Analysis of the autophagy gene expression profile of pancreatic cancer based on autophagy-related protein microtubule-associated protein 1A/1B-light chain 3

BACKGROUND Pancreatic cancer is a highly invasive malignant tumor. Expression levels of the autophagy-related protein microtubule-associated protein 1 A/1 B-light chain 3(LC3) and perineural invasion(PNI) are closely related to its occurrence and development. Our previous results showed that the high expression of LC3 was positively correlated with PNI in the patients with pancreatic cancer. In this study, we further searched for differential genes involved in autophagy of pancreatic cancer by gene expression profiling and analyzed their biological functions in pancreatic cancer, which provides a theoretical basis for elucidating the pathophysiological mechanism of autophagy in pancreatic cancer and PNI.AIM To identify differentially expressed genes involved in pancreatic cancer autophagy and explore the pathogenesis at the molecular level.METHODS Two sets of gene expression profiles of pancreatic cancer/normal tissue(GSE16515 and GSE15471) were collected from the Gene Expression Omnibus.Significance analysis of microarrays algorithm was used to screen differentially expressed genes related to pancreatic cancer. Gene Ontology(GO) analysis and Kyoto Encyclopedia of Genes and Genomes(KEGG) pathway analysis were used to analyze the functional enrichment of the differentially expressed genes. Protein interaction data containing only differentially expressed genes was downloaded from String database and screened. Module mining was carried out by Cytoscape software and ClusterOne plug-in. The interaction relationship between the modules was analyzed and the pivot nodes between the functional modules were determined according to the information of the functional modules and the data of reliable protein interaction network.RESULTS Based on the above two data sets of pancreatic tissue total gene expression, 6098 and 12928 differentially expressed genes were obtained by analysis of genes with higher phenotypic correlation. After extracting the intersection of the two differential gene sets, 4870 genes were determined. GO analysis showed that 14 significant functional items including negative regulation of protein ubiquitination were closely related to autophagy. A total of 986 differentially expressed genes were enriched in these functional items. After eliminating the autophagy related genes of human cancer cells which had been defined, 347 differentially expressed genes were obtained. KEGG pathway analysis showed that the pathways hsa04144 and hsa04020 were related to autophagy. In addition,65 clustering modules were screened after the protein interaction network was constructed based on String database, and module 32 contains the LC3 gene,which interacts with multiple autophagy-related genes. Moreover, ubiquitin C acts as a pivot node in functional modules to connect multiple modules related to pancreatic cancer and autophagy.CONCLUSION Three hundred and forty-seven genes associated with autophagy in human pancreatic cancer were concentrated, and a key gene ubiquitin C which is closely related to the occurrence of PNI was determined, suggesting that LC3 may influence the PNI and prognosis of pancreatic cancer through ubiquitin C.

Cloning and Sequencing of Kappa Light Chain Gene of a Mouse Monoclonal Antibody Directed Against Potato Virus Y

A cDNA library was constructed in λgt11 vectors, complementary to the mRNA isolated from a mouse hybridoma raised against potato virus Y(PVY). Thirty cDNA clones were selected from the cDNA library by in situ immunohybridization with goat anti-mouse kappa-chain-specific antibody conjugated to alkaline phosphatase, from which one clone, k6, having the largest insert was characterized by sequence analysis. The result shows that the immunoglobulin messenger RNA corresponding to k6 is 956 nucleotides in length excluding the poly(A) region, among which 31 bases code for the 5’ non-coding region, 57 for the leader sequence of the protein, 657 for the mature protein and 211 for the 3’ non-coding region. Comparison of deduced amino acid sequences of the protein and other kappa light chains shows that they share a 100% identity in their constant regions(CL) and 93.7% identity in their variable regions(VL). The kappa light chain encoded by k6 is considered to be specific to PVY since only one type of light chain is expressed in the hybridoma.

