treatment algorithms tailored to the individualized patient profiles in secondary BC care (effective protection against metastatic disease). Clinically relevant examples are provided, including mitochondrial health control and epigenetic regulatory mechanisms involved.

癌症(BC)是全球范围内最常见的女性恶性肿瘤。遗传改变和表观遗传区域转移之间的全面相互作用协同导致疾病发展和进展为转移性BC。DNA和组蛋白甲基化作为研究最多的表观遗传学修饰,代表了致癌过程中的常见和早期事件。为此,通过对DNA、RNA和组蛋白甲基化的调节,长非编码RNA(lncRNA)被认为是BC病理机制中有效的表观遗传学调节剂。反过来,DNA、RNA和组蛋白的甲基化状态可以影响lncRNA的表达水平,这表明了相关机制的相互作用。此外,lncRNA可能会发生甲基化,以应对实际的医疗条件,如肿瘤发展和治疗的恶性肿瘤。BC中全基因组甲基化状态和长非编码RNA表达水平之间的相互作用在很大程度上仍未被探索。根据证据,由于该领域的生物/医学研究非常分散,这种相互作用对不列颠哥伦比亚省发展和进展的相关性尚未得到系统分析。从上下文来看,这篇文章旨在:巩固关于不列颠哥伦比亚省全基因组甲基化状态和相应lncRNA表达模式的积累知识,并强调这种综合的多专业方法对高级不列颠哥伦比亚省管理的潜在好处。基于大数据分析和用于个性化数据解释的机器学习,所提出的方法证明了在具有成本效益的初级保健(次优健康条件和防止健康向疾病转变)中促进预测诊断和有针对性的预防的巨大潜力,以及在二级BC护理中根据个性化患者情况量身定制的先进治疗算法(有效预防转移性疾病)提供了临床相关的实例,包括所涉及的线粒体健康控制和表观遗传学调控机制。
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引用次数: 1
Ideal cardiovascular health metrics and life expectancy free of cardiovascular diseases: a prospective cohort study. 理想的心血管健康指标和无心血管疾病的预期寿命:一项前瞻性队列研究。
IF 6.5 2区 医学 Q1 Medicine Pub Date : 2023-05-20 eCollection Date: 2023-06-01 DOI: 10.1007/s13167-023-00322-8
Qiuyue Tian, Shuohua Chen, Jie Zhang, Cancan Li, Shouling Wu, Yanxiu Wang, Youxin Wang

Objectives: Whether cardiovascular health (CVH) metrics impact longevity with and without cardiovascular diseases (CVDs) has not been well established. This study aimed to investigate the association between CVH metrics and life expectancy in participants free of CVD events. We hypothesized that ideal CVH status was associated with increased life expectancy and assessed the effect of CVH status as a prevention target of longevity in the framework of predictive, preventive, and personalized medicine (PPPM/3PM).

Methods: A total of 92,795 participants in the Kailuan study were examined and thereafter followed up until 2020. We considered three transitions (from non-CVD events to incident CVD events, from non-CVD events to mortality, and from CVD events to mortality). The multistate lifetable method was applied to estimate the life expectancy.

Results: During a median follow-up of 13 years, 12,541 (13.51%) deaths occurred. Compared with poor CVH, ideal CVH attenuated the risk of incident CVD events and mortality without CVD events by approximately 58% and 27%, respectively. Women with ideal CVH at age 35 had a 5.00 (3.23-6.77) year longer life expectancy free of CVD events than did women with poor CVH metrics. Among men, ideal CVH was associated with a 6.74 (5.55-7.93) year longer life expectancy free of CVD events.

Conclusion: An ideal CVH status is associated with a lower risk of premature mortality and a longer life expectancy, either in the general population or in CVD patients, which are cost-effective ways for personalized medicine of potential CVD patients. Our findings suggest that the promotion of a higher CVH score or ideal CVH status would result in reduced burdens of CVD events and extended disease-free life expectancy, which offered an accurate prediction for primary care following the concept of PPPM/3PM.

Supplementary information: The online version contains supplementary material available at 10.1007/s13167-023-00322-8.

