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Mosaferi Z, Pirestani M, Arefian E, Gojani G, Kavousinasab N, Karimi P, Deilami A, Abrehdari-Tafreshi Z. Exploring the Relationship Between KRAS, NRAS, and BRAF Mutations and Clinical Characteristics in Iranian Colorectal Cancer Patients. J Gastrointest Cancer 2024; 55:1134-1143. [PMID: 38709419 DOI: 10.1007/s12029-024-01064-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 04/27/2024] [Indexed: 05/07/2024]
Abstract
BACKGROUND Patients with colorectal cancer can benefit from anti-EGFR (epidermal growth factor receptor) therapy. However, this therapy is not effective for treating colorectal cancers with constitutive activating mutations in the KRAS, NRAS, and BRAF genes. Molecular analysis of tumor tissue frequently informs treatment decisions for colorectal cancer. This study aims to identify KRAS, NRAS, and BRAF mutations in Iranian patients diagnosed with colorectal cancer and to assess the prevalence of these mutations relative to the tumor differentiation stage within these populations. METHODS From April 2018 to December 2022, 2000 specimens from patients with colorectal cancer were collected. Data on sex, age, and tumor differentiation stage were recorded for all samples. For mutation detection, the KRAS and NRAS exons (2, 3, and 4) were amplified using the Diatech kit, and a specific primer was used to amplify BRAF exon 15. Pyrosequencing was then performed. RESULTS Analysis of samples revealed that 1105 specimens (55.3%) contained mutations in at least one of the screened genes. Among the genes studied, the highest occurrence was the KRAS mutation at 47.4%, followed by NRAS at 5.3% and BRAF at 2.7%. Most KRAS mutations were found in exon 2 (89.7%), with the G12D mutation being the most prevalent at 32% of cases. There was a significant difference in the rate of KRAS mutations in women (52.5%) compared to men (43.5%) (P = 0.02). For NRAS, the majority mutations were observed in exon 3 (76.2%), with the Q61H mutation being the most prevalent at 28.5% of cases. There were no significant associations between the clinicopathological parameters and mutations. CONCLUSION The study's findings indicate a rising frequency of mutations in these genes in Iran, highlighting the need to screening mutations in the main exons of all three genes for effective colorectal cancer treatment strategies.
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Affiliation(s)
- Zahra Mosaferi
- Department of Cell and Molecular Biology, Tehran Medical Branch, Islamic Azad University, Tehran, Iran
| | - Majid Pirestani
- Parasitology & Entomology Dept, Faculty of Medical Sciences, Tarbiat Modares University, Tehran, Iran
| | - Ehsan Arefian
- Department of Microbiology, School of Biology, College of Sciences, University of Tehran, Tehran, Iran
- Pediatric Cell and Gene Therapy Research Center, & Tissue Research Institute, Tehran University of Medical Sciences, GeneTehran, Cell, Iran
| | - Goli Gojani
- National Institute of Genetic Engineering and Biotechnology (NIGEB), Tehran, Iran
| | - Nastaran Kavousinasab
- Department of Biology, Science and Research Branch, Islamic Azad University, Tehran, Iran
| | - Parto Karimi
- Department of Chemistry, Faculty of Chemistry, North Tehran Branch, Islamic Azad University, Tehran, Iran
| | - Azam Deilami
- Department of Cell and Molecular Biology, Tehran Medical Branch, Islamic Azad University, Tehran, Iran
| | - Zahra Abrehdari-Tafreshi
- Department of Cell and Molecular Biology, School of Biology, College of Sciences, University of Tehran, P. O. Box, Tehran, 14155-6455, Iran.
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Benmokhtar S, Laraqui A, Hilali F, Bajjou T, El Zaitouni S, Jafari M, Baba W, Elannaz H, Lahlou IA, Hafsa C, Oukabli M, Mahfoud T, Tanz R, Ichou M, Ennibi K, Dakka N, Sekhsokh Y. RAS/RAF/MAPK Pathway Mutations as Predictive Biomarkers in Middle Eastern Colorectal Cancer: A Systematic Review. Clin Med Insights Oncol 2024; 18:11795549241255651. [PMID: 38798959 PMCID: PMC11128178 DOI: 10.1177/11795549241255651] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/05/2023] [Accepted: 04/29/2024] [Indexed: 05/29/2024] Open
Abstract
Background This review article aims to investigate the prevalence and spectrum of rat sarcoma (RAS) and V-Raf Murine Sarcoma Viral Oncogene Homolog B (BRAF) mutations, and their connection with geographical location, clinicopathological features, and other relevant factors in colorectal cancer (CRC) patients in the Middle East. Methods A systematic literature review, employing the Preferred Reporting Items for Systematic Reviews and Meta-Analyses (PRISMA) framework, was conducted to investigate the association between the frequency of relevant mutations and the descriptive clinicopathological characteristics of CRC patients. Multiple electronic databases, including PubMed, Science Direct, Web of Science, Scopus, and Google Scholar, were searched to analyze the relevant literature. Results A total of 19 eligible studies comprising 2960 patients with CRC were included in this review. A comprehensive analysis of the collected literature data as well as descriptive and methodological insights is provided. Men were predominant in reviewed studies for the region, accounting for 58.6%. Overall, RAS mutation prevalence was 38.1%. Kirsten RAS Viral Oncogene Homolog (KRAS) mutations were the most common, accounting for 37.1% of cases and distributed among different exons, with the G12D mutation being the most frequent in exon 2 (23.2%) followed by G12V (13.7%), G13D (10.1%), G12C (5.1%), G12A (5.04%), and G12S (3.6%). Neuroblastoma RAS Viral Oncogene Homolog (NRAS) mutations were identified in 3.3% of tumor samples, with the most common mutation site located in exons 2, 3, and 4, and codon 61 being the most common location for the region. The total mutation frequency in the BRAF gene was 2.6%, with the V600E mutation being the most common. Conclusion The distribution patterns of RAS and BRAF mutations among CRC patients exhibit notable variations across diverse ethnic groups. Our study sheds light on this phenomenon by demonstrating a higher prevalence of KRAS mutations in CRC patients from the Middle East, as compared with those from other regions. The identification of these mutations and geographical differences is important for personalized treatment planning and could potentially aid in the development of novel targeted therapies. The distinct distribution patterns of RAS and BRAF mutations among CRC patients across different ethnic groups, as well as the regional variability in mutation prevalence, highlight the need for further research in this area.
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Affiliation(s)
- Soukaina Benmokhtar
- Royal School of Military Health Service, Sequencing Unit, Laboratory of Virology, Center of Virology, Infectious, and Tropical Diseases, Mohammed V Military Teaching Hospital, Faculty of Medicine and Pharmacy, Mohammed V University, Rabat, Morocco
- Laboratory of Biology of Human Pathologies and Genomic Center of Human Pathologies, Department of Biology, Faculty of Sciences, Mohammed V University, Rabat, Morocco
| | - Abdelilah Laraqui
- Royal School of Military Health Service, Sequencing Unit, Laboratory of Virology, Center of Virology, Infectious, and Tropical Diseases, Mohammed V Military Teaching Hospital, Faculty of Medicine and Pharmacy, Mohammed V University, Rabat, Morocco
- Laboratory of Biology of Human Pathologies and Genomic Center of Human Pathologies, Department of Biology, Faculty of Sciences, Mohammed V University, Rabat, Morocco
| | - Farida Hilali
- Laboratory of Research and Biosafety P3, Mohammed V Military Teaching Hospital, Faculty of Medicine and Pharmacy, Mohammed V University, Rabat, Morocco
| | - Tahar Bajjou
- Laboratory of Research and Biosafety P3, Mohammed V Military Teaching Hospital, Faculty of Medicine and Pharmacy, Mohammed V University, Rabat, Morocco
| | - Sara El Zaitouni
- Laboratory of Biology of Human Pathologies and Genomic Center of Human Pathologies, Department of Biology, Faculty of Sciences, Mohammed V University, Rabat, Morocco
| | - Meryem Jafari
- Laboratory of Biology of Human Pathologies and Genomic Center of Human Pathologies, Department of Biology, Faculty of Sciences, Mohammed V University, Rabat, Morocco
| | - Walid Baba
- Laboratory of Biology of Human Pathologies and Genomic Center of Human Pathologies, Department of Biology, Faculty of Sciences, Mohammed V University, Rabat, Morocco
| | - Hicham Elannaz
- Royal School of Military Health Service, Sequencing Unit, Laboratory of Virology, Center of Virology, Infectious, and Tropical Diseases, Mohammed V Military Teaching Hospital, Faculty of Medicine and Pharmacy, Mohammed V University, Rabat, Morocco
| | - Idriss Amine Lahlou
- Royal School of Military Health Service, Sequencing Unit, Laboratory of Virology, Center of Virology, Infectious, and Tropical Diseases, Mohammed V Military Teaching Hospital, Faculty of Medicine and Pharmacy, Mohammed V University, Rabat, Morocco
| | - Chahdi Hafsa
- Department of Medical Oncology, Mohammed V Military Teaching Hospital, Faculty of Medicine and Pharmacy, Mohammed V University, Rabat, Morocco
| | - Mohamed Oukabli
- Department of Pathology, Mohammed V Military Teaching Hospital, Faculty of Medicine and Pharmacy, Mohammed V University, Rabat, Morocco
| | - Tarik Mahfoud
- Center of Virology, Infectious and Tropical Diseases, Mohammed V Military Teaching Hospital, Faculty of Medicine and Pharmacy, Mohammed V University, Rabat, Morocco
| | - Rachid Tanz
- Center of Virology, Infectious and Tropical Diseases, Mohammed V Military Teaching Hospital, Faculty of Medicine and Pharmacy, Mohammed V University, Rabat, Morocco
| | - Mohamed Ichou
- Center of Virology, Infectious and Tropical Diseases, Mohammed V Military Teaching Hospital, Faculty of Medicine and Pharmacy, Mohammed V University, Rabat, Morocco
| | - Khaled Ennibi
- Royal School of Military Health Service, Sequencing Unit, Laboratory of Virology, Center of Virology, Infectious, and Tropical Diseases, Mohammed V Military Teaching Hospital, Faculty of Medicine and Pharmacy, Mohammed V University, Rabat, Morocco
- Center of Virology, Infectious and Tropical Diseases, Mohammed V Military Teaching Hospital, Faculty of Medicine and Pharmacy, Mohammed V University, Rabat, Morocco
| | - Nadia Dakka
- Laboratory of Biology of Human Pathologies and Genomic Center of Human Pathologies, Department of Biology, Faculty of Sciences, Mohammed V University, Rabat, Morocco
| | - Yassine Sekhsokh
- Laboratory of Research and Biosafety P3, Mohammed V Military Teaching Hospital, Faculty of Medicine and Pharmacy, Mohammed V University, Rabat, Morocco
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Shang P, Lu J, Song F, Zhao Y, Hong W, He Y, Shen W, Geng L. RNF43 is associated with genomic features and clinical outcome in BRAF mutant colorectal cancer. Front Oncol 2023; 13:1119587. [PMID: 37409251 PMCID: PMC10319416 DOI: 10.3389/fonc.2023.1119587] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/09/2022] [Accepted: 03/27/2023] [Indexed: 07/07/2023] Open
Abstract
Background Colorectal cancer (CRC) patients with BRAF mutation have very poor prognosis. It is urgent to search for prognostic factors of BRAF mutant CRC. RNF43 is a ENF ubiquitin ligase of Wnt signaling. Mutation of RNF43 has been observed frequently in various types of human cancers. However, few studies have evaluated the role of RNF43 in CRC. The present study aimed to explore the impact of RNF43 mutations on molecular characteristics and prognosis in BRAF mutant CRC. Methods Samples of 261 CRC patients with BRAF mutation were retrospectively analyzed. Tumor tissue and matched peripheral blood samples were collected and subjected to targeted sequencing with a panel of 1021 cancer-related genes. The association of molecular characteristics and survival in patients were then analyzed. 358 CRC patients with BRAF mutation from the cBioPortal dataset were used for further confirmation. Results This study was inspired by a CRC patient with BRAF V600E and RNF43 co-mutation, who achieved a best remission of 70% and a progression free survival (PFS) of 13 months. Genomic analysis indicated that RNF43 mutation affected the genomic characteristics of patients with BRAF mutation, including microsatellite instability (MSI), tumor mutation burden (TMB) and the proportion of common gene mutations. Survival analysis showed that RNF43 mutation was a predictive biomarker for better PFS and OS in BRAF mutant CRC. Conclusion Collectively, we identified that RNF43 mutations were correlated with favorable genomic features, resulting in a better clinical outcome for BRAF mutant CRC patients.
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Affiliation(s)
- Peipei Shang
- Oncology Department, Eastern Hepatobiliary Surgical Hospital, Shanghai, China
| | - Jiongjiong Lu
- Department of Special Treatment, Eastern Hepatobiliary Surgical Hospital, Shanghai, China
| | - Feihong Song
- Department of Special Treatment, Eastern Hepatobiliary Surgical Hospital, Shanghai, China
| | - Yijun Zhao
- Department of Special Treatment, Eastern Hepatobiliary Surgical Hospital, Shanghai, China
| | - Weipeng Hong
- Department of Medical Center, Geneplus-Beijing Ltd., Beijing, China
| | - Yuange He
- Department of Medical Center, Geneplus-Beijing Ltd., Beijing, China
| | - Weidong Shen
- Department of Medical Center, Geneplus-Beijing Ltd., Beijing, China
| | - Li Geng
- Department of Special Treatment, Eastern Hepatobiliary Surgical Hospital, Shanghai, China
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Chubarov AS, Oscorbin IP, Novikova LM, Filipenko ML, Lomzov AA, Pyshnyi DV. Allele-Specific PCR for PIK3CA Mutation Detection Using Phosphoryl Guanidine Modified Primers. Diagnostics (Basel) 2023; 13:diagnostics13020250. [PMID: 36673060 PMCID: PMC9858071 DOI: 10.3390/diagnostics13020250] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/28/2022] [Revised: 12/05/2022] [Accepted: 01/06/2023] [Indexed: 01/11/2023] Open
Abstract
Phosphoryl guanidine (PG) is the novel uncharged modification of internucleotide phosphates of oligonucleotides. Incorporating PG modification into PCR primers leads to increased discrimination between wild-type and mutated DNA, providing extraordinary detection limits in an allele-specific real-time polymerase chain reaction (AS-PCR). Herein, we used PG-modification to improve the specificity of AS primers with unfavorable Pyr/Pur primer's 3'-end mismatch in the template/primer complex. Two mutations of the PIK3CA gene (E542K, E545K) were chosen to validate the advantages of the PG modification. Several primers with PG modifications were synthesized for each mutation and assessed using AS-PCR with the plasmid controls and DNA obtained from formalin-fixed paraffin-embedded (FFPE) tissues. The assay allows the detection of 0.5% of mutated DNA on the wild-type DNA plasmid template's background with good specificity. Compared with ddPCR, the primers with PG-modification demonstrated 100% specificity and 100% sensitivity on the DNA from FFPE with mutation presence higher than 0.5%. Our results indicate the high potential of PG-modified primers for point mutation detection. The main principle of the developed methodology can be used to improve the specificity of primers regardless of sequences.
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Afolabi H, Md Salleh S, Zakaria Z, Seng CE, Mohd Nafil SNB, Abdul Aziz AAB, Wada Y, Irekeola A. A Systematic Review and Meta-analysis on the Occurrence of Biomarker Mutation in Colorectal Cancer among the Asian Population. BIOMED RESEARCH INTERNATIONAL 2022; 2022:5824183. [PMID: 35782059 PMCID: PMC9246611 DOI: 10.1155/2022/5824183] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 01/19/2022] [Accepted: 05/24/2022] [Indexed: 12/24/2022]
Abstract
Globally, colorectal carcinoma (CRC) is the third most common cancer and the third major cause of cancer-related death in both sexes. KRAS and BRAF mutations are almost mutually exclusively involved in the pathogenesis of CRC. Both are major culprits in treatment failure and poor prognosis for CRC. Method. A systematic review and meta-analysis of various research was done following the Preferred Reporting Items for Systematic Reviews and Meta-Analysis (PRISMA) guidelines. This trial is registered with PROSPERO CRD42021256452. The initial search included 646 articles; after the removal of noneligible studies, a total of 88 studies was finally selected. Data analysis was carried out using OpenMeta Analyst and Comprehensive Meta-Analysis 3.0 (CMA 3.0) software to investigate the prevalence of KRAS and BRAF mutations among patients with CRC in Asia. Results. The meta-analysis comprises of 25,525 sample sizes from Asia with most being male 15,743/25525 (61.7%). Overall prevalence of KRAS mutations was (59/88) 36.3% (95% CI: 34.5-38.2) with I 2 = 85.54% (P value < 0.001). In 43/59 studies, frequency of KRAS mutations was majorly in codon 12 (76.6% (95% CI: 74.2-78.0)) and less in codon 13 (21.0% (95% CI: 19.1-23.0)). Overall prevalence of BRAF mutations was 5.6% (95% CI: 3.9-8.0) with I 2 = 94.00% (P value < 0.001). When stratified according to location, a higher prevalence was observed in Indonesia (71.8%) while Pakistan has the lowest (13.5%). Conclusion. Total prevalence of KRAS and BRAF mutations in CRC was 36.6% and 5.6%, respectively, and the results conformed with several published studies on KRAS and BRAF mutations.