Insertional mutagenesis and cloning of HIV env 125 peptide gene by polymerase chain reaction

One oligonueleotide probe,HIV env 101-1,and two oligonucleotide primers,HIV env125-1 and HIV env 125-2,were designed with the aid of a computer and synthesized by a DNAsynthesizer.The env 125 peptide gene was amplified by polymerase chain reaetion(PCR).Beingidentified by electrophoresis and Southern blotting,the PCR product was cloned into plasmidpUC 19.The recombinant pENV 125,identified with X-gal selection and restriction mapping, wassequenced.The results showed that the cloned env 125 peptide gene contained the inserted EcoRⅠ site and ATG at the 5’end,Hind Ⅲ site and TAG at the 3’end.The sequence and readingframe were proved to be correct.

Cloning, sequencing and analyzing of the heavy chain V region genes of human polyreactive antibodies

The heavy chain variable region genes of 5 human polyreactive mAbs generated in our laboratory have been cloned and sequenced using polymerase chain reaction (PCR) technique. We found that 2 and 3 mAbs utilized genes of the VHIV and VHIII families, respectively. The former 2 VH segments were in germline configuration. A common VH segment, with the best similarity of 90.1 % to the published VHIII germline genes, was utilized by 2 different rearranged genes encoding the V regions of other 3 mAbs. This strongly suggests that the common VH segment is a unmutated copy of an unidentified germline VHIII gene. All these polyreactive mAbs displayed a large NDN region (VH-D-JH junction). The entire H chain V regions of these polyreactive mAbs are unusually basic. The analysis of the charge properties of these mAbs as well as those of other poly- and mono- reactive mAbs from literatures prompts us to propose that the charged amino acids with a particular distribution along the H chain V region,especially the binding sites (CDRs), may be an important structural feature involved in antibody polyreactivity.

刺葡萄STS基因克隆及其在不同光质下的表达水平

【目的】研究刺葡萄芪合酶(STS)基因的序列特征及其在不同光质处理下的表达水平,旨在为进一步解析STS基因通过响应光信号调控刺葡萄愈伤组织中白藜芦醇合成的分子机制提供依据。【方法】以刺葡萄愈伤组织为材料,利用逆转录PCR(RT-PCR)技术成功克隆获得了4个STS基因,对这些基因及其编码蛋白进行了生物信息学分析,并利用实时荧光定量PCR(RT-qPCR)检测其在不同光质下和不同培养阶段的表达水平。【结果】成功地从刺葡萄愈伤组织中克隆获得了VdSTS5、VdSTS6、VdSTS20、VdSTS21共4个基因,均含1179 bp完整开放阅读框(ORF),编码392个氨基酸残基,预测其编码的是亲水性、无信号肽的细胞质定位蛋白,磷酸化修饰主要发生在苏氨酸和丝氨酸位点上,蛋白质的二级结构主要由α-螺旋、无规则卷曲和延伸链组成,STS与查尔酮合成酶(CHS)的蛋白质序列具有高度同源性。4个VdSTS的蛋白质序列在系统进化树上处于3个不同的大分支中,其中,VdSTS5与VdSTS21处在不同的分支中,而VdSTS6与VdSTS20聚在同一分支中,葡萄属不同种之间的STS蛋白质序列相似度高,推测其可能具有相同的功能。启动子顺式作用元件预测发现,4个VdSTS启动子含有多个光响应元件,还含有转录因子识别和作用元件、激素作用元件等。光质显著影响4个VdSTS的表达,在白光、红光、黄光和黑暗处理下,VdSTS的总体表达水平较高,而在绿光和紫光处理下,VdSTS的总体表达水平较低;同时,VdSTS对不同光质的响应不仅存在着基因间的差异,还存在不同培养阶段的差异,VdSTS5在培养后期强烈响应黄光的调控,VdSTS6、VdSTS20在培养中期对黑暗和红光的响应最强,VdSTS21则在培养中期强烈响应红光的调控,这些基因表达水平的变化影响着刺葡萄愈伤组织中白藜芦醇的合成。【结论】4个VdSTS对光质的响应存在差异,可能在响应不同光质调控中对刺葡萄愈伤组织白藜芦醇的合成起到重要作用。

