Genomic Expression Profiling and Bioinformatics Analysis of Chronic Recurrent Multifocal Osteomyelitis

Objective. Chronic nonbacterial osteomyelitis (CNO) is an autoinflammatory bone disorder. Its most severe form is referred to as chronic recurrent multifocal osteomyelitis (CRMO). Currently, the exact molecular pathophysiology of CNO/CRMO remains unknown. No uniform diagnostic standard and treatment protocol were available for this disease. The aim of this study was to identify the differentially expressed genes (DEGs) in CRMO tissues compared to normal control tissues to investigate the mechanisms of CRMO. Materials. Microarray data from the GSE133378 (12 CRMO and 148 matched normal tissue samples) data sets were downloaded from the Gene Expression Omnibus (GEO) database. DEGs were identified using the limma package in the R software. Gene Ontology (GO) analysis, Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway analysis, and protein-protein interaction (PPI) network analysis were performed to further investigate the function of the identified DEGs. Results. This study identified a total of 1299 differentially expressed mRNAs, including1177 upregulated genes and 122 downregulated genes, between CRMO and matched normal tissue samples. GO analyses showed that DEGs were enriched in immune-related terms. KEGG pathway enrichment analyses showed that the DEGs were mainly related to oxidative phosphorylation, ribosome, and Parkinson disease. Eight modules were extracted from the gene expression network, including one module constituted with immune-related genes and one module constituted with ribosomal-related genes. Conclusion. Oxidative phosphorylation, ribosome, and Parkinson disease pathways were significantly associated with CRMO. The immune-related genes including IRF5, OAS3, and HLA-A, as well as numerous ribosomal-related genes, might be implicated in the pathogenesis of CRMO. The identification of these genes may contribute to the development of early diagnostic tools, prognostic markers, or therapeutic targets in CRMO.

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Expression of EGF receptors in canine prostate with proliferative inflammatory atrophy and carcinoma

Ciência Rural ◽

10.1590/0103-8478cr20170085 ◽

2017 ◽

Vol 47 (12) ◽

Author(s):

Mariana Batista Rodrigues Faleiro ◽

Lorena Cardoso Cintra ◽

Rosália Santos Amorim Jesuino ◽

Eugênio Gonçalves de Araújo ◽

Rafael Malagoli Rocha ◽

...

Keyword(s):

Gene Expression ◽

Gene Product ◽

Normal Tissue ◽

Prostatic Carcinoma ◽

Prostatic Tissue ◽

Egf Receptors ◽

Tissue Samples ◽

Proliferative Inflammatory Atrophy ◽

Erbb2 Mrna

ABSTRACT: Gene expression of ErbB1 and ErbB2, and immunostaining of EGFR (Her1) and Her2 (c-erbB-2) were evaluated in this study to ascertain whether these receptors are involved in the evolution of canine premalignant and malignant prostatic lesions, as proliferative inflammatory atrophy (PIA) and prostatic carcinoma (PC). With regards to the intensity of EGFR immunostaining, there was no difference between normal prostatic tissue and tissues with PIA or PC. In relation to Her2 immunostaining, there were differences between normal prostatic tissue and those with PIA and PC, as also differences between prostates with PIA and PC. There was no correlation between EGFR and Her2 immunostaining. ErbB1 gene product was detected in two normal tissue samples, in one with PIA, and in all samples with PC. ErbB2 mRNA was recorded in two canine samples with PIA, in all with PC, but was not detected in normal prostatic tissue. It was concluded that EGFR and Her2 play roles in canine PIA and PC, suggesting that those receptors may be involved in canine prostatic carcinogenesis.

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Transcriptional characterization of microenvironment and their prediction role for the prognosis of hepatocellular carcinoma after surgery.

Journal of Clinical Oncology ◽

10.1200/jco.2019.37.15_suppl.e15650 ◽

2019 ◽

Vol 37 (15_suppl) ◽

pp. e15650-e15650

Author(s):

Kehe Chen ◽

Haiming Wei ◽

Tianqi Liu ◽

Zhenxiang Chen ◽

Deng Pan ◽

...

