Differentially expressed long non-coding RNAs and mRNAs of cadmium exposure on learning disability of offspring rats

BACKGROUND

Cadmium (Cd) exposure has been found to have detrimental effects on the development of the central nervous system and cognitive ability in children. However, there is ongoing debate regarding the impact of maternal Cd exposure on the cognitive ability of offspring. In this study, we aimed to investigate the mechanisms underlying the influence of maternal Cd exposure on the cognitive ability of offspring rats.

METHODS

Here, we constructed a model of cadmium poisoning in first-generation rats through gavage. The cognitive and memory abilities of its offspring were evaluated by water maze experiment. Then, we used the gene chip to find out the key genes, and we performed qRT-PCR detection of these genes. Subsequently, enrichment analysis was employed to identify pathways. Finally, we constructed a co-expression network consisting of LncRNAs and mRNAs to elucidate the biological functions and regulatory mechanisms of LncRNAs.

RESULTS

The results of the water maze trial demonstrated that the offspring of rats exposed to cadmium in the first generation had reduced cognitive and memory abilities. Through an analysis of gene expression in the hippocampus of the cadmium-treated rats' offspring and the control group, we identified a correlation between the islet secretion pathway and the cognitive impairment observed in the offspring. Utilizing various algorithms, we identified Cpa1 and Prss1 as potential key genes associated with the cognitive impairment caused by cadmium. The results of qRT-PCR demonstrated a decrease in the expression levels of these genes in the hippocampus of the cadmium-treated rats' offspring. In addition, in the co-expression network, we observed that Cpa1 was co-expressed with 11 LncRNAs, while Prss1 was associated with 4 unexplored LncRNAs. Furthermore, we conducted an analysis to examine the relationship between Cpa1, Prss1-related transcription factors, and LncRNAs.

CONCLUSION

Overall, this study provides novel insights into the molecular effects of first generation Cd exposure on the cognitive ability of offspring. The target genes and signaling pathways investigated in this study could serve as potential targets for improving neurodevelopment and cognitive ability in children.

Development of a quadruple PCR-based gene microarray for detection of vaccine and wild-type classical swine fever virus, African swine fever virus and atypical porcine pestivirus

BACKGROUND

Classical swine fever (CSF), African swine fever (ASF), and atypical porcine pestivirus (APPV) are acute, virulent, and contagious viral diseases currently hampering the pig industry in China, which result in mummification or stillbirths in piglets and mortality in pigs. Diagnostic assays for the differentiation of infection and vaccination of CSFV, in addition to the detection of ASFV and APPV, are urgently required for better prevention, control, and elimination of these viral diseases in China.

METHODS

A quadruple PCR-based gene microarray assay was developed in this study to simultaneously detect wild-type and vaccine CSFV strains, ASFV and APPV according to their conserved regions. Forty-two laboratory-confirmed samples, including positive samples of 10 other swine viral diseases, were tested using this assay to confirm its high specificity.

RESULTS

This assay's limit of detections (LODs) for the wild-type and vaccine CSFV were 6.98 and 6.92 copies/µL. LODs for ASFV and APPV were 2.56 × 10 and 1.80 × 10 copies/µL, respectively. When compared with standard RT-PCR or qPCR for CSFV (GB/T 26875-2018), ASFV (MARR issue No.172), or APPV (CN108611442A) using 219 clinical samples, the coincidence was 100%. The results showed that this assay with high sensitivity could specifically distinguish ASFV, APPV, and CSFV, including CSFV infection and immunization.

CONCLUSION

This assay provides a practical, simple, economic, and reliable test for the rapid detection and accurate diagnosis of the three viruses and may have good prospects for application in an epidemiological investigation, prevention, and control and elimination of these three diseases.

Advances in multiplex molecular detection technologies for harmful algae

As the eutrophication of natural water bodies becomes more and more serious, the frequency of outbreaks of harmful algal blooms (HABs) mainly formed by harmful algae also increases. HABs have become a global ecological problem that poses a serious threat to human health and food safety. Therefore, it is extremely important to establish methods that can rapidly detect harmful algal species for early warning of HABs. The traditional morphology-based identification method is inefficient and inaccurate. In recent years, the rapid development of molecular biology techniques has provided new ideas for the detection of harmful algae and has become a research hotspot. The current molecular detection methods for harmful algal species mainly include fluorescence in situ hybridization, sandwich hybridization, and quantitative PCR (qPCR), but all of these methods can only detect single harmful algal species at a time. The establishment of methods for the simultaneous detection of multiple harmful algal species has become a new trend in the development of molecular detection technology because various harmful algal species may coexist in the natural water environment. The established molecular techniques for multiple detections of harmful algae mainly include gene chip, multiplex PCR, multiplex qPCR, massively parallel sequencing, antibody chip, and multiple isothermal amplification. This review mainly focuses on the principles, advantages and disadvantages, application progress, and application prospects of these multiple detection technologies, aiming at providing effective references not only for the fisheries but also for economic activities, environment, and human health.

Expression of IER3 in hepatocellular carcinoma: clinicopathology, prognosis, and potential regulatory pathways

Background

Immediate early response 3 (IER3) is correlated to the prognosis of several cancers, but the precise mechanisms underlying the regulation by IER3 of the occurrence and development of hepatocellular carcinoma (HCC) remain unknown.

Methods

The expression level of IER3 was examined by using in-house immunohistochemistry (IHC), public gene chip, and public RNA-sequencing (RNA-seq). The standardized mean difference (SMD) was calculated to compare the expression levels of IER3 between HCC patients and controls. The summary receiver operating characteristics (sROC) was plotted to comprehensively understand the discriminatory capability of IER3 between HCC and non-HCC group. The Kaplan-Meier curves and the combined hazard ratios (HRs) were used to determine the prognostic value of IER3 in HCC. Moreover, differentially expressed genes (DEGs) and co-expression genes (CEGs) were used to explored the molecular mechanisms of IER3 underlying HCC. hTFtarget was used to predict the transcription factors (TFs) of IER3. The binding site of TFs and the IER3 promoter region was forecasted using the JASPAR website. The relevant ChIP-seq data were used to determine whether TF peaks were present in the IER3 transcription initiation.

Results

A significantly increased expression of IER3 protein was found in HCC tissue relative to non-HCC tissue as detected by IHC (p < 0.001). Compared to 1,263 cases of non-HCC tissues, IER3 in 1483 cases of HCC tissues was upregulated (SMD = 0.42, 95% confidence interval [CI] [0.09-0.76]). The sROC showed that IER3 had a certain ability at differentiating HCC tissues (area under the curve (AUC) = 0.65, 95% CI [0.61-0.69]). Comprehensive analysis of the effect of IER3 on the prognosis of patients with HCC demonstrated that higher IER3 expression was associated with poor prognosis in HCC (HRs = 1.30, 95% CI [1.03-1.64]). Pathway enrichment analysis revealed that IER3-related genes were mostly enriched in the PI3K-Akt signaling pathway, cancer-related signaling pathways, the p53 signaling pathway, and other signaling pathways. Regulatory factor X5 (RFX5) was identified as a possible regulator of IER3-related TF.

