An Integrative CGH, MSI and Candidate Genes Methylation Analysis of Colorectal Tumors

Brim, Hassan; Abu‐Asab, Mones; Nouraie, Mehdi; Salazar, José; DeLeo, James M.; Razjouyan, Hadi; Mokarram, Pooneh; Schäffer, Alejandro A.; Naghibhossaini, Fakhraddin; Ashktorab, Hassan

doi:10.1371/journal.pone.0082185

Cited by 30 publications

(33 citation statements)

References 51 publications

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“…Regarding the LGR6 receptor, its promoter has been reported to be hypermethylated in approximately 20% of sporadic colorectal cancer [92]. Interestingly, higher methylation level was detected in early as compared to advanced stages [92][93][94]. Together, these studies evidence that expression of LGR receptors is epigenetically modulated in cancer.…”

Section: Epigeneticsmentioning

confidence: 79%

LGRs receptors as peculiar GPCRs involved in cancer

Garcia¹

2017

J Stem Cell Res Med

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G protein-coupled receptors (GPCRs) constitute the largest protein superfamily in mammalian genomes. The Leucine-rich repeat-containing G protein-coupled receptors LGR4, LGR5 and LGR6 belong to the type A rhodopsin-like family and are closely structurally related to the glycoprotein hormone receptors. They have the particularity to be expressed in stem/progenitor cells.LGRs commonly recognize R-spondins as ligands leading to Wnt signaling regulation. Whereas LGR4 plays an essential role during development and adult homeostasis and exerts a dominant function over its paralogues, the function of LGR5 still remains controversial. In cancer cells, LGRs identify tumor-initiating cells and their expression can be correlated with tumor stage and prognosis. The molecular events underlying deregulated expression of LGRs in cancer cells and potential new therapeutic approaches to target cancer cells are reviewed.

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Section: Epigeneticsmentioning

confidence: 79%

LGRs receptors as peculiar GPCRs involved in cancer

Garcia¹

2017

J Stem Cell Res Med

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“…The most regularly found kinds of mutations are G > A and G > T transitions (21). KRAS testing has a vital improvement in the treatment of CRCs, especially after metastasis (19,20,22). There are very few studies about the frequency of K-ras mutation from the Middle East and Iran; consequently, in the present study, we reviewed KRAS mutation rate and spectrum in previous studies from Iran.…”

Section: Kras Mutationmentioning

confidence: 98%

“…The basic tests identify five markers (NR-21, BAT-26, BA T -25, NR-27 and NR-24) to devise the simplest diagnostic assay (9). Previous reports have shown significant diversity regarding the most common marker for microsatellite testing; BAT 25, BAT26 and NR21 have been reported in HNPCC and sporadic CRCs (9)(10)(11)(12)(13)(14)(15)(16)(17)(18)(19)(20)(21)(22)(23)(24)(25)(26)(27)(28). Table 1 shows the reports from Iran that studied the frequency of MMR genes in both hereditary and sporadic colorectal cancers.…”

Section: Microsatellite Instability (Msi)mentioning

confidence: 99%

“…Table 1 shows the reports from Iran that studied the frequency of MMR genes in both hereditary and sporadic colorectal cancers. As it shows, the frequency of MSI in patients with HNPCC has been 29% -62.5% (9-25), there are not so many studies about the frequency of MSI in sporadic CRC from Iran; however, the reported frequencies of MMR have been from 19.4% to 66.6% (9)(10)(11)(12)(13)(14)(15)(16)(17)(18)(19)(20)(21)(22)(23)(24)(25).…”

Section: Microsatellite Instability (Msi)mentioning

confidence: 99%

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Molecular Biomarkers of Colorectal Cancer: A Review of Published Articles From Iran

Geramizadeh

2015

Ann Colorectal Res

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Context: Colorectal cancer is one of the most common cancers worldwide (the third most common cancer in the world) and is especially more common in Western countries; however, its incidence has been increased significantly during the last few years in Eastern countries such as Iran and considered as one of the five common cancers in this country. According to molecular pathways, numerous biomarkers have been identified for colorectal cancers which help patients' management. Evidence aquisition: In this study, we tried to review published articles about the molecular biomarkers of colorectal cancer from Iran. We searched medical databases such as google scholar, Scopus, PubMed, Magiran, SID and Iran Medex for keywords of "colon cancer, KRAS, BRAF, mismatch repair gene, Microsatellite instability, molecular genetics, molecular pathogenesis, biomarker and Iran" to find studies published about colorectal cancers from Iran regarding molecular biomarkers. Conclusion: This study showed that molecular biomarkers in colorectal cancer of Iranian patients are not so different from Western population.

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“…Although data acquisition software and imaging technology have improved chip logistics, sample measurement, and data collection, the heterogeneity of aCGH data obfuscates attempts to identify meaningful conclusionseven in instances of small sample number (Brim et al, 2012;2014).…”

Section: Introductionmentioning

confidence: 99%

A Systems Biology Interpretation of Array Comparative Genomic Hybridization (aCGH) Data through Phylogenetics

Abunimer

Salazar

Noursi

et al. 2016

OMICS: A Journal of Integrative Biology

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Array Comparative Genomic Hybridization (aCGH) is a rapid screening technique to detect gene deletions and duplications, providing an overview of chromosomal aberrations throughout the entire genome of a tumor, without the need for cell culturing. However, the heterogeneity of aCGH data obfuscates existing methods of data analysis. Analysis of aCGH data from a systems biology perspective or in the context of total aberrations is largely absent in the published literature. We present here a novel alternative to the functional analysis of aCGH data using the phylogenetic paradigm that is well-suited to high dimensional datasets of heterogeneous nature, but has not been widely adapted to aCGH data. Maximum parsimony phylogenetic analysis sorts out genetic data through the simplest presentation of the data on a cladogram, a graphical evolutionary tree, thus providing a powerful and efficient method for aCGH data analysis. For example, the cladogram models the multiphasic changes in the cancer genome and identifies shared early mutations in the disease progression, providing a simple yet powerful means of aCGH data interpretation. As such, applying maximum parsimony phylogenetic analysis to aCGH results allows for the differentiation between drivers and passenger genes aberrations in cancer specimens. In addition to offering a novel methodology to analyze aCGH results, we present here a crucial software suite that we wrote to carry out the analysis. In a broader context, we wish to underscore that phylogenetic analysis of aCGH data is a non-parametric method that circumvents the pitfalls and frustrations of standard analytical techniques that rely on parametric statistics. Organizing the data in a cladogram as explained in this research article provides insights into the disease common aberrations, as well as the disease subtypes and their shared aberrations (the synapomorphies) of each subtype. Hence, we report the method and make the software suite publicly and freely available at http://software.phylomcs.com so that researchers can test alternative and innovative approaches to the analysis of aCGH data.

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An Integrative CGH, MSI and Candidate Genes Methylation Analysis of Colorectal Tumors

Cited by 30 publications

References 51 publications

LGRs receptors as peculiar GPCRs involved in cancer

LGRs receptors as peculiar GPCRs involved in cancer

Molecular Biomarkers of Colorectal Cancer: A Review of Published Articles From Iran

A Systems Biology Interpretation of Array Comparative Genomic Hybridization (aCGH) Data through Phylogenetics

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