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1.
Artigo em Inglês | MEDLINE | ID: mdl-36478240

RESUMO

OBJECTIVES: To develop an unbiased objective for learning automatic coding algorithms from clinical records annotated with only partial relevant International Classification of Diseases codes, as annotation noise in undercoded clinical records used as training data can mislead the learning process of deep neural networks. MATERIALS AND METHODS: We use Medical Information Mart for Intensive Care III as our dataset. We employ positive-unlabeled learning to achieve unbiased loss estimation, which is free of misleading training signal. We then utilize reweighting mechanism to compensate for the imbalance between positive and negative samples. To further close the performance gap caused by poor quality annotation, we integrate the supervision provided by the automatic annotation tool Medical Concept Annotation Toolkit which can ease the heavy burden of manual validation. RESULTS: Our benchmarking results show that positive-unlabeled learning with reweighting outperforms competitive baseline methods over a range of missing label ratios. Integrating supervision provided by annotation tool further boosted the performance. DISCUSSION: Considering the annotation noise and severe imbalance, unbiased loss estimation and reweighting mechanism are both important for learning from undercoded clinical records. Unbiased loss requires the estimation of false negative ratios and estimation through trained models is practical and competitive. CONCLUSIONS: The combination of positive-unlabeled learning with reweighting and supervision provided by the annotation tool is a promising solution to learn from undercoded clinical records.

2.
Artigo em Inglês | MEDLINE | ID: mdl-36417969

RESUMO

OBJECTIVE: To quantify placebo effects and responses in randomized controlled trials (RCTs) on neck pain and explore how they would influence the treatment of neck pain. DATA SOURCES: We searched MEDLINE (PubMed), EMBASE (Ovid), CINAHL (EBSCO), Physiotherapy Evidence Database (PEDro), and World Health Organization (WHO) International Clinical Trials Registry Platform (ICTRP) from the inception of August 15, 2021, to identify relevant RCTs. STUDY SELECTION AND DATA EXTRACTION: The abstracts and full texts of potential studies were independently screened, and data extraction was also independently performed by two researchers. Scales of the score measuring neck pain and the scores both at baseline and the endpoint were extracted. DATA SYNTHESIS: A total of 60 RCTs were included. The mean improvement in the pain score after placebo treatment was 15.65 [MD = -15.65, 95% CI (-19.19, -12.12); P<0.05], which we defined as the placebo response. In the active groups, it was 25.91 [MD = -25.91, 95% CI (-29.15, -22.68); P<0.05], and in the no-treatment groups, it was 5.80 [MD = -5.80, 95% CI (13.28, 1.69); P=0.13]. Using the three MDs from the three groups, the placebo effect was calculated to accounts for 38.0% of the pain score improvement in the active group. CONCLUSIONS: The pain scores of patients with neck pain were reduced after treatment with placebos, but the magnitude of pain score reduction was not clinically significant enough. The 38.0% amount of pain score reduction in patients treated with active interventions was caused by placebo. Interventions with considerable clinically significance for neck pain were still required.

3.
Artigo em Inglês | MEDLINE | ID: mdl-36376170

RESUMO

PURPOSE: Numerous studies suggested methylation modifications play an important role in upper tract urothelial carcinoma (UTUC), but few have depicted DNA methylation architecture on the pathological process of UTUC. We aimed to better understand the pathogenesis of UTUC and provide precision medicine references when managing UTUC patients. METHODS: PubMed, Cochrane Library, EMBASE, and Scopus were searched for UTUC until December 31, 2020. Methodological quality assessment was conducted according to NIH recommendations. Meta-analysis was conducted to assess the prognostic effect of methylated genes. Kaplan-Meier survival analyses were performed to validate methylated genes and cytosine-phosphate-guanine (CpG) sites. RESULTS: Eleven studies (3619 patients) were eligible to investigate 12 methylated genes and 10 CpGs. The quality of all the studies was fair to good. Meta-analysis found the pooled effect of eligible methylated genes had a low risk of tumor recurrence (HR = 0·67; 95% CI: 0·51-0·87; P = ·003), but a high risk of tumor progression (HR = 1·60; 95% CI: 1·17-2·18; P = ·003) and cancer-specific mortality (HR = 1·35; 95% CI: 1·06-1·72; P = ·01). For individual methylation status of GDF15, HSPA2, RASSF1A, TMEFF2, and VIM, the pooled effect of each gene was found pleiotropic on both diagnosis and prognosis. Survival analysis suggested higher methylation of SPARCL1 had a better disease-specific survival (P = ·048). CONCLUSION: We combined meta-analysis and Kaplan-Meier survival analysis using the most updated evidence on the methylation of UTUC. Candidate biomarkers with essential diagnosis and prognosis function might provide precision medicine references for personalized therapies.

