BACKGROUND: The noninvasive collection of saliva samples for DNA analyses is simple, and its potential for research and diagnostic purposes is great. However, DNA isolates from such samples are often of inferior quality to those from blood. AIM: The aim of this study was to investigate the robustness and sensitivity of the ddPCR instrument for genetic analyses from saliva samples of poor quality by comparing their results to those obtained using an established method from blood samples. METHODS: Blood and saliva were collected from 47 university students, which was followed by manual isolation of DNA and analysis on droplet digital PCR (ddPCR). Results of analyses were supplemented with values of fractional abundances. RESULTS: ddPCR proved to be highly suitable for analysis of even low-quality saliva samples (concentrations as low as 0.79 ng/µL), especially when augmented by fractional abundance data. This combination yielded 100% agreement with results obtained from blood samples. CONCLUSION: This study verified the applicability of ddPCR as a sensitive and robust method of genetic diagnostic testing even from low-quality saliva isolates. This makes it potentially suitable for a wide range of applications and facilitates the performance of large epidemiological studies, even if sampling or sample processing is suboptimal.

• Klíčová slova
• blood, ddPCR, fractional abundance, manual isolation, point mutation, saliva,
• Publikační typ
• časopisecké články MeSH

For many years, activin A, encoded by Inhba, has been thought to be present in both mouse and human oocytes and preimplantation embryos. However, its deficiency does not impede the proper embryonic development of the embryo until birth. It has been suggested that the lack of a phenotype in zygotic knockout embryos may be masked by the presence of maternal protein deposited in the oocyte during oogenesis or provided from the reproductive tract. Therefore, to explore whether maternally supplied activin A is required for embryo development, we carried out a conditional Inhba knockout in oocytes using Zp3-Cre/LoxP strategy. By examining Inhba maternal and maternal/zygotic knockout embryos, individually recorded using time-lapse imaging, immunostained, and genotyped, we revealed that the maternal pool of activin A affects the dynamics of mouse preimplantation development. These alterations are accompanied by impaired mitochondrial activity in oocytes. Surprisingly, using the droplet digital polymerase chain reaction (ddPCR) approach, we provided evidence that the Inhba mRNA of zygotic origin is undetectable in mouse embryos.

• Klíčová slova
• Activin a, Ddpcr, Inhba, Maternal knockout, Preimplantation embryo,
• Publikační typ
• časopisecké články MeSH

BACKGROUND: Thrombophilic mutations in genes for factor V Leiden and factor II prothrombin are among the most important risk factors for developing the thromboembolic disease (TED), along with the use of oral contraceptives (OCs) or smoking. AIM: This study aimed to investigate the occurrence of risk factors in young women using droplet digital PCR (ddPCR) and, based on the results of this investigation, to perform a cost-benefit analysis of ddPCR-based screening in young women starting to take OCs compared to the treatment costs of patients who develop preventable TED in the Czech Republic. METHODS: In this cross-sectional study, female university students filled in a questionnaire and provided a blood sample for DNA isolation and ddPCR analysis of both aforementioned genetic risk factors. The results, along with data from literature and web search, were used for cost-benefit analysis valid for the Czech Republic. RESULTS: Out of 148 participants, 30 (20%) were smokers and 49 (33%) took OCs. A mutation was confirmed in 6 women (4.1%) in the factor V gene and in 3 women (2%) in the factor II gene, respectively. A model calculation on a cohort of 50,000 women starting to use contraceptives in the Czech Republic every year showed that at maximum compliance, (i.e., non-use of OC and smoking cessation), screening could prevent 68 cases of TED over the course of the mean period of OC use (5.7 years). Economically, the costs of testing in this cohort (2.25 mil. USD) would be significantly lower than prevented treatment costs (16 mil. USD at maximum compliance); the cost-benefit break-even point would be at 14.1% compliance. CONCLUSION: The cost-benefit analysis based on our results indicates that screening for factor V Leiden and factor II prothrombin in young women before starting to use OCs would, in the conditions of the Czech Republic, likely be highly economically effective.

• Klíčová slova
• ddPCR, factor II prothrombin, factor V Leiden, oral contraceptives, smoking, thrombophilic mutation,
• Publikační typ
• časopisecké články MeSH

BACKGROUND: Nowadays, modern treatment methods for cancer patients are based on targeting specific molecules involved in cellular signaling system associated with tumor initiation and progression. The success of such approach depends on a correctly chosen dia-gnostic test with high sensitivity that identifies the occurrence and level of bio-markers in patients to select those who will respond and benefit from the treatment. The development of new technologies and the upgrades of the known ones contribute to the innovations in molecular characterization of cancer, which allows the detection of patients mutational status with high sensitivity and specificity. PURPOSE: Here, we discuss the utilization of the third-generation type of polymerase chain reaction (PCR), droplet digital PCR (ddPCR), in the molecular dia-gnostics of oncology diseases. According to the studies reported in our review, ddPCR represents a promising tool in genetic profiling of cancer patients. Therefore, the optimization and precise validation may enable gradual implementation of ddPCR into clinical practice in the field of oncology.