目的:心血管健康(CVH)指标是否影响有或无心血管疾病(CVD)的寿命尚未得到很好的证实。本研究旨在调查无心血管疾病事件参与者的CVH指标与预期寿命之间的关系。我们假设理想的CVH状态与预期寿命的增加有关,并在预测性、预防性和个性化医学(PPPM/3PM)的框架下评估了CVH状态作为长寿预防目标的效果。方法:对开滦研究中的92795名参与者进行了检查,随后随访至2020年。我们考虑了三种转变(从非心血管疾病事件到偶发心血管疾病事件,从非心血管事件到死亡率,以及从心血管疾病事件至死亡率)。采用多状态寿命表方法对预期寿命进行了估算。结果:在13年的中位随访中,发生12541例(13.51%)死亡。与较差的CVH相比,理想的CVH将发生CVD事件的风险和无CVD事件的死亡率分别降低了约58%和27%。与CVH指标较差的女性相比,35岁时CVH理想的女性无CVD事件的预期寿命延长了5.00年(3.23-6.77)。在男性中,理想的CVH与6.74(5.55-7.93)年无CVD事件的预期寿命有关。结论:无论是在普通人群中还是在心血管疾病患者中,理想的CVH状态都与较低的过早死亡风险和较长的预期寿命有关,这是潜在心血管疾病患者个性化用药的成本效益高的方法。我们的研究结果表明,提高CVH评分或理想的CVH状态将减少CVD事件的负担,延长无病预期寿命,这为遵循PPPM/3PM概念的初级保健提供了准确的预测。补充信息:在线版本包含补充材料,可访问10.1007/s13167-023-00322-8。
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引用次数: 0
Short communication: unique metabolic signature of proliferative retinopathy in the tear fluid of diabetic patients with comorbidities - preliminary data for PPPM validation. 简短交流:糖尿病合并并发症患者泪液中增殖性视网膜病变的独特代谢特征——PPPM验证的初步数据。
IF 6.5 2区 医学 Q1 Medicine Pub Date : 2023-03-01 DOI: 10.1007/s13167-023-00318-4
Martina Kropp, Eline De Clerck, Trong-Tin Kevin Steve Vo, Gabriele Thumann, Vincenzo Costigliola, Olga Golubnitschaja
<p><p>Type 2 diabetes (T2DM) defined as the adult-onset type that is primarily not insulin-dependent, comprises over 95% of all diabetes mellitus (DM) cases. According to global records, 537 million adults aged 20-79 years are affected by DM that means at least 1 out of 15 persons. This number is projected to grow by 51% by the year 2045. One of the most common complications of T2DM is diabetic retinopathy (DR) with an overall prevalence over 30%. The total number of the DR-related visual impairments is on the rise, due to the growing T2DM population. Proliferative diabetic retinopathy (PDR) is the progressing DR and leading cause of preventable blindness in working-age adults. Moreover, PDR with characteristic systemic attributes including mitochondrial impairment, increased cell death and chronic inflammation, is an independent predictor of the cascading DM-complications such as ischemic stroke. Therefore, early DR is a reliable predictor appearing upstream of this "domino effect". Global screening, leading to timely identification of DM-related complications, is insufficiently implemented by currently applied reactive medicine. A personalised predictive approach and cost-effective targeted prevention shortly - predictive, preventive and personalised medicine (PPPM / 3PM) could make a good use of the accumulated knowledge, preventing blindness and other severe DM complications. In order to reach this goal, reliable stage- and disease-specific biomarker panels are needed characterised by an easy way of the sample