Irbesartan ameliorates diabetic kidney injury in db/db mice by restoring circadian rhythm and cell cycle

Background and Objectives

Irbesartan has been widely used in the clinical treatment of diabetic kidney disease (DKD). However, the molecular mechanism of its delay of DKD disease progression has not been fully elucidated. The aim of the present study was to investigate the mechanism of irbesartan in the treatment of DKD.

Materials and Methods

C57BL/KsJ db/db mice were randomly divided into the model group and irbesartan-treated group. After treatment with irbesartan for 12 weeks, the effects on blood glucose, body weight, 24-h urinary albumin, and renal injuries were evaluated. Microarray was used to determine the differentially expressed genes (DEGs) in the renal cortex of mice. |Log FC| <0.5 and false discovery rate (FDR) <0.25 were set as the screening criteria. Kyoto Encyclopedia of Genes and Genomes (KEGG), gene ontology (GO), protein-protein interaction (PPI) network and modules, and microRNA (miRNA)-DEGs network analysis were applied to analyze the DEGs. Furthermore, quantitative real-time polymerase chain reaction (qRT-PCR) was used to validate the results of microarray.

Results

The present study demonstrated irbesartan could significantly improve the renal function in db/db mice through decreasing 24-h urinary albumin and alleviating the pathological injury of kidney. Irbesartan may affect the expression of numerous kidney genes involved in circadian rhythm, cell cycle, micoRNAs in cancer, and PI3K-AKT signaling pathway. In the miRNA-DEGs network, miR-1970, miR-703, miR-466f, miR-5135, and miR-132-3p were the potential targets for irbesartan treatment. The validation test confirmed that key genes regulating circadian rhythm (Arntl, Per3, and Dbp) and cell cycle (Prc1, Ccna2, and Ccnb2) were restored in db/db mice on treatment with Irbesartan.

Conclusion

Generally, irbesartan can effectively treat DKD by regulating the circadian rhythm and cell cycle. The DEGs and pathways identified in the study will provide new insights into the potential mechanisms of irbesartan in the treatment of DKD.

IGF2BP3 as a Prognostic Biomarker in Well-Differentiated/Dedifferentiated Liposarcoma

BACKGROUND

Although IGF2BP3 has been implicated in tumorigenesis and poor outcomes in multiple cancers, its role in soft-tissue sarcoma (STS) remains unknown. Preliminary data have suggested an association with IGF2BP3 expression among patients with well-differentiated/dedifferentiated liposarcoma (WD/DD LPS), a disease where molecular risk stratification is lacking.

METHODS

We examined the survival associations of IGF2BP3 via univariate and multivariate Cox regression in three unique datasets: (1) the Cancer Genome Atlas (TCGA), (2) an in-house gene microarray, and (3) an in-house tissue microarray (TMA). A fourth dataset, representing an independent in-house TMA, was used for validation.

RESULTS

Within the TCGA dataset, IGF2BP3 expression was a poor prognostic factor uniquely in DD LPS (OS 1.6 vs. 5.0 years, p = 0.009). Within the microarray dataset, IGF2BP3 expression in WD/DD LPS was associated with worse survival (OS 7.7 vs. 21.5 years, p = 0.02). IGF2BP3 protein expression also portended worse survival in WD/DD LPS (OS 3.7 vs. 13.8 years, p < 0.001), which was confirmed in our validation cohort (OS 2.7 vs. 14.9 years, p < 0.001). In the multivariate model, IGF2BP3 was an independent risk factor for OS, (HR 2.55, p = 0.034).

CONCLUSION

IGF2BP3 is highly expressed in a subset of WD/DD LPS. Across independent datasets, IGF2BP3 is also a biomarker of disease progression and worse survival.

Subject clustering by IF-PCA and several recent methods

Subject clustering (i.e., the use of measured features to cluster subjects, such as patients or cells, into multiple groups) is a problem of significant interest. In recent years, many approaches have been proposed, among which unsupervised deep learning (UDL) has received much attention. Two interesting questions are 1) how to combine the strengths of UDL and other approaches and 2) how these approaches compare to each other. We combine the variational auto-encoder (VAE), a popular UDL approach, with the recent idea of influential feature-principal component analysis (IF-PCA) and propose IF-VAE as a new method for subject clustering. We study IF-VAE and compare it with several other methods (including IF-PCA, VAE, Seurat, and SC3) on 10 gene microarray data sets and eight single-cell RNA-seq data sets. We find that IF-VAE shows significant improvement over VAE, but still underperforms compared to IF-PCA. We also find that IF-PCA is quite competitive, slightly outperforming Seurat and SC3 over the eight single-cell data sets. IF-PCA is conceptually simple and permits delicate analysis. We demonstrate that IF-PCA is capable of achieving phase transition in a rare/weak model. Comparatively, Seurat and SC3 are more complex and theoretically difficult to analyze (for these reasons, their optimality remains unclear).

TRANSCRIPTOMICS OF NATURAL AND SYNTHETIC VITAMIN D IN HUMAN HEPATOCYTE LIPOTOXICITY

Vitamin D (VD) has been used to prevent non-alcoholic fatty liver disease (NAFLD), a condition of lipotoxicity associated with a defective metabolism and function of this vitamin. Different forms of VD are available and can be used for this scope, but their effects on liver cell lipotoxicity remain unexplored. In this study we compared a natural formulation rich in VD2 (Shiitake Mushroom extract or SM-VD2) with a synthetic formulation containing pure VD3 (SV-VD3) and the bioactive metabolite 1,25(OH)₂-D3. These were investigated in chemoprevention mode in human HepaRG liver cells supplemented with oleic and palmitic acid to induce lipotoxicity. All the different forms of VD showed similar efficacy in reducing the levels of lipotoxicity and the changes that lipotoxicity induced on the cellular transcriptome. However, the three forms of VD generated different gene fingerprints suggesting diverse, even if functionally convergent, cytoprotective mechanisms. Main differences were 1) the number of differentially expressed genes (SV-VD3 > 1,25(OH)₂-D3 > SM-VD2), 2) their identity that demonstrated significant gene homology between SM-VD2 and 1,25(OH)₂-D3, and 3) the number and type of biological functions identified by Ingenuity Pathway Analysis as relevant to liver metabolism and cytoprotection annotations. Immunoblot confirmed a different response of VDR and other VDR-related proteins to natural and synthetic VD formulations, including FXR, PXR, PPARγ/PGC-1α, and CYP3A4 and CYP24A1. In conclusion, different responses of the cellular transcriptome drive the cytoprotective effect of natural and synthetic formulations of VD in the free fatty acid-induced lipotoxicity of human hepatocytes.

Preliminary Study of the Distinctive Mechanism of Shenqi Compound in Treating Rats with Type 2 Diabetes Mellitus by Comparing with Metformin

BACKGROUND

In China, traditional Chinese medicine (TCM) has been used to treat type 2 diabetes mellitus (T2DM) for centuries.

METHODS

To investigate how the TCM ShenQi (SQC) formulation differs from metformin, four rat groups, including control, model, T2DM rats treated using SQC (SQC group), and T2DM rats treated using metformin (Met group), were constructed. The differentially expressed genes (DEGs) between SQC and metformin groups were screened, and the co-expression modules of the DEGs were constructed based on the weighted correlation network analysis (WGCNA) method. The correlation between modules and metabolic pathways was also calculated. The potential gene targets of SQC were obtained via the TCM systems pharmacology analysis.

RESULTS

A total of 962 DEGs between SQC and Met groups were screened, and these DEGs were significantly enriched in various functions, such as sensory perception of the chemical stimulus, NADH dehydrogenase (ubiquinone) activity, and positive regulation of the fatty acid metabolic process. In addition, seven co-expression modules were constructed after the redundancy-reduced process. Four of these modules involved specific activated or inhibited metabolic pathways. Moreover, 334 effective ingredients of SQC herbs were collected, and four genes (RNASE1 (ribonuclease A family member 1, pancreatic), ADRB1 (adrenoceptor beta 1), PPIF (peptidylprolyl isomerase F), and ALDH1B1 (aldehyde dehydrogenase 1 family member B1)) were identified as potential targets of SQC.

