Sanaz Savabkar; Shiva Irani; Masoud Alebouyeh; Reza Mirfakhraie; Ehsan Nazemalhosseini Mojarad; Mohammad reza Zali; Hamid Asadzadeh aghdaei
Volume 23, Issue 4 , 2021
Abstract
Background: Aberrant DNA methylation is a common molecular feature in colorectal cancer (CRC). Hypermethylation of miR-200b promoter, as an epigenetic factor, is involved in CRC tumorigenesis. The methylation status of miR-200b has been examined in CRC and adjacent normal tissues.
Objectives: ...
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Background: Aberrant DNA methylation is a common molecular feature in colorectal cancer (CRC). Hypermethylation of miR-200b promoter, as an epigenetic factor, is involved in CRC tumorigenesis. The methylation status of miR-200b has been examined in CRC and adjacent normal tissues.
Objectives: This study aimed to investigate miR-200b methylation in a series of colorectal adenomatous polyps, hyperplastic polyps, and adenocarcinoma tissues as precursors of CRC in the Iranian population for the first time.
Materials and Methods: In this cross-sectional study (2017-2018), the methylation status of the miR-200b promoter was investigated using methylation-specific PCR in 131 fresh samples, including 30 adenocarcinoma specimens, 17 tumor-adjacent normal tissues, 78 primary lesions (55 adenomatous polyps and 23 hyperplastic polyps) and 6 healthy individuals.
Results: Methylation of miR-200b was detected in adenocarcinoma samples (86%) and adenomatous polyps (85%); however, most of the hyperplastic polyps were unmethylated (69.6%). Neither control individuals nor tumor-adjacent normal tissues exhibited methylation in the miR-200b promoter. Aberrant methylation of miR-200b was significantly more common in tumor tissues and adenomatous polyps than in hyperplastic polyps (P<0.0001) and tumor-adjacent normal samples (P<0.0001).
Conclusion: Methylation status of the miR-200b promoter was significantly altered during CRC development and may be identified as an attractive biomarker for the early detection of the disease.
Mohammad Reza Jafari Nakhjavani; Amir Ghorbanihaghjo; Ozra Dabagh Asadollahipour; Sima Abedi Azar; Tala Pourlak; Aida Malek Mahdavi
Volume 21, Issue 5 , May 2019, , Pages 1-7
Abstract
Background: The role of vitamin D and cartilage oligomeric matrix protein (COMP) in knee osteoarthritis (OA) still remains con- troversial.Objectives: This study aimed to evaluate serum COMP and 25-hydroxy vitamin D concentrations in patients with knee OA in com- parison to healthy individuals and to ...
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Background: The role of vitamin D and cartilage oligomeric matrix protein (COMP) in knee osteoarthritis (OA) still remains con- troversial.Objectives: This study aimed to evaluate serum COMP and 25-hydroxy vitamin D concentrations in patients with knee OA in com- parison to healthy individuals and to find whether there is a relationship between serum COMP, 25-hydroxy vitamin D, and disease activity in knee OA.Methods: In a case-control study, 60 patients with knee OA were selected based on the criteria of the American College of Rheumatol- ogy referred to the Rheumatology Department of Tabriz University of Medical Sciences, Tabriz, Iran, from October 2017 to February 2018. Also, 28 healthy subjects matched regarding age and sex were selected. The patients were examined, and Western Ontario and McMaster Universities Osteoarthritis Index (WOMAC Index) was assessed. Serum levels of COMP and 25-hydroxy vitamin D were assessed by ELISA method.Results: The mean ± SD age of the patients and controls was 57.60 ± 10.63 and 56.46 ± 5.58 years, respectively. Serum COMP was significantly higher in OA patients (40.82 ± 10.04 pg/mL) than in healthy controls (27.01 ± 9.64 pg/mL) (P < 0.001). There were no statistically significant differences in serum 25-hydroxy vitamin D between the patients and control subjects (P = 0.361). Significant correlations were found between serum COMP concentration with WOMAC score (r = -0.290, P = 0.025) as well as the grade of OA (r = 0.362, P = 0.004). No statistically significant correlations were found between serum 25-hydroxy vitamin D level with WOMAC score (r = 0.102, P = 0.438) and the grade of OA (r = - 0.063, P = 0.630) as well as between serum COMP and 25-hydroxy vitamin D levels (P > 0.05).Conclusions: Based on the results of our study, Serum COMP levels correlated with disease characteristics in patients with os- teoarthritis. Although further studies are needed to confirm our results, COMP may be used as a possible novel marker to measure osteoarthritis development and progression.
