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Perez-Mayoral J, Gonzalez-Pons M, Centeno-Girona H, Montes-Rodríguez IM, Soto-Salgado M, Suárez B, Rodríguez N, Colón G, Sevilla J, Jorge D, Llor X, Xicola RM, Toro DH, Tous-López L, Torres-Torres M, Reyes JS, López-Acevedo N, Goel A, Rodríguez-Quilichini S, Cruz-Correa M. Molecular and Sociodemographic Colorectal Cancer Disparities in Latinos Living in Puerto Rico. Genes (Basel) 2023; 14:894. [PMID: 37107652 PMCID: PMC10138302 DOI: 10.3390/genes14040894] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/15/2023] [Revised: 04/05/2023] [Accepted: 04/07/2023] [Indexed: 04/29/2023] Open
Abstract
BACKGROUND The incidence of sporadic colorectal cancer (CRC) among individuals <50 years (early-onset CRC) has been increasing in the United States (U.S.) and Puerto Rico. CRC is currently the leading cause of cancer death among Hispanic men and women living in Puerto Rico (PRH). The objective of this study was to characterize the molecular markers and clinicopathologic features of colorectal tumors from PRH to better understand the molecular pathways leading to CRC in this Hispanic subpopulation. METHODS Microsatellite instability (MSI), CpG island methylator phenotype (CIMP), and KRAS and BRAF mutation status were analyzed. Sociodemographic and clinicopathological characteristics were evaluated using Chi-squared and Fisher's exact tests. RESULTS Of the 718 tumors analyzed, 34.2% (n = 245) were early-onset CRC, and 51.7% were males. Among the tumors with molecular data available (n = 192), 3.2% had MSI, 9.7% had BRAF, and 31.9% had KRAS mutations. The most common KRAS mutations observed were G12D (26.6%) and G13D (20.0%); G12C was present in 4.4% of tumors. A higher percentage of Amerindian admixture was significantly associated with early-onset CRC. CONCLUSIONS The differences observed in the prevalence of the molecular markers among PRH tumors compared to other racial/ethnic groups suggest a distinct molecular carcinogenic pathway among Hispanics. Additional studies are warranted.
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Affiliation(s)
| | - Maria Gonzalez-Pons
- University of Puerto Rico Comprehensive Cancer Center, San Juan, PR 00936, USA
| | | | | | | | - Belisa Suárez
- University of Puerto Rico Comprehensive Cancer Center, San Juan, PR 00936, USA
| | - Natalia Rodríguez
- School of Medicine, Universidad Central del Caribe, Bayamon, PR 00956, USA
| | - Giancarlo Colón
- School of Medicine, Universidad Central del Caribe, Bayamon, PR 00956, USA
| | - Javier Sevilla
- School of Medicine, Universidad Central del Caribe, Bayamon, PR 00956, USA
| | - Daphne Jorge
- School of Medicine, Ponce Health Sciences University, Ponce, PR 00716, USA
| | - Xavier Llor
- Department of Internal Medicine and Digestive Diseases, School of Medicine, Yale University, New Haven, CT 06520, USA
| | - Rosa M. Xicola
- Department of Internal Medicine and Digestive Diseases, School of Medicine, Yale University, New Haven, CT 06520, USA
| | - Doris H. Toro
- VA Caribbean Healthcare System, San Juan, PR 00921, USA
| | - Luis Tous-López
- Ashford Presbyterian Community Hospital, San Juan, PR 00907, USA
| | | | - José S. Reyes
- Ashford Presbyterian Community Hospital, San Juan, PR 00907, USA
| | | | - Ajay Goel
- Beckman Research Institute, City of Hope Comprehensive Cancer Center, Duarte, CA 91010, USA
| | | | - Marcia Cruz-Correa
- University of Puerto Rico Comprehensive Cancer Center, San Juan, PR 00936, USA
- Department of Medicine, Medical Sciences Campus, University of Puerto Rico, San Juan, PR 00935, USA
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Baba O, Bidikian A, Mukherji D, Shamseddin A, Temraz S, Fakhruddin N, Khazzouh M, Ghizzawi D, Abdel Khalek R, Zaatari G, Mahfouz R. Tumor profiling of KRAS, BRAF, and NRAS gene mutations in patients with colorectal cancer: A Lebanese major center cohort study. Gene 2022; 834:146646. [PMID: 35680020 DOI: 10.1016/j.gene.2022.146646] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/19/2022] [Revised: 04/16/2022] [Accepted: 06/02/2022] [Indexed: 02/07/2023]
Abstract
BACKGROUND In the era of precision medicine, treatment schemes for advanced Colorectal (CRC) disease include monoclonal antibodies which block the epidermal growth factor receptor (EGFR) implicated in tumor proliferation, invasion, migration and neovascularization. Resistance to these agents has been correlated with activating downstream mutations in KRAS, BRAF and NRAS genes, among others, leading to constitutive activation of the EGFR axis bypassing EGFR blockade. The assessment of tumor RASandBRAFmutational status has thus become standard clinical practice. While multiple investigations reported roughly mutations rates of 40% in KRAS, 7% in NRAS and 5-15 % in BRAF, numbers vary across different populations with limited data