TCR Dβ-Jβ sjTRECs检测方法的建立和应用

目的：建立检测TCR Dβ-Jβ sjTRECs的方法，并了解不同T细胞受体Dβ-Jβ之间T细胞受体删除DNA环(sjTRECs)在胸腺细胞和外周血T细胞中的形成情况。方法：利用巢式PCR分别扩增10例正常人外周血单个核细胞和3例正常胸腺细胞DNA中不同的Dβ片段和Jβ重排时形成的sjTRECs的情况，PCR产物进一步进行克隆和序列分析以确定结合区的位置。结果：可检测到Dβ1与5个Jβ1基因片段、Dβ2与4个Jβ2基因片段分别形成的sjTRECs，其中以Dβ1-Jβ1S1、Dβ1-Jβ1S2和Dβ2-Jβ2S2sjTRECs最常见，PCR产物经克隆和序列分析证实其形成Dβ-jβsjTRECs的情况。结论：成功地建立了检测Dβ-Jβ-sjTRECs的方法，为分析各TCRβ亚家族的sjTRECs含量和确定TCRβ naive细胞提供了新方法。     

扩增鼠源性mAb和人源性抗体κ轻链基因中引物的作用

目的比较扩增鼠源性mAb和人源性抗体Vκ基因中引物的作用.方法从5株抗HFRS病毒鼠源性mAb杂交瘤细胞系和人PBL中提取细胞总RNA.逆转录后,用不同的引物进行PCR扩增,克隆后测定核苷酸序列并比较不同引物的作用.结果 5株mAb杂交瘤细胞的Vκ基因及人源性抗体的Vκ基因,需采用不同的引物组合才可得到.结论 5'端引物在PCR扩增抗体Vκ基因中起重要作用.     

从兔外周血直接克隆IgG重链可变区 

目的 从兔外周血总RNA中直接扩增出IgG重链可变区基因。方法 先从IMGT/GENE-DB数据库中获取编码大耳白兔免疫球蛋白（Ig）重链可变区（VH）的3个胚系基因片段VSUB>H/SUB>（IGHV）、D（IGHD）和JSUB>H/SUB>（IGHJ）,以及编码γ重链恒定区（CH）基因Cγ（IGHG）的cDNA序列,然后设计嵌套引物,以兔外周血总RNA为模板,进行RT-PCR和Nested-PCR扩增,产物经胶回收后克隆到T载体,随机挑选白色克隆测序,最后将序列用Bioedit软件的Local Blast功能比对出Cγ的基因型,同时提交到IMGT/V-QUEST分析出所属的VH、D和JH胚系基因。结果 获得25个克隆的插入子序列,每个克隆均为兔IgG重链可变区的编码基因,且包含了完整的VSUB>H/SUB>、D、JSUB>H/SUB>胚系基因片段,以及Cγ基因     

人类白细胞抗原-DRB1第3外显子单链测序方法的建立及其多态性分析

目的 建立人类白细胞抗原(human leukocyte antigen,HLA)-DRB1第3外显子单链测序方法,并分析其多态性.方法 采用组特异性引物扩增HLA-DRB1第2和3外显子序列,扩增产物经双酶切后进行双向测序分析,采用Assign 3.5 SBT分析软件指定等位基因型.结果 PCR产物经直接测序后得到清晰的序列冬,并向IMGT/HLA数据库提交了HLA-DRB1*08:09和DRB1*12:02:01第3外显子全部序列.在检测的25个等位基因中,HLA-DRB1第3外显子全长序列中存在27个单核苷酸多态性位点,占第3外显子序列碱基总数的9.56%.建立的方法可有效区分HLA-DRB1*14∶01∶01/14∶54歧义标本,证实中国人群中存在HLA-DRB1*14∶01∶01.结论 本实验建立的HLA-DRB1第3外显子测序方法是可行的,HLA-DRB1第3外显子存在多态性.     