人LIGHT基因的克隆及其重组腺病毒载体的构建

目的 克隆人ＬＩＧＨＴ基因，构建其重组腺病毒载体，以研究ＬＩＧＨＴ过表达与腺病毒感染对细胞生长的影响。方法用ＲＴ－ＰＣＲ法从人外周血单个核细胞（ＰＢＭＣ）中克隆人的ＬＩＧＨＴ全长基因。将ＬＩＧＨＴ ｃＤＮＡ克隆到穿棱载体ｐＡｄＴｒａｃｋ－ＣＭＶ－ＬＩＧＨＴ重组质粒中，经酶切线性化后，将重组质粒ｐＡｄＴｒａｃｋ－ＣＭＶ－ＬＩＧＨＴ和骨架质粒ｐＡｄＥａｓｙ－１，以电穿孔法共转染大肠杆菌ＢＪ５１８３，获得重组腺病毒质粒。最后，将线性化的重组腺病毒质粒转染２９３细胞包装获得重组腺病毒，用荧光显微镜、ＰＣＲ及Ｗｅｓｔｅｒｎ ｂｌｏｔ分析ＬＩＧＨＴ基因的表达。 结果 用ＲＴ－ＰＣＲ法从人的ＰＢＭＣ中，扩增出７２３ ｂｐ的ｃＤＮＡ，测序证实为人ＬＩＧＨＴ基因。荧光显微镜、ＰＣＲ及Ｗｅｓｔｅｒｎ ｂｌｏｔ证实，ＬＩＧＨＴ重组腺病毒可感染２９３细胞，并在２９３细胞内进行有效的复制。结论成功地克隆了人ＬＩＧＨＴ基因，并构建了其重组腺病毒载体，为进一步研究ＬＩＧＨＴ基因的功能提供了条件。

人LIGHT胞外段基因的克隆及在大肠杆菌中的表达

目的:构建人LIGHT胞外段基因的原核表达载体,并在大肠杆菌中诱导表达。方法:从人外周血单核细胞来源的未成熟树突状细胞中提取总RNA,通过RT-PCR得到LIGHT胞外段基因,并将其克隆至pET32a(+)原核表达载体中,经双酶切鉴定及序列测定后的重组质粒转化入E.coli BL21,IPTG诱导表达目的蛋白,并用SDS-PAGE和Western blot进行检测。结果:RT-PCR扩增出了大小为543bp的LIGHT胞外段基因,经测序证明序列正确。SDS-PAGE和Western blot分析证实重组质粒可表达出Mr约为41000的蛋白。结论:成功地克隆了人LIGHT胞外段基因并在大肠杆菌中进行了表达为进一步研究LIGHT的功能打下了基础。

人LIGHT胞外区基因的克隆及融合蛋白的表达

目的:克隆人LIGHT胞外区基因(hsLIGHT),构建其原核表达质粒,并诱导其在大肠杆菌中表达融合蛋白。方法:采用RT-PCR方法从HL60细胞中扩增hsLIGHT,将其克隆入原核表达质粒pGEX-4T-2,构建其重组表达质粒pGEX-4T- 2/hsLIGHT,以不同浓度IPTG诱导表达,于不同时间经SDS-PAGE和Western blot分析、鉴定。结果:经RT-PCR扩增获得的 hsLIGHT序列与Genebank报道的LIGHT基因胞外区序列完全一致;SDS-PAGE和Western blot分析证实重组质粒可表达出相对分子量为47 000的蛋白,与GST-hsLIGHT融合蛋白分子量一致。结论:成功完成了人LIGHT胞外区基因的克隆及其原核表达质粒的构建,在大肠杆菌E．coli BL21中经IPTG诱导表达了融合蛋白GST-hsLIGHT,为进一步探讨LIGHT的抗肿瘤生物学活性、探索肿瘤免疫治疗新方法奠定了基础。

