FLJ39061 new gene expression in lymphoma and Functional Analysis
Author: Yan Lingling, Zhu Tao, Xiang-Yang Bai, Yun-
Ping Lu, Jian-Feng Zhou, Martin
【Abstract】 Objective To study the proliferation of lymphoma and reactive lymph nodes differences in gene expression, and high expression of genes FLJ39061 lymphoma preliminary analysis. Methods lymphoma and reactive hyperplasia of lymph node specimens of liquid nitrogen frozen lymph node biopsy specimens, the use of laser microdissection separation of
lymphocytes and lymphocytes in the mRNA extracted and cDNA microarray hybridization, scanning through the signal after treatment to obtain the expression of two differences in genes. Using bioinformatics methods a significant difference
between the preliminary analysis of new gene FLJ39061. The results of cDNA microarray identified 152 differentially expressed genes. Lymphoma-related gene FLJ39061 on the nature of effective prediction, the basic protein encoded by the gene identified as a nuclear protein, is likely to be one MAP kinase-activated protein kinase 2, precursors or isomers. Conclusion FLJ39061 may be used as kinase substrate phosphorylation regulates cell metabolism, and lymphoma related to the occurrence can be used as therapeutic targets
for further functional studies.
Key words lymphoma; cDNA microarray; FLJ39061; bio-
Expression of a Novel Gene FLJ39061 in Lymphoma and Its Function Analysis
Abstract: Objective To explore the differential expressed
genes in lymphoma and reactive lymph node and performed an initial analysis on a novel gene. Hypethetical Protein FIJ39061, which is highly expressed in lymphnode of lymphoma. Methods The samples were collected and flash frozen quickly to
maintain the integrity of mRNA. The mRNA of the tissue from the lymphoma and reactive lymph node are marked with biotin respectively and hybridized with expression profile microarray, and the differential expressed genes are obtained. Initial bioinformatics analysis is performed on a novel gene named FLJ39061 which have no functional researches at present. Its gene structure, genomic localization, the physical and chemical characteristics of the putative protein, subcellular localization, functional domain and so on are predicted, and
the systematic evolution analysis is performed on the similar proteins among several species. Results Using expression profile microarray, 152 differential expressed genes are uncovered. Efficient bioinformatics analysis have fundamentally identified that FLJ39061 is a nuclear protein, and probably is precursor or isomer of MAP kinase activated
protein kinase 2. Conclusion By bioinformatics analysis, FLJ39061 may involved in the phosphorylation regulation. It is anticipated that this project will advance our understanding of the molecular mechanisms in the neoplastic transformation of lymphoma and the new insights will help to identify promising molecular targets for therapeutic intervention.
Key words: Lymphoma; Expression profile microarray;
FLJ39061; Bioinformatics; MAPK
In recent years, there are incremental trend in the incidence of malignant lymphoma, and its pathogenesis is still unclear. With the gene chips, serial analysis of gene expression (SAGE), suppression subtractive hybridization (SSH) the development of high-throughput research methods, making
the molecular level to study the regulation of tumor-related
molecular mechanisms and regulatory pathways. Here the use of gene chips for laser capture microdissection to obtain gene expression profiles of lymphoma lymph node samples for analysis and found a T-cell lymphoma in the lymph nodes in the highly expressed genes FLJ39061, and its preliminary bioinformatics analysis, the basic clear The biological
function of this gene and significance for the future of
molecular biology experiments provided further information and methodological guidance.
1 Materials and methods
6 cases of lymphoma and reactive hyperplasia of lymph
node specimens from lymph node specimens, Huazhong University of Science and Technology, Tongji Hospital, Tongji Medical College in September 2005 ~ December 2005 hematology patients surgical specimens, including three pathologic findings
confirmed the lymphoma (2, called B-cell lymphoma, a known T-
cell lymphoma) and the other three patients with pathological lymph nodes were identified as reactive hyperplasia. Micro mRNA extraction reagents were purchased from Qiagen Company. CDNA microarray biochip companies using Affymetrix Human Genome U133 plus2.0 chips. The chip covers about 54 000 individual human gene sequences.
1.2.1 Total RNA extraction and purification of
Fresh lymph node tissue samples drawn after the bacteria
stored in cold fixative in the back lab. Frozen sections will be organized, laser capture micro-lymphoma cells, micro-
extraction of cells in the total RNA.
1.2.2 Micro-RNA in vitro amplification of
Using the T7 OligodT do reverse reaction, synthesis of
double-stranded cDNA with T7 RNA polymerase in vitro
transcription to do. unbiased linear amplification of mRNA for the future, with 1% agarose gel electrophoresis and UV spectrophotometer obtained aRNA purity and concentration.
1.2.3 cDNA microarray sample preparation and detection
After aRNA amplification carried out on the quality of identification, in order to biotin incorporation of reverse transcription, labeling aRNA. Followed by microarray hybridization.
1.2.4 cDNA microarray analysis of raw data
Gene chip every gene or EST from the 11 20 to 25 base
pairs of the probe composition. Hybridization signal data measured after deducting background values, using Wilcoxon signed-rank test probe hybridization signal intensity and the corresponding genes in control mismatch probe differences. To
0.05 as a significant difference in the standard. P ? 0.05 of
the gene as a positive gene. Comprehensive comparison of test results 6 times and returned to lymphoma and reactive hyperplasia of lymph nodes differentially expressed sequence information.
1.2.5 Bioinformatic analysis
Sequence of reference sequence and the basic notes from NCBI's GenBank database, using the genome map viewer watching location and gene structure. The use of Spidey Tools (http://www.ncbi.nlm.nih.gov/IEB/Research / Ostell / Spidey /)
will be aligned to the corresponding mRNA sequence of the genome sequence to verify the gene structure. Expasy site (http://www.expasy.org/) of the ProtParam tool to predict physical and chemical properties of proteins, ProtScale tool
to predict hydrophilicity profile. InterProScan  (http://www.ebi.ac.uk/InterProS can /) prediction of
protein functional domains and structural domains. PSORT II (http://psort.nibb.ac.jp/form2.html) predicted subcellular location information. SignalP3.0 Server
(http://www.cbs.dtu.dk/services/SignalP/) predicted a possible signal peptide cleavage site . TMHMM Server
(http://www.cbs.dtu.dk/services/TMHMM/) predicted transmembrane. Motif Scan (http://myhits.isb sib.ch / cgi