Comprehensive Analysis Of Gene Expression Profiles Research Articles

Comprehensive Gene Expression Profiling Analysis of Adipose Tissue in Male Individuals from Fat- and Thin-Tailed Sheep Breeds.

It has been shown that tail fat content varies significantly among sheep breeds and plays a significant role in meat quality. Recently, significant efforts have been made to understand the physiological, biochemical, and genomic regulation of fat deposition in sheep tails in order to unravel the mechanisms underlying energy storage and adipose tissue lipid metabolism. RNA-seq has enabled us to provide a high-resolution snapshot of differential gene expression between fat- and thin-tailed sheep breeds. Therefore, three RNA-seq datasets were meta-analyzed for the current work to elucidate the transcriptome profile differences between them. Specifically, we identified hub genes, performed gene ontology (GO) analysis, carried out enrichment analyses of the Kyoto Encyclopedia of Genes and Genomes (KEGG) pathways, and validated hub genes using machine learning algorithms. This approach revealed a total of 136 meta-genes, 39 of which were not significant in any of the individual studies, indicating the higher statistical power of the meta-analysis. Furthermore, the results derived from the use of machine learning revealed POSTN, K35, SETD4, USP29, ANKRD37, RTN2, PRG4, and LRRC4C as substantial genes that were assigned a higher weight (0.7) than other meta-genes. Among the decision tree models, the Random Forest ones surpassed the others in adipose tissue predictive power fat deposition in fat- and thin-tailed breeds (accuracy > 0.85%). In this regard, combining meta-analyses and machine learning approaches allowed for the identification of three important genes (POSTN, K35, SETD4) related to lipid metabolism, and our findings could help animal breeding strategies optimize fat-tailed breeds' tail sizes.

Cancer stem cell-mediated drug resistance: A comprehensive gene expression profile analysis in breast cancer.

Breast cancer is the most frequently diagnosed malignancy in women and a major public health concern. In the current report, differential expression of the breast cancer resistance promoting genes with a focus on breast cancer stem cell related elements as well as the correlation of their mRNAs with various clinicopathologic characteristics, including molecular subtypes, tumor grade/stage, and methylation status, have been investigated using METABRIC and TCGA datasets. To achieve this goal, we downloaded gene expression data of breast cancer patients from TCGA and METABRIC. Then, statistical analyses were used to assess the correlation between the expression levels of stem cell related drug resistant genes and methylation status, tumor grades, various molecular subtypes, and some cancer hallmark gene sets such as immune evasion, metastasis, and angiogenesis. According to the results of this study, a number of stem cell related drug resistant genes are deregulated in breast cancer patients. Furthermore, we observe negative correlations between methylation of resistance genes and mRNA expression. There is a significant difference in the expression of resistance-promoting genes between different molecular subtypes. As mRNA expression and DNA methylation are clearly related, DNA methylation might be a mechanism that regulates these genes in breast cancer cells. As indicated by the differential expression of resistance-promoting genes among various breast cancer molecular subtypes, these genes may function differently in different subtypes of breast cancer. In conclusion, significant deregulation of resistance-promoting factors indicates that these genes may play a significant role in the development of breast cancer.

Endothelial cell malfunction in unruptured intracranial aneurysm lesions revealed using a 3D-casted mold.

Intracranial aneurysms (IA) are major causes of devastating subarachnoid hemorrhages. They are characterized by a chronic inflammatory process in the intracranial arterial walls triggered and modified by hemodynamic force loading. Because IA lesion morphology is complex, the blood flow conditions loaded on endothelial cells in each portion of the lesion in situ vary greatly. We created a 3D-casted mold of the human unruptured IA lesion and cultured endothelial cells on this model; it was then perfused with culture media to model physiological flow conditions. Gene expression profiles of endothelial cells in each part of the IA lesion were then analyzed. Comprehensive gene expression profile analysis revealed similar gene expression patterns in endothelial cells from each part of the IA lesion but gene ontology analysis revealed endothelial cell malfunction within the IA lesion. Histopathological examination, electron microscopy, and immunohistochemical analysis indicated that endothelial cells within IA lesions are damaged and dysfunctional. Thus, our findings reveal endothelial cell malfunction in IA lesions and provided new insights into IA pathogenesis.