Conclusion

IER3 may be a potential prognostic marker for HCC. The molecular mechanisms of IER3 in HCC warrant further study.

Exploring the pathogenesis of type 2 diabetes mellitus intestinal damp-heat syndrome and the therapeutic effect of Gegen Qinlian Decoction from the perspective of exosomal miRNA

ETHNOPHARMACOLOGICAL RELEVANCE

Diabetes is a common, complex, chronic metabolic disease. A randomized, double-blind, placebo-parallel controlled clinical study has shown that Gegen Qinlian Decoction (GQD) can reduce glycosylated hemoglobin in type 2 diabetes mellitus (T2DM) intestinal damp-heat syndrome patients in a dose-dependent manner.

AIM

To explore the pathogenesis of T2DM intestinal damp-heat syndrome and the therapeutic effect of GQD from the perspective of exosomal microRNA (miRNA).

METHODS

Eligible patients were selected and treated with GQD for 3 months to evaluate their clinical efficacy. Effective cases were matched with healthy volunteers, and saliva samples were collected. Exosomal miRNA was extracted from saliva and analyzed by chip sequencing. Subsequently, the function of the differential gene and the signal transduction pathway were analyzed using bioinformatics technology. Finally, three target miRNAs were randomly selected from the T2DM group/healthy group, and two target miRNAs in the T2DM before treatment/after treatment group were randomly selected for qPCR verification. Finally, we conducted a correlation analysis of the miRNAs and clinical indicators. The registration number for this research is ChiCTR-IOR-15006626.

RESULTS

(1) The expression of exosomal miRNA chips showed that there were 14 differentially expressed miRNAs in the T2DM group/healthy group, and 26 differentially expressed miRNAs in the T2DM before treatment/after treatment group. (2) Enrichment results showed that in the T2DM group/healthy group, it was primarily related to cell development, body metabolism, TGF-β, and ErbB signaling pathways. In the T2DM before treatment/after treatment group, it was mainly related to cellular metabolic regulation processes, and insulin, Wnt, and AMPK signaling pathways. (3) The qPCR verification showed that the expressions of hsa-miR-9-5p, hsa-miR-150-5p, and hsa-miR-216b-5p in the T2DM group was higher (P<0.05). Following GQD treatment, hsa-miR-342-3p and hsa-miR-221-3p were significantly downregulated (P<0.05). (4) hsa-miR-9-5p was positively correlated with BMI (P<0.05), and hsa-miR-150-5p was positively correlated with total cholesterol and triglycerides (P<0.05). The GQD efficacy-related gene hsa-miR-342-3p was positively correlated with the patient's initial blood glucose level (P<0.05), and hsa-miR-221-3p was positively correlated with total cholesterol and triglycerides (P<0.05).

CONCLUSION

The exosomal miRNA expression profile and signaling pathways related to T2DM intestinal damp-heat syndrome and the efficacy of GQD were established, which provides an alternative strategy for precision traditional Chinese medicine treatment.

The value of gene chip detection of bronchoalveolar lavage fluid in the diagnosis of nontuberculous mycobacterial lung disease

BACKGROUND

Nontuberculous mycobacteria (NTM) are mycobacteria other than mycobacterium tuberculosis complex (MTBC) and mycobacterium leprae. NTM can cause infection in many human tissues and organs and is most commonly seen in the lungs. Clinically, the symptoms and signs of nontuberculous mycobacteria lung disease (NMLD) are very similar to those of tuberculosis (TB). Because most NTMs are resistant to conventional anti-TB drugs, the rapid diagnosis of NMLD is the key to treatment. This study aimed to use gene chip technology to examine bronchoalveolar lavage fluid (BALF) from NMLD patients to explore the value of this technique for the rapid diagnosis of NMLD in BALF.

METHODS

A retrospective analysis of 308 patients with NMLD treated at Fuzhou Pulmonary Hospital from January 2018 to June 2020 was performed. BALF was collected from the patients. Gene chip detection (Capital Bio Corporation, Chengdu, China) and BACTEC MGIT960 (Becton, Dickinson and Company, MD, USA) liquid culture were performed to compare the NTM positive detection rates between the two methods. The NTM strain isolated from liquid culture were identified by rDNA sequencing and the results of identification were compared with those of gene chip detection using BALF specimens.

RESULTS

A total of 221 cases of NTM were detected in 308 BALF specimens by the gene chip method; the positive rate was 71.75% (221/308). A total of 218 cases of NTM were detected by the liquid culture method, and the positive rate was 70.78% (218/308). There was no significant difference in the positive rate of NTM detected in BALF specimens between the two methods (χ2=0.138 P=0.804>0.05); 187 cases were detected with both sequencing and gene chip detection, and the coincidence rate of strain identification with the two methods reached 96.79% (181/187). Sequencing of 218 strains of NTM was carried out; eight species were identified, and the top four species were M. intracellulare (131/218, 60.09%), M. avium (48/218, 22.02%), M. abscessus (27/218, 12.38%), and M. kansasii (5/218, 2.29%).

CONCLUSIONS

Gene chip technology can rapidly detect NTM in BALF and accurately identify bacterial species. It has important clinical value in the early diagnosis and treatment of NMLD.

Microarray analysis of long non-coding RNA expression profiles in low high-density lipoprotein cholesterol disease

Background

Low high-density lipoprotein cholesterol (HDL-C) disease with unknown etiology has a high prevalence in the Xinjiang Kazak population. In this study, long noncoding RNAs (lncRNAs) that might play a role in low HDL-C disease were identified.

Methods

Plasma samples from 10 eligible individuals with low HDL disease and 10 individuals with normal HDL-C levels were collected. The lncRNA profiles for 20 Xinjiang Kazak individuals were measured using microarray analysis.

Results

Differentially expressed lncRNAs and mRNAs with fold-change values not less than 1.5 and FDR-adjusted P-values less than 0.05 were screened. Bioinformatic analyses, including Gene Ontology (GO), Kyoto Encyclopedia of Genes and Genomes (KEGG), and network analyses, were used to determine relevant signaling pathways and predict potential target genes. In total, 381 lncRNAs and 370 mRNAs were differentially expressed based on microarray analysis. Compared with those in healthy individuals, several lncRNAs were upregulated or downregulated in patients with low HDL-C disease, among which TCONS_00006679 was most significantly upregulated and TCONS_00011823 was most significantly downregulated. GO and KEGG pathway analyses as well as co-expression networks of lncRNAs and mRNAs revealed that the platelet activation pathway and cardiovascular disease were associated with low HDL-C disease.