CONCLUSION

Comparing SQC with metformin to treat T2DM rats revealed several potential gene targets. These genes provide clues for elucidating the therapeutic mechanisms of SQC.

Plant invasion reconstructs soil microbial assembly and functionality in coastal salt marshes

Microbiologically driven ecosystem processes can be profoundly altered by alien plant invasions. The understanding of ecological mechanisms orchestrating different microbial constituents and their roles in emerging functional properties under plant invasions is limited. Here, we investigated soil microbial communities and functions using high-throughput amplicon sequencing and GeoChip technology, respectively, along a chronological gradient of smooth cordgrass invasion in salt marshes located in the Yellow River Estuary, China. We found a positive correlation between microbial diversity and the duration age of invasion, and both bacterial and fungal communities exerted orderly changes with invasion. Soil microbial metabolic potential, as indicated by the abundance of microbial functional genes involved in biogeochemical cycling, decreased in response to invasion. As a consequence, declined soil microbial metabolisms by plant invasion facilitated the carbon accumulation in invaded salt marshes. Bacteria and fungi exhibited distinct contributions to assembly processes along the invasion gradient: bacterial communities were mainly driven by selection and dispersal limitation, while fungi were dramatically shaped by stochastic processes. Soil microbial-mediated functions were taxon-specific, as indicated by community-function relationships. This study demonstrates the distinct contributions of microbial constituents to microbial community assembly and functions and sheds light on the implications of plant invasion on microbiologically driven ecosystem processes in coastal wetlands.

Laryngeal Squamous Cell Carcinoma: Clinical Significance and Potential Mechanism of Cell Division Cycle 45

Background: Cell division cycle 45 (CDC45) plays an important role in the occurrence and development of numerous carcinomas, but its effect in laryngeal squamous cell carcinoma (LSCC) remains unclear. Materials and Methods: The messenger RNA and protein expression levels of CDC45 in LSCC were evaluated with a t test and the standard mean difference (SMD). The ability of CDC45 expression to distinguish the LSCC was assessed through receiver operating characteristic (ROC) curves. Gene set enrichment analysis (GSEA), protein-protein interaction, public databases, and online tools were used to explore the potential molecular mechanism of CDC45 in LSCC. Results: A high expression of CDC45 was identified in LSCC (SMD = 2.61, 95% confidence interval [1.62-3.61]). Through ROC curves, the expression of CDC45 makes it feasible to distinguish the LSCC group from the non-LSCC counterpart. CDC45 was relevant to the progression-free interval of LSCC patients (log-rank p = 0.03). GSEAs show that CDC45 is related to the cell cycle. CDC45, CDC6, KIF2C, and AURKB were identified as hub genes of LSCC. E2F1 may be the regulatory transcription factor of CDC45. Conclusions: High expression of CDC45 likely demonstrates carcinogenic effects in LSCC, and CDC45 is a potential target in screening and treatment of LSCC.

Identification of differentially expressed genes using microarray analysis and COL6A1 induction of bone metastasis in non-small cell lung cancer

Non-small cell lung cancer (NSCLC) is a major cause of cancer-associated mortality worldwide, and bone metastasis is the most prevalent event observed in patients with advanced NSCLC. However, the pathogenesis of bone metastases has not been fully elucidated. In the present study, differentially expressed genes (DEGs) were identified by gene expression microarray analysis of NSCLC tissue samples with or without bone metastases. Subsequently, collagen type 6A1 (COL6A1) was chosen as the target gene through Ingenuity Pathway Analysis and reverse transcription-quantitative (RT-q) PCR validation of the top eight DEGs. COL6A1 was overexpressed or knocked down, and the proliferation and invasion of NSCLC cells was assessed using Cell Counting Kit-8, colony formation and Transwell invasion assays. Additionally, the osteogenic capacity of HOB and hES-MP 002.5 cells was assessed using RT-qPCR, western blotting, Alizarin Red and alkaline phosphatase staining. A total of 364 DEGs were identified in NSCLC tissues with bone metastases compared with NSCLC tissues without bone metastases, including 140 upregulated and 224 downregulated genes. Gene Ontology analysis results demonstrated that the upregulated and downregulated genes were primarily enriched in 'cellular process', 'metabolic process' and 'biological regulation'. Kyoto Encyclopedia of Genes and Genomes pathway enrichment analysis revealed that the upregulated genes were primarily enriched in 'cysteine and methionine metabolism', 'oxidative phosphorylation' and 'ribosome', whereas the downregulated genes were primarily enriched in the 'transcriptional misregulation in cancer', 'ribosome' and 'mitophagy-animal' pathways. COL6A1 was highly expressed in NSCLC tissue samples with bone metastases. Functionally, COL6A1 overexpression induced the proliferation and invasion of HARA cells, and its knockdown inhibited the proliferation and invasion of HARA-B4 cells. Finally, it was demonstrated that HOB and hES-MP 002.5 cells exhibited osteogenic capacity, and overexpression of COL6A1 in HARA cells increased the adhesion of these cells to the osteoblasts, whereas knockdown of COL6A1 in HARA-B4 cells reduced their adhesive ability. In conclusion, COL6A1 may serve as a potential diagnostic marker and therapeutic target for bone metastasis in NSCLC.

Obesogenic diet exposure alters uterine natural killer cell biology and impairs vasculature remodeling in mice†

Prepregnancy obesity associates with adverse reproductive outcomes that impact maternal and fetal health. While obesity-driven mechanisms underlying adverse pregnancy outcomes remain unclear, local uterine immune cells are strong but poorly studied candidates. Uterine immune cells, particularly uterine natural killer cells (uNKs), play central roles in orchestrating developmental events in pregnancy. However, the effect of obesity on uNK biology is poorly understood. Using an obesogenic high-fat/high-sugar diet (HFD) mouse model, we set out to examine the effects of maternal obesity on uNK composition and establishment of the maternal-fetal interface. HFD exposure resulted in weight gain-dependent increases in systemic inflammation and rates of fetal resorption. While HFD did not affect total uNK frequencies, HFD exposure did lead to an increase in natural cytotoxicity receptor-1 expressing uNKs as well as overall uNK activity. Importantly, HFD-associated changes in uNK coincided with impairments in uterine artery remodeling in mid but not late pregnancy. Comparison of uNK mRNA transcripts from control and HFD mice identified HFD-directed changes in genes that play roles in promoting activity/cytotoxicity and vascular biology. Together, this work provides new insight into how obesity may impact uNK processes central to the establishment of the maternal-fetal interface in early and mid pregnancy. Moreover, these findings shed light on the cellular processes affected by maternal obesity that may relate to overall pregnancy health.

Exploring the Protective Effect of ShenQi Compound on Skeletal Muscle in Diabetic Macrovasculopathy Mice

OBJECTIVE

ShenQi compound (SQC) is a traditional herbal formula, which has been used to treat Type 2 diabetes mellitus (T2DM) and complications for years. The aim of this study was to explore the preventive and protective effects of SQC recipe on the skeletal muscle of diabetic macrovasculopathy mice, which provides a theoretical basis for the clinical use of this formula.

METHODS

We evaluated the effect of SQC in a diabetic vasculopathy mouse model by detecting a series of blood indicators (blood glucose, lipids and insulin) and performing histological observations. Meanwhile, we explored the molecular mechanism of SQC treatment on skeletal muscle by genome expression profiles.

RESULTS

The results indicated that SQC could effectively improve blood glucose, serum lipids (total cholesterol (TC), Triglyceride (TG), high-density lipoprotein cholesterol (HDL-C) and low-density lipoprotein cholesterol (LDL-C)) and insulin (INS) levels in diabetic vasculopathy mice, as well as alleviating skeletal muscle tissue damage for diabetic macrovasculopathy. Meanwhile, compared with rosiglitazone, SQC showed a better effect on blood glucose fluctuation. Moreover, the gene microarray analysis indicated that SQC might improve T2DM by affecting biological functions related to cell death and cell adhesion. Moreover, 7 genes (Celsr2, Rilpl1, Dlx6as, 2010004M13Rik, Anapc13, Gm6097, Ddx39b) might be potential therapeutic targets of SQC.

