Prognosis and predictive value of KIT exon 11 deletion in GISTs.
Ontology highlight
ABSTRACT:
SUBMITTER: Bachet JB
PROVIDER: S-EPMC2713701 | biostudies-other | 2009 Jul
REPOSITORIES: biostudies-other
Similar Datasets
Project description:Background & Aims: In gastrointestinal stromal tumors (GIST) KIT exon 11 deletions are associated with poor prognosis. The aim of this study was to determine the gene expression profile of GIST carrying KIT exon 11 deletions and to identify genes associated with poor prognosis. Methods: Expression profiling was performed on 9 tumors with KIT exon 11 deletions and 7 without KIT exon 11 mutations using oligonucleotide microarrays. In addition, gene expression profiles for 35 GISTs were analysed by meta-analysis. Differentially expressed genes were identified and confirmed by qPCR. Expression of CD133 (prominin-1) protein (AC133) was also examined by tissue microarray (TMA) analysis of 204 GISTs from a population-based study in Western Sweden. Survival analysis was performed using Cox regression model. Results: Gene expression profiling, meta-analysis and qPCR demonstrated up-regulation of the stem cell marker CD133 in GIST carrying KIT exon 11 deletions. Immunohistochemical analysis on TMA confirmed CD133 expression in 28% of all tumors. CD133 positivity was frequent in gastric GIST (48%) versus small intestinal GIST (4%). CD133 positivity was also frequent in GIST with KIT exon 11 mutations (41%) compared to tumors with mutations in KIT exon 9, PDGFRA, or wild-type tumors (0-17%). There was no significant correlation between CD133 staining and NIH risk score. Survival analysis demonstrated significant correlation between presence of CD133 and shorter overall survival. Conclusions: The stem cell marker CD133 is expressed in a subset of predominantly gastric GIST with KIT exon 11 mutations and associated with poor prognosis.
2010-06-30 | GSE14755 | GEO
Project description:Background & Aims: In gastrointestinal stromal tumors (GIST) KIT exon 11 deletions are associated with poor prognosis. The aim of this study was to determine the gene expression profile of GIST carrying KIT exon 11 deletions and to identify genes associated with poor prognosis. Methods: Expression profiling was performed on 9 tumors with KIT exon 11 deletions and 7 without KIT exon 11 mutations using oligonucleotide microarrays. In addition, gene expression profiles for 35 GISTs were analysed by meta-analysis. Differentially expressed genes were identified and confirmed by qPCR. Expression of CD133 (prominin-1) protein (AC133) was also examined by tissue microarray (TMA) analysis of 204 GISTs from a population-based study in Western Sweden. Survival analysis was performed using Cox regression model. Results: Gene expression profiling, meta-analysis and qPCR demonstrated up-regulation of the stem cell marker CD133 in GIST carrying KIT exon 11 deletions. Immunohistochemical analysis on TMA confirmed CD133 expression in 28% of all tumors. CD133 positivity was frequent in gastric GIST (48%) versus small intestinal GIST (4%). CD133 positivity was also frequent in GIST with KIT exon 11 mutations (41%) compared to tumors with mutations in KIT exon 9, PDGFRA, or wild-type tumors (0-17%). There was no significant correlation between CD133 staining and NIH risk score. Survival analysis demonstrated significant correlation between presence of CD133 and shorter overall survival. Conclusions: The stem cell marker CD133 is expressed in a subset of predominantly gastric GIST with KIT exon 11 mutations and associated with poor prognosis. Tumors with and without KIT exon 11 deletion were compared using a common reference design.
2010-06-30 | E-GEOD-14755 | biostudies-arrayexpress
Project description:BackgroundGastrointestinal stromal tumors (GISTs) with different types of mutations exhibit different clinical characteristics and prognosis. This study aimed to evaluate the prognostic value of mutations in KIT and PDGFRA in a large-scale cohort of GIST patients with current therapy including surgery and imatinib.MethodsA total of 1163 patients diagnosed with GISTs between January 2006 and December 2018 were enrolled in this study. Mutation analysis was performed for exons 9, 11, 13, and 17 of KIT and exons 12 and 18 of PDGFRA. Mutations were grouped into 12 categories according to the gene, exon, and involved codons; they were analyzed considering the clinical characteristics, disease-free survival (DFS), and overall survival (OS) of patients with GISTs.ResultsIn low-risk GISTs, we identified two predictors of worse DFS: tumor origin in the rectum and KIT exon 11 deletion involving two or more codons. In high-risk GISTs treated with R0 resection and imatinib, patients with KIT exon 11 homozygous mutations and KIT intron 10/exon 11 junction deletions demonstrated the highest recurrence rate, indicating that these mutations can be independent prognostic factors of DFS. The presence of KIT exon 11 homozygous mutations also independently influenced OS.ConclusionLow-incidence mutations such as KIT exon 11 homozygous mutations or intron 10/exon 11 junction deletions in GISTs should be carefully evaluated to explore novel treatment strategies, as tumors with these mutations have a high recurrence rate and a very poor prognosis after surgery followed by imatinib adjuvant treatment.