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Affiliation(s)
- Hafeez Afolabi
- Department of General Surgery, School of Medical Sciences, Universiti Sains Malaysia Hospital, Malaysia
| | - Salzihan Md Salleh
- Department of Pathology, School of Medical Sciences, Health Campus, Universiti Sains Malaysia, Kubang Kerian, 16150 Kelantan, Malaysia
| | - Zaidi Zakaria
- Department of General Surgery, School of Medical Sciences, Universiti Sains Malaysia Hospital, Malaysia
| | - Ch'ng Ewe Seng
- Department of Pathology, School of Medical Sciences, Health Campus, Universiti Sains Malaysia, Kubang Kerian, 16150 Kelantan, Malaysia
| | - Siti Norasikin Binti Mohd Nafil
- Department of Pathology, School of Medical Sciences, Health Campus, Universiti Sains Malaysia, Kubang Kerian, 16150 Kelantan, Malaysia
| | - Ahmad Aizat Bin Abdul Aziz
- School of Medical Sciences, Hospital Universiti Sains Malaysia HUSM, Universiti Sains Malaysia USM, Kubang Kerian, 16150 Kelantan, Malaysia
| | - Yusuf Wada
- Department of Medical Microbiology and Parasitology, School of Medical Sciences, Health Campus, Universiti Sains Malaysia, Kubang Kerian, 16150 Kelantan, Malaysia
| | - Ahmad Irekeola
- Department of Medical Microbiology and Parasitology, School of Medical Sciences, Health Campus, Universiti Sains Malaysia, Kubang Kerian, 16150 Kelantan, Malaysia
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Sir-Mendoza F, González-Martínez F, Madera M. Prevalence of KRAS, PIK3CA, BRAF and AXIN2 gene mutations in colorectal cancer and its relationship with dental agenesis: a systematic review. REVISTA DE LA FACULTAD DE MEDICINA 2021. [DOI: 10.15446/revfacmed.v71n1.95595] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022] Open
Abstract
Introduction: The study of allelic and genotypic frequencies contributes to determining the distribution of genetic variants in different populations and their possible association with biomarkers. This knowledge could improve the decision-making process regarding the management of some diseases such as colorectal cancer (CRC), in which the detection of clinical biomarkers such as dental agenesis could be crucial in clinical practice.
Objective: To evaluate the available scientific evidence on the prevalence of KRAS, PIK3CA, BRAF and AXIN2 mutations and their possible association with dental agenesis in people with CRC.
Materials and methods: A systematic search was conducted in PubMed, EMBASE and Cochrane Library databases using the following search strategy: type of studies: observational studies reporting the prevalence of KRAS, PIK3CA, BRAF and AXIN2 mutations in people diagnosed with CRC and their possible association with dental agenesis; publication language: English and Spanish; publication period: 2010-2020; search terms: “Genes”, “RAS”, “Kras”, “PIK3CA”, “BRAF”, “AXIN2”, “Mutation”, “Polymorphism”, “Colorectal Neoplasms”, “Colorectal Cancer”, used in different combinations (“AND” and “OR”).
Results: The initial search yielded 403 records, but only 30 studies met the eligibility criteria. Of these, 11, 5, 5 and 1 only reported the prevalence of PIK3CA, KRAS, BRAF and AXIN2 mutations, respectively; while 8 reported the prevalence of more than one of these mutations in patients with CRC. The prevalence of KRAS (p.Gly12Asp), PIK3CA (p.Glu545Lys), and BRAF (p.Val600Glu) mutations ranged from 20.5% to 54%, 3.5% to 20.2%, and 2.5% to 12.1%, respectively. There were no findings regarding the association between the occurrence of these mutations and dental agenesis.
Conclusions: KRAS mutations were the most prevalent; however, there is no evidence on the association between dental agenesis and the occurrence of KRAS, PIK3CA and BRAF germline mutations in individuals with CRC.
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Sanaei MJ, Baghery Saghchy Khorasani A, Pourbagheri-Sigaroodi A, Shahrokh S, Zali MR, Bashash D. The PI3K/Akt/mTOR axis in colorectal cancer: Oncogenic alterations, non-coding RNAs, therapeutic opportunities, and the emerging role of nanoparticles. J Cell Physiol 2021; 237:1720-1752. [PMID: 34897682 DOI: 10.1002/jcp.30655] [Citation(s) in RCA: 25] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/02/2021] [Revised: 11/02/2021] [Accepted: 11/24/2021] [Indexed: 02/06/2023]
Abstract
Colorectal cancer (CRC) is one of the deadliest human malignancies worldwide. Several molecular pathways have been demonstrated to be involved in the initiation and development of CRC which among them, the overactivation of the phosphatidyl-inositol 3-kinase (PI3K)/Akt/mTOR axis is of importance. The current review aims to unravel the mechanisms by which the PI3K/Akt/mTOR pathway affects CRC progression; and also, to summarize the original data obtained from international research laboratories on the oncogenic alterations and polymorphisms affecting this pathway in CRC. Besides, we provide a special focus on the regulatory role of noncoding RNAs targeting the PI3K/Akt/mTOR pathway in this malignancy. Questions on how this axis is involved in the inhibition of apoptosis, in the induction of drug resistance, and the angiogenesis, epithelial to mesenchymal transition, and metastasis are also responded. We also discussed the PI3K/Akt pathway-associated prognostic and predictive biomarkers in CRC. In addition, we provide a general overview of PI3K/Akt/mTOR pathway inhibition whether by chemical-based drugs or by natural-based medications in the context of CRC, either as monotherapy or in combination with other therapeutic agents; however, those treatments might have life-threatening side effects and toxicities. To the best of our knowledge, the current review is one of the first ones highlighting the emerging roles of nanotechnology to overcome challenges related to CRC therapy in the hope that providing a promising platform for the treatment of CRC.
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Affiliation(s)
- Mohammad-Javad Sanaei
- Department of Hematology and Blood Banking, School of Allied Medical Sciences, Shahid Beheshti University of Medical Sciences, Tehran, Iran
| | | | - Atieh Pourbagheri-Sigaroodi
- Department of Hematology and Blood Banking, School of Allied Medical Sciences, Shahid Beheshti University of Medical Sciences, Tehran, Iran
| | - Shabnam Shahrokh
- Gastroenterology and Liver Diseases Research Center, Research Institute for Gastroenterology and Liver Diseases, Shahid Beheshti University of Medical Sciences, Tehran, Iran
| | - Mohammad Reza Zali
- Gastroenterology and Liver Diseases Research Center, Research Institute for Gastroenterology and Liver Diseases, Shahid Beheshti University of Medical Sciences, Tehran, Iran
| | - Davood Bashash
- Department of Hematology and Blood Banking, School of Allied Medical Sciences, Shahid Beheshti University of Medical Sciences, Tehran, Iran
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Yari A, Samoudi A, Afzali A, Karam ZM, Karimaldini NK, Abadi MFS, Ziasistani M, Zangouey MR, Dabiri S. Mutation Status and Prognostic Value of KRAS and BRAF in Southeast Iranian Colorectal Cancer Patients: First Report from Southeast of Iran. J Gastrointest Cancer 2021; 52:557-568. [PMID: 32495109 DOI: 10.1007/s12029-020-00426-8] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022]
Abstract
MAIN PURPOSE This study aimed to determine any association of KRAS and BRAF mutations in colorectal cancer with clinicopathological features and overall survival (OS) of Southeast Iranian colorectal cancer (CRC) patients. METHODS Overall, KRAS and BRAF status were assessed in 100 Iranian CRC subjects. A hundred consecutive stages I-IV CRC patients, who underwent surgical tumor resection from February 2012 to August 2015, were prospectively attained from three centers and were enrolled in the research. Direct sequencing and real-time PCR methods were used to the detection of KRAS and BRAF mutations, respectively. Logistic regression models were used to detect associations of KRAS and BRAF mutations with clinical/clinicopathological features. Kaplan-Meier model was used to estimate overall survival. RESULTS In total, KRAS and BRAF mutations were detected in 29 (29%) and 7 (7%) of 100 CRC patients, respectively. BRAF mutations that all comprised V600E and KRAS mutations were found in codon 12, 13, and 61 (72.4%, 20.7 and 6.9%), respectively. In a multivariate analysis, older age (≥ 60) was significantly associated with higher KRAS mutations rate and high BRAF mutation rate was significantly associated with older age (≥ 60) and poorly differentiated tumors. KRAS and BRAF mutant vs. wild type of KRAS and BRAF, 5-year OS was 62.1% vs. 71.8% (p value > 0.05) and 57.1% vs. 67.7% (p value > 0.05), respectively. CONCLUSION Mutations were found in both KRAS and BRAF genes in Iranian colorectal cancers patients and were associated with clinical/clinicopathologic features. Our data emphasizes the importance of these molecular features in Iranian CRC patients.
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Affiliation(s)
- Abolfazl Yari
- Student Research Committee, Kerman University of Medical Sciences, Kerman, Iran
- Department of Pathology, Pathology and Stem Cell Research Center, Afzalipour School of Medicine, Kerman University of Medical Sciences, 22 Bahman Blvd., Kerman, Iran
| | - Arash Samoudi
- Student Research Committee, Kerman University of Medical Sciences, Kerman, Iran
- Department of Immunology, Afzalipour School of Medicine, Kerman University of Medical Sciences, Kerman, Iran
| | - Asiyeh Afzali
- Department of Medical Laboratory of Sciences, Iran University of Medical Sciences, Tehran, Iran
| | - Zahra Miri Karam
- Student Research Committee, Kerman University of Medical Sciences, Kerman, Iran
- Physiology Research Center, Kerman University of Medical Sciences, Kerman, Iran
| | - Negin Khaje Karimaldini
- Department of Pathology, Pathology and Stem Cell Research Center, Afzalipour School of Medicine, Kerman University of Medical Sciences, 22 Bahman Blvd., Kerman, Iran
| | - Maryam Fekri Soofi Abadi
- Department of Pathology, Pathology and Stem Cell Research Center, Afzalipour School of Medicine, Kerman University of Medical Sciences, 22 Bahman Blvd., Kerman, Iran
| | - Mahsa Ziasistani
- Department of Pathology, Pathology and Stem Cell Research Center, Afzalipour School of Medicine, Kerman University of Medical Sciences, 22 Bahman Blvd., Kerman, Iran
| | - Mohammad Reza Zangouey
- Department of Immunology, Afzalipour School of Medicine, Kerman University of Medical Sciences, Kerman, Iran
| | - Shahriar Dabiri
- Department of Pathology, Pathology and Stem Cell Research Center, Afzalipour School of Medicine, Kerman University of Medical Sciences, 22 Bahman Blvd., Kerman, Iran.
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El agy F, el Bardai S, El Otmani I, Benbrahim Z, Karim IMH, Mazaz K, Benjelloun EB, Ousadden A, El Abkari M, Ibrahimi SA, Chbani L. Mutation status and prognostic value of KRAS and NRAS mutations in Moroccan colon cancer patients: A first report. PLoS One 2021; 16:e0248522. [PMID: 33784337 PMCID: PMC8009361 DOI: 10.1371/journal.pone.0248522] [Citation(s) in RCA: 13] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/12/2020] [Accepted: 02/27/2021] [Indexed: 12/12/2022] Open
Abstract
This study aimed to estimate the incidence of KRAS, NRAS, and BRAF mutations in the Moroccan population, and investigate the associations of KRAS and NRAS gene mutations with clinicopathological characteristics and their prognosis value. To achieve these objectives, we reviewed medical and pathology reports for 210 patients. RAS testing was investigated by Sanger sequencing and Pyrosequencing technology. BRAF (exon 15) status was analyzed by the Sanger method. The expression of MMR proteins was evaluated by Immunohistochemistry. KRAS and NRAS mutations were found in 36.7% and 2.9% of 210 patients, respectively. KRAS exon 2 mutations were identified in 76.5% of the cases. RAS-mutated colon cancers were significantly associated with female gender, presence of vascular invasion, classical adenocarcinoma, moderately differentiated tumors, advanced TNM stage III-IV, left colon site, higher incidence of distant metastases at the time of diagnostic, microsatellite stable phenotype, lower number of total lymph nodes, and higher means of positive lymph nodes and lymph node ratio. KRAS exon 2-mutated colon cancers, compared with KRAS wild-type colon cancers were associated with the same clinicopathological features of RAS-mutated colon cancers. NRAS-mutated patients were associated with lower total lymph node rate and the presence of positive lymph node. Rare RAS-mutated tumors, compared with wild-type tumors were more frequently moderately differentiated and associated with lower lymph node rate. We found that KRAS codon 13-mutated, tumors compared to codon 12-mutated tumors were significantly correlated with a higher death cases number, a lower rate of positive lymph, lower follow-up time, and poor overall survival. Our findings show that KRAS and NRAS mutations have distinct clinicopathological features. KRAS codon 13-mutated status was the worst predictor of prognosis at all stages in our population.
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Affiliation(s)
- Fatima El agy
- Faculty of Medicine and Pharmacy, Laboratory of Biomedical and Translational Research, Sidi Mohamed Ben Abdellah University, Fez, Morocco
- Laboratory of Anatomic Pathology and Molecular Pathology, University Hospital Hassan II, Sidi Mohamed Ben Abdellah University, Fez, Morocco
- * E-mail:
| | - Sanae el Bardai
- Laboratory of Anatomic Pathology and Molecular Pathology, University Hospital Hassan II, Sidi Mohamed Ben Abdellah University, Fez, Morocco
| | - Ihsane El Otmani
- Faculty of Medicine and Pharmacy, Laboratory of Biomedical and Translational Research, Sidi Mohamed Ben Abdellah University, Fez, Morocco
- Laboratory of Anatomic Pathology and Molecular Pathology, University Hospital Hassan II, Sidi Mohamed Ben Abdellah University, Fez, Morocco
- Unit of Medical Genetics and Oncogenetics, University Hospital Hassan II, Sidi Mohamed Ben Abdellah University, Fez, Morocco
| | - Zineb Benbrahim
- Department of Oncology, University Hospital Hassan II, Sidi Mohamed Ben Abdellah University, Fez, Morocco
| | - Ibn Majdoub Hassani Karim
- Department of General Surgery, University Hospital Hassan II, Sidi Mohamed Ben Abdellah University, Fez, Morocco
| | - Khalid Mazaz
- Department of General Surgery, University Hospital Hassan II, Sidi Mohamed Ben Abdellah University, Fez, Morocco
| | - El Bachir Benjelloun
- Department of General Surgery, University Hospital Hassan II, Sidi Mohamed Ben Abdellah University, Fez, Morocco
| | - Abdelmalek Ousadden
- Department of General Surgery, University Hospital Hassan II, Sidi Mohamed Ben Abdellah University, Fez, Morocco
| | - Mohammed El Abkari
- Department of Gastroenterology, University Hospital Hassan II, Sidi Mohamed Ben Abdellah University, Fez, Morocco
| | - Sidi Adil Ibrahimi
- Department of General Surgery, University Hospital Hassan II, Sidi Mohamed Ben Abdellah University, Fez, Morocco
| | - Laila Chbani
- Faculty of Medicine and Pharmacy, Laboratory of Biomedical and Translational Research, Sidi Mohamed Ben Abdellah University, Fez, Morocco
- Laboratory of Anatomic Pathology and Molecular Pathology, University Hospital Hassan II, Sidi Mohamed Ben Abdellah University, Fez, Morocco
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10
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UGT1A1 Polymorphism for Irinotecan Dose Escalation in Patients with BRAF-Mutated Metastatic Colorectal Cancer Treated with First-Line Bevacizumab and FOLFIRI. JOURNAL OF ONCOLOGY 2021; 2021:6686517. [PMID: 33777142 PMCID: PMC7972843 DOI: 10.1155/2021/6686517] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 11/15/2020] [Revised: 02/12/2021] [Accepted: 02/25/2021] [Indexed: 12/22/2022]
Abstract
Background Patients with metastatic colorectal cancer (mCRC) and BRAF V600E mutation have a poor prognosis, with a median progression-free survival (PFS) of only 5–7 months after initial therapy. The current standard first-line chemotherapy for these patients includes FOLFOX or FOLFIRI plus bevacizumab. In this study, we explored the effects and oncological outcomes of UGT1A1 polymorphism for irinotecan escalation in patients with BRAF-mutated mCRC. Patients and Methods. This retrospective study included 17 patients with BRAF-mutated mCRC between April 2016 and December 2019. UGT1A1 genotyping was performed on all patients prior to initiating bevacizumab plus FOLFIRI chemotherapy. The primary endpoint was PFS, and the secondary endpoints were toxicity, response rate, disease control rate, and overall survival (OS). Results Fifteen and two patients had UGT1A1 1∗/1∗ and 1∗/28∗, respectively. Eight underwent irinotecan dose escalation with tolerable adverse effects (AEs), and nine maintained an irinotecan dose of 180 mg/m2 or required deescalation to 150 mg/m2 due to intolerable AEs. After a median follow-up period of 15.7 (range, 3–54) months, the median PFS and OS were 9.4 and 15.7 months, respectively. Grade 3/4 AEs were observed in three (6%) patients. The disease control and partial response rates were 64.7% and 11.8%, respectively, indicating that most patients (14, 82.3%) could maintain this as a first-line line therapy with stable disease or proceed to second-line therapy if disease progression occurred, thereby maintaining acceptable performance status. Conclusions The oncological outcomes of patients with BRAF-mutated mCRC treated using FOLFIRI plus bevacizumab with irinotecan dose escalation as a first-line therapy are acceptable with tolerable AEs; this may be a feasible treatment option in such patients. Pretherapeutic UGT1A1 genotyping-guided dose adjustment can achieve favorable outcomes.
