Identification and validation of key genes associated with non-small-cell lung cancer

Non-small-cell lung cancer (NSCLC) is one of the main causes of death induced by cancer globally. However, the molecular aberrations in NSCLC patients remain unclearly. In the present study, four messenger RNA microarray datasets (GSE18842, GSE40275, GSE43458, and GSE102287) were downloaded from the Gene Expression Omnibus (GEO) database. Differentially expressed genes (DEGs) between NSCLC tissues and adjacent lung tissues were obtained from GEO2R and the overlapping DEGs were identified. Moreover, functional and pathway enrichment were performed by Funrich, while the protein–protein interaction (PPI) network construction were obtained from STRING and hub genes were visualized and identified by Cytoscape software. Furthermore, validation, overall survival (OS) and tumor staging analysis of selected hub genes were performed by GEPIA. A total of 367 DEGs (95 upregulated and 272 downregulated) were obtained through gene integration analysis. The PPI network consisted of 94 nodes and 1036 edges in the upregulated DEGs and 272 nodes and 464 edges in the downregulated DEGs, respectively. The PPI network identified 46 upregulated and 27 downregulated hub genes among the DEGs, and six (such as CENPE, NCAPH, MYH11, LRRK2, HSD17B6, and A2M) of that have not been identified to be associated with NSCLC so far. Moreover, the expression differences of the mentioned hub genes were consistent with that in lung adenocarcinoma and lung squamous cell carcinoma in the TCGA database. Further analysis showed that all the six hub genes were associated with tumor staging except MYH11, while only the upregulated DEG CENPE was associated with the worse OS of patients with NSCLC. In conclusion, the current study showed that CENPE, NCAPH, MYH11, LRRK2, HSD17B6, and A2M might be the key genes contributed to tumorigenesis or tumor progression in NSCLC, further functional study is needed to explore the involved mechanisms.     

Restoration of miR-29b exerts anti-cancer effects on glioblastoma

Background

Methylation plays an important role in the etiology and pathogenesis of colorectal cancer (CRC). This study aimed to identify aberrantly methylated-differentially expressed genes (DEGs) and pathways in CRC by comprehensive bioinformatics analysis.

Methods

Data of gene expression microarrays (GSE68468, GSE44076) and gene methylation microarrays (GSE29490, GSE17648) were downloaded from GEO database. Aberrantly methylated-DEGs were obtained by GEO2R. Functional and enrichment analyses of selected genes were performed using DAVID database. Protein–protein interaction (PPI) network was constructed by STRING and visualized in Cytoscape. MCODE was used for module analysis of the PPI network.

Results

Totally 411 hypomethylation-high expression genes were identified, which were enriched in biological processes of response to wounding or inflammation, cell proliferation and adhesion. Pathway enrichment showed cytokine–cytokine receptor interaction, p53 signaling and cell cycle. The top 5 hub genes of PPI network were CAD, CCND1, ATM, RB1 and MET. Additionally, 239 hypermethylation-low expression genes were identified, which demonstrated enrichment in biological processes including cell–cell signaling, nerve impulse transmission, etc. Pathway analysis indicated enrichment in calcium signaling, maturity onset diabetes of the young, cell adhesion molecules, etc. The top 5 hub genes of PPI network were EGFR, ACTA1, SST, ESR1 and DNM2. After validation in TCGA database, most hub genes still remained significant.

Conclusion

In summary, our study indicated possible aberrantly methylated-differentially expressed genes and pathways in CRC by bioinformatics analysis, which may provide novel insights for unraveling pathogenesis of CRC. Hub genes including CAD, CCND1, ATM, RB1, MET, EGFR, ACTA1, SST, ESR1 and DNM2 might serve as aberrantly methylation-based biomarkers for precise diagnosis and treatment of CRC in the future.

     

Ratio of Intratumoral Macrophage Phenotypes Is a Prognostic Factor in Epithelioid Malignant Pleural Mesothelioma

Hypothesis

The tumor micro-environment and especially the different macrophage phenotypes appear to be of great influence on the behavior of multiple tumor types. M1 skewed macrophages possess anti-tumoral capacities, while the M2 polarized macrophages have pro-tumoral capacities. We analyzed if the macrophage count and the M2 to total macrophage ratio is a discriminative marker for outcome after surgery in malignant pleural mesothelioma (MPM) and studied the prognostic value of these immunological cells.

