Myoepithelial carcinoma of salivary glands is an underrecognized and challenging entity with a broad morphologic spectrum, including an EWSR1-rearranged clear cell variant. Myoepithelial carcinoma is generally aggressive with largely unknown genetic features. A retrospective review of Salivary Gland Tumor Registry in Pilsen searching for the key words "clear cell myoepithelial carcinoma," "hyalinizing clear cell," and "clear cell malignant myoepithelioma" yielded 94 clear cell myoepithelial carcinomas (CCMCs) for molecular analysis of EWSR1 rearrangement using fluorescence in situ hybridization (FISH). Tumors positive for EWSR1 gene rearrangement were tested by next-generation sequencing (NGS) using fusion-detecting panels. NGS results were confirmed by reverse-transcription polymerase chain reaction or by FISH. Twenty-six tumors originally diagnosed as CCMC (26/94, 27.6%) revealed split signals for EWSR1 by FISH. Six of these tumors (6/26, 23%) displayed amplification of the EWSR1 locus. Fifteen cases were analyzable by NGS, whereas 9 were not, and tissue was not available in 2 cases. None of the CCMCs with EWSR1 rearrangements detected by FISH had an EWSR1 fusion transcript. Fusion transcripts were detected in 6 cases (6/15, 40%), including LIFR-PLAG1 and CTNNB1-PLAG1, in 2 cases each, and CHCHD7-PLAG1 and EWSR1-ATF1 fusions were identified in 1 case each. Seven cases, including those with PLAG1 fusion, were positive for PLAG1 rearrangement by FISH, with notable exception of CHCHD7-PLAG1, which is an inversion not detectable by FISH. One single case with EWSR1-ATF1 fusion in NGS showed ATF1 gene rearrangement by FISH and was reclassified as clear cell carcinoma (CCC). In addition, another 4 cases revealed ATF1 rearrangement by FISH and were reclassified as CCC as well. Moreover, 12/68 (17%) CCMCs with intact EWSR1 gene were selected randomly and analyzed by NGS. PLAG1 fusions were found in 5 cases (5/12, 41.6%) with LIFR (2 cases), FGFR1 (2 cases), and CTNNB1 (1 case) as partner genes. Overall, PLAG1 gene rearrangements were detected in 10/38 (26%) tested cases. None of the tumors had SMARCB1 loss by immunohistochemistry as a possible explanation for the EWSR1 abnormalities in FISH. Novel findings in our NGS study suggest that EWSR1-FISH positive CCMC is a gene fusion-driven disease with frequent oncogenic PLAG1 fusions, including LIFR-PLAG1 and CTNNB1-PLAG1 in most cases. Productive EWSR1 fusions are found only in a minority of EWSR1-ATF1-rearranged cases, which were in part reclassifiable as CCCs. Detectable EWSR1-FISH abnormality in CCMCs without gene fusion perhaps represents a passenger mutation with minor or no oncologic effect.