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11
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Yari A, Afzali A, Aalipour M, Nakheai M, Zahedi MJ. KRAS and BRAF mutations in Iranian colorectal cancer patients: A systematic review and meta-analysis. CASPIAN JOURNAL OF INTERNAL MEDICINE 2021; 11:355-369. [PMID: 33680376 PMCID: PMC7911761 DOI: 10.22088/cjim.11.4.355] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 11/20/2022]
Abstract
Background: Mutations in the EGFR signaling pathway play an important role in the development of colorectal cancer (CRC). Mutations in these genes, like KRAS and BRAF, affect the treatment strategies and associated with poor prognosis and relative resistance to anti-EGFR therapies. Our aim was to conduct a systematic and meta-analysis on all studies that have been conducted on the prevalence of these gene mutations in Iranian CRC patients. Methods: Four science citation index databases (MEDLINE, EMBASE, Web of Science and Cochrane library) and local databases were searched up to March 2018 with related keywords. Two reviewers independently screened and extracted the data. Quality of all included studies was assessed using an adapted checklist from STROBE. A random-effect model was used to calculate the total prevalence of KRAS and BRAF mutations in CRC subjects by the event rate (ER). Meta-regression was utilized to explore heterogeneity causes. Results: In total, from 573 records, 23 eligible studies (2662 patients) were included for data extraction and analysis. In 18 of 23 included studies, the prevalence of KRAS mutations was 33.9% (95% CI=30.1-37.9) with I2=65.17 (p<0.001). The occurrence of KRAS mutations in codon 12 and 13 was 76.9% (95% CI = 70.4-82.3%) with I2=84.88 (p<0.001) and 23.5% (95% CI=17.9-30.3) with I2=85.85 (p<0.001), respectively. In 9 of 23 studies, the BRAF mutation rate was 3.2% (95% CI=0.003-13.6) with I2=88.61 (p<0.001). Conclusion: The prevalence of these mutations in CRC patients shows a significant difference in the different regions of Iran, which is probably due to environmental and racial factors.
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Affiliation(s)
- Abolfazl Yari
- Student Research Committee, Kerman University of Medical Sciences, Kerman, Iran.,Department of Medical Genetics, Afzalipour School of Medicine, Kerman University of Medical Sciences, Kerman, Iran
| | - Asiyeh Afzali
- Department of Medical Laboratory of Sciences, Iran University of Medical Sciences, Tehran, Iran
| | - Mostafa Aalipour
- Department of Immunology, Afzalipour School of Medicine, Kerman University of Medical Sciences, Kerman, Iran
| | - Mehran Nakheai
- Department of Epidemiology and Biostatistics, School of Public Health, Kerman University of Medical Sciences, Kerman, Iran
| | - Mohammad Javad Zahedi
- Gastroenterology and Hepatology Research Center, Department of Internal Medicine, Kerman University of Medical Sciences, Kerman, Iran
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12
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Abstract
Adaptive enrichment designs for clinical trials may include rules that use interim data to identify treatment-sensitive patient subgroups, select or compare treatments, or change entry criteria. A common setting is a trial to compare a new biologically targeted agent to standard therapy. An enrichment design's structure depends on its goals, how it accounts for patient heterogeneity and treatment effects, and practical constraints. This article first covers basic concepts, including treatment-biomarker interaction, precision medicine, selection bias, and sequentially adaptive decision making, and briefly describes some different types of enrichment. Numerical illustrations are provided for qualitatively different cases involving treatment-biomarker interactions. Reviews are given of adaptive signature designs; a Bayesian design that uses a random partition to identify treatment-sensitive biomarker subgroups and assign treatments; and designs that enrich superior treatment sample sizes overall or within subgroups, make subgroup-specific decisions, or include outcome-adaptive randomization.
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Affiliation(s)
- Peter F Thall
- Department of Biostatistics, M.D. Anderson Cancer Center, University of Texas, Houston, Texas 77030, USA
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13
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Liu J, Tang L, Yi J, Li G, Lu Y, Xu Y, Zhao S, Mao R, Li X, Ren L, Wang K. Unique characteristics of CpG island methylator phenotype (CIMP) in a Chinese population with colorectal cancer. BMC Gastroenterol 2019; 19:173. [PMID: 31690257 PMCID: PMC6833289 DOI: 10.1186/s12876-019-1086-x] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 03/28/2019] [Accepted: 10/02/2019] [Indexed: 12/21/2022] Open
Abstract
Background Molecular characteristics of CpG island methylator phenotype (CIMP) in colorectal cancer (CRC) have been well documented in Western, but not in Chinese, populations. Methods We investigated the incidence of CIMP, BRAF/KRAS mutation, and microsatellite instability (MSI) in a Chinese population with CRC (n = 401) and analysed associations between CIMP status and clinicopathological and molecular features. Results A total of 41 cases, 310 cases, and 40 cases were classified as CIMP-high, CIMP-low, and CIMP-negative, respectively. We detected a significantly low incidence of BRAF mutation in adenomas (2%) and CRC (0.7%), and a relatively low incidence of KRAS mutation (24.9%) compared with that in other populations. We also detected a relatively low incidence of CIMP-high (10.2%), which was significantly associated with younger age (≤49 years of age), female sex, and proximal tumour location. Conclusions This study revealed unique characteristics of CIMP in a Chinese population with colorectal cancer. Developing specific CIMP markers based on unique populations or ethnic groups will further help to fully elucidate CIMP pathogenesis.
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Affiliation(s)
- Jiang Liu
- Department of Reproduction and Genetics, the First Affiliated Hospital of Kunming Medical University, Kunming, 650032, Yunnan, China.,Yunnan Engineering Technology Center of Digestive Disease, Kunming, 650032, Yunnan, China.,Kunming Engineering Technology Center of Digestive Disease, Kunming, 650032, Yunnan, China
| | - Li Tang
- Department of Reproduction and Genetics, the First Affiliated Hospital of Kunming Medical University, Kunming, 650032, Yunnan, China
| | - Jinhua Yi
- Department of Gastrointestinal Surgery, the First Affiliated Hospital of Kunming Medical University, Yunnan Institute of Digestive Disease, Kunming, 650032, Yunnan, China.,Yunnan Engineering Technology Center of Digestive Disease, Kunming, 650032, Yunnan, China.,Kunming Engineering Technology Center of Digestive Disease, Kunming, 650032, Yunnan, China
| | - Guimei Li
- Public Technical Service Center, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, 650032, Yunnan, China.,Kunming Biological Diversity Regional Center of Large Apparatus and Equipments, Chinese Academy of Sciences, Kunming, 650032, Yunnan, China
| | - Youwang Lu
- Department of Reproduction and Genetics, the First Affiliated Hospital of Kunming Medical University, Kunming, 650032, Yunnan, China.,Yunnan Engineering Technology Center of Digestive Disease, Kunming, 650032, Yunnan, China.,Kunming Engineering Technology Center of Digestive Disease, Kunming, 650032, Yunnan, China
| | - Yu Xu
- Department of Gastrointestinal Surgery, the First Affiliated Hospital of Kunming Medical University, Yunnan Institute of Digestive Disease, Kunming, 650032, Yunnan, China.,Yunnan Engineering Technology Center of Digestive Disease, Kunming, 650032, Yunnan, China.,Kunming Engineering Technology Center of Digestive Disease, Kunming, 650032, Yunnan, China
| | - Shuhua Zhao
- Department of Reproduction and Genetics, the First Affiliated Hospital of Kunming Medical University, Kunming, 650032, Yunnan, China
| | - Rui Mao
- School of Stomatology, Kunming Medical University, Kunming, 650500, Yunnan, China
| | - Xiaolu Li
- Public Technical Service Center, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, 650032, Yunnan, China.,Kunming Biological Diversity Regional Center of Large Apparatus and Equipments, Chinese Academy of Sciences, Kunming, 650032, Yunnan, China
| | - Li Ren
- Department of Reproductive Gynecology, the First People's Hospital of Yunnan Province, Kunming, 650031, Yunnan, China
| | - Kunhua Wang
- Department of Gastrointestinal Surgery, the First Affiliated Hospital of Kunming Medical University, Yunnan Institute of Digestive Disease, Kunming, 650032, Yunnan, China. .,Yunnan Engineering Technology Center of Digestive Disease, Kunming, 650032, Yunnan, China. .,Kunming Engineering Technology Center of Digestive Disease, Kunming, 650032, Yunnan, China.
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14
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Moosazadeh M, Sadough A, Afshari M, Barzegari S, Janbabaee G, Tabrizi R, Akbari M, Alizadeh-Navaei R, Hedayatizadeh-Omran A, Rostami-Maskopaee F. Prevalence of BRAF gene mutation in samples of primary and metastatic colorectal cancer: A meta-analysis. Eur J Cancer Care (Engl) 2019; 28:e13160. [PMID: 31482595 DOI: 10.1111/ecc.13160] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/09/2018] [Revised: 06/23/2019] [Accepted: 08/01/2019] [Indexed: 02/05/2023]
Abstract
INTRODUCTION Understanding the prevalence and biology of BRAF gene can improve the treatment methods of cancerous patients. This study aims to estimate the prevalence of BRAF gene mutation in samples of primary and metastatic colorectal cancer using meta-analysis method. METHODS We searched PubMed, Scopus, ScienceDirect, Ovid and Google Scholar motor engine using MeSH terms of relevant keywords. During the screening phase, titles, abstracts and full texts were reviewed and risk of bias was assessed for all selected papers based on Newcastle-Ottawa Scale (NOS) checklist. The results of the primary studies were combined using meta-analysis. RESULTS Of 95 eligible studies entered into the meta-analysis, prevalence of BRAF gene mutation had been assessed among 19,484 primary tumour samples as well as 12,256 metastatic samples. The total prevalence of BRAF gene mutation among primary tumour samples was estimated as of 10.16% (8.09-12.22) in the world, 0.41% (0-1.89) in EMRO region, 10.06% (7.54-12.59) in EURO region, 10.33% (7.24-13.43) in SEARO region and 11.33% (7.29-15.37) in WPRO region. The pooled estimates for BRAF gene mutation in metastatic samples were 6.53% (5.09-7.96), 8.07% (5.57-10.56), 5.38% (3.75-7.02) and 5.55% (1.72-9.38) for all regions, EURO, WPRO and PAHO regions respectively. CONCLUSION Our results showed evidences of BRAF gene mutation in one-tenth of primary colorectal tumour samples in EURO, PAHO, SEARO and WPRO regions which was considerably higher than that of the EMRO region.
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Affiliation(s)
- Mahmood Moosazadeh
- Health Sciences Research center, Addiction Institute, Mazandaran University of Medical Sciences, Sari, Iran
| | - Azita Sadough
- Traditional Medicine and History of Medical science Research center, Faculty of Iranian medicine, Babol University of Medical Science, Babol, Iran
| | - Mahdi Afshari
- Department of Community Medicine, Zabol University of Medical Sciences, Zabol, Iran
| | - Saeed Barzegari
- Department of Health Information Management, School of Allied Medical Sciences, Tehran University of Medical Sciences, Tehran, Iran
| | - Ghasem Janbabaee
- Gastrointestinal Cancer Research Center, Faculty of Medicine, Mazandaran University of Medical Sciences, Sari, Iran
| | - Reza Tabrizi
- Health Policy Research Center, Student Research Committee, Institute of Health, Shiraz University of Medical Sciences, Shiraz, Iran
| | - Maryam Akbari
- Health Policy Research Center, Student Research Committee, Institute of Health, Shiraz University of Medical Sciences, Shiraz, Iran
| | - Reza Alizadeh-Navaei
- Gastrointestinal cancer research center, Mazandaran University of Medical Sciences, Sari, Iran
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15
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KRAS, NRAS, BRAF, HER2 and microsatellite instability in metastatic colorectal cancer - practical implications for the clinician. Radiol Oncol 2019; 53:265-274. [PMID: 31553708 PMCID: PMC6765160 DOI: 10.2478/raon-2019-0033] [Citation(s) in RCA: 82] [Impact Index Per Article: 16.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/16/2019] [Accepted: 06/24/2019] [Indexed: 12/13/2022] Open
Abstract
Background Colorectal cancer is a successful model of genetic biomarker development in oncology. Currently, several predictive or prognostic genetic alterations have been identified and are used in clinical practice. The RAS gene family, which includes KRAS and NRAS act as predictors for anti-epithelial growth factor receptor treatment (anti-EGFR), and it has been suggested that NRAS mutations also play a role in prognosis: patients harboring NRAS alterations have a significantly shorter survival compared to those with wild type tumours. BRAF V600E mutations are rare and occur mostly in tumors located in the ascending colon in elderly female patients. BRAF is instrumental in establishing prognosis: survival is shorter by 10-16 months in BRAF-mutant patients, and BRAF may be a negative prognostic factor for patients who undergo hepatic or pulmonary metastasectomy. Moreover, this mutation is used as a negative predictive factor for anti-EGFR therapies. Two new biomarkers have recently been added to the metastatic colorectal cancer panel: HER2 and microsatellite instability. While HER2 is still being investigated in different prospective studies in order to validate its prognostic role, microsatellite instability already guides clinical decisions in substituted with advanced colorectal cancer. Conclusions There are current evidences that support using above mentioned genetic biomarkers to better identify the right medicine that is supposed to be used in the right patient. This approach contributes to a more individualized patient-oriented treatment in daily clinical practice.
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16
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Korphaisarn K, Pongpaibul A, Roothumnong E, Pongsuktavorn K, Thamlikitkul L, Anekpuritanang T, Poungvarin N, Thongnoppakhun W, Pithukpakorn M. High Frequency of KRAS Codon 146 and FBXW7 Mutations in Thai Patients with Stage II-III Colon Cancer. Asian Pac J Cancer Prev 2019; 20:2319-2326. [PMID: 31450901 PMCID: PMC6852819 DOI: 10.31557/apjcp.2019.20.8.2319] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/11/2019] [Indexed: 12/24/2022] Open
Abstract
Background: KRAS, NRAS, and BRAF gene mutations are the most clinically relevant and frequently reported in
colorectal cancer (CRC). Although data on these genes are frequently reported in several counties, data specific to these
genes among Thai population are scarce. The aim of this study was to investigate and identify molecular alterations
associated with colon cancer in Thai population, and to determine the impact of these genetic aberrations on clinical
outcome. Methods: DNA from 108 archived formalin-fixed, paraffin-embedded (FFPE) tissue samples that histologically
confirmed adenocarcinoma of stage II-III colon cancer between 2010 and 2012 at Siriraj Hospital (Bangkok, Thailand)
were extracted. Gene mutational analysis was performed by next-generation sequencing (NGS) using an Oncomine
Solid Tumor DNA kit (Thermo Fisher Scientific, Inc., Waltham, MA, USA). Results: A total of 22 somatic gene
mutations were detected. The mutation frequency observed in KRAS, NRAS, BRAF, PIK3CA, and FBXW7 mutations
was 47.2%, 1.9%, 1.9%, 12%, and 14.8%, respectively. KRAS mutation codon 12, 13, 59, 61, 117, and 146 mutations
were identified in 29.6%, 8.3%, 1.8%, 0.9%, 0.0%, and 8.3%, respectively. KRAS Exon 4 had better DFS compared
with Exon 2 and 3. Conclusions: This study is the first to comprehensively report hotspot mutations using NGS in Thai
colon cancer patients. The most commonly identified gene mutation frequencies among Thai patients (KRAS, NRAS,
BRAF, TP53, and PIK3CA) were similar to the gene mutation frequencies reported in Western population, except for
subgroup of KRAS codon 146 and FBXW7 mutations that had a slightly higher frequency.