• Klíčová slova
• cancer, ddPCR, molecular dia­gnostics, tumor bio­markers,
• MeSH
• lidé MeSH
• nádory diagnóza   genetika   MeSH
• polymerázová řetězová reakce metody   MeSH
• reziduální nádor diagnóza   genetika   MeSH
• Check Tag
• lidé MeSH
• Publikační typ
• časopisecké články MeSH
• přehledy MeSH

BACKGROUND: B chromosomes are classified as dispensable genomic components tolerated by cells, which are transmitted to progeny despite providing no benefit in most cases. They have been observed in over 2800 species of plants, animals and fungi, including numerous maize accessions. As maize is one of the most important crops worldwide, research on the maize B chromosome has been pioneering in the field. The characteristic of the B chromosome is its irregular inheritance. This results in offspring with a different number of B chromosomes compared to the parents. However, the exact number of B chromosomes in the studied plants is a crucial piece of information. Currently, assessing the number of B chromosomes in maize largely depends on cytogenetic analyses, which are laborious and time-consuming. We present an alternative approach based on the droplet digital PCR technique (ddPCR), which is faster, more efficient and provides the results within one day with the same level of accuracy. RESULTS: In this study, we report a rapid and straightforward protocol for determining the number of B chromosomes in maize plants. We developed a droplet digital PCR assay using specific primers and a TaqMan probe for the B-chromosome-linked gene and a single-copy reference gene on maize chromosome 1. The performance of the assay was successfully verified by comparison with the results of cytogenetic analyses performed in parallel. CONCLUSIONS: The protocol significantly improves the efficiency of B chromosome number assessment in maize compared to cytogenetic approaches. The assay has been developed to target conserved genomic regions and can therefore be applied to a wide range of diverged maize accessions. This universal approach can be modified for chromosome number detection in other species, not only for the B chromosome but also for any other chromosome in aneuploid constitution.

• Klíčová slova
• B chromosome, Direct PCR, FISH, Maize, ddPCR,
• Publikační typ
• časopisecké články MeSH

UNLABELLED: In the course of time, scientific communities have a growing interest in understanding ethano medicines. The Putranjiva roxburghii, a native plant of the Indian Subcontinent is described as a "Child amulet tree" in Ayurveda. Based on the fact that this herbal medicine has an indispensable component of integrative medicine, the present study was planned to assess the effect of ethanolic dried extract of Putranjiva seeds on the motility of X and Y-bearing bovine spermatozoa. The in-vitro effect of seed extract diluted in S-TALP medium on bull semen has been evaluated by Computer Assisted Semen Analysis (CASA) shows a marked increase in the motility of spermatozoa. Motile and non-motile spermatozoa have been separated by glass wool column from the control as well as treated group. The X and Y-bearing sperm quantification have been carried out by droplet digital polymerase chain reaction (ddPCR). The extract didn't exert any differential effect on the motility and viability of X and Y chromosome-bearing spermatozoa. The transcriptome profiling (RNA-Seq) identified 93 differentially expressed genes between the extract treated and control group. It unveils the up-regulation of CATSPER, AKAP3, SPAG, ADAM1B, ADAM2 and ADAM32 genes that are involved in increasing sperm motility. Transcriptome profile also unveil the expression of ZAR1, CYP17A1, APPL2, HOXB4 and SP9 genes involved with embryonic development processes in Putranjiva extract-treated motile spermatozoa. The results envisaged the medicinal value of Putranjiva herb on increased fertility due to combinatory effect like increased sperm motility and favourableness on embryogenesis. The study ruled out the possibility of herbs having any biased effect on the selection of either male or female-bearing spermatozoa in the bull. SUPPLEMENTARY INFORMATION: The online version contains supplementary material available at 10.1007/s13205-022-03452-4.