4.
Front Microbiol ; 13: 931431, 2022.
Artigo em Inglês | MEDLINE | ID: mdl-36329847

RESUMO

Objective: Rheumatoid arthritis (RA) is a chronic inflammatory joint disease, which is associated with progressive disability, systemic complications, and early death. But its etiology and pathogenesis are not fully understood. We aimed to investigate the alterations in plasma metabolite profiles, gut bacteria, and fungi and their role of them in the pathogenesis of RA. Methods: Metabolomics profiling of plasma from 363 participants including RA (n = 244), systemic lupus erythematosus (SLE, n = 50), and healthy control (HC, n = 69) were performed using the ultra-high performance liquid chromatography-quadrupole time-of-flight mass spectrometry. The differentially expressed metabolites were selected among groups and used to explore important metabolic pathways. Gut microbial diversity analysis was performed by 16S rRNA sequencing and ITS sequencing (RA = 195, HC = 269), and the specific microbial floras were identified afterward. The diagnosis models were established based on significant differential metabolites and microbial floras, respectively. Results: There were 63 differential metabolites discovered between RA and HC groups, mainly significantly enriched in the arginine and proline metabolism, glycine, serine, and threonine metabolism, and glycerophospholipid metabolism between RA and HC groups. The core differential metabolites included L-arginine, creatine, D-proline, ornithine, choline, betaine, L-threonine, LysoPC (18:0), phosphorylcholine, and glycerophosphocholine. The L-arginine and phosphorylcholine were increased in the RA group. The AUC of the predictive model was 0.992, based on the combination of the 10 differential metabolites. Compared with the SLE group, 23 metabolites increased and 61 metabolites decreased in the RA group. However, no significant metabolic pathways were enriched between RA and SLE groups. On the genus level, a total of 117 differential bacteria genera and 531 differential fungal genera were identified between RA and HC groups. The results indicated that three bacteria genera (Eubacterium_hallii_group, Escherichia-Shigella, Streptococcus) and two fungal genera (Candida and Debaryomyces) significantly increased in RA patients. The AUC was 0.80 based on a combination of six differential bacterial genera and the AUC was 0.812 based on a combination of seven differential fungal genera. Functional predictive analysis displayed that differential bacterial and differential fungus both were associated with KEGG pathways involving superpathway of L-serine and glycine biosynthesis I, arginine, ornithine, and proline interconversion. Conclusion: The plasma metabolism profile and gut microbe profile changed markedly in RA. The glycine, serine, and threonine metabolism and arginine and proline metabolism played an important role in RA.

5.
Cancer Med ; 2022 Sep 07.
Artigo em Inglês | MEDLINE | ID: mdl-36069056

RESUMO

BACKGROUND: Many observational epidemiology studies discovered that kidney cancer and impaired kidney function have a bidirectional relationship. However, it remains unclear whether these two kinds of traits are causally linked. In this study, we aimed to investigate the bidirectional causal relation between kidney cancer and kidney function biomarkers (creatinine-based estimated glomerular filtration rate (eGFRcrea), cystatin C-based estimated glomerular filtration rate (eGFRcys), blood urea nitrogen (BUN), serum urate, and urinary albumin-to-creatinine ratio (UACR)). METHODS: For both directions, single-nucleotide polymorphisms (SNPs), as genetic instruments, for the five kidney function traits were selected from up to 1,004,040 individuals, and SNPs for kidney cancer were from 408,786 participants(1338 cases). In the main analysis, we applied two state-of-the-art MR methods, namely, contamination mixture and Robust Adjusted Profile Score to downweight the effect of weak instrument bias, pleiotropy, and extreme outliers. We additionally conducted traditional MR analyses as sensitivity analyses. Summary-level data of European ancestry were extracted from UK Biobank, Chronic Kidney Disease Genetics Consortium, and Kaiser Permanente. RESULTS: Based on 99 SNPs, we found that the eGFRcrea had a significant negative causal effect on the risk of kidney cancer (OR = 0.007, 95% CI:2.6 × 10-4 -0.569, p = 0.041). After adjusting for body composition or diabetes, urate had a significant negative causal effect on kidney cancer (OR <1, p < 0.05). For UACR, it showed a strong causal effect on kidney cancer, after adjusting for body composition (OR = 14.503, 95% CI: 2.546-96.001, p = 0.032). Due to lacking significant signals and effect power for the reverse MR, further investigations are warranted. CONCLUSIONS: Our study suggested a potential causal effect of damaged kidney function on kidney cancer. EGFRcrea and UACR might be causally associated with kidney cancer, especially when patients were comorbid with obesity or diabetes. We called for larger sample-size studies to further unravel the underlying causal relationship and the exact mechanism.