Conclusions

Potential target genes integrin beta-3 (ITGB3) and thromboxane A2 receptor (TBXA2R) were regulated by the lncRNAs AP001033.3–201 and AC068234.2–202, respectively. Both genes were associated with cardiovascular disease and were involved in the platelet activation pathway. AP001033.3–201 and AC068234.2–202 were associated with low HDL-C disease and could play a role in platelet activation in cardiovascular disease. These results reveal the potential etiology of dyslipidemia in the Xinjiang Kazakh population and lay the foundation for further validation using large sample sizes.

Prevalence of nontuberculous mycobacteria in a tertiary hospital in Beijing, China, January 2013 to December 2018

BACKGROUND

To investigate the species distribution of non-tuberculous mycobacteria (NTM) among tuberculosis (TB) specimens collected from January 2013 to December 2018 at Peking Union Medical Hospital (Beijing), China. NTM species identification was carried out by DNA microarray chip.

RESULTS

Mycobacterial species were detected in 1514 specimens from 1508 patients, among which NTM accounted for 37.3% (565/1514), increasing from a proportion of 15.6% in 2013 to 46.1% in 2018 (P < 0.001). Among the 565 NTM positive specimens, the majority (55.2%) were from female patients. Furthermore, patients aged 45-65 years accounted for 49.6% of the total patients tested. Among 223 NTM positive specimens characterized further, the majority (86.2%) were from respiratory tract, whilst 3.6 and 3.1% were from lymph nodes and pus, respectively. Mycobacterium intracellulare (31.8%) and Mycobacterium chelonae / Mycobacterium abscessus (21.5%) were the most frequently detected species, followed by M. avium (13.5%), M. gordonae (11.7%), M. kansasii (7.6%), and others.

CONCLUSION

The proportion of NTM among mycobacterial species detected in a tertiary hospital in Beijing, China, increased rapidly from year 2013 to 2018. Middle-aged patients are more likely to be infected with NTM, especially females. Mycobacterium intracellulare and Mycobacterium chelonae/ Mycobacterium abscessus were the most frequently detected NTM pathogens. Accurate and timely identification of NTM is important for diagnosis and treatment.

Small-cell variant renal oncocytoma: Case report on its clinicopathological and genetic characteristics and literature review

INTRODUCTION

Small-cell variant of RO is a rare subtype of renal tumor that can be easily misdiagnosed. To date, only 20 cases had been reported, with its genetic alterations largely unknown due to insufficient information.

MATERIALS AND METHODS

We report a case of the tumor with genetic characterization using exome sequencing chip. We also reviewed literature on this lesion to summarize clinicopathological presentation and differential diagnosis of the tumor.

DISCUSSION

Grossly, the tumor is yellow to grayish brown, with clear boundary, central scar, or cystic degeneration. Microscopically, small-cell variant RO show scant eosinophilic cytoplasm with small-round nuclei, arranged in small acini and tubules. Nucleoli and necrosis are rarely observed. Immunohistochemically, the tumor is positive for EMA, cytokeratin 18, CD117 and E-cadherin. Genetically, 4745 differentially expressed genes in this tumor, which encode tricarboxylic acid cycle enzymes and are involved in mitochondrial respiratory chain. This result strongly supports the diagnosis of small cell variant of RO. Findings from the molecular genetic analysis of our case suggests that metabolic pathway-related genes (PIK3R5, PI3KCB, PLA2G4E, PLA2G2A, PLA2G6, PLCB4, PLCG2) may be exploited as potential targets for diagnosis and treatment when necessary. These genes may provide new clues for future research.

CONCLUSION

Small-cell variant of RO is considered benign renal neoplasms with good prognosis. A histochemical and immunohistochemical stains assist in diagnosis of this tumor. Definitive diagnosis can help avoid unnecessary total renal nephrectomy. The exact mechanism of Small-cell variant of RO remains to be further investigated.

Genomic and GeneChip expression profiling reveals the inhibitory effects of Amorphophalli Rhizoma in TNBC cells

ETHNOPHARMACOLOGICAL RELEVANCE

Amorphophalli Rhizoma has been widely used as an adjuvant treatment for advanced or metastatic breast cancer, pancreatic cancer, hepatoma, and malignant lymphoma, but its molecular mechanism of action for treatment of metastatic triple-negative breast cancer (TNBC) is generally poorly understood.

AIM OF THE STUDY

To investigate genomic changes related to the inhibitory effect of Amorphophalli Rhizoma and to elucidate the molecular mechanism of this inhibition in MDA-MB-231 TNBC cells.

MATERIALS AND METHODS

Gene chip analysis was employed to explore genomic changes caused by Amorphophalli Rhizoma in TNBC cells. Potential classical signaling pathways, upstream regulators, functions, regulatory effects and gene interaction networks were analyzed by Ingenuity Pathway Analysis (IPA). Real-time quantitative PCR (RT-qPCR) and RNA interference (RNAi) assays were used to clarify the roles of potential target genes.

RESULTS

In total, 536 significantly upregulated and 648 significantly downregulated genes were identified between the group treated with Amorphophalli Rhizoma extract and that treated with vehicle. Many of these differentially expressed genes (DEGs) in TNBC cells are involved in DNA replication, recombination and repair, the cell cycle, and cellular assembly and organization. Attenuation of KNL1, OLFML2A, RTKN2 and SGO1 gene expression by Amorphophalli Rhizoma significantly induced cell cycle arrest and suppressed cell proliferation and migration.

CONCLUSIONS

The inhibitory effects of Amorphophalli Rhizoma in TNBC cells likely occur through regulation of the spindle checkpoint, chromosomal and centrosomal instability, and cell membrane stability.

[Transcription factors analysis of subchondral bone in early experimental osteoarthritis based on gene expression profiles]

OBJECTIVE

To identify the master transcription factors (TF) that might be responsible for the gene expression alteration of OA.

METHODS

Raw expression data for rat OA model(GSE30322) was downloaded from NCBI GEO database. Microarray data analysis for rat and human was carried out separately using functions from limma packagein R, gene expression was considered as significantly changed between conditions if adjusted P-value<0.05 and the absolute value of fold change>=2. iRegulon was applied to differentially up-regulated and down-regulated genes in OA separately.

RESULTS

(1)15 TFs, including FOXN4, NANOS1, E2F6, RAD21, MECOM, ETS1, MEF2A, POU2F3, BRCA1, GATA3, ZNF706, ZBTB33, SUZ12, DBP and SETDB1, were identified as the potential master TFs of up-regulated DEGs with statistical significance. (2)12 TFs, including ARID3A, YY1, RDBP, ATF1, CRX, TAF1, XBP1, SOX3, E2F4, PGR, TIMM8A and HOXA2, were identified as the potential master TFs of down-regulated DEGs with statistical significance.

CONCLUSIONS

The newly identified TFs maybe play important roles in pathogenesis of early experimental osteoarthritis, and our study provides new diagnostic markers or therapeutic targets for OA.