specifically from the Middle East. METHODS This is a retrospective observational Laboratory information system (LIS) chart review of all the patients with pathologically confirmed colorectal carcinoma (CRC) or metastatic CRC who underwent KRAS, NRAS and/or BRAF mutational analysis testing at the Molecular Diagnostics Laboratory of the American University of Beirut Medical Center (AUBMC) from January 2012 to December 2018, inclusive. Data retrieved included the results of mutation testing performed for KRAS, NRAS and BRAF genes, the age, gender, and tumor location for each patient. Analysis of the mutations was performed using polymerase chain reaction (PCR) hybridization StripAssay® (ViennaLab, Vienna, Austria). RESULTS 130 (47.6%) out of 273 histologically confirmed CRC cases, had positive KRAS mutations, namely in codons 12 (82%), 13 (17%), 146 (1.5%), 117 (0.75%), or 61 (0.75%). Two patients had two concomitant mutations: 12 + 12 (different mutations) and 12 + 146. Of 203 CRC cases tested for NRAS mutations, 16 (7.8%) were found to be positive for a mutation in codon 12 (37.5%), 61 (37.5%), or 13 (12.5%). Two patients had two concomitant mutations: 12 + 13 and 59 + 61. Of 172 CRC cases tested for BRAF mutations, 2 (1.2 %) were positive for the V600E -. CONCLUSION This retrospective study is the first to report the frequencies of KRAS, NRAS and BRAF gene mutations in a Lebanese CRC cohort diagnosed and managed at a tertiary care center. The frequencies of the studied somatic gene mutations were similar to previously reported cohorts in other populations however the rate of BRAF mutation was lower in this cohort than expected.
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Affiliation(s)
- Omar Baba
- Department of Pathology and Laboratory Medicine, American University of Beirut Medical Center, Beirut, Lebanon
| | - Aram Bidikian
- Faculty of Medicine. American University of Beirut, Beirut, Lebanon
| | - Deborah Mukherji
- Department of Internal Medicine. American University of Beirut Medical Center, Beirut, Lebanon
| | - Ali Shamseddin
- Department of Internal Medicine. American University of Beirut Medical Center, Beirut, Lebanon
| | - Sally Temraz
- Department of Internal Medicine. American University of Beirut Medical Center, Beirut, Lebanon
| | - Najla Fakhruddin
- Department of Pathology and Laboratory Medicine, American University of Beirut Medical Center, Beirut, Lebanon
| | - Mira Khazzouh
- Department of Pathology and Laboratory Medicine, American University of Beirut Medical Center, Beirut, Lebanon
| | - Diana Ghizzawi
- Department of Pathology and Laboratory Medicine, American University of Beirut Medical Center, Beirut, Lebanon
| | - Rabab Abdel Khalek
- Department of Pathology and Laboratory Medicine, American University of Beirut Medical Center, Beirut, Lebanon
| | - Ghazi Zaatari
- Department of Pathology and Laboratory Medicine, American University of Beirut Medical Center, Beirut, Lebanon
| | - Rami Mahfouz
- Department of Pathology and Laboratory Medicine, American University of Beirut Medical Center, Beirut, Lebanon.
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Saharti S. KRAS/NRAS/BRAF Mutation Rate in Saudi Academic Hospital Patients With Colorectal Cancer. Cureus 2022; 14:e24392. [PMID: 35619874 PMCID: PMC9124608 DOI: 10.7759/cureus.24392] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 03/26/2022] [Indexed: 12/13/2022] Open
Abstract
Background: KRAS/NRAS/BRAF mutations are prognostic and predictive molecular biomarkers for colorectal cancers (CRCs). CRC has different frequencies in the population for mutations such as KRAS, NRAS, and BRAF. The aim of this study is to verify the frequency of the somatic KRAS/NRAS/BRAF mutations in Saudi academic hospital patients diagnosed with CRC and compare it with those estimated at the local and national levels. Methods: Out of 280 colorectal carcinomas diagnosed between 2018 and 2021 (primary and secondary), 97 (34.6%) were evaluated by Next Generation Sequencing (NGS) for colorectal cancer molecular markers. Four of these failed the PCR amplification, while 93 were successfully tested. KRAS, NRAS, and BRAF mutation rates and clinical pathological characteristics were recorded. Results: In this retrospective study, almost half of the tested samples were reported to have a clinically significant mutation (46/93 positive calls, while others were triple-negative). We found that the most prevalent mutation in KRAS (45.2%) was followed by NRAS (2.2%) and BRAF (2.2%). KRAS p.G12D accounted for the most frequently resulting variant (17/42, 40.5%). Second in ranking is KRAS p. G12V (6/42, 14.3%). Conclusion: This study is the first to describe the frequency of triple mutations in the city of Jeddah. The findings are consistent with previous research conducted in the Middle East and other local Saudi centers.