Methods

8 MPM patients who received induction chemotherapy and surgical treatment were matched on age, sex, tumor histology, TNM stage and EORTC score with 8 patients who received chemotherapy only. CD8 positive T-cells and the total macrophage count, using the CD68 pan-macrophage marker, and CD163 positive M2 macrophage count were determined in tumor specimens prior to treatment.

Results

The number of CD68 and CD163 cells was comparable between the surgery and the non-surgery group, and was not related to overall survival (OS) in both the surgery and non-surgery group. However, the CD163/CD68 ratio did correlate with OS in both in the total patient group (Pearson r −0.72, p<0.05). No correlation between the number of CD8 cells and prognosis was found.

Conclusions

The total number of macrophages in tumor tissue did not correlate with OS in both groups, however, the CD163/CD68 ratio correlates with OS in the total patient group. Our data revealed that the CD163/CD68 ratio is a potential prognostic marker in epithelioid mesothelioma patients independent of treatment but cannot be used as a predictive marker for outcome after surgery.     

NALP1 基因与骨肉瘤细胞的相关研究

目的:探讨NALP1基因在骨肉瘤细胞株MG-63、U-2OS中的表达,以及高表达NALP1基因对于骨肉瘤细胞体外凋亡的影响。方法:使用RT-PCR、Western-blot法检测骨肉瘤细胞株MG-63、U-2OS中的mRNA及蛋白表达水平并与人成骨细胞株hFOB1.19比较。将NALP1基因转染质粒PcDNA3.1,将重组质粒转染骨肉瘤细胞,分成高表达基因组、空质粒组及对照组,加入抗肿瘤药物顺铂及甲氨蝶呤促使肿瘤细胞凋亡,使用流式细胞仪测定各组肿瘤细胞凋亡率。结果:通过统计分析,骨肉瘤细胞株MG-63、U-2OS中的mRNA及蛋白表达水平均低于人成骨细胞株hFOB1.19(P<0.05),NALP1高表达组的肿瘤细胞凋亡率明显高于空白质粒组及对照组。结论:上调骨肉瘤细胞株MG-63、U-2OS中的NALP1的表达量可以促进肿瘤细胞凋亡。     

Identification of pivotal genes associated with the prognosis of gastric carcinoma through integrated analysis

Purpose: Detecting and diagnosing gastric cancer (GC) during its early period remains greatly difficult. Our analysis was performed to detect core genes correlated with GC and explore their prognostic values.Methods: Microarray datasets from the Gene Expression Omnibus (GEO) ({"type":"entrez-geo","attrs":{"text":"GSE54129","term_id":"54129"}}GSE54129) and The Cancer Genome Atlas (TCGA)-stomach adenocarcinoma (STAD) datasets were applied for common differentially co-expressed genes using differential gene expression analysis and Weighted Gene Co-expression Network Analysis (WGCNA). Functional enrichment analysis and protein–protein interaction (PPI) network analysis of differentially co-expressed genes were performed. We identified hub genes via the CytoHubba plugin. Prognostic values of hub genes were explored. Afterward, Gene Set Enrichment Analysis (GSEA) was used to analyze survival-related hub genes. Finally, the tumor-infiltrating immune cell (TIC) abundance profiles were estimated.Results: Sixty common differentially co-expressed genes were found. Functional enrichment analysis implied that cell–cell junction organization and cell adhesion molecules were primarily enriched. Hub genes were identified using the degree, edge percolated component (EPC), maximal clique centrality (MCC), and maximum neighborhood component (MNC) algorithms, and serpin family E member 1 (SERPINE1) was highly associated with the prognosis of GC patients. Moreover, GSEA demonstrated that extracellular matrix (ECM) receptor interactions and pathways in cancers were correlated with SERPINE1 expression. CIBERSORT analysis of the proportion of TICs suggested that CD8⁺ T cell and T-cell regulation were negatively associated with SERPINE1 expression, showing that SERPINE1 may inhibit the immune-dominant status of the tumor microenvironment (TME) in GC.Conclusions: Our analysis shows that SERPINE1 is closely correlated with the tumorigenesis and progression of GC. Furthermore, SERPINE1 acts as a candidate therapeutic target and prognostic biomarker of GC.     