collection, high sensitivity and specificity of analyses. In the current study, we tested the hypothesis that non-invasively collected tear fluid is a robust source for the analysis of ocular and systemic (DM-related complications) biomarker patterns suitable for differential diagnosis of stable DR versus PDR. Here, we report the first results of the comprehensive ongoing study, in which we correlate individualised patient profiles (healthy controls versus patients with stable D as well as patients with PDR with and without co-morbidities) with their metabolic profiles in the tear fluid. Comparative mass spectrometric analysis performed has identified following metabolic clusters which are differentially expressed in the groups of comparison: acylcarnitines, amino acid & related compounds, bile acids, ceramides, lysophosphatidyl-choline, nucleobases & related compounds, phosphatidyl-cholines, triglycerides, cholesterol esters, and fatty acids. Our preliminary data strongly support potential clinical utility of metabolic patterns in the tear fluid indicating a unique metabolic signature characteristic for the DR stages and PDR progression. This pilot study creates a platform for validating the tear fluid biomarker patterns to stratify T2DM-patients predisposed to the PDR. Moreover, since PDR is an independent predictor of severe T2DM-related complications such as ischemic stroke, our international project aims to create an analytical pro
2型糖尿病(T2DM)定义为成人发病类型,主要不依赖胰岛素,占所有糖尿病(DM)病例的95%以上。根据全球记录,5.37亿20-79岁的成年人患有糖尿病,这意味着每15人中至少有1人患有糖尿病。预计到2045年,这一数字将增长51%。T2DM最常见的并发症之一是糖尿病视网膜病变(DR),总患病率超过30%。由于2型糖尿病人群的增加,dr相关的视力损害的总数正在上升。增殖性糖尿病视网膜病变(PDR)是进展中的糖尿病视网膜病变,是导致工作年龄成人可预防性失明的主要原因。此外,PDR具有线粒体损伤、细胞死亡增加和慢性炎症等系统性特征,是级联性dm并发症(如缺血性卒中)的独立预测因子。因此,早期DR是出现在这种“多米诺效应”上游的可靠预测指标。全球筛查导致及时识别dm相关并发症,但目前应用的反应性药物尚未充分实施。个性化预测方法和具有成本效益的针对性预防-短期预测、预防和个性化医学(PPPM / 3PM)可以很好地利用积累的知识,预防失明和其他严重糖尿病并发症。为了实现这一目标,需要可靠的阶段和疾病特异性生物标志物面板,其特点是样品收集方法简单,分析灵敏度高,特异性高。在目前的研究中,我们验证了一种假设,即非侵入性收集的泪液是分析眼部和全身(dm相关并发症)生物标志物模式的可靠来源,适用于鉴别诊断稳定型DR与PDR。在这里,我们报告了全面的正在进行的研究的第一个结果,在该研究中,我们将个体化患者的资料(健康对照组与稳定D患者以及有或没有合并症的PDR患者)与其泪液中的代谢资料联系起来。进行的比较质谱分析确定了以下代谢簇,这些代谢簇在比较组中有差异表达:酰基肉碱、氨基酸及相关化合物、胆汁酸、神经酰胺、溶血磷脂酰胆碱、核碱基及相关化合物、磷脂酰胆碱、甘油三酯、胆固醇酯和脂肪酸。我们的初步数据有力地支持了泪液代谢模式的潜在临床应用,表明了DR分期和PDR进展的独特代谢特征。这项初步研究为验证泪液生物标志物模式以对易患PDR的t2dm患者进行分层创建了一个平台。此外,由于PDR是严重t2dm相关并发症(如缺血性卒中)的独立预测因子,我们的国际项目旨在创建适用于糖尿病护理健康风险评估的“诊断树”(是/否)分析原型。
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引用次数: 3
New insight of metabolomics in ocular diseases in the context of 3P medicine. 在3P医学背景下代谢组学在眼部疾病中的新见解。
IF 6.5 2区 医学 Q1 Medicine Pub Date : 2023-03-01 DOI: 10.1007/s13167-023-00313-9
Quyan Zhang, Nan Wang, Yuhua Rui, Yang Xia, Siqi Xiong, Xiaobo Xia

