Edible plant derived exosome-like nanoparticles(ELNs)have been shown to have multiple nutraceutical functions.However,the diversity of plant materials makes the plant derived ELN study challenging.More efforts are sti...Edible plant derived exosome-like nanoparticles(ELNs)have been shown to have multiple nutraceutical functions.However,the diversity of plant materials makes the plant derived ELN study challenging.More efforts are still needed to explore the feasible isolation methods of edible plant derived ELNs and the possible roles of food-derived ELNs in improving human health.In this study,a size exclusion chromatography based method was compared with the traditional ultracentrifugation method to isolate blueberry derived ELNs(B-ELNs),and the miRNA profile of B-ELNs was analyzed by high-throughput sequencing.A total of 36 miRNAs were found to be enriched in B-ELNs compared with berry tissue,and their potential cross-kingdom human gene targets were further predicted.Results showed that size exclusion chromatography was effective for B-ELN isolation.The most abundant miRNAs in B-ELNs mainly belonged to the miR166 family and miR396 family.Target gene prediction indicated that B-ELNs could potentially regulate pathways related to the human digestive system,immune system and infectious diseases.展开更多
The spikelet number per spike(SNS)contributes greatly to grain yield in wheat.Identifying various genes that control wheat SNS is vital for yield improvement.This study used a recombinant inbred line population genoty...The spikelet number per spike(SNS)contributes greatly to grain yield in wheat.Identifying various genes that control wheat SNS is vital for yield improvement.This study used a recombinant inbred line population genotyped by the Wheat55K single-nucleotide polymorphism array to identify two major and stably expressed quantitative trait loci(QTLs)for SNS.One of them(QSns.sau-2SY-2D.1)was reported previously,while the other(QSns.sau-2SY-7A)was newly detected and further analyzed in this study.QSns.sau-2SY-7A had a high LOD value ranging from 4.46 to 16.00 and explained 10.21-40.78%of the phenotypic variances.QSns.sau-2SY-7A was flanked by the markers AX-110518554 and AX-110094527 in a 4.75-cM interval on chromosome arm 7AL.The contributions and interactions of both major QTLs were further analyzed and discussed.The effect of QSns.sau-2SY-7A was successfully validated by developing a tightly linked kompetitive allele specific PCR marker in an F_(2:3) population and a panel of 101 high-generation breeding wheat lines.Furthermore,several genes including the previously reported WHEAT ORTHOLOG OF APO1(WAPO1),an ortholog of the rice gene ABERRANT PANICLE ORGANIZATION 1(APO1)related to SNS,were predicted in the interval of QSns.sau-2SY-7A.In summary,these results revealed the genetic basis of the multi-spikelet genotype of wheat line 20828 and will facilitate subsequent fine mapping and breeding utilization of the major QTLs.展开更多
Objective The aim of the study was to summarize the diagnostic value of miR-21 as a biomarker in oral squamous cell carcinoma(OSCC)using a review of the literature and data from the cancer genome atlas(TCGA)database.M...Objective The aim of the study was to summarize the diagnostic value of miR-21 as a biomarker in oral squamous cell carcinoma(OSCC)using a review of the literature and data from the cancer genome atlas(TCGA)database.Methods Data from TCGA database was sorted and analyzed by bioinformatics to determine the expression level of miR-21 in OSCC.Further,we searched for relevant articles in Embase,PubMed/Medline,Scopus,and Web of Science published before March 2021,extracted the data,and conducted quality assessment.The bivariate meta-analysis model with Stata 16.0 was used to analyze the diagnostic value of miR-21 for OSCC.Results A total of 304 related articles were identified,and seven were selected for meta-analysis.The diagnostic results after analysis were as follows:sensitivity 0.76[95%confidence interval(CI),0.57-0.88];specificity 0.77(95%CI,0.58-0.89);positive likelihood ratio 3.34(95%CI,1.58-7.08);negative likelihood ratio 0.31(95%CI,0.15-0.63);diagnostic odds ratio 10.75(95%CI,2.85-40.51);and area under the curve 0.83(95%CI,0.80-0.86).The Deeks’funnel chart showed that there was no potential bias(P=0.54).Prediction analysis of the potential target genes of miR-21 was performed via the biological website,and DAVID was used to cross target genes for gene ontology(GO)annotation function analysis.Conclusion The results showed that miR-21-3p and miR-21-5p were significantly more highly expressed in OSCC tissues than in normal tissues(P<0.05),and the results of the meta-analysis indicated that they could be used as potential biomarkers in the diagnosis of OSCC.In addition,58 potential target genes of miR-21 were significantly enriched in 28 GO annotation functional pathways,which provided a biological basis for further clinical diagnostic value research.展开更多