6.
Mol Genet Genomic Med ; 10(11): e2047, 2022 Nov.
Artigo em Inglês | MEDLINE | ID: mdl-36124564

RESUMO

BACKGROUND: Patients with impaired kidney function were found at a high risk of COVID-19 hospitalization and mortality in many observational, cross-sectional, and hospital-based studies, but evidence from large-scale prospective cohorts has been lacking. We aimed to examine the association of kidney function-related biomarkers and their genetic predisposition with the risk of developing severe COVID-19 in population-based data. METHODS: We analyzed data from UK Biobank to examine the prospective association of abnormal kidney function biomarkers with severe COVID-19, defined by laboratory-confirmed COVID-19 hospitalizations. Using genotype data, we constructed polygenic risk scores (PRS) to represent an individual's overall genetic risk for these biomarkers. We also identified tipping points where the risk of severe COVID-19 began to increase significantly for each biomarker. RESULTS: Of the 502,506 adults, 1650 (0.32%) were identified as severe COVID-19, before August 12, 2020. High levels of cystatin C (OR: 1.3; 95% CI: 1.2-1.5; FDR = 1.5 × 10-5 ), serum creatinine (OR: 1.7; 95% CI: 1.3-2.1; p = 3.5 × 10-4 ; FDR = 3.5 × 10-4 ), microalbuminuria (OR: 1.4; 95% CI: 1.2-1.6; FDR = 4 × 10-4 ), and UACR (urinary albumin creatinine ratio; OR: 1.4; 95% CI: 1.2-1.6; p = 3.5 × 10-4 ; FDR = 3.5 × 10-4 ) were found significantly associated with severe COVID-19. Individuals with top 10% of PRS for elevated cystatin C, urate, and microalbuminuria had 28% to 43% higher risks of severe COVID-19 than individuals with bottom 30% PRS (p < 0.05). Tipping-point analyses further supported that severe COVID-19 could occur even when the values of cystatin C, urate (male), and microalbuminuria were within their normal value ranges (OR >1.1, p < 0.05). CONCLUSIONS: Findings from this study might point to new directions for clinicians and policymakers in optimizing risk-stratification among patients based on polygenic risk estimation and tipping points of kidney function markers. Our results call for further investigation to develop a better strategy to prevent severe COVID-19 outcomes among patients with genetic predisposition to impaired kidney function. These findings could provide a new tool for clinicians and policymakers in the future especially if we need to live with COVID-19 for a long time.


Assuntos
COVID-19 , Insuficiência Renal , Adulto , Humanos , Masculino , Cistatina C/urina , COVID-19/genética , Predisposição Genética para Doença , Estudos Transversais , Ácido Úrico , Albuminúria/genética , Biomarcadores , Rim
7.
BMC Med Inform Decis Mak ; 22(1): 174, 2022 07 01.
Artigo em Inglês | MEDLINE | ID: mdl-35778708

RESUMO

BACKGROUND: People live a long time in pre-diabetes/early diabetes without a formal diagnosis or management. Heterogeneity of progression coupled with deficiencies in electronic health records related to incomplete data, discrete events, and irregular event intervals make identification of pre-diabetes and critical points of diabetes progression challenging. METHODS: We utilized longitudinal electronic health records of 9298 patients with type 2 diabetes or prediabetes from 2005 to 2016 from a large regional healthcare delivery network in China. We optimized a generative Markov-Bayesian-based model to generate 5000 synthetic illness trajectories. The synthetic data were manually reviewed by endocrinologists. RESULTS: We build an optimized generative progression model for type 2 diabetes using anchor information to reduce the number of parameters learning in the third layer of the model from [Formula: see text] to [Formula: see text], where [Formula: see text] is the number of clinical findings, [Formula: see text] is the number of complications, [Formula: see text] is the number of anchors. Based on this model, we infer the relationships between progression stages, the onset of complication categories, and the associated diagnoses during the whole progression of type 2 diabetes using electronic health records. DISCUSSION: Our findings indicate that 55.3% of single complications and 31.8% of complication patterns could be predicted early and managed appropriately to potentially delay (as it is a progressive disease) or prevented (by lifestyle modifications that keep patient from developing/triggering diabetes in the first place). CONCLUSIONS: The full type 2 diabetes patient trajectories generated by the chronic disease progression model can counter a lack of real-world evidence of desired longitudinal timeframe while facilitating population health management.