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Affiliation(s)
- Krittiya Korphaisarn
- Division of Medical Oncology, Department of Medicine, Faculty of Medicine, Siriraj Hospital, Mahidol University, Bangkok, Thailand. ,Siriraj Center of Research Excellence in Precision Medicine, Faculty of Medicine, Siriraj Hospital, Mahidol University, Bangkok, Thailand
| | - Ananya Pongpaibul
- Department of Pathology, Faculty of Medicine, Siriraj Hospital, Mahidol University, Bangkok, Thailand
| | - Ekkapong Roothumnong
- Siriraj Center of Research Excellence in Precision Medicine, Faculty of Medicine, Siriraj Hospital, Mahidol University, Bangkok, Thailand.,Division of Medical Genetics, Faculty of Medicine, Siriraj Hospital, Mahidol University, Bangkok, Thailand.,Division of Medical Genetics Research and Laboratory, Faculty of Medicine, Siriraj Hospital, Mahidol University, Bangkok, Thailand
| | - Khontawan Pongsuktavorn
- Siriraj Center of Research Excellence in Precision Medicine, Faculty of Medicine, Siriraj Hospital, Mahidol University, Bangkok, Thailand.,Division of Medical Genetics Research and Laboratory, Faculty of Medicine, Siriraj Hospital, Mahidol University, Bangkok, Thailand
| | - Lucksamon Thamlikitkul
- Division of Medical Oncology, Department of Medicine, Faculty of Medicine, Siriraj Hospital, Mahidol University, Bangkok, Thailand.
| | - Tauangtham Anekpuritanang
- Department of Pathology, Faculty of Medicine, Siriraj Hospital, Mahidol University, Bangkok, Thailand
| | - Naravat Poungvarin
- Department of Clinical Pathology, Faculty of Medicine, Siriraj Hospital, Mahidol University, Bangkok, Thailand
| | - Wanna Thongnoppakhun
- Siriraj Center of Research Excellence in Precision Medicine, Faculty of Medicine, Siriraj Hospital, Mahidol University, Bangkok, Thailand.,Division of Medical Genetics Research and Laboratory, Faculty of Medicine, Siriraj Hospital, Mahidol University, Bangkok, Thailand
| | - Manop Pithukpakorn
- Siriraj Center of Research Excellence in Precision Medicine, Faculty of Medicine, Siriraj Hospital, Mahidol University, Bangkok, Thailand.,Division of Medical Genetics, Faculty of Medicine, Siriraj Hospital, Mahidol University, Bangkok, Thailand.,Division of Medical Genetics Research and Laboratory, Faculty of Medicine, Siriraj Hospital, Mahidol University, Bangkok, Thailand
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17
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Fu X, Huang Y, Fan X, Deng Y, Liu H, Zou H, Wu P, Chen Z, Huang J, Wang J, Lin H, Huang S, Tan X, Lan P, Wang L, Wang JP. Demographic trends and KRAS/BRAF V600E mutations in colorectal cancer patients of South China: A single-site report. Int J Cancer 2019; 144:2109-2117. [PMID: 30414169 DOI: 10.1002/ijc.31973] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/09/2018] [Accepted: 10/22/2018] [Indexed: 12/20/2022]
Abstract
The incidence of colorectal cancer (CRC) is increasing in China. Here, we aimed to evaluate the latest demographic trends and KRAS/BRAF mutations status of Chinese CRC. Five thousand five hundred and forty-six CRC patients diagnosed from 2010 to 2017 were involved. KRAS exon 2 and BRAFV600E mutations were detected by Sanger sequencing and high-resolution melting analysis or allelic-specific probe method. Gene mutation profiles and clinicopathologic characteristics of 5495 patients were analyzed. The joinpoint regression model was used to predict the demographic data in 2018. We found KRAS exon 2 and BRAFV600E mutation rates were 37.7 and 2.8% in CRC patients. Tumors with KRAS exon 2 mutations were more likely to be present in female and patients aged older than 75 years, right colon and have well-differentiated histology. Tumors with BRAFV600E mutations were more likely to be present in the female, right colon and have poorly differentiated histology. From 2010 to 2017, the percentage of colon cancer and tubular adenocarcinoma in CRC increased substantially (from 39.3 to 51.8%, from 78.6 to 93.4%, respectively). The percentage of right colon cancer increased from 18.3 to 20.5%, which predictively may keep at 22.6% in 2018. The rise trends for patients with moderate differentiation tumor or KRAS exon 2 mutated tumor were apparent (from 50.3 to 78.6%, from 32.8 to 39.7%, respectively). In conclusion, in recent 8 years, there is a shift to the colon, especially right colon in the incidence of Chinese CRC. Moreover tubular adenocarcinoma is becoming the primary histology type.
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Affiliation(s)
- Xinhui Fu
- Guangdong Institute of Gastroenterology, The Sixth Affiliated Hospital, Sun Yat-sen University, Guangzhou, China.,Guangdong Provincial Key Laboratory of Colorectal and Pelvic Floor Diseases, the Sixth Affiliated Hospital, Sun Yat-sen University, Guangzhou, China.,Department of Pathology, The Sixth Affiliated Hospital, Sun Yat-sen University, Guangzhou, China
| | - Yan Huang
- Department of Pathology, The Sixth Affiliated Hospital, Sun Yat-sen University, Guangzhou, China
| | - Xinjuan Fan
- Department of Pathology, The Sixth Affiliated Hospital, Sun Yat-sen University, Guangzhou, China
| | - Yanhong Deng
- Department of Medical Oncology, The Sixth Affiliated Hospital, Sun Yat-sen University, Guangzhou, China
| | - Huanliang Liu
- Guangdong Institute of Gastroenterology, The Sixth Affiliated Hospital, Sun Yat-sen University, Guangzhou, China.,Guangdong Provincial Key Laboratory of Colorectal and Pelvic Floor Diseases, the Sixth Affiliated Hospital, Sun Yat-sen University, Guangzhou, China
| | - Hongzhi Zou
- Guangdong Institute of Gastroenterology, The Sixth Affiliated Hospital, Sun Yat-sen University, Guangzhou, China.,Guangdong Provincial Key Laboratory of Colorectal and Pelvic Floor Diseases, the Sixth Affiliated Hospital, Sun Yat-sen University, Guangzhou, China
| | - Peihuang Wu
- Guangdong Institute of Gastroenterology, The Sixth Affiliated Hospital, Sun Yat-sen University, Guangzhou, China.,Guangdong Provincial Key Laboratory of Colorectal and Pelvic Floor Diseases, the Sixth Affiliated Hospital, Sun Yat-sen University, Guangzhou, China
| | - Zhiting Chen
- Guangdong Institute of Gastroenterology, The Sixth Affiliated Hospital, Sun Yat-sen University, Guangzhou, China.,Guangdong Provincial Key Laboratory of Colorectal and Pelvic Floor Diseases, the Sixth Affiliated Hospital, Sun Yat-sen University, Guangzhou, China.,Department of Pathology, The Sixth Affiliated Hospital, Sun Yat-sen University, Guangzhou, China
| | - Jinglin Huang
- Guangdong Institute of Gastroenterology, The Sixth Affiliated Hospital, Sun Yat-sen University, Guangzhou, China.,Guangdong Provincial Key Laboratory of Colorectal and Pelvic Floor Diseases, the Sixth Affiliated Hospital, Sun Yat-sen University, Guangzhou, China.,Department of Pathology, The Sixth Affiliated Hospital, Sun Yat-sen University, Guangzhou, China
| | - Jingxuan Wang
- Guangdong Institute of Gastroenterology, The Sixth Affiliated Hospital, Sun Yat-sen University, Guangzhou, China.,Guangdong Provincial Key Laboratory of Colorectal and Pelvic Floor Diseases, the Sixth Affiliated Hospital, Sun Yat-sen University, Guangzhou, China
| | - Hanjie Lin
- Guangdong Institute of Gastroenterology, The Sixth Affiliated Hospital, Sun Yat-sen University, Guangzhou, China.,Guangdong Provincial Key Laboratory of Colorectal and Pelvic Floor Diseases, the Sixth Affiliated Hospital, Sun Yat-sen University, Guangzhou, China.,Department of Pathology, The Sixth Affiliated Hospital, Sun Yat-sen University, Guangzhou, China
| | - Shuhui Huang
- Department of Pathology, The Sixth Affiliated Hospital, Sun Yat-sen University, Guangzhou, China
| | - Xiaoli Tan
- Guangdong Institute of Gastroenterology, The Sixth Affiliated Hospital, Sun Yat-sen University, Guangzhou, China.,Guangdong Provincial Key Laboratory of Colorectal and Pelvic Floor Diseases, the Sixth Affiliated Hospital, Sun Yat-sen University, Guangzhou, China.,Department of Pathology, The Sixth Affiliated Hospital, Sun Yat-sen University, Guangzhou, China
| | - Ping Lan
- Guangdong Institute of Gastroenterology, The Sixth Affiliated Hospital, Sun Yat-sen University, Guangzhou, China.,Department of GI Surgery, The Sixth Affiliated Hospital, Sun Yat-sen University, Guangzhou, China
| | - Lei Wang
- Department of GI Surgery, The Sixth Affiliated Hospital, Sun Yat-sen University, Guangzhou, China
| | - Jian-Ping Wang
- Guangdong Institute of Gastroenterology, The Sixth Affiliated Hospital, Sun Yat-sen University, Guangzhou, China.,Guangdong Provincial Key Laboratory of Colorectal and Pelvic Floor Diseases, the Sixth Affiliated Hospital, Sun Yat-sen University, Guangzhou, China
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18
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Fu XH, Chen ZT, Wang WH, Fan XJ, Huang Y, Wu XB, Huang JL, Wang JX, Lin HJ, Tan XL, Wang L, Wang JP. KRAS G12V Mutation is an Adverse Prognostic Factor of Chinese Gastric Cancer Patients. J Cancer 2019; 10:821-828. [PMID: 30854087 PMCID: PMC6400811 DOI: 10.7150/jca.27899] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/15/2018] [Accepted: 12/14/2018] [Indexed: 12/13/2022] Open
Abstract
This study aims to investigate the molecular characteristics of Chinese gastric cancer patients. In our study, the KRAS, BRAF, and PIK3CA mutation status of 485 GC patients were analyzed by Sanger sequencing. Kaplan-Meier analysis was used to plot survival curves according to different genotypes. The results show that the frequency of KRAS, BRAF and PIK3CA mutations were 4.1%, 1.2% and 3.5%, respectively. BRAF mutations were significantly concentrated in stage III and IV gastric cancer (P=0.009). KRAS G12V mutation carriers have much shorter OS than other mutation carriers and wild-type group patients (P=0.013). In conclusion, only the KRAS G12V mutation has an adverse effect on patient survival.
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Affiliation(s)
- Xin-Hui Fu
- Guangdong Institute of Gastroenterology, The Sixth Affiliated Hospital, Sun Yat-sen University, Guangdong, China.,Guangdong Provincial Key Laboratory of Colorectal and Pelvic Floor Diseases, The Sixth Affiliated Hospital, Sun Yat-sen University, Guangdong, China.,Department of Pathology, The Sixth Affiliated Hospital, Sun Yat-sen University, Guangdong, China
| | - Zhi-Ting Chen
- Guangdong Institute of Gastroenterology, The Sixth Affiliated Hospital, Sun Yat-sen University, Guangdong, China.,Guangdong Provincial Key Laboratory of Colorectal and Pelvic Floor Diseases, The Sixth Affiliated Hospital, Sun Yat-sen University, Guangdong, China.,Department of Pathology, The Sixth Affiliated Hospital, Sun Yat-sen University, Guangdong, China
| | - Wen-Hui Wang
- Department of Information and Technology, The Sixth Affiliated Hospital, Sun Yat-sen University, Guangdong, China
| | - Xin-Juan Fan
- Department of Pathology, The Sixth Affiliated Hospital, Sun Yat-sen University, Guangdong, China
| | - Yan Huang
- Department of Pathology, The Sixth Affiliated Hospital, Sun Yat-sen University, Guangdong, China
| | - Xiao-Bin Wu
- Department of GI Surgery, The Sixth Affiliated Hospital, Sun Yat-sen University, Guangdong, China
| | - Jing-Lin Huang
- Guangdong Institute of Gastroenterology, The Sixth Affiliated Hospital, Sun Yat-sen University, Guangdong, China.,Guangdong Provincial Key Laboratory of Colorectal and Pelvic Floor Diseases, The Sixth Affiliated Hospital, Sun Yat-sen University, Guangdong, China.,Department of Pathology, The Sixth Affiliated Hospital, Sun Yat-sen University, Guangdong, China
| | - Jing-Xuan Wang
- Guangdong Institute of Gastroenterology, The Sixth Affiliated Hospital, Sun Yat-sen University, Guangdong, China.,Guangdong Provincial Key Laboratory of Colorectal and Pelvic Floor Diseases, The Sixth Affiliated Hospital, Sun Yat-sen University, Guangdong, China.,Department of Pathology, The Sixth Affiliated Hospital, Sun Yat-sen University, Guangdong, China
| | - Han-Jie Lin
- Guangdong Institute of Gastroenterology, The Sixth Affiliated Hospital, Sun Yat-sen University, Guangdong, China.,Guangdong Provincial Key Laboratory of Colorectal and Pelvic Floor Diseases, The Sixth Affiliated Hospital, Sun Yat-sen University, Guangdong, China.,Department of Pathology, The Sixth Affiliated Hospital, Sun Yat-sen University, Guangdong, China
| | - Xiao-Li Tan
- Guangdong Institute of Gastroenterology, The Sixth Affiliated Hospital, Sun Yat-sen University, Guangdong, China.,Guangdong Provincial Key Laboratory of Colorectal and Pelvic Floor Diseases, The Sixth Affiliated Hospital, Sun Yat-sen University, Guangdong, China.,Department of Pathology, The Sixth Affiliated Hospital, Sun Yat-sen University, Guangdong, China
| | - Lei Wang
- Department of GI Surgery, The Sixth Affiliated Hospital, Sun Yat-sen University, Guangdong, China
| | - Jian-Ping Wang
- Guangdong Institute of Gastroenterology, The Sixth Affiliated Hospital, Sun Yat-sen University, Guangdong, China.,Guangdong Provincial Key Laboratory of Colorectal and Pelvic Floor Diseases, The Sixth Affiliated Hospital, Sun Yat-sen University, Guangdong, China
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19
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Yang Q, Huo S, Sui Y, Du Z, Zhao H, Liu Y, Li W, Wan X, Liu T, Zhang G. Mutation Status and Immunohistochemical Correlation of KRAS, NRAS, and BRAF in 260 Chinese Colorectal and Gastric Cancers. Front Oncol 2018; 8:487. [PMID: 30416987 PMCID: PMC6212577 DOI: 10.3389/fonc.2018.00487] [Citation(s) in RCA: 22] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/09/2018] [Accepted: 10/10/2018] [Indexed: 12/12/2022] Open
Abstract
KRAS, NRAS and BRAF are kinases involved in the RAS-RAF-MAPK signaling pathway and also potential tumor-driven genes. Patients with KRAS/NRAS/BRAF mutations are resistant to anti-EGFR monoclonal antibody therapy. The main purpose of this study is to investigate the mutation status and distribution of KRAS/NRAS/BRAF in Chinese colorectal and gastric cancers, and to explore the histopathological changes and related immunohistochemical marker changes caused by these mutations. The mutation status of KRAS (exons 2, codon 12/13), NRAS (exons 2/3/4, codon 12/13/59/61/117/146) and BRAF (exons 15, codon 600) were detected by amplification refractory mutation system polymerase chain reaction (ARMS-PCR) in 86 colon cancer, 140 rectal cancer and 34 gastric cancer tissues. Then, the frequencies and distribution of KRAS/NRAS/BRAF mutations were described in detail. Furthermore, the relationship between KRAS/NRAS/BRAF mutations and the features of histopathological and related immunohistochemical markers were analyzed. The results showed that KRAS/NRAS/BRAF mutation rates in colon cancer were 44.2, 1.2, and 3.5%; in rectal cancer were 37.1, 4.3, and 0.7%; in gastric cancer were none, none and 2.9%. The mutation rate of KRAS in female (48.8%) is significantly higher than that of male (27.8%), and the mutation rate increased with the higher degree of differentiation. Additionally, the mutation rate of BRAF detected by ARMS-PCR (1.77%) was significantly lower than that by immunohistochemistry (4.11%). It also showed that the KRAS/NRAS/BRAF mutation status had a certain relationship with the expression of some immunohistochemical markers. This study provides more data support for clinical research on KRAS/NRAS/BRAF mutation in CRCs or gastric cancers.
