[show abstract][hide abstract] ABSTRACT: Double-strand DNA breaks (DSBs) are continuously induced in cells by endogenously generated free radicals and exogenous genotoxic agents such as ionizing radiation. DSBs activate the kinase activity in sensor proteins such as ATM and DNA-PK, initiating a complex DNA damage response that coordinates various DNA repair pathways to restore genomic integrity. In this study, we report the unexpected finding that homologous chromosomes contact each other at the sites of DSBs induced by either radiation or the endonuclease I-PpoI in human somatic cells. Contact involves short segments of homologous chromosomes and is centered on a DSB in active genes but does not occur at I-PpoI sites in intergenic DNA. I-PpoI-induced contact between homologous genes is abrogated by the transcriptional inhibitors actinomycin D and α-amanitin and requires the kinase activity of ATM but not DNA-PK. Our findings provide documentation of a common transcription-related and ATM kinase-dependent mechanism that induces contact between allelic regions of homologous chromosomes at sites of DSBs in human somatic cells.
Proceedings of the National Academy of Sciences 05/2012; 109(24):9454-9. · 9.74 Impact Factor
[show abstract][hide abstract] ABSTRACT: Molecular testing for mutations activating the mitogen-associated protein kinase signaling pathway is being used to help diagnose thyroid carcinomas. However, the prevalence of these mutations in thyroid lymphomas has not been reported. Therefore, we studied the prevalence of BRAF, NRAS, HRAS, and KRAS mutations in 33 thyroid lymphomas and correlated the mutational status with the clinical, pathological, cytogenetic, and immunophenotypic findings. Eleven cases were also tested for PAX8/PPARγ translocations. The lymphomas included 25 diffuse large B-cell lymphomas, 6 extranodal marginal-zone lymphomas of mucosa-associated lymphoid tissue type, and 2 follicular lymphomas. Seventeen diffuse large B-cell lymphomas were germinal center type, six non-germinal center type, and two unclassifiable (Hans algorithm). None of the cases had an associated thyroid carcinoma. Mutations of the BRAF gene were identified in six (24%) diffuse large B-cell lymphomas (D594G in three germinal center diffuse large B-cell lymphomas, K601N in two germinal center diffuse large B-cell lymphomas, and V600E in one non-germinal center diffuse large B-cell lymphoma) and of the NRAS gene in two (8%) non-germinal center diffuse large B-cell lymphomas (Q61K and Q61H). BRAF and NRAS mutations were not found in any extranodal marginal-zone lymphomas of mucosa-associated lymphoid tissue type or follicular lymphomas. HRAS and KRAS mutations were not identified in any of the cases, nor were PAX8/PPARγ translocations found. Thus, interpretation of finding a BRAF or NRAS mutation in the thyroid, particularly in preoperative thyroid aspirates, must take into account the differential diagnosis of a lymphoma. In addition to the diagnostic importance, our data also demonstrate that alteration in the mitogen-associated protein kinase pathway may have a role in the pathogenesis of some large B-cell lymphomas of the thyroid with potential therapeutic implications.
Modern Pathology 05/2012; 25(9):1203-11. · 5.25 Impact Factor
[show abstract][hide abstract] ABSTRACT: Papillary thyroid carcinoma (PTC) has relatively indolent behavior, although some tumors recur and disseminate to distant sites. The aggressive biological behavior of PTC is difficult to predict. MicroRNAs (miRNAs) are dysregulated in various tumors types, and some of them serve as markers of poor prognosis. In this study, we evaluated miRNA expression as a marker of more aggressive behavior in PTC.
miRNA array was used to identify a subset of differentially expressed miRNAs between aggressive and nonaggressive PTC. These miRNAs were further validated by real-time RT-PCR in a cohort of 17 PTC with local tumor recurrence or distant metastases and 15 PTC with no extrathyroidal dissemination and correlated with BRAF, RAS, and RET/PTC mutations and MET expression.
The miRNA array identified miR-146b, miR-221, miR-222, miR-155, miR-31 upregulation and miR-1, miR-34b, miR-130b, miR-138 downregulation in aggressive compared with nonaggressive PTC. Significant miRNA deregulation was confirmed in the validation cohort, with upregulation of miR-146b and miR-222 and downregulation of miR-34b and miR-130b seen in aggressive PTC. Among BRAF-positive tumors, miR-146b showed strong association with aggressive PTC. MET was identified as a potential target gene for 2 downregulated miRNAs (miR-34b and miR-1), and significantly higher level of MET expression was observed in aggressive PTC.
