Ivana Tichá

Screening for genomic rearrangements in BRCA1 and BRCA2 genes in Czech high-risk breast/ovarian cancer patients: high proportion of population specific alterations in BRCA1 gene

Large genomic rearrangements (LGR) represent substantial proportion of pathogenic mutations in the BRCA1 gene, whereas the frequency of rearrangements in the BRCA2 gene is low in many populations. We screened for LGRs in BRCA1 and BRCA2 genes by multiplex ligation-dependent probe amplification (MLPA) in 521 unrelated patients negative for BRCA1/2 point mutations selected from 655 Czech high-risk breast and/or ovarian cancer patients. Besides long range PCR, a chromosome 17-specific oligonucleotide-based array comparative genomic hybridization (aCGH) was used for accurate location of deletions. We identified 14 patients carrying 8 different LGRs in BRCA1 that accounted for 12.3% of all pathogenic BRCA1 mutations. No LGRs were detected in the BRCA2 gene. In a subgroup of 239 patients from high-risk families, we found 12 LGRs (5.0%), whereas two LGRs were revealed in a subgroup of 282 non-familial cancer cases (0.7%). Five LGRs (deletion of exons 1–17, 5–10, 13–19, 18–22 and 21–24) were novel; two LGRs (deletion of exons 5–14 and 21–22) belong to the already described Czech-specific mutations; one LGR (deletion of exons 1–2) was reported from several countries. The deletions of exons 1–17 and 5–14, identified each in four families, represented Czech founder mutations. The present study indicates that screening for LGRs in BRCA1 should include patients from breast or ovarian cancer families as well as high-risk patients with non-familial cancer, in particular cases with early-onset breast or ovarian cancer. On the contrary, our analyses do not support the need to screen for LGRs in the BRCA2 gene. Implementation of chromosome-specific aCGH could markedly facilitate the design of primers for amplification and sequence analysis of junction fragments, especially in deletions overlapping gene boundaries.

Lack of large intragenic rearrangements in dihydropyrimidine dehydrogenase (DPYD) gene in fluoropyrimidine-treated patients with high-grade toxicity

PurposeDeficiency of dihydropyrimidine dehydrogenase (DPD) has been associated with severe fluoropyrimidines (FP) toxicity. Mutations in DPD-coding gene (DPYD) were shown to increase the risk of severe toxicity in FP-treated cancer patients. However, the majority of DPYD alterations characterized in these patients has been considered as polymorphisms and known deleterious mutations are rare and present in only limited subgroup of patients with high toxicity. Recently, the common fragile site FRA1E was mapped within DPYD locus but intragenic rearrangements in DPYD gene were not studied so far.MethodsWe performed the analysis of intragenic rearrangements of DPYD using multiplex ligation-dependent probe amplification in 68 patients with high-grade gastrointestinal and/or hematological toxicity developed at the beginning of FP treatment.ResultsWe did not detect any deletion/duplication of one or more DPYD exons in analyzed patients.ConclusionsWe assume that rearrangements in DPYD gene play insignificant role in the development of serious FP-related toxicity.

Native Red Electrophoresis – A new method suitable for separation of native proteins

A new type of native electrophoresis was developed to separate and characterize proteins. In this modification of the native blue electrophoresis, the dye Ponceau Red S is used instead of Coomassie Brilliant Blue to impose uniform negative charge on proteins to enable their electrophoretic separation according to their relative molecular masses. As Ponceau Red S binds less tightly to proteins, in comparison with Coomassie Blue, it can be easily removed after the electrophoretic separation and a further investigation of protein properties is made possible (e.g. an enzyme detection or electroblotting). The tested proteins also kept their native properties (enzyme activity or aggregation state).