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Affiliation(s)
- Qiwei Yang
- Medical Research Center, The Second Hospital of Jilin University, Changchun, China
| | - Sibo Huo
- Department of General Surgery, The Second Hospital of Jilin University, Changchun, China
| | - Yujie Sui
- Medical Research Center, The Second Hospital of Jilin University, Changchun, China
| | - Zhenwu Du
- Medical Research Center, The Second Hospital of Jilin University, Changchun, China.,Department of Orthopedics, The Second Hospital of Jilin University, Changchun, China
| | - Haiyue Zhao
- Center of Reproductive Medicine and Center of Prenatal Diagnosis, The First Hospital of Jilin University, Changchun, China
| | - Yu Liu
- Department of General Surgery, The Second Hospital of Jilin University, Changchun, China
| | - Wei Li
- Department of General Surgery, The Second Hospital of Jilin University, Changchun, China
| | - Xin Wan
- Department of General Surgery, The Second Hospital of Jilin University, Changchun, China
| | - Tongjun Liu
- Department of General Surgery, The Second Hospital of Jilin University, Changchun, China
| | - Guizhen Zhang
- Medical Research Center, The Second Hospital of Jilin University, Changchun, China.,Department of Orthopedics, The Second Hospital of Jilin University, Changchun, China
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20
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Chat-Uthai N, Vejvisithsakul P, Udommethaporn S, Meesiri P, Danthanawanit C, Wongchai Y, Teerapakpinyo C, Shuangshoti S, Poungvarin N. Development of ultra-short PCR assay to reveal BRAF V600 mutation status in Thai colorectal cancer tissues. PLoS One 2018; 13:e0198795. [PMID: 29879227 PMCID: PMC5991739 DOI: 10.1371/journal.pone.0198795] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/17/2017] [Accepted: 05/25/2018] [Indexed: 02/06/2023] Open
Abstract
The protein kinase BRAF is one of the key players in regulating cellular responses to extracellular signals. Somatic mutations of the BRAF gene, causing constitutive activation of BRAF, have been found in various types of human cancers such as malignant melanoma, and colorectal cancer. BRAF V600E and V600K, most commonly observed mutations in these cancers, may predict response to targeted therapies. Many techniques suffer from a lack of diagnostic sensitivity in mutation analysis in clinical samples with a low cancer cell percentage or poor-quality fragmented DNA. Here we present allele-specific real-time PCR assay for amplifying 35- to 45-base target sequences in BRAF gene. Forward primer designed for BRAF V600E detection is capable of recognizing both types of BRAF V600E mutation, i.e. V600E1 (c.1799T>A) and V600E2 (c.1799_1800delTGinsAA), as well as complex tandem mutation caused by nucleotide changes in codons 600 and 601. We utilized this assay to analyze Thai formalin-fixed paraffin-embedded tissues. Forty-eight percent of 178 Thai colorectal cancer tissues has KRAS mutation detected by highly sensitive commercial assays. Although these DNA samples contain low overall yield of amplifiable DNA, our newly-developed assay successfully revealed BRAF V600 mutations in 6 of 93 formalin-fixed paraffin-embedded colorectal cancer tissues which KRAS mutation was not detected. Ultra-short PCR assay with forward mutation-specific primers is potentially useful to detect BRAF V600 mutations in highly fragmented DNA specimens from cancer patients.
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Affiliation(s)
- Nunthawut Chat-Uthai
- Research Division, Faculty of Medicine Siriraj Hospital, Mahidol University, Bangkok, Thailand
| | | | - Sutthirat Udommethaporn
- Clinical Molecular Pathology Laboratory, Department of Clinical Pathology, Faculty of Medicine Siriraj Hospital, Mahidol University, Bangkok, Thailand
| | - Puttarakun Meesiri
- Clinical Molecular Pathology Laboratory, Department of Clinical Pathology, Faculty of Medicine Siriraj Hospital, Mahidol University, Bangkok, Thailand
| | - Chetiya Danthanawanit
- Clinical Molecular Pathology Laboratory, Department of Clinical Pathology, Faculty of Medicine Siriraj Hospital, Mahidol University, Bangkok, Thailand
| | - Yannawan Wongchai
- Research Division, Faculty of Medicine Siriraj Hospital, Mahidol University, Bangkok, Thailand
| | - Chinachote Teerapakpinyo
- Chulalongkorn GenePRO Center, Research Affairs, Faculty of Medicine, Chulalongkorn University, Bangkok, Thailand
| | - Shanop Shuangshoti
- Chulalongkorn GenePRO Center, Research Affairs, Faculty of Medicine, Chulalongkorn University, Bangkok, Thailand
- Department of Pathology, Faculty of Medicine, Chulalongkorn University, Bangkok, Thailand
| | - Naravat Poungvarin
- Clinical Molecular Pathology Laboratory, Department of Clinical Pathology, Faculty of Medicine Siriraj Hospital, Mahidol University, Bangkok, Thailand
- * E-mail:
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21
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Jia S, Zhang R, Lin G, Peng R, Gao P, Han Y, Fu Y, Ding J, Wu Q, Zhang K, Xie J, Li J. A novel cell line generated using the CRISPR/Cas9 technology as universal quality control material for KRAS G12V mutation testing. J Clin Lab Anal 2018; 32:e22391. [PMID: 29380513 DOI: 10.1002/jcla.22391] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/15/2017] [Accepted: 12/30/2017] [Indexed: 01/06/2023] Open
Abstract
BACKGROUND KRAS mutations are the key indicator for EGFR monoclonal antibody-targeted therapy and acquired drug resistance, and their accurate detection is critical to the clinical decision-making of colorectal cancer. However, no proper quality control material is available for the current detection methods, particularly next-generation sequencing (NGS). The ideal quality control material for NGS needs to provide both the tumor mutation gene and the matched background genomic DNA, which is uncataloged in public databases, to accurately distinguish germline polymorphisms and somatic mutations. METHODS We developed a novel KRAS G12V mutant cell line using the clustered regularly interspaced short palindromic repeat (CRISPR)/CRISPR-associated protein 9 (Cas9) technique to make up for the deficiencies in existing quality control material and further validated the feasibility of the cell line as quality control material by amplification refractory mutation system (ARMS), Sanger sequencing, digital PCR (dPCR), and NGS. RESULTS We verified that the edited cell line specifically had the G12V mutation, and the validation results presented a high consistency among the four methods of detection. The three cell lines screened contained the G12V mutation and the mutation allele fractions of G12V-1, G12V-2, and G12V-3 were 52.01%, 82.06%, and 17.29%, respectively. CONCLUSION The novel KRAS G12V cell line generated using the CRISPR/Cas9 gene editing system is suitable as a quality control material for all current detection methods and provides a new direction in the development of quality control material.
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Affiliation(s)
- Shiyu Jia
- Peking University Fifth School of Clinical Medicine, National Center for Clinical Laboratories, National Center of Gerontology, Beijing Hospital, Beijing, China.,National Center for Clinical Laboratories, National Center of Gerontology, Beijing Hospital, Beijing, China.,Beijing Engineering Research Center of Laboratory Medicine, Beijing Hospital, Beijing, China
| | - Rui Zhang
- National Center for Clinical Laboratories, National Center of Gerontology, Beijing Hospital, Beijing, China.,Beijing Engineering Research Center of Laboratory Medicine, Beijing Hospital, Beijing, China
| | - Guigao Lin
- National Center for Clinical Laboratories, National Center of Gerontology, Beijing Hospital, Beijing, China.,Beijing Engineering Research Center of Laboratory Medicine, Beijing Hospital, Beijing, China
| | - Rongxue Peng
- National Center for Clinical Laboratories, National Center of Gerontology, Beijing Hospital, Beijing, China.,Beijing Engineering Research Center of Laboratory Medicine, Beijing Hospital, Beijing, China.,Graduate School, Chinese Academy of Medical Sciences, Peking Union Medical College, Beijing, China
| | - Peng Gao
- National Center for Clinical Laboratories, National Center of Gerontology, Beijing Hospital, Beijing, China.,Beijing Engineering Research Center of Laboratory Medicine, Beijing Hospital, Beijing, China.,Graduate School, Chinese Academy of Medical Sciences, Peking Union Medical College, Beijing, China
| | - Yanxi Han
- National Center for Clinical Laboratories, National Center of Gerontology, Beijing Hospital, Beijing, China.,Beijing Engineering Research Center of Laboratory Medicine, Beijing Hospital, Beijing, China
| | - Yu Fu
- National Center for Clinical Laboratories, National Center of Gerontology, Beijing Hospital, Beijing, China.,Beijing Engineering Research Center of Laboratory Medicine, Beijing Hospital, Beijing, China.,Graduate School, Chinese Academy of Medical Sciences, Peking Union Medical College, Beijing, China
| | - Jiansheng Ding
- National Center for Clinical Laboratories, National Center of Gerontology, Beijing Hospital, Beijing, China.,Beijing Engineering Research Center of Laboratory Medicine, Beijing Hospital, Beijing, China.,Graduate School, Chinese Academy of Medical Sciences, Peking Union Medical College, Beijing, China
| | - Qisheng Wu
- National Center for Clinical Laboratories, National Center of Gerontology, Beijing Hospital, Beijing, China.,Beijing Engineering Research Center of Laboratory Medicine, Beijing Hospital, Beijing, China.,Graduate School, Chinese Academy of Medical Sciences, Peking Union Medical College, Beijing, China
| | - Kuo Zhang
- National Center for Clinical Laboratories, National Center of Gerontology, Beijing Hospital, Beijing, China.,Beijing Engineering Research Center of Laboratory Medicine, Beijing Hospital, Beijing, China
| | - Jiehong Xie
- National Center for Clinical Laboratories, National Center of Gerontology, Beijing Hospital, Beijing, China.,Beijing Engineering Research Center of Laboratory Medicine, Beijing Hospital, Beijing, China
| | - Jinming Li
- Peking University Fifth School of Clinical Medicine, National Center for Clinical Laboratories, National Center of Gerontology, Beijing Hospital, Beijing, China.,National Center for Clinical Laboratories, National Center of Gerontology, Beijing Hospital, Beijing, China.,Beijing Engineering Research Center of Laboratory Medicine, Beijing Hospital, Beijing, China
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22
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First-decade patient with colorectal cancer carrying both germline and somatic mutations in APC gene. BMC Cancer 2017; 17:849. [PMID: 29237421 PMCID: PMC5729288 DOI: 10.1186/s12885-017-3878-0] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/10/2016] [Accepted: 12/05/2017] [Indexed: 01/05/2023] Open
Abstract
Background Colorectal carcinoma (CRC) is one of the most common causes of cancer-related deaths. The mean age of patients with CRC ranges from 49 to 60 years. Pediatric CRC is unusual, which often escapes early diagnosis because of a lack of awareness of its occurrence in children. The association between the mutation of APC and the occurrence of CRC in the first decade of life remains unknown. Case presentation We report a 10-year-old child with CRC; he was diagnosed with stage IIIB advanced transverse colon cancer without distal metastases. We detected a heterozygous germline mutation at c.5465 T > A in both blood and tissue samples and a heterozygous somatic mutation at c.7397C > T in the tissue sample. Both of these mutations can cause CRC tumorigenesis in the first decade of life. Conclusions The rare genetic features of this 10-year-old patient might be the predisposing cause of pediatric CRC. Therefore, screening patients with early-onset CRC through clinical and genetic characterizations is suggested.
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23
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Słomka M, Sobalska-Kwapis M, Wachulec M, Bartosz G, Strapagiel D. High Resolution Melting (HRM) for High-Throughput Genotyping-Limitations and Caveats in Practical Case Studies. Int J Mol Sci 2017; 18:ijms18112316. [PMID: 29099791 PMCID: PMC5713285 DOI: 10.3390/ijms18112316] [Citation(s) in RCA: 59] [Impact Index Per Article: 8.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/07/2017] [Revised: 10/06/2017] [Accepted: 10/31/2017] [Indexed: 01/02/2023] Open
Abstract
High resolution melting (HRM) is a convenient method for gene scanning as well as genotyping of individual and multiple single nucleotide polymorphisms (SNPs). This rapid, simple, closed-tube, homogenous, and cost-efficient approach has the capacity for high specificity and sensitivity, while allowing easy transition to high-throughput scale. In this paper, we provide examples from our laboratory practice of some problematic issues which can affect the performance and data analysis of HRM results, especially with regard to reference curve-based targeted genotyping. We present those examples in order of the typical experimental workflow, and discuss the crucial significance of the respective experimental errors and limitations for the quality and analysis of results. The experimental details which have a decisive impact on correct execution of a HRM genotyping experiment include type and quality of DNA source material, reproducibility of isolation method and template DNA preparation, primer and amplicon design, automation-derived preparation and pipetting inconsistencies, as well as physical limitations in melting curve distinction for alternative variants and careful selection of samples for validation by sequencing. We provide a case-by-case analysis and discussion of actual problems we encountered and solutions that should be taken into account by researchers newly attempting HRM genotyping, especially in a high-throughput setup.
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Affiliation(s)
- Marcin Słomka
- Biobank Lab, Department of Molecular Biophysics, Faculty of Biology and Environmental Protection, University of Łódź, Pilarskiego 14/16, 90-231 Łódź, Poland.
- BBMRI.pl Consortium, 54-066 Wrocław, Poland.
| | - Marta Sobalska-Kwapis
- Biobank Lab, Department of Molecular Biophysics, Faculty of Biology and Environmental Protection, University of Łódź, Pilarskiego 14/16, 90-231 Łódź, Poland.
- BBMRI.pl Consortium, 54-066 Wrocław, Poland.
| | - Monika Wachulec
- Department of Molecular Biophysics, Faculty of Biology and Environmental Protection, University of Łódź, Pomorska 141/143, 90-236 Łódź, Poland.
| | - Grzegorz Bartosz
- Department of Molecular Biophysics, Faculty of Biology and Environmental Protection, University of Łódź, Pomorska 141/143, 90-236 Łódź, Poland.
| | - Dominik Strapagiel
- Biobank Lab, Department of Molecular Biophysics, Faculty of Biology and Environmental Protection, University of Łódź, Pilarskiego 14/16, 90-231 Łódź, Poland.
- BBMRI.pl Consortium, 54-066 Wrocław, Poland.
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24
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Fujiyoshi K, Yamaguchi T, Kakuta M, Takahashi A, Arai Y, Yamada M, Yamamoto G, Ohde S, Takao M, Horiguchi SI, Natsume S, Kazama S, Nishizawa Y, Nishimura Y, Akagi Y, Sakamoto H, Akagi K. Predictive model for high-frequency microsatellite instability in colorectal cancer patients over 50 years of age. Cancer Med 2017; 6:1255-1263. [PMID: 28544821 PMCID: PMC5463087 DOI: 10.1002/cam4.1088] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/30/2017] [Revised: 04/02/2017] [Accepted: 04/09/2017] [Indexed: 12/19/2022] Open
Abstract
Microsatellite instability (MSI) is an important biomarker for screening for Lynch syndrome, and also of response to immune checkpoint inhibitors. The aim of this study is to create a predictive model to determine which elderly patients with colorectal cancer (CRC) should undergo MSI and/or immunohistochemistry testing on the basis of clinicopathological data. We analyzed a test cohort of CRC patients aged ≥50 years (n = 2219) by multivariate logistic regression analyses to identify predictors of high‐frequency MSI (MSI‐H). The created prediction model was validated in an external cohort (n = 992). The frequency of MSI‐H was 5.5% among CRC patients aged ≥ 50 years. The following five predictors of MSI‐H were identified in the test cohort: female (1 point), mucinous component (2 points), tumor size ≥ 60 mm (2 points), location in proximal colon (3 points), and BRAF mutation (6 points). The area under curve (AUC) in the receiver‐operating characteristic (ROC) analysis of this prediction model was 0.832 (95% confidence interval: 0.790–0.874). The sensitivity and specificity were 74.4% and 77.7%, respectively, for a cut‐off score of 4 points. The receiver‐operating characteristic curve of the validation cohort also showed an AUC of 0.856 (95% CI: 0.806–0.905). This prediction model is useful to select elderly CRC patients who should undergo MSI testing, and who may benefit from treatment with 5‐FU‐based adjuvant chemotherapy and cancer immunotherapy.