Metabolomics refers to the high-through untargeted or targeted screening of metabolites in biofluids, cells, and tissues. Metabolome reflects the functional states of cells and organs of an individual, influenced by genes, RNA, proteins, and environment. Metabolomic analyses help to understand the interaction between metabolism and phenotype and reveal biomarkers for diseases. Advanced ocular diseases can lead to vision loss and blindness, reducing patients' quality of life and aggravating socio-economic burden. Contextually, the transition from reactive medicine to the predictive, preventive, and personalized (PPPM / 3P) medicine is needed. Clinicians and researchers dedicate a lot of efforts to explore effective ways for disease prevention, biomarkers for disease prediction, and personalized treatments, by taking advantages of metabolomics. In this way, metabolomics has great clinical utility in the primary and secondary care. In this review, we summarized much progress achieved by applying metabolomics to ocular diseases and pointed out potential biomarkers and metabolic pathways involved to promote 3P medicine approach in healthcare.

代谢组学是指生物体液、细胞和组织中代谢物的高通量非靶向或靶向筛选。代谢组反映了个体细胞和器官的功能状态,受基因、RNA、蛋白质和环境的影响。代谢组学分析有助于了解代谢和表型之间的相互作用,并揭示疾病的生物标志物。晚期眼病可导致视力丧失和失明,降低患者的生活质量,加重社会经济负担。因此,需要从反应性医学向预测性、预防性和个性化(PPPM / 3P)医学过渡。临床医生和研究人员致力于利用代谢组学的优势,探索疾病预防、疾病预测的生物标志物和个性化治疗的有效途径。因此,代谢组学在初级和二级医疗中具有很大的临床应用价值。本文综述了代谢组学在眼科疾病研究中取得的进展,并指出了潜在的生物标志物和代谢途径,以促进3P医学方法在医疗保健中的应用。
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引用次数: 5
Multi-omics and immune cells' profiling of COVID-19 patients for ICU admission prediction: in silico analysis and an integrated machine learning-based approach in the framework of Predictive, Preventive, and Personalized Medicine. COVID-19患者的多组学和免疫细胞分析用于ICU入院预测:预测、预防和个性化医学框架下的计算机分析和基于机器学习的综合方法
IF 6.5 2区 医学 Q1 Medicine Pub Date : 2023-03-01 DOI: 10.1007/s13167-023-00317-5
Kun Zhu, Zhonghua Chen, Yi Xiao, Dengming Lai, Xiaofeng Wang, Xiangming Fang, Qiang Shu

Background: Intensive care unit admission (ICUA) triage has been urgent need for solving the shortage of ICU beds, during the coronavirus disease 2019 (COVID-19) surge. In silico analysis and integrated machine learning (ML) approach, based on multi-omics and immune cells (ICs) profiling, might provide solutions for this issue in the framework of predictive, preventive, and personalized medicine (PPPM).

Methods: Multi-omics was used to screen the synchronous differentially expressed protein-coding genes (SDEpcGs), and an integrated ML approach to develop and validate a nomogram for prediction of ICUA. Finally, the independent risk factor (IRF) with ICs profiling of the ICUA was identified.

Results: Colony-stimulating factor 1 receptor (CSF1R) and peptidase inhibitor 16 (PI16) were identified as SDEpcGs, and each fold change (FCij) of CSF1R and PI16 was selected to develop and validate a nomogram to predict ICUA. The area under curve (AUC) of the nomogram was 0.872 (95% confidence interval (CI): 0.707 to 0.950) on the training set, and 0.822 (95% CI: 0.659 to 0.917) on the testing set. CSF1R was identified as an IRF of ICUA, expressed in and positively correlated with monocytes which had a lower fraction in COVID-19 ICU patients.

Conclusion: The nomogram and monocytes could provide added value to ICUA prediction and targeted prevention, which are cost-effective platform for personalized medicine of COVID-19 patients. The log2fold change (log2FC) of the fraction of monocytes could be monitored simply and economically in primary care, and the nomogram offered an accurate prediction for secondary care in the framework of PPPM.

Supplementary information: The online version contains supplementary material available at 10.1007/s13167-023-00317-5.

