Spectrum of mutations in gastrointestinal stromal tumor patients - a population-based study from Slovakia

The novel KIT exon 11 germline mutation K558N is associated with gastrointestinal stromal tumor, mastocytosis, and seminoma development

Familial gastrointestinal stromal tumors (GIST) are dominant genetic disorders that are caused by germline mutations of the type III receptor tyrosine kinase KIT. While sporadic mutations are frequently found in mastocytosis and GISTs, germline mutations of KIT have only been described in 39 families until now. We detected a novel germline mutation of KIT in exon 11 (p.Lys-558-Asn; K558N) in a patient from a kindred with several GISTs harboring different secondary somatic KIT mutations. Structural analysis suggests that the primary germline mutation alone is not sufficient to release the autoinhibitory region of KIT located in the transmembrane domain. Instead, the KIT kinase module becomes constitutively activated when K558N combines with different secondary somatic mutations. The identical germline mutation in combination with an additional somatic KIT mutation was detected in a second patient of the kindred with seminoma while a third patient within the family had a cutaneous mastocytosis. These findings suggest that the K558N mutation interferes with the juxtamembranous part of KIT, since seminoma and mastocystosis are usually not associated with exon 11 mutations.

Prevalence and significance of M541L single nucleotide polymorphism in the central European cohort of gastrointestinal stromal tumor patients

BACKGROUND

Single nucleotide polymorphisms can create a genetic microenvironment in some tumors that affects the course of treatment, resistance, etc. Whether single nucleotide polymorphisms have an impact on gastrointestinal stromal tumor (GIST) development and disease progression is not yet accurately verified. KIT SNP^M541L in exon 10 correlates with a worse prognosis of many cancers. The impact of KIT SNP^M541L in GISTs is relatively unknown and, therefore, its analyses could have potential in patient therapy and could provide more detailed information on tumor character, clinical presentation, or tumor behavior in treatment.

AIM

The aim of the study was the analysis of the biological and clinical significance of the KIT SNP^M541L polymorphism in exon 10.

MATERIALS AND METHODS

Paraffin sample tissues were obtained from the National GIST Register in Martin. Retrospective samples from 177 GIST patients were divided into several groups. Detection of SNP^M541L was performed by Sanger sequencing. Statisitical analyses were performed to determine the prevalence of KIT SNP^M541L in the Slovak GIST cohort, to search for correlation between c-KIT status and clinicopathological, molecular and biological data.

RESULTS

Overall, 29 samples out of 177 showed KIT SNP^M541L polymorphism.

CONCLUSION

Our results do not support the association between KIT SNP^M541L and increased risk of relapse in localized primary GISTs. Additionally, we found a positive correlation between KIT SNP^M541L occurrence and earlier onset of relapse in PDGFRa and WT subgroup of GISTs.

BRAF mutations in KIT/PDGFRA positive gastrointestinal stromal tumours (GISTs): Is their frequency underestimated?

BRAF V600E mutations in GISTs are considered to be one of the mutational events in KIT/PDGFRA negative or positive GISTs, respectively. BRAF mutated GISTs usually do not respond to imatinib treatment, even more GISTs with imatinib sensitive KIT mutation. However, they are almost phenotypically and morphologically identical with KIT/PDGFRA positive GISTs. In general, due to the small number of BRAF mutations in GIST and because of the rarity of concomitant BRAF/KIT or BRAF/PDGFRA mutations, their frequency may be depreciated. The aim of this study was BRAF mutation detection in KIT/PDGFRA positive GISTs and their verification by other molecular methods. We applied the sensitive droplet digital PCR on 35 randomly selected KIT/PDGFRA positive GISTs to detect V600E mutations. We have established two criteria for the evaluation of samples: false positive rate (FPR) based on the negative controls; Limit of Detection (LoD) based on the serial dilution of positive control from RKO cell line harboring heterozygous V600E mutation in constant wild-type DNA background. Results from ddPCR were verified by other molecular methods: allele-specific PCR, dideoxysequencing, competitive allele-specific TaqMan PCR (castPCR). FPR was determined as 5 (∼4.4) positive droplets, and LoD was assessed to 3.4293 copies/μL what is the method sensitivity of 0.0162 %. We identified eight KIT/PDGFRA positive patients with concomitant V600E mutation. The five of them were in coexistence with KIT mutation and three with PDGFRA mutation. We also included the liver metastasis, but data from primary tumour were not available. We achieved the very high sensitivity of the ddPCR method for detecting BRAF mutation in GISTs to have importance from the point of view of therapy.