CONCLUSION

All these results indicate that SQC is an effective preventive and protective drug for skeletal muscle in diabetic macrovasculopathy, and could alleviate skeletal muscle tissue damage through affecting biological functions related to cell death and cell adhesion.

Exploration of SQC Formula Effect on Type 2 Diabetes Mellitus by Whole Transcriptome Profile in Rats

BACKGROUND

Type 2 diabetes mellitus (T2DM) is a chronic metabolic disease that has turned out to be a pandemic all over the world. In China, some traditional Chinese herbal formulas have enjoyed a high reputation in T2DM treatment for centuries.

METHODS

In this study, ShenQi compound (SQC) is proposed, a formula that has been performed on T2DM clinical therapeutics in China for many years. The efficacy of SQC in a diabetic rat model by measuring food and water intake and examining islet microcirculatory index involves islets microvessel quantity and density, islets size, pancreatic microvascular wall thickness is evaluated. Meanwhile, gene microarray experiments were performed to explore the molecular mechanism of SQC treatment. In addition, a western medicine, metformin, was employed as a comparison.

RESULTS

The results indicated that SQC could effectively improve polydipsia, polyphagia and weight loss caused by diabetes as well as pancreatic tissue damage and vascular injury for T2DM. Meanwhile, the gene microarray experiments indicated that SQC may improve the T2DM by affecting the biological functions related to detection of chemical stimulus involved in sensory perception of smell, G-protein coupled receptor signaling pathway, cytoplasmic translation. In addition, SQC presented curative effect by the regulated function associated with translation, while metformin presented curative effect by the regulated function associated coagulation.

CONCLUSION

SQC is an effective therapeutic drug on T2DM, and presents curative effect by regulated function associated with translation.

Long non‑coding RNA MEG3 suppresses epithelial‑to‑mesenchymal transition by inhibiting the PSAT1‑dependent GSK‑3β/Snail signaling pathway in esophageal squamous cell carcinoma

Esophageal squamous cell carcinoma (ESCC) is the main subtype of esophageal cancer in China, and the prognosis of patients remains poor mainly due to the occurrence of lymph node and distant metastasis. The long non‑coding RNA (lncRNA) maternally expressed gene 3 (MEG3) has been shown to have tumor‑suppressive properties and to play an important role in epithelial‑to‑mesenchymal transition (EMT) in some solid tumors. However, whether MEG3 is involved in EMT in ESCC remains unclear. In the present study, the MEG3 expression level and its association with tumorigenesis were determined in 43 tumor tissues of patients with ESCC and in ESCC cells using reverse transcription‑quantitative PCR analysis. Gene microarray analysis was performed to detect differentially expressed genes (DEGs). Based on the functional annotation results, the effects of ectopic expression of MEG3 on cell growth, migration, invasion and EMT were assessed. MEG3 expression level was found to be markedly lower in tumor tissues and cells. Statistical analysis revealed that MEG3 expression was significantly negatively associated with lymph node metastasis and TNM stage in ESCC. Fluorescence in situ hybridization assay demonstrated that MEG3 was expressed mainly in the nucleus. Ectopic expression of MEG3 inhibited cell proliferation, migration, invasion and cell cycle progression in EC109 cells. Gene microarray results demonstrated that 177 genes were differentially expressed ≥2.0 fold in MEG3‑overexpressing cells, including 23 upregulated and 154 downregulated genes. Functional annotation revealed that the DEGs were mainly involved in amino acid biosynthetic process, mitogen‑activated protein kinase signaling, and serine and glycine metabolism. Further experiments indicated that the ectopic expression of MEG3 significantly suppressed cell proliferation, migration, invasion and EMT by downregulating phosphoserine aminotransferase 1 (PSAT1). In pathological tissues, PSAT1 and MEG3 were significantly negatively correlated, and high expression of PSAT1 predicted poor survival. Taken together, these results suggest that MEG3 may be a useful prognostic biomarker and may suppress EMT by inhibiting the PSAT1‑dependent glycogen synthase kinase‑3β/Snail signaling pathway in ESCC.

Gene Expression in Human Polymorphonuclear Neutrophils (PMNs) Stimulated by Bacillus Calmette-Guérin (BCG)

Neutrophils are the most abundant leukocytes in the blood. Moreover, neutrophils form the first line of host immune defense against bacterial and fungal invasion, and also play an important part in inflammatory and immune system responses. Intravesical bacillus Calmette-Guérin (BCG) has been shown to reduce and delay tumor progression to muscle-invasive disease after transurethral resection of bladder tumors (TRUBTs). Following intravesical BCG, neutrophils gather around tissues infected by BCG in the early stage of inflammatory and immune responses. In our previous study, we reported that BCG induced the formation of neutrophil extracellular traps (NETs), which play an important role in tumor treatment. Therefore, in the present study, we analyzed the gene expression profile of neutrophils stimulated by BCG through high-throughput arrays, which helped us determine the potential roles of neutrophils in BCG immunotherapy. The results showed that the expression of neutrophil genes led to changes in the early stage of BCG stimulation. The changed genes were involved in many functions of neutrophils such as mobility, proliferation, and secretion of cytokines, chemokines, and adhesion molecules. These changes in neutrophil biological functions may play an essential role in BCG induction of inflammatory and immune responses, and in anti-tumor processes.

Integrated assessment of CDK1 upregulation in thyroid cancer

Cyclin-dependent kinase 1 (CDK1) has a unique role in cell cycle regulation, as it is crucial for cell cycle progression and cell division. The aim of the present study was to use a combination of various detection methods to examine the expression and clinical significance of CDK1 in thyroid cancer (THCA). We used in-house tissue microarrays, immunohistochemistry, public RNA-sequencing, gene microarrays, and meta-analyses to conduct a comprehensive analysis of the role of CDK1 in the occurrence and development of THCA. CDK1 protein expression was notably higher in THCA tissues than in non-cancer tissues as evidenced by the in-house tissue microarrays. The expression of CDK1 protein was also significantly higher in pathologic T3-T4 than in T1-T2 samples. The pooled standardized mean difference (SMD) for CDK1 was 0.71 (95% CI, 0.46-0.95) including a total of 931 THCA and 585 non-cancerous thyroid tissue samples. An aggregation of the immunohistochemistry results and the RNA-sequencing/microarray findings gave a pooled SMD for CDK1 expression of 2.13 (95% CI, 1.30-2.96). The final area under curve (AUC) for the summarized receiver operating characteristic (sROC) was 0.7941 using all 1102 cases of THCA and 672 cases of controls. KEGG analysis with the co-expressed genes of CDK1 in THCA demonstrated the top enriched pathways to be the cell cycle, thyroid hormone synthesis, autoimmune thyroid disease, etc. In summary, we reveal the overexpression of CDK1 in THCA based on multiple detection methods that combine independent cohorts. However, further studies are required to elucidate the molecular mechanisms of CDK1 that promotes the biological aggressiveness of THCA cells.

Case report: Novel GJB2 variant c.113T>C associated with autosomal recessive non-syndromic hearing loss (ARNSHL) in a Han family

RATIONALE

Molecular mechanism underlying the autosomal recessive non-syndromic hearing loss (ARNSHL) is still plausible. Pathogenic mutations of the gap junction beta 2 protein (GJB2) are reported to be the primary causes of ARNSHL.

PATIENT CONCERNS

A propositus was diagnosed as ARNSHL with bilateral congenital profound hearing loss.

DIAGNOSIS

With microarray and target gene sequencing testing methods, a novel GJB2 mutant was found to be associated with ARNSHL in this Han Chinese family.

INTERVENTIONS/OUTCOMES

Based on the finding in this research, prenatal screening of GJB2 mutation and genetic counseling are recommended to this family for their next pregnancy. Our interventions allow the family to plan informatively.