A comprehensive gene expression profile analysis of prostate cancer cells resistant to paclitaxel and the potent target to reverse resistance.

Background: Paclitaxel resistance is the major clinical obstacle in the chemotherapy of prostate cancer (PCa), but the resistant mechanism is less investigated.Purpose: To establish two paclitaxel-resistant PCa cells, provide a comprehensive gene expression profile analysis of resistant cells and the potential target to reverse resistance.Methods: Two Paclitaxel-resistant PCa cells (PC3/PR, LNcap/PR) were established by gradually increasing drug concentration. MTT and transwell assays were performed to detect drug sensitivity, cell proliferation and migration abilities. RNA-Sequencing (RNA-seq) and bioinformatic analyses were performed to identify abnormally expressed genes (AEGs) in resistant cells, and annotate the biological functions of AEGs. The role of the candidate AEG, TLR-4, on the resistant phenotypes was further investigated.Results: The resistance index of resistant cells was 2-3, and they showed a slower proliferation and increased migration ability. 4741 AEGs were screened out (Log2fold change absolute: log2FC(abs) > 1) in the resistant cells, and they were enriched in 2'-5'-oligoadenylate synthetase activity and chemical carcinogenesis. A number of AEGs, CCND2, IGFBP3, FOS, SHH, ZEB2, and members of FGF, FGFR and WNT families were also identified to be involved in cancer- and resistant phenotype-related processes. Finally, TLR-4 was validated significantly increased in resistant cells, and knockdown of TLR-4 increased drug-sensitivity, inhibited the proliferation and migration abilities.Conclusions: The study provided a comprehensive gene expression profile of paclitaxel-resistant PCa cells, and TLR-4 could be a potential target to reverse paclitaxel resistance.

Comprehensive gene expression analysis of IDH1/2 mutant biliary cancers (BC).

4598 Background: Isocitrate dehydrogenases (IDH) mutations (mut) identify a distinct subtype of BC that has yet to be fully characterized. We recently showed that IDH1/2 mutant (mIDH) BC harbor specific gene alterations involving chromatin remodeling and DNA repair, and a differential immune markers profile compared to other mIDH GI tumors. Here we aim to further dissect the molecular profile of mIDH BC through a comprehensive gene expression profiling analysis. Methods: 524 BC samples (303 intrahepatic cholangiocarcinoma, IHCC, 67 extrahepatic cholangiocarcinoma, EHCC, 141 gallbladder, 13 unspecified) collected between February to December of 2019 were included. Samples were analyzed using NextGen DNA sequencing (NextSeq, 592 gene panel), whole transcriptome RNA sequencing (NovaSeq) and immunohistochemistry (Caris Life Sciences, Phoenix, AZ). EBseq was used to identify differentially expressed genes in mIDH vs wild type (WT) tumors with control for FDR ( Q < 0.2). Pathway and functional enrichment analysis was performed using g:Profiler and Enrichr. Results: mIDH frequency in our cohort was 11.4% (60/524), with higher prevalence of IDH1 mut (8.8%). IHCC showed the highest mut prevalence: IDH1 13.5%, IDH2 4.6%. mIDH was more common in females ( P = 0.0036). A total of 774 genes were significantly differentially expressed between mIDH and WT: 582 underexpressed (Fold change, FC: 0.025~0.699); 192 overexpressed (FC: 1.43~3.3). Pathway enrichment showed a significant decrease of gene expression in cytokine-cytokine receptor interaction ( Q = 0.002) and inflammatory response genes ( Q = 0.005) in mIDH. Interferon-γ- and PD1 signaling-related genes expression was significantly lower in mIDH vs WT ( Q = 0.02) including IFNG (FC 0.32), NKG7 (FC 0.36), CD8B (FC 0.37), BATF (FC 0.40), PD1 (FC 0.53), SLAMF6 (FC 0.55) and PD-L2 (FC 0.60). Wnt and cadherin signaling were also enriched for altered expression in several genes in mIDH BC ( Q = 3.86e-7 and < 0.00001, respectively). Conclusions: To our knowledge, this is the largest and most extensive gene expression profiling study focused on mIDH BC. Our data show for the first time a distinct gene expression profile characterizing mIDH tumors which display significant downregulation of inflammatory response pathways and immune-related genes. These findings contribute to further the understanding of mIDH BC and may inform the future development of rational combination therapies.