| S-EPMC7520349 | biostudies-literature
Project description:Background and aimsConsidering the indication of adjuvant therapy, the recurrence risk for primary gastrointestinal stromal tumor (GIST) after surgery needs to be accurately estimated. However, current risk stratification schemes may still have room for improvement. This study seeks to analyze prognostic factors for primary GISTs from 3 aspects, including clinicopathological parameters, immunohistochemical biomarkers, and gene mutational status, and attempts to find novel valuable factors predicting the malignancy potential of GISTs.MethodsRetrospective data from 114 primary GIST patients after R0 resection were collected. Clinicopathological data was obtained from medical records and re-evaluated. Immunohistochemical analysis was performed using the Tissue Microarray method for Ki67, p16, p27, p53, SKP2, CD133, and actin. KIT gene exons 9, 11, 13, and 17 and PDGFRα gene exons 12 and 18 were tested for mutations using PCR.ResultsUnivariate analysis revealed the following factors as poor prognostic indicators for relapse-free survival with a median follow-up of 50 months: male gender, gastrointestinal bleeding, mitotic index >5/50HPFs, tumor size >5 cm, non-gastric site, necrosis, epithelioid or mixed cell type, surrounding tissue invasion, Ki67>5%, p16>20%, p53 index >10, SKP2>10%, and KIT exon 11 deletion. Besides mitotic index, tumor size and site, SKP2 high expression (RR = 2.91, 95% CI: 1.41-5.99, P = 0.004) and KIT exon 11 deletion (RR = 2.73, 95% CI: 1.04-7.16, P = 0.041) were also independent risk factors in multivariate analysis, with gastrointestinal bleeding also showing a trend towards significance (RR = 1.88, 95% CI: 0.98-3.64, P = 0.059). In addition, gastrointestinal bleeding and SKP2 high expression showed a good ability to stratify high-risk patients further.ConclusionOur results show that gastrointestinal bleeding, SKP2 high expression, and KIT exon 11 deletions may be useful indicators of high recurrence risk for primary GIST patients.
| S-EPMC3656858 | biostudies-literature
Project description:Background Gastrointestinal stromal tumors (GIST) are the most common mesenchymal neoplasms in the gastrointestinal (GI) tract. The mutation of C-KIT is considered to be the crucial step in the tumorigenesis. Targeted therapies are being developed focusing these mutations. Various exon mutations of GIST responded in varied patterns to this targeted therapy. This study was carried out to evaluate the C-KIT exon 11, exon 9 and BRAF V600E mutations among GIST specimens. Methods This retrospective study was carried out among 20 DNA extracted specimens from paraffin blocks of GIST received in our tertiary teaching institution for a period of three years. DNA sequencing was carried out for mutational analyses on C-KIT exon 9, C-KIT exon 11 and BRAF V600E genes using Sanger sequencing. Results Histologically, majority of the tumors had spindle cell morphology. About 19 cases were positive for CD117. The analysis of type of mutations showed that three cases carried Exon 11 and three cases carried Exon 9 mutations. BRAF V600E mutation was seen in one case. Conclusion It is essential to conduct molecular studies on GISTs in order to get a clear understanding of the pathogenesis and behavior pattern. This will also help in designing targeted therapies and assessing recurrence. With the advent of rapidly evolving personalized therapy, the evaluation of genetic mutations is essential for diagnosis and prognostic value.
| S-EPMC7174865 | biostudies-literature
Project description:Gastrointestinal stromal tumors (GISTs) are common mesenchymal neoplasms in the gastrointestinal tract of humans and dogs. Little is known about the pathogenesis of these tumors. This study evaluated the role of c-KIT in canine GISTs; specifically, we investigated activating mutations in exons 8, 9, 11, 13, and 17 of c-KIT and exons 12, 14, and 18 of platelet-derived growth factor receptor, alpha polypeptide (PDGFRA), all of which have been implicated in human GISTs.Seventeen canine GISTs all confirmed to be positive for KIT immunostaining were studied. Exons 8, 9, 11, 13 and 17 of c-KIT and exons 12, 14, and 18 of PDGFRA, were amplified from DNA isolated from formalin-fixed paraffin-embedded samples.Of these seventeen cases, six amplicons of exon 11 of c-KIT showed aberrant bands on gel electrophoresis. Sequencing of these amplicons revealed heterozygous in-frame deletions in six cases. The mutations include two different but overlapping six base pair deletions. Exons 8, 9, 13, and 17 of c-KIT and exons 12, 14, and 18 of PDGFRA had no abnormalities detected by electrophoresis and sequencing did not reveal any mutations, other than synonymous single nucleotide polymorphisms (SNPs) found in exon 11 of c-KIT and exons 12 and 14 of PDGFRA.The deletion mutations detected in canine GISTs are similar to those previously found in the juxtamembrane domain of c-KIT in canine cutaneous mast cell tumors in our laboratory as well as to those reported in human GISTs. Interestingly, none of the other c-KIT or PDGFRA exons showed any abnormalities in our cases. This finding underlines the critical importance of c-KIT in the pathophysiology of canine GISTs. The expression of KIT and the identification of these activating mutations in c-KIT implicate KIT in the pathogenesis of these tumors. Our results indicate that mutations in c-KIT may be of prognostic significance and that targeting KIT may be a rational approach to treatment of these malignant tumors. This study further demonstrates that spontaneously occurring canine GISTs share molecular features with human GISTs and are an appropriate model for human GISTs.