Background:DNA methylation and gene expression are known to play important roles in the etiology of human diseases such as prostate cancer(PCa).However,it has not yet been possible to incorporate information of DNA me...Background:DNA methylation and gene expression are known to play important roles in the etiology of human diseases such as prostate cancer(PCa).However,it has not yet been possible to incorporate information of DNA methylation and gene expression into polygenic risk scores(PRSs).Here,we aimed to develop and validate an improved PRS for PCa risk by incorporating genetically predicted gene expression and DNA methylation,and other genomic information using an integrative method.Methods:Using data from the PRACTICAL consortium,we derived multiple sets of genetic scores,including those based on available single-nucleotide polymorphisms through widely used methods of pruning and thresholding,LDpred,LDpred-funt,AnnoPred,and EBPRS,as well as PRS constructed using the genetically predicted gene expression and DNA methylation through a revised pruning and thresholding strategy.In the tuning step,using the UK Biobank data(1458 prevalent cases and 1467 controls),we selected PRSs with the best performance.Using an independent set of data from the UK Biobank,we developed an integrative PRS combining information from individual scores.Furthermore,in the testing step,we tested the performance of the integrative PRS in another independent set of UK Biobank data of incident cases and controls.Results:Our constructed PRS had improved performance(C statistics:76.1%)over PRSs constructed by individual benchmark methods(from 69.6%to 74.7%).Furthermore,our new PRS had much higher risk assessment power than family history.The overall net reclassification improvement was 69.0%by adding PRS to the baseline model compared with 12.5%by adding family history.Conclusions:We developed and validated a new PRS which may improve the utility in predicting the risk of developing PCa.Our innovative method can also be applied to other human diseases to improve risk prediction across multiple outcomes.展开更多
基金supported by the National Natural Science Foundation of China(31701561)。
文摘Edible plant derived exosome-like nanoparticles(ELNs)have been shown to have multiple nutraceutical functions.However,the diversity of plant materials makes the plant derived ELN study challenging.More efforts are still needed to explore the feasible isolation methods of edible plant derived ELNs and the possible roles of food-derived ELNs in improving human health.In this study,a size exclusion chromatography based method was compared with the traditional ultracentrifugation method to isolate blueberry derived ELNs(B-ELNs),and the miRNA profile of B-ELNs was analyzed by high-throughput sequencing.A total of 36 miRNAs were found to be enriched in B-ELNs compared with berry tissue,and their potential cross-kingdom human gene targets were further predicted.Results showed that size exclusion chromatography was effective for B-ELN isolation.The most abundant miRNAs in B-ELNs mainly belonged to the miR166 family and miR396 family.Target gene prediction indicated that B-ELNs could potentially regulate pathways related to the human digestive system,immune system and infectious diseases.
基金supported by the projects from the Applied Basic Research Programs of Science and Technology Department of Sichuan Province, China (2020YJ0140 and 2021YJ0503)the International Science and Technology Cooperation and Exchanges Program of Science and Technology Department of Sichuan Province, China (2021YFH0083 and 2022YFH0053)+1 种基金the National Natural Science Foundation of China (31971937 and 31970243)the Key Projects of Scientific and Technological Activities for Overseas Students of Sichuan Province, China
文摘The spikelet number per spike(SNS)contributes greatly to grain yield in wheat.Identifying various genes that control wheat SNS is vital for yield improvement.This study used a recombinant inbred line population genotyped by the Wheat55K single-nucleotide polymorphism array to identify two major and stably expressed quantitative trait loci(QTLs)for SNS.One of them(QSns.sau-2SY-2D.1)was reported previously,while the other(QSns.sau-2SY-7A)was newly detected and further analyzed in this study.QSns.sau-2SY-7A had a high LOD value ranging from 4.46 to 16.00 and explained 10.21-40.78%of the phenotypic variances.QSns.sau-2SY-7A was flanked by the markers AX-110518554 and AX-110094527 in a 4.75-cM interval on chromosome arm 7AL.The contributions and interactions of both major QTLs were further analyzed and discussed.The effect of QSns.sau-2SY-7A was successfully validated by developing a tightly linked kompetitive allele specific PCR marker in an F_(2:3) population and a panel of 101 high-generation breeding wheat lines.Furthermore,several genes including the previously reported WHEAT ORTHOLOG OF APO1(WAPO1),an ortholog of the rice gene ABERRANT PANICLE ORGANIZATION 1(APO1)related to SNS,were predicted in the interval of QSns.sau-2SY-7A.In summary,these results revealed the genetic basis of the multi-spikelet genotype of wheat line 20828 and will facilitate subsequent fine mapping and breeding utilization of the major QTLs.
基金Supported by a grant from the National Natural Science Foundation of China(No.81402298).