基于TCR基因位点的FT-aCGH分析鉴定T-ALL中异常TCR Vβ-IgH重排

目的:鉴定T细胞-急性淋巴母细胞白血病(T-ALL)异常基因重排。方法:利用基于T细胞受体(TCR)基因位点的精细定位的寡核苷酸阵列比较基因组杂交(FT-aCGH)技术分析1例T-ALL样本与对照组基因组DNA的差异,了解7号和14号染色体TCRβ、TCRγ和TCRαδ位点上可能的断裂点位置,根据所提供的初步结果,根据断裂点涉及的基因序列设计特异引物,采用连接介导PCR(LM-PCR)和序列分析等方法分析与之发生重排的基因序列。结果:FT-aCGH结果显示所检测T-ALL样本中,各TCR基因位点都存在断裂点,经过LM-PCR和序列分析,以及利用PCR和特异引物检测基因组DNA结果确定了T-ALL克隆为Vα8-Jα22基因重排,并发现了7号染色体在TCRβ基因位点,Vβ20-1基因片段与14号染色体位于免疫球蛋白重链区基因位点的IgHVII-26-2基因片段发生异常重排,形成t(7;14)(q34;q32)染色体易位。结论:利用FT-aCGH和LM-PCR技术在1例T-ALL中发现了一种新的Vβ20-1-IgHVII-26-2异常重排,这种异常重排有可能可以作为该肿瘤克隆的生物标记物。     

HLA-Cw基因全长序列分子克隆及测序方法的建立

目的 建立可靠的HLA-Cw基因全长序列的分子克隆和测序技术.方法 设计合成HLA-Cw基因全长序列PCR引物和探索PCR反应体系,采用长距离PCR技术,扩增HLA-Cw基因非翻泽区(untranslated region,5'-UTR)区、8个外显子、7个内含子和3'-UTR区,全长约4.5 kb.PCR产物纯化后进行分子克隆,筛选阳性克隆,提取质粒DNA,采用自行设计的测序引物进行全长双向测序.12份已经AlleleSEQR HLA-Cw测序分型试剂盒进行PCR产物直接测序、基因型已知的样本,分别用TaKaRa LATaq酶和Stratagene Pfu Taq DNA聚合酶进行HLA-Cw基因全长扩增,以及PCR产物分子克隆和序列测定,克隆测序结果分别与PCR产物直接测序结果进行对比分析.结果 PCR扩增获得了特异性目的 片段,测序获得了HLA-Cw基因-962～3576位碱基全长序列.克隆测序结果的对比表明,Pfu酶保真性高于LA Taq酶.比较本文测定的Cw*010201与Cw*07020101等位基因序列,在5'上游-962～-284位碱基区域存在11个单核苷酸多态(single nucleotide polymorphisms,SNPs)和2个插入(或)缺失多态性位点;3'-UTR下游3067～3576位碱基区域存在11个SNPs和1个插入(或)缺失.结论 建立了HLA-Cw基因全长序列分子克隆及测序方法,在HLA-Cw基因全长序列分子多态性及表达调控等研究领域,具有广泛应用前景.     

HLA-Cw基因全长序列分子克隆及测序方法的建立

目的 建立可靠的HLA-Cw基因全长序列的分子克隆和测序技术.方法 设计合成HLA-Cw基因全长序列PCR引物和探索PCR反应体系,采用长距离PCR技术,扩增HLA-Cw基因非翻泽区(untranslated region,5'-UTR)区、8个外显子、7个内含子和3'-UTR区,全长约4.5 kb.PCR产物纯化后进行分子克隆,筛选阳性克隆,提取质粒DNA,采用自行设计的测序引物进行全长双向测序.12份已经AlleleSEQR HLA-Cw测序分型试剂盒进行PCR产物直接测序、基因型已知的样本,分别用TaKaRa LATaq酶和Stratagene Pfu Taq DNA聚合酶进行HLA-Cw基因全长扩增,以及PCR产物分子克隆和序列测定,克隆测序结果分别与PCR产物直接测序结果进行对比分析.结果 PCR扩增获得了特异性目的 片段,测序获得了HLA-Cw基因-962～3576位碱基全长序列.克隆测序结果的对比表明,Pfu酶保真性高于LA Taq酶.比较本文测定的Cw*010201与Cw*07020101等位基因序列,在5'上游-962～-284位碱基区域存在11个单核苷酸多态(single nucleotide polymorphisms,SNPs)和2个插入(或)缺失多态性位点;3'-UTR下游3067～3576位碱基区域存在11个SNPs和1个插入(或)缺失.结论 建立了HLA-Cw基因全长序列分子克隆及测序方法,在HLA-Cw基因全长序列分子多态性及表达调控等研究领域,具有广泛应用前景.     