Comprehensive analysis of gene-expression profile in chronic obstructive pulmonary disease.

ObjectiveTo investigate the gene-expression profile of chronic obstructive pulmonary disease (COPD) patients and explore the possible therapeutic targets.MethodsThe microarray raw dataset GSE29133, including three COPD samples and three normal samples, was obtained from Gene Expression Omnibus. After data preprocessing with the Affy package, Student’s t-test was employed to identify the differentially expressed genes (DEGs). The up- and downregulated DEGs were then pooled for gene-ontology and pathway-enrichment analyses using the Database for Annotation, Visualization and Integrated Discovery (DAVID). The upstream regulatory elements of these DEGs were also explored by using Whole-Genome rVISTA. Furthermore, we constructed a protein–protein interaction (PPI) network for DEGs. The surfactant protein D (SP-D) serum level and HLA-A gene frequency in COPD patients and healthy controls were also measured by enzyme-linked immunosorbent assay (ELISA) and real-time polymerase chain reaction, respectively.ResultsA total of 39 up- and 15 downregulated DEGs were screened. Most of the upregulated genes were involved in the immune response process, while the downregulated genes were involved in the steroid metabolic process. Moreover, we also found that HLA-A has the highest degree in the PPI network. The SP-D serum level and HLA-A gene frequency in COPD patients were significantly higher than those in healthy controls (13.62±2.09 ng/mL vs 10.28±2.86 ng/mL; 62.5% vs 12.5%; P<0.05).ConclusionOur results may help further the understanding of the mechanisms of COPD. The identified DEGs, especially HLA-A, may serve as diagnosis markers for COPD.

NF-κB Subunit c-Rel Cooperates with Myc and Mutated p53 to Confer Significantly Worse Survival in Patients with Diffuse Large B-Cell Lymphoma: A Report from the International DLBCL Rituximab-CHOP Consortium Program