Assuntos
Diabetes Mellitus Tipo 2 , Estado Pré-Diabético , Teorema de Bayes , China/epidemiologia , Diabetes Mellitus Tipo 2/complicações , Humanos , Estado Pré-Diabético/complicações , Estado Pré-Diabético/epidemiologia
8.
Gastrointest Endosc ; 96(5): 787-795.e6, 2022 11.
Artigo em Inglês | MEDLINE | ID: mdl-35718070

RESUMO

BACKGROUND AND AIMS: The clinical application of GI endoscopy for the diagnosis of multiple diseases using artificial intelligence (AI) has been limited by its high false-positive rates. There is an unmet need to develop a GI endoscopy AI-assisted diagnosis system (GEADS) to improve diagnostic accuracy and clinical utility. METHODS: In this retrospective, multicenter study, a convolutional neural network was trained to assess upper GI diseases based on 26,228 endoscopic images from Dazhou Central Hospital that were randomly assigned (3:1:1) to a training dataset, validation dataset, and test dataset, respectively. To validate the model, 6 external independent datasets comprising 51,372 images of upper GI diseases were collected. In addition, 1 prospective dataset comprising 27,975 images was collected. The performance of GEADS was compared with endoscopists with 2 professional degrees of expertise: expert and novice. Eight endoscopists were in the expert group with >5 years of experience, whereas 3 endoscopists were in the novice group with 1 to 5 years of experience. RESULTS: The GEADS model achieved an accuracy of .918 (95% confidence interval [CI], .914-.922), with an F1 score of .884 (95% CI, .879-.889), recall of .873 (95% CI, .868-.878), and precision of .890 (95% CI, .885-.895) in the internal validation dataset. In the external validation datasets and 1 prospective validation dataset, the diagnostic accuracy of the GEADS ranged from .841 (95% CI, .834-.848) to .949 (95% CI, .935-.963). With the help of the GEADS, the diagnosing accuracies of novice and expert endoscopists were significantly improved (P < .001). CONCLUSIONS: The AI system can assist endoscopists in improving the accuracy of diagnosing upper GI diseases.


Assuntos
Inteligência Artificial , Gastroenteropatias , Humanos , Gastroscopia/métodos , Estudos Retrospectivos , Redes Neurais de Computação , Algoritmos , Gastroenteropatias/diagnóstico por imagem
9.
Urol Oncol ; 40(8): 383.e11-383.e21, 2022 08.
Artigo em Inglês | MEDLINE | ID: mdl-35659483

RESUMO

Numerous studies suggested that non-coding RNA modifications play an important role in upper tract urothelial carcinoma (UTUC), but few have depicted the architecture of non-coding RNA on the pathological process of UTUC. We aimed to better understand the pathogenesis of UTUC and provide precision medicine references of non-coding RNA when managing UTUC patients. PubMed, Cochrane Library, Embase, and Scopus were searched for UTUC until December 31, 2020. Methodological quality assessment was conducted according to NIH recommendations. Enrichment analyses and network analyses were conducted to explore the interactions of miRNA with genes and other non-coding RNAs. Survival analyses were performed to validate the novel genes. A total of 12 pairs of UTUC tumors and adjacent normal tissues were also included to validate the gene expressions regulated by miRNAs from the miRNA-gene network. Thirteen studies with 945 patients were eligible, investigating 106 miRNAs mutations. The quality of all the studies was fair to good. Most miRNAs were enriched in tissue/organs, diseases, and specific anti-cancer drugs (false discovery rate <0.05). Other non-coding RNAs, i.e.,: miR-34a, DLGAP1-AS1, USP39, and RNA5SP479, were highlighted by network analyses to have potential in the pathogenesis of UTUC. Top hub genes in the miRNA-gene network, namely ZNF460, NUFIP2, and E2F3, were all validated by survival analysis(P < 0.05). Using own cohort data, the differential expression analyses identified 368 overlapped significant genes, including above 3 hub genes (false discovery rate <0.05). Novel biomarkers identified in our studies might play essential roles in UTUC, from the perspectives of the molecule, tissue/organ, diagnosis, treatment, and prognosis. Candidate biomarkers could be significant references for personalized and target therapies.