HLA-Cw基因全长序列分子克隆及测序方法的建立

目的 建立可靠的HLA-Cw基因全长序列的分子克隆和测序技术.方法 设计合成HLA-Cw基因全长序列PCR引物和探索PCR反应体系,采用长距离PCR技术,扩增HLA-Cw基因非翻泽区(untranslated region,5'-UTR)区、8个外显子、7个内含子和3'-UTR区,全长约4.5 kb.PCR产物纯化后进行分子克隆,筛选阳性克隆,提取质粒DNA,采用自行设计的测序引物进行全长双向测序.12份已经AlleleSEQR HLA-Cw测序分型试剂盒进行PCR产物直接测序、基因型已知的样本,分别用TaKaRa LATaq酶和Stratagene Pfu Taq DNA聚合酶进行HLA-Cw基因全长扩增,以及PCR产物分子克隆和序列测定,克隆测序结果分别与PCR产物直接测序结果进行对比分析.结果 PCR扩增获得了特异性目的 片段,测序获得了HLA-Cw基因-962～3576位碱基全长序列.克隆测序结果的对比表明,Pfu酶保真性高于LA Taq酶.比较本文测定的Cw*010201与Cw*07020101等位基因序列,在5'上游-962～-284位碱基区域存在11个单核苷酸多态(single nucleotide polymorphisms,SNPs)和2个插入(或)缺失多态性位点;3'-UTR下游3067～3576位碱基区域存在11个SNPs和1个插入(或)缺失.结论 建立了HLA-Cw基因全长序列分子克隆及测序方法,在HLA-Cw基因全长序列分子多态性及表达调控等研究领域,具有广泛应用前景.     

HLA新等位基因B*5618的序列分析

目的识别确认中国汉族人群中的HLA新等位基因。方法采用聚合酶链反应-序列特异性寡核苷酸探针(polymerase chain reaction-sequence specific oligonucleotide probes,PCR-SSOP)方法、聚合酶链反应-序列特异性引物(PCR-sequence specific primer,PCR-SSP)方法以及基因测序分型(sequence-based typing,SBT)技术,发现1个与HLA-B*5610等位基因相近的未知等位基因。以基因特异性引物单独扩增B*56基因并对第2、3、4外显子进行双向测序,序列经BLAST验证并分析该基因与B*5610基因的核苷酸序列差异。结果该基因为新的等位基因,其序列已被GenBank接受(编号为EF016753)。新等位基因与最接近的B*5610相比,在第3外显子上有4个核苷酸的不同,即第379位C→G(密码子127CTG→GTG,氨基酸127Leu→Val);第412位A→G(密码子138AAC→GAC,氨基酸138Asn→Asp);第419位T→C、第420位A→C(密码子140TTA→TCC,氨基酸140Leu→Ser)。结论该等位基因为新的HLA-B等位基因,2006年9月已被世界卫生组织HLA因子命名委员会正式命名为HLA-B*5618。     

HLA-A*02:251新等位基因克隆测序鉴定及序列分析

目的 鉴定中国人群人类白细胞抗原(human leukocyte antigen,HLA)A*02:251新等位基因,分析新等位基因遗传特征.方法 采用聚合酶链反应-测序分型法(polymerase chain reaction-sequence based typing,PCR-SBT)对组织配型健康供、患者进行HLA基因分型,发现先证者核苷酸杂合序列与已知序列不匹配,不能指定先证者HLA等位基因型,对先证者DNA扩增HLA-A位点第2～4外显子,PCR产物经克隆到PMD18-T质粒载体中以获得单链核苷酸序列,对克隆所得产物进行HLA-A基因的第2～4外显子双向测序分析.结果 发现先证者的一个HLA-A*02:06:01基因被确认,而另一个HLA-A基因为新等位基因,其序列被GenBank接受(编号为HM245348).新等位基因序列通过IMGT/HLA 数据库BLAST,与最相近的A*02:01:01:01相比,在第3外显子上有1个核苷酸的不同,即第383位 G>C,密码子 128 GAG→GAC,氨基酸由谷氨酸(Glu)→天门冬氨酸(Asp).供、患者HLA-A、B、C、DQB1位点等位基因不匹配.结论 该等位基因为新的HLA-A*02:251等位基因.中国人群HLA-A 位点第3外显子核苷酸序列存在多态性.