背景:在2019冠状病毒病(COVID-19)激增期间,迫切需要重症监护病房(ICUA)入院分诊,以解决ICU床位短缺问题。基于多组学和免疫细胞(ic)分析的计算机分析和集成机器学习(ML)方法可能在预测、预防和个性化医学(PPPM)框架中为这一问题提供解决方案。方法:采用多组学方法筛选同步差异表达蛋白编码基因(SDEpcGs),并采用集成ML方法建立并验证预测ICUA的nomogram。最后,确定了ICUA的独立风险因素(IRF)。结果:将集落刺激因子1受体(CSF1R)和肽酶抑制剂16 (PI16)鉴定为SDEpcGs,选取CSF1R和PI16的每一个fold change (FCij)来建立并验证预测ICUA的nomogram。训练集的曲线下面积(AUC)为0.872(95%置信区间(CI): 0.707 ~ 0.950),测试集的曲线下面积(AUC)为0.822(95%置信区间(CI): 0.659 ~ 0.917)。CSF1R被鉴定为ICUA的IRF,在COVID-19 ICU患者中表达,并与单核细胞比例较低呈正相关。结论:nomogram和monocytes可为ICUA预测和针对性预防提供附加价值,是COVID-19患者个性化用药的高性价比平台。在初级保健中,单核细胞分数的log2fold change (log2FC)可以简单、经济地监测,在PPPM框架下,nomogram可以准确预测二级保健。补充信息:在线版本包含补充资料,下载地址:10.1007/s13167-023-00317-5。
{"title":"Multi-omics and immune cells' profiling of COVID-19 patients for ICU admission prediction: in silico analysis and an integrated machine learning-based approach in the framework of Predictive, Preventive, and Personalized Medicine.","authors":"Kun Zhu,&nbsp;Zhonghua Chen,&nbsp;Yi Xiao,&nbsp;Dengming Lai,&nbsp;Xiaofeng Wang,&nbsp;Xiangming Fang,&nbsp;Qiang Shu","doi":"10.1007/s13167-023-00317-5","DOIUrl":"https://doi.org/10.1007/s13167-023-00317-5","url":null,"abstract":"<p><strong>Background: </strong>Intensive care unit admission (ICUA) triage has been urgent need for solving the shortage of ICU beds, during the coronavirus disease 2019 (COVID-19) surge. In silico analysis and integrated machine learning (ML) approach, based on multi-omics and immune cells (ICs) profiling, might provide solutions for this issue in the framework of predictive, preventive, and personalized medicine (PPPM).</p><p><strong>Methods: </strong>Multi-omics was used to screen the synchronous differentially expressed protein-coding genes (SDEpcGs), and an integrated ML approach to develop and validate a nomogram for prediction of ICUA. Finally, the independent risk factor (IRF) with ICs profiling of the ICUA was identified.</p><p><strong>Results: </strong>Colony-stimulating factor 1 receptor (CSF1R) and peptidase inhibitor 16 (PI16) were identified as SDEpcGs, and each fold change (FC<sub>ij</sub>) of CSF1R and PI16 was selected to develop and validate a nomogram to predict ICUA. The area under curve (AUC) of the nomogram was 0.872 (95% confidence interval (CI): 0.707 to 0.950) on the training set, and 0.822 (95% CI: 0.659 to 0.917) on the testing set. CSF1R was identified as an IRF of ICUA, expressed in and positively correlated with monocytes which had a lower fraction in COVID-19 ICU patients.</p><p><strong>Conclusion: </strong>The nomogram and monocytes could provide added value to ICUA prediction and targeted prevention, which are cost-effective platform for personalized medicine of COVID-19 patients. The log<sub>2</sub>fold change (log<sub>2</sub>FC) of the fraction of monocytes could be monitored simply and economically in primary care, and the nomogram offered an accurate prediction for secondary care in the framework of PPPM.</p><p><strong>Supplementary information: </strong>The online version contains supplementary material available at 10.1007/s13167-023-00317-5.</p>","PeriodicalId":54292,"journal":{"name":"Epma Journal","volume":"14 1","pages":"101-117"},"PeriodicalIF":6.5,"publicationDate":"2023-03-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC9942629/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"10828639","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"医学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
引用次数: 2
Correction to: A nomogram model for the risk prediction of type 2 diabetes in healthy eastern China residents: a 14‑year retrospective cohort study from 15,166 participants. 修正:中国东部健康居民2型糖尿病风险预测的nomogram模型:来自15,166名参与者的14年回顾性队列研究。
IF 6.5 2区 医学 Q1 Medicine Pub Date : 2023-03-01 DOI: 10.1007/s13167-022-00297-y
Tiancheng Xu, Decai Yu, Weihong Zhou, Lei Yu

[This corrects the article DOI: 10.1007/s13167-022-00295-0.].