Stratification of patients with colorectal cancer without the recorded family history

Colorectal cancer (CRC) is a multifactorial disease and one of the most malignant tumours. In addition to the sporadic form, familial occurrences, particularly hereditary non-polyposis CRC-Lynch syndrome (LS)-are often observed. LS is caused by a germline mutation in mismatch repair (MMR) genes, whose task it is to correct errors in the DNA structure that result from its replication. The aim of the present study was to stratify CRC patients using molecular diagnostics and next generation sequencing, according to the chosen criteria [positive for microsatellite instability (MSI) and negative for a BRAF mutation and MutL homolog 1 (MLH1) methylation], and subsequently to detect pathological germline mutations in MMR genes in Slovak patients. To exclude patients with MSI from further testing, the present study detected the BRAF V600E mutation and examined MLH1 methylation status. From the 300 CRC patients, 37 cases with MSI were identified. In the MSI-positive samples, 13 cases of BRAF V600E mutation were recorded. In 24 BRAF-negative patients, 11 cases of epigenetic methylation of MLH1 and 12 cases without MLH1 methylation suspected for LS were detected, and it was not possible to analyse the methylation phenotype of 1 sample. Thus, the present study reports the novel deletion of four nucleotides, 1627_1630del AAAG (Glu544Lysfs*26) in MSH6, probably associated with LS. A second case with a nonsense mutation in MSH was also detected, namely MMR_c.1030C>T (p.Q344X).

KIT exon 11 and PDGFRA exon 18 gene mutations in gastric GIST: proposal of a short panel for predicting therapeutic response

Background

GIST is the most common mesenchymal tumor of gastrointestinal tract and is more frequent in stomach. Its main mutations affect KIT and PDGFRA genes. Full genetic analysis panels are currently used to study mutations in GIST and other tumors. Considering that in gastric GIST KIT gene mutations in exon 11 are sensitive to IM whereas PDGFRΑ gene mutations in exon 18 (D842V) are resistant to the same drug, the aim of this study is to focus on these two molecular targets as a short alternative panel for predicting therapeutic response in gastric GIST which might optimize resources.

Methods

The genotypes of 38 cases of primary GIST were determined by performing bidirectional DNA sequencing.

Results

Exon 11 of KIT gene showed mutations in 65.3% and the exon 18 of PDGFRA gene showed 9% of cases. So it was possible to determine a subgroup of tumors which presented mutations in KIT exon 11 and PDGFRA exon 18.

Conclusion

Considering all of the foregoing analyzed globally, the application of short panel has impact on the cost and time of release of results to the physician, allowing a rapid approach to patients eligible for treatment with the target therapy.

Somatic mutational spectrum analysis in a prospective series of 104 gastrointestinal stromal tumors