Abstract：

Objective To identify a novel human leukocyte antigen (HLA) allele A*02:251 and analyze the sequences in Chinese population. Methods Routine HLA-A, -B, -DRB1 high resolution genotyping for healthy Chinese donors and patients was performed with polymerase chain reaction-sequence based typing. An unknown HLA-A allele was initially detected by HLA typing in the healthy donor. Genomic DNA of the HLA-A locus in the proband was amplified, the amplified product was cloned by PMD18-T to split the two alleles, and selected clones were sequenced. Results The sequencing results showed that a normal A*02:06:01 and a novel A*02:251 variant allele were identified. The sequence of the novel allele has been submitted to GenBank (HM245348). Nucleotide sequence alignments with HLA-A allele from the IMGT/HLA Sequence Database showed that the novel A*02 variant allele differed from the closest allele A*02:01:01:01 by nt 383 G>C (codon 128 GAG>GAC) in exon 3, which resulted in one amino acid substitution of Glu>Asp. The HLA-A, B, C and DQB1 alleles of the healthy donor did not match with that of the patient. Conclusion This novel allele is officially designated as HLA-A*02:251 by World Health Organization(WHO) Nomenclature Committee (Submission ID HWS10010755). The sequence of HLA-A locus in exon 3 is confirmed to be polymorphic in Chinese population.     

Nomenclature and overview of the mouse (Mus musculus and Mus sp.) immunoglobulin kappa (IGK) genes

'Nomenclature and overview of the mouse (Mus musculus and Mus sp.) immunoglobulin kappa (IGK) Genes', the 19th report of the 'IMGT Locus in Focus' section, provides the first complete list of all the mouse (M. musculus) IGK genes. The mouse (M. musculus) locus spans 3,200 kb. The total number of mouse (M. musculus) IGK genes per haploid genome is 164 (174 if the orphons are included). The functional genomic repertoire comprises 93 IGKV belonging to 18 subgroups, 5 IGKJ and 1 IGKC gene. IMGT gene names and definitions of the mouse (M. musculus) IGK genes on chromosome 6 and IGK orphons are provided with the gene functionality and the number of alleles, according to the concepts of IMGT-ONTOLOGY and to rules of the IMGT Scientific chart, with the accession numbers of the IMGT reference sequences. These tables and figures are available at the IMGT Marie-Paule page of IMGT, the international ImMunoGeneTics database (http://imgt.cines.fr) created by Marie-Paule Lefranc, Université Montpellier II, CNRS, France.     

乙肝免疫球蛋白抗体的多样性

目的 基于重链可变区的编码基因序列对乙肝免疫球蛋白（HBIG）中的IgG抗体进行分类。方法 借用文献提供的引物,以HBsAb强阳性健康个体外周血中的总RNA为模板进行RT-PCR和Nested-PCR扩增,通过将产物克隆到T载体、随机挑选测序,分析并统计出插入子的V_H-J_H-C_γ组
合方式。结果 共获得56个有效克隆,全部为人V_H3-D-J_H-C_γ序列,可分成49种序列,其中5种序列有2或3个序列完全相同的克隆。4个Cγ功能基因也全部出现,其中IGHG2频率最高（28次）;23个V_H3功能基因有11个出现,其中频率最高的是IGHV3-23（29次）;23个D功能基因有16个出
现,其中频率最高的是IGHD1-26（8次）;6个J_H 功能基因则全部出现,其中频率最高的是IGHJ4（33次）。V_H3-D-J_H组合有33种,频率最高的是IGHV3-23/IGHD1-26/IGHJ4（8次）,其中5种与IGHG2拼接,但这5种V_H3-D-J_H-C_γ2序列仍有明显的差异。结论 成功地从HBsAb强阳性健康个体外周血中克隆到由VH3亚家族参与重排的IgG重链可变区序列;初步证实可变区序列不仅在V_H3-D-J_H-C_γ组合方式上具有极大的多样性,而且在序列上也具有明显的差异性;基于可变区测序对IgG抗体或B细胞进行分类是可行的,但需大大提高挑取克隆的数量或改用新一代大规模测序技术。     