| S-EPMC2970610 | biostudies-literature
Project description:ObjectiveThe aim of the present study was to analyze mutations of the mast/stem cell growth factor receptor Kit (KIT) gene in patients with melanoma from Eastern Siberia regions of the Russian Federation.MethodsKIT gene mutations in exons 11 and 13 were analyzed by Sanger sequencing in 57 tumor samples obtained from patients with KIT-positive melanomas localized in preferable locations.ResultMutations were identified in 21% of patients. Among them, multiple mutations were identified in five patients. A total of 18 mutations were observed in the KIT gene, of which three were deletions and fourteen substitution mutations. Age, gender and clinicopathological characteristics of patients with cutaneous KIT-positive melanoma in Eastern Siberia corresponded to the European population. According to computational prediction tools, all mutations were evaluated as potentially harmful.ConclusionThe six novel mutations reported in the present study expand our knowledge on the molecular pathogenesis of melanoma, which can be used to further explore methods to improve disease therapeutic strategies.
| S-EPMC10762753 | biostudies-literature
Project description:Codelink® Whole Mouse Genome Bioarrays (GE/Amersham) of one sample of WT, D6, D54, WT/D6, WT/D54 and MIGR NIH3T3 cells, cultivated in the four different conditions (SCF+, SCF- and imatinib 1 or 5 µM), were used for the analysis of differential gene expression. Our aim was to choose the best candidate genes for low density array analysis. We first selected genes differentially expressed between WT and hemizygous samples grown in the SCF+ condition, whose fold change was superior or equal to 2 and whose expression for at least one of the sample was greater than 1.3 (commonly admitted threshold for low density arrays). We selected then 83 and 126 genes more that were differentially expressed between D6 and D54 cell lines (fold change ≥ 2; gene amplification > 1.3) in SCF+ or SCF- condition, respectively. Finally we obtained a list of 235 genes in which 94 were available for Taqman® low density array (Applied®).
2012-01-01 | GSE33968 | GEO
Project description:Ellis-van Creveld syndrome (EVC) is a rare genetic disorder characterized by chondral and ectodermal dysplasia. Clinical features may include polydactyly, growth retardation, short ribs, and heart defects. The exact prevalence is still unclear; however, the Amish community in the United States is the most common community to report this rare disease. Until now, only six cases have been reported in Saudi Arabia so far. This is the first case to be reported in the Jazan region. Jazan covers an area of 11,671 km² and has a population of 1,567,547 at the 2017 census. This region has the highest population density with a high consanguinity marriage rate. We present a case of EVC with typical clinical findings, which was confirmed by homozygous mutation in the EVC2 gene in the region of Jazan, Saudi Arabia. Besides the six cases that were reported from Saudi Arabia, this makes it a total of seven cases. The prenatal findings are considered a good predictor of the disease outcome. More effort is needed in making a national registry of rare disorders to report such cases and provide more awareness among highly consanguinity marriage communities.
| S-EPMC8491797 | biostudies-literature
Project description:BackgroundExome sequencing allows researchers to study the human genome in unprecedented detail. Among the many types of variants detectable through exome sequencing, one of the most over looked types of mutation is internal deletion of exons. Internal exon deletions are the absence of consecutive exons in a gene. Such deletions have potentially significant biological meaning, and they are often too short to be considered copy number variation. Therefore, to the need for efficient detection of such deletions using exome sequencing data exists.ResultsWe present ExonDel, a tool specially designed to detect homozygous exon deletions efficiently. We tested ExonDel on exome sequencing data generated from 16 breast cancer cell lines and identified both novel and known IEDs. Subsequently, we verified our findings using RNAseq and PCR technologies. Further comparisons with multiple sequencing-based CNV tools showed that ExonDel is capable of detecting unique IEDs not found by other CNV tools.ConclusionsExonDel is an efficient way to screen for novel and known IEDs using exome sequencing data. ExonDel and its source code can be downloaded freely at https://github.com/slzhao/ExonDel.
| S-EPMC4288651 | biostudies-literature