Macrophage Polarization Reflects T Cell Composition of Tumor Microenvironment in Pediatric Classical Hodgkin Lymphoma and Has Impact on Survival

Macrophages have been implicated in the pathogenesis of classical Hodgkin lymphoma (cHL) and have been suggested to have a negative impact on outcome. Most studies addressing the role of macrophages in cHL have relied on identification of macrophages by generic macrophage antigens, e.g., CD68. We have therefore conducted an in situ analysis of macrophage polarization in a series of 100 pediatric cHL (pcHL) cases using double staining immunohistochemistry, combining CD68 or CD163 with pSTAT1 (M1-like) or CMAF (M2-like). M1- or M2-polarised microenvironment was defined by an excess of one population over the other (>1.5). Expression of STAT1 and LYZ genes was also evaluated by RT-qPCR. Patients <14 years and EBV+ cases displayed higher numbers of CD68+pSTAT1+ cells than older children and EBV- cases, respectively (P=0.01 and P=0.02). A cytotoxic tumor microenvironment, defined by a CD8+/FOXP3+ ratio >1.5 was associated with higher numbers of CD68+pSTAT1+ (P=0.025) and CD163+pSTAT1+ macrophages (P<0.0005). Levels of STAT1 and LYZ expression were associated with the numbers of CD68+pSTAT1+ macrophages. EBV+ cHL cases disclosed a predominant M1 polarized microenvironment similar to Th1 mediated inflammatory disorders, while EBV- cHL showed a predominant M2 polarized microenvironment closer to Th2 mediated inflammatory diseases. Better overall-survival (OS) was observed in cases with higher numbers of CD163+pSTAT1+ macrophages (P=0.02) while larger numbers of CD163+CMAF+ macrophages were associated with worse progression-free survival (PFS) (P=0.02). Predominant M1-like polarization as disclosed by CD163+pSTAT1+/CD163+CMAF+ ratio > 1.5 was associated with better OS (P= 0.037). In conclusion, macrophage polarization in pcHL correlates with prevalent local T cell response and may be influenced by the EBV-status of neoplastic cells. Besides, M1-like and M2-like macrophages displayed differential effects on outcome in pcHL.     

Identification of hub genes and pathways in adrenocortical carcinoma by integrated bioinformatic analysis

Adrenocortical carcinoma (ACC), a rare malignant neoplasm originating from adrenal cortical cells, has high malignancy and few treatments. Therefore, it is necessary to explore the molecular mechanism of tumorigenesis, screen and verify potential biomarkers, which will provide new clues for the treatment and diagnosis of ACC. In this paper, three gene expression profiles (GSE10927, GSE12368 and GSE90713) were downloaded from the Gene Expression Omnibus (GEO) database. Differentially expressed genes (DEGs) were obtained using the Limma package. Gene ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) pathways were enriched by DAVID. Protein‐protein interaction (PPI) network was evaluated by STRING database, and PPI network was constructed by Cytoscape. Finally, GEPIA was used to validate hub genes’ expression. Compared with normal adrenal tissues, 74 up‐regulated DEGs and 126 down‐regulated DEGs were found in ACC samples; GO analysis showed that up‐regulated DEGs were enriched in organelle fission, nuclear division, spindle, et al, while down‐regulated DEGs were enriched in angiogenesis, proteinaceous extracellular matrix and growth factor activity; KEGG pathway analysis showed that up‐regulated DEGs were significantly enriched in cell cycle, cellular senescence and progesterone‐mediated oocyte maturation; Nine hub genes (CCNB1, CDK1, TOP2A, CCNA2, CDKN3, MAD2L1, RACGAP1, BUB1 and CCNB2) were identified by PPI network; ACC patients with high expression of 9 hub genes were all associated with worse overall survival (OS). These hub genes and pathways might be involved in the tumorigenesis, which will offer the opportunities to develop the new therapeutic targets of ACC.     