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The potential of PIK3CA, KRAS, BRAF, and APC hotspot mutations as a non-invasive detection method for colorectal cancer. Mol Cell Probes 2022; 63:101807. [DOI: 10.1016/j.mcp.2022.101807] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/14/2021] [Revised: 03/09/2022] [Accepted: 03/09/2022] [Indexed: 02/07/2023]
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Abudabous A, Drah M, Aldehmani M, Parker I, Alqawi O. KRAS mutations in patients with colorectal cancer in Libya. Mol Clin Oncol 2021; 15:197. [PMID: 34462653 PMCID: PMC8375022 DOI: 10.3892/mco.2021.2359] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/19/2020] [Accepted: 12/17/2020] [Indexed: 11/27/2022] Open
Abstract
Large prospective clinical trials have demonstrated that colorectal cancers (CRCs) with wild-type KRAS respond favorably to anti-epidermal growth factor receptor treatment, thus making mutational analysis obligatory prior to treatment. In our study, frozen CRC tissues from Libyan patients were analyzed for KRAS and HRAS mutations in codons 12/13 by direct sequencing and the correlations with clinical and pathological parameters were investigated. A total of 34 CRC cases, comprising 19 men and 15 women (age range, 24-87 years), were subjected to systematic analysis for RAS mutations. Although HRAS mutations were not detected in any of the patients in the study group, KRAS codon 12/13 mutations were present in 38.2% (13/34) of the patients. The frequent types of codon 12 mutations were glycine to aspartate (G12D, 46.1%); glycine to valine (G12V, 30.8%) and glycine to cysteine (G12C, 15.4%), while the codon 13 mutations were glycine to aspartate (G13D, 7.7%). G→A mutations occurred in 53.8% (7/13) of the patients, while G→T mutations occurred in 46.2% (6/13) of the patients. Mutations occurred at the first base of codon 12 or 13 in 2/13 (15.4%) and at the second base in 11/13 (84.6%) patients. There was no significant association between clinicopathological characteristics and KRAS mutation status, except the site of the tumors harboring KRAS mutations, which was as follows: The frequency was higher among tumors located in the left colon (8/13, 61.5%) compared to other sites (P=0.027). KRAS mutations were correlated with advanced age, with 10/13 being aged >50 years and affected 8/15 female patients (53%) compared with 5/19 male patients (26%). The highest frequency of KRAS mutations was observed in highly differentiated CRCs (8/13).
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Affiliation(s)
- Asma Abudabous
- Department of Life Sciences, The Libyan Academy, Misurata 218-51, Libya
| | - Mustafa Drah
- Department of Zoology, Faculty of Science, Misurata University, Misurata 218-51, Libya
| | | | - Iqbal Parker
- Department of Integrative Biomedical Sciences and Institute of Infectious Disease and Molecular Medicine, Faculty of Health Sciences, University of Cape Town, Cape Town 7925, South Africa
| | - Omar Alqawi
- Biotechnology Research Centre, National Cancer Institute-Misurata, Misurata 218-51, Libya
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Siraj AK, Pratheeshkumar P, Divya SP, Parvathareddy SK, Bu R, Masoodi T, Kong Y, Thangavel S, Al-Sanea N, Ashari LH, Abduljabbar A, Al-Homoud S, Al-Dayel F, Al-Kuraya KS. TGFβ-induced SMAD4-dependent Apoptosis Proceeded by EMT in CRC. Mol Cancer Ther 2019; 18:1312-1322. [PMID: 31053577 DOI: 10.1158/1535-7163.mct-18-1378] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/18/2018] [Revised: 04/28/2019] [Accepted: 04/29/2019] [Indexed: 11/16/2022]
Abstract
Colorectal cancer is one of the leading causes of cancer-related deaths worldwide. In Saudi Arabia, colorectal cancer is more aggressive and presents at younger age, warranting new treatment strategies. Role of TGFβ/Smad4 signaling pathway in initiation and progression of colorectal cancer is well documented. This study examined the role of TGFβ/Smad4 signaling pathway in a large cohort of Saudi patients with colorectal cancer, followed by in vitro analysis to dissect the dual role of TGFβ on inducing epithelial-to-mesenchymal transition (EMT) and apoptosis. Our study demonstrated high frequency of Smad4 alterations with low expression of Smad4 protein identifying a subgroup of aggressive colorectal cancer to be an independent marker for poor prognosis. Functional studies using colorectal cancer cells show that TGFβ induces Smad4-dependent EMT followed by apoptosis. Induction of mesenchymal transcriptional factors, Snail1 and Zeb1, was essential for TGFβ-induced apoptosis. Our results indicate that KLF5 acts as an oncogene in colorectal cancer cells regardless of Smad4 expression and inhibition of KLF5 is requisite for TGFβ-induced apoptosis. Furthermore, TGFβ/Smad4 signal inhibits the transcription of KLF5 that in turn switches Sox4 from tumor promoter to suppressor. A high incidence of Smad4 alterations were found in the Saudi patients with colorectal cancer. Functional study results indicate that TGFβ induces Smad4-dependent EMT followed by apoptosis in colorectal cancer cells.