GeneChip analysis of resistant Mycobacterium tuberculosis with previously treated tuberculosis in Changchun

Background

With the widespread use of rifampicin and isoniazid, bacterial resistance has become a growing problem. Additionally, the lack of relevant baseline information for the frequency of drug-resistant tuberculosis (TB) gene mutations is a critical issue, and the incidence of this infection in the city of Changchun has not investigated to date. However, compared with the slow traditional methods of drug susceptibility testing, recently developed detection methods, such as rifampicin and isoniazid resistance-related gene chip techniques, allow for rapid, easy detection and simultaneous testing for mutation frequency and drug resistance.

Methods

In this study, the rifampicin and isoniazid resistance-related gene mutation chip method was employed for an epidemiological investigation. To assess the gene mutation characteristics of drug-resistant TB and evaluate the chip method, we tested 2143 clinical specimens from patients from the infectious diseases hospital of Changchun city from January to December 2016. The drug sensitivity test method was used as the reference standard.

Results

The following mutation frequencies of sites in the rifampicin resistance gene rpoB were found: Ser531Leu (52.6%), His526Tyr (12.3%), and Leu511Pro (8.8%). The multidrug-resistance (MDR)-TB mutation frequency was 34.7% for rpoB Ser531Leu and katG Ser315Thr, 26.4% for rpoB Ser531Leu and inhA promoter − 15 (C → T), and 10.7% for rpoB His526Tyr and katG Ser315Thr. In addition, drug susceptibility testing served as a reference standard. In previously treated clinical cases, the sensitivity and specificity of GeneChip were 83.1 and 98.7% for rifampicin resistance, 79.9 and 99.6% for isoniazid resistance, and 74.1 and 99.8% for MDR-TB.

Conclusions

Our experimental results show that the chip method is accurate and reliable; it can be used to detect the type of drug-resistant gene mutation in clinical specimens. Moreover, this study can be used as a reference for future research on TB resistance baselines.

Electronic supplementary material

The online version of this article (10.1186/s12879-018-3131-8) contains supplementary material, which is available to authorized users.

Differences in gene expression profile between vocal cord Leukoplakia and normal larynx mucosa by gene chip

BACKGROUND

Long non-coding RNAs (lncRNAs) play an important role in tumorigenesis. Vocal cord leukoplakia is a precancerous lesion in otolaryngological practice. Till now, the expression patterns and functions of lncRNAs in vocal cord leukoplakia have not been well understood. In this study, we used microarrays to investigate the aberrantly expressed lncRNAs and mRNAs in vocal cord leukoplakia and adjacent non-neoplastic tissues.

METHODS

Gene Ontology and pathway analyses were performed to determine the significant function and pathways of the differentially expressed mRNAs. qRT-PCR was performed to further validate the expression of selected lncRNAs and mRNAs in vocal cord leukoplakia.

RESULTS

Our study identified 170 differentially expressed lncRNAs and 99 differentially expressed mRNAs, including 142 up-regulated lncRNAs and 28 down-regulated lncRNAs, and 54 up-regulated mRNAs and 45 down-regulated mRNAs. Among these, XLOC_000605 and DLX6-AS1 were the most aberrantly expressed lncRNAs. Furthermore, we identified an antisense lncRNA (LOC100506801), an enhancer-like lncRNA (AK057351) and three long intergenetic noncoding RNAs including XLOC_008001, XLOC_011989 and XLOC_007341.

CONCLUSIONS

Our results revealed that many lncRNAs were differentially expressed between vocal cord leukoplakia tissues and normal tissue, suggesting that they may play a key role in vocal cord leukoplakia tumorigenesis.

Comparison of gene expression profiles induced by fresh or ozone-oxidized black carbon particles in A549 cells

Epidemiological studies have showed an association between black carbon (BC) exposure and adverse health effects. This study intends to investigate the influence of oxidation processes in atmosphere on the initial cellular responses of BC. The changes of gene expressions induced by fresh BC (FBC) and ozone-oxidized BC (OBC) in human lung epithelial A549 cells were analyzed. And their toxic effects presented by viability, LDH release and DNA damage were compared. Totally 47, 000 genes in A549 cells were examined using Affymetrix Human U133 plus 2.0 chips. Some of the differentially expressed genes were verified by reverse transcription-quantitative polymerase chain reaction (RT-qPCR). The results showed that 1446 genes (including 756 up-regulated and 690 down-regulated) and 1594 genes (including 788 up-regulated and 806 down-regulated genes) were significantly changed by FBC and OBC respectively. Only 4 of 14 (FBC)/15 (OBC) oxidative stress related genes, up- or down-regulated by FBC and OBC, were identical; 13 of 29 (FBC)/31 (OBC) inflammation related genes, and 6 of 20 (FBC)/18 (OBC) autophagy related genes were identical. No obvious differences were observed between the toxic effects of FBC and OBC. The cytotoxicity of OBC and FBC in A549 cells is at least partially induced by oxidative stress and consequent inflammation or autophagy process. Previous studies indicated that OBC may be more toxic than FBC. However, our results suggested that FBC and OBC might lead to diverse toxic endpoints through activating different molecular pathways.

Influence of SKF38393 on changes of gene profile in rat prefrontal cortex during chronic paradoxical sleep deprivation

Chronic paradoxical sleep deprivation (CSD) can induce dramatic physiological and neurofunctional changes in rats, including decreased body weight, reduced learning and memory, and declined locomotor function. SKF38393, a dopamine D1 receptor agonist, can reverse the above damages. However, the mechanism of CSD syndrome and reversal role of SKF38393 remains largely unexplained. To preliminarily elucidate the mechanism of the neural dysfunction caused by CSD, in the present study we use gene chips to examine the expression profile of more than 28,000 transcripts in the prefrontal cortex (PFC). Rats were sleep deprived by modified multi-platform method for 3 weeks. Totally 59 transcripts showed differential expressions in CSD group in contrast to controls; they included transcripts coding for caffeine metabolism, circadian rhythm, drug metabolism and some amino acid metabolism pathway. Among the 59 transcripts, 39 increased their expression and 20 decreased. Two transcripts can be specifically reversed with SKF38393, one of them is Homer1, which is related to 20 functional classifications and coding for Glutamatergic synapse pathway. Our findings in the present study indicate that long-term sleep deprivation may trigger the changes of some certain functions and pathways in the PFC, and lead to the dysfunction of this advanced neuron, and the activation of D1 receptor by SKF38393 might ameliorate these changes via modulation of some transcripts such as Homer1, which is involved in the Ca(2+) pathway and MAPK pathway related to Glutamatergic synapse pathway.

The Screening of Genes Sensitive to Long-Term, Low-Level Microwave Exposure and Bioinformatic Analysis of Potential Correlations to Learning and Memory

OBJECTIVE

To gain a better understanding of gene expression changes in the brain following microwave exposure in mice. This study hopes to reveal mechanisms contributing to microwave-induced learning and memory dysfunction.