We demonstrate that miR-146b, miR-222, miR-34b, miR-130b are differentially expressed in aggressive compared with nonaggressive PTC. Among BRAF-positive tumors, overexpression of miR-146b was associated with aggressive behavior, suggesting that it may further refine the prognostic importance of BRAF.
Annals of Surgical Oncology 07/2011; 18(7):2035-41. · 4.12 Impact Factor
[show abstract][hide abstract] ABSTRACT: Ionizing radiation is a well-known mutagen and a risk factor for thyroid cancer. MicroRNAs (miRNAs) play an important role in the regulation of gene expression on post-transcriptional level and are dysregulated in thyroid cancer. The goal of this study was to investigate the effects of acute exposure to 1 and 10 Gy of γ-irradiation on miRNA expression in normal human thyroid cells.
Expression of 319 miRNAs was studied in primary cultures of normal human thyroid cells 4 and 24 hours postirradiation using a miRNA expression array with further confirmation of miRNAs expression by reverse transcription-polymerase chain reaction.
We identified 30 miRNAs that were unregulated or downregulated more than twofold after irradiation as compared to nonirradiated thyroid cells, with no significant difference found between 1 and 10 Gy of radiation. Four distinct patterns of miRNA expression change were observed: miRNAs downregulated at 4 hours and returned to normal levels at 24 hours, miRNAs upregulated at 4 hours and returned to normal levels at 24 hours, and miRNAs either upregulated or downregulated at both time points. No dysregulation of miRNAs known to occur in thyroid cancer was observed.
Acute exposure of thyroid cells to γ-radiation results in several specific patterns of miRNA response. It appears that alteration in miRNA expression seen 4-24 hours after irradiation has no direct association with carcinogenesis. However, it is likely to affect other cell functions, such as DNA repair.
Thyroid: official journal of the American Thyroid Association 02/2011; 21(3):261-6. · 2.60 Impact Factor
[show abstract][hide abstract] ABSTRACT: MicroRNA (miRNA) expression is deregulated in lung cancer, and some miRNAs are associated with poor prognosis and survival. In this study, we investigated the miRNA expression in lung adenocarcinomas with different oncogenic mutations, including EGFR-positive, KRAS-positive and EGFR/KRAS-negative tumors. The expression of 319 miRNAs was evaluated by Exiqon/Luminex microarray, and expression of individual miRNAs was validated by individual RT-PCR assays (Applied Biosystems). Overall, miRNA expression was similar among three mutationally different groups with most upregulated miRNAs being miR-20a, miR-328, miR-34c and miR-18b and most downregulated miRNAs being miR-32, miR-137 and miR-342. Four miRNAs (miR-155, miR-25, miR-495 and miR-7g) were expressed differently among these tumors. miR-155 was upregulated only in EGFR/KRAS-negative group, miR-25 was upregulated only in EGFR-positive group and miR-495 was upregulated only in KRAS-positive adenocarcinomas. In opposite, let-7g was downregulated in all three groups, with more significant downregulation in EGFR/KRAS-negative adenocarcinomas. Principal component analysis (PCA) revealed significant correlation between miRNA expression patterns and somatic mutations. In this study, we demonstrated that despite the similarity in miRNA expression among lung adenocarcinomas with different somatic mutations, some miRNAs showed unique expression patterns, which were in strong correlation with the mutation type, suggesting different carcinogenic pathway for these tumors. These miRNAs can be further explored for their diagnostic and prognostic use.