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Affiliation(s)
- Abdul K Siraj
- Human Cancer Genomic Research, King Faisal Specialist Hospital and Research Center, Riyadh, Saudi Arabia
| | - Poyil Pratheeshkumar
- Human Cancer Genomic Research, King Faisal Specialist Hospital and Research Center, Riyadh, Saudi Arabia
| | - Sasidharan Padmaja Divya
- Human Cancer Genomic Research, King Faisal Specialist Hospital and Research Center, Riyadh, Saudi Arabia
| | | | - Rong Bu
- Human Cancer Genomic Research, King Faisal Specialist Hospital and Research Center, Riyadh, Saudi Arabia
| | - Tariq Masoodi
- Human Cancer Genomic Research, King Faisal Specialist Hospital and Research Center, Riyadh, Saudi Arabia
| | - Yan Kong
- Human Cancer Genomic Research, King Faisal Specialist Hospital and Research Center, Riyadh, Saudi Arabia
| | - Saravanan Thangavel
- Human Cancer Genomic Research, King Faisal Specialist Hospital and Research Center, Riyadh, Saudi Arabia
| | - Nasser Al-Sanea
- Department of Surgery, Colorectal Unit, Riyadh, Saudi Arabia
| | - Luai H Ashari
- Department of Surgery, Colorectal Unit, Riyadh, Saudi Arabia
| | | | - Samar Al-Homoud
- Department of Surgery, Colorectal Unit, Riyadh, Saudi Arabia
| | - Fouad Al-Dayel
- Department of Pathology, King Faisal Specialist Hospital and Research Centre, Riyadh, Saudi Arabia
| | - Khawla S Al-Kuraya
- Human Cancer Genomic Research, King Faisal Specialist Hospital and Research Center, Riyadh, Saudi Arabia.
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Clinical, Pathological, and Molecular Characteristics of CpG Island Methylator Phenotype in Colorectal Cancer: A Systematic Review and Meta-analysis. Transl Oncol 2018; 11:1188-1201. [PMID: 30071442 PMCID: PMC6080640 DOI: 10.1016/j.tranon.2018.07.008] [Citation(s) in RCA: 42] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/10/2018] [Revised: 07/10/2018] [Accepted: 07/10/2018] [Indexed: 02/07/2023] Open
Abstract
BACKGROUND: CpG island methylator phenotype (CIMP) tumors, comprising 20% of colorectal cancers, are associated with female sex, age, right-sided location, and BRAF mutations. However, other factors potentially associated with CIMP have not been robustly examined. This meta-analysis provides a comprehensive assessment of the clinical, pathologic, and molecular characteristics that define CIMP tumors. METHODS: We conducted a comprehensive search of the literature from January 1999 through April 2018 and identified 122 articles, on which comprehensive data abstraction was performed on the clinical, pathologic, molecular, and mutational characteristics of CIMP subgroups, classified based on the extent of DNA methylation of tumor suppressor genes assessed using a variety of laboratory methods. Associations of CIMP with outcome parameters were estimated using pooled odds ratio or standardized mean differences using random-effects model. RESULTS: We confirmed prior associations including female sex, older age, right-sided tumor location, poor differentiation, and microsatellite instability. In addition to the recognized association with BRAF mutations, CIMP was also associated with PIK3CA mutations and lack of mutations in KRAS and TP53. Evidence of an activated immune response was seen with high rates of tumor-infiltrating lymphocytes (but not peritumoral lymphocytes), Crohn-like infiltrates, and infiltration with Fusobacterium nucleatum bacteria. Additionally, CIMP tumors were associated with advance T-stage and presence of perineural and lymphovascular invasion. CONCLUSION: The meta-analysis highlights key features distinguishing CIMP in colorectal cancer, including molecular characteristics of an active immune response. Improved understanding of this unique molecular subtype of colorectal cancer may provide insights into prevention and treatment.
