Comprehensive molecular screening by next generation sequencing reveals a distinctive mutational profile of KIT/PDGFRA genes and novel genomic alterations: results from a 20-year cohort of patients with GIST from north-western Greece

Introduction

Gastrointestinal stromal tumours (GIST) are mesenchymal neoplasms that usually carry an activating mutation in KIT or platelet-derived growth factor receptor alpha (PDGFRA) genes with predictive and prognostic significance. We investigated the extended mutational status of GIST in a patient population of north-western Greece in order to look at geopraphic/genotypic distinctive traits.

Patient and methods

Clinicopathological and molecular data of 38 patients diagnosed from 1996 to 2016 with GIST in the region of Epirus in Greece were retrospectively assessed. Formalin-fixed paraffin-embedded tumours were successfully analysed for mutations in 54 genes with oncogenic potential. Next generation sequencing was conducted by using the Ion AmpliSeqCancer Hotspot Panel V.2 for DNA analysis (Thermofisher Scientific).

Results

Among 38 tumours, 24 (63.16%) and seven (18.42%) of the tumours harboured mutations in the KIT and PDGFRA genes, respectively, while seven (18.42%) tumours were negative for either KIT or PDGFRA mutation. No mutations were detected in five (13.16%) cases. Concomitant mutations of BRAF and fibroblast growth factor receptor 3 (FGFR3) genes were observed in two patients with KIT gene mutation. Two patients with KIT/PDGFRA wild-type GIST had mutations in either KRAS or phosphatidylinositol-4,5-bisphosphate 3-kinase catalytic subunit alpha (PIK3CA) genes. There was no significant survival difference regarding the exonic site of mutation in either KIT or PDGFRA gene. The presence of a mutation in pathway effectors downstream of KIT or PDGFRA, such as BRAF, KRAS or PIK3CA, was associated with poor prognosis. Adverse prognosticators were also high mitotic index and the advanced disease status at diagnosis.

Conclusions

We report comparable incidence of KIT and PDGFRA mutation in patients with GIST from north-western Greece as compared with cohorts from other regions. Interestingly, we identified rare mutations on RAS, BRAF and PIK3CA genes in patients with poor prognosis.

Abstract P1-03-08: Different genomic rearrangements account for 17% of BRCA1/2 mutations in Greece

AIM: The aim of this study was to further delineate the extent and nature of mutations in the BRCA1 and BRCA2 genes, responsible for hereditary breast and ovarian cancer in Greek families.

MATERAILS & METHODS: Genomic DNA was isolated from whole peripheral blood of patients referred to our center for mutation analysis of the BRCA1 and BRCA2 genes. Patients were included on the basis of affected family members, types of cancer present in the family and age at diagnosis of breast cancer in the proband. Families were subdivided into high, medium and low risk depending on the number of affected family members, types of cancer diagnosed in the family and age at diagnosis of affected family members. In total, 675 families have been analyzed by our group in the past 4 years. Mutation analysis in all cases included sequencing of the coding region and the splice sites of the two genes. In addition, MLPA analysis was carried in 585 of the patients.

RESULTS: In total, a pathogenic mutation has been identified in 12% of the 675 patients analyzed. Of the 78 mutations identified in total, 13 (17%) were large genomic rearrangements. These were deletions of exons 8, 20, 23, 23-24 and the entire BRCA1 gene, in addition to a duplication of exons 3-8 of the BRCA1 gene. As far as BRCA2 is involved deletions of exons 3, 15 and the entire BRCA2 gene were detected. All deletions were confirmed by use of other MLPA probe sets and/or relative quantitation by Real Time PCR. Of the rearrangements identified, two, namely deletions of exon 20 and exons 23-24 of the BRCA1 gene were identified in more than one unrelated families. In addition, the recurrent mutations 5382insC and G1738R, which have been previously identified as founder mutations in the Greek population, were identified in multiple unrelated analyzed families.

CONCLUSIONS: Our results indicate that different large genomic rearrangements account for an important proportion (17%) of the mutations in the BRCA1 and BRCA2 genes, in Greek families at risk of carrying a germline mutation as judged by family / personal history. The use of the available technologies for the identification of such mutational events is therefore necessary when carrying out complete analysis of the genes in high risk families of Greek background.

