scholarly journals A Novel Approach for Pathway Analysis of GWAS Data Highlights Role of BMP Signaling and Muscle Cell Differentiation in Colorectal Cancer Susceptibility – Erratum

2017 ◽  
Vol 20 (2) ◽  
pp. 186-186 ◽  
Author(s):  
Aniket Mishra ◽  
Stuart MacGregor
Keyword(s):  
Colorectal Cancer ◽  
Cell Differentiation ◽  
Medical Research ◽  
Pathway Analysis ◽  
Cancer Susceptibility ◽  
Bmp Signaling ◽  
Cancer Family ◽  
Muscle Cell Differentiation ◽  
Novel Approach

The publishers regret to announce that the affiliation for the above paper was incorrectly inserted. The correct affiliation is below:Aniket Mishra1, Genetics and Epidemiology of Colorectal Cancer Consortium (GECCO) and the Colorectal Cancer Family Registry (CCFR), and Stuart MacGregor11 Statistical Genetics, QIMR Berghofer Medical Research Institute, Brisbane, Queensland, Australia

scholarly journals A Novel Approach for Pathway Analysis of GWAS Data Highlights Role of BMP Signaling and Muscle Cell Differentiation in Colorectal Cancer Susceptibility

2017 ◽  
Vol 20 (1) ◽  
pp. 1-9 ◽  
Author(s):  
Aniket Mishra ◽  
Stuart MacGregor
Keyword(s):  
Colorectal Cancer ◽  
Cell Differentiation ◽  
Muscle Cell ◽  
Complex Traits ◽  
Meta Analysis ◽  
Bmp Signaling ◽  
Genome Wide Association Studies ◽  
Muscle Cell Differentiation ◽  
Gene Sets ◽  
Wide Range

Genome-wide association studies (GWAS) have revolutionized the field of gene mapping. As the GWAS field matures, it is becoming clear that for many complex traits, a proportion of the missing heritability is attributable to common variants of individually small effect. Detecting these small effects individually can be difficult, and statistical power would be increased if relevant variants could be grouped together for testing. Here, we propose a VEGAS2Pathway approach that aggregates association strength of individual markers into pre-specified biological pathways. It accounts for gene size and linkage disequilibrium between markers using simulations from the multivariate normal distribution. Pathway size is taken into account via a resampling approach. Importantly, since the approach only requires summary data, the method can easily be applied in all GWASs, including meta-analysis, singleton-based, family-based, and DNA-pooling-based designs. This approach is implemented in a user-friendly web page https://vegas2.qimrberghofer.edu.au and a command line tool. The web implementation uses gene-sets from the gene ontology (GO), curated gene-sets from MSigDB (containing canonical pathways and gene-sets from BIOCARTA, REACTOME, KEGG databases), PANTHER, and pathway commons databases, enabling analysis of a wide range of complex traits. We applied this method on a colorectal cancer GWAS meta-analysis data set (10,934 cases, 12,328 controls) from the Genetics and Epidemiology of Colorectal Cancer Consortium (GECCO). We report statistically significant enrichment of association signal for the ‘BMP signaling’ and ‘muscle cell differentiation’ pathways, suggesting a possible role for these pathways onto the risk of colorectal cancer.

scholarly journals Study of the Relationship between Microbiome and Colorectal Cancer Susceptibility Using 16SrRNA Sequencing

2020 ◽  
Vol 2020 ◽  
pp. 1-17 ◽  
Author(s):  
Wanxin Liu ◽  
Ren Zhang ◽  
Rong Shu ◽  
Jinjing Yu ◽  
Huan Li ◽  
...  
Keyword(s):  
Colorectal Cancer ◽  
Gut Microbiota ◽  
Cancer Susceptibility ◽  
Precancerous Lesions ◽  
Bacterial Community Composition ◽  
Intestinal Flora ◽  
Control Group ◽  
Healthy Controls ◽  
Healthy Individuals