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Affiliation(s)
- Kenji Fujiyoshi
- Division of Molecular Diagnosis and Cancer Prevention, Saitama Cancer Center, Saitama, Japan.,Department of Surgery, Kurume University, Fukuoka, Japan
| | - Tatsuro Yamaguchi
- Department of Surgery, Tokyo Metropolitan Cancer and Infectious Diseases Center Komagome Hospital, Tokyo, Japan.,Hereditary Tumor Research Project, Tokyo Metropolitan Cancer and Infectious Diseases Center Komagome Hospital, Tokyo, Japan
| | - Miho Kakuta
- Division of Molecular Diagnosis and Cancer Prevention, Saitama Cancer Center, Saitama, Japan
| | - Akemi Takahashi
- Division of Molecular Diagnosis and Cancer Prevention, Saitama Cancer Center, Saitama, Japan
| | - Yoshiko Arai
- Division of Molecular Diagnosis and Cancer Prevention, Saitama Cancer Center, Saitama, Japan
| | - Mina Yamada
- Division of Molecular Diagnosis and Cancer Prevention, Saitama Cancer Center, Saitama, Japan
| | - Gou Yamamoto
- Division of Molecular Diagnosis and Cancer Prevention, Saitama Cancer Center, Saitama, Japan
| | - Sachiko Ohde
- Center for Clinical Epidemiology, Graduate School of Public Health Planning Office, St. Luke's International University, OMURA Susumu & Mieko Memorial, St. Luke's Center for Clinical Academia, Tokyo, Japan
| | - Misato Takao
- Department of Surgery, Tokyo Metropolitan Cancer and Infectious Diseases Center Komagome Hospital, Tokyo, Japan.,Department of Digestive Tract and General Surgery, Saitama Medical Center, Saitama Medical University, Saitama, Japan
| | - Shin-Ichiro Horiguchi
- Department of Pathology, Tokyo Metropolitan Cancer and Infectious Diseases Center Komagome Hospital, Tokyo, Japan
| | - Soichiro Natsume
- Department of Surgery, Tokyo Metropolitan Cancer and Infectious Diseases Center Komagome Hospital, Tokyo, Japan
| | - Shinsuke Kazama
- Division of Gastroenterological Surgery, Saitama Cancer Center, Saitama, Japan
| | - Yusuke Nishizawa
- Division of Gastroenterological Surgery, Saitama Cancer Center, Saitama, Japan
| | - Yoji Nishimura
- Division of Gastroenterological Surgery, Saitama Cancer Center, Saitama, Japan
| | - Yoshito Akagi
- Department of Surgery, Kurume University, Fukuoka, Japan
| | - Hirohiko Sakamoto
- Division of Gastroenterological Surgery, Saitama Cancer Center, Saitama, Japan
| | - Kiwamu Akagi
- Division of Molecular Diagnosis and Cancer Prevention, Saitama Cancer Center, Saitama, Japan
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25
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Obliosca JM, Cheng SY, Chen YA, Llanos MF, Liu YL, Imphean DM, Bell DR, Petty JT, Ren P, Yeh HC. LNA Thymidine Monomer Enables Differentiation of the Four Single-Nucleotide Variants by Melting Temperature. J Am Chem Soc 2017; 139:7110-7116. [PMID: 28463488 DOI: 10.1021/jacs.7b03395] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022]
Abstract
High-resolution melting (HRM) analysis of DNA is a closed-tube single-nucleotide polymorphism (SNP) detection method that has shown many advantages in point-of-care diagnostics and personalized medicine. While recently developed melting probes have demonstrated significantly improved discrimination of mismatched (mutant) alleles from matched (wild-type) alleles, no effort has been made to design a simple melting probe that can reliably distinguish all four SNP alleles in a single experiment. Such a new probe could facilitate the discovery of rare genetic mutations at lower cost. Here we demonstrate that a melting probe embedded with a single locked thymidine monomer (tL) can reliably differentiate the four SNP alleles by four distinct melting temperatures (termed the "4Tm probe"). This enhanced discriminatory power comes from the decreased melting temperature of the tL·C mismatched hybrid as compared to that of the t·C mismatched hybrid, while the melting temperatures of the tL-A, tL·G and tL·T hybrids are increased or remain unchanged as compared to those of their canonical counterparts. This phenomenon is observed not only in the HRM experiments but also in the molecular dynamics simulations.
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Affiliation(s)
- Judy M Obliosca
- Department of Biomedical Engineering, Cockrell School of Engineering, University of Texas at Austin , Austin, Texas 78712, United States
| | - Sara Y Cheng
- Department of Physics, College of Natural Sciences, University of Texas at Austin , Austin, Texas 78712, United States
| | - Yu-An Chen
- Department of Biomedical Engineering, Cockrell School of Engineering, University of Texas at Austin , Austin, Texas 78712, United States
| | - Mariana F Llanos
- Department of Chemistry, Department of Chemistry, Furman University , Greenville, South Carolina 29613, United States
| | - Yen-Liang Liu
- Department of Biomedical Engineering, Cockrell School of Engineering, University of Texas at Austin , Austin, Texas 78712, United States
| | - Darren M Imphean
- Department of Biomedical Engineering, Cockrell School of Engineering, University of Texas at Austin , Austin, Texas 78712, United States
| | - David R Bell
- Department of Biomedical Engineering, Cockrell School of Engineering, University of Texas at Austin , Austin, Texas 78712, United States
| | - Jeffrey T Petty
- Department of Chemistry, Department of Chemistry, Furman University , Greenville, South Carolina 29613, United States
| | - Pengyu Ren
- Department of Biomedical Engineering, Cockrell School of Engineering, University of Texas at Austin , Austin, Texas 78712, United States
| | - Hsin-Chih Yeh
- Department of Biomedical Engineering, Cockrell School of Engineering, University of Texas at Austin , Austin, Texas 78712, United States
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26
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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: 40] [Impact Index Per Article: 5.0] [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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Kudryavtseva AV, Lipatova AV, Zaretsky AR, Moskalev AA, Fedorova MS, Rasskazova AS, Shibukhova GA, Snezhkina AV, Kaprin AD, Alekseev BY, Dmitriev AA, Krasnov GS. Important molecular genetic markers of colorectal cancer. Oncotarget 2016; 7:53959-53983. [PMID: 27276710 PMCID: PMC5288236 DOI: 10.18632/oncotarget.9796] [Citation(s) in RCA: 78] [Impact Index Per Article: 9.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/21/2015] [Accepted: 05/21/2016] [Indexed: 02/06/2023] Open
Abstract
Colorectal cancer (CRC) ranks third in the incidences of cancer morbidity and mortality worldwide. CRC is rather heterogeneous with regard to molecular genetic characteristics and pathogenic pathways. A wide spectrum of biomarkers is used for molecular subtype determination, prognosis, and estimation of sensitivity to different drugs in practice. These biomarkers can include germline and somatic mutations, chromosomal aberrations, genomic abnormalities, gene expression alterations at mRNA or protein level and changes in DNA methylation status. In the present review we discuss the most important and well-studied CRC biomarkers, and their potential clinical significance and current approaches to molecular classification of colorectal tumors.
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Affiliation(s)
- Anna V. Kudryavtseva
- Engelhardt Institute of Molecular Biology, Russian Academy of Sciences, Moscow, Russia
- National Medical Research Radiological Centre, Ministry of Healthcare of the Russian Federation, Moscow, Russia
| | - Anastasia V. Lipatova
- Engelhardt Institute of Molecular Biology, Russian Academy of Sciences, Moscow, Russia
| | - Andrew R. Zaretsky
- Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry, Russian Academy of Sciences, Moscow, Russia
| | - Alexey A. Moskalev
- Engelhardt Institute of Molecular Biology, Russian Academy of Sciences, Moscow, Russia
| | - Maria S. Fedorova
- Engelhardt Institute of Molecular Biology, Russian Academy of Sciences, Moscow, Russia
- National Medical Research Radiological Centre, Ministry of Healthcare of the Russian Federation, Moscow, Russia
| | | | - Galina A. Shibukhova
- National Medical Research Radiological Centre, Ministry of Healthcare of the Russian Federation, Moscow, Russia
| | | | - Andrey D. Kaprin
- National Medical Research Radiological Centre, Ministry of Healthcare of the Russian Federation, Moscow, Russia
| | - Boris Y. Alekseev
- National Medical Research Radiological Centre, Ministry of Healthcare of the Russian Federation, Moscow, Russia
| | - Alexey A. Dmitriev
- Engelhardt Institute of Molecular Biology, Russian Academy of Sciences, Moscow, Russia
| | - George S. Krasnov
- Engelhardt Institute of Molecular Biology, Russian Academy of Sciences, Moscow, Russia
- Orekhovich Institute of Biomedical Chemistry, Russian Academy of Medical Sciences, Moscow, Russia
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Rapid Identification of FGFR2 Gene Mutations in Taiwanese Patients With Endometrial Cancer Using High-resolution Melting Analysis. Appl Immunohistochem Mol Morphol 2016; 23:532-7. [PMID: 25517871 DOI: 10.1097/pai.0000000000000114] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/04/2023]
Abstract
OBJECTIVES Mutations in fibroblast growth factor receptor 2 (FGFR2) gene have been reported in endometrial cancer and mutant FGFR2 has been pointed out as a potential therapeutic target. The aim of the current study was to use a high-resolution melting (HRM) analysis to identify FGFR2 hotspot mutations and to investigate the occurrence of these mutations in the Taiwanese population with endometrial cancer. DESIGN AND METHODS HRM analysis was designed to characterize the FGFR2 hotspot mutations. DNAs were extracted from 72 cases of fresh-frozen endometrial cancer tissues for FGFR2 mutational analysis by HRM analysis. The 6 exons of FGFR2 were screened by HRM analysis. All results were confirmed by direct sequencing. RESULTS We have identified the 6 reported mutations in the FGFR2 gene. The mutation c.879C>T (p.Q289P) was first reported in endometrial cancer. Each mutation could be readily and accurately identified in the difference plot curves. The frequency of FGFR2 hotspot mutations is 9.7% (7/72) in patients with endometrial cancer in the Taiwanese population. CONCLUSIONS HRM analysis is rapid, feasible, and a reliable diagnostic method for the detection of FGFR2 mutations in a clinical setting. Our results indicated the prevalence of FGFR2 mutational status in the Taiwanese population with endometrial cancer.
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koochak A, Rakhshani N, Niya MHK, Tameshkel FS, Sohrabi MR, Babaee MR, Rezvani H, Bahar B, Imanzade F, Zamani F, Khonsari MR, Ajdarkosh H, Hemmasi G. Mutation Analysis of KRAS and BRAF Genes in Metastatic Colorectal Cancer: a First Large Scale Study from Iran. Asian Pac J Cancer Prev 2016; 17:603-8. [DOI: 10.7314/apjcp.2016.17.2.603] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022] Open
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Chang YC, Chang JG, Liu TC, Lin CY, Yang SF, Ho CM, Chen WTL, Chang YS. Mutation analysis of 13 driver genes of colorectal cancer-related pathways in Taiwanese patients. World J Gastroenterol 2016; 22:2314-2325. [PMID: 26900293 PMCID: PMC4735005 DOI: 10.3748/wjg.v22.i7.2314] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 06/14/2015] [Revised: 10/28/2015] [Accepted: 12/01/2015] [Indexed: 02/06/2023] Open
Abstract
AIM: To investigate the driver gene mutations associated with colorectal cancer (CRC) in the Taiwanese population.
METHODS: In this study, 103 patients with CRC were evaluated. The samples consisted of 66 men and 37 women with a median age of 59 years and an age range of 26-86 years. We used high-resolution melting analysis (HRM) and direct DNA sequencing to characterize the mutations in 13 driver genes of CRC-related pathways. The HRM assays were conducted using the LightCycler® 480 Instrument provided with the software LightCycler® 480 Gene Scanning Software Version 1.5. We also compared the clinicopathological data of CRC patients with the driver gene mutation status.
RESULTS: Of the 103 patients evaluated, 73.79% had mutations in one of the 13 driver genes. We discovered 18 novel mutations in APC, MLH1, MSH2, PMS2, SMAD4 and TP53 that have not been previously reported. Additionally, we found 16 de novo mutations in APC, BMPR1A, MLH1, MSH2, MSH6, MUTYH and PMS2 in cancerous tissues previously reported in the dbSNP database; however, these mutations could not be detected in peripheral blood cells. The APC mutation correlates with lymph node metastasis (34.69% vs 12.96%, P = 0.009) and cancer stage (34.78% vs 14.04%, P = 0.013). No association was observed between other driver gene mutations and clinicopathological features. Furthermore, having two or more driver gene mutations correlates with the degree of lymph node metastasis (42.86% vs 24.07%, P = 0.043).
CONCLUSION: Our findings confirm the importance of 13 CRC-related pathway driver genes in the development of CRC in Taiwanese patients.
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Molecular spectrum of KRAS, NRAS, BRAF and PIK3CA mutations in Chinese colorectal cancer patients: analysis of 1,110 cases. Sci Rep 2015; 5:18678. [PMID: 26691448 PMCID: PMC4687048 DOI: 10.1038/srep18678] [Citation(s) in RCA: 82] [Impact Index Per Article: 9.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/11/2015] [Accepted: 11/23/2015] [Indexed: 02/07/2023] Open
Abstract
Mutations in genes such as KRAS, NRAS, BRAF and PIK3CA have become an important part of colorectal carcinoma evaluation. The aim of this study was to screen for mutations in these genes in Chinese patients with colorectal cancer (CRC) and to explore their correlations with certain clinicopathological parameters. We tested mutations in the KRAS (exons 2, 3 and 4), NRAS (exons 2, 3 and 4), PIK3CA (exon 20) and BRAF (exon 15) genes using reverse transcriptase-polymerase chain reaction (RT-PCR) and Sanger sequencing in a large cohort of 1,110 Chinese CRC patients who underwent surgical resection at one of three major teaching hospitals located in different regions of China. The prevalence rates of KRAS, NRAS, BRAF and PIK3CA mutations were 45.4%, 3.9%, 3.1% and 3.5%, respectively. Mutant KRAS was associated with the mucinous subtype and greater differentiation, while mutant BRAF was associated with right-sided tumors and poorer differentiation. Our results revealed differences in the genetic profiles of KRAS, NRAS, PIK3CA and BRAF at mutation hotspots between Chinese CRC patients and those of Western countries, while some of these gene features were shared among patients from other Asian countries.
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Ye JX, Liu Y, Qin Y, Zhong HH, Yi WN, Shi XY. KRAS and BRAF gene mutations and DNA mismatch repair status in Chinese colorectal carcinoma patients. World J Gastroenterol 2015; 21:1595-1605. [PMID: 25663779 PMCID: PMC4316102 DOI: 10.3748/wjg.v21.i5.1595] [Citation(s) in RCA: 47] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 07/17/2014] [Revised: 10/28/2014] [Accepted: 12/08/2014] [Indexed: 02/06/2023] Open
Abstract
AIM: To investigate gene mutations and DNA mismatch repair (MMR) protein abnormality in Chinese colorectal carcinoma (CRC) patients and their correlations with clinicopathologic features.
METHODS: Clinical and pathological information for 535 patients including 538 tumors was reviewed and recorded. Mutation analyses for exon 2 of KRAS gene and exon 15 of BRAF gene were performed by Sanger sequencing except that in 9 tumors amplification refractory mutation system PCR was used. Expression of MMR proteins including MHL1, MSH2, MSH6 and PMS2 was evaluated by immunohistochemistry. Correlations of KRAS and BRAF mutation status and the expression status of MMR proteins with age, gender, cancer stage, location, and histology were analyzed. Correlations between KRAS or BRAF mutations and MMR protein expression were also explored.
RESULTS: The overall frequencies of KRAS and BRAF mutations were 37.9% and 4.4%, respectively. KRAS mutations were more common in patients ≥ 50 years old (39.8% vs 22% in patients < 50 years old, P < 0.05). The frequencies of BRAF mutants were higher in tumors from females (6.6% vs males 2.8%, P < 0.05), located in the right colon (9.6% vs 2.1% in the left colon, 1.8% in the rectum, P < 0.01), with mucinous differentiation (9.8% vs 2.8% without mucinous differentiation, P < 0.01), or being poorly differentiated (9.5% vs 3.4% well/moderately differentiated, P < 0.05). MMR deficiency was strongly associated with proximal location (20.5% in the right colon vs 9.2% in the left colon and 5.1% in the rectum, P < 0.001), early cancer stage (15.0% in stages I-II vs 7.7% in stages III-IV, P < 0.05), and mucinous differentiation (20.2% vs 9.2% without mucin, P < 0.01). A higher frequency of MLH1/PMS2 loss was found in females (9.2% vs 4.4% in males, P < 0.05), and MSH2/MSH6 loss tended to be seen in younger (<50 years old) patients (12.0% vs 4.0% ≥ 50 years old, P < 0.05). MMR deficient tumors were less likely to have KRAS mutations (18.8% vs 41.7% in MMR proficient tumors, P < 0.05) and tumors with abnormal MLH1/PMS2 tended to harbor BRAF mutations (15.4% vs 4.2% in MMR proficient tumors, P < 0.05).