Assuntos
Carcinoma de Células de Transição , MicroRNAs , Neoplasias da Bexiga Urinária , Neoplasias Urológicas , Carcinoma de Células de Transição/patologia , Humanos , MicroRNAs/genética , Proteínas Nucleares/metabolismo , Prognóstico , Proteínas de Ligação a RNA , Proteases Específicas de Ubiquitina/metabolismo , Neoplasias da Bexiga Urinária/genética , Neoplasias Urológicas/patologia
10.
Res Synth Methods ; 13(5): 622-631, 2022 Sep.
Artigo em Inglês | MEDLINE | ID: mdl-35716041

RESUMO

Little research has been conducted to assess which specific databases should be searched when performing a systematic review (SR) on acupuncture. The current study aimed to identify key databases and the optimal database combination to retrieve randomized controlled trials (RCTs) on acupuncture for inclusion in SRs. A systematic search for SRs in the field of acupuncture was conducted in order to identify target databases and RCTs were extracted from the SRs that had searched all target databases. The proportions of SRs that had achieved 100%, 95%, or 90% recall of RCTs and the total recall of RCTs in various combinations of target databases were calculated. Sensitivity analysis was performed on those SRs that included 10 or more RCTs. CNKI, WanFang, VIP, PubMed, CENTRAL and Embase were regarded as target databases. A total of 4349 acupuncture RCTs were extracted from 286 SRs. Searching all six target databases retrieved 99.3% of all RCTs while 99.1% were recalled by searching the combination of CNKI, WanFang, PubMed and CENTRAL. There were no significant differences on total recall of RCTs (p = 0.549) or in the proportion of SRs with 90% recall of RCTs (97.2% vs. 97.6%; p = 0.794) between searching the above four and the full six target databases. Most results were similar in the sensitivity analysis. The combined retrieval power of CNKI, WanFang, PubMed and CENTRAL was considered an efficient choice to retrieve acupuncture RCTs included in SRs.


Assuntos
Terapia por Acupuntura , Terapia por Acupuntura/métodos , Bases de Dados Factuais , Estudos Epidemiológicos , Ensaios Clínicos Controlados Aleatórios como Assunto
12.
Future Oncol ; 18(14): 1777-1791, 2022 May.
Artigo em Inglês | MEDLINE | ID: mdl-35137603

RESUMO

Background: The CyberKnife© system combines real-time image guidance and a dynamic tracking system to implement frameless radiotherapy. This umbrella review is aimed to evaluate the effectiveness and safety of CyberKnife. Methods: A comprehensive search of health technology assessments and systematic reviews was performed among the Embase, PubMed and other grey databases until July 2020. Treatment outcomes were extracted, and the quality of included studies were assessed using AMSTAR-2. Results: Nineteen studies were eligible. CyberKnife not only had a wide range of applications, long overall survival and great local control, but also had a limited toxicity and good cost-effectiveness compared with other radiotherapy equipment. Conclusion: Despite the relatively low quality of the evidence, our findings can still provide a decision reference for policymakers.


An umbrella review on the effectiveness and safety of the CyberKnife© system was performed by comprehensively searching for all related publications. The CyberKnife system had excellent effect on treatment of cancer and some noncancer diseases, with limited toxicity. Additionally, it was a cost-effective treatment compared with other types of radiotherapy. Despite the relatively low quality of the included evidence, our findings can still provide a comprehensive decision reference for policymakers of patients, government and hospitals.


Assuntos
Radiocirurgia , Humanos , Radiocirurgia/efeitos adversos , Radiocirurgia/métodos , Resultado do Tratamento
13.
Urol Int ; 106(4): 352-359, 2022.
Artigo em Inglês | MEDLINE | ID: mdl-34350887

RESUMO

BACKGROUND: Hemostatic agents (HAs) are used to achieve hemostasis and prevent postoperative complications in multiple surgeries, but the role of HAs is ambiguous during partial nephrectomy (PN), so this study aimed to assess the role of HAs in PN. METHODS: PubMed, Embase, CENTRAL and ClinicalTrials.gov were searched for randomized controlled trials and cohort studies regarding the comparison of HA use alone and standard suturing during PN on January 17, 2020. RevMan 5.3 was used to conduct meta-analysis. Sensitivity analyses and subgroup analyses were performed based on surgical procedures and HA types. RESULTS: Six studies involving 1,066 patients were included. The quality of studies was moderate to high. There were significant reductions in warm ischemia time (mean difference [MD] = -6.30 min, 95% confidence interval [CI] -7.70 to -4.90, p < 0.00001), operative time (MD = -19.81 min, 95% CI -27.54 to -12.08, p < 0.00001), and estimated blood loss (MD = -108.62 mL, 95% CI -177.27 to -39.9, p = 0.002) in the HA group, and HA use alone did not increase postoperative complications. The results were similar in the subgroup analyses and sensitivity analyses. CONCLUSION: HA may be an effective and safe surgical material in PN, which can improve postoperative outcomes. High-quality and randomly designed studies are needed to validate the applicability.