Gastrointestinal stromal tumors (GISTs) are mesenchymal tumors distinguished by driver mutations in proto-oncogenes KIT or PDGFRA in 85-90% of cases. These mutations have been linked to the response to imatinib, a multikinase inhibitor, and have independent prognostic impact. Here, we describe the prospective study of the molecular characteristics of 104 GISTs from French adult patients analyzed routinely through the National Hospital Program of Molecular Cancer Diagnosis. All patients with GISTs diagnosed at the University Hospital of Besançon between August 2005 and October 2014 were prospectively included in the present study. KIT, PDGFRA and KRAS-codons 12 and 13 as well as BRAF codon 600 mutations were analyzed by Sanger sequencing or SNaPshot. KIT and PDGFRA mutations were detected in 71.2 and 19.2% of the cases, respectively. A total of 43 different mutations were detected of which 13 had never been described. As expected, KIT exon 9 and PDGFRA exon 18 mutations were associated with small bowel and gastric localizations respectively. No mutation was found in KRAS and BRAF. Molecular studies are critical to improve the management of GISTs. Our study enhances the current knowledge by describing 13 new mutations in KIT. A common molecular pattern in all KIT exon 11 substitutions is also described for the first time in this study but its significance remains unknown since genetic and environmental risk factors favoring the development of GISTs such as DNA repair defects and exposure to carcinogens are not currently known.

Detection of mutations in the BRAF gene in patients with KIT and PDGFRA wild-type gastrointestinal stromal tumors

Gastrointestinal stromal tumors (GISTs) are characterized by mutations in exons 9, 11, 13, and 17 of KIT or exons 12, 14, and 18 of PDGFRA gene. However, approximately 10 to 15 % of GISTs lack the mutations in KIT and PDGFRA, and these are referred to as wild-type GISTs which are less sensitive to tyrosine-kinase inhibitors. The aim of this study was to detect BRAF mutations in patients with wild-type GISTs. We applied a sensitive allele-specific PCR, which was optimized using the V600E mutation-harboring cell line RKO, followed by verification of the results by dideoxy sequencing. We selected 149 GIST patients without detectable mutations in KIT and PDGFRA genes from the Slovak national GIST register and analyzed biopsy specimens for the presence of BRAF mutations in exon 15. We identified nine patients with the V600E mutation. The BRAF-driven GISTs were primary gastric (n = 3), small intestinal (n = 3), colon (n = 1), and of uncertain origin (n = 1). We also included a liver metastasis of a patient with a simultaneous KIT exon 11-mutated intra-abdominal metastasis. We conclude that genome analysis of wild-type GISTs for mutations should include the BRAF gene, as its mutation status contributes to understanding of pathogenesis and might be important for decisions on therapy.

Molecular and Immunohistochemical Study of Platelet Derived Growth Factor Receptor Alpha in KIT Negative Gastrointestinal Stromal Tumors; the First Report from Iran

BACKGROUND

Gastrointestinal stromal tumors (GISTs) are potentially malignant tumors; however their behavior and response to treatment is dependent on the type of mutation and immunohistochemical expression of antigens. It is recommended to perform routine molecular and immunohistochemical tests in KIT and platelet derived growth factor receptor alpha (PDGFRA) molecules for making decision regarding targeted therapy and prediction of the behavior of the tumor.

Objectives: There has been no study from Iran regarding the PDGFRA mutational analysis in GISTs. In this study, for the first time from Iran, we performed immunohistochemical and molecular analysis of PDGFRA molecule on GISTs.

METHODS

In a cross-sectional study during 7 years (2008-2014) on 50 untreated non-recurrent non-metastatic newly diagnosed GISTs, molecular analysis and immunohistochemical staining for PDGFRA were performed and findings were compared with different clinicopathological characteristics..

RESULTS

During the 7 years, 50 cases of GISTs according to the above mentioned criteria were found. 17 cases were negative for KIT mutation. Of them, 15 (30%) were positive for either exon 12 or 18 mutation of PDGFRA. These cases showed more epithelioid morphology and the number of mitotic figures were lower than PDFRA negative GISTs. Also according to the criteria for risk assessment, it seems that PDGFRA mutant GISTs are rarely in the high risk category.

CONCLUSION

PDGFRA mutant GISTs are common in Iranian population and it is recommended to perform mutation analysis for PDGFRA in every GIST with wild type KIT and epithelioid morphology.