Citation Format: Angela Apessos, Eirini Papadopoulou, Vassiliki Metaxa-Mariatou, Konstantinos Agiannitopoulos, Christos Markopoulos, Vasileios Venizelos, Grigorios Xepapadakis, Maria Vasilaki-Antonatou, Antonios Keramopoulos, Nikolaos Bredakis, Aristeidis Tsiftsoglou, Georgios Kesisis, Stylianos Kakolyris, Nikolaos Touroutoglou, Ioannis Natsiopoulos, Konstantinos Papazisis, Georgios Nasioulas. Different genomic rearrangements account for 17% of BRCA1/2 mutations in Greece [abstract]. In: Proceedings of the Thirty-Seventh Annual CTRC-AACR San Antonio Breast Cancer Symposium: 2014 Dec 9-13; San Antonio, TX. Philadelphia (PA): AACR; Cancer Res 2015;75(9 Suppl):Abstract nr P1-03-08.

Novel germline mutations of the MEN1 gene in Greek families with multiple endocrine neoplasia type 1

INTRODUCTION

Multiple endocrine neoplasia type 1 (MEN1) is an autosomal dominant hereditary disorder associated with mutations of the MEN1 gene and characterized by the combined occurrence of tumours of the parathyroid glands, the pancreatic islet cells and the anterior pituitary.

AIM

To identify MEN1 gene mutations and characterize clinical manifestations in Greek patients with MEN1.

PATIENTS AND METHODS

We studied four unrelated index patients with MEN1, 17 relatives and 100 control subjects. Among the relatives, seven were clinically and/or biochemically affected, while 10 were unaffected. DNA extraction, polymerase chain reaction (PCR) and direct sequencing of the MEN1 exons 2-10 and exon/intron boundaries were performed according to standard procedures.

RESULTS

We identified novel MEN1 gene mutations in three out of four index patients (75%) and in all affected (100%) relatives. Novel mutations included: a frameshift mutation in exon 4 (c.684_685insG) at codon 229 (index patient A); a frameshift mutation in exon 8 (c.1160_1170dupAGGAGCGGCCG) involving codons 387-390 (index patient B); and a missense mutation in exon 4 (c.776T > C), which substitutes leucine with proline at codon 259 (L259P) (index patient C). In the fourth index patient, a common polymorphism (D418D) was detected.

CONCLUSIONS

This is the first report to reveal a high prevalence of novel MEN1 gene mutations among Greek MEN1 patients with apparent absence of genotype-phenotype correlation. Because of the small number of patients examined, the high prevalence detected might be a chance phenomenon.

Subtype C1 persistent infection of HHV-8 in a PEL patient

PEL, a rare type of lymphoma constituting less than 5% of NHLs, has been recently identified as a distinct clinical and pathological entity among the B-cell lymphomas, with characteristic morphologic, immunophenotypic, molecular and viral features. ICC, PCR, RT-PCR and sequencing were carried out in biologicals samples from a 44-year-old, non-smoker Caucasian male patient of Greek nationality, HIV-1 negative and HCV positive. The ICC results showed CD30 + , Vimentin + , EMA + , Ki67 + , Pankeratin- and negative to B and T antibodies. In addition, HHV-8 was detected in pleural fluid. Examination of blood samples of the patient over a period of nearly two years showed a persistent infection of HHV-8. Phylogenetic analysis revealed a close relation to the C1 variant of HHV-8. The samples was also found EBV negative by PCR. Using a combination of clinical, morphological, immunohistochemical features and molecular biology techniques in this study we document a PEL case with persistent HHV-8 of genotype C1 infection.

The implications of using mutagenic primers in combination with Taq polymerase having proofreading activity

Polymerases with proofreading activity provide high fidelity PCR amplifications. In this study we examined the consequences of using a Taq polymerase with proofreading activity, such as Optimase Taq polymerase, in combination with 4 different mutagenic reverse primers for the amplification of a 345-bp FII PCR product. The amplifications were performed with Optimase Taq polymerase (Transgenomic), and Taq DNA polymerase-recombinant (Invitrogen), without proofreading activity. Mutation screening was carried out by DHPLC and restriction fragment analysis. The usage of Optimase Taq polymerase results in complete reversion of the first and second mutated nucleotide introduced at the 3' end of the mutagenic reverse primer. It also partially reverses the missense nucleotide introduced in the third position of the mutagenic primer and leads to misleading DHPLC and restriction fragment analysis patterns. Nevertheless it cannot perform such an activity when an abnormal nucleotide is introduced in the fourth position.