Jin Zheng; Hong Chen; Ying Pan; Xin Yue
Volume 19, Issue 10 , October 2017, , Pages 1-8
Abstract
Background: Breast cancer (BC) is one of the leading causes of cancer-related mortality among females worldwide. There is no effective treatment for it, since the molecular mechanism underlying BC still remains unclear.Objectives: The current study aimed at identifying the hub pathways for BC based on ...
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Background: Breast cancer (BC) is one of the leading causes of cancer-related mortality among females worldwide. There is no effective treatment for it, since the molecular mechanism underlying BC still remains unclear.Objectives: The current study aimed at identifying the hub pathways for BC based on pathway crosstalk networks (PCNs), and revealing the molecular mechanisms underlying BC.Methods: The current case-control bioinformatics analysis used the already published microarray data of BC. The currentfoundation-application study was performed in Moffitt cancer center, USA, in 2010. To begin with, the gene expression profile of BC (access number E-GEOD-10780), which included 185 samples (143 normal controls and 42 BC samples), was recruited from ArrayExpress database. Then, data pretreatment method was used. Next, the original pathways (OPs), original protein-protein interaction (PPI) network (OPPIN), and attract OPs (AOPs) were obtained. Then, the construction of background PCN (BPCN) and cancer PCN (CPCN) was performed, following by the degree analysis of pathways in the BPCN and CPCN to further identify hub pathways. Moreover, the cross-talks for hub pathways were extracted and termed as hub cross-talks.Results: There were 300 nodes and 42,293 edges in BPCN, and 283 nodes and 25,750 edges in CPCN. According to the degree results, it was found that the degree distribution of pathways for BPCN was concentrated, while that of CPCN was dispersed. Moreover, the degree of original pathways in BPCN was greater than that of the majority of AOPs in CPCN. Based on the threshold of RankProd < 0.01 and false discovery rate of AOP < 0.01, thirteen significant pathways were detected. Using the threshold of impact factor > 240, a total of 4 hub pathways including glycolysis/gluconeogenesis, Alzheimer disease, carbon metabolism, and hepatitis C virus (HCV) infection were identified.Conclusions: Hub pathways such as glycolysis/gluconeogenesis and Alzheimer disease might be the potential signatures for BC therapy.
Caixia Wang; Shaoyong Luan; Ming Li; Ruiyun Zhang; Xiuxia Chen
Volume 19, Issue 3 , March 2017, , Pages 1-7
Abstract
Background: The exact interacting factor that response to the infection for neonatal sepsis is still needed to urgently to be disclosed.Objectives: This research was aimed to explore the potential biomarkers and illuminate the underlying molecular mechanisms associated with neonatal sepsis via identifying ...
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Background: The exact interacting factor that response to the infection for neonatal sepsis is still needed to urgently to be disclosed.Objectives: This research was aimed to explore the potential biomarkers and illuminate the underlying molecular mechanisms associated with neonatal sepsis via identifying differential modules (DMs).Methods: This is a case-control bioinformatics analysis using already published microarray data of neonatal sepsis. This study was conducted in Qingdao, China from September 2015 to May 2016. We recruited the gene expression profile of neonatal sepsis from the Array Express database (http://www.ebi.ac.uk/arrayexpress) under the accessing number of E-GEOD-25504, which included 27 neonatal samples with a confirmed blood culture-positive test for sepsis (bacterial infected cases) as well as 35 matched controls. Meanwhile, the human protein-protein interaction (PPI) data was collected from the database of Search Tool for the Retrieval ofInteracting Genes/Proteins (STRING, http://string-db.org). All of the data was preprocessed. Then, the differential co expression network (DCN) was constructed by integrating co-expression analysis and differential expression analysis. Next, a systemic module searching strategy, which contained seed genes selection, module searching and refinement of modules, was performed by select DMs.Results: Starting from the gene expression data and PPI data, the DCN that included 430 edges (covering 324 nodes) was constructed, in which each edge was assigned a weight value. From the DCN, we selected a total of 16 seed genes. Starting from these seed genes, a total of 3 modules were identified from the DCN based on the systemic module algorithm. Of them, only one module (Module 3) was considered as DM under P < 0.05. This DM was involved in the progress of ribosome biogenesis in eukaryotes.Conclusions: In the present study, we identified a key gene RPS16 and a significant module involved in ribosome biogenesis in eukaryotes that were related to neonatal sepsis, which might be potential biomarkers for early detection and therapy for neonatal sepsis
