Úvod a cíl: Primární diagnostika distálních biliárních striktur může být někdy svízelná a obtížná. Je známo, že kartáčková cytologie (BC – brush cytology) má v těchto případech nízkou diagnostickou senzitivitu. Fluorescenční in situ hybridizace (FISH) byla popsána jako užitečná doplňková metoda u pacientů se strikturami žlučových cest. Cílem naší studie bylo stanovit diagnostickou výtěžnost BC, FISH a jejich kombinace (BC + FISH) v primární diagnostice distálních biliárních striktur. Metodika: Tato prospektivní studie byla provedena v období od dubna 2019 do ledna 2021. Do studie byli postupně zařazeni pacienti s dosud nebioptovanými biliárními strikturami, kteří podstoupili první endoskopickou retrográdní cholangiopankreatografii (ERCP) na našem pracovišti. Byly provedeny cytologické a FISH analýzy vzorků tkáně odebraných ze dvou standardizovaných transpapilárních odběrů „kartáčkem“ z distálních striktur. Postoperační histologie nebo výsledky 12měsíčního sledování pacientů byly považovány za zlatý standard pro stanovení konečné diagnózy. Výsledky: Do studie bylo zařazeno celkem 109 pacientů. Sedm pacientů bylo z konečné analýzy vyřazeno a 26 mělo proximální stenózu. Ze zbývajících 76 pacientů (61,8 % mužů, průměrný věk 67,6 let, rozmezí 25–89 let) s distální stenózou byl podíl benigních a maligních striktur 25 (32,9 %), resp. 51 (67,1 %). Z podskupiny maligních striktur tvořilo 17,7 % cholangiokarcinom, 74,5 % nádory pankreatu a 7,8 % jiné nádory. Ve srovnání se samotnou BC zvýšila FISH senzitivitu z 0,373 % na 0,706 % (p = 0,0007) při mírném poklesu specificity (p = 0,045). Závěr: Duální modalita hodnocení tkáně pomocí BC + FISH má lepší senzitivitu pro primární diagnózu distálních biliárních striktur ve srovnání se samotnou BC.
Background and aim: Primary diagnosis of the distal biliary stricture can be sometime difficult. Brush cytology (BC) is known to have low diagnostic sensitivity in these cases. Fluorescence in situ hybridization (FISH) has been reported as a useful adjunctive test in patients with biliary strictures. We aimed to determine performance characteristics of BC, FISH and their combination (BC + FISH) in the primary diagnosis of distal biliary strictures. Methods: This single-center prospective study was conducted between April 2019 and January 2021. Consecutive patients with unsampled biliary strictures undergoing first ERCP in our institution were included. Cytological and FISH analysis of tissue specimens from two standardized transpapillary brushings from the distal strictures were provided. Histopathological confirmation after surgery or 12-month follow-up was regarded as the reference standard for the final diagnosis. Results: A total of 109 patients were enrolled. Seven patients were lost from the final analysis and 26 suffered proximal stenosis. Of the 76 remaining patients (61.8% males, mean age 67.6, range 25–89 years) with distal stenosis, the proportions of benign and malignant strictures were 25 (32.9%) and 51 (67.1%), respectively. Of the subgroup of malignant strictures, 17.7% were cholangiocarcinoma, 74.5% were pancreatic tumors and 7.8% others. In comparison to BC alone, FISH increased the sensitivity from 0.373% to 0.706% (p = 0.0007) with a slight decrease in specificity (p = 0.045). Conclusions: Dual modality tissue evaluation using BC + FISH has better sensitivity for the primary diagnosis of distal biliary strictures, compared to BC alone.