Molecular analysis of GISTs: evaluation of sequencing and dHPLC

Gastrointestinal stromal tumors (GISTs) are the most common mesenchymal tumors of the gastrointestinal tract and are characterized by mutations in the proto-oncogene KIT (c-kit). To date, the detection of genomic alterations of the c-kit gene has been based mostly on direct sequencing. However, sequencing is an expensive and time-consuming approach. Since the technology of WAVE DNA Fragment Analysis System (Transgenomic, Inc., Worcester, MA) (dHPLC) is available in our laboratory, we decided to evaluate its use. Sixteen patients with small/large intestine, stomach tumors were included in the study. Immunohistochemical evaluation was performed on formalin-fixed, paraffin-embedded specimens with the polyclonal antibody CD117 for the KIT protein. After DNA extraction and isolation from paraffin-embedded sections, a nested PCR approach was applied to amplify sequences of exon 11 of the c-kit gene. dHPLC and the ABI Prism 310 Genetic Analyzer (Applied Biosystems, Bedford, MA) were used respectively for screening and identification of genomic alterations. Immunohistochemical analysis revealed strong and diffuse KIT expression in each of the 16 paraffin-embedded sections examined. dHPLC analysis in two temperatures showed the presence of genomic alterations in 8 out of 16 (50%) samples examined. Subsequently, sequence analysis of exon 11 in those samples revealed c-kit alterations in only 8 out of 16 (50%) samples. These were five deletions, one of which was an in-frame deletion one-point mutation and one insertion. Furthermore, the sensitivity of both methods was compared by using different mixtures of a wild-type and a sample with a deletion in exon 11. dHPLC was shown to be able to detect genomic alterations in all four different sample mixtures, whereas with sequence analysis genomic alterations were detected only in the 1:2 and 1:4 sample mixtures. In conclusion, we showed that dHPLC is an efficient and accurate, as well as a more sensitive, method for screening of genomic alterations in exon 11 of the c-kit gene, compared to sequence analysis.

Human herpesvirus type 8 genotypes in iatrogenic, classic and AIDS-associated Kaposi's sarcoma from Greece

BACKGROUND

Kaposi's sarcoma-associated herpesvirus (KSHV)/human herpesvirus 8 (HHV-8) is consistently found in almost all observed Kaposi's sarcomas (KS), whether AIDS-associated, iatrogenic or classic. To our knowledge no data are available on the genetic polymorphism of HHV-8 from Greece. We report the study of 15 renal transplant recipients with KS, 5 with AIDS-associated KS, 11 with classic KS and 60 healthy individuals from Greece.

MATERIALS AND METHODS

Polymerase chain reaction (PCR) was carried out on DNA extracted from peripheral-blood mononuclear cells (PBMC) or KS cutaneous biopsies, using specific primers for the HHV-8, KS330 fragment from ORF-26 (233 bp) and the highly variable region (VR1) from ORF-K1 (363 bp).

RESULTS

HHV-8 DNA was detected in 30 out of 31 (97%) KS cases, regardless of their clinico-pathological subtype and in 10 out of 60 (16.7%) healthy individuals. Sequencing of the ORF26 fragment demonstrated that the 40 HHV-8 strains were of the A and C sub-types. Furthermore, sequencing of the ORF-K1 showed that these HHV-8 strains of Greek origin were of the A1, A4, C1 or C3 sub-type.

CONCLUSION

Our findings imply a possible link of the C3 subtype of HHV-8 in renal transplant-related KS cases (iatrogenic KS) in Greece, a link of the A4 subtype in AIDS-associated KS cases and a potential involvement of the A1 subtype in Greek classic KS incidences, as HHV-8 strains among healthy individual tested belong to the C1, C3 or A1 subtypes.