- MeSH
- DNA vazebné proteiny genetika MeSH
- dospělí MeSH
- genová přestavba MeSH
- lidé středního věku MeSH
- lidé MeSH
- myoepiteliální nádor genetika MeSH
- nádory slinných žláz genetika MeSH
- onkogenní fúze MeSH
- protein EWS vázající RNA genetika MeSH
- senioři MeSH
- stanovení celkové genové exprese MeSH
- Check Tag
- dospělí MeSH
- lidé středního věku MeSH
- lidé MeSH
- mužské pohlaví MeSH
- senioři MeSH
- ženské pohlaví MeSH
- Publikační typ
- časopisecké články MeSH
- práce podpořená grantem MeSH
Oncocytomas (OCs) in salivary glands are rare benign tumors composed of mitochondria-rich epithelial cells (oncocytes), mostly localized in the parotid gland. The treatment of choice is simple excision. Extensive oncocytic metaplasia of pleomorphic adenoma (PA) and myoepithelioma (ME) can be diagnostically challenging and may camouflage the correct diagnosis. These tumors should be treated more carefully compared with OC, given the risk of frequent recurrences and the possibility of malignant transformation. We have investigated 89 oncocytic lesions from our files, including OC (n = 74) and metaplastic oncocytic variant of PA/ME (n = 15). All OCs were stained for S100 protein and SOX10. The tumors with immunohistochemical expression of one or both markers were tested by next-generation sequencing (NGS). The NGS results were confirmed by reverse transcription-polymerase chain reaction (RT-PCR) and/or fluorescence in situ hybridization (FISH). Ten cases originally diagnosed as OC, and 1 low-grade uncertain oncocytic tumor (11/74) revealed nuclear-cytoplasmic and/or nuclear positivity for S100 protein and/or SOX10, respectively. Fusion transcripts CHCHD7-PLAG1 and GEM-PLAG1 were found in 2 cases (1 fusion in each), and these were confirmed by RT-PCR and PLAG1 break-apart FISH probe, respectively. Another 5 cases were positive for PLAG1 rearrangement by FISH. In the control group of 15 oncocytic PA/ME, 4/15 tested tumors harbored gene fusions including NFT3-PLAG1, CHCHD7-PLAG1, FBXO32-PLAG1, and C1orf116-PLAG1 (1 fusion in each case) as detected by NGS. Two fusions were confirmed by RT-PCR, 1 case by FISH, and 1 case was not analyzable by FISH. We additionally tested 24 OCs negative for S100 protein and SOX10 by immunohistochemistry (IHC) and by FISH for rearrangement of PLAG1 gene, but none of them were positive. SOX10 and/or S100 protein immunopositivity in conjunction with rearrangement of the PLAG1 gene assisted in reclassification of a subset of oncocytomas as oncocytic variants of PA and ME. Therefore, we recommend to include S100 protein and SOX10 IHC when diagnosing tumors with predominantly oncocytoma-like differentiation. In addition, by NGS, 3 new gene fusions were detected in oncocytic ME, including NTF3-PLAG1, FBXO32-PLAG1, and GEM-PLAG1, and a new fusion C1orf116-PLAG1 was detected in oncocytic PA.
- MeSH
- dospělí MeSH
- lidé středního věku MeSH
- lidé MeSH
- myoepiteliální nádor diagnóza genetika MeSH
- nádorové biomarkery analýza MeSH
- nádory slinných žláz diagnóza genetika MeSH
- onkogenní fúze MeSH
- oxyfilní adenom diagnóza genetika MeSH
- pleomorfní adenom diagnóza genetika MeSH
- proteiny S100 analýza biosyntéza MeSH
- retrospektivní studie MeSH
- senioři nad 80 let MeSH
- senioři MeSH
- transkripční faktory SOXE analýza biosyntéza MeSH
- Check Tag
- dospělí MeSH
- lidé středního věku MeSH
- lidé MeSH
- mužské pohlaví MeSH
- senioři nad 80 let MeSH
- senioři MeSH
- ženské pohlaví MeSH
- Publikační typ
- časopisecké články MeSH
- práce podpořená grantem MeSH
Although lichenized fungi are among the most reliable indicators of forest quality and represent a considerable part of forest biodiversity, methods maximizing completeness of their species lists per area are lacking. Employing a novel methodological approach including a multi-expert competition and a search for local hot-spot plots, we have obtained outstanding data about epiphytic lichen biota in a part of the largest Central European virgin forest reserve Uholka-Shyrokyi Luh situated in Ukrainian Carpathians. Our field research consisted of two four-day periods: (1) an overall floristic survey and a search for spots with raised lichen diversity, and (2) survey in four one-hectare plots established in lichen diversity hot-spots along an altitudinal gradient. Recorded alpha-diversities in plots ranged from 181-228 species, but estimated species richness is in the range 207-322 species. Detected gamma-diversity was 387 species; estimates are 409-484 species. 93% of the species found in the forest were recorded in plots, but only 65% outside the plots. This underlines the high-efficiency of the multi-expert competitive survey in diversity hot-spot plots. Species richness in each one-hectare plot was equal to the numbers of species obtained by floristic surveys of much larger old-growth forest areas in Central Europe. Gamma-diversity detected in the Uholka primeval forest far exceeded all numbers achieved in Central European old-growth forests. Our method appears to be both effective (it obtains a more nearly complete inventory of species) and practical (the resources required are not unreasonably large).