A lot of previous studies have recently reported that the gut microbiota influences the development of colorectal cancer (CRC) in Western countries, but the role of the gut microbiota in Chinese population must be investigated fully. The goal of this study was to determine the role of the gut microbiome in the initiation and development of CRC. We collected fecal samples of 206 Chinese individuals: 59 with polyp (group P), 54 with adenoma (group A), 51 with colorectal cancer (group CC), and 42 healthy controls (group HC).16S ribosomal RNA (rRNA) was used to compare the microbiota community structures among healthy controls, patients with polyp, and those with adenoma or colorectal cancer. Our study proved that intestinal flora, as a specific indicator, showed significant differences in its diversity and composition. Sobs, Chao, and Ace indexes of group CC were significantly lower than those of the healthy control group (CC group: Sobs, Chao, and Ace indexes were 217.3 ± 69, 4265.1 ± 80.7, and 268.6 ± 78.1, respectively; HC group: Sobs, Chao, and Ace indexes were 228.8 ± 44.4, 272.9 ± 58.6, and 271.9 ± 57.2, respectively). When compared with the healthy individuals, the species richness and diversity of intestinal flora in patients with colorectal cancer were significantly reduced: PCA and PCoA both revealed that a significant separation in bacterial community composition between the CC group and HC group (with PCA using the first two principal component scores of PC1 14.73% and PC2 10.34% of the explained variance, respectively; PCoA : PC1 = 14%, PC2 = 9%, PC3 = 6%). Wilcox tests was used to analyze differences between the two groups, it reveals that Firmicutes (P=0.000356), Fusobacteria (P=0.000001), Proteobacteria (P=0.000796), Spirochaetes (P=0.013421), Synergistetes (P=0.005642) were phyla with significantly different distributions between cases and controls. The proportion of microorganism composition is varying at different stages of colon cancer development: Bacteroidetes (52.14%) and Firmicutes (35.88%) were enriched in the healthy individuals; on the phylum level, the abundance of Bacteroidetes (52.14%-53.92%-52.46%–47.06%) and Firmicutes (35.88%-29.73%-24.27%–25.36%) is decreasing with the development of health-polyp-adenomas-CRC, and the abundance of Proteobacteria (9.33%-12.31%-16.51%–22.37%) is increasing. PCA and PCOA analysis showed there was no significant (P<0.05) difference in species similarity between precancerous and carcinogenic states. However, the composition of the microflora in patients with precancerous lesions (including patients with adenoma and polyp) was proved to have no significant disparity (P<0.05). Our study provides insights into new angles to dig out potential biomarkers in diagnosis and treatment of colorectal cancer and to provide scientific advice for a healthy lifestyle for the sake of gut microbiota.

The role of smooth muscle cell differentiation in the mechanism of obliteration of processus vaginalis

2004 ◽  
Vol 39 (7) ◽  
pp. 1018-1023 ◽  
Author(s):  
Munevver Hosgor ◽  
Irfan Karaca ◽  
Erdener Ozer ◽  
Gulsun Erdag ◽  
Cagnur Ulukus ◽  
...  
Keyword(s):  
Smooth Muscle ◽  
Cell Differentiation ◽  
Smooth Muscle Cell ◽  
Muscle Cell ◽  
Processus Vaginalis ◽  
Muscle Cell Differentiation ◽  
Smooth Muscle Cell Differentiation

scholarly journals TrkB induced metastatic potential of cancer by suppression of BMP mediated tumor inhibitory activity

2020 ◽  
Author(s):  
Min Soo Kim ◽  
Wook Jin
Keyword(s):  
Breast Cancer ◽  
Colorectal Cancer ◽  
Inhibitory Activity ◽  
Metastatic Potential ◽  
Bmp Signaling ◽  
Unique Role ◽  
Akt Activation ◽  
Growth Inhibitory ◽  
Growth Inhibitory Activity

AbstractOur previous observations also demonstrate that TrkB expression in breast cancer induces metastatic potential by both JAK2/STAT3 and PI3K/AKT activation and induced metastasis of breast cancer mediated suppression of RUNX3 and KEAP1 expression by TrkB. Also, TrkB induced metastatic potential of cancer and suppressed the growth inhibitory activity in response to BMP signaling by preventing BMRRI/BMPRII complex formation. The previous report BMP-2 and BMP4 trigger tumor inhibitory activity in colorectal cancer by upregulation of RUNX3 expression. Although TrkB may regulate tumor inhibitory activity by BMP-induced upregulation of RUNX3, it is not still fully understood how TrkB signaling adjusts to inhibit BMP signaling-mediated tumor suppression.Our findings provide important molecular insights into TrkB-mediated modulation of BMP signaling has remained unknown, and none of the studies still reported a correlation between TrkB and BMP signaling. Our current study surprisingly showed that unique role of TrkB in the regulation of BMP-induced tumor inhibitory activity and BMP-2-induced RUNX3 expression.

Su1069 – The Role of Rare Variants in Muc4 in Gastric Cancer Susceptibility in Gastric Cancer Family

2019 ◽  
Vol 156 (6) ◽  
pp. S-500
Author(s):  
Yoon Jin Choi ◽  
Nayoung Kim ◽  
Cheol Min Shin ◽  
Dong Ho Lee
Keyword(s):  
Gastric Cancer ◽  
Rare Variants ◽  
Cancer Susceptibility ◽  
Cancer Family

Role of Tumor Necrosis Factor Gene Polymorphism (-308 and -238) in Colorectal Cancer Susceptibility

2007 ◽  
Vol 102 ◽  
pp. S559-S560
Author(s):  
Mehrnoosh Tashakori ◽  
Babak Noorinayer ◽  
Azadeh Safaee ◽  
Faramarz Derakhshan ◽  
Mohammad Reza Zali
Keyword(s):  
Colorectal Cancer ◽  
Tumor Necrosis Factor ◽  
Gene Polymorphism ◽  
Tumor Necrosis ◽  
Cancer Susceptibility ◽  
Factor Gene ◽  
Tumor Necrosis Factor Gene ◽  
Necrosis Factor
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