Modern Pathology 12/2010; 23(12):1577-82. · 5.25 Impact Factor
[show abstract][hide abstract] ABSTRACT: The MECT1/MAML2 translocation is identified in a large proportion of mucoepidermoid carcinomas (MEC) of the salivary gland and is an emerging favorable prognosticator. However, there are conflicting data on this translocation's specificity, restriction to low/intermediate MEC, and strength as a prognosticator. We present our experience with the MECT1/MAML2 translocation in a large cohort of MECs to address these issues. We analyzed 55 salivary MEC and 36 potential MEC mimics (24 Warthin tumors, 5 oncocytomas, 3 squamous cell carcinomas, 2 squamoid salivary duct carcinomas, 1 lymphoepithelial cyst, 1 Schneiderian carcinoma ex papilloma) for presence of the MECT1/MAML2 translocation by fluorescent in-situ hybridization (FISH) and real-time RT-PCR. Overall, MECT1/MAML2 translocation was present in 36/55 (66%) of MEC whereas all 36 non-MEC were negative for translocation. Low or intermediate-grade MEC had a higher frequency of translocation (75%) than high-grade MEC (46%) (P=0.039). Translocation positive cases had a better disease-specific survival (log rank P=0.026) although 2 patients still died of disease. Within high-grade MEC, MECT1/MAML2 positive tumors had lower rates of anaplasia (P=0.001), and mitotic counts (P=0.012). Thus, MECT1/MAML2 translocation is highly specific for MEC and imparts a better prognosis. However, it is frequent even within high-grade MEC and can be seen in lethal cases suggesting that translocation status should not supersede conventional parameters. There are 2 distinct subgroups within high-grade MEC, and the translocation negative tumors may actually be more appropriately categorized as another tumor type (such as adenosquamous carcinoma).
The American journal of surgical pathology 08/2010; 34(8):1106-21. · 4.06 Impact Factor
[show abstract][hide abstract] ABSTRACT: Novel mutations in the isocitrate dehydrogenase 1 (IDH1) and 2 (IDH2) genes have been identified in a large proportion of diffuse gliomas. Tumors with IDH1/2 mutations have distinctive clinical characteristics, including a less aggressive course. The aim of this study was to develop and evaluate the performance of a novel real-time PCR and post-PCR fluorescence melting curve analysis assay for the detection of IDH1 and IDH2 mutations in routine formalin-fixed, paraffin-embedded tissues of brain biopsies. Using the established assay, we tested 67 glial neoplasms, 57 non-neoplastic conditions that can often mimic gliomas (eg, radiation changes, viral infections, infarctions, etc), and 44 noncentral nervous system tumors. IDH1 and IDH2 mutations were detected in 72% of lower grade diffuse gliomas and in 17% of glioblastomas. The IDH1 mutation was the most common (93%), with the most frequent subtype being R132H (88%). These mutations were not identified in non-neoplastic glioma mimickers and in noncentral nervous system tumors including thyroid carcinomas. The results of this assay had a 100% correlation with the results obtained by conventional sequencing. In summary, we report here the real-time PCR/fluorescence melting curve analysis assay that provides rapid and sensitive detection of IDH mutations in formalin-fixed, paraffin-embedded tissues, and is therefore useful as a powerful adjunct diagnostic tool for refining histopathological diagnosis of brain lesions and guiding patient management.
The Journal of molecular diagnostics: JMD 07/2010; 12(4):487-92. · 3.48 Impact Factor
[show abstract][hide abstract] ABSTRACT: Mutations in isocitrate dehydrogenase enzyme isoforms 1 (IDH1) and 2 (IDH2) have been identified in many adult astrocytomas and oligodendrogliomas. These mutations are targeted to specific codons (e.g. R132 in IDH1 and R172 in IDH2), making assays to detect them in clinical specimens feasible. We describe a simple and accurate molecular assay for detection of IDH1/2 mutations on routine formalin-fixed paraffin-embedded tissues. Using this polymerase chain reaction-based assay, we tested 75 glial neoplasms and 57 nonneoplastic conditions that can mimic gliomas including radiation changes, viral infections, and infarcts. Of the gliomas, 37 (49%) were positive for IDH1 or IDH2 mutations; the most common mutation was IDH1 (97%). Two of 12 gangliogliomas were positive for IDH1 mutation, and both had unfavorable clinical outcomes (p < 0.03). None of the nonneoplastic cases were positive for IDH mutations. The assay detected IDH mutations in biopsy material containing mostly glioma and in concomitant near-miss stereotactic core biopsies that were otherwise equivocal for the presence of glioma by light microscopy. These results indicate that testing for IDH1/2 mutations can be effectively performed in a clinical setting and can enhance the accuracy of diagnosis of gliomas when traditional diagnostic methods are not definitive.
Journal of Neuropathology and Experimental Neurology 11/2009; 68(12):1319-25. · 4.35 Impact Factor