Objective： This study aimed to comprehensively assess Epstein-Barr virus（EBV）-induced methylation alterations of B cell across whole genome.Methods： We compared DNA methylation patterns of primary B cells and corr...Objective： This study aimed to comprehensively assess Epstein-Barr virus（EBV）-induced methylation alterations of B cell across whole genome.Methods： We compared DNA methylation patterns of primary B cells and corresponding lymphoblastoid cell lines（LCLs） from eight participants. The genome-wide DNA methylation profiles were compared at over 850,000 genome-wide methylation sites.Results： DNA methylation analysis revealed 87,732 differentially methylated Cp G sites, representing approximately 12.41% of all sites in LCLs compared to primary B cells. The hypermethylated and hypomethylated Cp G sites were about 22.75% or 77.25%, respectively. Only 0.8% of hypomethylated sites and 4.5% of hypermethylated sites were located in Cp G islands, whereas 8.0% of hypomethylated sites and 16.3% of hypermethylated sites were located in shore（N_shore and S_shore）. Using principal component analysis of the DNA methylation profiles, primary B cells and LCLs could be accurately predicted. Gene Ontology（GO） and Kyoto Encyclopedia of Genes and Genomes（KEGG） analysis of differently methylated genes revealed that most of the top GO biological processes were related to cell activation and immune response, and some top enrichment pathways were related with activation and malignant transformation of human B cells.Conclusions： Our study demonstrated genome-wide DNA methylation variations between primary B cells and corresponding LCLs, which might yield new insight on the methylation mechanism of EBV-induced immortalization.展开更多
Background:Blood-based cell-free DNA(cfDNA)methylation testing has emerged as a promising approach for multi-cancer early detection(MCED),holding the potential to improve cancer survival rates.However,traditional bisu...Background:Blood-based cell-free DNA(cfDNA)methylation testing has emerged as a promising approach for multi-cancer early detection(MCED),holding the potential to improve cancer survival rates.However,traditional bisulfite-based methods often encounter sensitivity limitations in detecting early-stage malignancies or certain cancer types.In the INSPECTOR study,we developed a MCED and cancer signal origin(CSO)system specifically designed for early-stage or hard-to-detect cancers,including those of the lung,breast,colorectum,liver,esophagus,stomach,pancreas,and ovary.Methods:We established a comprehensive methylation marker discovery database(n=6,342)by integrating public datasets(n=4,699)and in-house samples(n=1,643),all processed using human TET(hTET)enzyme-assisted whole-methylome sequencing(GM-seq).This enabled the design of a targeted panel encompassing 155,362 methylated CpG sites.Leveraging hTET-assisted high-depth next-generation sequencing(NGS),our blood test achieved amedian unique depth of 1,093×.Multicenter case-control cohorts,including various pathological subtypes,were used for training,validation,and independent validation of MCED and CSO models,and to verify the clinical feasibility.Results:Clinical validation was conducted across multi-center case-control cohorts,including 1,071 participants in the training set,581 in the validation set,and 824 in the independent validation set.TheMCEDassay demonstrated robust performancewith a specificity of 99.1%and sensitivity of 83.2%in the training set,99.0%and 81.8%in the validation set,and comparable results in the independent validation set(99.0%specificity,81.9%sensitivity).Notably,sensitivity reached 65.5%for stage I cancers,79.7%for stage II,and 71.3%for stages I-II combined.The sensitivities for different cancer types were as follows:esophageal(79.2%),gastric(76.1%),colorectal(86.2%),pancreatic(66.7%),liver(100.0%),lung(72.9%),breast(88.9%),and ovarian(87.9%).The CSO model exhibited strong accuracy,with top-1 cancer origin prediction rates of 87.9%(validation)and 87.4%(independent validation),rising to 95.1%and 94.5%for top-2 predictions,respectively.For stage I cancers specifically,the top-1 accuracy was 85.5%.Conclusions:These findings underscore the efficacy of the hTET-assisted cfDNA methylation sequencing system across diverse cancer types,particularly in early stages.Enzyme-assisted NGS test of methylated cfDNA thus enhances the clinical utility of non-invasive blood-based screening.展开更多
Recently an article published in Molecular Cell reveals the mechanism of a nuclear N6-methyladenosine（m^6A）reader,the YTH domain-containing protein 1（YTHDC1）,in regulating pre-m RNA splicing[1].Meanwhile,two addit...Recently an article published in Molecular Cell reveals the mechanism of a nuclear N6-methyladenosine（m^6A）reader,the YTH domain-containing protein 1（YTHDC1）,in regulating pre-m RNA splicing[1].Meanwhile,two additional articles published in Nature and Nature Chemical Biology report the展开更多