CONCLUSION: The frequency of sporadic CRCs having BRAF mutation, MLH1 deficiency and MSI in Chinese population may be lower than that in the Western population.
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BRAF V600E mutation and KRAS codon 13 mutations predict poor survival in Chinese colorectal cancer patients. BMC Cancer 2014; 14:802. [PMID: 25367198 PMCID: PMC4233032 DOI: 10.1186/1471-2407-14-802] [Citation(s) in RCA: 43] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/27/2014] [Accepted: 10/17/2014] [Indexed: 11/25/2022] Open
Abstract
Background Mutations in KRAS, BRAF and PIK3CA are the most common somatic alterations found in the colorectal cancer (CRC) patients from Western countries; but their prevalence and prognostic value have not been adequately assessed in Asian patients. The aim of this study was to determine the mutation frequencies of these genes in Chinese CRC patients and to investigate their impact on prognosis. Methods The sequences of exon 2 of KRAS, exon 15 of BRAF and exons 9 and 20 of PIK3CA were evaluated by PCR and direct sequencing using DNA extracted from formalin-fixed paraffin-embedded (FFPE) tissues from primary CRC tumors of 214 patients (colon/rectum: 126/88). Results KRAS, BRAF and PIK3CA mutations were identified in 44.9% (96/214), 4.2% (9/214) and 12.3% (26/212) CRCs, respectively. The most frequent mutations in KRAS, BRAF and PIK3CA were G12D, V600E and H1047R, respectively. All BRAF and 80.8% PIK3CA mutations were from colon cancer patients. BRAF V600E was associated with advanced TNM (P < 0.001), more distant metastases (P = 0.025), and worse overall survival (OS, P < 0.001; multivariate HR = 4.2, P = 0.004) in colon cancer patients. Compared with KRAS wt/BRAF wt CRC patients (N = 109), those with KRAS codon 13 mutations (N = 25) had significantly worse OS (P = 0.016; multivariate HR = 2.7, P = 0.011), whereas KRAS codon 12-mutated cases were not significantly associated with survival. Among the three most common KRAS mutations, G13D (N = 23) showed significant association with poor OS (P = 0.024; multivariate HR = 2.6, P = 0.016) compared with KRAS wt/BRAF wt patients. Conclusion Our findings indicate that PI3K/RAS-RAF signaling pathway genes are frequently mutated in Chinese CRC patients, but have different characteristics than found in Western patients. BRAF V600E is an independent prognostic factor for Chinese patients. Our finding that KRAS codon 13 mutations (in particular G13D) are associated with inferior survival in BRAF wild-type CRCs in Chinese patients was not reported thus far. Our data emphasizes the importance of prospective evaluation of molecular features in CRC patients, because a single mutation type may represent a distinct biologic effect and clinical implication. Electronic supplementary material The online version of this article (doi:10.1186/1471-2407-14-802) contains supplementary material, which is available to authorized users.
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Li L, Ma BB. Colorectal cancer in Chinese patients: current and emerging treatment options. Onco Targets Ther 2014. [PMID: 25336973 DOI: 10.2147/ott.s48409ott-7-1817] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022] Open
Abstract
Colorectal cancer is the second most common cancer in Hong Kong and its incidence is rising in economically developed Chinese cities, including Hong Kong and Shanghai. Several studies conducted in the People's Republic of China have characterized the unique molecular epidemiology of familial colorectal cancer syndromes and molecular biomarkers such as microsatellite instability and genetic mutations (eg, KRAS, NRAS, BRAF, PIK3CA, ERCC1) in Chinese populations. Interethnic differences in anticancer drug response and toxicity have been well described in many cancers, and this review examined the literature with regard to the tolerance of Chinese patients to commonly used chemotherapeutic regimens and targeted therapies for metastatic colorectal cancer. Studies on the pharmacogenomic differences in drug metabolizing and DNA repair enzymes between Chinese, North Asians, and Caucasian patients were also reviewed.
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Affiliation(s)
- Leung Li
- Department of Clinical Oncology, Prince of Wales Hospital, Hong Kong Cancer Institute, Sha Tin, Hong Kong
| | - Brigette By Ma
- Department of Clinical Oncology, Prince of Wales Hospital, Hong Kong Cancer Institute, Sha Tin, Hong Kong ; State Key Laboratory of South China, Sir YK Pao Cancer Center, Hong Kong Cancer Institute, Sha Tin, Hong Kong
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Li L, Ma BBY. Colorectal cancer in Chinese patients: current and emerging treatment options. Onco Targets Ther 2014; 7:1817-28. [PMID: 25336973 PMCID: PMC4199792 DOI: 10.2147/ott.s48409] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/15/2023] Open
Abstract
Colorectal cancer is the second most common cancer in Hong Kong and its incidence is rising in economically developed Chinese cities, including Hong Kong and Shanghai. Several studies conducted in the People's Republic of China have characterized the unique molecular epidemiology of familial colorectal cancer syndromes and molecular biomarkers such as microsatellite instability and genetic mutations (eg, KRAS, NRAS, BRAF, PIK3CA, ERCC1) in Chinese populations. Interethnic differences in anticancer drug response and toxicity have been well described in many cancers, and this review examined the literature with regard to the tolerance of Chinese patients to commonly used chemotherapeutic regimens and targeted therapies for metastatic colorectal cancer. Studies on the pharmacogenomic differences in drug metabolizing and DNA repair enzymes between Chinese, North Asians, and Caucasian patients were also reviewed.
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Affiliation(s)
- Leung Li
- Department of Clinical Oncology, Prince of Wales Hospital, Hong Kong Cancer Institute, Sha Tin, Hong Kong
| | - Brigette BY Ma
- Department of Clinical Oncology, Prince of Wales Hospital, Hong Kong Cancer Institute, Sha Tin, Hong Kong
- State Key Laboratory of South China, Sir YK Pao Cancer Center, Hong Kong Cancer Institute, Sha Tin, Hong Kong
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Bisht S, Ahmad F, Sawaimoon S, Bhatia S, Das BR. Molecular spectrum of KRAS, BRAF, and PIK3CA gene mutation: determination of frequency, distribution pattern in Indian colorectal carcinoma. Med Oncol 2014; 31:124. [PMID: 25073438 DOI: 10.1007/s12032-014-0124-3] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/17/2014] [Accepted: 07/05/2014] [Indexed: 12/20/2022]
Abstract
Molecular evaluation of KRAS, BRAF, and PIK3CA mutation has become an important part in colorectal carcinoma evaluation, and their alterations may determine the therapeutic response to anti-EGFR therapy. The current study demonstrates the evaluation of KRAS, BRAF, and PIK3CA mutation using direct sequencing in 204 samples. The frequency of KRAS, BRAF, and PIK3CA mutations was 23.5, 9.8, and 5.9 %, respectively. Five different substitution mutations at KRAS codon 12 (G12S, G12D, G12A, G12V, and G12C) and one substitution type at codon 13 (G13D) were observed. KRAS mutations were significantly higher in patients who were >50 years, and were associated with moderate/poorly differentiated tumors and adenocarcinomas. All mutations in BRAF gene were of V600E type, which were frequent in patients who were ≤ 50 years. Unlike KRAS mutations, BRAF mutations were more frequent in well-differentiated tumors and right-sided tumors. PIK3CA-E545K was the most recurrent mutation while other mutations detected were T544I, Q546R, H1047R, G1049S, and D1056N. No significant association of PIK3CA mutation with age, tumor differentiation, location, and other parameters was noted. No concomitant mutation of KRAS and BRAF mutations was observed, while, interestingly, five cases showed concurrent mutation of KRAS and PIK3CA mutations. In conclusion, to our knowledge, this is the first study to evaluate the PIK3CA mutation in Indian CRC patients. The frequency of KRAS, BRAF, and PIK3CA was similar to worldwide reports. Furthermore, identification of molecular markers has unique strengths, and can provide insights into the pathogenic process and help optimize personalized prevention and therapy.
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Affiliation(s)
- Swati Bisht
- Research and Development, SRL Limited, Plot No 1, Prime Square Building, S.V. Road, Goregaon (W), Mumbai, 400062, India
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Siraj AK, Bu R, Prabhakaran S, Bavi P, Beg S, Al Hazmi M, Al-Rasheed M, Alobaisi K, Al-Dayel F, AlManea H, Al-Sanea N, Uddin S, Al-Kuraya KS. A very low incidence of BRAF mutations in Middle Eastern colorectal carcinoma. Mol Cancer 2014; 13:168. [PMID: 25005754 PMCID: PMC4109832 DOI: 10.1186/1476-4598-13-168] [Citation(s) in RCA: 29] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/27/2014] [Accepted: 06/24/2014] [Indexed: 02/08/2023] Open
Abstract
Background Recent studies emphasize the role of BRAF as a genetic marker for prediction, prognosis and risk stratification in colorectal cancer. Earlier studies have reported the incidence of BRAF mutations in the range of 5-20% in colorectal carcinomas (CRC) and are predominantly seen in the serrated adenoma-carcinoma pathway characterized by microsatellite instability (MSI-H) and hypermethylation of the MLH1 gene in the setting of the CpG island methylator phenotype (CIMP). Due to the lack of data on the true incidence of BRAF mutations in Saudi Arabia, we sought to analyze the incidence of BRAF mutations in this ethnic group. Methods 770 CRC cases were analyzed for BRAF and KRAS mutations by direct DNA sequencing. Results BRAF gene mutations were seen in 2.5% (19/757) CRC analyzed and BRAF V600E somatic mutation constituted 90% (17/19) of all BRAF mutations. BRAF mutations were significantly associated with right sided tumors (p = 0.0019), MSI-H status (p = 0.0144), CIMP (p = 0.0017) and a high proliferative index of Ki67 expression (p = 0.0162). Incidence of KRAS mutations was 28.6% (216/755) and a mutual exclusivity was noted with BRAF mutations (p = 0.0518; a trend was seen). Conclusion Our results highlight the low incidence of BRAF mutations and CIMP in CRC from Saudi Arabia. This could be attributed to ethnic differences and warrant further investigation to elucidate the effect of other environmental and genetic factors. These findings indirectly suggest the possibility of a higher incidence of familial hereditary colorectal cancers especially Hereditary non polyposis colorectal cancer (HNPCC) syndrome /Lynch Syndrome (LS) in Saudi Arabia.
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Affiliation(s)
| | | | | | | | | | | | | | | | | | | | | | | | - Khawla S Al-Kuraya
- Human Cancer Genomic Research, Research Center, King Faisal Specialist Hospital and Research Center, MBC#98-16, P,O, Box 3354 Riyadh 11211, Saudi Arabia.
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Chang YS, Hsu HT, Ko YC, Yeh KT, Chang SJ, Lin CY, Chang JG. Combined mutational analysis of RAS, BRAF, PIK3CA, and TP53 genes in Taiwanese patients with oral squamous cell carcinoma. Oral Surg Oral Med Oral Pathol Oral Radiol 2014; 118:110-116.e1. [DOI: 10.1016/j.oooo.2014.03.016] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/02/2013] [Revised: 03/13/2014] [Accepted: 03/20/2014] [Indexed: 11/17/2022]
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Ogino S, Lochhead P, Giovannucci E, Meyerhardt JA, Fuchs CS, Chan AT. Discovery of colorectal cancer PIK3CA mutation as potential predictive biomarker: power and promise of molecular pathological epidemiology. Oncogene 2014; 33:2949-55. [PMID: 23792451 PMCID: PMC3818472 DOI: 10.1038/onc.2013.244] [Citation(s) in RCA: 104] [Impact Index Per Article: 10.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/21/2013] [Revised: 04/26/2013] [Accepted: 04/27/2013] [Indexed: 12/18/2022]
Abstract
Regular use of aspirin reduces incidence and mortality of various cancers, including colorectal cancer. Anticancer effect of aspirin represents one of the 'Provocative Questions' in cancer research. Experimental and clinical studies support a carcinogenic role for PTGS2 (cyclooxygenase-2), which is an important enzymatic mediator of inflammation, and a target of aspirin. Recent 'molecular pathological epidemiology' (MPE) research has shown that aspirin use is associated with better prognosis and clinical outcome in PIK3CA-mutated colorectal carcinoma, suggesting somatic PIK3CA mutation as a molecular biomarker that predicts response to aspirin therapy. The PI3K (phosphatidylinositol-4,5-bisphosphonate 3-kinase) enzyme has a pivotal role in the PI3K-AKT signaling pathway. Activating PIK3CA oncogene mutations are observed in various malignancies including breast cancer, ovarian cancer, brain tumor, hepatocellular carcinoma, lung cancer and colon cancer. The prevalence of PIK3CA mutations increases continuously from rectal to cecal cancers, supporting the 'colorectal continuum' paradigm, and an important interplay of gut microbiota and host immune/inflammatory reaction. MPE represents an interdisciplinary integrative science, conceptually defined as 'epidemiology of molecular heterogeneity of disease'. As exposome and interactome vary from person to person and influence disease process, each disease process is unique (the unique disease principle). Therefore, MPE concept and paradigm can extend to non-neoplastic diseases including diabetes mellitus, cardiovascular diseases, metabolic diseases, and so on. MPE research opportunities are currently limited by paucity of tumor molecular data in the existing large-scale population-based studies. However, genomic, epigenomic and molecular pathology testings (for example, analyses for microsatellite instability, MLH1 promoter CpG island methylation, and KRAS and BRAF mutations in colorectal tumors) are becoming routine clinical practices. In order for integrative molecular and population science to be routine practice, we must first reform education curricula by integrating both population and molecular biological sciences. As consequences, next-generation hybrid molecular biological and population scientists can advance science, moving closer to personalized precision medicine and health care.
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Affiliation(s)
- S Ogino
- 1] Department of Pathology, Brigham and Women's Hospital, Harvard Medical School, Boston, MA, USA [2] Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA, USA [3] Department of Epidemiology, Harvard School of Public Health, Boston, MA, USA
| | - P Lochhead
- Institute of Medical Sciences, University of Aberdeen, Aberdeen, UK
| | - E Giovannucci
- 1] Department of Epidemiology, Harvard School of Public Health, Boston, MA, USA [2] Department of Nutrition, Harvard School of Public Health, Boston, MA, USA [3] Channing Division of Network Medicine, Department of Medicine, Brigham and Women's Hospital, Harvard Medical School, Boston, MA, USA
| | - J A Meyerhardt
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA, USA
| | - C S Fuchs
- 1] Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA, USA [2] Channing Division of Network Medicine, Department of Medicine, Brigham and Women's Hospital, Harvard Medical School, Boston, MA, USA
| | - A T Chan
- 1] Channing Division of Network Medicine, Department of Medicine, Brigham and Women's Hospital, Harvard Medical School, Boston, MA, USA [2] Division of Gastroenterology, Massachusetts General Hospital, Boston, MA, USA
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Kim JH, Kang GH. Molecular and prognostic heterogeneity of microsatellite-unstable colorectal cancer. World J Gastroenterol 2014; 20:4230-4243. [PMID: 24764661 PMCID: PMC3989959 DOI: 10.3748/wjg.v20.i15.4230] [Citation(s) in RCA: 72] [Impact Index Per Article: 7.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 09/25/2013] [Revised: 01/30/2014] [Accepted: 02/20/2014] [Indexed: 02/06/2023] Open
Abstract
Colorectal cancers (CRCs) with a high level of microsatellite instability (MSI-H) are clinicopathologically distinct tumors characterized by predominance in females, proximal colonic localization, poor differentiation, mucinous histology, tumor-infiltrating lymphocytes, a Crohn’s-like lymphoid reaction and a favorable prognosis. In terms of their molecular features, MSI-H CRCs are heterogeneous tumors associated with various genetic and epigenetic alterations, including DNA mismatch repair deficiency, target microsatellite mutations, BRAF mutations, a CpG island methylator phenotype-high (CIMP-H) status, and a low level of genomic hypomethylation. The molecular heterogeneity of MSI-H CRCs also depends on ethnic differences; for example, in Eastern Asian countries, relatively low frequencies of CIMP-H and BRAF mutations have been observed in MSI-H CRCs compared to Western countries. Although the prognostic features of MSI-H CRCs include a favorable survival of patients and low benefit of adjuvant chemotherapy, there may be prognostic differences based on the molecular heterogeneity of MSI-H CRCs. Here, we have reviewed and discussed the molecular and prognostic features of MSI-H CRCs, as well as several putative prognostic or predictive molecular markers, including HSP110 expression, beta2-microglobulin mutations, myosin 1a expression, CDX2/CK20 expression, SMAD4 expression, CIMP status and LINE-1 methylation levels.