Assuntos
Hemostáticos , Neoplasias Renais , Hemostáticos/uso terapêutico , Humanos , Neoplasias Renais/cirurgia , Nefrectomia/efeitos adversos , Nefrectomia/métodos , Complicações Pós-Operatórias/prevenção & controle , Complicações Pós-Operatórias/cirurgia , Resultado do Tratamento , Isquemia Quente
14.
Biomolecules ; 13(1)2022 Dec 20.
Artigo em Inglês | MEDLINE | ID: mdl-36671391

RESUMO

This study was conducted to investigate oropharyngeal microbiota alterations during the progression of coronavirus disease 2019 (COVID-19) by analyzing these alterations during the infection and clearance processes of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2). The diagnosis of COVID-19 was confirmed by using positive SARS-CoV-2 quantitative reverse transcription polymerase chain reaction (RT-qPCR). The alterations in abundance, diversity, and potential function of the oropharyngeal microbiome were identified using metatranscriptomic sequencing analyses of oropharyngeal swab specimens from 47 patients with COVID-19 (within a week after diagnosis and within two months after recovery from COVID-19) and 40 healthy individuals. As a result, in the infection process of SARS-CoV-2, compared to the healthy individuals, the relative abundances of Prevotella, Aspergillus, and Epstein-Barr virus were elevated; the alpha diversity was decreased; the beta diversity was disordered; the relative abundance of Gram-negative bacteria was increased; and the relative abundance of Gram-positive bacteria was decreased. After the clearance of SARS-CoV-2, compared to the healthy individuals and patients with COVID-19, the above disordered alterations persisted in the patients who had recovered from COVID-19 and did not return to the normal level observed in the healthy individuals. Additionally, the expressions of several antibiotic resistance genes (especially multi-drug resistance, glycopeptide, and tetracycline) in the patients with COVID-19 were higher than those in the healthy individuals. After SARS-CoV-2 was cleared, the expressions of these genes in the patients who had recovered from COVID-19 were lower than those in the patients with COVID-19, and they were different from those in the healthy individuals. In conclusion, our findings provide evidence that potential secondary infections with oropharyngeal bacteria, fungi, and viruses in patients who have recovered from COVID-19 should not be ignored; this evidence also highlights the clinical significance of the oropharyngeal microbiome in the early prevention of potential secondary infections of COVID-19 and suggests that it is imperative to choose appropriate antibiotics for subsequent bacterial secondary infection in patients with COVID-19.


Assuntos
COVID-19 , Coinfecção , Infecções por Vírus Epstein-Barr , Microbiota , Humanos , SARS-CoV-2/genética , Herpesvirus Humano 4 , Microbiota/genética , Bactérias
15.
Clin Epigenetics ; 13(1): 48, 2021 03 04.
Artigo em Inglês | MEDLINE | ID: mdl-33663610

RESUMO

BACKGROUND: DNA methylation age (mAge), a methylation biomarker for the aging process, might serve as a more accurate predictor of morbidity and aging status than chronological age. We evaluated the role of multiple factors, including fat deposition, cardiometabolic risk factors and lifestyle weight-loss intervention, on the deviation of mAge from chronological age (mAge deviation) or 18-month change in mAge (∆mAge). In this sub-study of the CENTRAL magnetic resonance imaging weight-loss trial, we evaluated mAge by a validated 240-CpG-based prediction formula at baseline and after 18-month intervention of either low fat (LF) or mediterranean/low carbohydrate (MED/LC) diets. RESULTS: Among 120 CENTRAL participants with abdominal obesity or dyslipidemia, mAge (mean ± SD: 60.3 ± 7.5 years) was higher than the chronological age (48.6 ± 9.3 years) but strongly correlated (r = 0.93; p = 3.1 × 10-53). Participants in the lowest tertile of mAge deviation from their chronological age had significantly lower waist-circumference, visceral adipose tissue, intrahepatic fat (IHF) content, fasting-glucose and HOMA-IR, as compared with participants in the highest sex-specific residual tertile (p < 0.05 for all). IHF% remained associated with greater mAge deviation after further adjustments (ß = 0.23; p = 0.02). After 18-month weight-loss lifestyle intervention, mAge remained significantly correlated with chronological age (r = 0.94, p = 1.5 × 10-55). mAging occurred, with no difference between lifestyle intervention groups (∆ = 0.9 ± 1.9 years in MED/LC vs. ∆ = 1.3 ± 1.9 years in LF; p = 0.2); however, we observed a mAging attenuation in successful weight losers (> 5% weight loss) vs. weight-loss failures ( ∆ = 0.6 years vs. ∆ = 1.1 years; p = 0.04), and in participants who completed the trial with healthy liver fat content (< 5% IHF) vs. participants with fatty liver (∆ = 0.6 years vs. ∆ = 1.8 years; p = 0.003). Overall, 18 months of weight-loss lifestyle intervention attenuated the mAging of the men, mainly the older, by 7.1 months than the expected (p < 0.05). CONCLUSIONS: Lifestyle weight-loss intervention may attenuate mAging. Deviation of mAge from chronological age might be related to body fat distribution and glycemic control and could indicate biological age, health status and the risk for premature cardiometabolic diseases. TRIAL REGISTRATION: ClinicalTrials.gov NCT01530724. Registered 10 February 2012, https://clinicaltrials.gov/ct2/show/study/NCT01530724 .


