Circulating endometrial cells (CECs) have emerged as a new biomarker of advanced disease in women with endometriosis. The identification of several subtypes of CECs (e.g., stem cell-like, epithelial, glandular, stromal) has opened the way for characterization of endometriosis-associated CECs. This study focused on the isolation and characterization of CECs and disseminated endometrial cells (DECs) in patients with spontaneous pneumothorax (SP). The primary objective was to differentiate between cancer and non-cancer cells in patients with no previous cancer diagnosis. The MetaCell® size-based separation protocol was used to enrich CECs/DECs. Evaluation of the captured cells by 3D microscopy was performed using a NANOLIVETM microscope using a holographic approach. Based on gene expression analysis (GEA), we can conclude that mitochondria are much more active in primary tumors compared to endometriosis tissue (e.g. MT-ND1, MT-ATP6 genes). The culture of DECs is made of stromal, stem and immune cells. In vitro culture of DECs is characterized by an increase in the epithelial marker KRT18. Similarly, NFE2L2, a proerythroid factor, is also elevated. Further, a significant decrease in the amount of stem and immune cells was observed in the cell culture of DECs. The data presented here show how morphologically plastic the changes in the mitochondrial network can be and how cells can reflect them at the level of gene expression. The markers identified could help in the accompanying diagnostic process of the spontaneous pneumothorax in women of reproductive age.
- MeSH
- dospělí MeSH
- endometrióza * patologie diagnóza genetika MeSH
- endometrium patologie metabolismus MeSH
- lidé MeSH
- mitochondrie * metabolismus patologie MeSH
- pneumotorax * patologie diagnóza MeSH
- stanovení celkové genové exprese metody MeSH
- Check Tag
- dospělí MeSH
- lidé MeSH
- ženské pohlaví MeSH
- Publikační typ
- časopisecké články MeSH
Single-cell RNA sequencing (scRNA-seq) methods are widely used in life sciences, including immunology. Typical scRNA-seq analysis pipelines quantify the abundance of particular transcripts without accounting for alternative splicing. However, a well-established pan-leukocyte surface marker, CD45, encoded by the PTPRC gene, presents alternatively spliced variants that define different immune cell subsets. Information about some of the splicing patterns in particular cells in the scRNA-seq data can be obtained using isotype-specific DNA oligo-tagged anti-CD45 antibodies. However, this requires generation of an additional sequencing DNA library. Here, we present IDEIS, an easy-to-use software for CD45 isoform quantification that uses single-cell transcriptomic data as the input. We showed that IDEIS accurately identifies canonical human CD45 isoforms in datasets generated by 10× Genomics 5' sequencing assays. Moreover, we used IDEIS to determine the specificity of the Ptprc splicing pattern in mouse leukocyte subsets.
- MeSH
- alternativní sestřih MeSH
- analýza jednotlivých buněk metody MeSH
- antigeny CD45 * genetika metabolismus MeSH
- leukocyty metabolismus imunologie MeSH
- lidé MeSH
- myši MeSH
- protein - isoformy genetika MeSH
- sekvenční analýza RNA metody MeSH
- software * MeSH
- stanovení celkové genové exprese metody MeSH
- transkriptom MeSH
- zvířata MeSH
- Check Tag
- lidé MeSH
- myši MeSH
- zvířata MeSH
- Publikační typ
- časopisecké články MeSH
We investigated gene expression patterns in Lutzomyia and Phlebotomus sand fly vectors of leishmaniases. Using quantitative PCR, we assessed the expression stability of potential endogenous control genes commonly used in dipterans. We analyzed Lutzomyia longipalpis and Phlebotomus papatasi samples from L3 and L4 larval stages, adult sand flies of different sexes, diets, dsRNA injection, and Leishmania infection. Six genes were evaluated: actin, α-tubulin, GAPDH, 60 S ribosomal proteins L8 and L32 (RiboL8 and RiboL32), and elongation factor 1-α (EF1-α). EF1-α was among the most stably expressed along with RiboL8 in L. longipalpis larvae and RiboL32 in adults. In P. papatasi, EF1-α and RiboL32 were the top in larvae, while EF1-α and actin were the most stable in adults. RiboL8 and actin were the most stable genes in dissected tissues and infected guts. Additionally, five primer pairs designed for L. longipalpis or P. papatasi were effective in PCR with Lutzomyia migonei, Phlebotomus duboscqi, Phlebotomus perniciosus, and Sergentomyia schwetzi cDNA. Furthermore, L. longipalpis RiboL32 and P. papatasi α-tubulin primers were suitable for qPCR with cDNA from the other four species. Our research provides tools to enhance relative gene expression studies in sand flies, facilitating the selection of endogenous control for qPCR.
- MeSH
- esenciální geny * MeSH
- hmyz - vektory genetika MeSH
- hmyzí geny MeSH
- larva genetika MeSH
- Leishmania genetika MeSH
- Phlebotomus * genetika MeSH
- Psychodidae genetika MeSH
- stanovení celkové genové exprese metody MeSH
- zvířata MeSH
- Check Tag
- mužské pohlaví MeSH
- ženské pohlaví MeSH
- zvířata MeSH
- Publikační typ
- časopisecké články MeSH
Nonalcoholic fatty liver disease (NAFLD) is a chronic liver disease characterized by the accumulation of fat in the liver in the absence of excessive alcohol consumption or a secondary cause of hepatic steatosis. The prevalence of NAFLD is increasing worldwide and its management has become a public health concern. Animal models are traditionally used to elucidate disease mechanisms and identify potential drug targets; however, their translational aspects in human diseases have not been fully established. This study aimed to clarify the utility of animal models for translational research by assessing their relevance to human diseases using gene expression analysis. Weighted gene co-expression network analysis of liver tissues from Western diet (WD)-induced NAFLD mice was performed to identify the modules associated with disease progression. Moreover, the similarity of the gene co-expression network across species was evaluated using module preservation analysis. Nineteen disease-associated modules were identified. The brown module was positively associated with disease severity, and functional analyses indicated that it may be involved in inflammatory responses in immune cells. Moreover, the gene co-expression network of the brown module was highly preserved in human NAFLD liver gene expression datasets. These results indicate that WD-induced NAFLD mice have similar gene co-expression networks (especially genes associated with inflammatory responses) to humans and are thought to be a useful experimental tool for preclinical research on NAFLD. Keywords: Nonalcoholic fatty liver disease (NAFLD), Weighted gene co-expression network analysis (WGCNA), Western diet (WD).
