In accordance with previous reports, the sequences related to phosporylated protein segments occur in conserved variable domains of immunoglobulins including first of all certain N-terminally located segments. Consequ...In accordance with previous reports, the sequences related to phosporylated protein segments occur in conserved variable domains of immunoglobulins including first of all certain N-terminally located segments. Consequently, we look here for the sequences 1) composing human and mouse proteins different from antigen receptors, 2) identical with or highly similar to nucleotide sequence representatives of conserved variable immunoglobulin segments and 3) identical with or closely related to phosphorylation sites. More precisely, we searched for the corresponding actual pairs of DNA and protein sequence segments using five-step bilingual approach employing among others a) different types of BLAST searches, b) two in-principle-different machine-learning methods predicting phosphorylated sites and c) two large databases recording existing phosphorylation sites. The approach identified seven existing phosphorylation sites and thirty-seven related human and mouse segments achieving limits for several predictions or phylogenic parameters. Mostly serines phosporylated with ataxia-telangiectasia-related kinase (involved in regulation of DNA-double-strand-break repair) were indicated or predicted in this study. Hypermutation motifs, located in effective positions of the selected sequence segments, occurred significantly less frequently in transcribed than non-transcribed DNA strands suggesting thus the incidence of mutation events. In addition, marked differences between the numbers and proportions of human and mouse cancer-related sequence items were found in different steps of selection process. The possible role of hypermutation changes within the selected segments and the observed structural relationships are discussed here with respect to DNA damage, carcinogenesis, cancer vaccination, ageing and evolution. Taken together, our data represent additional and sometimes perhaps complementary information to the existing databases of empirically proven phosphorylation sites or pathogenically important spots.展开更多
Sequence similarities were found between protein and DNA sequences encoding certain part of conserved variable immunoglobulin domains (i.e. conserved IgV) and phosphorylation sites. Hypermutation motifs were then indi...Sequence similarities were found between protein and DNA sequences encoding certain part of conserved variable immunoglobulin domains (i.e. conserved IgV) and phosphorylation sites. Hypermutation motifs were then indicated in the majority of the corresponding non-IgV nucleotide sequences. According to database confirmations or double prediction of phosphorylation sites, 80% of the selected human and mouse IgV-related phosphorylation sites or their highly probable candidates exhibited substrate relationship to ataxia-telangiectasia-mutated kinase known as ATM. In accordance with literature data, inactivation of ATM by mutations can participate in the mechanisms of carcinogenesis, neurodegeneration and possibly also in aging. In agreement with this relationship, some of the selected IgV-/ATM-related segments formed molecules specifically involved in carcinogenesis. The selected IgV-related sequence segments were also similar to certain segments of higher plants containing immunoglobulin-like repeats and related regions. Bioinformatic analysis of some selected plant sequences then indicated the presence of catalytic domains composing serine/threonine/tyrosine receptor/receptor-like kinases, which are considered important structures for evolution of very early and part of later Ig-domain-related immunity. The analyzed conserved domain similarities also suggested certain interesting structural and phylogenic relationships, which need to be further investigated. This review in fact briefly summarizes the findings on the subject from the last twenty years.展开更多