Assuntos
Envelhecimento/genética , Distribuição da Gordura Corporal/estatística & dados numéricos , Imageamento por Ressonância Magnética/métodos , Redução de Peso/genética , Adulto , Idoso , Fatores de Risco Cardiometabólico , Ilhas de CpG , Metilação de DNA , Dieta com Restrição de Carboidratos/métodos , Dieta com Restrição de Gorduras/métodos , Dislipidemias/dietoterapia , Dislipidemias/genética , Epigenômica , Fígado Gorduroso/genética , Feminino , Intolerância à Glucose/genética , Nível de Saúde , Humanos , Estilo de Vida , Masculino , Pessoa de Meia-Idade , Obesidade Abdominal/dietoterapia , Obesidade Abdominal/genética
16.
Nat Immunol ; 22(10): 1219-1230, 2021 10.
Artigo em Inglês | MEDLINE | ID: mdl-34556881

RESUMO

Blind mole rats (BMRs) are small rodents, characterized by an exceptionally long lifespan (>21 years) and resistance to both spontaneous and induced tumorigenesis. Here we report that cancer resistance in the BMR is mediated by retrotransposable elements (RTEs). Cells and tissues of BMRs express very low levels of DNA methyltransferase 1. Following cell hyperplasia, the BMR genome DNA loses methylation, resulting in the activation of RTEs. Upregulated RTEs form cytoplasmic RNA-DNA hybrids, which activate the cGAS-STING pathway to induce cell death. Although this mechanism is enhanced in the BMR, we show that it functions in mice and humans. We propose that RTEs were co-opted to serve as tumor suppressors that monitor cell proliferation and are activated in premalignant cells to trigger cell death via activation of the innate immune response. Activation of RTEs is a double-edged sword, serving as a tumor suppressor but contributing to aging in late life via the induction of sterile inflammation.


Assuntos
Elementos de DNA Transponíveis/imunologia , Imunidade Inata/imunologia , Ratos-Toupeira/imunologia , Neoplasias/imunologia , Animais , Carcinogênese/imunologia , Linhagem Celular Tumoral , Proliferação de Células/fisiologia , Células Cultivadas , DNA/imunologia , Células HeLa , Humanos , Camundongos , Camundongos Endogâmicos C57BL , Camundongos Nus , Ratos , Transdução de Sinais/imunologia
17.
Elife ; 102021 09 13.
Artigo em Inglês | MEDLINE | ID: mdl-34515027

RESUMO

Background: Identifying environmentally responsive genetic loci where DNA methylation is associated with coronary heart disease (CHD) may reveal novel pathways or therapeutic targets for CHD. We conducted the first prospective epigenome-wide analysis of DNA methylation in relation to incident CHD in the Asian population. Methods: We did a nested case-control study comprising incident CHD cases and 1:1 matched controls who were identified from the 10 year follow-up of the China Kadoorie Biobank. Methylation level of baseline blood leukocyte DNA was measured by Infinium Methylation EPIC BeadChip. We performed the single cytosine-phosphate-guanine (CpG) site association analysis and network approach to identify CHD-associated CpG sites and co-methylation gene module. Results: After quality control, 982 participants (mean age 50.1 years) were retained. Methylation level at 25 CpG sites across the genome was associated with incident CHD (genome-wide false discovery rate [FDR] < 0.05 or module-specific FDR < 0.01). One SD increase in methylation level of identified CpGs was associated with differences in CHD risk, ranging from a 47 % decrease to a 118 % increase. Mediation analyses revealed 28.5 % of the excessed CHD risk associated with smoking was mediated by methylation level at the promoter region of ANKS1A gene (P for mediation effect = 0.036). Methylation level at the promoter region of SNX30 was associated with blood pressure and subsequent risk of CHD, with the mediating proportion to be 7.7 % (P = 0.003) via systolic blood pressure and 6.4 % (P = 0.006) via diastolic blood pressure. Network analysis revealed a co-methylation module associated with CHD. Conclusions: We identified novel blood methylation alterations associated with incident CHD in the Asian population and provided evidence of the possible role of epigenetic regulations in the smoking- and blood pressure-related pathways to CHD risk. Funding: This work was supported by National Natural Science Foundation of China (81390544 and 91846303). The CKB baseline survey and the first re-survey were supported by a grant from the Kadoorie Charitable Foundation in Hong Kong. The long-term follow-up is supported by grants from the UK Wellcome Trust (202922/Z/16/Z, 088158/Z/09/Z, 104085/Z/14/Z), grant (2016YFC0900500, 2016YFC0900501, 2016YFC0900504, 2016YFC1303904) from the National Key R&D Program of China, and Chinese Ministry of Science and Technology (2011BAI09B01).