LESSONS

In this family, we discovered 2 heterozygous carriers of c.113T>C variation in the GJB2 gene. The propositus, who had profound hearing loss, had inherited the c.113T>C variation from his normal mother and the c.235delC from his father.

Unraveling the role of the transcriptional regulator VirS in low pH-induced responses of Mycobacterium tuberculosis and identification of VirS inhibitors

The ability of Mycobacterium tuberculosis to respond and adapt to various stresses such as oxygen/nitrogen radicals and low pH inside macrophages is critical for the persistence of this human pathogen inside its host. We have previously shown that an AraC/XylS-type transcriptional regulator, VirS, which is induced in low pH, is involved in remodeling the architecture of the bacterial cell envelope. However, how VirS influences gene expression to coordinate these pH responses remains unclear. Here, using a genetic biosensor of cytoplasmic pH, we demonstrate that VirS is required for the intracellular pH maintenance in response to acidic stress and inside acidified macrophages. Furthermore, we observed that VirS plays an important role in blocking phagosomal-lysosomal fusions. Transcriptomics experiments revealed that VirS affects the expression of genes encoding metabolic enzymes, cell-wall envelope proteins, efflux pumps, ion transporters, detoxification enzymes, and transcriptional regulators expressed under low-pH stress. Employing electrophoretic mobility-shift assays, DNA footprinting, and in silico analysis, we identified a DNA sequence to which VirS binds and key residues in VirS required for its interaction with DNA. A significant role of VirS in M. tuberculosis survival in adverse conditions suggested it as a potential anti-mycobacterial drug target. To that end, we identified VirS inhibitors in a virtual screen; the top hit compounds inhibited its DNA-binding activity and also M. tuberculosis growth in vitro and inside macrophages. Our findings establish that VirS mediates M. tuberculosis responses to acidic stress and identify VirS-inhibiting compounds that may form the basis for developing more effective anti-mycobacterial agents.

Gene Expression Differences in Pediatric Lymphatic Malformations: Size Really Matters

Lymphatic malformations (LMs) are congenital vascular anomalies characterized by dilated and cystic lymphatic channels. They are subdivided into macrocystic and microcystic lesions based upon the predominant size of the cysts involved. However, significant differences in clinical characteristics, treatment outcomes, and prognosis between macrocytic and microcytic disease suggest variation in underlying biologic and genetic influences. Indirect differential expression analysis revealed that 426 genes are significantly different (p < 0.01) in a small sample of LM subtypes. Functional analyses on the differentially expressed gene sets showed that microcystic LM gene expression favors a prooncogenic profile with upregulation of MYC target genes and cell cycle proteins, whereas macrocystic expression demonstrates hypoxic events that lead to angiogenesis and cell proliferation. Therefore, microcystic and macrocystic LMs, although histologically and physiologically similar, may occur under the influence of vastly different biological pathways and mechanisms of action.

Histone deacetylase inhibitors prevent persistent hypersensitivity in an orofacial neuropathic pain model

Chronic orofacial pain is a significant health problem requiring identification of regulating processes. Involvement of epigenetic modifications that is reported for hindlimb neuropathic pain experimental models, however, is less well studied in cranial nerve pain models. Three independent observations reported here are the (1) epigenetic profile in mouse trigeminal ganglia (TG) after trigeminal inflammatory compression (TIC) nerve injury mouse model determined by gene expression microarray, (2) H3K9 acetylation pattern in TG by immunohistochemistry, and (3) efficacy of histone deacetylase (HDAC) inhibitors to attenuate development of hypersensitivity. After TIC injury, ipsilateral whisker pad mechanical sensitization develops by day 3 and persists well beyond day 21 in contrast to sham surgery. Global acetylation of H3K9 decreases at day 21 in ipsilateral TG . Thirty-four genes are significantly (p < 0.05) overexpressed in the ipsilateral TG by at least two-fold at either 3 or 21 days post-trigeminal inflammatory compression injury. The three genes most overexpressed three days post-trigeminal inflammatory compression nerve injury are nerve regeneration-associated gene ATF3, up 6.8-fold, and two of its regeneration-associated gene effector genes, Sprr1a and Gal, up 174- and 25-fold, respectively. Although transcription levels of 25 of 32 genes significantly overexpressed three days post-trigeminal inflammatory compression return to constitutive levels by day 21, these three regeneration-associated genes remain significantly overexpressed at the later time point. On day 21, when tissues are healed, other differentially expressed genes include 39 of the top 50 upregulated and downregulated genes. Remarkably, preemptive manipulation of gene expression with two HDAC inhibitors (HDACi's), suberanilohydroxamic acid (SAHA) and MS-275, reduces the magnitude and duration of whisker pad mechanical hypersensitivity and prevents the development of a persistent pain state. These findings suggest that trigeminal nerve injury leads to epigenetic modifications favoring overexpression of genes involved in nerve regeneration and that maintaining transcriptional homeostasis with epigenetic modifying drugs could help prevent the development of persistent pain.

The immunomodulatory peptide bursopentin (BP5) enhances proliferation and induces sIgM expression in DT40 cells

BACKGROUND

In the recent past, many studies have been focused on extracts of BF and multiple biologically active factors and their effects on humoral immune system in chickens and birds. However, the mechanism of those immunomodulatory peptides on the B lineage cells proliferation and antibody production in chicken is fairly unknown. DT40 cell line, an avian leucosis virus-induced chicken pre-B cell line, expresses immunoglobulin M (IgM) isotype B cell reporter in the plasma membrane. There are many evidences suggesting that DT40 cells are best characterized as a bursal stem cell line. Because of the unique characteristics of DT40 cell line, it has been widely used to observe biological processes of pre-B lymphocyte cell within living cells.

METHODS

The chicken B cell line DT40 was cultured in Roswell Park Memorial Institute (RPMI) 1640 medium and cytotoxicity was studied. Also, effect of BP5 on cell proliferation and cell cycle distribution of DT40 cells was studied. Also, the effect of BP5 on sIgM mRNA expression was studied by using real-time PCR.

OBJECTIVES

To investigat the effects of Bursopentin (Cys-Lys-Arg-Val-Tyr, BP5) on a chicken promyelocyte cell line DT40, assays of cell proliferation, cell cycle distribution, detection of surface immunoglobulin G (sIgM) mRNA expression and gene microarray analysis were performed.

RESULTS

The results showed that BP5 displayed concentration-dependent effects on the proliferation, cell cycle, and sIgM mRNA expression in DT40 cells. And the analysis of expression profiles identified a signature set of 3022 genes (1254 up regulated genes, 1762 down regulated genes), which clearly discriminated the BP5-treated DT40 cells from control with high certainty (P≤0.02). The results of microarray analysis were confirmed by quantitative reverse transcription-polymerase chain reaction for 12 of the differentially expressed genes.

CONCLUSION

Theses findings showed the immuno-activity effect of BP5 on B lymphocyte and indicated that BP5 treatment regulated eight signaling pathways, in which Toll-like signaling pathway was the most significant enrichment pathway.

Key pathway and gene alterations in the gastric mucosa associated with obesity and obesity-related diabetes

BACKGROUND AND OBJECTIVE

The stomach plays an important role in obesity and obesity-related diabetes; yet, little is known about key pathways in the gastric mucosa associated with obesity and diabetes.

METHODS

We performed gene microarray and real time-polymerase chain reaction (RT-PCR) on gut mucosa samples from control subjects (CON), patients with simple obesity (OB), and patients with obesity and comorbid diabetes (OD) (n = 3 per group). Gene ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway analyses were used to predict the functional significance of differentially expressed genes.

RESULTS

In total, 262 genes were upregulated and 265 genes were downregulated in the OB group whereas 1756 genes were upregulated and 1053 genes were downregulated in the OD group compared with the CON group. Of these, 23 were co-regulated in both comparisons. Seven differentially expressed genes were validated by RT-PCR (NRIP3, L1CAM, TPO, P2RY1, OR8A1, ADAMTS19, and ASIC3). A functional analysis revealed that genes differentially expressed between the OB or OD and CON groups played crucial roles in metabolic, T cell, and G-protein coupled receptor biological processes, and primarily participated in the PI3K-Akt and AGE-RAGE signaling pathways.