Construction of miRNA-mRNA network for the identification of key biological markers and their associated pathways in IgA nephropathy by employing the integrated bioinformatics analysis

BackgroundAbout half-century ago, Immunoglobulin A nephropathy (IgAN) was discovered as a complicated disease with frequent clinical symptoms. Until now, exact mechanism underlying the pathogenesis of IgAN is poorly known. Therefore, current study was aimed to understand the molecular mechanism of IgAN by identifying the key miRNAs and their targeted hub genes. The key miRNAs might contribute to the diagnosis and therapy of IgAN, and could turn out to be a new star in the field of IgAN.MethodsThe microarray datasets were downloaded from Gene Expresssion Omnibus (GEO) database and analyzed using R package (LIMMA) in order to obtain differential expressed genes (DEGs). Then, the hub genes were identified using cytoHubba plugin of cytoscpae tool and other bioinformatics approaches including protein-protein interaction (PPI) network analysis, module analysis, and miRNA-hub gene network construction was also performed.ResultsA total of 348 DEGs were identified, of which 107 were upregulated genes and 241 were downregulated genes. Subsequently, the 12 overlapped genes were predicted from cytoHubba, and considered as hub genes. Moreover, a network among miRNA-hub genes was created to explore the correlation between the hub genes and their targeted miRNAs. Network construction ultimately lead to the identification of nine gene named FN1, EGR1, FOS, JUN, SERPINE1, MMP2, ATF3, MYC, and IL1B and one novel key miRNA namely, has-miR-144-3p as biomarker for diagnosis and therapy of IgAN.ConclusionThis study updates the information and yield a new perspective in context of understanding the pathogenesis and development of IgAN. In future, key miRNAs might be capable of improving the personalized detection and therapies for IgAN. In vivo and in vitro investigation of miRNAs and pathway interaction is essential to delineate the specific roles of the novel miRNAs, which may help to further reveal the mechanisms underlying IgAN.     

紫外辐照恢复早期耐辐射奇球菌的转录组学分析（英文）

目的 耐辐射奇球菌是一种对紫外线、电离、干燥和化学试剂具有较强抗性的极端微生物。然而，该菌在紫外辐照后恢复早期的分子响应还不完全清楚。本文的目的是揭示耐辐射奇球菌在这一阶段的转录组响应。方法 本研究采用RNA-seq技术，测定了正常和紫外辐照培养条件下耐辐射奇球菌的转录组。为确定关键的差异表达基因及其调控关系，进行了功能富集分析。选取部分关键差异表达基因，进行实时定量PCR实验验证。利用以往研究中的转录组数据，寻找紫外辐照、电离辐射和干燥胁迫条件下公共的差异表达基因。构建了蛋白质-蛋白质相互作用网络；对蛋白质互作网络中的枢纽基因和主要模块进行了鉴定；对这些枢纽基因和模块进行了功能富集分析。结果 紫外辐照后的恢复早期，上调基因数量是下调基因数量的2倍以上，且多数与应激反应和DNA修复有关。恢复早期的修复途径主要有单链退火（SSA）途径（涉及基因：ddr A-D）、非同源端连接（NHEJ）途径（涉及基因：lig B、ppr A）和核苷酸切除修复（NER）途径（涉及基因：uvr A-C），前两种途径为同源重组（HR）做准备，而NER途径去除紫外线照射带来的嘧啶二聚体。通过比较紫外辐照、电离辐...     

LncRNAs related key pathways and genes in ischemic stroke by weighted gene co-expression network analysis (WGCNA)

BackgroundIschemic stroke (IS) was a significant public health concern and long-chain noncoding RNAs (lncRNAs) were gaining particular importance in stroke biology, however, the potential mechanism of lncRNAs in IS was not fully understood.MethodsIn this study, three diagnosed patients with IS and three controls were selected to establish the lncRNA library. Weighted gene co-expression network analysis (WGCNA) was applied to screen key lncRNA modules associated with IS. The key lncRNAs were identified by module membership (MM) and gene significance (GS). The Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway enrichment analysis was used to identify the key pathways and protein-protein interaction (PPI) network method was used to identify the key genes.ResultsA total of 3627 lncRNAs were investigated, followed by an analysis of 17 modules, and only one module was highly associated with the IS. The top 10 lncRNAs were identified based on GS and MM. KEGG pathways analysis revealed the top two pathways of the Human T cell Lymphotropic Virus-1 (HTLV-1) infection and the mTOR signaling pathway might influence the progress of IS. Further, genes meeting the top two degree (AKT1 and MAPK14) were selected as the hub genes in the PPI network.ConclusionTo summarize, this study identified the key pathways and genes, which might serve as biomarkers and targets for precise diagnosis and treatment of IS in the future.     