文摘Objective The aim of the study was to summarize the diagnostic value of miR-21 as a biomarker in oral squamous cell carcinoma(OSCC)using a review of the literature and data from the cancer genome atlas(TCGA)database.Methods Data from TCGA database was sorted and analyzed by bioinformatics to determine the expression level of miR-21 in OSCC.Further,we searched for relevant articles in Embase,PubMed/Medline,Scopus,and Web of Science published before March 2021,extracted the data,and conducted quality assessment.The bivariate meta-analysis model with Stata 16.0 was used to analyze the diagnostic value of miR-21 for OSCC.Results A total of 304 related articles were identified,and seven were selected for meta-analysis.The diagnostic results after analysis were as follows:sensitivity 0.76[95%confidence interval(CI),0.57-0.88];specificity 0.77(95%CI,0.58-0.89);positive likelihood ratio 3.34(95%CI,1.58-7.08);negative likelihood ratio 0.31(95%CI,0.15-0.63);diagnostic odds ratio 10.75(95%CI,2.85-40.51);and area under the curve 0.83(95%CI,0.80-0.86).The Deeks’funnel chart showed that there was no potential bias(P=0.54).Prediction analysis of the potential target genes of miR-21 was performed via the biological website,and DAVID was used to cross target genes for gene ontology(GO)annotation function analysis.Conclusion The results showed that miR-21-3p and miR-21-5p were significantly more highly expressed in OSCC tissues than in normal tissues(P<0.05),and the results of the meta-analysis indicated that they could be used as potential biomarkers in the diagnosis of OSCC.In addition,58 potential target genes of miR-21 were significantly enriched in 28 GO annotation functional pathways,which provided a biological basis for further clinical diagnostic value research.
基金NIH,Grant/Award Number:R03 AG070669Canadian Institutes of Health Research,European Commission’s Seventh Framework Programme grant agreement,Grant/Award Number:HEALTH-F2-2009-223175+11 种基金Cancer Research UK,Grant/Award Numbers:C5047/A7357,C1287/A10118,C1287/A16563,C5047/A3354,C5047/A10692,C16913/A6135The National Institute of Health(NIH)Cancer Post-Cancer GWAS,Grant/Award Number:1 U19 CA 148537-01The National Health and Medical Research Council,Australia,Grant/Award Numbers:126402,209057,251533,396414,450104,504700,504702,504715,623204,940394,614296US National Institutes of Health(NIH),Grant/Award Number:U19 CA 148537Prostate cancer SuscEptibility(ELLIPSE),Grant/Award Number:X01HG007492Center for Inherited Disease Research(CIDR),Grant/Award Number:HHSN268201200008INIH NCI,Grant/Award Number:U01 CA188392European Community’s Seventh Framework Programme,Grant/Award Number:223175Post-Cancer GWAS initiative,Grant/Award Numbers:1U19 CA148537,1U19 CA148065,1U19 CA148112U.S.National Institutes of Health,National Cancer Institute,Grant/Award Numbers:U01-CA98233,U01-CA98710,U01-CA98216,U01-CA98758Swedish Cancer Foundation,Grant/Award Numbers:09-0677,11-484,12-823Swedish Research Council,Swedish Research Council,Grant/Award Numbers:K2010-70X-20430-04-3,2014-2269。
文摘Background:DNA methylation and gene expression are known to play important roles in the etiology of human diseases such as prostate cancer(PCa).However,it has not yet been possible to incorporate information of DNA methylation and gene expression into polygenic risk scores(PRSs).Here,we aimed to develop and validate an improved PRS for PCa risk by incorporating genetically predicted gene expression and DNA methylation,and other genomic information using an integrative method.Methods:Using data from the PRACTICAL consortium,we derived multiple sets of genetic scores,including those based on available single-nucleotide polymorphisms through widely used methods of pruning and thresholding,LDpred,LDpred-funt,AnnoPred,and EBPRS,as well as PRS constructed using the genetically predicted gene expression and DNA methylation through a revised pruning and thresholding strategy.In the tuning step,using the UK Biobank data(1458 prevalent cases and 1467 controls),we selected PRSs with the best performance.Using an independent set of data from the UK Biobank,we developed an integrative PRS combining information from individual scores.Furthermore,in the testing step,we tested the performance of the integrative PRS in another independent set of UK Biobank data of incident cases and controls.Results:Our constructed PRS had improved performance(C statistics:76.1%)over PRSs constructed by individual benchmark methods(from 69.6%to 74.7%).Furthermore,our new PRS had much higher risk assessment power than family history.The overall net reclassification improvement was 69.0%by adding PRS to the baseline model compared with 12.5%by adding family history.Conclusions:We developed and validated a new PRS which may improve the utility in predicting the risk of developing PCa.Our innovative method can also be applied to other human diseases to improve risk prediction across multiple outcomes.