CONCLUSIONS

Obesity and obesity-related diabetes are associated with important gene expression and pathway alterations in the stomach.

Gene expression profiling: identification of gene expression in human MSC chondrogenic differentiation

Understanding the mechanisms that govern cell fate will lead to the development of techniques for the induction of human mesenchymal stem cell differentiation into desired cell outcomes and the production of an autologous source of tissue for regenerative medicine. Here, we demonstrate that stem cells derived from adult bone marrow grown with 3D pellets take on characteristics similar to human cartilage. The NFAT signaling pathway is primarily linked to cell differentiation and influences chondrogenic differentiation. Based on our previous results that alterations in the expression of the NFATc1 gene affect chondrogenesis, we screened a microarray and identified 29 genes with altered expression, including 13 up-regulated (fold change ≥ 2) and 16 down-regulated (fold change ≤ 2) genes, compared with the control group. We then used RT-PCR to validate the chip data. Gene ontology and pathway analyses were performed on these altered genes. We found that these altered genes function in the complement and coagulation cascades, metabolism, biosynthesis, transcriptional regulation, proteolysis, and intracellular signaling pathways, such as the cytoplasmic calcineurin-dependent signaling pathway, the cyclin-dependent kinase inhibitor 2C signaling pathway, the MAPK signaling pathway, and the insulin signaling pathway. Our study suggests that these pathways may play important roles in chondrogenesis, which could be useful in the design of biomaterials.

Gene expression profiling of human bone marrow mesenchymal stem cells during osteogenic differentiation

OBJECTIVE

Osteogenesis is a multiple-step process through which osteoblasts are derived from bone marrow mesenchymal stem cells (MSCs) with multilineage differentiation potential. This study aimed to analyze gene expression profiling during osteogenic differentiation of MSCs.

MATERIALS AND METHODS

Human MSCs were isolated and induced for differentiation in osteogenic medium. Full-genome gene expression microarrays and gene ontology analysis were performed.

RESULTS

A total of 1,680 differentially expressed genes in differentiated MSCs were identified including 430 upregulated and 1,250 downregulated. Moreover, pathway-act-network analysis showed that cell cycle, p53 signaling pathway and focal adhesion, had high degree (>5). The ribonucleotide reductase M1, thymidine kinase 1 and histone cluster 1 H3e also showed high degree (>10). Polymerase chain reaction analysis confirmed the differential expression of insulin-like growth factor binding protein 3, SMAD family member 3, transforming growth factor beta 2, and fibroblast growth factor 14 in differentiated MSCs.

CONCLUSIONS

Gene expression profiling provides a foundation to reveal the mechanisms that regulate osteogenic differentiation of MSCs.

Weight Gain and Impaired Glucose Metabolism in Women Are Predicted by Inefficient Subcutaneous Fat Cell Lipolysis

Adipocyte mobilization of fatty acids (lipolysis) is instrumental for energy expenditure. Lipolysis displays both spontaneous (basal) and hormone-stimulated activity. It is unknown if lipolysis is important for future body weight gain and associated disturbed glucose metabolism, and this was presently investigated in subcutaneous adipocytes from two female cohorts before and after ≥10-year follow-up. High basal and low stimulated lipolysis at baseline predicted future weight gain (odds ratios ≥4.6) as well as development of insulin resistance and impaired fasting glucose/type 2 diabetes (odds ratios ≥3.2). At baseline, weight gainers displayed lower adipose expression of several established lipolysis-regulating genes. Thus, inefficient lipolysis (high basal/low stimulated) involving altered gene expression is linked to future weight gain and impaired glucose metabolism and may constitute a treatment target. Finally, low stimulated lipolysis could be accurately estimated in vivo by simple clinical/biochemical measures and may be used to identify risk individuals for intensified preventive measures.

Gene microarray analysis revealed a potential crucial gene RACK1 in oral squamous cell carcinoma (OSCC)

Oral squamous cell carcinoma (OSCC) is the sixth most common cancer worldwide, which appears as a consequence of multiple molecular genetic events in various chromosomes and genes. In order to unveil the possible mechanisms underlying OSCC tumorigenesis, the OSCC-related gene expression variance and the gene interaction network should be further investigated. Herein, we conducted the NimbleGen Human Gene Expression Microarray to analyze expression heterogeneity between OSCC primary tumor tissue and its adjacent normal tissue from two patients. A total number of 7872 out of 32,448 detected genes are differentially expressed in OSCC. Gene ontology (GO) analysis demonstrated that these differentially expressed transcripts were critical in a series of metabolic processes, cancer-related signal pathways, and biological regulations. KEGG signaling pathway enrichment suggested a number of pathways (metabolic process and immune response) which are frequently enrolled during cancer progression. 15 most differential regulated genes between OSCC tumor and non-tumor were confirmed by quantitative reverse transcription polymerase chain reaction (qRT-PCR). Furthermore, the interaction network analysis of these confirmed genes by STRING database showed the two subunits of RACK1 had direct interaction with 14 differential proteins. This bioinformatics research lends support about the critical role of RACK1 which functions as a key node protein driving OSCC development.

High-throughput proteomics integrated with gene microarray for discovery of colorectal cancer potential biomarkers

Proteins, as executives of genes' instructions, are responsible for cellular phenotypes. Integrating proteomics with gene microarray, we conducted this study to identify potential protein biomarkers of colorectal cancer (CRC). Isobaric tags with related and absolute quantitation (iTRAQ) labeling mass spectrometry (MS) was applied to screen and identify differentially expressed proteins between paired CRC and adjacent normal mucosa. Meanwhile, Affymetrix U133plus2.0 microarrays were used to perform gene microarray analysis. Verification experiments included immunohistochemistry (IHC), western blot and enzyme-linked immunosorbent assay (ELISA) of selected proteins. Overall, 5469 differentially expressed proteins were detected with iTRAQ-MS from 24 matched CRC and adjacent normal tissues. And gene microarray identified 39859 differential genes from 52 patients. Of these, 3083 differential proteins had corresponding differentially expressed genes, with 245 proteins and their genes showed >1.5-fold change in expression level. Gene ontology enrichment analysis revealed that up-regulated proteins were more involved in cell adhesion and motion than down-regulated proteins. In addition, up-regulated proteins were more likely to be located in nucleus and vesicles. Further verification experiments with IHC confirmed differential expression levels of 5 proteins (S100 calcium-binding protein A9, annexin A3, nicotinamide phosphoribosyltransferase, carboxylesterase 2 and calcium activated chloride channel A1) between CRC and normal tissues. Besides, western blot showed a stepwise increase of annexin A3 abundance in normal colorectal mucosa, adenoma and CRC tissues. ELISA results revealed significantly higher serum levels of S100 calcium-binding protein A9 and annexin A3 in CRC patients than healthy controls, validating diagnostic value of these proteins. Cell experiments showed that inhibition of annexin A3 could suppress CRC cell proliferation and aggressiveness. S100 calcium-binding protein A9, annexin A3, nicotinamide phosphoribosyltransferase, carboxylesterase 2 and calcium activated chloride channel A1 were probably potential biomarkers of colorectal cancer. Annexin A3 was a potentially valuable therapeutic target of CRC.