- Klíčová slova
- biliární striktura,
- MeSH
- hybridizace in situ fluorescenční * metody MeSH
- lidé MeSH
- nemoci žlučových cest * diagnóza MeSH
- prospektivní studie MeSH
- stenóza diagnóza MeSH
- žlučové cesty patologie MeSH
- Check Tag
- lidé MeSH
Cervids are characterized by their greatest karyotypic diversity among mammals. A great diversity of chromosome numbers in notably similar morphological groups leads to the existence of several complexes of cryptic species and taxonomic uncertainties. Some deer lineages, such as those of Neotropical deer, stand out for a rapid chromosomal reorganization and intraspecific chromosome polymorphisms, which have not been properly explored yet. For that reason, we contribute to the study of deer karyotype diversity and taxonomy by producing and characterizing new molecular cytogenetic markers for the gray brocket deer (Subulo gouazoubira), a deer species that retained the hypothetical ancestral karyotype of Cervidae. We used bacterial artificial chromosome (BAC) clones derived from the cattle genome (Bos taurus) as markers, which were hybridized on S. gouazoubira metaphase chromosomes. In total, we mapped 108 markers, encompassing all gray brocket deer chromosomes, except the Y chromosome. The detailed analysis of fluorescent in situ hybridization results showed 6 fissions and 1 fusion as interchromosomal rearrangements that have separated cattle and gray brocket deer karyotypes. Each group of BAC probes derived from bovine chromosome pairs 1, 2, 5, 6, 8, and 9 showed hybridization signals on 2 different chromosomes, while pairs 28 and 26 are fused in tandem in a single acrocentric chromosome in S. gouazoubira. Furthermore, the BAC markers detected the occurrence of intrachromosomal rearrangements in the S. gouazoubira chromosomes homologous to pair 1 and the X chromosome of cattle. We present a karyotypic map of the 108 new markers, which will be of great importance for future karyotypic evolution studies in cervids and, consequently, help in their conservation and taxonomy resolution.
Most patients with chronic lymphocytic leukaemia (CLL) are nowadays diagnosed without any symptoms and do not require therapy. A prognostic score identifying patients within this large group who are at high risk of disease progression would be highly beneficial. The recently published International Prognostic Score for Early asymptomatic patients (IPS-E) uses combination of absolute lymphocyte count (ALC) >15 × 109 /l, palpable lymphadenopathy, and unmutated immunoglobulin heavy-chain variable-region (IGHV) gene to predict the time to first-line therapy (TTFT). Patients at low, intermediate, and high risk had estimated 5-year TTFT of 8%, 28%, and 61%. We performed an external validation of the IPS-E score using an unselected, consecutive group of 130 Binet A patients. The 5-year TTFT was 11%, 36%, and 78% (C-statistic 0·74). Furthermore, we propose an alternative system (AIPS-E) using cytogenetic aberrations instead of palpable lymphadenopathy. This system yielded 5-year TTFT of 14%, 40%, and 72%. These results were externally validated in 388 Binet A patients from five Czech centres; the 5-year TTFT was 16%, 37%, and 80% (C-statistic 0·74). In conclusion, we have successfully validated the IPS-E score for patients with early stage CLL. In addition, we propose a modified scoring system, the AIPS-E, combining IGHV, fluorescence in situ hybridisation, and ALC.
- MeSH
- čas zasáhnout při rozvinutí nemoci statistika a číselné údaje MeSH
- chromozomální aberace statistika a číselné údaje MeSH
- chronická lymfatická leukemie krev diagnóza mortalita patologie MeSH
- geny pro těžké řetězce imunoglobulinů genetika MeSH
- hybridizace in situ fluorescenční metody MeSH
- kohortové studie MeSH
- lidé MeSH
- lymfadenopatie diagnóza MeSH
- palpace metody MeSH
- počet lymfocytů metody MeSH
- prognóza MeSH
- progrese nemoci MeSH
- rizikové faktory MeSH
- senioři MeSH
- staging nádorů metody MeSH
- výzkumný projekt trendy MeSH
- Check Tag
- lidé MeSH
- mužské pohlaví MeSH
- senioři MeSH
- ženské pohlaví MeSH
- Publikační typ
- časopisecké články MeSH
- práce podpořená grantem MeSH
- Geografické názvy
- Česká republika MeSH
The widely distributed ray-finned fish genus Carassius is very well known due to its unique biological characteristics such as polyploidy, clonality, and/or interspecies hybridization. These biological characteristics have enabled Carassius species to be successfully widespread over relatively short period of evolutionary time. Therefore, this fish model deserves to be the center of attention in the research field. Some studies have already described the Carassius karyotype, but results are inconsistent in the number of morphological categories for individual chromosomes. We investigated three focal species: Carassius auratus, C. carassius and C. gibelio with the aim to describe their standardized diploid karyotypes, and to study their evolutionary relationships using cytogenetic tools. We measured length (q+plength) of each chromosome and calculated centromeric index (i value). We found: (i) The relationship between q+plength and i value showed higher similarity of C. auratus and C. carassius. (ii) The variability of i value within each chromosome expressed by means of the first quartile (Q1) up to the third quartile (Q3) showed higher similarity of C. carassius and C. gibelio. (iii) The fluorescent in situ hybridization (FISH) analysis revealed higher similarity of C. auratus and C. gibelio. (iv) Standardized karyotype formula described using median value (Q2) showed differentiation among all investigated species: C. auratus had 24 metacentric (m), 40 submetacentric (sm), 2 subtelocentric (st), 2 acrocentric (a) and 32 telocentric (T) chromosomes (24m+40sm+2st+2a+32T); C. carassius: 16m+34sm+8st+42T; and C. gibelio: 16m+22sm+10st+2a+50T. (v) We developed R scripts applicable for the description of standardized karyotype for any other species. The diverse results indicated unprecedented complex genomic and chromosomal architecture in the genus Carassius probably influenced by its unique biological characteristics which make the study of evolutionary relationships more difficult than it has been originally postulated.