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Abstract
PIK3CA, the catalytic subunit of PI3K, is mutated in many different tumors, including colorectal cancer (CRC). Mutations of PIK3CA have been reported in 10–20% of CRC, about 80% of mutations found in two hot spots in exon 9 and exon 20. In RAS wild-type CRC, PIK3CA mutations have been associated with a worse clinical outcome and with a negative prediction of a response to targeted therapy by anti-EGFR monoclonal antibodies. However, these findings have not been confirmed in all studies and subsequent more detailed analysis has revealed that these effects may be restricted to mutations in Exon 20. Finally, mutations in PIK3CA may be the long sought biomarker for successful adjuvant therapy with aspirin in patients with CRC. Therefore, PIK3CA mutations appear to be a promising predictive biomarker; however, further data are needed to conclusively define the impact of somatic mutations in the PIK3CA gene for the management of patients with CRC.
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Affiliation(s)
- Gieri Cathomas
- Institut für Pathologie, Kantonsspital Baselland , Liestal , Switzerland
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Chen D, Wang YY, Chuai ZR, Huang JF, Wang YX, Liu K, Zhang LQ, Yang Z, Shi DC, Liu Q, Huang Q, Fu WL. High-resolution melting analysis for accurate detection of BRAF mutations: a systematic review and meta-analysis. Sci Rep 2014; 4:4168. [PMID: 24566771 PMCID: PMC3933866 DOI: 10.1038/srep04168] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/20/2013] [Accepted: 02/03/2014] [Indexed: 12/24/2022] Open
Abstract
The high-resolution melting curve analysis (HRMA) might be a good alternative method for rapid detection of BRAF mutations. However, the accuracy of HRMA in detection of BRAF mutations has not been systematically evaluated. We performed a systematic review and meta-analysis involving 1324 samples from 14 separate studies. The overall sensitivity of HRMA was 0.99 (95% confidence interval (CI) = 0.75–0.82), and the overall specificity was very high at 0.99 (95% CI = 0.94–0.98). The values for the pooled positive likelihood ratio, negative likelihood ratio, and diagnostic odds ratio were 68.01 (95% CI = 25.33–182.64), 0.06 (95% CI = 0.03–0.11), and1263.76 (95% CI = 393.91–4064.39), respectively. The summary receiver operating characteristic curve for the same data shows an area of 1.00 and a Q* value of 0.97. The high sensitivity and specificity, simplicity, low cost, less labor or time and rapid turnaround make HRMA a good alternative method for rapid detection of BRAF mutations in the clinical practice.
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Affiliation(s)
- Dong Chen
- Department of Laboratory Medicine, Southwest Hospital, Third Military Medical University, Chongqing, PR China
| | - Yan-Yan Wang
- Research and service centre of laboratory medicine, Chengdu Military general Hospital, Chengdu, PR China
| | - Zheng-Ran Chuai
- Department of Laboratory Medicine, Southwest Hospital, Third Military Medical University, Chongqing, PR China
| | - Jun-Fu Huang
- Department of Laboratory Medicine, Southwest Hospital, Third Military Medical University, Chongqing, PR China
| | - Yun-Xia Wang
- Department of Laboratory Medicine, Southwest Hospital, Third Military Medical University, Chongqing, PR China
| | - Kai Liu
- Research Center for Nutrition and Food Safety, Institute of Military Preventive Medicine, Third Military Medical University, Chongqing, PR China
| | - Li-Qun Zhang
- Department of Laboratory Medicine, Southwest Hospital, Third Military Medical University, Chongqing, PR China
| | - Zhao Yang
- Department of Laboratory Medicine, Southwest Hospital, Third Military Medical University, Chongqing, PR China
| | - Da-Chuan Shi
- Department of Laboratory Medicine, Southwest Hospital, Third Military Medical University, Chongqing, PR China
| | - Qian Liu
- Department of Laboratory Medicine, Southwest Hospital, Third Military Medical University, Chongqing, PR China
| | - Qing Huang
- Department of Laboratory Medicine, Southwest Hospital, Third Military Medical University, Chongqing, PR China
| | - Wei-Ling Fu
- Department of Laboratory Medicine, Southwest Hospital, Third Military Medical University, Chongqing, PR China
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Xue Q, Sun K, Deng HJ, Lei ST, Dong JQ, Li GX. Anti-miRNA-221 sensitizes human colorectal carcinoma cells to radiation by upregulating PTEN. World J Gastroenterol 2013; 19:9307-9317. [PMID: 24409057 PMCID: PMC3882403 DOI: 10.3748/wjg.v19.i48.9307] [Citation(s) in RCA: 40] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 08/14/2013] [Revised: 09/29/2013] [Accepted: 10/14/2013] [Indexed: 02/06/2023] Open
Abstract
AIM: To investigate the regulative effect of miRNA (miR)-221 on colorectal carcinoma (CRC) cell radiosensitivity and the underlying mechanisms.
METHODS: A human CRC-derived cell line was cultured conventionally and exposed to different doses of X-rays (0, 2, 4, 6 and 8 Gy). The total RNA and protein of the cells were extracted 24 h after irradiation, and the alteration of miR-221 and phosphatase and tensin homolog deleted on chromosome 10 (PTEN) gene mRNA expression was detected by real-time reverse transcriptase polymerase chain reaction (PCR). The protein alteration of PTEN in the cells was detected by Western blotting. Caco2 cells were pretreated with or without anti-PTEN-siRNA prior to the addition of pre-miR-221 or anti-miR-221 using Lipofectamine 2000. Colony formation assay and flow cytometry analysis were used to measure the surviving cell fraction and the sensitizing enhancement ratio after irradiation. Additionally, PTEN 3′-untranslated region fragment was PCR amplified and inserted into a luciferase reporter plasmid. The luciferase reporter plasmid construct was then transfected into CRC cells together with pre-miR-221 or anti-miR-221, and the luciferase activity in the transfected cells was detected.
RESULTS: The X-ray radiation dose had a significant effect on the expression of miR-221 and PTEN protein in human Caco2 cells in a dose-dependent manner. The miR-221 expression level improved gradually with the increase in irradiation dose, while the PTEN protein expression level reduced gradually. miR-221 expression was significantly reduced in the anti-miR-221 group compared with the pre-miR-221 and negative control groups (P < 0.01). Anti-miR-221 upregulated expression of PTEN protein and enhanced the radiosensitivity of Caco2 cells (P < 0.01). Moreover, the inhibitory effect was dramatically abolished by pretreatment with anti-PTEN-siRNA, suggesting that the enhancement of radiosensitivity was indeed mediated by PTEN. A significant increase of luciferase activity was detected in CRC cells that were cotransfected with the luciferase reporter plasmid construct and anti-miR-221 (P < 0.01).
CONCLUSION: Anti-miR-221 can enhance the radiosensitivity of CRC cells by upregulating PTEN.
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Shen Y, Wang J, Han X, Yang H, Wang S, Lin D, Shi Y. Effectors of epidermal growth factor receptor pathway: the genetic profiling ofKRAS, BRAF, PIK3CA, NRAS mutations in colorectal cancer characteristics and personalized medicine. PLoS One 2013; 8:e81628. [PMID: 24339949 PMCID: PMC3858242 DOI: 10.1371/journal.pone.0081628] [Citation(s) in RCA: 80] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/14/2013] [Accepted: 10/23/2013] [Indexed: 12/30/2022] Open
Abstract
Mutations in KRAS oncogene are recognized biomarkers that predict lack of response to anti- epidermal growth factor receptor (EGFR) antibody therapies. However, some patients with KRAS wild-type tumors still do not respond, so other downstream mutations in BRAF, PIK3CA and NRAS should be investigated. Herein we used direct sequencing to analyze mutation status for 676 patients in KRAS (codons 12, 13 and 61), BRAF (exon 11 and exon 15), PIK3CA (exon 9 and exon 20) and NRAS (codons12, 13 and 61). Clinicopathological characteristics associations were analyzed together with overall survival (OS) of metastatic colorectal cancer patients (mCRC). We found 35.9% (242/674) tumors harbored a KRAS mutation, 6.96% (47/675) harbored a BRAF mutation, 9.9% (62/625) harbored a PIK3CA mutation and 4.19% (26/621) harbored a NRAS mutation. KRAS mutation coexisted with BRAF, PIK3CA and NRAS mutation, PIK3CA exon9 mutation appeared more frequently in KRAS mutant tumors (P = 0.027) while NRAS mutation almost existed in KRAS wild-types (P<0.001). Female patients and older group harbored a higher KRAS mutation (P = 0.018 and P = 0.031, respectively); BRAF (V600E) mutation showed a higher frequency in colon cancer and poor differentiation tumors (P = 0.020 and P = 0.030, respectively); proximal tumors appeared a higher PIK3CA mutation (P<0.001) and distant metastatic tumors shared a higher NRAS mutation (P = 0.010). However, in this study no significant result was found between OS and gene mutation in mCRC group. To our knowledge, the first large-scale retrospective study on comprehensive genetic profile which associated with anti-EGFR MoAbs treatment selection in East Asian CRC population, appeared a specific genotype distribution picture, and the results provided a better understanding between clinicopathological characteristics and gene mutations in CRC patients.
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Affiliation(s)
- Yinchen Shen
- Department of Medical Oncology, Cancer Institute/Hospital, Peking Union Medical College and Chinese Academy of Medical Sciences, Beijing, China
- Beijing Key Laboratory of Clinical Study on Anticancer Molecular Targeted Drugs, Beijing, China
| | - Jianfei Wang
- Department of Medical Oncology, Cancer Institute/Hospital, Peking Union Medical College and Chinese Academy of Medical Sciences, Beijing, China
- Beijing Key Laboratory of Clinical Study on Anticancer Molecular Targeted Drugs, Beijing, China
| | - Xiaohong Han
- Department of Medical Oncology, Cancer Institute/Hospital, Peking Union Medical College and Chinese Academy of Medical Sciences, Beijing, China
- Beijing Key Laboratory of Clinical Study on Anticancer Molecular Targeted Drugs, Beijing, China
| | - Hongying Yang
- Department of Pathology, Cancer Institute/Hospital, Peking Union Medical College and Chinese Academy of Medical Sciences, Beijing, China
| | - Shuai Wang
- Department of Medical Oncology, Cancer Institute/Hospital, Peking Union Medical College and Chinese Academy of Medical Sciences, Beijing, China
- Beijing Key Laboratory of Clinical Study on Anticancer Molecular Targeted Drugs, Beijing, China
| | - Dongmei Lin
- Department of Pathology, Cancer Institute/Hospital, Peking Union Medical College and Chinese Academy of Medical Sciences, Beijing, China
| | - Yuankai Shi
- Department of Medical Oncology, Cancer Institute/Hospital, Peking Union Medical College and Chinese Academy of Medical Sciences, Beijing, China
- Beijing Key Laboratory of Clinical Study on Anticancer Molecular Targeted Drugs, Beijing, China
- * E-mail:
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Chang YS, Chang SJ, Yeh KT, Lin TH, Chang JG. RAS, BRAF, and TP53 gene mutations in Taiwanese colorectal cancer patients. ACTA ACUST UNITED AC 2013; 36:719-24. [PMID: 24356563 DOI: 10.1159/000356814] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/19/2022]
Abstract
BACKGROUND Colorectal cancer (CRC) plays an important role in cancer mortality and morbidity. This study examined colorectal tissues for RAS, BRAF, and TP53 gene mutations to assess their value as indicators of outcomes of CRC therapy. MATERIAL AND METHODS DNA was extracted from tissues taken from 165 patients with CRC. RAS gene mutations (exons 2 and 3) were detected by primer extension analysis. BRAF gene mutations (V600E) were detected by high resolution melting (HRM) analysis. TP53 gene mutations (exons 5-8) were detected by direct sequencing. RESULTS RAS, BRAF, and TP53 mutations occurred in 36.97% (61/165), 4.24% (7/165), and 37.58% (62/165), respectively. The KRAS mutation is a predictor for poor 5-year survival (p = 0.05), and the co-presence of KRAS and TP53 mutations correlates with lymph node involvement (p = 0.029), tumor stage (p = 0.029), and poor survival (p = 0.021). Multivariate analysis adjusted for tumor size, histologic grade, lymph node metastasis, sex, and age also indicated that KRAS mutations correlate significantly with overall survival (p = 0.036). CONCLUSION The KRAS mutation is not present in about one-third of CRC patients, and therefore other gene mutations need to be investigated to better understand the molecular mechanisms of CRC and its treatment.
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Affiliation(s)
- Ya-Sian Chang
- Epigenome Research Center, China Medical University Hospital, Taichung, Taiwan
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Chang YS, Lin IL, Yeh KT, Chang JG. Rapid detection of K-, N-, H-RAS, and BRAF hotspot mutations in thyroid cancer using the multiplex primer extension. Clin Biochem 2013; 46:1572-7. [PMID: 23792105 DOI: 10.1016/j.clinbiochem.2013.06.005] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/07/2013] [Revised: 05/20/2013] [Accepted: 06/09/2013] [Indexed: 12/11/2022]
Abstract
OBJECTIVES The objective of this study is to develop a multiplex PCR and primer extension to detect K-, N-, H-RAS, and BRAF mutations. DESIGN AND METHODS DNA samples were isolated from 76 thyroid cancer patients. Multiplex amplification of exons 2 and 3 of three RAS genes and exon 15 of the BRAF gene using three pairs of primers was performed in a single tube. The products were split into three tubes. First, we used nine different-sized N-RAS and BRAF primers to detect base changes in N-RAS and BRAF. The other two tubes used seven separate different-sized K-RAS and H-RAS primers to detect base changes. RESULTS We compared these results with direct sequencing. The two methods generated identical results, but our method was superior to direct sequencing in terms of the amount of work and time involved. CONCLUSIONS We present a rapid method to detect mutations of K-, N-, H-RAS, and BRAF in human cancers.
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Affiliation(s)
- Ya-Sian Chang
- Epigenome Research Center, China Medical University Hospital, Taichung, Taiwan
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Rosty C, Young JP, Walsh MD, Clendenning M, Sanderson K, Walters RJ, Parry S, Jenkins MA, Win AK, Southey MC, Hopper JL, Giles GG, Williamson EJ, English DR, Buchanan DD. PIK3CA activating mutation in colorectal carcinoma: associations with molecular features and survival. PLoS One 2013; 8:e65479. [PMID: 23785428 PMCID: PMC3681782 DOI: 10.1371/journal.pone.0065479] [Citation(s) in RCA: 110] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/28/2013] [Accepted: 04/25/2013] [Indexed: 12/24/2022] Open
Abstract
Mutations in PIK3CA are present in 10 to 15% of colorectal carcinomas. We aimed to examine how PIK3CA mutations relate to other molecular alterations in colorectal carcinoma, to pathologic phenotype and survival. PIK3CA mutation testing was carried out using direct sequencing on 757 incident tumors from the Melbourne Collaborative Cohort Study. The status of O-6-methylguanine-DNA methyltransferase (MGMT) was assessed using both immunohistochemistry and methyLight techniques. Microsatellite instability, CpG island phenotype (CIMP), KRAS and BRAF V600E mutation status, and pathology review features were derived from previous reports. PIK3CA mutation was observed in 105 of 757 (14%) of carcinomas, characterized by location in the proximal colon (54% vs. 34%; P<0.001) and an increased frequency of KRAS mutation (48% vs. 25%; P<0.001). High-levels of CIMP were more frequently found in PIK3CA-mutated tumors compared with PIK3CA wild-type tumors (22% vs. 11%; P = 0.004). There was no difference in the prevalence of BRAF V600E mutation between these two tumor groups. PIK3CA-mutated tumors were associated with loss of MGMT expression (35% vs. 20%; P = 0.001) and the presence of tumor mucinous differentiation (54% vs. 32%; P<0.001). In patients with wild-type BRAF tumors, PIK3CA mutation was associated with poor survival (HR 1.51 95% CI 1.04-2.19, P = 0.03). In summary, PIK3CA-mutated colorectal carcinomas are more likely to develop in the proximal colon, to demonstrate high levels of CIMP, KRAS mutation and loss of MGMT expression. PIK3CA mutation also contributes to significantly decreased survival for patients with wild-type BRAF tumors.
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Affiliation(s)
- Christophe Rosty
- Cancer and Population Studies Group, Queensland Institute of Medical Research, Herston, Australia.
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