analysis, the level of KRAS mRNA expression was an independent prognostic factor in both TCGA (hazard ratio [HR], 1.570; 95% confidence interval [CI], 1.026–2.403; p = 0.038) and METABRIC (HR, 1.254; 95% CI, 1.087–1.446; p = 0.002) databases. The prognostic impact of mRNA expression was effective only for luminal A subtype (p < 0.001 in METABRIC). Positive correlation was observed between mRNA expression and copy number alteration (CNA) (r = 0.577, p < 0.001 in TCGA; ρ = 0.343, p < 0.001 in METABRIC). Methylation showed negative correlations with both mRNA expression and CNA (r = −0.272, p < 0.001 in TCGA). The expression of mRNA had little association with the mutation status in breast cancers, having a mutation frequency of approximately 0.6%.CONCLUSION: KRAS mRNA expression was significantly associated with breast cancer prognosis. It was found to be an independent prognostic factor for breast cancer. Prognostic role of KRAS mRNA expression was effective only in luminal A subtype. Further studies are needed to validate the prognostic role of KRAS mRNA expression in breast cancer, thus paving a way for clinical application of KRAS in practice.]]>
Breast Neoplasms ; Breast ; Classification ; Genome ; Methylation ; Multivariate Analysis ; Mutation Rate ; Phenobarbital ; Prognosis ; ras Proteins ; RNA ; RNA, Messenger

EGFR and KRAS mutations are two of the most common mutations that are present in lung cancer. Screening and detecting these mutations are of issue these days, and many different methods and tissue samples are currently used to effectively detect these two mutations. In this study, we aimed to evaluate the testing for EGFR and KRAS mutations by pyrosequencing method, and compared the yield of cytology versus histology specimens in a consecutive series of patients with lung cancer. We retrospectively reviewed EGFR and KRAS mutation results of 399 (patients with EGFR mutation test) and 323 patients (patients with KRAS mutation test) diagnosed with lung cancer in Konkuk University Medical Center from 2008 to 2014. Among them, 60 patients had received both EGFR and KRAS mutation studies. We compared the detection rate of EGFR and KRAS tests in cytology, biopsy, and resection specimens. EGFR and KRAS mutations were detected in 29.8% and 8.7% of total patients, and the positive mutation results of EGFR and KRAS were mutually exclusive. The detection rate of EGFR mutation in cytology was higher than non-cytology (biopsy or resection) materials (cytology: 48.5%, non-cytology: 26.1%), and the detection rate of KRAS mutation in cytology specimens was comparable to non-cytology specimens (cytology: 8.3%, non-cytology: 8.7%). We suggest that cytology specimens are good alternatives that can readily substitute tissue samples for testing both EGFR and KRAS mutations. Moreover, pyrosequencing method is highly sensitive in detecting EGFR and KRAS mutations in lung cancer patients.
Adult ; Aged ; Aged, 80 and over ; Carcinoma, Non-Small-Cell Lung/genetics/metabolism/*pathology ; DNA Mutational Analysis ; DNA, Neoplasm/chemistry/metabolism ; Female ; Humans ; Lung Neoplasms/genetics/metabolism/*pathology ; Male ; Middle Aged ; Mutation ; Receptor, Epidermal Growth Factor/*genetics/metabolism ; Retrospective Studies ; ras Proteins/*genetics/metabolism

This study was aimed to characterize clinicopathological features and prognosis of patients with adenosquamous lung carcinoma (ASC). Among the 2531 patients with lung cancer who underwent surgery between January 2000 and June 2012 in our hospital, 59 were histologically diagnosed as having ASC. The clinicopathological features and follow-up data of ASC patients were collected and analyzed statistically. Superior lobectomy was accomplished in 40 patients, middle and inferior lobectomy in 3, lobectomy plus partial resection of contralateral lung in 5, partial lung resection in 4, and pneumonectomy in 7. Moreover, 22 cases were found to be adenocarcinoma-predominant, and 18 to be squamous cell carcinoma-predominant. The median survival time was 13.6 months, and the 1-, 3-, and 5-year survival rates were 59.9%, 36.4% and 31.2%, respectively. Of the 52 cases with tissue specimens available, 11 had an EGFR mutation (21.2%) and 2 had a KRAS mutation (3.8%). Multivariate analysis showed that histology subtype, pleural invasion, TNM stage, and postoperative treatment were all independent prognostic factors. The data from the current study demonstrated that SCC-predominant histology represents a better prognosis of ASC. Histology subtype, pleural invasion, TNM stage, and postoperative treatment are independent prognostic factors for ASC and adjuvant therapy may help control the disease.
Adult ; Aged ; Carcinoma, Adenosquamous ; genetics ; pathology ; surgery ; Diagnosis, Differential ; Female ; Humans ; Lung Neoplasms ; genetics ; pathology ; surgery ; Male ; Middle Aged ; Mutation ; Prognosis ; Proto-Oncogene Proteins p21(ras) ; genetics ; Receptor, Epidermal Growth Factor ; genetics ; Retrospective Studies ; Survival Analysis