Analysis of the potential pathways and target genes in spinal cord injury using bioinformatics methods

Spinal cord injury (SCI) remains to be the most devastating type of trauma for patients because of long lasting disability and limited response to the acute drug administration and efforts at rehabilitation. With the purpose to identify potential targets for SCI treatment and to gain more insights into the mechanisms of SCI, the microarray data of GSE2270, including 119 raphe magnus (RM) samples and 125 sensorimotor cortex (SMTC) samples, was downloaded from the Gene Expression Omnibus database. Differentially expressed genes (DEGs) were screened in RM group and SMTC group compared with their corresponding controls, respectively. A protein–protein interaction (PPI) network was constructed based on the common DEGs identified in both RM group and SMTC group. Gene ontology (GO) and pathway enrichment analyses of the overlapping DEGs were performed. Furthermore, the common DEGs enriched in each pathway were analyzed to identify significant regulatory elements. Totally, 173 overlapping DEGs (130 up-regulated and 43 down-regulated) were identified in both RM and SMTC samples. These overlapping DEGs were enriched in different GO terms. Pathway enrichment analysis revealed that DEGs were mainly related to inflammation and immunity. CD68 molecule (CD68) was a hub protein in the PPI network. Moreover, the regulatory network showed that ras-related C3 botulinum toxin substrate 2 (RAC2), CD44 molecule (CD44), and actin related protein 2/3 complex (ARPC1B) were hub genes. RAC2, CD44, and ARPC1B may be significantly involved in the pathogenesis of SCI by participating significant pathways such as extracellular matrix-receptor signaling pathway and Toll-like receptor signaling pathway.     

RNA sequence analysis identified bone morphogenetic protein-2 (BMP2) as a biomarker underlying form deprivation myopia

PurposeForm deprivation myopia (FDM) is an urgent public issue characterized by pathological changes, but the underlying mechanism remained unclear. The aim was to investigate bone morphogenetic proteins (BMPs) utilizing the pathogenesis of FDM.Material and methodsGene expression omnibus (GEO) database was used to analyze one mRNA profile (GSE89325) of FDM. Sixteen retina samples (8 FDM and 8 controls) were randomly divided into seven groups for differential gene expression analysis in R. software. The gene pathway and protein-protein interaction (PPI) analysis were performed by the DAVID and STRING databases. Cytoscape was used to draw the PPI network. The gene ontology (GO) enrichment and Kyoto encyclopedia of genes and Genomes (KEGG) analysis were determined to achieve gene annotation and visualization.ResultsA total of 18420 differentially expressed genes (DEGs) were identified associated with FDM. The only non-significant gene (BEND6) was separately analyzed between two groups. Thirteen hub genes were discovered, ACVR1, ACVR2A, ACVR2B, RGMB, BMPR2, BMPR1A, BMP2, BMPR1B, CHRD, PTH, PTH1R, PTHLH, and WNT9A. The expression alteration in FDM were mainly enriched in cytokine-cytokine, and neuroactive ligand receptor interaction pathways. BMP2 was the key gene in myopia progression.ConclusionsOf clinical perspective, our findings reveal that expression of BMP2 as an underlying mechanism of FDM, providing an insight for therapeutic interventions.     