METHODS

Mice were exposed to whole body 2100 MHz microwaves with specific absorption rates (SARs) of 0.45 W/kg, 1.8 W/kg, and 3.6 W/kg for 1 hour daily for 8 weeks. Differentially expressing genes in the brains were screened using high-density oligonucleotide arrays, with genes showing more significant differences further confirmed by RT-PCR.

RESULTS

The gene chip results demonstrated that 41 genes (0.45 W/kg group), 29 genes (1.8 W/kg group), and 219 genes (3.6 W/kg group) were differentially expressed. GO analysis revealed that these differentially expressed genes were primarily involved in metabolic processes, cellular metabolic processes, regulation of biological processes, macromolecular metabolic processes, biosynthetic processes, cellular protein metabolic processes, transport, developmental processes, cellular component organization, etc. KEGG pathway analysis showed that these genes are mainly involved in pathways related to ribosome, Alzheimer's disease, Parkinson's disease, long-term potentiation, Huntington's disease, and Neurotrophin signaling. Construction of a protein interaction network identified several important regulatory genes including synbindin (sbdn), Crystallin (CryaB), PPP1CA, Ywhaq, Psap, Psmb1, Pcbp2, etc., which play important roles in the processes of learning and memorye.

CONCLUSION

Long-term, low-level microwave exposure may inhibit learning and memory by affecting protein and energy metabolic processes and signaling pathways relating to neurological functions or diseases.

Homozygosity mapping and sequencing identify two genes that might contribute to pointing behavior in hunting dogs

BACKGROUND

The domestic dog represents an important model for studying the genetics of behavior. In spite of technological advances in genomics and phenomics, the genetic basis of most specific canine behaviors is largely unknown. Some breeds of hunting dogs exhibit a behavioral trait called "pointing" (a prolonged halt of movement to indicate the position of a game animal). Here, the genomes of pointing dogs (Large Munsterlander and Weimaraner) were compared with those of behaviorally distinct herding dogs (Berger des Pyrenées and Schapendoes). We assumed (i) that these four dog breeds initially represented inbred populations and (ii) that selective breeding for pointing behavior promotes an enrichment of the genetic trait in a homozygous state.

RESULTS

The homozygosity mapping of 52 dogs (13 of each of the four breeds) followed by subsequent interval resequencing identified fixed genetic differences on chromosome 22 between pointers and herding dogs. In addition, we identified one non-synonomous variation in each of the coding genes SETDB2 and CYSLTR2 that might have a functional consequence. Genetic analysis of additional hunting and non-hunting dogs revealed consistent homozygosity for these two variations in six of seven pointing breeds.

CONCLUSIONS

Based on the present findings, we propose that, together with other genetic, training and/or environmental factors, the nucleotide and associated amino acid variations identified in genes SETDB2 and CYSLTR2 contribute to pointing behavior.

Enhanced amino acid utilization sustains growth of cells lacking Snf1/AMPK

The metabolism of proliferating cells shows common features even in evolutionary distant organisms such as mammals and yeasts, for example the requirement for anabolic processes under tight control of signaling pathways. Analysis of the rewiring of metabolism, which occurs following the dysregulation of signaling pathways, provides new knowledge about the mechanisms underlying cell proliferation. The key energy regulator in yeast Snf1 and its mammalian ortholog AMPK have earlier been shown to have similar functions at glucose limited conditions and here we show that they also have analogies when grown with glucose excess. We show that loss of Snf1 in cells growing in 2% glucose induces an extensive transcriptional reprogramming, enhances glycolytic activity, fatty acid accumulation and reliance on amino acid utilization for growth. Strikingly, we demonstrate that Snf1/AMPK-deficient cells remodel their metabolism fueling mitochondria and show glucose and amino acids addiction, a typical hallmark of cancer cells.

Comparative proteomic analysis provides new insights into cadmium accumulation in rice grain under cadmium stress

Rice is one of the most important staple crops. During the growth season, rice plants are inevitably subjected to numerous stresses, among which heavy metal stress represented by cadmium contamination not only hindering the yield of rice but also affecting the food safety by Cd accumulating in rice grains. The mechanism of Cd accumulation in rice grains has not been well elucidated. In this study, we compare the proteomic difference between two genotypes with different Cd accumulation ability in grains. Verification of differentially expressed protein-encoding genes was analyzing by quantitative PCR (QPCR) and reanalysis of microarray expression data. Forty-seven proteins in total were successfully identified through proteomic screening. GO and KEGG enrichment analysis showed Cd accumulation triggered stress-related pathways in the cells, and strongly affecting metabolic pathways. Many proteins associated with nutrient reservoir and starch-related enzyme were identified in this study suggesting that a considerably damage on grain quality was caused. The results also implied stress response was initiated by the abnormal cells and the transmission of signals may mediated by reactive oxygen species (ROS). Our research will provide new insights into Cd accumulation in rice grain under Cd stress.

Gene expression profiles associated with osteoblasts differentiated from bone marrow stromal cells

OBJECTIVE

To study the changes of gene expression profiles associated with osteoblasts differentiated from rat bone marrow stromal cells in vitro by gene chip technique.

METHODS

rat Bone marrow stromal cells were isolated and cultured, and differentiation was induced by dexamethasone, β-glycerol phosphate and vitamin C. Cellular mRNA was extracted and reverse transcribed into cDNA, thus related genes expression differences were detected by gene expression profile chip.

RESULTS

Calcifying nodules were visible in the induced cells. There were 27.7% genes expressed differentially, three times more than the normal and induced cells, and some genes were related to transcription, translation, glycosylation modification. Extracellular matrix, signal molecules and metabolism were up-regulated.

CONCLUSIONS

The gene chip technique can be used to detect the multi-gene different expression in the differentiation-induced rat BMSCs, and these differentially expressed genes are necessary genes related to rat BMSCs proliferation and induction of osteoblastic differentiation.

Genes involved in immunity and apoptosis are associated with human presbycusis based on microarray analysis

CONCLUSIONS

Genes involved in immunity and apoptosis were associated with human presbycusis. CCR3 and GILZ played an important role in the pathogenesis of presbycusis, probably through regulating chemokine receptor, T-cell apoptosis, or T-cell activation pathways.

OBJECTIVES

To identify genes associated with human presbycusis and explore the molecular mechanism of presbycusis.

METHODS

Hearing function was tested by pure-tone audiometry. Microarray analysis was performed to identify presbycusis-correlated genes by Illumina Human-6 BeadChip using the peripheral blood samples of subjects. To identify biological process categories and pathways associated with presbycusis-correlated genes, bioinformatics analysis was carried out by Gene Ontology Tree Machine (GOTM) and database for annotation, visualization, and integrated discovery (DAVID). Quantitative RT-PCR (qRT-PCR) was used to validate the microarray data.