Global epidemiology of gastrointestinal stromal tumours (GIST): A systematic review of population-based cohort studies

BACKGROUND

Gastrointestinal stromal tumours (GISTs) are rare, yet the most common mesenchymal tumour within the digestive tract. Lack of diagnostic criteria and no specific code in the ICD system has prevented epidemiological evaluation except from overt malignant cases in the past. A global estimate of incidence and disease patterns has thus not been available.

METHODS

A systematic literature search of all available population-based studies on GIST published between January 2000 and December 2014 were reviewed. Descriptive epidemiological data are presented.

RESULTS

The search found 29 studies of more than 13,550 patients from 19 countries that reported sufficient data for regional or national population-based statistics. Age at diagnosis ranged from 10 to 100 years, with median age being mid 60s across most studies. Gender distribution was equal across studies. On average, 18% of patients had an incidental diagnosis (range from 5% to 40%). Anatomical location of primary tumour in 9747 GISTs demonstrated gastric location as the most frequent (55.6%) followed by small bowel (31.8%), colorectal (6.0%), other/various location (5.5%) and oesophagus (0.7%). Most studies reported incidence at 10-15 per million per year. Notably, lowest incidence was in China (Shanxi province) with 4.3 per million per year. Highest incidence rates were reported also from China (Hong Kong and Shanghai areas), and in Taiwan and Norway (Northern part), with up to 19-22 per million per year.

CONCLUSIONS

Epidemiology of GIST demonstrates some consistent features across geographical regions. Whether the reported extreme differences in incidence reflect real variation in population risk warrants further investigation.

Correlation between mutational status and survival and second cancer risk assessment in patients with gastrointestinal stromal tumors: a population-based study

BACKGROUND

Gastrointestinal stromal tumors are sarcomas of the digestive tract characterized by mutations mainly located in the c-KIT or in the platelet-derived growth factor receptor (PDGFR)-alpha genes. Mutations in the BRAF gene have also been described. Our purpose is to define the distribution of c-KIT, PDGFR and BRAF mutations in a population-based cohort of gastrointestinal stromal tumors (GIST) patients and correlate them with anatomical site, risk classification and survival. In addition, as most of the GIST patients have a long survival, second cancers are frequently diagnosed in them. We performed a second primary cancer risk assessment.

METHODS

Our analysis was based on data from Tarragona and Girona Cancer Registries. We identified all GIST diagnosed from 1996 to 2006 and performed a mutational analysis of those in which paraffin-embedded tissue was obtained. Observed (OS) and relative survival (RS) were calculated according to risk classifications and mutational status. Multivariate analysis of variables for observed survival and was also done.

RESULTS

A total of 132 GIST cases were found and we analyzed mutations in 108 cases. We obtained 53.7% of mutations in exon 11 and 7.4% in exon 9 of c-KIT gene; 12% in exon 18 and 1.9% in exon 12 of PDGFR gene and 25% of cases were wild type GIST. Patients with mutations in exon 11 of the c-KIT gene had a 5-year OS and RS of 59.6% and 66.3%, respectively. Patients with mutations in exon 18 of the PDGFR gene had a 5-year OS and RS of 84.6% and 89.7%. In multivariate analysis, only age and risk group achieved statistical significance for observed survival. GIST patients had an increased risk of second cancer with a hazard ratio of 2.47.

CONCLUSIONS

This population-based study shows a spectrum of mutations in the c-KIT and PDGFR genes in GIST patients similar to that previously published. The OS and RS of GIST with the exon 18 PDGFR gene mutation could indicate that this subgroup of patients may be less aggressive and have a good prognosis, although less sensitive to treatment at recurrence. In our study, GIST patients have an increased risk of developing a second neoplasm.