Objective:To evaluate the prognostic significance of RELamplification, expression and c-Rel activation in DLBCL patients and to identify potential mechanisms for impact of c-Rel activation on patient survival.Patients and Design: The study cohort consists 460 de novo DLBCL patients (median follow-up, 46.8 moths) treated with R-CHOP. We assessed the nuclear expression/activation of c-Rel and other NF-κB subunits by immunohistochemistry, REL gene amplification by fluorescence in situ hybridization, and gene expression profiling using Affymetrix GeneChips array. Correlations between expression of nuclear c-Rel, REL mRNA, and expression of TP53, MDM2, MDM4, MYC, BCL2, AKT1, NFKB1, RELA, NFKB2, and RELB, both at the mRNA and protein levels were analyzed using t-tests. The prognostic significance of c-Rel activation, REL mRNA expression, and REL amplification was evaluated in the overall cohort, and different subgroups stratified by COO, status of TP53 mutation (wide type/WT, or mutated/MUT) and expression, Myc, Bcl-2 overexpression, and nuclear expression of other NF-κB subunits.Results:Nuclear c-Rel expression was observed in 29.6% of DLBCL patients and did not correlate with REL mRNA levels (P=0.95) and COO (P=0.77). In contrast, REL mRNA was significantly higher in germinal center B-like (GCB) subtype (P<0.0001). In GCB-DLBCL, nuclear c-Rel expression was associated with significantly lower Myc, p53, MDM4, and pAKT protein levels but not at the transcriptional level. In contrast, in ABC-DLBCL, c-Rel activation was associated with significantly higher MUT-TP53mRNA level and reduced pAKT expression.Correspondingly to the lack of associations with reduced Myc, pAKT, and p53 in ABC-DLBCL, nuclear c-Rel expression showed prognostic impact only in ABC- but not in GCB- DLBCL, especially when it was concurrent with Myc overexpression (P<0.0001 for OS and P=0.0012 for PFS). Importantly, patients with c-Rel activation and p53 mutations had significantly worse survival (for OS, hazard ratio, 3.56; P=0.0011; median survival, 16.2 vs 87.3 months. For PFS, hazard ratio, 3.976; P=0.0004; median survival, 10.4 vs 55.5 months) compared with other MUT-p53 DLBCL patients. The additive impact of c-Rel activation to TP53 mutations was more apparent in the ABC-DLBCL subtype, in which c-Rel activation was associated with significantly upregulated MUT-TP53 transcription (P=0.0087). Conversely, MUT-p53 expression was associated significantly with upregulated REL mRNA expression (P=0.0021), predominantly in the ABC-DLBCL subtype (P=0.0047). Only in ABC-DLBCL patients, TP53 mutations were associated with elevated nuclear c-Rel levels with a borderline P value (P=0.05).In addition to the association of nuclear p65 in GCB-DLBCL (P=0.003), and p50, NFKB1 and RELA mRNA in ABC-DLBCL (P=0.0023), the prognostic significance of c-Rel appears to depend on p50 (P=0.08) and p65 expression (P=0.12). Also, supporting that c-Rel transactivates anti-apoptotic BCL2L1/BCLXL by previous studies, there was no significant difference in survival of ABC-DLBCL patients with isolated BCL2 overexpression and with nuclear c-Rel expression. Comprehensive gene-expression profiling analysis and cell line study are undergoing in order to identify pathways to activate c-Rel and oncogenic mechanisms for c-Rel–mediated chemoresistance.REL amplification was predominantly observed in GCB-DLBCL (frequency, 7%) and correlated with significantly higher mRNA level (P<0.0001). However, REL amplification did not correlation with nuclear c-Rel expression or patient survival, illustrating the importance of posttranslational regulations in c-Rel activation and function. Consistent with the adverse impact of c-Rel activation at the protein level, a strong trend toward poor survival was observed for elevated RELmRNA in ABC- but not in GCB-DLBCL.Conclusions: Nuclear c-Rel activation was associated with reduced level of proteins whose degradation involves with ubiquitin-proteasome in GCB-DLBCL, and upregulated TP53 transcription in ABC-DLBCL. Reciprocal regulation of c-Rel and MUT-p53 at the transcriptional level may underlie the synergetic adverse effect of c-Rel activation and TP53 mutations. c-Rel cooperated with Myc and conferred significantly worse survival in ABC-DLBCL patients. These subsets of c-Rel+ DLBCL patients likely will benefit from c-Rel targeted therapies. DisclosuresNo relevant conflicts of interest to declare.

Towards understanding the role of orphan nuclear receptor NR4A2 in Th17 cell-mediated central nervous system autoimmunity: An experimental approach using an animal model of multiple sclerosis