RESULTS

Microarray analysis identified 469 up-regulated genes and 323 down-regulated genes. Both the dominant biological processes by Gene Ontology (GO) analysis and the enriched pathways by Kyoto encyclopedia of genes and genomes (KEGG) and BIOCARTA showed that genes involved in immunity and apoptosis were associated with presbycusis. In addition, CCR3, GILZ, CXCL10, and CX3CR1 genes showed consistent difference between groups for both the gene chip and qRT-PCR data. The differences of CCR3 and GILZ between presbycusis patients and controls were statistically significant (p < 0.05).

Cytotoxicity and genome-wide microarray analysis of intestinal smooth muscle cells in response to hexavalent chromium induction

Chronic ingestion of high concentrations of hexavalent chromium [Cr(VI)] in drinking water induces intestinal tumors in mice; however, information on its toxicity on intestinal smooth muscle cells is limited. The present study aimed to assess the in vitro and in vivo toxicological effects of Cr(VI) on intestinal smooth muscle cells. Human intestinal smooth muscle cells (HISM cells) were cultured with different concentrations of Cr(VI) to evaluate effects on cell proliferation ability, oxidative stress levels, and antioxidant system. Furthermore, tissue sections in Cr(VI) exposed rabbits were analyzed to evaluate toxicity on intestinal muscle cells in vivo. Gene chips were utilized to assess differential gene expression profiles at the genome-wide level in 1 μmol/L Cr(VI) treated cells. Intestinal tissue biopsy results showed that Cr(VI) increased the incidences of diffuse epithelial hyperplasia in intestinal jejunum but caused no obvious damage to the structure of the muscularis. Cell proliferation analysis revealed that high concentrations (≥64 μmol/L) but not low concentrations of Cr(VI) (≤16 μmol/L) significantly inhibited the growth of HISM cells. For oxidative stress levels, the expression of reactive oxygen species (ROS) and nitric oxide (NO) was elevated at high concentrations (≥64 μmol/L) but not at low concentrations of Cr(VI) (≤16 μmol/L). In addition, dose-dependent increases in the activity of oxidized glutathione (GSSH)/total-glutathione (T-GSH) were also observed. Gene chip screened 491 differentially expressed genes including genes associated with cell apoptosis, oxidations, and cytoskeletons. Some of these differentially expressed genes may be unique to smooth muscle cells in response to Cr(VI) induction.

MiRNA expression profiling of rectal adenocarcinoma

AIM: To compare the expression profile of microRNA (miRNA) between rectal adenocarcinoma and normal rectal mucosal tissue to identify genes possibly associated with the development of rectal cancer.

METHODS: MiRNA expression profiling of two rectal adenocarcinoma samples and two normal rectal tissue samples was performed using miRNA microarray. The possible targets of miRNAs were predicated using bioinformatic tools.

RESULTS: Fifty-five miRNAs were found to be differentially expressed between rectal adenocarcinoma and normal tissues, with thirty-seven miRNAs up-regulated while eighteen down-regulated. Bioinformatic analyses indicated that ZFHX4 may be the target of miR-375, and that BACH2 and FZD3 may be the targets of miR-31.

CONCLUSION: There is a specific miRNA expression profile in rectal adenocarcinoma. MiRNAs play an important role in the development of rectal adenocarcinoma. Target mRNAs were primarily identified and worthy of further study.

DNMT1: an emerging target in the treatment of invasive urinary bladder cancer

OBJECTIVES

More than 14,000 people die from invasive urothelial carcinoma (iUC) of the urinary bladder each year in the USA, and more effective therapies are needed. Naturally occurring canine iUC very closely resembles the disease in humans and serves as a highly relevant translational model for novel therapy of human iUC. Work was undertaken to identify new targets for anticancer therapy in dogs with the goal of translating successful therapeutic strategies into humans with iUC.

MATERIALS AND METHODS

Microarray expression analyses were conducted on mRNA extracted from canine normal bladder (n = 4) and iUC tissues (n = 4) using Genome Array 1.0 and analyzed by GeneSpring GX 11, with the stringency of P < 0.02 and a ≥ 2-fold change. The genes thus identified were further analyzed for functional and pathway analysis using Protein ANalysis THrough Evolutionary Relationships (PANTHER) Classification System. In selecting genes for further study, consideration was given for evidence of a role of the gene in human iUC. From these analyses, DNA methyltransferase 1 (DNMT1) was selected for further study. Immunohistochemistry (IHC) of canine normal bladder and iUC tissues was performed to confirm the microarray expression analyses. The effects of targeting DNMT1 in vitro was assessed through MTT assay and Western blot of canine iUC cells treated with 5-azacitidine (5-azaC) and trichostatin A (TSA).

RESULTS

DNMT1 was expressed in 0 of 6 normal canine bladder samples and in 10 of 22 (45%) canine iUC samples. The proliferation of canine iUC cells was inhibited by 5-azaC (at concentrations ≥ 5 μm) and by TSA (at concentrations ≥ 0.1 μm). Western blot results were supportive of DNMT1-related effects having a role in the antiproliferative activity.

CONCLUSIONS

Microarray expression analyses on canine tissues identified DNMT1 as a potentially "targetable" gene. Expression of DNMT1 in canine iUC was confirmed by IHC, and in vitro studies confirmed that drugs that inhibit DNMT1 have antiproliferative effects. These findings are similar to those recently reported in human iUC and are also in line with results of a preclinical (prehuman) trial of 5-azaC in dogs with naturally occurring iUC. DNMT1 has excellent potential as a target for iUC therapy in humans.

Screening of genes differentially expressed between human esophageal squamous cell carcinoma and tumor-adjacent normal tissue using gene chip technology

AIM: To screen differentially expressed genes between human esophageal squamous cell carcinoma and tumor-adjacent normal tissue to lay a theoretical basis for finding molecular markers specific for esophageal squamous cell carcinoma.

METHODS: Total RNA was extracted from human esophageal squamous cell carcinoma and tumor adjacent normal tissue specimens and cDNA was synthesized by reverse transcription. Probes were prepared by labeling the synthesized cDNA with Cy3-dUTP and hybridized with gene chips to screen differentially expressed genes. Bioinformatic tools were used for characterization of differentially expressed genes obtained.

RESULTS: According to the expression ratio of >4.0 or <0.25, a total of 1 113 differentially expressed genes were identified, including 464 up-regulated and 649 down-regulated ones. Bioinformatic analysis identified a variety of known functional genes. RT-PCR analysis confirmed that three genes were differentially expressed between human esophageal squamous cell carcinoma and tumor adjacent normal tissue.

CONCLUSION: Gene chip technology is highly efficient and reliable in screening genes differentially expressed in esophageal squamous cell carcinoma. The occurrence and development of esophageal squamous cell carcinoma is the result of expression of many cancer-related genes.