目的观察健脾解毒方对脾虚肝癌大鼠模型的抗癌作用与T细胞受体β链超变区第3互补决定区(the third complementary-determining region of the variable region of T cell receptorβ-chain,TCRVβCDR3)基因谱系的关系。方法将大鼠按随...目的观察健脾解毒方对脾虚肝癌大鼠模型的抗癌作用与T细胞受体β链超变区第3互补决定区(the third complementary-determining region of the variable region of T cell receptorβ-chain,TCRVβCDR3)基因谱系的关系。方法将大鼠按随机数字法分为空白对照组(正常组,灌胃生理盐水,每日1次),脾虚模型组(脾虚组),肝癌模型组(肝癌组),脾虚肝癌模型组(脾虚肝癌组),健脾解毒方(中药)高、中、低剂量(75.00、37.50、18.75 g/kg灌胃,每日1次)组和胸腺五肽(5 mg/kg,肌肉注射,每周2次)组(西药组),每组8只。采用苦寒泻下法制备脾虚模型,原位移植法制备肝癌模型。基因扫描检测大鼠胸腺、肝、肝癌20个TCRVβCDR3亚家族基因片段谱系。结果中药中、高剂量健脾解毒方可延缓肝癌的体积增长(P<0.05),且其肝指数和胸腺指数与正常组相当(P>0.05)。正常胸腺组织和肝组织TCRVβCDR3亚家族数量(20、19)、基因片段数量(220、113)、谱系准高斯分布比例(100%、42.1%)、片段荧光峰面积(6 539±2 325、1 238±439)在各组中均处于最高水平。中药中、高剂量组胸腺和肝组织TCRVβCDR3表达接近正常组,西药组、脾虚组和肝癌组居中,脾虚肝癌组最差。西药组肝癌组织TCRVβCDR3表达最佳。结论健脾解毒方对肝癌细胞增殖的抑制作用可能与其增强TCRVβCDR3基因谱系表达有关。展开更多
Background Clinical studies suggest that the dysfunction of T cells and B cells may play an essential role in the pathogenesis of idiopathic nephrotic syndrome(INS),but laboratory evidence is lacking.Therefore,this st...Background Clinical studies suggest that the dysfunction of T cells and B cells may play an essential role in the pathogenesis of idiopathic nephrotic syndrome(INS),but laboratory evidence is lacking.Therefore,this study explored T-cell receptor(TCR)and B-cell receptor(BCR)profiling in children with idiopathic nephrotic syndrome.Methods High-throughput sequencing technology was used to profile the TCR and BCR repertoires in children with INS.Peripheral blood was collected from ten INS patients,including five vinculin autoantibody-positive patients and five vin-culin autoantibody-negative patients,before and after treatment.TCR and BCR libraries were constructed by 5'-RACE and sequenced by a DNBSEQ-T7 sequencer,and sequence analyses were performed using ReSeqTools,FastP,MiXCR,and VDJtools.Results The TRA(T-cell receptorα),TRG(T-cell receptor y),and IGH(immunoglobulin heavy chain)repertoires of the INS group were occupied by highly abundant clonotypes,whereas small clonotypes occupied the healthy group,especially TRA.A significant increase in the Shannon-Weaver index was observed for the TRA and TRG repertoires after treatment in vinculin autoantibody-negative patients,but a significant increase in the IGH repertoire after treatment was observed in vinculin autoantibody-positive patients.The frequency of some V-J pairs was significantly enriched in steroid-sensitive nephrotic syndrome patients.The usage frequency of the V and J genes was skewed in patients,which seemed not related to immunosuppressive therapy.However,after effective treatment,dynamic changes in the size of the individual clonotype were observed.Conclusion T-cell and B-cell immunity contribute to the pathogenesis of different INSs.展开更多
文摘In accordance with previous reports, the sequences related to phosporylated protein segments occur in conserved variable domains of immunoglobulins including first of all certain N-terminally located segments. Consequently, we look here for the sequences 1) composing human and mouse proteins different from antigen receptors, 2) identical with or highly similar to nucleotide sequence representatives of conserved variable immunoglobulin segments and 3) identical with or closely related to phosphorylation sites. More precisely, we searched for the corresponding actual pairs of DNA and protein sequence segments using five-step bilingual approach employing among others a) different types of BLAST searches, b) two in-principle-different machine-learning methods predicting phosphorylated sites and c) two large databases recording existing phosphorylation sites. The approach identified seven existing phosphorylation sites and thirty-seven related human and mouse segments achieving limits for several predictions or phylogenic parameters. Mostly serines phosporylated with ataxia-telangiectasia-related kinase (involved in regulation of DNA-double-strand-break repair) were indicated or predicted in this study. Hypermutation motifs, located in effective positions of the selected sequence segments, occurred significantly less frequently in transcribed than non-transcribed DNA strands suggesting thus the incidence of mutation events. In addition, marked differences between the numbers and proportions of human and mouse cancer-related sequence items were found in different steps of selection process. The possible role of hypermutation changes within the selected segments and the observed structural relationships are discussed here with respect to DNA damage, carcinogenesis, cancer vaccination, ageing and evolution. Taken together, our data represent additional and sometimes perhaps complementary information to the existing databases of empirically proven phosphorylation sites or pathogenically important spots.