Overexpression of RHEB is associated with metastasis and poor prognosis in hepatocellular carcinoma

Aberrant expression of Ras homolog enriched in brain (RHEB) has been observed in a variety of cancer tissues and is closely associated with clinicopathological features. However, the expression profile of RHEB in patients with hepatocellular carcinoma (HCC) and its clinical signature with underlying mechanisms have not been explored thus far. To analyze the association between RHEB expression and clinicopathological features, the RHEB expression levels were determined in the present study using gene microarrays, immunohistochemistry and western blotting in 60 liver cancer tissues and 35 normal liver tissues. Downregulation of RHEB expression in liver cancer cell lines was achieved by RNA interfering technology to explore its biological function in HCC. RHEB expression was high in liver cancer tissues, with an increase of 2.00±0.19-fold compared with normal tissues and of 2.00±0.27-fold compared with adjacent non-cancer tissues. RHEB expression increased along with the clinical staging of HCC, and the overall survival and mortality of patients were closely correlated to RHEB levels, micro-vascular invasion, hepatitis B virus-DNA titer, tumor differentiation and pathological satellites (P<0.05). After knocking down RHEB in SMMC-7721 cells, the growth of liver cancer cells was significantly reduced. The majority of cells were blocked in S-phase, and their colony-forming and proliferating abilities significantly decreased (P<0.05). In vivo, upon downregulation of RHEB expression, the tumorigenic ability of HCC significantly decreased (P<0.05). These data suggest that RHEB expression is a significant prognostic factor and may be important in HCC cell growth. The present study highlights the importance of RHEB as a novel prognostic marker of HCC.

Identification of genes involved in enterovirus 71 infected SK-N-SH cells

The enterovirus 71 (EV71) is the major pathogen of hand-foot-and-mouth disease (HFMD) and has been associated with severe neurological disease in children under 5 years of age. The molecular mechanisms underlying the response of human neural cells to EV71 infection still remain unclear. In this study, the genome microarray was employed to perform transcriptome profiling analysis in human neuroblastoma SK-N-SH cells infected by EV71. The results indicated that EV71 infection lead to altered expression of 87 human mRNA. The up-regulated gene mainly include the cytokine and chemokine, ubiquitin mediated proteolysis, Toll-like receptor signaling pathway, p53 signaling pathway, apoptosis, leukocyte transendothelial migration, MAPK signaling pathway and Jak-STAT signaling pathway, etc. Finally, the microarray results were validated using real-time RT-PCR and ELISA in the RNA and protein level, respectively. Our results suggested that the high fatality rate of EV71 infection probably derived from a severe immune response caused by cytokines and chemokines. The findings will help to better understand the host responses to EV71 infection and provide the potential strategy for prevention and control of EV71 infection.

Molecular Fingerprint for Terminal Abdominal Aortic Aneurysm Disease

Background

Clinical decision making in abdominal aortic aneurysms (AAA) relies completely on diameter. At this point, improved decision tools remain an unmet medical need. Our goal was to identify changes at the molecular level specifically leading up to AAA rupture.

Methods and Results

Aortic wall tissue specimens were collected during open elective (eAAA; n=31) or emergency repair of ruptured AAA (rAAA; n=17), and gene expression was investigated using microarrays. Identified candidate genes were validated with quantitative real‐time polymerase chain reaction in an independent sample set (eAAA: n=46; rAAA: n=18). Two gene sets were identified, 1 set containing 5 genes linked to terminal progression, that is, positively associated with progression of larger AAA, and with rupture (HILPDA,ANGPTL4,LOX,SRPX2,FCGBP), and a second set containing 5 genes exclusively upregulated in rAAA (ADAMTS9,STC1,GFPT2,GAL3ST4,CCL4L1). Genes in both sets essentially associated with processes related to impaired tissue remodeling, such as angiogenesis and adipogenesis. In gene expression experiments we were able to show that upregulated gene expression for identified candidate genes is unique for AAA. Functionally, the selected upregulated factors converge at processes coordinated by the canonical HIF‐1α signaling pathway and are highly expressed in fibroblasts but not inflammatory cells of the aneurysmatic wall. Histological quantification of angiogenesis and exploration of the HIF‐1α network in rAAA versus eAAA shows enhanced microvessel density but also clear activation of the HIF‐1α network in rAAA.

Conclusions

Our study shows a specific molecular fingerprint for terminal AAA disease. These changes appear to converge at activation of HIF‐1α signaling in mesenchymal cells. Aspects of this cascade might represent targets for rupture risk assessment.

Comprehensive analysis of long non-coding RNA PVT1 gene interaction regulatory network in hepatocellular carcinoma using gene microarray and bioinformatics

PVT1 has been reported to be involved in the tumorigenesis and development of different cancers. However, the role of PVT1 in hepatocellular carcinoma (HCC) remains unclear. In this study, we applied gene microarray analysis to detect differentially expressed genes (DEGs) between PVT1 RNAi groups and controls. We initially investigated and confirmed PVT1 expression in HCC using The Cancer Genome Atlas (TCGA). The potential genes and pathways associated with PVT1 were also analyzed. We also performed bioinformatics analyses (Gene Ontology (GO), pathway, Kyoto Encyclopedia of Genes and Genomes (KEGG), and network analyses) to explore the underlying pathways and networks of these potential genes. We selected DLC1 for further analysis. Based on the TCGA database, PVT1 was markedly up-regulated in HCC, whereas DLC1 was down-regulated. Moreover, PVT1 expression negatively correlated with DLC1 in HCC, an observation that has been further validated in different cohorts with Oncomine. High expression of PVT1 was positively associated with gender, race, vascular invasion and pathological grade in HCC. Additionally, the ROC curve indicated that both PVT1 and DLC1 have high diagnostic value in HCC. We speculated that PVT1 might play a significant role in HCC development and progression via regulation of various pathways and genes, especially DLC1 and the Hippo signaling pathway. However, this mechanism should be confirmed by functional experiments.

MDG-1, a Potential Regulator of PPARα and PPARγ, Ameliorates Dyslipidemia in Mice

Hyperlipidemia is a serious epidemic disease caused by lipid metabolism disorder, which is harmful to human health. MDG-1, a β-d-fructan polysaccharide extracted from Ophiopogon japonicus, has been shown to improve abnormal blood lipid levels and alleviate diabetes. However, the underlying mechanism on hyperlipidemia is largely unknown. In this study, male C57BL/6 mice were randomly separated into three groups, respectively: low-fat diet (Con), high-fat diet (HFD), and high-fat diet plus 5‰ MDG-1 (HFD + MDG-1). Body weight was measured and the serum lipid levels were analyzed. Using gene microarray, various core pathways, together with levels of gene expression within hepatocytes, were analyzed. RT-PCR was used to confirm the identity of the differentially expressed genes. MDG-1 could prevent obesity in HFD-induced mice and improve abnormal serum lipids. Besides, MDG-1 could regulate hyperlipidemia symptoms, specifically, and decrease fasting blood glucose, improve glucose tolerance, and ameliorate insulin resistance. According to results from gene microarray, most of the identified pathways were involved in the digestion and absorption of fat, biosynthesis, and catabolism of fatty acids as well as the secretion and biological synthesis of bile acids. Furthermore, MDG-1 may act upon peroxisome proliferator-activated receptors (PPAR) α and γ, activating PPARα whilst inhibiting PPARγ, thus having a potent hypolipidemic effect.

Bioinformatics and co-expression network analysis of differentially expressed lncRNAs and mRNAs in hippocampus of APP/PS1 transgenic mice with Alzheimer disease

APP/PS1 transgenic mice with Alzheimer disease (AD) are widely used as a reliable animal model in studies about behaviors, physiology, biochemistry and histomorphology of AD, but few studies have been conducted to investigate the role of lncRNAs in this model. In this study, lncRNA microarray was employed to detect the gene expression profile and lncRNA expression profile in the mouse brain. Then, bioinformatics was used to predict the differentially expressed genes related to AD (n=20). Among different lncRNAs (n=249), 99 were downregulated and 150 upregulated. Co-expression network was applied to analyze the co-expression of differential lncRNAs and different genes. In network, lncRNA Gm13498 and lncRNA 1700030L20Rik correlated with the most genes and their degrees were 6 and 5, respectively. Then, the function and signal transduction pathways related to the differentially co-expressed lncRNAs were analyzed with bioinformatics, and results showed that these lncRNAs were involved in the systemic development of neurons, intercellular communication, regulation of action potential of neurons, development and differentiation of oligodendrocytes, neurotransmitters transmission, and neuronal regeneration. Realtime PCR was employed to detect the expression of relevant lncRNAs and differentially expressed RNAs in 10 samples, and results were consistent with above findings from microarray.