人LIGHT基因的克隆及其在293T细胞中的表达

目的 克隆人LIGHT分子的全长cDNA ,构建重组真核表达质粒pCI neo LIGHT并在 2 93T细胞上获得稳定表达。方法 从人T细胞cDNA文库中用PCR技术克隆人LIGHT全长cDNA ,装入T Easy载体 ,测序证实后 ,将LIGHTcDNA装入质粒pCI neo中构建真核表达载体。用电穿孔法转染 2 93T细胞 ,经G418筛选后 ,用流式细胞仪检测LIGHT分子的表达。结果 测序证实克隆的LIGHT全长cDNA阅读框正确完整 ,酶切证实LIGHT pCI neo中LIGHT插入方向正确。转染的2 93T细胞经G418筛选 3个月后 ,流式细胞仪检测有 78 69%的细胞表达人LIGHT分子。结论 成功克隆LIGHT基因并获得稳定表达膜型LIGHT分子的 2 93T细胞系。

Lnc RNA SNHG14通过调节miR-206表达来促进卵巢癌的发展

目的探讨长链非编码RNA(Lnc RNA)小核仁RNA宿主基因14(SNHG14)在卵巢癌组织中的表达,以及Lnc RNA SNHG14通过微小RNA(miR)-206影响卵巢癌的增殖、迁移和侵袭能力。方法收集58例行卵巢癌根治手术患者的癌组织及其邻近的癌旁组织(距离癌组织>3 cm),将其进行细胞培养,待细胞融合度达到70%左右时进行细胞转染,分别转染阴性对照质粒(si-NC组)、SNHG14高表达质粒(si-SNHG14组);采用实时荧光定量聚合酶链式反应(qRT-PCR)检测卵巢癌组织与癌旁组织中SNHG14、miR-206表达量,采用细胞增殖活性检测试剂盒(CCK-8)实验、平板克隆形成实验、Matrigel侵袭实验分别检测SNHG14对卵巢癌细胞的增殖能力、克隆形成数、迁移及侵袭;双荧光素酶报告实验检测Lnc RNA SNHG14与miR-206的靶向关系。结果与癌旁组织的(1.01±0.08)、(1.00±0.07)比较,卵巢癌组织中SNHG14表达量(2.56±0.57)升高、而miR-206表达量(0.36±0.11)降低(P<0.05);通过Pearson法检测卵巢癌组织中SNHG14与miR-206的相关性显示,SNHG14与miR-206呈负相关(r=-0.803,P<0.01)。与si-NC组的(1.01±0.06)、(1.00±0.08)比较,si-SNHG14组的SNHG14表达量(0.27±0.07)降低、miR-206表达量(2.96±0.45)升高(P<0.05);si-SNHG14组的吸光度(OD值)(0.29±0.05)较si-NC组的(0.79±0.06)降低,克隆形成数(52.35±7.37)较si-NC组的(120.51±19.34)减少(P<0.05)。si-SNHG14组的迁移细胞数(43.11±5.87)、侵袭细胞数(49.66±11.01)均较si-NC组的(117.11±10.48)、(122.30±12.97)明显减少(P<0.05)。采用starbase预测与SNHG14可互补结合的miR-206。转染miR-206 mimics可降低含有野生型载体的卵巢癌细胞的荧光素酶活性(P<0.05),而未能抑制含有突变型载体的卵巢癌细胞的荧光素酶活性(P>0.05)。结论卵巢癌组织和卵巢癌细胞中Lnc RNA SNHG14的表达会升高,Lnc RNA SNHG14可靶向miR-206,从而调节卵巢癌细胞的增殖、克隆形成、迁移和侵袭。