Native polyacrylamide electrophoresis in the presence of Ponceau Red to study oligomeric states of protein complexes

Native polyacrylamide electrophoresis in the presence of two reversible protein anionic stains (Ponceau S and Ponceau 2R) was used to study the oligomeric states of soluble proteins. A mild binding of the used protein stains to nondissociated protein oligomers imposed a charge shift on the proteins resulting into separation of protein species according to their size under physiological conditions. Adsorbed stains could be easily removed after electrophoresis by washing of polyacrylamide gel with buffer and protein complexes could be visualized either by the detection of their enzyme activity or by using a nonspecific protein stain. The specific detection of enzyme activity of glycosidases, lactate dehydrogenase, or phosphatases was shown as an example.

Expression of Glut-1 in Malignant Melanoma and Melanocytic Nevi: an Immunohistochemical Study of 400 Cases

The glucose transporter-1 (Glut-1) is a cell membrane glycoprotein involved in glucose uptake. An increased expression of Glut-1 is an important cell adaptation mechanism against hypoxia. An upregulation of Glut-1 can be found in several types of malignant tumors, which are able to reprogram their metabolism from oxidative phosphorylation to aerobic glycolysis (Warburg effect). However, the data regarding melanocytic lesions is equivocal. We performed comprehensive immunohistochemical analysis of the Glut-1 expression in 225 malignant melanomas (MM) and 175 benign nevi. Only the membranous expression of Glut-1 was regarded as positive. The expression of Glut-1 (the cut-off for positivity was determined as H-score 15) was found in 69/225 malignant melanomas. The number of positive cases and the H-score of Glut-1 increased where there was a higher Breslow thickness (p < 0.00001) when comparing pT1- pT4 MM groups. All benign nevi were classified as negative. In conclusion, the membranous expression of Glut-1 is a common feature of a malignant melanoma but this type of expression is very rare in benign melanocytic nevi. Our results suggest that the membranous expression of Glut-1 can be used as a surrogate marker in the assessing of the biological nature of benign and malignant melanocytic lesions. However, despite its high specificity, the sensitivity of this marker is relatively low. Moreover, due to the fact that the increased expression of Glut-1 correlates with a shorter survival period (10-year disease free survival, recurrence free survival and metastasis free survival and MFS), it can be used as a prognostically adverse factor.

Lymphoepithelioma-like carcinoma of the endometrium: Case report of a rare tumour with comprehensive immunohistochemical and molecular analysis

We are reporting a case of endometrial lymphoepithelioma-like carcinoma (LELC) in a 63-year-old female. Microscopically, the tumor consisted of groups of tumor cells surrounded by dense lymphoplasmacytic infiltrate. Immunohistochemically, the tumour cells were positive for cytokeratins AE1/AE3, EMA, PAX8, p16, and estrogen receptors. Protein p53 showed an aberrant type of expression. Molecular genetic analysis revealed mutations in the TP53 and PIKP53CA genes. Based on our results, we believe that the tumor represents an unusual morphological variant of endometrial serous carcinoma.To the best of our knowledge, only six cases of LELC arising in endometrium have been reported in literature to date.

Detection of EGFR Mutations in Circulating Tumor DNA (ctDNA) Retrieved from Plasma – Interlaboratory Quality Assessment in the Czech Republic