Keyword(s):

Gene Expression ◽

Hepatocellular Carcinoma ◽

Antigen Processing ◽

Tissue Samples ◽

Ffpe Tumor ◽

Group A ◽

One Year ◽

Group B ◽

Immune Related Genes ◽

The Impact

e15650 Background: Hepatocellular carcinoma (HCC) is one of the most common prevalent fatal cancers worldwide with poor prognosis due to high incidence of recurrence. For patients with HCC, surgical treatment is a potentially cutative therapy. However, the puzzle in the therapy was the rapid recurrence after surgery. The purpose of this study was to integrate the impact of different immune context present in HCC microenvironment on patients’ prognosis, provide the molecular prediction clue of HCC recurrence. Methods: RNA targeted sequencing was performed on 12 primary tumor specimens from HCC patients. Transcripts of 395 immune related genes expressed in FFPE tumor samples were analyzed. The lima package was used to analyze the different expressed genes (DEGs) between patients with different prognosis. The gene set variance analysis (GSVA) analysis was performed to explore gene sets enrichment related to the recurrence post-resection. Results: 15 DEGs were detected in tissue samples between the two groups (group A: patients who relapsed within one year after surgery; group B: patients who hadn't relapsed beyond two years after surgery). The Antigen processing pathway enrichment may associate with the favorable prognosis (p < 0.05). HLA-A gene expression in group A was lower than that in group B; The gene expression of IL23A, TP63, ALOX15B, BUB1, CXCR2, CCL20, CLEC4C, PTK7, MPO, IL1B, MMP9, GAGE2C, GAGE2A, GAGE2E, DMBT1, FOXM1 in group A was higher than that in group B. Additionally, the combination of 3 genes (TP63, IL23A and BUB1) can distinguish the patients recurrent within 1 year or beyond 2 years post-resection. The joint diagnostic equation is logit (Y = 1) = 0.073 +0.740 *(TP63) + 0.589 * (IL23A)+0.959(BUB1), (Optimal threshold: 0.667, specificity: 1, sensitivity: 0.833). Conclusions: Our results suggest that RNA-seq of immune related genes from FFPE sample can effectively profile the specific landscape of tumor immune microenvironment and predict the survival of HCC. 3 genes’ expression (TP63, IL23A and BUB1) might correlate with recurrence in HCC patients after surgery.

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Gene expression profiling of multiple leiomyomata uteri and matched normal tissue from a single patient

Fertility and Sterility ◽

10.1016/j.fertnstert.2008.03.071 ◽

2009 ◽

Vol 91 (6) ◽

pp. 2650-2663 ◽

Cited By ~ 17

Author(s):

Irina K. Dimitrova ◽

Jennifer K. Richer ◽

Michael C. Rudolph ◽

Nicole S. Spoelstra ◽

Elaine M. Reno ◽

...

Keyword(s):

Gene Expression ◽

Gene Expression Profiling ◽

Expression Profiling ◽

Normal Tissue ◽

Single Patient ◽

Matched Normal Tissue

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Elevated miRNA Inversely Correlates with E-cadherin Gene Expression in Tissue Biopsies from Crohn Disease Patients in contrast to Ulcerative Colitis Patients

BioMed Research International ◽

10.1155/2020/4250329 ◽

2020 ◽

Vol 2020 ◽

pp. 1-7

Author(s):

Małgorzata Guz ◽

Tomasz Dworzański ◽

Witold Jeleniewicz ◽

Marek Cybulski ◽

Joanna Kozicka ◽

...