The 3 ′ part of the immunoglobulin κ locus of the mouse

A detailed restriction map of a 430-kb contig comprising the single Cκ, the 5 Jκ and the adjoining 22 Vκ gene segments is presented. The first 12 Vκ genes following the JκCκ region belong to the Vκ21 family, the subsequent ones to the closely related families Vκ8 and Vκ19/28. Previous difficulties in cloning all Vκ21 genes can now be explained by the presence of a duplicated region in this part of the locus. The structure was established by analysis of yeast artificial chromosome, bacterial artificial chromosome and cosmid clones and by the so-called long template PCR technique. The distance between Cκ and the proximal Vκ21 gene is 22 kb and the average distances between the Vκ genes are about 20 kb. Of the 12 Vκ21 genes 5 were sequenced for the first time and 8 of the 12 genes were found to be expressed. Of the 10 Vκ8 and Vκ19/28 germline genes 9 are new; expression products of 8 of the 10 genes were known. The known 5 ′ , 3 ′ polarities allow to specify for the 22 Vκ genes whether they are rearranged to the JκCκ element by a deletion or an inversion mechanism. Also the formation of interesting rearrangement products in classical cell lines as MPC11, MOPC41 and PC 7043 can be explained now. The non-Vκ sequence L10 whose rearrangement by inversion has been described earlier (Hoechtl and Zachau, Nature 1983. 302:260 – 263) was now localized downstream of JκCκ.     

Nomenclature of the human immunoglobulin kappa (IGK) genes

'Nomenclature of the Human Immunoglobulin Kappa (IGK) Genes', the 17th report of the 'IMGT Locus in Focus' section, provides the first complete list of all the human IGK genes. In the most frequent haplotypes, the human IGK locus spans 1,820 kb and the IGKV genes are organized in two clusters separated by 800 kb. In those haplotypes where both the proximal and distal IGKV clusters are present, the total number of human IGK genes per haploid genome is 82 (107 genes if the orphons are included) of which 37-41 are functional. If only the proximal IGKV cluster is present, which is found in a rare haplotype, the total number of genes per haploid genome is 46 (71 genes if the orphons are included) of which 23-25 genes are functional. IMGT/HUGO gene names and definitions of the human IGK genes on chromosome 2p11.2, and IGK orphons on chromosomes 1, 2, 15, and 22 are provided with the gene functionality and the number of alleles according to the rules of the IMGT Scientific chart, with the accession numbers of the IMGT reference sequences, and the accession ID of the Genome Database GDB and NCBI LocusLink databases in which all the IMGT human IGK genes have been entered. The tables are available at the IMGT Marie-Paule page from IMGT, the international ImMunoGeneTics database (http://imgt.cines.fr:8104) created by Marie-Paule Lefranc, Université Montpellier II, CNRS, France.     

Universal PCR amplification of mouse immunoglobulin gene variable regions: the design of degenerate primers and an assessment of the effect of DNA polymerase 3' to 5' exonuclease activity

Degenerate primers were designed for PCR amplification of unknown mouse immunoglobulin (Ig) light (L) and heavy (H) chain variable (V) genes. Each subgroup of mouse Ig gene sequences [Kabat, E.A., Wu, T. T., Perry, H.H., Gottesman, K.S., Foeller, C., 1991. Sequences of Proteins of Immunological Interest, 5th edn. US Department of Health and Human Services, Public Health Service, NIH.] was analyzed, and highly degenerate primers in the framework one (FR1) region were designed. A single highly degenerate FR1 primer sufficed for the amplification of light chains; for heavy chains, a series of FR1 primers was used. At the same time, we assessed the effect of 3' to 5' exonuclease activity of DNA polymerase on the utilization of these degenerate primers. Using Taq polymerase, which lacks 3' to 5' exonuclease activity, we successfully amplified the Ig VL and VH genes expressed in more than a hundred monoclonal hybridoma cell lines reactive against a phosphonamidate hapten. Sequence analysis of the cloned VL and VH genes, 52 of each, showed that they are derived from multiple germline families (10 of the 17 VL families and 9 of the 14 VH families) as recently defined [Martinez, C., Lefranc, M., 1998. The mouse (Mus musculus) immunoglobulin kappa variable (IGKV) genes and joining (IGKJ) segments. Exp. Clin. Immunogenet. 15, 184.]. The universality of our primers was also demonstrated by successful amplification of other mouse hybridoma cell lines that are specific to different antigens.     