The Clinical Significance of the CD163+ and CD68+ Macrophages in Patients with Hepatocellular Carcinoma

Our previous study has found that the abundance of peritumoral CD68⁺ macrophages was associated with poor prognosis in hepatocellular carcinoma (HCC) after resection. However, CD68 staining could not discriminate the protumoral or tumoricidal subpopulations from pan-macrophages. CD163 is a marker of alternatively activated macrophages. In this study, the clinical significance of CD163⁺ cells in tumors and peritumoral liver tissues was evaluated in a cohort of 295 patients with HCC after curative resection. We found that the density of CD163⁺ cells was well correlated with that of CD68⁺ cells in both tumors and peritumoral liver tissues but was much more. Immunostaining on consecutive sections and flow cytometry assay on surgical resected specimens further supported the findings that the CD163⁺ cells was more abundant than CD68⁺ cells. The density of peritumoral CD68⁺ cells was associated with poor recurrence-free survival (RFS) and poor overall survival (OS) (P = 0.004 and P = 0.001, respectively), whereas the CD163⁺ cells have no prognostic values either in tumors or in peritumoral liver tissues. In another cohort of 107 HCC patients, preoperative plasma concentration of soluble form of CD163 (sCD163) was associated with active hepatitis-related factors but not associated with the markers of tumor invasion. In conclusion, both the CD163⁺ cells local infiltration and plasma sCD163 were of limited significance in HCC, and they were more likely markers related to active hepatitis rather than tumor progression.     

Identification of immune-associated signatures and potential therapeutic targets for pulmonary arterial hypertension

Pulmonary arterial hypertension (PAH) comprises a heterogeneous group of diseases with diverse aetiologies. It is characterized by increased pulmonary arterial pressure and right ventricular (RV) failure without specific drugs for treatment. Emerging evidence suggests that inflammation and autoimmune disorders are common features across all PAH phenotypes. This provides a novel idea to explore the characteristics of immunological disorders in PAH and identify immune-related genes or biomarkers for specific anti-remodelling regimens. In this study, we integrated three gene expression profiles and performed Gene Ontology (GO) and KEGG pathway analysis. CIBERSORT was utilized to estimate the abundance of tissue-infiltrating immune cells in PAH. The PPI network and machine learning were constructed to identify immune-related hub genes and then evaluate the relationship between hub genes and differential immune cells using ImmucellAI. Additionally, we implemented molecular docking to screen potential small-molecule compounds based on the obtained genes. Our findings demonstrated the density and distribution of infiltrating CD4 T cells in PAH and identified four immune-related genes (ROCK2, ATHL1, HSP90AA1 and ACTR2) as potential targets. We also listed 20 promising molecules, including TDI01953, pemetrexed acid and radotinib, for PAH treatment. These results provide a promising avenue for further research into immunological disorders in PAH and potential novel therapeutic targets.     

Network pharmacology and molecular docking analyses on Lianhua Qingwen capsule indicate Akt1 is a potential target to treat and prevent COVID‐19

ObjectivesCoronavirus disease 2019 (COVID‐19) is rapidly spreading worldwide. Lianhua Qingwen capsule (LQC) has shown therapeutic effects in patients with COVID‐19. This study is aimed to discover its molecular mechanism and provide potential drug targets.Materials and MethodsAn LQC target and COVID‐19–related gene set was established using the Traditional Chinese Medicine Systems Pharmacology database and seven disease‐gene databases. Gene ontology (GO), Kyoto Encyclopedia of Genes and Genomes (KEGG) enrichment analysis and protein‐protein interaction (PPI) network were performed to discover the potential mechanism. Molecular docking was performed to visualize the patterns of interactions between the effective molecule and targeted protein.ResultsA gene set of 65 genes was generated. We then constructed a compound‐target network that contained 234 nodes of active compounds and 916 edges of compound‐target pairs. The GO and KEGG indicated that LQC can act by regulating immune response, apoptosis and virus infection. PPI network and subnetworks identified nine hub genes. The molecular docking was conducted on the most significant gene Akt1, which is involved in lung injury, lung fibrogenesis and virus infection. Six active compounds of LQC can enter the active pocket of Akt1, namely beta‐carotene, kaempferol, luteolin, naringenin, quercetin and wogonin, thereby exerting potential therapeutic effects in COVID‐19.ConclusionsThe network pharmacological strategy integrates molecular docking to unravel the molecular mechanism of LQC. Akt1 is a promising drug target to reduce tissue damage and help eliminate virus infection.     