- MeSH
- chromozomy genetika MeSH
- diploidie MeSH
- fylogeneze MeSH
- genetická variace genetika MeSH
- genom genetika MeSH
- hybridizace in situ fluorescenční metody MeSH
- kapři genetika MeSH
- karas zlatý genetika MeSH
- karyotyp MeSH
- karyotypizace metody MeSH
- mapování chromozomů metody MeSH
- polyploidie MeSH
- ryby genetika MeSH
- zvířata MeSH
- Check Tag
- mužské pohlaví MeSH
- ženské pohlaví MeSH
- zvířata MeSH
- Publikační typ
- časopisecké články MeSH
BACKGROUND: The blood flukes of genus Schistosoma are the causative agent of schistosomiasis, a parasitic disease that infects more than 200 million people worldwide. Proteases of schistosomes are involved in critical steps of host-parasite interactions and are promising therapeutic targets. We recently identified and characterized a group of S1 family Schistosoma mansoni serine proteases, including SmSP1 to SmSP5. Expression levels of some SmSPs in S. mansoni are low, and by standard genome sequencing technologies they are marginally detectable at the method threshold levels. Here, we report their spatial gene expression patterns in adult S. mansoni by the high-sensitivity localization assay. METHODOLOGY: Highly sensitive fluorescence in situ RNA hybridization (FISH) was modified and used for the localization of mRNAs encoding individual SmSP proteases (including low-expressed SmSPs) in tissues of adult worms. High sensitivity was obtained due to specifically prepared tissue and probes in combination with the employment of a signal amplification approach. The assay method was validated by detecting the expression patterns of a set of relevant reference genes including SmCB1, SmPOP, SmTSP-2, and Sm29 with localization formerly determined by other techniques. RESULTS: FISH analysis revealed interesting expression patterns of SmSPs distributed in multiple tissues of S. mansoni adults. The expression patterns of individual SmSPs were distinct but in part overlapping and were consistent with existing transcriptome sequencing data. The exception were genes with significantly low expression, which were also localized in tissues where they had not previously been detected by RNA sequencing methods. In general, SmSPs were found in various tissues including reproductive organs, parenchymal cells, esophagus, and the tegumental surface. CONCLUSIONS: The FISH-based assay provided spatial information about the expression of five SmSPs in adult S. mansoni females and males. This highly sensitive method allowed visualization of low-abundantly expressed genes that are below the detection limits of standard in situ hybridization or by RNA sequencing. Thus, this technical approach turned out to be suitable for sensitive localization studies and may also be applicable for other trematodes. The results suggest that SmSPs may play roles in diverse processes of the parasite. Certain SmSPs expressed at the surface may be involved in host-parasite interactions.
- MeSH
- exprese genu * MeSH
- hybridizace in situ fluorescenční metody normy MeSH
- proteiny červů genetika MeSH
- RNA metabolismus MeSH
- Schistosoma mansoni enzymologie genetika MeSH
- serinové proteasy genetika MeSH
- stanovení celkové genové exprese MeSH
- zvířata MeSH
- Check Tag
- mužské pohlaví MeSH
- ženské pohlaví MeSH
- zvířata MeSH
- Publikační typ
- časopisecké články MeSH
So-called oncocytic papillary renal cell carcinoma (OPRCC) is a poorly defined variant of papillary renal cell carcinoma. Since its first description, several studies were published with conflicting results, and thus precise definition is lacking. A cohort of 39 PRCCs composed of oncocytic cells were analyzed. Cases were divided into 3 groups based on copy number variation (CNV) pattern. The first group consisted of 23 cases with CNV equal to renal oncocytoma. The second group consisted of 7 cases with polysomy of chromosomes 7 and 17 and the last group of 9 cases included those with variable CNV. Epidemiologic, morphologic and immunohistochemical features varied among the groups. There were not any particular histomorphologic features correlating with any of the genetic subgroups. Further, a combination of morphologic, immunohistochemical, and molecular-genetic features did not allow to precisely predict biologic behavior. Owing to variable CNV pattern in OPRCC, strict adherence to morphology and immunohistochemical profile is recommended, particularly in limited samples (i.e., core biopsy). Applying CNV pattern as a part of a diagnostic algorithm can be potentially misleading. OPRCC is a highly variable group of tumors, which might be misdiagnosed as renal oncocytoma. Using the term OPRCC as a distinct diagnostic entity is, thanks to its high heterogeneity, questionable.