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Siraj AK, Masoodi T, Bu R, Pratheeshkumar P, Al-Sanea N, Ashari LH, Abduljabbar A, Alhomoud S, Al-Dayel F, Alkuraya FS, Al-Kuraya KS. MED12 is recurrently mutated in Middle Eastern colorectal cancer. Gut 2018; 67:663-671. [PMID: 28183795 PMCID: PMC5868237 DOI: 10.1136/gutjnl-2016-313334] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 10/31/2016] [Revised: 01/05/2017] [Accepted: 01/12/2017] [Indexed: 01/31/2023]
Abstract
OBJECTIVE Colorectal cancer (CRC) is a common cancer and a leading cause of cancer deaths. Previous studies have identified a number of key steps in the evolution of CRC but our knowledge of driver mutations in CRC remains incomplete. Recognising the potential of studying different human populations to reveal novel insights in disease pathogenesis, we conducted genomic analysis of CRC in Saudi patients. DESIGN In the discovery phase of the study, we conducted whole genome sequencing of tumour and corresponding germline DNA in 27 patients with CRC. In addition to known driver mutations, we identified three MED12 somatic mutations. In the replication phase, we employed a next-generation sequencing approach to capture and sequence MED12 and other candidate genes in a larger sample of 400 patients with CRC and confirmed the enrichment for recurrent MED12 mutations. RESULTS In order to gain insight into a plausible biological mechanism for the potential role of MED12 mutations in CRC, we studied CRC cell lines that differ substantially in the expression level of MED12, and found the latter to be correlated inversely with transforming growth factor (TGF)-β signalling and directly with apoptosis in response to chemotherapeutic agents. Importantly, these correlations were replicated when MED12 expression was experimentally manipulated. CONCLUSIONS Our data expand the recently described role of MED12 as a tumour suppressor in other cancers to include CRC, and suggest TGF-β signalling as a potential mediator of this effect.
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Affiliation(s)
- Abdul K Siraj
- Human Cancer Genomic Research, King Faisal Specialist Hospital and Research Centre, Riyadh, Saudi Arabia
| | - Tariq Masoodi
- Human Cancer Genomic Research, King Faisal Specialist Hospital and Research Centre, Riyadh, Saudi Arabia
| | - Rong Bu
- Human Cancer Genomic Research, King Faisal Specialist Hospital and Research Centre, Riyadh, Saudi Arabia
| | - Poyil Pratheeshkumar
- Human Cancer Genomic Research, King Faisal Specialist Hospital and Research Centre, Riyadh, Saudi Arabia
| | - Nasser Al-Sanea
- Department of Surgery and Colorectal Section, King Faisal Specialist Hospital and Research Centre, Riyadh, Saudi Arabia
| | - Luai H Ashari
- Department of Surgery and Colorectal Section, King Faisal Specialist Hospital and Research Centre, Riyadh, Saudi Arabia
| | - Alaa Abduljabbar
- Department of Surgery and Colorectal Section, King Faisal Specialist Hospital and Research Centre, Riyadh, Saudi Arabia
| | - Samar Alhomoud
- Department of Surgery and Colorectal Section, King Faisal Specialist Hospital and Research Centre, Riyadh, Saudi Arabia
| | - Fouad Al-Dayel
- Department of Pathology and Laboratory Medicine, King Faisal Specialist Hospital and Research Centre, Riyadh, Saudi Arabia
| | - Fowzan S Alkuraya
- Department of Genetics, King Faisal Specialist Hospital and Research Centre, Riyadh, Saudi Arabia,Department of Anatomy and Cell Biology, College of Medicine, Alfaisal University, Riyadh, Saudi Arabia
| | - Khawla S Al-Kuraya
- Human Cancer Genomic Research, King Faisal Specialist Hospital and Research Centre, Riyadh, Saudi Arabia
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Wang H, Luo J, Liu C, Niu H, Wang J, Liu Q, Zhao Z, Xu H, Ding Y, Sun J, Zhang Q. Investigating MicroRNA and transcription factor co-regulatory networks in colorectal cancer. BMC Bioinformatics 2017; 18:388. [PMID: 28865443 PMCID: PMC5581471 DOI: 10.1186/s12859-017-1796-4] [Citation(s) in RCA: 31] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/22/2016] [Accepted: 08/21/2017] [Indexed: 02/06/2023] Open
Abstract