小鼠LIGHT胞外段基因原核表达质粒的构建及表达

目的构建含有LIGHT胞外段的原核表达载体,并在大肠杆菌中诱导表达。方法从由小鼠骨髓来源的未成熟树突状细胞中提取总RNA,经RT-PCR扩增LIGHT胞外段,克隆至原核表达载体pET-24a(+)中,构建重组表达质粒pET24-LIGHTECD。重组质粒经酶切鉴定及序列测定后,转化E.coli BL21,IPTG诱导表达,并用SDS-PAGE和Western blot进行检测。结果RT-PCR扩增出了525bp LIGHT胞外段的cDNA,经测序证实其序列正确。SDS-PAGE和Western blot分析证实重组质粒可表达出相对分子质量为20000的LIGHT胞外段蛋白。结论成功地克隆了小鼠LIGHT胞外段基因并在大肠杆菌中进行了表达,为进一步研究LIGHT的功能打下了基础。

Epidemiology and molecular genetics of congenital cataracts

Congenital cataract is a crystallin severe blinding disease and genetic factors in disease development are important. Crystallin growth is under a combination of genes and their products in time and space to complete the coordination role of the guidance. Congenital cataract-related genes, included crystallin protein gene (CRYAA, CRYAB, CRYBA1/A3, CRYBA4, CRYBB1, CRYBB2, CRYBB3, CRYGC, CRYGD, CRYGS), gap junction channel protein gene (GJA1, GJA3, GJA8), membrane protein gene (GJA3, GJA8, MIP, LIM2), cytoskeletal protein gene (BF-SP2), transcription factor genes (HSF4, MAF, PITX3, PAX6), ferritin light chain gene (FTL), fibroblast growth factor (FGF) and so on. Currently, there are about 39 genetic loci isolated to which primary cataracts have been mapped, although the number is constantly increasing and depends to some extent on definition. We summarized the recent advances on epidemiology and genetic locations of congenital cataract in this review.

Screen for stage-specific expression genes between tail bud stage and heartbeat beginning stage in embryogenesis of gynogenetic silver crucian carp

A systemic study was initiated to identify stage-specific expression genes in fish embryogenesis by using suppression subtractive hybridization (SSH) technique. In this study, we presented a preliminary result on screen for stage-specific expression genes between tail bud stage (TBS) and heartbeat beginning stage (HBS) in gynogenetic silver crucian carp (Carassius auratus gibelio). Two SSH plasmid libraries specific for TBS embryos and HBS embryos were constructed, and stage-specific expression genes were screened between the two stages. 1963 TBS positive clones and 2466 HBS positive clones were sampled to PCR amplification, and 1373 TBS and 1809 HBS PCR positive clones were selected to carry out dot blots. 169 TBS dot blot positive clones and 272 HBS dot blot positive clones were sequenced. Searching GenBank by using these nucleotide sequences indicated that most of the TBS dot blot positive clones could not be found homologous sequences in the database, while known genes were mainly detected from HBS dot blot positive clones. Of the 79 known genes, 20 were enzymes or kinases involved in important metabolism of embryonic development. Moreover, specific expressions of partial genes were further confirmed by virtual northern blots. This study is the first step for making a large attempt to study temporal and spatial control of gene expression in the gynogenetic fish embryogenesis.

Cloning of differentially expressed genes in human hepatocellular carcinoma and nontumor liver

INTRODUCTIONThe mechanism of hepatocellular carcinoma(HCC)is still unclear,although some genes have been found to play a role in the transformation of liver cells,and a variety of studies have described differences in gene expression which distinguished tumor from nontumor[1-6].The new genes,especially the functional genes directly related with tumor are still worth being found.The purpose of our study is to find the different genes between human liver tumor and normal tissues using suppression subtractive hybridization.

Differentially expressed genes in hepatocellular carcinoma induced by woodchuck hepatitis B virus in mice

INTRODUCTIONHepatocellular carcinoma(HCC)is one of the major causes of death in the word.The mechanism of carcinogenesis is unknown,although it is widely accepted that HBV and HCV are clsely related to liver cancer[1-5[1-5].Previously,a variety of studies have described the differences in gene expression which distinguished tumor from nontumor[6-11].Cloning of the genes,especially the genes associated with HBV and HCV,is still very important to account for the development of liver cancer.