Keyword(s):

Gene Expression ◽

Ulcerative Colitis ◽

Crohn Disease ◽

Normal Tissue ◽

Normal Mucosa ◽

Normal Colonic Mucosa ◽

Adjacent Normal Tissue ◽

Tissue Samples ◽

Mesenchymal Transition ◽

E Cadherin

Inflammatory bowel disease (IBD) comprises ulcerative colitis (UC) and Crohn disease (CD). Similar symptoms, but different treatment procedures for both diseases require precise diagnosis. MicroRNAs (miRNAs) are major posttranscriptional players that regulate the expression of genes during the inflammation and thus could be appropriate biomarkers for differentiation between UC and CD. For this purpose, we analyzed the expression of miR-21-3p, miR-31-3p, miR-125b-1-3p, miR-146a-3p, miR-155-5p, and E-cadherin (CDH1) genes associated with IBD, in 67 tissue samples: 28 inflamed mucosa samples (n=16 UC, n=12 CD), 28 adjacent normal colonic mucosa (n=16 UC, n=12 CD), and 11 normal mucosa from healthy patients using reverse transcription real-time RT-PCR. We found all analyzed miRNAs were significantly overexpressed in UC tissue as compared to adjacent normal tissue of patients with UC, as well as to normal mucosa from healthy controls. Four miRNAs (except miR-125b-1-3p) were significantly upregulated in CD lesions as compared to adjacent normal tissue of patients with CD, and four miRNAs, except miR-146a-3p, were significantly higher in CD samples compared to normal mucosa from healthy individuals. In the CD group, we found an inverse correlation between miR-155-5p or miR-146a-3p expressions and CDH1expression in inflamed mucosa. This type of correlation was also detected for miR-213p in adjacent normal tissue and CDH1 in inflamed mucosa, as well as between miR-155-5p and CDH1 in adjacent normal tissue. Elevated miRNA expression is characteristic for IBD-mediated inflammation process and inversely correlated with CDH1 gene expression, which suggest involvement of epithelial to mesenchymal transition (EMT) in IBD development.

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GEO Data Mining Identifies OLR1 as a Potential Biomarker in NSCLC Immunotherapy

Frontiers in Oncology ◽

10.3389/fonc.2021.629333 ◽

2021 ◽

Vol 11 ◽

Author(s):

Bin Liu ◽

Ziyu Wang ◽

Meng Gu ◽

Cong Zhao ◽

Teng Ma ◽

...

Keyword(s):

Gene Expression ◽

Lung Cancer ◽

Expression Profiles ◽

Statistical Significance ◽

Linear Regression Analysis ◽

Gene Expression Profiles ◽

Multiple Linear Regression Analysis ◽

Tissue Samples ◽

Potential Biomarker ◽

Immune Related Genes

Non-small cell lung cancer (NSCLC) is the most common type of lung cancer. The tumor immune microenvironment (TME) in NSCLC is closely correlated to tumor initiation, progression, and prognosis. TME failure impedes the generation of an effective antitumor immune response. In this study, we attempted to explore TME and identify a potential biomarker for NSCLC immunotherapy. 48 potential immune-related genes were identified from 11 eligible Gene Expression Omnibus (GEO) data sets. We applied the CIBERSORT computational approach to quantify bulk gene expression profiles and thereby infer the proportions of 22 subsets of tumor-infiltrating immune cells (TICs); 16 kinds of TICs showed differential distributions between the tumor and control tissue samples. Multiple linear regression analysis was used to determine the correlation between TICs and 48 potential immune-related genes. Nine differential immune-related genes showed statistical significance. We analyzed the influence of nine differential immune-related genes on NSCLC immunotherapy, and OLR1 exhibited the strongest correlation with four well-recognized biomarkers (PD-L1, CD8A, GZMB, and NOS2) of immunotherapy. Differential expression of OLR1 showed its considerable potential to divide TICs distribution, as determined by non-linear dimensionality reduction analysis. In immunotherapy prediction analysis with the comparatively reliable tool TIDE, patients with higher OLR1 expression were predicted to have better immunotherapy outcomes, and OLR1 expression was potentially highly correlated with PD-L1 expression, the average of CD8A and CD8B, IFNG, and Merck18 expression, T cell dysfunction and exclusion potential, and other significant immunotherapy predictors. These findings contribute to the current understanding of TME with immunotherapy. OLR1 also shows potential as a predictor or a regulator in NSCLC immunotherapy.

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