Background Colorectal cancer (CRC) is one of the most common malignancies worldwide with poor prognosis. Studies have showed that abnormal microRNA (miRNA) expression can affect CRC pathogenesis and development through targeting critical genes in cellular system. However, it is unclear about which miRNAs play central roles in CRC’s pathogenesis and how they interact with transcription factors (TFs) to regulate the cancer-related genes. Results To address this issue, we systematically explored the major regulation motifs, namely feed-forward loops (FFLs), that consist of miRNAs, TFs and CRC-related genes through the construction of a miRNA-TF regulatory network in CRC. First, we compiled CRC-related miRNAs, CRC-related genes, and human TFs from multiple data sources. Second, we identified 13,123 3-node FFLs including 25 miRNA-FFLs, 13,005 TF-FFLs and 93 composite-FFLs, and merged the 3-node FFLs to construct a CRC-related regulatory network. The network consists of three types of regulatory subnetworks (SNWs): miRNA-SNW, TF-SNW, and composite-SNW. To enhance the accuracy of the network, the results were filtered by using The Cancer Genome Atlas (TCGA) expression data in CRC, whereby we generated a core regulatory network consisting of 58 significant FFLs. We then applied a hub identification strategy to the significant FFLs and found 5 significant components, including two miRNAs (hsa-miR-25 and hsa-miR-31), two genes (ADAMTSL3 and AXIN1) and one TF (BRCA1). The follow up prognosis analysis indicated all of the 5 significant components having good prediction of overall survival of CRC patients. Conclusions In summary, we generated a CRC-specific miRNA-TF regulatory network, which is helpful to understand the complex CRC regulatory mechanisms and guide clinical treatment. The discovered 5 regulators might have critical roles in CRC pathogenesis and warrant future investigation. Electronic supplementary material The online version of this article (10.1186/s12859-017-1796-4) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Hao Wang
- Department of Pathology, Nanfang Hospital, Southern Medical University, Guangzhou, 510515, China.,Department of Pathology, College of Basic Medicine, Southern Medical University, Guangzhou, 510515, China
| | - Jiamao Luo
- Department of Pathology, Nanfang Hospital, Southern Medical University, Guangzhou, 510515, China.,Department of Pathology, College of Basic Medicine, Southern Medical University, Guangzhou, 510515, China
| | - Chun Liu
- Department of Pathology, Nanfang Hospital, Southern Medical University, Guangzhou, 510515, China.,Department of Pathology, College of Basic Medicine, Southern Medical University, Guangzhou, 510515, China
| | - Huilin Niu
- Department of Pathology, Nanfang Hospital, Southern Medical University, Guangzhou, 510515, China.,Department of Pathology, College of Basic Medicine, Southern Medical University, Guangzhou, 510515, China
| | - Jing Wang
- Center for Quantitative Sciences, Vanderbilt University School of Medicine, Nashville, TN, 37232, USA
| | - Qi Liu
- Center for Quantitative Sciences, Vanderbilt University School of Medicine, Nashville, TN, 37232, USA
| | - Zhongming Zhao
- School of Biomedical Informatics, The University of Texas Health Science Center at Houston, Houston, TX, 77030, USA.,Center for Precision Health, School of Biomedical Informatics, The University of Texas Health Science Center at Houston, Houston, TX, 77030, USA
| | - Hua Xu
- School of Biomedical Informatics, The University of Texas Health Science Center at Houston, Houston, TX, 77030, USA
| | - Yanqing Ding
- Department of Pathology, Nanfang Hospital, Southern Medical University, Guangzhou, 510515, China.,Department of Pathology, College of Basic Medicine, Southern Medical University, Guangzhou, 510515, China
| | - Jingchun Sun
- School of Biomedical Informatics, The University of Texas Health Science Center at Houston, Houston, TX, 77030, USA.
| | - Qingling Zhang
- Department of Pathology, Nanfang Hospital, Southern Medical University, Guangzhou, 510515, China. .,Department of Pathology, College of Basic Medicine, Southern Medical University, Guangzhou, 510515, China.