OBJECTIVETo investigate mutations frequencies of KRAS,NRAS and BRAF genes in colorectal carcinoma.

METHODSTissue specimens from 200 colorectal cancer patients at diagnosis were collected and subject to KRAS,NRAS and BRAF mutation analyses by PCR-based direct DNA sequencing targeting exons 2, 3 and 4 of KRAS gene, exons 2, 3 and 4 of NRAS gene and exon 15 of BRAF gene.

RESULTSActivating mutations were detected in KRAS (44%, 88/200), NRAS (2%, 4/200) and BRAF (5%, 10/200) in this study cohort.Among KRAS mutations, 64.8% (57/88) occurred in codon 12 and 12.5% (11/88) occurred in codon 13. KRAS gene mutation in exon 3 mainly involved codons 59 and 61. KRAS gene mutation in exon 4 mainly involved codons 117 and 146.

CONCLUSIONSMutations at exon 2 of KRAS gene have the highest frequency in colorectal carcinoma. Expanding the detection sites of KRAS gene combined with NRAS and BRAF genes may help to identify patients who will most likely benefit from targeted therapies.

Base Sequence ; Codon ; Colorectal Neoplasms ; genetics ; DNA Mutational Analysis ; Exons ; Female ; Genes, ras ; Humans ; Mutation ; Proto-Oncogene Proteins ; Proto-Oncogene Proteins B-raf ; genetics ; Sequence Analysis, DNA

Colorectal Neoplasms ; genetics ; DNA Mutational Analysis ; standards ; Humans ; Mutation ; Proto-Oncogene Proteins B-raf ; genetics ; ras Proteins ; genetics

OBJECTIVETo compare the application values of real-time quantitative PCR-Sanger sequencing and TaqMan probe method in the detection of KRAS and BRAF mutations, and to correlate KRAS/BRAF mutations with the clinicopathological characteristics in colorectal carcinomas.

METHODSGenomic DNA of the tumor cells was extracted from formalin fixed paraffin embedded (FFPE) tissue samples of 344 colorectal carcinomas by microdissection. Real-time quantitative PCR-Sanger sequencing and TaqMan probe method were performed to detect the KRAS/BRAF mutations. The frequency and types of KRAS/BRAF mutations, clinicopathological characteristics and survival time were analyzed.

RESULTSKRAS mutations were detected in 39.8% (137/344) and 38.7% (133/344) of 344 colorectal carcinomas by using real-time quantitative PCR-Sanger sequencing and TaqMan probe method, respectively. BRAF mutation was detected in 4.7% (16/344) and 4.1% (14/344), respectively. There was no significant correlation between the two methods. The frequency of the KRAS mutation in female was higher than that in male (P < 0.05). The frequency of the BRAF mutation in colon was higher than that in rectum. The frequency of the BRAF mutation in stage III-IV cases was higher than that in stageI-II cases. The frequency of the BRAF mutation in signet ring cell carcinoma was higher than that in mucinous carcinoma and nonspecific adenocarcinoma had the lowest mutation rate. The frequency of the BRAF mutation in grade III cases was higher than that in grade II cases (P < 0.05). The overall concordance for the two methods of KRAS/BRAF mutation detection was 98.8% (kappa = 0.976). There was statistic significance between BRAF and KRAS mutations for the survival time of colorectal carcinomas (P = 0.039). There were no statistic significance between BRAF mutation type and BRAF/KRAS wild type (P = 0.058).

CONCLUSIONS(1) Compared with real-time quantitative PCR-Sanger sequencing, TaqMan probe method is better with regard to handling time, efficiency, repeatability, cost and equipment. (2) The frequency of the KRAS mutation is correlated with gender. BRAF mutation is correlated with primary tumor site, TNM stage, histological types and histological grades.(3) BRAF gene mutation is an independent prognostic marker for colorectal carcinomas.