Identifying factors that influence species interactions is central to research in symbiotic systems. While lichens represent iconic models of symbiosis and play important roles in understanding the biology of symbiotic interactions, patterns of interactions in lichen symbionts and mechanisms governing these relationships are not well characterized. This is due, in part to the fact that current taxonomic approaches for recognizing diversity in lichen symbionts commonly fail to accurately reflect actual species diversity. In this study, we employed DNA-based approaches to circumscribed candidate species-level lineages in rock-posy lichen symbionts (mycobiont=Rhizoplaca s. lat. species; photobiont=Trebouxia species). Our results revealed a high degree of cryptic diversity in both the myco- and photobionts in these lichens. Using the candidate species circumscribed here, we investigated the specificity of the symbionts toward their partners and inferred the relative importance of various factors influencing symbiont interactions. Distinct mycobiont species complexes, ecozones, and biomes are significantly correlated with the occurrence of photobiont OTUs, indicating that complex interactions among mycobiont lineages, ecogeography, and microhabitat determine interactions between photobionts and their mycobionts in lichen symbiosis. One-to-one specificity between mycobiont and photobiont species was not found, with the exception of R. maheui that associated with a single Trebouxia OTU that was not found with other Rhizoplaca s. lat. species. We estimated the most recent common ancestor of the core Rhizoplaca group at c. 62.5Ma, similar in age to the diverse parmelioid core group in the well-studied family Parmeliaceae. However, in contrast to Parmeliaceae, species in Rhizoplaca were found to associate with a narrow range of photobionts. Our study provides important perspectives into species diversity and interactions in iconic lichen symbiotic systems and establishes a valuable framework for continuing research into rock-posy lichens.
Trebouxia aggregata (Archibald) Gärtner (phylum Chlorophyta, family Trebouxiaceae), a lichen symbiotic alga, has been identified as host of the well-known herbaceous plant virus Cauliflower mosaic virus (CaMV, family Caulimoviridae). The alga had been isolated from Xanthoria parietina more than 70 years ago and has been maintained in a collection since that time. The CaMV detected in this collection entry has now been completely sequenced. The virus from T. aggregata is mechanically transmissible to a herbaceous host and induces disease symptoms there. Its genome differs by 173 nt from the closest European CaMV-D/H isolate from cauliflower. No site under positive selection was found on the CaMV genome from T. aggregata. We therefore assume that the virus's presence in this alga was not sufficiently long to fix any specific changes in its genome. Apart from this symbiotic alga, CaMV capsid protein sequences were amplified from many other non-symbiotic algae species maintained in a collection (e.g., Oonephris obesa, Elliptochloris sp., Microthamnion kuetzingianum, Chlorella vulgaris, Pseudococcomyxa sp.). CaMV-free Chlorella vulgaris was treated with CaMV to establish virus infection. The virus was still detected there after five passages. The virus infection is morphologically symptomless on Chlorella algae and the photosynthesis activity is slightly decreased in comparison to CaMV-free alga culture. This is the first proof as to the natural presence of CaMV in algae and the first demonstration of algae being artificially infected with this virus.
- MeSH
- Caulimovirus klasifikace genetika izolace a purifikace MeSH
- Chlorophyta virologie MeSH
- DNA virů chemie izolace a purifikace MeSH
- elektronová mikroskopie MeSH
- molekulární sekvence - údaje MeSH
- sekvence nukleotidů MeSH
- sekvenční seřazení MeSH
- výročí a významné události MeSH
- zlato chemie MeSH
- Publikační typ
- časopisecké články MeSH
- práce podpořená grantem MeSH