• Klíčová slova
• CASA, Infertility, Putranjiva roxburghii, RNA-sequence profiling, ddPCR,
• Publikační typ
• časopisecké články MeSH

OBJECTIVES: Molecular screening plays a major role in prognostic categorization and subsequent definition of treatment strategies for acute myeloid leukemia. The possibility of using IDH1/2 mutations as a marker for the monitoring of minimal residual disease (MRD) is still under investigation and remains unclear. METHODS: In this retrospective study, we evaluated 90 patients with de novo AML using Sanger sequencing (exon 4, IDH1 and IDH2). For subsequent MRD monitoring were used both methods, massive parallel sequencing and droplet digital PCR (ddPCR). RESULTS: We identified 22 patients (24%) who harboured mutations in IDH1 or IDH2 genes. Fourteen (64%) of them had other commonly used MRD markers (insertion in NPM1 and partial tandem duplication of MLL, MLL-PTD). Eight of the 22 patients had IDH1 mutations, 13 had IDH2 mutations and 1 had both IDH1 and IDH2 mutations. In our cohort, this IDH1/2 marker responded to the treatment in all of the patients and reflected the onset of the relapse very well. NPM1 mutation based MRD monitoring was more sensitive and predicted relapse earlier but IDH1/2 based monitoring was more sensitive than a method based on MLL-PTD. Both massive parallel sequencing and ddPCR were competent to monitor MRD using IDH1/2. Nevertheless, ddPCR was able to achieve a higher sensitivity in some cases and moreover this method can analyse a single sample without significant price increases. CONCLUSION: Given these data, we conclude that IDH1/2 mutations can be used as a reliable and cost-effective marker for MRD monitoring.

• Klíčová slova
• Acute myeloid leukemia, IDH1 and IDH2 mutations, Minimal residual disease, NGS, ddPCR,
• MeSH
• akutní myeloidní leukemie diagnóza   enzymologie   genetika   terapie   MeSH
• dospělí MeSH
• exony MeSH
• genetická predispozice k nemoci * MeSH
• genetické asociační studie MeSH
• indukce remise MeSH
• isocitrátdehydrogenasa chemie   genetika   metabolismus   MeSH
• kohortové studie MeSH
• lidé středního věku MeSH
• lidé MeSH
• mutace * MeSH
• mutační analýza DNA MeSH
• následné studie MeSH
• nemocnice univerzitní MeSH
• nukleofosmin MeSH
• prognóza MeSH
• retrospektivní studie MeSH
• reziduální nádor MeSH
• senioři MeSH
• substituce aminokyselin MeSH
• Check Tag
• dospělí MeSH
• lidé středního věku MeSH
• lidé MeSH
• mužské pohlaví MeSH
• senioři MeSH
• ženské pohlaví MeSH
• Publikační typ
• časopisecké články MeSH
• Geografické názvy
• Česká republika MeSH
• Názvy látek
• IDH1 protein, human MeSH Prohlížeč
• IDH2 protein, human MeSH Prohlížeč
• isocitrátdehydrogenasa MeSH
• NPM1 protein, human MeSH Prohlížeč
• nukleofosmin MeSH

BACKGROUND: Melanoma is the most aggressive skin cancer with ability to recur also after early-stage tumor surgery. The aim was to identify early-stage melanoma patients at high risk of recurrence using liquid biopsy, estimating of mutated BRAF ctDNA and the level of tumor marker S100B in plasma. METHODS: Eighty patients were enrolled in the study. BRAF V600E mutation was determined in FFPE tissue and plasma samples using ultrasensitive ddPCR with pre-amplification. The level of S100B was determined in plasma by immunoassay chemiluminescent method. RESULTS: The best prediction of melanoma recurrence after surgery was observed in patients with combined high level of S100B (S100Bhigh) and ctDNA BRAFV600E (BRAFmut) in preoperative (57.1% vs. 12.5%, p = 0.025) as well as postoperative blood samples (83.3% vs. 14.3%, resp., p = 0.001) in comparison with low S100B and BRAF wild-type. Similarly, patients with preoperative and postoperative S100Bhigh and BRAFmut experienced worse prognosis (DFI p = 0.05, OS p = 0.131 and DFI p = 0.001, OS = 0.001, resp.). CONCLUSION: We observed the benefit of the estimation of combination of S100B and ctDNA BRAFmut in peripheral blood for identification of patients at high risk of recurrence and unfavorable prognosis. SIGNIFICANCE: There is still no general consensus on molecular markers for deciding the appropriateness of adjuvant treatment of early-stage melanoma. We have shown for the first time that the combined determination of the ctDNA BRAFmut oncogene (liquid biopsy) and the high level of tumor marker S100B in pre- and postoperative plasma samples can identify patients with the worst prognosis and the highest risk of tumor recurrence. Therefore, modern adjuvant therapy would be appropriate for these patients with resectable melanoma, regardless of disease stage.