BACKGROUND Detection of EGFR mutations in tumor tissue represents a standard testing procedure in patients with non-small cell lung cancer. Molecular testing of circulating tumor DNA (ctDNA) in plasma enables detection of mutations in cases where tumor specimens are unavailable or when monitoring of therapeutic responses is necessary. In addition, according to the recent literature, ctDNA better reflects the heterogeneity of the neoplastic cell population than isolated tumor lesion or metastasis. We report a national interlaboratory evaluation aimed at assessing the analytical quality of ctDNA EGFR testing in plasma across seven reference laboratories in the Czech Republic. MATERIAL AND METHODS Aliquots of 13 plasma samples were sent to 7 laboratories and consisted of commercially available 2ml plasma specimens of genomic DNA with mutant allelic frequencies of 5, 0.5, 0.05, and 0% of the most common sensitizing mutations (deletion in exon 19, L858R) and the resistance mutation T790M. DNA extraction and EGFR testing were performed according to standard procedures. In 6/7 laboratories the cobas® EGFR Mutation Test v2 was used. One laboratory employed the Super-ARMS® EGFR Mutation Detection Kit. RESULTS In total, 91 genotypes were determined with an overall error rate of 24.2% (22/91). The overall error rates were 3.2% (2/63) for the 0.5% mutation frequency and 0% for the 5% mutation frequency (0/35), respectively. No false positive results were reported. The cobas® method achieved consistent results with the 0.05% mutation frequency for the exon 19 deletion. For L858R and T790M mutations, the threshold was above the 0.5% frequency. CONCLUSIONS The results show that EGFR testing for ctDNA in plasma has limited sensitivity, especially for detection of the T790M mutation. Particularly, in ctDNA testing of very low mutated DNA plasma fractions (below 0.01%), emphasis should be placed on the use of highly sensitive molecular methods. The outcomes of this quality assessment confirm the need for rebiopsy in patients with negative plasma results because of a higher false negative rate in comparison to tissue testing. Key words: circulating DNA - liquid biopsy - epidermal growth factor receptor - non-small cell lung cancer - quality control This work was supported by grants of AstraZeneca and the project of the Ministry of Health number 00064203 (Motol University Hospital). The authors declare they have no potential confl icts of interest concerning drugs, products, or services used in the study. The Editorial Board declares that the manuscript met the ICMJE recommendation for biomedical papers. Submitted: 4. 6. 2018 Accepted: 1. 8. 2018.

Evaluation of Inflammatory Cells (Tumor Infiltrating Lymphocytes) in Solid Tumors

BACKGROUND The tumor microenvironment plays an important role in tumorigenesis and the tumor-host relationship. An important part of the tumor microenvironment is inflammatory infiltration. Its evaluation in solid tumors has prognostic meaning and appears also to be predictive of outcome, which is particularly important for predicting responses to immune checkpoint inhibitors. However, the methodology used to assess inflammatory infiltration is problematic, because it has been standardized only for certain types of tumors. OBJECTIVE The present study provides an overview of current issues related to the evaluation of inflammatory cells (tumor infiltrating lymphocytes) in solid tumors, specifically in tumors of the breast, lung, head and neck, gastrointestinal tract, female genital tract, urogenital tract, brain, malignant mesothelioma, and malignant melanoma. Various methodologies for evaluation are mentioned, including the efforts that are being made to standardize these methodologies and the importance of immunophenotyping inflammatory infiltrates. With regard to clinical meaning, prognostic and predictive significance are also discussed. CONCLUSION The evaluation of TILs in solid tumors often has predictive value; however, the results have been equivocal. There is also ambiguity about the predictive use of this marker. Despite all the methodological developments, which have resulted in the implementation of complicated technologies (image analysis, multiplex fluorescence immunohistochemistry, and mass spectrometry) for the evaluation of the various aspects of inflammatory infiltrates present in tumors, including their functional characteristics, there is still a need for standardization and development of inexpensive and universally available methodologies to enable the wide use of TIL evaluations in clinical settings. The recently proposed unified methodology may be used in all solid tumors and could help resolve one of the main limitations of the routine use of TIL, i.e., the inconsistent approach to assessment.Key words: solid tumors - tumor-infiltratig lymphocytes - inflammatory cells This work was supported by program of the Czech Ministry of Health No. RVO-VFN 64165 and AZV project No. 16-30954A, Charles University and OPPK (CZ.2.16/3.1.00/24509). The authors declare they have no potential conflicts of interest concerning drugs, products, or services used in the study. The Editorial Board declares that the manuscript met the ICMJE recommendation for biomedical papers.Submitted: 24. 9. 2017Accepted: 3. 10. 2017.