Mesenchymal stem cells display different gene expression profiles compared to hyaline and elastic chondrocytes

Cartilage has a poor intrinsic repair capacity, requiring surgical intervention to effect biological repair. Tissue engineering technologies or regenerative medicine strategies are currently being employed to address cartilage repair. Mesenchymal stem cells (MSCs) are considered to be an excellent cell source for this application. However, the different gene expression profiles between the MSCs and differentiated cartilage remain unclear. In this report, we first examined the gene expression profiles between the MSCs, hyaline and elastic chondrocytes, and then identify candidate genes, which may be important in the process of MSC differentiation into hyaline and elastic cartilage. Several hundred differentially expressed genes were screened initially by microarray, including 417 simultaneously up-regulated genes in both hyaline and elastic chondrocytes, with 313 down-regulated genes. Several genes were identified that were up-regulated in hyaline chondrocytes while down-regulated in elastic chondrocytes. Both RT-PCR and western blot analysis were consistent with those results obtained by microarray analysis. Chondromodulinl (Chm1) was found to be highly expressed in MSCs differentiating to hyaline and elastic cartilage. Both collagen type II, alpha 1 (Col2a1) and cartilage homeo protein 1 (Cart1) were also highly upregulated and may be important early differentiation of MSCs to hyaline cartilage.

Diagnostic value of gene chip test for detection of H.pylori infection and relationship between H.pylori virulence factors and the severity of gastroduodenal lesions

AIM: To investigate the diagnostic value of gene chip test for detection of Helicobacter pylori (H.pylori) infection in children, and to assess the relationship between H.pylori virulence factors and the severity of gastroduodenal lesions.

METHODS: A total of 30 children with symptoms of the digestive system, such as abdominal pain, vomiting, melena and hematemesis, underwent the ¹³C breath test at Beijing Children's Hospital from October 2007 to April 2008. A gene chip test was then performed for positive cases. The sensitivity and specificity of the gene chip test were analyzed. Gastroscopy was performed in patients diagnosed with H.pylori infection by both of the above methods. The pathological changes in gastroduodenal lesions were examined by gastroscopy to assess the relationship between H.pylori virulence factors and the severity of H.pylori. The results were analyzed by the Kappa test.

RESULTS: The gene chip test has a sensitivity of 93.7%, a specificity of 60%, and a rate of missed diagnosis of 6.3%. The coincidence rate between the ¹³C breath test and gene chip test is 89.1%, showing a good consistency. H.pylori CagA antibody was detected in 96.6% (29/30) of the patients, while the detection rate of VacA antibody is 3.3%. H.pylori carrying CagA may have a stronger pathogenicity. The presence of CagA antibody was often related with gastritis, peptic ulcer and Henoch-Schonlein syndrome (abdominal type), while the presence of VacA antibody predicted more severe pathological manifestations.

CONCLUSION: The gene chip test has a high specificity and sensitivity in detection of H.pylori infection, and is useful for finding the relationship between H.pylori virulence factors and the severity of disease.

Relationship between distribution of HBV genotypes and liver diseases in Lhasa

AIM: To study the distribution of HBV genotypes and the clinical relevance of genotype with hepatitis B in Lhasa, Tibet Autonomous Region of China.

METHODS: Ninety two HBV-infected cases were analyzed for genotypes using gene chip technology. And association between its epidemiology, DNA content, liver function, gender and ethnicity was investigated.

RESULTS: Seventy-three HBV DNA positive cases with varying genotypes showed significant differences (χ² = 7.179, P < 0.05). Among HBV DNA positive samples, there were 32 cases of e antigen positive, and no significant difference was observed in the DNA content but significant difference was detected in the national e antigen positive rate (χ² = 8.423, P < 0.05). Genotypes B and C were mostly present in the Han nationality, while D-type existed mainly in Tibetan. ALB was lower in type D,C than in B, but GLB was higher in B. CHB and LC were mainly present in patients D and C genotypes (F = 3.832, P < 0.05).

CONCLUSION: The HBV genotype DNA load shows no difference and no significant association between liver function enzymes and disease conditions, and protein changes are more notable. Patients with C or D genotype are more vulnerable to disease progression than those with B genotype in Lhasa, Tibet region.

Liver regeneration-related gene signaling pathways in female mice transplanted bone marrow from male mice

AIM: To probe into the mechanism underlying the transformation of bone marrow into hepatic cells.

METHODS: Inter-sexual bone marrow transplantation models were induced by transplanting bone marrow from male mice into the liver cells from female mice. Female Balb/C mice were randomly divided model group and normal control group. The oligo-necleotide acid chip with mouse gene expression spectrum was selected, and reverse transcription enzyme was used to synthesize the fluorescence-labeled cDNA probe. The probe and gene expression microchip were hybridized to observe changes of gene expression in the liver issues, and genes with a different hybrid signal ratio were selected and the changes of liver regeneration-related gene pathways in female mice transplanted bone marrow from male mice were analyzed.

RESULTS: A significance difference in the expression of genes was found in liver tissue from the female mice transplanted bone marrow from male mice after 6 mo between the model and normal control groups. Eight hundred and sixty-five genes had different expressions, including 447 recognized functional genes, of which 92 were up-regulated genes and 355 down-regulated genes. The up-regulated genes involving the signal pathways of HGF, TGF-β, focal adhesion, JAK-Stat and VEGF could promote the proliferation and differentiation of hepatic cells. The down-regulated genes could inhibit the activation of TGF-β signaling pathways and the negative effect of liver regeneration, thus contributing to the proliferation and differentiation of liver cells.

CONCLUSION: The gene expression spectrum is remarkably changed in liver tissue from female mice transplanted bone marrow from male mice by activating gene signal pathways and inhibiting liver regeneration.

Detection of HBV genotypes in Lhasa by gene chip

AIM: To investigate the distribution and characteristics of HBV genotypes in Lhasa.

METHODS: A total of 92 serum samples were collected from chronic hepatitis patients in Lhasa infected with HBV. Oligonucleotide probes were designed according to the DNA sequences from GenBank and used to prepare the genotyping chip. The fragments of HBV S gene were amplified using nested PCR. The genotypes were identified by gene chip and then confirmed by sequencing. The phylogeny was analyzed with BioEdit software. The relationship with hepatitis markers, DNA load, gender and race was also analyzed.

RESULTS: Among the 73 patients positive for HBV DNA, 13 (17.8%) were genotype B, 18 (24.7%) genotype C, 39 (53.4%) genotype D, and 3 (4.1%) mixed genotype B/D. The distribution of the genotypes was not associated with serum HBV markers, HBV DNA load or gender, but was significantly associated with nationality (χ² = 7.179, P < 0.05). Genotype B (9/13) was mostly distributed in the Han region, and genotypes C (12/18) and D (28/39) in Tibet. In addition, we selected 7 cases of genotype B, 6 of genotype C, 16 of genotype D, and 3 of mixed genotype B/D, identified by HBV typing chip which were further confirmed by sequencing, and the results of these two methods were consistent.