Cellular and molecular properties associated with osteosarcoma cells

Osteosarcoma cells are recognized by abnormal function that causes a primary bone tumor. Osteosarcoma cells U₂OS and SAOS‐2 were analyzed for the expression of cell surface markers. High expression was quantified for hyaloronidase receptor (CD‐44) > moderate for integrins (CD‐51 and ‐61), > and lower for selectins (CD‐62). High mitotic capacity were demonstrated by gene expression (measured by RT‐PCR) and the protein level (measured by FACS) for cFOS, cMYC, and cJUN. The basic definition of osteosarcoma is excessive production of pathological osteoid. Expression of mRNA for matrix genes osteocalcin, osteonectin, and biglycan was studied. Osteocalcin and osteonectin were detected in RNA from primary cultured marrow stromal, trabecular bone cells, and osteosarcoma cell lines (U₂OS, SAOS‐2). mRNA for biglycan was detected only in primary cells and MG‐63 cell line and was undetectable in RNA from U₂OS, SAOS‐2 osteosarcoma cell lines and by RNA extracted from bone biopsies of osteosarcoma patients. The absence of biglycan message observed in osteosarcoma samples provides evidence for the alterations in the extra cellular matrix which result with non‐mineralized osteoid produced by the osteosarcoma cells. J. Cell. Biochem. 84: 108–114, 2002. © 2001 Wiley‐Liss, Inc.     

The Downregulation of MiR-182 Is Associated with the Growth and Invasion of Osteosarcoma Cells through the Regulation of TIAM1 Expression

BackgroundOsteosarcoma is the most common primary bone malignancy in children and young adults. Increasing results suggest that discovery of microRNAs (miRNAs) might provide a novel therapeutical target for osteosarcoma.MethodsMiR-182 expression level in osteosarcoma cell lines and tissues were assayed by qRT-PCR. MiRNA mimics or inhibitor were transfected for up-regulation or down-regulation of miR-182 expression. Cell function was assayed by CCK8, migration assay and invasion assay. The target genes of miR-182 were predicated by bioinformatics algorithm (TargetScan Human).ResultsMiR-182 was down-regulated in osteosarcoma tissues and cell lines. Overexpression of miR-182 inhibited tumor growth, migration and invasion. Subsequent investigation revealed that TIAM1 was a direct and functional target of miR-182 in osteosarcoma cells. Overexpression of miR-182 impaired TIAM1-induced inhibition of proliferation and invasion in osteosarcoma cells.ConclusionsDown-expression of miR-182 in osteosarcoma promoted tumor growth, migration and invasion by targeting TIAM1. MiR-182 might act as a tumor suppressor gene whose down-regulation contributes to the progression and metastasis of osteosarcoma, providing a potential therapy target for osteosarcoma patients.     

The omics based study for the role of superoxide dismutase 2 (SOD2) in keratinocytes: RNA sequencing,antibody-chip array and bioinformatics approaches

Abstract

In this study, we aimed to identify critical factors associated with superoxide dismutase 2 (SOD2) in human keratinocytes through gene and protein expression profiling approaches. After recombinant SOD2 was exogenously added to culture media, we conducted serial OMICS studies, which included RNA sequencing analysis, integrated antibody-chip arrays, and the implementation of bioinformatics algorithms, in order to reveal genes and proteins that are possibly associated with SOD2 in keratinocytes. These approaches identified several novel genes and proteins in keratinocytes that are associated with exogenous SOD2. These novel genes included DCT, which was up-regulated, and CD38, GPR151, HCK, KIT, and AFP, which were down-regulated. Among them, CD38 and KIT were also predicted as hub proteins in PPI mappings. By integrating the datasets obtained from these complementary high-throughput OMICS studies and utilizing the strengths of each method, we obtained new insights into the functional role of externally added SOD2 in skin cells and into several critical genes that are thought to play important roles in SOD2-associated skin function. The approach used here could help contribute to our clinical understanding of SOD2-associated applications and may be broadly applicable to a wider range of diseases. Abbreviations SOD2 superoxide dismutase 2

DAVID the database for annotation, visualization and integrated discovery

KEGG Kyoto Encyclopedia of Genes and Genomes

PPI protein–protein interactions

HTS High-throughput screening

Communicated by Ramaswamy H. Sarma