STUDY OF ECK GENE EXON-3 FROM HUMAN NORMAL TISSUE AND BREAST CANCER CELL LINE

Objective To establish a method cloning the exon 3 of eck gene from normal tissue and ZR 75 1 cell line (a human breast cancer cell line)and study whether these genes exist mutant. Methods Designed a pair of specific primers and amplified the exon 3 of eck gene fragment from the extracted genomic DNA derived from normal epithelial cells from skin tissue and ZR 75 1 cell line respectively by PCR technique. Transformed the E.coil. JM109 with recombinant plamids constructed by inserting the amplified fragments into medium vector pUCm T and sequenced these amplified fragments after primary screening of endonuclease restriction digestion and PCR amplification. Results ① Obtained the genomic DNA of human normal epithelial cells and ZR 75 1 cell line respectively. ② Obtained the amplified fragments of human exon 3 of eck gene through PCR technique. ③ Obtained the cloning vectors of exon 3 of eck gene of human normal epithelial cells and ZR 75 1 cell line respectively. ④ ZR 75 1 cell line exists mutation of nucleotides. Conclusion Successfully established the method of cloning the human exon 3 of eck gene and found some mutations in the detected samples. This study lays a foundation for further studying the function of eck gene in tumorgenesis.

Amplification,cloning,sequencing and expression of the gene encoding the major surface antigen of Toxoplasma gondii isolated in China

According to the published gene sequence of the major surface antigen (P30) of Toxoplasma gondii, a pair of primers were designed and synthesized. Using polymerase chain reaction (PCR), the coding sequences of P30 gene were amplified from a Chinese strain of T. gondii, The amplified gene fragment and plasmid pB220 were digested with EcoRI and BamHI and then ligated. The inserted gene fragment was sequenced by the chain termination method, the reading reveals that nucleotide sequence determined was the same as the P30 sequecne of RH strain pubilished by Burg (1988), except that one base was changed. The recombinant plasmid containing P30 gene was transformed to E. coli DH5α.After temperature inducing culture, the total cellular proteins were analysed by SDS-PAGE and Western blot. The results show that the p30 gene cloned into the plasmid could express in E. coli, and the expression product had immunogenicity.

Cloning and sequencing of the fourth exon of transforming growth factor α gene

Using normal brain cell geneomic DNA as a template,transforming growth factor(TGFa)-IV exon gene was amplified by polymerase chain reaction(PCR). The sequence of amplified fragment was analysed with a DNA sequencing kit.The results showed that the cloned fragment is proved to be the TGFa-IV exon gene.

THE CLONING OF HUMAN NEUROTROPHIN-3 GENE

In the present study, we have cloned the gene of human neurotrophin3 (hNT3) from the genomic DNA of white blood cells (WBC) by polymerase chain reaction (PCR). The amplification products were cloned into pUC19 and sequenced. Genomic sequence comparison of the cloned fragment and the reported hNT3 (GenBank M61180) reveals 7 base differences: 1 in the signal peptide, 3 in the prepro peptide, and 3 in the mature hNT3. Except the 2 varied bases (16th, T to G; 285th, A to C) in the signal peptide and prosequence resulted in the change of their encoded aminoacids (TyrAsp; GlnHis), the other varied bases have no influence on their respective encoded aminoacids, and all the changes have no influence on the open reading frame (ORF) of the hNT3.

Cloning of polyadenylated mRNA fragments of Escherichia coli with restriction display-polymerase chain reaction

Objective:To investigate the polyadenylation of mRNA in E. Coli. Methods: The mRNA of E. Coli was enriched from the total RNA with oligo(dT)-cellulose, prior to reverse transcription using oligo(dT)18as the primer. Double-stranded cDNA was subsequently synthesized, which was subjected to digestion with Sau3A I to produce multiple gene fragments for ligation with the adapters. PCR was carried out in 10 groups according to 10 different pairs of the selective primers, and the PCR products were then cloned into T-vectors. Results: More than 100 gene fragments had been cloned, 30 of which were sequenced. Conclusion:Polyadenylation of E. Coli mRNA may not be a biochemical curiosity but a general attribute of bacterial mRNA.