• Klíčová slova
• BRAF V600E, S100B, ctDNA, ddPCR, melanoma,
• MeSH
• dospělí MeSH
• lidé středního věku MeSH
• lidé MeSH
• lokální recidiva nádoru * genetika   krev   MeSH
• melanom * genetika   krev   patologie   diagnóza   chirurgie   MeSH
• mutace * MeSH
• nádorové biomarkery * krev   genetika   MeSH
• nádory kůže * krev   genetika   patologie   diagnóza   chirurgie   MeSH
• prediktivní hodnota testů MeSH
• prognóza MeSH
• protoonkogenní proteiny B-Raf * genetika   krev   MeSH
• S-100 kalcium vázající protein G, podjednotka beta * krev   genetika   MeSH
• senioři nad 80 let MeSH
• senioři MeSH
• staging nádorů MeSH
• tekutá biopsie metody   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
• Názvy látek
• BRAF protein, human MeSH Prohlížeč
• nádorové biomarkery * MeSH
• protoonkogenní proteiny B-Raf * MeSH
• S-100 kalcium vázající protein G, podjednotka beta * MeSH
• S100B protein, human MeSH Prohlížeč

Mouse wild-derived strains (WDSs) combine the advantages of classical laboratory stocks and wild animals, and thus appear to be promising tools for diverse biomedical and evolutionary studies. We employed 18 WDSs representing three non-synanthropic species (Mus spretus, Mus spicilegus, and M. macedonicus) and three house mouse subspecies (Mus musculus musculus, M. m. domesticus, M. m. castaneus), which are all important human commensals to explore whether the number of major urinary protein (MUP) genes and their final protein levels in urine are correlated with the level of commensalism. Contrary to expectations, the MUP copy number (CN) and protein excretion in the strains derived from M. m. castaneus, which is supposed to be the strongest commensal, were not significantly different from the non-commensal species. Regardless of an overall tendency for higher MUP amounts in taxa with a higher CN, there was no significant correlation at the strain level. Our study thus suggests that expansion of the Mup cluster, which appeared before the house mouse diversification, is unlikely to facilitate commensalism with humans in three house mouse subspecies. Finally, we found considerable variation among con(sub)specific WDSs, warning against generalisations of results based on a few strains.

• Klíčová slova
• MUP excretion, Mus musculus, copy number variation, ddPCR, proteomics, synanthropy,
• MeSH
• biologická evoluce MeSH
• divoká zvířata * MeSH
• lidé MeSH
• myši MeSH
• symbióza * genetika   MeSH
• zvířata MeSH
• Check Tag
• lidé MeSH
• myši MeSH
• zvířata MeSH
• Publikační typ
• časopisecké články MeSH
• práce podpořená grantem MeSH

Cellular leiomyoma (CL) represents an uncommon variant of uterine leiomyoma with limited data concerning its immunohistochemical and molecular profile. We performed a comprehensive analysis of 52 CL cases all of which were analyzed immunohistochemically. Molecular analysis was possible in 32 cases with sufficient DNA, and 38 cases with sufficient RNA. The immunohistochemical results showed a high expression of smooth muscle markers (calponin (100%), desmin (100%), smooth muscle actin (98.1%), caldesmon (96.1%), transgelin (96.1%), smooth muscle myosin heavy chain (86.5%), and smoothelin (61.5%)). Concerning markers of endometrial stromal differentiation, the expression of CD10 was observed in 65.4% cases (42.2% with H-score > 50), and IFITM1 in 36.5% cases (1.9% with H-score > 50). 36.5% showed HMGA2 overexpression at the IHC level, associated with increased mRNA expression in 14/14 cases. The rearrangement of the HMGA2 gene was detected in 13.2%. Chromosome 1p deletion was found in 19.3%, while 9.4% of tumors showed a pathogenic mutation in the MED12 gene. In conclusion, CL is immunohistochemically characterized by a high expression of "smooth muscle" markers commonly associated with a co-expression of "endometrial stromal" markers, where IFITM1 shows superior performance compared to CD10 regarding its specificity for differentiation from endometrial stromal tumors. The sensitivity of smoothelin in CL seems rather low, but no data is available to assess its specificity. On a molecular level, the most common mutually exclusive aberration in CL affects HMGA2, followed by chromosome 1p deletions and MED12 mutations.

• Klíčová slova
• Cellular leiomyoma, Chromosome 1p, HMGA2, MED12, NGS, ddPCR,
• MeSH
• chromozomy chemie   metabolismus   MeSH
• leiomyom * patologie   MeSH
• lidé MeSH
• mediátorový komplex genetika   metabolismus   MeSH
• mutace MeSH
• nádory dělohy * patologie   MeSH
• nádory endometria * genetika   MeSH
• neprilysin analýza   MeSH
• protein HMGA2 MeSH
• Check Tag
• lidé MeSH
• ženské pohlaví MeSH
• Publikační typ
• časopisecké články MeSH
• Názvy látek
• HMGA2 protein, human MeSH Prohlížeč
• MED12 protein, human MeSH Prohlížeč
• mediátorový komplex MeSH
• neprilysin MeSH
• protein HMGA2 MeSH