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10
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Yang JF, Noffsinger AE, Agrawal D, Yang QH. Colorectal cancer anatomic distribution patterns remain the same after sessile serrated adenoma/polyp considered cancer precursor: a 9-year comparison study from community-based endoscopy centers. J Gastrointest Oncol 2016; 7:917-923. [PMID: 28078114 DOI: 10.21037/jgo.2016.07.02] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 01/16/2023] Open
Abstract
BACKGROUND The overall incidence of colorectal cancer (CRC) in the United States has steadily decreased. However, the incidence of right-sided CRC remains unchanged for the past two decades. The serrated neoplastic pathway (sessile serrated adenoma/polyp, SSA/P) has been considered an important pathway of colorectal carcinogenesis, especially in the right-sided CRC. The aim of this study was to compare CRC anatomic distribution patterns in a 9-year interval in the general population before and after SSA/P was recognized and treated as a CRC precursor. METHODS The Miraca Life Sciences (MLS) pathology database was queried for all primary CRCs diagnosed between 8/3/2000 to 12/31/2005 (control group) and 1/1/2014 to 12/31/2014 (current group). Patients' demographics, clinical information, and pathology reports were collected and analyzed. RESULTS A total of 5,602 patients with 5,685 CRCs were identified, of which 2,728 patients with 2,765 CRCs in current group and 2,874 patients with 2,920 CRCs in control group. Overall, there were no statistical differences in the current group in regards to the anatomical distribution patterns of CRCs in the proximal, right-sided, distal, and left-sided colon or genders compared with the control group (all P>0.05). Among the current group, there were 33 (1.2%) patients with 38 (1.4%) CRCs arising in SSA/Ps [serrated carcinomas (SCAs)], of which 33 (86.8%) were in the right-sided colon and 5 (13.2%) in the left-sided colon. Twenty-three (69.7%) SCA patients were female with significant advanced age than male (76.4 vs. 69.6, P=0.023). CONCLUSIONS The overall current CRC anatomic distribution patterns after SSA/Ps managed as CRC precursor remain the same in the patients' population from the community-based endoscopy centers in the U.S. It is suggested that the current SSA/P management might need to be further modified.
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Affiliation(s)
- Juliana F Yang
- Division of Digestive and Liver Diseases, The University of Texas Southwestern Medical Center, Dallas, TX, USA
| | | | - Deepak Agrawal
- Division of Digestive and Liver Diseases, The University of Texas Southwestern Medical Center, Dallas, TX, USA
| | - Qing-Hua Yang
- Miraca Life Sciences Research Institute, Irving, TX, USA
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Al-Shamsi HO, Jones J, Fahmawi Y, Dahbour I, Tabash A, Abdel-Wahab R, Abousamra AOS, Shaw KR, Xiao L, Hassan MM, Kipp BR, Kopetz S, Soliman AS, McWilliams RR, Wolff RA. Molecular spectrum of KRAS, NRAS, BRAF, PIK3CA, TP53, and APC somatic gene mutations in Arab patients with colorectal cancer: determination of frequency and distribution pattern. J Gastrointest Oncol 2016; 7:882-902. [PMID: 28078112 DOI: 10.21037/jgo.2016.11.02] [Citation(s) in RCA: 37] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 12/12/2022] Open
Abstract
BACKGROUND The frequency rates of mutations such as KRAS, NRAS, BRAF, and PIK3CA in colorectal cancer (CRC) differ among populations. The aim of this study was to assess mutation frequencies in the Arab population and determine their correlations with certain clinicopathological features. METHODS Arab patients from the Arab Gulf region and a population of age- and sex-matched Western patients with CRC whose tumors were evaluated with next-generation sequencing (NGS) were identified and retrospectively reviewed. The mutation rates of KRAS, NRAS, BRAF, PIK3CA, TP53, and APC were recorded, along with clinicopathological features. Other somatic mutation and their rates were also identified. Fisher's exact test was used to determine the association between mutation status and clinical features. RESULTS A total of 198 cases were identified; 99 Arab patients and 99 Western patients. Fifty-two point seven percent of Arab patients had stage IV disease at initial presentation, 74.2% had left-sided tumors. Eighty-nine point two percent had tubular adenocarcinoma and 10.8% had mucinous adenocarcinoma. The prevalence rates of KRAS, NRAS, BRAF, PIK3CA, TP53, APC, SMAD, FBXW7 mutations in Arab population were 44.4%, 4%, 4%, 13.1%, 52.5%, 27.3%, 2% and 3% respectively. Compared to 48.4%, 4%, 4%, 12.1%, 47.5%, 24.2%, 11.1% and 0% respectively in matched Western population. Associations between these mutations and patient clinicopathological features were not statistically significant. CONCLUSIONS This is the first study to report comprehensive hotspot mutations using NGS in Arab patients with CRC. The frequency of KRAS, NRAS, BRAF, TP53, APC and PIK3CA mutations were similar to reported frequencies in Western population except SMAD4 that had a lower frequency and higher frequency of FBXW7 mutation.