Novel genes in brain tissues of EAE-induced normal and obese mice: Upregulation of metal ion-binding protein genes in obese-EAE mice

Experimental autoimmune encephalomyelitis (EAE) is an inflammatory autoimmune disease of the central nervous system resulting from degeneration of the myelin sheath. This study is aimed to identify differentially expressed genes (DEGs) in the brain of EAE-induced normal diet (ND) mice and high-fat diet (HFD)-induced obese mice, and to identify novel genes responsible for elucidating the mechanism of the disease. Purified mRNA samples from the brain tissue were analyzed for gene microarray and validated by real-time RT-PCR. DEGs were identified if significant changes greater than 1.5-fold or less than 0.66-fold were observed (p<0.05). Pathway construction and functional categorization were performed using the Kyoto encyclopedia of genes and genomes pathways and gene ontology (GO) analysis. HFD-EAE mice showed more severe disease symptoms than ND-EAE mice. From GO study, fold changes of HFD-EAE to ND-EAE genes indicated that the genes were significantly associated to the pathways related with the immune response, antigen presentation, and complement activation. The genes related with metal ion-binding proteins were upregulated in HFD-EAE and ND-EAE mice. Upregulation of Cul9, Mast2, and C4b expression is significantly higher in HFD-EAE mice than ND-EAE mice. Cul9, Mast2, C4b, Psmb8, Ly86, and Ms4a6d were significantly upregulated in both ND- and HFD-EAE mice. Fcgr4, S3-12, Gca, and Zdhhc4 were upregulated only in ND-EAE, and Xlr4b was upregulated only in HFD-EAE mice. And significant upregulated genes of metal ion-binding proteins (Cul9 and Mast2) were observed in HFD-EAE mice.

Gene expression profiling of human bone marrow-derived mesenchymal stem cells during adipogenesis

INTRODUCTION

Adipogenesis comprises multiple processes by which mesenchymal stem cells differentiate into adipocytes. To increase our knowledge of the mechanism underlying adipogenic differentiation of human bone marrow mesenchymal stem cells (hMSCs), we performed full-genome gene expression microarray and gene ontology analyses of induced differentiation of hMSCs.

MATERIAL AND METHODS

Adipogenic differentiation of hMSCs was induced by an adipogenic medium, and total RNA was extracted from undifferentiated hMSCs (day 0) and differentiated adipocytes (day 14). Then microarray hybridization of RNA samples was performed. The GeneChip Operating Software was used to analyze the hybridization data to identify differentially expressed genes, which were performed Gene Ontology categorization and pathway analysis. Pathway-act-network and genes-act-network were built according to the Kyoto Encyclopedia of Genes and Genomes database. Some differentially expressed genes were subjected to qRT-PCR to verify the microarray data.

RESULTS

We detected a total of 3,821 differentially expressed genes, of which 753 were upregulated and 3,068 downregulated. These genes were well represented in a variety of functional categories, including collagen fibril organization, brown fat cell differentiation, cell division, and S phase of mitotic cell cycle. Subsequently, pathway analysis was conducted, and significant pathways (from top 50) were selected for pathway-act-network analysis, which indicated that the mitogen-activated protein kinase (MAPK) pathway and cell cycle were of high degrees (> 10). Gene-act-network analysis showed that insulin-like growth factor 1 receptor (IGF1R), histone deacetylase 1 (HDAC1), HDAC2, MAPK13, MAPK8, phosphoinositide-3-kinase regulatory subunit 1 (PI3KR1), and PI3KR2 also had high degrees (> 18).

CONCLUSIONS

Collectively, these data provide novel information and could serve as a basis for future study to clarify the mechanisms underlying adipocyte differentiation of hMSCs.

A regulatory gene network related to the porcine umami taste receptor (TAS1R1/TAS1R3)

Taste perception plays an important role in the mediation of food choices in mammals. The first porcine taste receptor genes identified, sequenced and characterized, TAS1R1 and TAS1R3, were related to the dimeric receptor for umami taste. However, little is known about their regulatory network. The objective of this study was to unfold the genetic network involved in porcine umami taste perception. We performed a meta-analysis of 20 gene expression studies spanning 480 porcine microarray chips and screened 328 taste-related genes by selective mining steps among the available 12,320 genes. A porcine umami taste-specific regulatory network was constructed based on the normalized coexpression data of the 328 genes across 27 tissues. From the network, we revealed the 'taste module' and identified a coexpression cluster for the umami taste according to the first connector with the TAS1R1/TAS1R3 genes. Our findings identify several taste-related regulatory genes and extend previous genetic background of porcine umami taste.

Microarray analysis of potential genes in the pathogenesis of recurrent oral ulcer

Recurrent oral ulcer seriously threatens patients' daily life and health. This study investigated potential genes and pathways that participate in the pathogenesis of recurrent oral ulcer by high throughput bioinformatic analysis. RT-PCR and Western blot were applied to further verify screened interleukins effect. Recurrent oral ulcer related genes were collected from websites and papers, and further found out from Human Genome 280 6.0 microarray data. Each pathway of recurrent oral ulcer related genes were got through chip hybridization. RT-PCR was applied to test four recurrent oral ulcer related genes to verify the microarray data. Data transformation, scatter plot, clustering analysis, and expression pattern analysis were used to analyze recurrent oral ulcer related gene expression changes. Recurrent oral ulcer gene microarray was successfully established. Microarray showed that 551 genes involved in recurrent oral ulcer activity and 196 genes were recurrent oral ulcer related genes. Of them, 76 genes up-regulated, 62 genes down-regulated, and 58 genes up-/down-regulated. Total expression level up-regulated 752 times (60%) and down-regulated 485 times (40%). IL-2 plays an important role in the occurrence, development and recurrence of recurrent oral ulcer on the mRNA and protein levels. Gene microarray can be used to analyze potential genes and pathways in recurrent oral ulcer. IL-2 may be involved in the pathogenesis of recurrent oral ulcer.

Effects of curcumin on the gene expression profile of L-02 cells

Curcumin has been utilized in the treatment and prevention of disease, including cancer and cardiovascular disease, but the molecular mechanism behind such numerous effects remains unclear. To explore the molecular mechanism and action sites of curcumin at the cellular level, human hepatic L-02 cells were used to assess these effects. Microarray technology was employed to detect the gene expression of L-02 cells treated with curcumin. According to the microarray results and the data from the National Center for Biotechnology Information, the present study classified and concluded that these curcumin-sensitive genes were associated with diseases and their signaling pathway. The study supports the evidence for treating cancer and cardiovascular disease, and found certain potential marker genes for conducting systematic research into the effects of curcumin. A total of 80 genes were identified as significantly differentially expressed between samples treated with and without curcumin. Curcumin is capable of developing physiological reactions and functions by regulating the gene expression and affecting its signal transduction pathway. Tumor protein p63, MYC-associated factor X and certain other genes associated with tumors act on a potential therapeutic target, while apolipoprotein B receptor and oxysterol-binding protein-like 7, and their signaling pathways may be involved in the cardioprotective effects of curcumin.

Conditional Density Estimation in Measurement Error Problems

This paper is motivated by a wide range of background correction problems in gene array data analysis, where the raw gene expression intensities are measured with error. Estimating a conditional density function from the contaminated expression data is a key aspect of statistical inference and visualization in these studies. We propose re-weighted deconvolution kernel methods to estimate the conditional density function in an additive error model, when the error distribution is known as well as when it is unknown. Theoretical properties of the proposed estimators are investigated with respect to the mean absolute error from a "double asymptotic" view. Practical rules are developed for the selection of smoothing-parameters. Simulated examples and an application to an Illumina bead microarray study are presented to illustrate the viability of the methods.

Gene microarray analysis of the lncRNA expression profile in human urothelial carcinoma of the bladder

OBJECTIVE

To analyze the expression profile variation of lncRNAs in normal urinary bladder tissue and urothelial carcinoma of the urinary bladder through microarray technology. The differentially expressed lncRNAs were identified and classified, and their biological information was analyzed. The data obtained in the study will prove helpful for the diagnosis, treatment, and prevention of urothelial carcinoma of the bladder.