[这更正了文章DOI: 10.1007/s13167-022-00295-0]。
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引用次数: 4
Diagnostic accuracy of autoverification and guidance system for COVID-19 RT-PCR results. COVID-19 RT-PCR结果自动验证和引导系统的诊断准确性。
IF 6.5 2区 医学 Q1 Medicine Pub Date : 2023-03-01 DOI: 10.1007/s13167-022-00310-4
Yingmu Cai, Mengyu Liu, Zhiyuan Wu, Cuihong Tian, Song Qiu, Zhen Li, Feng Xu, Wei Li, Yan Zheng, Aijuan Xu, Longxu Xie, Xuerui Tan
<p><strong>Background: </strong>To date, most countries worldwide have declared that the pandemic of COVID-19 is over, while the WHO has not officially ended the COVID-19 pandemic, and China still insists on the personalized dynamic COVID-free policy. Large-scale nucleic acid testing in Chinese communities and the manual interpretation for SARS-CoV-2 nucleic acid detection results pose a huge challenge for labour, quality and turnaround time (TAT) requirements. To solve this specific issue while increase the efficiency and accuracy of interpretation, we created an autoverification and guidance system (AGS) that can automatically interpret and report the COVID-19 reverse transcriptase-polymerase chain reaction (RT-PCR) results relaying on computer-based autoverification procedure and then validated its performance in real-world environments. This would be conductive to transmission risk prediction, COVID-19 prevention and control and timely medical treatment for positive patients in the context of the predictive, preventive and personalized medicine (PPPM).</p><p><strong>Methods: </strong>A diagnostic accuracy test was conducted with 380,693 participants from two COVID-19 test sites in China, the Hong Kong Hybribio Medical Laboratory (<i>n</i> = 266,035) and the mobile medical shelter at a Shanghai airport (<i>n</i> = 114,658). These participants underwent SARS-CoV-2 RT-PCR from March 28 to April 10, 2022. All RT-PCR results were interpreted by laboratorians and by using AGS simultaneously. Considering the manual interpretation as gold standard, the sensitivity, specificity, positive predictive value (PPV), negative predictive value (NPV) and accuracy were applied to evaluate the diagnostic value of the AGS on the interpretation of RT-PCR results.</p><p><strong>Results: </strong>Among the 266,035 samples in Hong Kong, there were 16,356 (6.15%) positive, 231,073 (86.86%) negative, 18,606 (6.99%) indefinite, 231,073 (86.86%, negative) no retest required and 34,962 (13.14%, positive and indefinite) retest required; the 114,658 samples in Shanghai consisted of 76 (0.07%) positive, 109,956 (95.90%) negative, 4626 (4.03%) indefinite, 109,956 (95.90%, negative) no retest required and 4702 (4.10%, positive and indefinite) retest required. Compared to the fashioned manual interpretation, the AGS is a procedure of high accuracy [99.96% (95%CI, 99.95-99.97%) in Hong Kong and 100% (95%CI, 100-100%) in Shanghai] with perfect sensitivity [99.98% (95%CI, 99.97-99.98%) in Hong Kong and 100% (95%CI, 100-100%) in Shanghai], specificity [99.87% (95%CI, 99.82-99.90%) in Hong Kong and 100% (95%CI, 99.92-100%) in Shanghai], PPV [99.98% (95%CI, 99.97-99.99%) in Hong Kong and 100% (95%CI, 99.99-100%) in Shanghai] and NPV [99.85% (95%CI, 99.80-99.88%) in Hong Kong and 100% (95%CI, 99.90-100%) in Shanghai]. The need for manual interpretation of total samples was dramatically reduced from 100% to 13.1% and the interpretation time fell from 53 h to 26 min in Hong Kong; while
背景:迄今为止,世界上大多数国家已经宣布新冠肺炎大流行结束,而世卫组织尚未正式结束新冠肺炎大流行,中国仍然坚持个性化的动态无疫政策。中国社区大规模核酸检测和人工解读新冠病毒核酸检测结果,对劳动力、质量和周转时间(TAT)要求提出了巨大挑战。为了解决这一具体问题,同时提高解释的效率和准确性,我们创建了一个自动验证和指导系统(AGS),该系统可以根据基于计算机的自动验证程序自动解释和报告COVID-19逆转录聚合酶链反应(RT-PCR)结果,然后在实际环境中验证其性能。这将有助于预测、预防和个性化医疗(PPPM)背景下的传播风险预测、COVID-19防控和阳性患者的及时治疗。方法:对来自中国两个COVID-19检测点、香港杂交生物医学实验室(n = 266,035)和上海机场移动医疗中心(n = 114,658)的380,693名参与者进行诊断准确性测试。这些参与者在2022年3月28日至4月10日期间接受了SARS-CoV-2 RT-PCR检测。所有RT-PCR结果由实验室人员和AGS同时进行解释。以人工解释为金标准,以敏感性、特异性、阳性预测值(PPV)、阴性预测值(NPV)和准确性评价AGS对RT-PCR结果解释的诊断价值。结果:香港266035份样本中,阳性16356份(6.15%),阴性231073份(86.86%),不确定18606份(6.99%),不需要复验231073份(86.86%),需要复验34962份(13.14%,阳性和不确定);上海市114,658份样本中,阳性76份(0.07%),阴性109,956份(95.90%),不确定4626份(4.03%),不需要复验109,956份(95.90%),需要复验4702份(4.10%,阳性和不确定)。与传统的人工口译相比,AGS具有较高的准确度[99.96% (95%CI, 99.95-99.97%)在香港,100% (95%CI, 99.95- 99.98%)在上海,100% (95%CI, 100-100%)],完美的灵敏度[99.98% (95%CI, 99.97-99.98%)在香港,100% (95%CI, 100-100%)在上海],特异性[99.87% (95%CI, 99.82-99.90%)在香港,100% (95%CI, 99.92-100%)在上海],PPV [99.98% (95%CI, 99.97-99.99%)在香港,100% (95%CI, 99.99-100%)在上海]和NPV [99.85% (95%CI, 99.95- 100%),(香港为99.80-99.88%),上海为100% (95%CI, 99.90-100%)]。在香港,人工解译总样本的需求从100%大幅降低到13.1%,解译时间从53 h下降到26 min;在上海,人工解译总样本的比例从100%下降到4.1%,解译时间从20 h下降到16 min。结论:AGS是一种准确性高的方法,可显著减轻RT-PCR大规模筛查SARS-CoV-2的工作量和时间挑战。建议将其作为一种强大的SARS-CoV-2筛查、诊断和预测系统,在PPPM的概念下,为及时结束COVID-19大流行做出贡献。