Although details of its pathogenesis remain elusive, multiple sclerosis (MS) is now widely accepted as an autoimmune disease of the central nervous system (CNS) in which autoreactive helper T cells play a pivotal role in triggering pathogenic cascades. Recently developed drugs and ongoing clinical trials clearly reflect the significance of targeting pathogenic immune cells, such as T helper 17 (Th17) cells, for MS treatment. Through comprehensive gene expression profiling analysis, we previously showed that the orphan nuclear receptor, NR4A2, is selectively upregulated in peripheral blood T cells from relapsing–remitting MS patients. Furthermore, using experimental autoimmune encephalomyelitis, an animal model of MS, we have shown that NR4A2 is selectively upregulated in peripheral blood T cells and T cells from inflamed CNS tissues. T cells expressing NR4A2 in vivo were induced only when immunized with self-peptide, not with irrelevant exogenous peptides. Accordingly, interleukin-17 (IL-17)-producing helper T cells exclusively express NR4A2, whether or not they secrete interferon (IFN)-γ, suggesting that NR4A2-expressing T cells represent a pathogenic Th17 subset during autoimmunity. Therefore, NR4A2 could be a useful biomarker to estimate pathogenic Th17 cell behavior in MS patients. In addition, a blockade of NR4A2 expression in differentiating Th17 cells with small interfering RNA not only abolished IL-17 secretion, but also Th17-related genes, such as IL-21, c-Maf and IL-23 receptor. Finally, in vivo administration of NR4A2-specific small interfering RNA significantly ameliorated experimental autoimmune encephalomyelitis, implying that NR4A2 is essential for triggering MS/experimental autoimmune encephalomyelitis, and could serve as a novel therapeutic target of the diseases.

Gene expression profiling of bovine mammary gland epithelial cells stimulated with lipoteichoic acid plus peptidoglycan from Staphylococcus aureus.

A Gram-positive bacterium, Staphylococcus aureus is known to be one of the major pathogenic bacteria responsible for causing bovine mastitis. Among the various cell wall components of S. aureus, lipoteichoic acid (LTA) and peptidoglycan (PGN) are closely associated with inflammatory responses. However, the role of LTA and PGN derived from S. aureus in bovine mastitis has not been clearly elucidated. In this study, we characterized the gene expression profile of a bovine mammary gland epithelial cell line, MAC-T cells, in the presence of LTA and PGN from S. aureus. LTA plus PGN, but not LTA or PGN alone, activated MAC-T cells. The analysis of transcriptional profiles using an Affymetrix genechip microarray showed that stimulation with LTA plus PGN produced a total of 2019 (fold change >1.2) differentially expressed genes (DEGs), with 801 up-regulated genes and 1218 down-regulated genes. Of the up-regulated genes, 14 inflammatory mediator-related DEGs, 22 intra-cellular signaling molecule-related DEGs, and 15 transcription factor-related DEGs were observed, whereas among the down-regulated DEGs 17 inflammation-related DEGs were found. The microarray results were confirmed using real-time RT-PCR of 18 genes with substantial changes in expression (9 each from the up-regulated and down-regulated DEGs). These results provide a comprehensive analysis of gene-expression profiles elicited by S. aureus LTA and PGN in MAC-T cells, contributing to an understanding of the pathogenesis for S. aureus-induced bovine mastitis.

Comprehensive analysis of differentially expressed rice actin depolymerizing factor gene family and heterologous overexpression of OsADF3 confers Arabidopsis Thaliana drought tolerance.

BackgroundActin depolymerizing factors (ADFs) are small actin-binding proteins. Many higher-plant ADFs has been known to involve in plant growth, development and pathogen defense. However, in rice the temporal and spatial expression of OsADF gene family and their relationship with abiotic stresses tolerance is still unknown.ResultsHere we reported the first comprehensive gene expression profile analysis of OsADF gene family. The OsADF genes showed distinct and overlapping gene expression patterns at different growth stages, tissues and abiotic stresses. We also demonstrated that both OsADF1 and OsADF3 proteins were localized in the nucleus. OsADF1 and OsADF3 were preferentially expressed in vascular tissues. Under ABA or abiotic stress treatments, OsADF3::GUS activity was enhanced in lateral roots and root tips. Ectopically overexpressed OsADF3 conferred the mannitol- and drought-stress tolerance of transgenic Arabidopsis seedlings by increasing germination rate, primary root length and survival. Several drought-tolerance responsive genes (RD22, ABF4, DREB2A, RD29A, PIP1; 4 and PIP2; 6) were upregulated in transgenic Arabidopsis under drought stress.ConclusionsThese results suggested that OsADF gene family may participate in plant abiotic stresses response or tolerance and would facilitate functional validation of other OsADF genes.Electronic supplementary materialThe online version of this article (doi:10.1186/1939-8433-5-33) contains supplementary material, which is available to authorized users.