Adenocarcinoma ; genetics ; pathology ; Adenocarcinoma, Mucinous ; genetics ; pathology ; Adult ; Aged ; Aged, 80 and over ; Carcinoma, Signet Ring Cell ; genetics ; pathology ; Colonic Neoplasms ; genetics ; pathology ; Colorectal Neoplasms ; genetics ; pathology ; DNA Mutational Analysis ; Female ; Humans ; Male ; Middle Aged ; Mutation ; Neoplasm Grading ; Neoplasm Staging ; Oligonucleotide Probes ; Proto-Oncogene Proteins ; genetics ; Proto-Oncogene Proteins B-raf ; genetics ; Proto-Oncogene Proteins p21(ras) ; Real-Time Polymerase Chain Reaction ; Rectal Neoplasms ; genetics ; pathology ; Sequence Analysis, DNA ; Sex Factors ; Young Adult ; ras Proteins ; genetics

This study was aimed to explore whether multiple common gene mutations of leukemia synergistically involved in acute promyelocytic leukemia (APL) pathogenesis, and to investigate their relevance to clinical features, cytogenetics and molecular risk stratification. 84 specimens of admitted de novo APL patients from February 2005 to October 2010 were collected, the gene mutations of bone marrow mononuclear cells and clinical features of mutation-positive patients were analyzed by genomic DNA-PCR. The results indicated that the prevalence of mutations was 60.7% (51/84), in which the mutations with the highest incidence were found as FLT3-ITD, reaching 27.4% (23/84). Next, there were 12 cases WT1 mutation, 9 for FLT3-TKD, 7 for TET2, 5 for N-RAS, 4 for ASXL1, 2 for EZH2 mutation and 1 positive case in MLL-PTD, IDH1 and CBL mutation respectively. No mutation was found in other JAK1, DNMT3, c-Kit, NPM1, IDH2, RUNX1 and JAK2 (V617F) common leukemia-related genes. Combined analysis with clinical data demonstrated that the patients with FLT3-ITD mutation displayed higher white blood cell counts, while the patients with N-RAS mutation showed lower platelet counts. Overall survival of these patients was obviously shorten as compared with patients with wild-type. This difference between mutant and wild-type of all above mentioned cases was statistically significant (P < 0.05). The difference between APL with simple t (15;17) and additional abnormal karyotype was not statistically significant. It is concluded that the FLT3-ITD mutation is recurrent genetic change in APL, and together with N-RAS mutation indicates poor prognosis. Additional abnormal karyotype does not associate with prognosis of APL.
Adolescent ; Adult ; Aged ; Child ; DNA Mutational Analysis ; DNA-Binding Proteins ; genetics ; Enhancer of Zeste Homolog 2 Protein ; Female ; Genes, ras ; Humans ; Leukemia, Promyelocytic, Acute ; genetics ; Male ; Middle Aged ; Mutation ; Nuclear Proteins ; genetics ; Polycomb Repressive Complex 2 ; genetics ; Prognosis ; Proto-Oncogene Proteins ; genetics ; Proto-Oncogene Proteins c-kit ; genetics ; Repressor Proteins ; genetics ; Tandem Repeat Sequences ; Young Adult ; fms-Like Tyrosine Kinase 3 ; genetics

OBJECTIVETo analyze immunophenotypes and gene mutations of colorectal precancerous lesions and adenocarcinoma, and to compare the difference of carcinogenetic mechanisms between the two precancerous lesions.

METHODSFifty-three cases of colorectal serrated lesions including 30 hyperplastic polyps, 20 sessile serrated adenomas (SSA) and 3 mixed polyps were collected from January 2006 to June 2012.Forty-five cases of traditional adenomas and 50 cases of colorectal adenocarcinomas were also recruited. Thirty hyperplastic polyps, 20 cases of SSA, 3 mixed polyps and 45 traditional adenomas were investigated by immunohistochemistry for the expression of DNA mismatch repair (MMR) proteins (MLH1, MSH2 and MSH6) and DNA methyltransferase MGMT. Mutations of KRAS, BRAF and PIK3CA genes in 10 cases of SSAs, 10 traditional adenomas, 1 mixed polyps and 50 colorectal adenocarcinomas were analyzed by PCR followed by direct Sanger sequencing.