{"title":"Diagnostic accuracy of autoverification and guidance system for COVID-19 RT-PCR results.","authors":"Yingmu Cai,&nbsp;Mengyu Liu,&nbsp;Zhiyuan Wu,&nbsp;Cuihong Tian,&nbsp;Song Qiu,&nbsp;Zhen Li,&nbsp;Feng Xu,&nbsp;Wei Li,&nbsp;Yan Zheng,&nbsp;Aijuan Xu,&nbsp;Longxu Xie,&nbsp;Xuerui Tan","doi":"10.1007/s13167-022-00310-4","DOIUrl":"https://doi.org/10.1007/s13167-022-00310-4","url":null,"abstract":"&lt;p&gt;&lt;strong&gt;Background: &lt;/strong&gt;To date, most countries worldwide have declared that the pandemic of COVID-19 is over, while the WHO has not officially ended the COVID-19 pandemic, and China still insists on the personalized dynamic COVID-free policy. Large-scale nucleic acid testing in Chinese communities and the manual interpretation for SARS-CoV-2 nucleic acid detection results pose a huge challenge for labour, quality and turnaround time (TAT) requirements. To solve this specific issue while increase the efficiency and accuracy of interpretation, we created an autoverification and guidance system (AGS) that can automatically interpret and report the COVID-19 reverse transcriptase-polymerase chain reaction (RT-PCR) results relaying on computer-based autoverification procedure and then validated its performance in real-world environments. This would be conductive to transmission risk prediction, COVID-19 prevention and control and timely medical treatment for positive patients in the context of the predictive, preventive and personalized medicine (PPPM).&lt;/p&gt;&lt;p&gt;&lt;strong&gt;Methods: &lt;/strong&gt;A diagnostic accuracy test was conducted with 380,693 participants from two COVID-19 test sites in China, the Hong Kong Hybribio Medical Laboratory (&lt;i&gt;n&lt;/i&gt; = 266,035) and the mobile medical shelter at a Shanghai airport (&lt;i&gt;n&lt;/i&gt; = 114,658). These participants underwent SARS-CoV-2 RT-PCR from March 28 to April 10, 2022. All RT-PCR results were interpreted by laboratorians and by using AGS simultaneously. Considering the manual interpretation as gold standard, the sensitivity, specificity, positive predictive value (PPV), negative predictive value (NPV) and accuracy were applied to evaluate the diagnostic value of the AGS on the interpretation of RT-PCR results.&lt;/p&gt;&lt;p&gt;&lt;strong&gt;Results: &lt;/strong&gt;Among the 266,035 samples in Hong Kong, there were 16,356 (6.15%) positive, 231,073 (86.86%) negative, 18,606 (6.99%) indefinite, 231,073 (86.86%, negative) no retest required and 34,962 (13.14%, positive and indefinite) retest required; the 114,658 samples in Shanghai consisted of 76 (0.07%) positive, 109,956 (95.90%) negative, 4626 (4.03%) indefinite, 109,956 (95.90%, negative) no retest required and 4702 (4.10%, positive and indefinite) retest required. Compared to the fashioned manual interpretation, the AGS is a procedure of high accuracy [99.96% (95%CI, 99.95-99.97%) in Hong Kong and 100% (95%CI, 100-100%) in Shanghai] with perfect sensitivity [99.98% (95%CI, 99.97-99.98%) in Hong Kong and 100% (95%CI, 100-100%) in Shanghai], specificity [99.87% (95%CI, 99.82-99.90%) in Hong Kong and 100% (95%CI, 99.92-100%) in Shanghai], PPV [99.98% (95%CI, 99.97-99.99%) in Hong Kong and 100% (95%CI, 99.99-100%) in Shanghai] and NPV [99.85% (95%CI, 99.80-99.88%) in Hong Kong and 100% (95%CI, 99.90-100%) in Shanghai]. The need for manual interpretation of total samples was dramatically reduced from 100% to 13.1% and the interpretation time fell from 53 h to 26 min in Hong Kong; while","PeriodicalId":54292,"journal":{"name":"Epma Journal","volume":"14 1","pages":"119-129"},"PeriodicalIF":6.5,"publicationDate":"2023-03-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC9755791/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"10794430","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"医学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
引用次数: 1
Diabetic retinopathy as the leading cause of blindness and early predictor of cascading complications-risks and mitigation. 糖尿病视网膜病变作为失明的主要原因和级联并发症的早期预测因子-风险和缓解
IF 6.5 2区 医学 Q1 Medicine Pub Date : 2023-03-01 DOI: 10.1007/s13167-023-00314-8
Martina Kropp, Olga Golubnitschaja, Alena Mazurakova, Lenka Koklesova, Nafiseh Sargheini, Trong-Tin Kevin Steve Vo, Eline de Clerck, Jiri Polivka, Pavel Potuznik, Jiri Polivka, Ivana Stetkarova, Peter Kubatka, Gabriele Thumann