文摘Sequence similarities were found between protein and DNA sequences encoding certain part of conserved variable immunoglobulin domains (i.e. conserved IgV) and phosphorylation sites. Hypermutation motifs were then indicated in the majority of the corresponding non-IgV nucleotide sequences. According to database confirmations or double prediction of phosphorylation sites, 80% of the selected human and mouse IgV-related phosphorylation sites or their highly probable candidates exhibited substrate relationship to ataxia-telangiectasia-mutated kinase known as ATM. In accordance with literature data, inactivation of ATM by mutations can participate in the mechanisms of carcinogenesis, neurodegeneration and possibly also in aging. In agreement with this relationship, some of the selected IgV-/ATM-related segments formed molecules specifically involved in carcinogenesis. The selected IgV-related sequence segments were also similar to certain segments of higher plants containing immunoglobulin-like repeats and related regions. Bioinformatic analysis of some selected plant sequences then indicated the presence of catalytic domains composing serine/threonine/tyrosine receptor/receptor-like kinases, which are considered important structures for evolution of very early and part of later Ig-domain-related immunity. The analyzed conserved domain similarities also suggested certain interesting structural and phylogenic relationships, which need to be further investigated. This review in fact briefly summarizes the findings on the subject from the last twenty years.
文摘目的观察健脾解毒方对脾虚肝癌大鼠模型的抗癌作用与T细胞受体β链超变区第3互补决定区(the third complementary-determining region of the variable region of T cell receptorβ-chain,TCRVβCDR3)基因谱系的关系。方法将大鼠按随机数字法分为空白对照组(正常组,灌胃生理盐水,每日1次),脾虚模型组(脾虚组),肝癌模型组(肝癌组),脾虚肝癌模型组(脾虚肝癌组),健脾解毒方(中药)高、中、低剂量(75.00、37.50、18.75 g/kg灌胃,每日1次)组和胸腺五肽(5 mg/kg,肌肉注射,每周2次)组(西药组),每组8只。采用苦寒泻下法制备脾虚模型,原位移植法制备肝癌模型。基因扫描检测大鼠胸腺、肝、肝癌20个TCRVβCDR3亚家族基因片段谱系。结果中药中、高剂量健脾解毒方可延缓肝癌的体积增长(P<0.05),且其肝指数和胸腺指数与正常组相当(P>0.05)。正常胸腺组织和肝组织TCRVβCDR3亚家族数量(20、19)、基因片段数量(220、113)、谱系准高斯分布比例(100%、42.1%)、片段荧光峰面积(6 539±2 325、1 238±439)在各组中均处于最高水平。中药中、高剂量组胸腺和肝组织TCRVβCDR3表达接近正常组,西药组、脾虚组和肝癌组居中,脾虚肝癌组最差。西药组肝癌组织TCRVβCDR3表达最佳。结论健脾解毒方对肝癌细胞增殖的抑制作用可能与其增强TCRVβCDR3基因谱系表达有关。
基金supported by the Natural Science Foundation of Zhejiang Province(LY22H050001)the National Natural Science Foundation of China(82270741,U20A20351)+1 种基金the Key Project of Provincial Ministry Coconstruction,Health Science,and Technology Project Plan of Zhejiang Province(WKJ-ZJ-2128)Yiluqihang Shenmingyuanyang Medical Development and Scientific Research Fund Project on Kidney Diseases(SMYY20220301001).
文摘Background Clinical studies suggest that the dysfunction of T cells and B cells may play an essential role in the pathogenesis of idiopathic nephrotic syndrome(INS),but laboratory evidence is lacking.Therefore,this study explored T-cell receptor(TCR)and B-cell receptor(BCR)profiling in children with idiopathic nephrotic syndrome.Methods High-throughput sequencing technology was used to profile the TCR and BCR repertoires in children with INS.Peripheral blood was collected from ten INS patients,including five vinculin autoantibody-positive patients and five vin-culin autoantibody-negative patients,before and after treatment.TCR and BCR libraries were constructed by 5'-RACE and sequenced by a DNBSEQ-T7 sequencer,and sequence analyses were performed using ReSeqTools,FastP,MiXCR,and VDJtools.Results The TRA(T-cell receptorα),TRG(T-cell receptor y),and IGH(immunoglobulin heavy chain)repertoires of the INS group were occupied by highly abundant clonotypes,whereas small clonotypes occupied the healthy group,especially TRA.A significant increase in the Shannon-Weaver index was observed for the TRA and TRG repertoires after treatment in vinculin autoantibody-negative patients,but a significant increase in the IGH repertoire after treatment was observed in vinculin autoantibody-positive patients.The frequency of some V-J pairs was significantly enriched in steroid-sensitive nephrotic syndrome patients.The usage frequency of the V and J genes was skewed in patients,which seemed not related to immunosuppressive therapy.However,after effective treatment,dynamic changes in the size of the individual clonotype were observed.Conclusion T-cell and B-cell immunity contribute to the pathogenesis of different INSs.