RESULTS(1) Only 3 cases of hyperplastic polyps lost MLH1 expression, and none of SSAs or traditional adenomas showed loss of MLH1. The negative expression rates of MSH2, MSH6 and MGMT in hyperplastic polyps and SSA were significantly higher than those of traditional adenomas. (2) KRAS mutation was found in 5/10 cases of SSAs, 5/10 traditional adenomas and 1/1 mixed polyps. (3) Colorectal adenocarcinomas harbored the mutations of KRAS (48%, 24/50), BRAF (6%, 3/50) and PIK3CA (4%, 2/50).

CONCLUSIONSImmunophenotypic and gene mutation profiles are different between colorectal serrated lesion and traditional adenoma. Alterations of MMR and MGMT expression play important roles in the pathogenesis of "serrated neoplasm". KRAS mutation is a significant genetic change in the early phase of colorectal carcinogenesis.

Adaptor Proteins, Signal Transducing ; metabolism ; Adenocarcinoma ; genetics ; metabolism ; Adenoma ; genetics ; metabolism ; Aged ; Class I Phosphatidylinositol 3-Kinases ; Colonic Polyps ; genetics ; metabolism ; Colorectal Neoplasms ; genetics ; metabolism ; DNA Mismatch Repair ; DNA Modification Methylases ; metabolism ; DNA Repair Enzymes ; metabolism ; DNA, Neoplasm ; metabolism ; DNA-Binding Proteins ; metabolism ; Female ; Humans ; Hyperplasia ; Immunophenotyping ; Male ; Middle Aged ; MutL Protein Homolog 1 ; MutS Homolog 2 Protein ; metabolism ; Nuclear Proteins ; metabolism ; Phosphatidylinositol 3-Kinases ; genetics ; Point Mutation ; Precancerous Conditions ; genetics ; metabolism ; Proto-Oncogene Proteins ; genetics ; Proto-Oncogene Proteins B-raf ; genetics ; Proto-Oncogene Proteins p21(ras) ; Sequence Analysis, DNA ; Tumor Suppressor Proteins ; metabolism ; ras Proteins ; genetics

Adenosine Triphosphate ; metabolism ; Colorectal Neoplasms ; diagnosis ; genetics ; DNA Methylation ; Diphosphates ; metabolism ; Glioma ; diagnosis ; genetics ; Humans ; Isocitrate Dehydrogenase ; genetics ; Janus Kinase 2 ; genetics ; Mutation ; Myeloproliferative Disorders ; diagnosis ; genetics ; Polymorphism, Single Nucleotide ; Proto-Oncogene Proteins ; genetics ; Proto-Oncogene Proteins p21(ras) ; Sequence Analysis, DNA ; methods ; Templates, Genetic ; ras Proteins ; genetics

BACKGROUND: N-ras mutations are one of the most commonly detected abnormalities of myeloid origin. N-ras mutations result in a constitutively active N-ras protein that induces uncontrolled cell proliferation and inhibits apoptosis. We analyzed N-ras mutations in adult patients with AML at a particular institution and compared pyrosequencing analysis with a direct sequencing method for the detection of N-ras mutations. METHODS: We analyzed 90 bone marrow samples from 83 AML patients. We detected N-ras mutations in codons 12, 13, and 61 using the pyrosequencing method and subsequently confirmed all data by direct sequencing. Using these methods, we screened the N-ras mutation quantitatively and determined the incidence and characteristic of N-ras mutation. RESULTS: The incidence of N-ras mutation was 7.2% in adult AML patients. The patients with N-ras mutations showed significant higher hemoglobin levels (P=0.022) and an increased incidence of FLT3 mutations (P=0.003). We observed 3 cases with N-ras mutations in codon 12 (3.6%), 2 cases in codon 13 (2.4%), and 1 case in codon 61 (1.2%). All the mutations disappeared during chemotherapy. CONCLUSIONS: There is a low incidence (7.2%) of N-ras mutations in AML patients compared with other populations. Similar data is obtained by both pyrosequencing and direct sequencing. This study showed the correlation between the N-ras mutation and the therapeutic response. However, pyrosequencing provides quantitative data and is useful for monitoring therapeutic responses.
Adult ; Aged ; Aged, 80 and over ; Antineoplastic Agents/therapeutic use ; Bone Marrow/metabolism ; Codon ; Cytogenetic Analysis ; Female ; Hemoglobins/metabolism ; Humans ; Incidence ; Leukemia, Myeloid, Acute/drug therapy/epidemiology/*genetics ; Male ; Middle Aged ; Mutation ; Sequence Analysis, DNA ; fms-Like Tyrosine Kinase 3/genetics ; ras Proteins/*genetics