Proliferative diabetic retinopathy (PDR) the sequel of diabetic retinopathy (DR), a frequent complication of diabetes mellitus (DM), is the leading cause of blindness in the working-age population. The current screening process for the DR risk is not sufficiently effective such that often the disease is undetected until irreversible damage occurs. Diabetes-associated small vessel disease and neuroretinal changes create a vicious cycle resulting in the conversion of DR into PDR with characteristic ocular attributes including excessive mitochondrial and retinal cell damage, chronic inflammation, neovascularisation, and reduced visual field. PDR is considered an independent predictor of other severe diabetic complications such as ischemic stroke. A "domino effect" is highly characteristic for the cascading DM complications in which DR is an early indicator of impaired molecular and visual signaling. Mitochondrial health control is clinically relevant in DR management, and multi-omic tear fluid analysis can be instrumental for DR prognosis and PDR prediction. Altered metabolic pathways and bioenergetics, microvascular deficits and small vessel disease, chronic inflammation, and excessive tissue remodelling are in focus of this article as evidence-based targets for a predictive approach to develop diagnosis and treatment algorithms tailored to the individual for a cost-effective early prevention by implementing the paradigm shift from reactive medicine to predictive, preventive, and personalized medicine (PPPM) in primary and secondary DR care management.

增殖性糖尿病视网膜病变(PDR)是糖尿病视网膜病变(DR)的后遗症,是糖尿病(DM)的常见并发症,是导致劳动年龄人口失明的主要原因。目前对DR风险的筛查程序不够有效,因此往往在发生不可逆转的损害之前未发现该疾病。糖尿病相关的小血管疾病和神经视网膜病变形成恶性循环,导致DR转化为PDR,其眼部特征包括线粒体和视网膜细胞过度损伤、慢性炎症、新生血管形成和视野缩小。PDR被认为是其他严重糖尿病并发症(如缺血性中风)的独立预测因子。“多米诺骨牌效应”是级联性糖尿病并发症的高度特征,其中DR是分子和视觉信号受损的早期指标。线粒体健康控制与DR管理具有临床相关性,多组泪液分析可用于DR预后和PDR预测。代谢途径和生物能量学改变、微血管缺陷和小血管疾病、慢性炎症和过度组织重塑是本文的重点,作为基于证据的预测方法的目标,开发针对个体的诊断和治疗算法,通过实施从反应性药物到预测、预防、以及个性化医疗(PPPM)在初级和二级DR护理管理中的应用。
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引用次数: 20
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