- MeSH
- biopsie dutou jehlou normy MeSH
- chromozomální aberace MeSH
- chybná diagnóza MeSH
- diferenciální diagnóza MeSH
- dospělí MeSH
- hybridizace in situ fluorescenční metody MeSH
- imunohistochemie metody MeSH
- karcinom z renálních buněk epidemiologie genetika patologie MeSH
- lidé středního věku MeSH
- lidé MeSH
- nádorové biomarkery metabolismus MeSH
- nádory ledvin diagnóza genetika patologie MeSH
- oxyfilní adenom diagnóza genetika patologie MeSH
- oxyfilní buňky metabolismus patologie MeSH
- překrývající se geny genetika MeSH
- senioři nad 80 let MeSH
- senioři MeSH
- staging nádorů metody MeSH
- variabilita počtu kopií segmentů DNA genetika 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
Repetitive DNAs comprise large portion of eukaryote genomes. In genome projects, the assembly of repetitive DNAs is challenging due to the similarity between repeats, which generate ambiguities for alignment. Fluorescence in situ hybridization (FISH) is a powerful technique for the physical mapping of various sequences on chromosomes. This technique is thus very helpful in chromosome-based genome assemblies, providing information on the fine architecture of genomes and their evolution. However, various protocols are currently used for FISH mapping, most of which are relatively laborious and expensive, or work properly only with a specific type of probes or sequences, and there is a need for a universal and affordable FISH protocol. Here we tested a FISH protocol for mapping of different DNA repeats, such as multigene families (rDNAs, U snDNAs, histone genes), satellite DNAs, microsatellites, transposable elements, DOP-PCR products, and telomeric motif (TTAGG)n, on the chromosomes of various insects and other arthropods. Different cell types and stages obtained from diverse tissues were used. The FISH procedure proved high quality and reliable results in all experiments performed. We obtained data on the chromosomal distribution of DNA repeats in representatives of insects and other arthropods. Thus, our results allow us to conclude that the protocol is universal and requires only time adjustment for chromosome/DNA denaturation. The use of this FISH protocol will facilitate studies focused on understanding the evolution and role of repetitive DNA in arthropod genomes.
- MeSH
- členovci genetika MeSH
- DNA genetika MeSH
- fluorescence MeSH
- hmyz genetika MeSH
- hybridizace in situ fluorescenční metody MeSH
- mapování chromozomů metody MeSH
- molekulární evoluce MeSH
- multigenová rodina genetika MeSH
- repetitivní sekvence nukleových kyselin genetika MeSH
- telomery genetika MeSH
- zvířata MeSH
- Check Tag
- zvířata MeSH
- Publikační typ
- časopisecké články MeSH
Duckweeds represent a small, free-floating aquatic family (Lemnaceae) of the monocot order Alismatales with the fastest growth rate among flowering plants. They comprise five genera (Spirodela, Landoltia, Lemna, Wolffiella, and Wolffia) varying in genome size and chromosome number. Spirodela polyrhiza had the first sequenced duckweed genome. Cytogenetic maps are available for both species of the genus Spirodela (S. polyrhiza and S. intermedia). However, elucidation of chromosome homeology and evolutionary chromosome rearrangements by cross-FISH using Spirodela BAC probes to species of other duckweed genera has not been successful so far. We investigated the potential of chromosome-specific oligo-FISH probes to address these topics. We designed oligo-FISH probes specific for one S. intermedia and one S. polyrhiza chromosome (Fig. 1a). Our results show that these oligo-probes cross-hybridize with the homeologous regions of the other congeneric species, but are not suitable to uncover chromosomal homeology across duckweeds genera. This is most likely due to too low sequence similarity between the investigated genera and/or too low probe density on the target genomes. Finally, we suggest genus-specific design of oligo-probes to elucidate chromosome evolution across duckweed genera.