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Affiliation(s)
- Humaid O Al-Shamsi
- Department of Gastrointestinal Medical Oncology, the University of Texas MD Anderson Cancer Center, Houston, Texas, USA;; Khalifa Bin Zayed Al Nahyan Foundation, Abu Dhabi, United Arab Emirates;; Sheikh Khalifa Bin Zayed Al Nahyan Institute for Personalized Cancer Therapy, the University of Texas MD Anderson Cancer Center, Houston, Texas, USA
| | - Jeremy Jones
- Department of Oncology, Mayo Clinic, Rochester, Minnesota, USA
| | - Yazan Fahmawi
- Department of Gastrointestinal Medical Oncology, the University of Texas MD Anderson Cancer Center, Houston, Texas, USA
| | - Ibrahim Dahbour
- Department of Gastrointestinal Medical Oncology, the University of Texas MD Anderson Cancer Center, Houston, Texas, USA
| | - Aziz Tabash
- Department of Gastrointestinal Medical Oncology, the University of Texas MD Anderson Cancer Center, Houston, Texas, USA
| | - Reham Abdel-Wahab
- Department of Gastrointestinal Medical Oncology, the University of Texas MD Anderson Cancer Center, Houston, Texas, USA;; Clinical Oncology Department, Assiut University, Assiut, Egypt
| | - Ahmed O S Abousamra
- Department of Gastrointestinal Medical Oncology, the University of Texas MD Anderson Cancer Center, Houston, Texas, USA
| | - Kenna R Shaw
- Sheikh Khalifa Bin Zayed Al Nahyan Institute for Personalized Cancer Therapy, the University of Texas MD Anderson Cancer Center, Houston, Texas, USA
| | - Lianchun Xiao
- Department of Gastrointestinal Medical Oncology, the University of Texas MD Anderson Cancer Center, Houston, Texas, USA
| | - Manal M Hassan
- Department of Gastrointestinal Medical Oncology, the University of Texas MD Anderson Cancer Center, Houston, Texas, USA
| | - Benjamin R Kipp
- Department of Laboratory Medicine and Pathology, Mayo Clinic, Rochester, Minnesota, USA
| | - Scott Kopetz
- Department of Gastrointestinal Medical Oncology, the University of Texas MD Anderson Cancer Center, Houston, Texas, USA
| | - Amr S Soliman
- Department of Epidemiology, the University of Nebraska Medical Center, Omaha, Nebraska, USA
| | | | - Robert A Wolff
- Department of Gastrointestinal Medical Oncology, the University of Texas MD Anderson Cancer Center, Houston, Texas, USA
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Alqahtani M, Grieu F, Carrello A, Amanuel B, Mashour M, Alattas R, Al-Saleh K, Alsheikh A, Alqahtani S, Iacopetta B. Screening for Lynch Syndrome in Young Colorectal Cancer Patients from Saudi Arabia Using Microsatellite Instability as the Initial Test. Asian Pac J Cancer Prev 2016; 17:1917-23. [DOI: 10.7314/apjcp.2016.17.4.1917] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022] Open
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13
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Al Moustafa AE, Al-Antary NTM. Specific gene patterns and molecular pathways related to human carcinogenesis in different populations among various geographic locations. Cancer 2016; 122:1134-5. [PMID: 26849403 DOI: 10.1002/cncr.29905] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
Affiliation(s)
- Ala-Eddin Al Moustafa
- College of Medicine Biomedical Research Centre, Qatar University, Doha, Qatar.,Department of Oncology, McGill University, Montreal, Quebec, Canada.,Research Cancer Centre, Aleppo University Syrian Society Against Cancer, Aleppo, Syria
| | - Noor T M Al-Antary
- College of Medicine Biomedical Research Centre, Qatar University, Doha, Qatar
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14
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Siraj AK, Beg S, Al-Kuraya KS. Reply to specific gene patterns and molecular pathways related to human carcinogenesis in different populations among various geographic locations. Cancer 2016; 122:1135-7. [PMID: 26849248 DOI: 10.1002/cncr.29904] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022]
Affiliation(s)
- Abdul K Siraj
- Human Cancer Genomic Research, King Faisal Specialist Hospital and Research Centre, Riyadh, Saudi Arabia
| | - Shaham Beg
- Human Cancer Genomic Research, King Faisal Specialist Hospital and Research Centre, Riyadh, Saudi Arabia
| | - Khawla S Al-Kuraya
- Human Cancer Genomic Research, King Faisal Specialist Hospital and Research Centre, Riyadh, Saudi Arabia.,Department of Pathology, College of Medicine Alfaisal University, Riyadh, Saudi Arabia
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