Molecular analysis of Kaposi's sarcoma occurring during haemodialysis

Human Herpesvirus 8 (HHV-8) has been implicated in the pathogenesis of Kaposi's sarcoma (KS). In this paper we attempted to confirm the connection between dialysis, HHV-8, and KS by examining the case of an elderly haemodialysis nonimmunosuppressed male patient with end-stage renal disease, who developed KS. By using PCR we have verified the presence of DNA from two different genomic regions (ORF 26 and ORF K1) of HHV-8. In addition, our RT-PCR results suggest active replication of HHV-8 in blood and KS lesions of the patient. Phylogenetic analysis revealed identical DNA sequence to ORF K1, and a close relation to its C1 variant. In conclusion, we document the case of KS and HHV-8 coexistence in a Greek elderly patient undergoing regular haemodialysis. Furthermore, our results indicate that factors other than immunosuppression could lead to KS development possibly due to activation of HHV-8.

Documentation of Legionella pneumophila and Mycobacterium tuberculosis co-existence in a patient with acute respiratory distress syndrome

BACKGROUND

Bacterial lung infections are common causes of ARDS and, despite intensive research for decades, the mortality rate remains very high. Only two reports suggest the co-existence of Legionnaires' disease and pulmonary tuberculosis based mainly on clinical presentation and serologic results for Legionella and positive cultures for Mycobacterium tuberculosis (M. tuberculosis).

MATERIALS AND METHODS

A variety of specimens from a 61-year-old man was used for detection of Legionella pneumophila (L. pneumophila) and M. tuberculosis by PCR. Further identification of the pathogens was carried out by sequence analysis.

RESULTS

L. pneumophila region mip was detected in bronchial washings, bronchoalveolar lavage and urine specimens of the patient. M. tuberculosis regions IS6110 and mtp40 were detected in endo-bronchial secretions and bronchoalveolar lavage.

CONCLUSION

By using polymerase chain reaction (PCR) and DNA sequencing we documented L. pneumophila and M. tuberculosis co-existence, in multiple specimens of a patient presenting with acute respiratory distress syndrome (ARDS). Furthermore, the efficacy of the specific antibiotic treatment, based on the PCR results, suggest the co-existence of these two pathogens.

The impact of heterozygosity for the factor V Leiden and factor II G20210A mutations on the risk of thrombosis in Greek patients

AIM

There is growing evidence that a number of genetic risk factors predispose independently to venous thrombosis and the coexistence of defective genes is involved in the manifestation and recurrence of thrombotic events. The goal of this study was to examine the efficiency of the selection criteria for performing a genetic test for the factor V G1691A (Leiden) and factor II G20210A mutations.

METHODS

Blood samples were drawn from 119 patients referred to us by their physicians. FV and prothrombin (FII) mutations were detected by polymerase chain reaction (PCR) followed by digestion with restriction endonucleases MnlI (FV), HindIII and MspI (FII).

RESULTS

Patient carrier frequencies were 16.8% and 10.08% for FV Leiden and FII G20210A, respectively. Heterozygosity for FII G20210A was observed in 10.0% of FV Leiden carriers whereas FV Leiden homozygosity was noted in 1.68% of the patients. Genotype frequencies were in conformity with Hardy-Weinberg equilibrium by the chi square goodness of fit test.

CONCLUSION

The obtained data provided a substantial genetic explanation of the thrombotic phenotype in approximately 25% of the patients and thus the physicians selection criteria were sufficient for genetic testing. Furthermore, coinheritance of both genetic defects were significantly associated with increased thrombosis risk and that of recurrent thrombosis.

Elastin distribution in the myometrial and vascular smooth muscle of the human uterus

Magnetic resonance imaging and transvaginal ultrasonography in women of reproductive age suggest that the myometrium consists of inner and outer layers. It was hypothesized that these structural and functional differences in the myometrium might be associated with a variation in elastin distribution. Fifty-one hysterectomy specimens representing all phases of the normal menstrual cycle were studied by immunocytochemistry, orcein staining and image analysis. Elastin was present within the outer myometrial smooth muscle, but was less widely distributed in the inner smooth muscle. Immunoreactivity and staining were observed in the myometrial arteries and arterioles and within the basal portions of endometrial arterioles. Elastin was also present in perivascular tissue, particularly near the large vessels. More extravascular (i.e. perivascular and smooth muscle) elastin was present in the outer myometrium in all cases, although no distinct layering was observed. Semi-quantitative analysis of the elastin distribution in 11 full thickness specimens demonstrated a decreasing gradient from outer to inner myometrium rather than distinct layering. Contrary to previous reports, these data suggest that the external region of the myometrium is more elastic than the inner region and that elastin is found throughout the arteriolar tree of the human uterus.