Identification of a possible therapeutic target through pathogenic T cell analysis of multiple sclerosis

Multiple sclerosis is an autoimmune disease affecting the central nervous system (CNS), in which Th17 and Th1 cells are involved. Comprehensive gene expression profiling analysis employing DNA microarray showed that NR4A2, an orphan nuclear receptor, is strongly upregulated in the peripheral blood T cells derived from MS patients. Further analysis revealed that NR4A2 plays a pivotal role for mediating production of inflammatory cytokines from pathogenic T cells. In experimental autoimmune encephalomyelitis (EAE), an animal model of MS, NR4A2 was selectively upregulated in the CNS-infiltrating T cells and the peripheral blood T cells. Intriguingly, a forced expression of NR4A2 augmented promoter activities of IL-17 and IFN-gamma genes, leading to an excessive production of these cytokines by splenic T cells. In contrast, treatment with siRNA specific for NR4A2 resulted in a significant reduction in the production of IL-17 and IFN-gamma. Furthermore, treatment with NR4A2-specific siRNA reduced the ability of encephalitogenic T cells to adoptively transfer EAE in recipient mice. These results imply that NR4A2 is an essential transcription factor for triggering the inflammatory cascade in MS/EAE and may serve as a novel therapeutic target of the diseases.

Modulation of gene expression in cholesterol-lowering effect of electroacupuncture at Fenglong acupoint (ST40): A cDNA microarray study

The aim of this study was to demonstrate the cholesterol-lowering effect of electroacupuncture (EA) at the acupoint of Fenglong (ST40) in mice and to investigate its molecular mechanism by using genome-wide gene expression profile analysis. Mice with hypercholesterolemia induced by a high-cholesterol diet were randomly divided into EA at ST40 group (EG), EA at non-acupoint group (ENG), and simvastatin group (DG). A lipid profile of both the plasma and liver indicated that EA at ST40 had the same hypocholesterolemic effect as that of simvastatin, while EA at non-acupoint failed to produce the same effect. The global gene expression profile showed that EA at ST40 not only regulated the expression of genes which were directly involved in the cholesterol metabolism in the liver, but also significantly affected the expression of genes involved in signal transduction, transcription regulation, cell cycle, cell adhesion, immunity and stress. The gene expression pattern was further verified by real-time RT-PCR. The mechanism by which EA at ST40 regulated liver cholesterol metabolism is discussed. We conclude that the hypocholesterolemic effect is specific to EA at ST40 and not due to general electrical stimulation of muscles. The comprehensive gene expression profile analysis appears particularly useful in the search for EA-induced changes in cholesterol regulation.

Identification ofBorrelia burgdorferiOuter Surface Proteins

Several Borrelia burgdorferi outer surface proteins have been identified over the past decade that are up-regulated by temperature- and/or mammalian host-specific signals as this spirochete is transmitted from ticks to mammals. Given the potential role(s) that these differentially up-regulated proteins may play in B. burgdorferi transmission and Lyme disease pathogenesis, much attention has recently been placed on identifying additional borrelial outer surface proteins. To identify uncharacterized B. burgdorferi outer surface proteins, we previously performed a comprehensive gene expression profiling analysis of temperature-shifted and mammalian host-adapted B. burgdorferi. The combined microarray analyses revealed that many genes encoding known and putative outer surface proteins are down-regulated in mammalian host-adapted B. burgdorferi. At the same time, however, several different genes encoding putative outer surface proteins were found to be up-regulated during the transmission and infection process. Among the putative outer surface proteins identified, biochemical and surface localization analyses confirmed that seven (Bb0405, Bb0689, BbA36, BbA64, BbA66, BbA69, and BbI42) are localized to the surface of B. burgdorferi. Furthermore, enzyme-linked immunosorbent assay analysis using serum from tick-infested baboons indicated that all seven outer surface proteins identified are immunogenic and that antibodies are generated against all seven during a natural infection. Specific antibodies generated against all seven of these surface proteins were found to be bactericidal against B. burgdorferi, indicating that these newly identified outer surface proteins are prime candidates for analysis as second-generation Lyme disease vaccinogens.