以鼠源重链Fd片段为模板导向筛选人源性抗γ-精浆蛋白抗体轻链

目的:以鼠源抗γ-sm抗体重链Fd片段为模板,筛选人源性抗人γ-精浆蛋白抗体轻链。方法:利用RT-PCR从前列腺癌患者外周血淋巴细胞扩增出全套的人抗体轻链基因,克隆入含鼠源性抗γ-sm抗体重链Fd片段的噬粒载体pComb3X/mFd中,电转化大肠杆菌XL1-Blue后建立人-鼠杂合的Fab抗体库。通过稀释滴定、限制性酶切和随机测序,对所建杂合库的库容、重组率和多样性分别进行鉴定,以M13K07辅助噬菌体超感染,利用亲和纯化的γ-sm为抗原,对挽救展示的噬菌体抗体库进行3轮淘筛和克隆鉴定。最后对筛选出的杂合抗体进行初步的功能检测。结果:构建成功1.2×107CFU、重组率为90%、多样性好的杂合人-鼠噬菌体抗体库。利用纯化的γ-sm3轮亲和淘筛后,5个克隆成功诱导表达特异性的pIII融合抗体。ELISA进一步检测表明,5个克隆均呈特异性阳性反应,其中2个克隆亲和力较高,测序显示其所含轻链基因序列完全相同,可变区来源于IGKV4-101胚系基因家族。结论:利用鼠源Fd片段为模板,导向筛选杂合噬菌体库,成功筛选到人源性抗人γ-精浆蛋白抗体轻链。     

The telostei immunoglobulin light IGL1 and IGL2 V, J and C genes

'Teleostei Immunoglobulin Light IGL1 and IGL2 V, J and C Genes', the 12th report of the 'IMGT Locus in Focus' section, comprises 8 tables: (1) 'Teleostei IGL1V genes'; (2) 'Teleostei germline IGL1J genes'; (3) 'Teleostei IGL1C genes and alleles'; (4) 'Teleostei IGL2V genes'; (5) 'Teleostei germline IGL2J genes'; (6) 'Teleostei IGL2C genes and alleles'; (7) 'FR-IMGT and CDR-IMGT length of the Teleostei IGL1V genes', and (8) 'FR-IMGT and CDR-IMGT length of the Teleostei IGL2V genes'. These tables are available on the IMGT Marie-Paule page from IMGT, the international ImMunoGeneTics database (http://imgt.cines.fr: 8104) created in 1989 by Marie-Paule Lefranc, Université Montpellier II, CNRS, France.     

A high-affinity macaque antibody Fab with human-like framework regions obtained from a small phage display immune library

Tetanus toxoid was used as a model antigen for the immunization of Macaca fascicularis. Using peripheral blood as a template, specific Fab-encoding genes were amplified by PCR on the fourth day after the final boost, and cloned in a phagemidic vector (pComb3X) as a small immune library (5 x 10(5) clones). A high-affinity Fab (Kd = 4 x 10(-10) M), 6-ATT, was isolated from this library by panning. The genes encoding 6-ATT were found to be similar to human immunoglobulin germline genes, and were assigned to subgroups of human V, (D) or J genes by IMGT/V-QUEST. Overall, the Fab variable domain framework regions were 93% identical to the representative genes and alleles of the human subgroups, this level of identity being similar to that between genes of the same human subgroup. This strategy could be used for the isolation of high-affinity, human-like Fab fragments directed against numerous antigens.