Assuntos
Doença das Coronárias/epidemiologia , Metilação de DNA , Epigenoma , Adulto , Estudos de Casos e Controles , China/epidemiologia , Doença das Coronárias/genética , Feminino , Humanos , Masculino , Pessoa de Meia-Idade , Prevalência , Estudos Prospectivos
18.
J Clin Epidemiol ; 129: 12-20, 2021 01.
Artigo em Inglês | MEDLINE | ID: mdl-32987161

RESUMO

OBJECTIVES: The objective of the study was to evaluate the consistency of risk of bias assessments for overlapping randomized controlled trials (RCTs) included in systematic reviews (SRs) on acupuncture. STUDY DESIGN AND SETTING: Databases were searched for acupuncture SRs. A weighted kappa (κ) statistic was calculated, and logistic regression was used to explore the factors of disagreements. RESULTS: We included 241 RCTs from 109 SRs on acupuncture. The percentage disagreements ranged from 25% to 44%, with moderate agreement for random sequence generation (κ = 0.57), allocation concealment (κ = 0.50), and incomplete outcome data (κ = 0.50), besides fair agreement for blinding of participants and personnel (κ = 0.44), blinding of outcome assessment (κ = 0.31), and selective reporting (κ = 0.39). Only 19% RCTs were evaluated completely consistent. Methodological quality (random sequence generation, odds ratio (OR) = 3.46), international cooperation (allocation concealment, OR = 0.14; incomplete outcome data, OR = 0.14; selective reporting, OR = 0.05), and risk of bias reporting completeness score (selective reporting, OR = 0.53) significantly affected the relative odds of disagreements. CONCLUSION: The level of agreement varied from fair to moderate agreement depending on the risk of bias domain. Methodological quality appears to be an overarching factor to account for disagreements.


Assuntos
Terapia por Acupuntura , Viés , Avaliação de Resultados em Cuidados de Saúde/métodos , Ensaios Clínicos Controlados Aleatórios como Assunto , Revisões Sistemáticas como Assunto/métodos , Bases de Dados Factuais/estatística & dados numéricos , Métodos Epidemiológicos , Humanos , Ensaios Clínicos Controlados Aleatórios como Assunto/normas , Reprodutibilidade dos Testes , Risco
20.
Epigenetics ; 16(12): 1283-1294, 2021 12.
Artigo em Inglês | MEDLINE | ID: mdl-33319642

RESUMO

IgA nephropathy (IgAN) is the most common primary glomerular disease in China and worldwide. The proliferation of B cells is known to be associated with both risk and prognosis of IgAN, but the epigenetic mechanism underlying this association is unknown. In this study we carried out the first Epigenome-wide Association Study (EWAS) by using the latest Infinium Methylation EPIC BeadChip on 184 B cell-specific samples (92 case/control pairs) for Chinese IgAN population. After rigorous data normalization and residual batch effect correction, linear mixed effect model was used to detect methylation CpG sites associated with IgAN adjusting for age, gender and smoking. False discovery rate (FDR) less than 10% was used to account for multiple testing. Weighted gene co-methylation networks were generated to identify gene modules highly correlated with IgAN. A permutation test was performed to account for the potential effect of overfitting. After adjusting clinical covariates and potential technical batch effects, three CpGs corresponding to PCDH17, TERT, WDR82 genes and three in the intergenic regions passed the genome-wide significant threshold. Methylation network analysis identified an additional IgAN associated gene module, containing 72 significant CpGs including GALNT6, IQSEC1, CDC16 and SYS1, involved in the pathway related to tubular atrophy/interstitial fibrosis of IgAN. These results suggested important DNA methylation and gene targets in CD19+ B cells for the pathogenesis of IgAN.


Assuntos
Epigenoma , Glomerulonefrite por IGA , Estudos de Casos e Controles , Metilação de DNA , Epigênese Genética , Estudo de Associação Genômica Ampla , Glomerulonefrite por IGA/genética , Humanos
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