Molecular spectrum of c-KIT and PDGFRA gene mutations in gastro intestinal stromal tumor: determination of frequency, distribution pattern and identification of novel mutations in Indian patients

KIT and PDGFRA gene mutations are the major genetic alterations seen in gastrointestinal stromal tumors (GISTs) and are being used clinically for predicting response to imatinib therapy. In the current study, we set out to explore the frequency and distribution pattern of c-KIT (exons 9, 11 and 13) and PDGFRA (exons 12 and 18) by direct sequencing in a series of 70 Indian GIST cases. Overall, 27 (38.5 %) and 4 (5.7 %) of the cases had c-KIT and PDGFRA mutations, respectively. Majority of KIT mutations involved exon 11 (85.7 %), followed by exon 9 (14.3 %), while none showed exon 13 mutation. Most exon 9 mutations showed Ala503-Tyr504 duplication, while one had novel point mutation at codon 476 (S476G). In contrast to exon 9 mutations, most exon 11 mutations were in-frame deletions (79 %, 19/24), predominantly at codons 550-560, while remaining exon 11 mutant cases were point mutations at codons 559, 560, 568, 573 and 575. Interestingly, P573T, Q556_V560delinsH, Q575H and Q575_P577 were novel variations observed in exon 11. The PDGFRA mutations were seen mostly in exon 18, which showed point mutation at codon 842 (D842V), while exon 12 showed a novel indel variation (V561_H570delinsT). No significant correlation between c-KIT/PDGFRA mutations and clinicopathological data was observed. In conclusion, this study highlights the frequency and distribution pattern of c-KIT/PDGFRA mutation in Indian cohort. The current study identified novel variations that added new insights into the genetic heterogeneity of GIST patients. Furthermore, this is the first study to report the presence of PDGFRA mutation from Indian subcontinent.

Advances in research of gastrointestinal stromal tumors

Gastrointestinal stromal tumors (GISTs) are the most common mesenchymal tumors of the gastrointestinal tract, arising from the interstitial cells of Cajal (ICCs), primarily in the stomach and small intestine. The growth of most GISTs is driven by the mutations of genes encoding oncogenic receptor tyrosine kinase KIT or platelet derived growth factor receptor alpha (PDGFRα). The pathogenesis of GISTs may involve ICCs, microRNAs (miRNAs), signaling pathways, DNA methylation, and KIT or PDGFRα gene mutations. This article systematically describes the advances in research of GISTs in terms of clinical features, imaging characteristics, endoscopic features, histopathological features, diagnosis and therapies.

Prognostic value of mutational characteristics in gastrointestinal stromal tumors: a single-center experience in 275 cases

The objective of this study was to investigate the impact of KIT/PDGFRA mutations on the prognosis of gastrointestinal stromal tumors (GISTs). In the present study, genotype analyses were performed based on GIST samples from 275 patients. The relationship between mutation and clinicopathological characteristics were explored. All factors were evaluated for their impacts on relapse-free survival (RFS). Briefly, the results of genotype analyses showed that mutations were identified in 258 (93.8 %) patients, and deletion was the most frequent type of mutation accounting for 47.3 % (122/258) of all mutation cases, followed by substitution (87/258, 33.7 %) and duplication (49/258, 19.0 %). Moreover, for KIT exon 11 mutation, the most frequently involved area was from codon 557 to 560. Deep analyses showed that the mutation types were correlated with tumor location (P = 0.005), tumor size (P = 0.022), mitosis rate (P < 0.001), risk grade (P < 0.001), and relapse (P = 0.004). Furthermore, delW557-K558 correlated with mitosis rate (P = 0.042) and relapse (P = 0.036), and delTyr568/570 correlated with tumor origin (P = 0.018). Most importantly, mitotic rate [HR = 2.901 (95 % CI 1.094-7.695), P = 0.032] and risk grade [HR = 9.629 (95 % CI 1.997-46.416), P = 0.005] would be the representative traditional prognostic factors, and deletion with >3 codons would be an novel independent predictor of poor outcome for RFS in GIST patients with deletion mutation of KIT exon 11 [HR = 7.970 (95 % CI 1.774-35.803), P = 0.007]. All results indicated that mutation determined clinicopathological features and prognosis of GISTs, and more than three codons involvement may be a novel adverse indicator.