CONCLUSION: Gene chip technology can be used for HBV genotyping. HBV genotypes distributed in Lhasa include B, C, D and B/D, of which genotype D is the predominant strain.

Establishment and selection of genes expressing differently in a human colon carcinoma LoVo/5-FU cell line

AIM: To establish a Lovo/5-FU of human drug-resistance colon carcinoma cell line, and to screen possible drug resistance-associated genes.

METHODS: LoVo/5-FU of a human drug-resistance colon carcinoma cell line was induced by continuously exposing human colon carcinoma cells to gradually increasing concentrations of 5-FU. The growth law was observed and the growth curve protracted. The drug resistance of LoVo/5-FU was measured by MTT assay and the drug resistant index (RI) was calculated. Genes expressing differently between LoVo/5-FU and its parent cell line Lovo were screened using a gene chip, and several selected associated drug resistance genes were confirmed by reverse transcription-polymerase chain reaction (RT-PCR).

RESULTS: Compared with parental cells, the resistance cell line had a slower growth rate and larger morphology. The LoVo/5-FU cell line showed drug resistance to 5-FU, adriamycin (ADM), mitomycin (MMC), but not to cisplatin (CDDP) (RI: 7.69, 2.78, 1.43, and 0.96). There were 425 differently expressed genes associated with drug resistance by the gene chip screening method. The possible drug resistance-related genes included CYP1B1, NAT2, RNF20, SNAI2, and MAP3K2. The expression of CYP1B1 had a significant difference between the LoVo/5-FU cell line and the parent cell line (Cy5/Cy3 = 5.877). RT-PCR results were consistent with the gene chip results.

CONCLUSION: The altered biological properties of LoVo/5-FU may be related to its drug resistance phenotype. Several genes, such as CYP1B1, are possibly involved in the mechanism of drug resistance.

Gene expression profile differences in gastric cancer, pericancerous epithelium and normal gastric mucosa by gene chip

AIM: To study the difference of gene expression in gastric cancer (T), pericancerous epithelium (P) and normal tissue of gastric mucosa (C), and to screen an associated novel gene in early gastric carcinogenesis by oligonucleotide microarray.

METHODS: U133A (Affymetrix, Santa Clara, CA) gene chip was used to detect the gene expression profile difference in T, P and C, respectively. Bioinformatics was used to analyze the detected results.

RESULTS: When gastric cancer was compared with normal gastric mucosa, 766 genes were found, with a difference of more than four times in expression levels. Of the 766 genes, 530 were up-regulated (Signal Log Ratio [SLR]>2), and 236 were down-regulated (SLR<-2). When pericancerous epithelium was compared with normal gastric mucosa, 64 genes were found, with a difference of more than four times in expression levels. Of the 64 genes, 50 were up-regulated (SLR>2), and 14 were down-regulated (SLR<-2). Compared with normal gastric mucosa, a total of 143 genes with a difference in expression levels (more than four times, either in cancer or in pericancerous epithelium) were found in gastric cancer (T) and pericancerous epithelium (P). Of the 143 genes, 108 were up-regulated (SLR>2), and 35 were down-regulated (SLR<-2).

CONCLUSION: To apply a gene chip could find 143 genes associated with the genes of gastric cancer in pericancerous epithelium, although there were no pathological changes in the tissue slices. More interesting, six genes of pericancerous epithelium were up-regulated in comparison with genes of gastric cancer and three genes were down-regulated in comparison with genes of gastric cancer. It is suggested that these genes may be related to the carcinogenesis and development of early gastric cancer.

Identify lymphatic metastasis-associated genes in mouse hepatocarcinoma cell lines using gene chip

AIM: In order to obtain lymphogenous metastasis-associated genes, we compared the transcriptional profiles of mouse hepatocarcinoma cell lines Hca-F with highly lymphatic metastasis potential and Hca-P with low lymphatic metastasis potential.

METHODS: Total RNA was isolated from Hca-F and Hca-P cells and synthesized into double-stranded cDNA. In vitro transcription double-stranded cDNA was labeled with biotin (i.e., biotin-labeled cRNA, used as the probe). The cRNA probes hybridized with Affymetrix GeneChip^® MOE430A (containing 22690 transcripts, including 14500 known mouse genes and 4371 ESTs) respectively and the signals were scanned by the GeneArray Scanner. The results were then analyzed by bioinformatics.

RESULTS: Out of the 14500 known genes investigated, 110 (0.8%) were up regulated at least 2³ fold. Among the total 4371 ESTs, 17 ESTs (0.4%) (data were not presented) were up regulated at least 2³ fold. According to the Gene Ontology and TreeView analysis, the 110 genes were further classified into two groups: differential biological process profile and molecular function profile.

CONCLUSION: Using high-throughput gene chip method, a large number of genes and their cellular functions about angiogenesis, cell adhesion, signal transduction, cell motility, transport, microtubule-based process, cytoskeleton organization and biogenesis, cell cycle, transcription, chaperone activity, motor activity, protein kinase activity, receptor binding and protein binding might be involved in the process of lymphatic metastasis and deserve to be used as potential candidates for further investigation. Cyclin D1, Fosl1, Hsp47, EGFR and AR, and Cav-1 are selected as the possible candidate genes of the metastatic phenotype, which need to be validated in later experiments. ESTs (data were not presented) might indicate novel genes associated with lymphatic metastasis. Validating the function of these genes is helpful to identify the key or candidate gene/pathway responsible for lymphatic metastasis, which might be used as the diagnostic markers and the therapeutic targets for lymphatic metastasis.

Gene expression profile of liver regeneration induced by monosodium L-glutamate in rat

AIM: By analyzing the gene expression profile in the regenerated liver tissue, to study the molecular mechanism of liver regeneration disturbance induced by monosodium L-glutamate (MSG) in rat.

METHODS: Both rats (control group) and MSG-rats (model group) were operated to excise the left and middle lobes of liver (about 68% of all the liver) 6 weeks after birth. The rats were executed at 5th day after operation, and the regenerated liver tissues were frozen by liquid nitrogen. A gene chip with 1176 genes was used to detect the differentially expressed genes in the regenerated liver tissue. mRNAs were extracted from the regenerated liver tissue and 33P labeled cDNA probes were prepared by RT-PCR. The probes were hybridized with the gene chip. The data were analyzed with Microsoft Access and Excel to determine the differentially expressed genes.

RESULTS: In the 1176 examined genes, there were 256 differentially expressed genes in model group in contrast with control group, with 40 genes up-regulated and 216 gene down-regulated. Among them, there were 10 genes associated with cell receptors, 15 genes associated with transcription, 9 genes associated with cell adhesion receptor, 98 genes associated with metabolism, 9 genes associated with post-translational modification/protein folding, and 11 genes associated with protein turnover.

CONCLUSION: The gene expression profile of the MSG-indcued liver regeneration is significantly different from partial hepatectomy-induced liver regeneration in rat.