基金supported by grants from National Natural Science Foundation of China (No. 81160249, 81301886 and 81760525)Science Foundation of Peking University Cancer Hospital (No. 2017 Zizhu-1)+4 种基金Open Project funded by Key Laboratory of Carcinogenesis and Translational ResearchMinistry of Education/Beijing (2017 Open Project-3)Beijing Municipal Science & Technology Commission (No. Z171100001017136)Beijing Natural Science Foundation (No. 7171001)West China First-Class Discipline Construction Project in Basic Medicine funded by Ningxia Medical University
文摘Objective： This study aimed to comprehensively assess Epstein-Barr virus（EBV）-induced methylation alterations of B cell across whole genome.Methods： We compared DNA methylation patterns of primary B cells and corresponding lymphoblastoid cell lines（LCLs） from eight participants. The genome-wide DNA methylation profiles were compared at over 850,000 genome-wide methylation sites.Results： DNA methylation analysis revealed 87,732 differentially methylated Cp G sites, representing approximately 12.41% of all sites in LCLs compared to primary B cells. The hypermethylated and hypomethylated Cp G sites were about 22.75% or 77.25%, respectively. Only 0.8% of hypomethylated sites and 4.5% of hypermethylated sites were located in Cp G islands, whereas 8.0% of hypomethylated sites and 16.3% of hypermethylated sites were located in shore（N_shore and S_shore）. Using principal component analysis of the DNA methylation profiles, primary B cells and LCLs could be accurately predicted. Gene Ontology（GO） and Kyoto Encyclopedia of Genes and Genomes（KEGG） analysis of differently methylated genes revealed that most of the top GO biological processes were related to cell activation and immune response, and some top enrichment pathways were related with activation and malignant transformation of human B cells.Conclusions： Our study demonstrated genome-wide DNA methylation variations between primary B cells and corresponding LCLs, which might yield new insight on the methylation mechanism of EBV-induced immortalization.
基金the Ethics Committee of the Cancer Prevention Center,Sun Yat-sen University(SL-B2023-717-01)Chinese PLA General Hospital(S2021-427-01)+2 种基金The Sixth Affiliated Hospital of Sun Yat-sen University(2024ZSLYEC-361)Gansu Provincial Cancer Hospital(IRB-PJ-2024-043)Shenzhen Bao’an District Songgang People’s Hospital(PY202408020003).
文摘Background:Blood-based cell-free DNA(cfDNA)methylation testing has emerged as a promising approach for multi-cancer early detection(MCED),holding the potential to improve cancer survival rates.However,traditional bisulfite-based methods often encounter sensitivity limitations in detecting early-stage malignancies or certain cancer types.In the INSPECTOR study,we developed a MCED and cancer signal origin(CSO)system specifically designed for early-stage or hard-to-detect cancers,including those of the lung,breast,colorectum,liver,esophagus,stomach,pancreas,and ovary.Methods:We established a comprehensive methylation marker discovery database(n=6,342)by integrating public datasets(n=4,699)and in-house samples(n=1,643),all processed using human TET(hTET)enzyme-assisted whole-methylome sequencing(GM-seq).This enabled the design of a targeted panel encompassing 155,362 methylated CpG sites.Leveraging hTET-assisted high-depth next-generation sequencing(NGS),our blood test achieved amedian unique depth of 1,093×.Multicenter case-control cohorts,including various pathological subtypes,were used for training,validation,and independent validation of MCED and CSO models,and to verify the clinical feasibility.Results:Clinical validation was conducted across multi-center case-control cohorts,including 1,071 participants in the training set,581 in the validation set,and 824 in the independent validation set.TheMCEDassay demonstrated robust performancewith a specificity of 99.1%and sensitivity of 83.2%in the training set,99.0%and 81.8%in the validation set,and comparable results in the independent validation set(99.0%specificity,81.9%sensitivity).Notably,sensitivity reached 65.5%for stage I cancers,79.7%for stage II,and 71.3%for stages I-II combined.The sensitivities for different cancer types were as follows:esophageal(79.2%),gastric(76.1%),colorectal(86.2%),pancreatic(66.7%),liver(100.0%),lung(72.9%),breast(88.9%),and ovarian(87.9%).The CSO model exhibited strong accuracy,with top-1 cancer origin prediction rates of 87.9%(validation)and 87.4%(independent validation),rising to 95.1%and 94.5%for top-2 predictions,respectively.For stage I cancers specifically,the top-1 accuracy was 85.5%.Conclusions:These findings underscore the efficacy of the hTET-assisted cfDNA methylation sequencing system across diverse cancer types,particularly in early stages.Enzyme-assisted NGS test of methylated cfDNA thus enhances the clinical utility of non-invasive blood-based screening.
基金supported by the National Basic Research Program of China (973 ProgramGrant No.2014CB964900)the National Natural Science Foundation of China (Grant Nos.21432002,21372022,and 21210003)
文摘Recently an article published in Molecular Cell reveals the mechanism of a nuclear N6-methyladenosine（m^6A）reader,the YTH domain-containing protein 1（YTHDC1）,in regulating pre-m RNA splicing[1].Meanwhile,two additional articles published in Nature and Nature Chemical Biology report the