MATERIALS AND METHODS

Three specimens of urothelial carcinoma of the bladder and three specimens of normal bladder tissue were identified by histology. The total RNA was isolated from the bladder urothelial carcinomas and normal tissue and purified. The targets were mixed and hybridized with the genes on the microarray, which contained thirty thousand lncRNAs. The bladder urothelial carcinomas were then compared with the normal bladder tissue. The lncRNAs that were differentially expressed between the two groups were identified based on the signal-to-noise ratios using the Agilent Feature Extraction software and were analyzed with the Agilent Genespring GX software (Agilent). The outcome was obtained, and the biological information of these genes was deposited in GenBank.

RESULTS

The expression profile of lncRNAs was significantly different between normal bladder tissue and urothelial carcinoma of the bladder. Compared with normal bladder tissue, 1,122 lncRNAs exhibited at least a twofold, significant difference (P < 0.05) and are thus regarded as differentially expressed lncRNAs. Of these, 734 and 388 lncRNAs were upregulated and down regulated. The differentially expressed lncRNAs in the urothelial carcinoma of the bladder are distributed on every chromosome, and most of these lncRNAs are distributed on chromosomes 1, 2, 3, 4, 6, and X.

CONCLUSIONS

Urothelial carcinoma of the bladder is a complicated disease that involves the regulation of multiple genes and the participation of multiple chromosomes. Some of the differentially expressed lncRNAs that were upregulated, such as AK124776, lincRNA-RAB12-1, KRT8P25, RP11-474J18.4, AC000110.1, KRT8P13, KRT8P10, BC072678, and downregulated, such as nc-HOXB9-206, RP11-160A10.2, nc-HOXA11-86, nc-HOXD10-7, nc-HOXB9-205, CES4, nc-HOXD12-3, systematic research on these lncRNAs will help clarify the mechanisms of urothelial carcinoma of the bladder and guide the early diagnosis and treatment of this cancer in the future.

Intratumoral regulatory T cells with higher prevalence and more suppressive activity in hepatocellular carcinoma patients

Regulatory T cells (Treg) play a vital role in immunosuppressive crosstalk; however, Tregs from different locations lead to different clinical outcomes. Our aim was, therefore, to compare the prevalences and suppressive phenotypes of Tregs in the peripheral blood, peritumor, and intratumor of patients with hepatocellular carcinoma (HCC). METHODS : The frequencies and phenotypes of CD4(+) CD25(+) CD127(low/-) CD49d(-) Tregs in the periphery, peritumor, and intratumor of 78 HCC patients and 12 healthy controls were evaluated by flow cytometry. Treg-cell suppressive activity was determined using an in vitro CD154 expression assay. Tregs from tumor and paired peritumor were then hybridized using an Agilent whole genome oligo microarray, and selected genes were validated by real-time polymerase chain reaction. Functional analysis of the microarray data was performed using Kyoto Encyclopedia of Genes and Genomes and Gene Ontology analyses. RESULTS : Intratumoral Tregs exhibited higher frequencies and more suppressive phenotypic functions than those in peritumor and periphery, whereas there was no difference between the latter two. Functional analysis showed that complement cascades, p53, and glycosylphosphatidylinositol-anchor biosynthesis pathways were significantly upregulated in intratumoral Tregs; the salivary secretion pathway was significantly downregulated in intratumoral Tregs, and immune cells and tumor-immuno-related Gene Ontology terms were significantly affected. CONCLUSIONS : Tregs in different locations exhibited different functional statuses. A higher prevalence and more suppressive phenotype suggested a critical role for intratumoral Tregs in the formation of multicellular immunosuppressive networks. HCC immunotherapy may be improved, therefore, by specific locational Tregs elimination or suppression.

miRNA and mRNA expression profiling identifies members of the miR-200 family as potential regulators of epithelial-mesenchymal transition in pterygium

The current study investigates whether microRNA (miRNA) regulators of epithelial-mesenchymal transition (EMT), tissue fibrosis, and angiogenesis are differentially expressed in human primary pterygium. Genome-wide miRNA and mRNA expression profiling of paired pterygium and normal conjunctiva was performed in the context of conventional excision of pterygium with autotransplantation of conjunctiva (n = 8). Quantitative real time polymerase chain reaction (qRT-PCR) was used to validate the expression of key molecules previously detected by microarray. In pterygium, 25 miRNAs and 31 mRNAs were significantly differentially expressed by more than two-fold compared to normal conjunctiva. 14 miRNAs were up-regulated (miR-1246, -486, -451, -3172, -3175, -1308, -1972, -143, -211, -665, -1973, -18a, 143, and -663b), whereas 11 were down-regulated (miR-675, -200b-star, -200a-star, -29b, -200b, -210, -141, -31, -200a, -934, and -375). Unsupervised hierarchical cluster analysis demonstrated that members of the miR-200 family were coexpressed and down-regulated in pterygium. The molecular and cellular functions that were most significant to the miRNA data sets were cellular development, cellular growth and proliferation, and cellular movement. qRT-PCR confirmed the expression of 15 of the 16 genes tested and revealed that miR-429 was down-regulated by more than two-fold in pterygium. The concerted down-regulation of four members from both clusters of the miR-200 family (miR-200a/-200b/-429 and miR-200c/-141), which are known to regulate EMT, and up-regulation of the predicted target and mesenchymal marker fibronectin (FN1), suggest that EMT could potentially play a role in the pathogenesis of pterygium and might constitute promising new targets for therapeutic intervention in pterygium.

An gene expression pattern

DNA microarray technology has become a powerful tool in the arsenal of the molecular biologist. Capitalizing on high-precision robotics and the wealth of DNA sequences annotated from the genomes of a large number of organisms, the manufacture of microarrays is now possible for the average academic laboratory with the funds and motivation. Microarray production requires attention to both biological and physical resources, including DNA libraries, robotics, and qualified personnel. Although the fabrication of microarrays is a very labor-intensive process, production of quality microarrays individually tailored on a project-by-project basis will help researchers shed light on future scientific questions.

Metabolism and regulation of gene expression by 4-oxoretinol versus all-trans retinoic acid in normal human mammary epithelial cells

We previously demonstrated that 4-oxoretinol (4-oxo-ROL) activated retinoic acid receptors (RARs) in F9 stem cells. We showed that 4-oxo-ROL inhibited the proliferation of normal human mammary epithelial cells (HMECs). To understand the mechanisms by which 4-oxo-ROL regulates HMEC growth we examined gene expression profiles following 4-oxo-ROL or all-trans retinoic acid (tRA). We also compared growth inhibition by tRA, 4-oxo-ROL, or 4-oxo-RA. All three retinoids inhibited HMEC proliferation. Gene expression analyses indicated that 4-oxo-ROL and tRA modulated gene expression in closely related pathways. The expression of many genes, e.g. ATP-binding cassette G1 (ABCG1); adrenergic receptorbeta2 (ADRB2); ras-related C3 botulinum toxin substrate (RAC2); and short-chain dehydrogenase/reductase 1 gene (SDR1) was changed after 4-oxo-ROL or tRA. Metabolism of these retinoids was analyzed by high-performance liquid chromatography (HPLC). In 1 microM tRA treated HMECs all of the tRA was found intracellularly, and tRA was the predominant intracellular retinoid. In 1 microM 4-oxo-ROL treated HMECs most 4-oxo-ROL was esterified to 4-oxoretinyl esters, no tRA was detected, and 4-oxo-ROL and 4-oxo-RA were observed intracellularly. In 1 microM 4-oxoretinoic acid (4-oxo-RA) treated HMECs little intracellular 4-oxo-RA was detected; most 4-oxo-RA was in the medium. Our results indicate that: (a) 4-oxo-ROL regulates gene expression and inhibits proliferation of HMECs; (b) 4-oxo-ROL and tRA regulate some of the same genes; (c) more tRA is found in cells, as compared to 4-oxoretinoic acid, when each drug is added at the same concentration in the medium; and (d) the mechanism by which 4-oxo-ROL exerts its biological activity does not involve intracellular tRA production.