Expression profiles of two types of human knee-joint cartilage.

We have performed a comprehensive analysis of gene-expression profiles in human articular cartilage (hyaline cartilage) and meniscus (fibrocartilage) by means of a cDNA microarray consisting of 23,040 human genes. Comparing the profiles of the two types of cartilage with those of 29 other normal human tissues identified 24 genes that were specifically expressed in both cartilaginous tissues; these genes might be involved in maintaining phenotypes common to cartilage. We also compared the cartilage profiles with gene expression in human mesenchymal stem cells (hMSC), and detected 22 genes that were differentially expressed in cells representing the two cartilaginous lineages, 11 specific to each type, which could serve as markers for predicting the direction of chondrocyte differentiation. Our data should also provide useful information about regeneration of cartilage, especially in support of efforts to identify cartilage-specific molecules as potential agents for therapeutic approaches to joint repair.

Influence of O‐glycans in IgA1 hinge on its biological activity in human mesangial cells: A comprehensive gene expression profiling analysis using cDNA array

Background: The IgA1 molecule, which is predominantly deposited in glomeruli of IgA nephropathy, has the characteristic O-glycan side chain in its hinge region. Several lines of evidence have demonstrated that underglycosylated IgA1 acquires self-aggregation1 and binding affinities to the extra-cellular matrix,1,2 resulting in deposition in the glomeruli.3,4 However, there is little information concerning actual biological activities of the underglycosylated IgA1 deposited in glomeruli, which lead to mesangial cell proliferation and/or matrix expansion. Aim: To clarify the influence of O-glycan side chain in the hinge of IgA1 on its biological activity in mesangial cells, we performed a comprehensive gene expression profiling analysis of human cultured mesangial cells stimulated by enzymatically underglycosylated IgA1 using cDNA array. Methods: IgA1 was purified by affinity chromatography using anti IgA column followed by Jacalin column. Asialo/agalacto IgA1 was obtained by enzyme digestion using sialidase and β-galactosidase. Heat aggregated IgA1 was obtained by incubation at 63°C for 150 min. Cultured human mesangial cells were stimulated for 3 h by non-treated IgA1, heat aggregated IgA1 or asialo/agalacto IgA1, respectively, and total RNA was obtained. Only the enzyme stimulation was performed as a negative control for asialo/agalacto IgA1. After DNase treatment, isotope labelled probes were prepared by reverse transcription and hybridized to the Atlas Human 1.2 Array (CLONTECH, Palo Alto, CA, USA) according to the manufacturer’s protocol. A total of 1176 arrayed genes were quantitatively evaluated using BAS. Results: Expression profiles of 1176 genes were obtained. In all experiments, none of the three negative controls on the cDNA array was detected. The expression profiles of mesangial cells by each IgA1 stimulation resembled one another, but they were widely different from that of mononuclear cells. On the whole, 10% of the genes expressed in the mesangial cells were up-regulated by asialo/agalacto IgA1 stimulation compared to that by enzyme stimulation. The results suggested that under-O-glycosylated IgA1 has a biological function in human mesangial cells in vitro. In good agreement with previous studies,5 heat aggregated IgA1 stimulation up-regulated IL-6 and TNF-α expressions in mesangial cells compared to by non-treated IgA1. Asialo/agalacto IgA1 stimulation also up-regulated these molecules, suggesting its pathogenetic role in IgA nephropathy. However, since a similar tendency was revealed by enzyme stimulation alone, further study may be necessary to establish these observations. Conclusion. In the present study, we investigated the comprehensive expression profiles of mesangial cells stimulated by various types of IgA1 using cDNA array. This approach may serve as a useful database not only to evaluate the biological activities of under-O-glycosylated IgA1 but also to elucidate the pathogenesis of IgA nephropathy.