- MeSH
- Araceae klasifikace genetika růst a vývoj MeSH
- chromozomy rostlin genetika MeSH
- druhová specificita MeSH
- fylogeneze MeSH
- genom rostlinný * MeSH
- hybridizace in situ fluorescenční metody MeSH
- karyotypizace MeSH
- molekulární evoluce * MeSH
- oligonukleotidové sondy chemie genetika MeSH
- Publikační typ
- časopisecké články MeSH
- práce podpořená grantem MeSH
Selection of non-small-cell lung cancer patients for treatment relies on the detection of expression of anaplastic lymphoma kinase (ALK) and ROS proto-oncogene 1 (ROS1) protein by immunohistochemistry (IHC). We evaluated staining performance for different IHC protocols and laboratory characteristics, and their influence on ALK and ROS1 interpretation during external quality assessment schemes between 2015 and 2018. Participants received five formalin-fixed, paraffin-embedded cases for staining by their routine protocol, whereafter at least two pathologists scored them simultaneously under a multihead microscope and awarded a graded expert staining score (ESS) from 1 to 5 points based on staining quality. European Conformity in Vitro Diagnostic kits (such as D5F3) revealed a better ALK ESS compared with laboratory-developed tests. ESS was indifferent to the applied antibody dilution or a recent protocol change. Lower ESSs were observed for higher antibody incubation times and temperatures. ESS for various ROS1 protocols were largely similar. Overall, for both markers, ESS improved over time and for repeated external quality assessment participation but was independent of laboratory setting or experience. Except for ROS1, ESS positively correlated with laboratory accreditation. IHC stains with lower ESS correlated with increased error rates in ALK and ROS1 interpretation and analysis failures. Laboratory characteristics differently affected staining quality and interpretation, and laboratories should assess both aspects, and less common protocols need improvement in staining performance.
- MeSH
- anaplastická lymfomová kináza metabolismus MeSH
- hybridizace in situ fluorescenční metody MeSH
- imunohistochemie metody MeSH
- laboratoře nemocniční MeSH
- lidé MeSH
- nádory plic metabolismus MeSH
- nemalobuněčný karcinom plic metabolismus MeSH
- patologové MeSH
- protoonkogen Mas MeSH
- protoonkogenní proteiny metabolismus MeSH
- senzitivita a specificita MeSH
- tyrosinkinasy metabolismus MeSH
- Check Tag
- lidé MeSH
- Publikační typ
- časopisecké články MeSH
- hodnotící studie MeSH
- práce podpořená grantem MeSH
Turtles, a speciose group consisting of more than 300 species, demonstrate karyotypes with diploid chromosome numbers ranging from 2n = 26 to 2n = 68. However, cytogenetic analyses have been conducted only to 1/3rd of the turtle species, often limited to conventional staining methods. In order to expand our knowledge of the karyotype evolution in turtles, we examined the topology of the (TTAGGG)n telomeric repeats and the rDNA loci by fluorescence in situ hybridization (FISH) on the karyotypes of two emydids: the Sicilian pond turtle, Emys trinacris, and the yellow-bellied slider, Trachemys scripta scripta (family Emydidae). Furthermore, AT-rich and GC-rich chromosome regions were detected by DAPI and CMA3 stains, respectively. The cytogenetic analysis revealed that telomeric sequences are restricted to the terminal ends of all chromosomes and the rDNA loci are localized in one pair of microchromosomes in both species. The karyotype of the Sicilian endemic E. trinacris with diploid number 2n = 50, consisting of 13 pairs of macrochromosomes and 12 pairs of microchromosomes, is presented here for first time. Our comparative examination revealed similar cytogenetic features in Emys trinacris and the closely related E. orbicularis, as well as to other previously studied emydid species, demonstrating a low rate of karyotype evolution, as chromosomal rearrangements are rather infrequent in this group of turtles.
- MeSH
- cytogenetika metody MeSH
- hybridizace in situ fluorescenční metody MeSH
- karyotyp * MeSH
- molekulární evoluce * MeSH
- ribozomální DNA genetika MeSH
- telomery genetika MeSH
- želvy genetika MeSH
- zvířata MeSH
- Check Tag
- ženské pohlaví MeSH
- zvířata MeSH
- Publikační typ
- časopisecké články MeSH
- práce podpořená grantem MeSH