- MeSH
- játra metabolismus patologie MeSH
- lidé MeSH
- modely nemocí na zvířatech * MeSH
- myši inbrední C57BL * MeSH
- myši MeSH
- nealkoholová steatóza jater * genetika metabolismus etiologie patologie MeSH
- stanovení celkové genové exprese metody MeSH
- transkriptom * MeSH
- západní dieta * škodlivé účinky MeSH
- zvířata MeSH
- Check Tag
- lidé MeSH
- mužské pohlaví MeSH
- myši MeSH
- zvířata MeSH
- Publikační typ
- časopisecké články MeSH
OBJECTIVES: Small extracellular vesicles (EVs) contain various signaling molecules, thus playing a crucial role in cell-to-cell communication and emerging as a promising source of biomarkers. However, the lack of standardized procedures impedes their translation to clinical practice. Thus, we compared different approaches for high-throughput analysis of small EVs transcriptome. METHODS: Small EVs were isolated from 150 μL of serum. Quality and quantity were assessed by dynamic light scattering, transmission electron microscopy, and Western blot. Comparison of RNA extraction efficiency was performed, and expression of selected genes was analyzed by RT-qPCR. Whole transcriptome analysis was done using microarrays. RESULTS: Obtained data confirmed the suitability of size exclusion chromatography for isolation of small EVs. Analyses of gene expression showed the best results in case of samples isolated by Monarch Total RNA Miniprep Kit. Totally, 7,182 transcripts were identified to be deregulated between colorectal cancer patients and healthy controls. The majority of them were non-coding RNAs with more than 70 % being lncRNAs, while protein-coding genes represented the second most common gene biotype. CONCLUSIONS: We have optimized the protocol for isolation of small EVs and their RNA from low volume of sera and confirmed the suitability of Clariom D Pico Assays for transcriptome profiling.
- MeSH
- extracelulární vezikuly * genetika metabolismus MeSH
- gelová chromatografie MeSH
- lidé MeSH
- RNA MeSH
- stanovení celkové genové exprese * metody MeSH
- Check Tag
- lidé MeSH
- Publikační typ
- časopisecké články MeSH
Spatial transcriptomics is revolutionizing modern biology, offering researchers an unprecedented ability to unravel intricate gene expression patterns within tissues. From pioneering techniques to newly commercialized platforms, the field of spatial transcriptomics has evolved rapidly, ushering in a new era of understanding across various disciplines, from developmental biology to disease research. This dynamic expansion is reflected in the rapidly growing number of technologies and data analysis techniques developed and introduced. However, the expanding landscape presents a considerable challenge for researchers, especially newcomers to the field, as staying informed about these advancements becomes increasingly complex. To address this challenge, we have prepared an updated review with a particular focus on technologies that have reached commercialization and are, therefore, accessible to a broad spectrum of potential new users. In this review, we present the fundamental principles of spatial transcriptomic methods, discuss the challenges in data analysis, provide insights into experimental considerations, offer information about available resources for spatial transcriptomics, and conclude with a guide for method selection and a forward-looking perspective. Our aim is to serve as a guiding resource for both experienced users and newcomers navigating the complex realm of spatial transcriptomics in this era of rapid development. We intend to equip researchers with the necessary knowledge to make informed decisions and contribute to the cutting-edge research that spatial transcriptomics offers.
- MeSH
- lidé MeSH
- stanovení celkové genové exprese * metody MeSH
- transkriptom * MeSH
- výpočetní biologie metody MeSH
- zvířata MeSH
- Check Tag
- lidé MeSH
- zvířata MeSH
- Publikační typ
- časopisecké články MeSH
- přehledy MeSH
Lithium (Li) is one of the most effective drugs for treating bipolar disorder (BD), however, there is presently no way to predict response to guide treatment. The aim of this study is to identify functional genes and pathways that distinguish BD Li responders (LR) from BD Li non-responders (NR). An initial Pharmacogenomics of Bipolar Disorder study (PGBD) GWAS of lithium response did not provide any significant results. As a result, we then employed network-based integrative analysis of transcriptomic and genomic data. In transcriptomic study of iPSC-derived neurons, 41 significantly differentially expressed (DE) genes were identified in LR vs NR regardless of lithium exposure. In the PGBD, post-GWAS gene prioritization using the GWA-boosting (GWAB) approach identified 1119 candidate genes. Following DE-derived network propagation, there was a highly significant overlap of genes between the top 500- and top 2000-proximal gene networks and the GWAB gene list (Phypergeometric = 1.28E-09 and 4.10E-18, respectively). Functional enrichment analyses of the top 500 proximal network genes identified focal adhesion and the extracellular matrix (ECM) as the most significant functions. Our findings suggest that the difference between LR and NR was a much greater effect than that of lithium. The direct impact of dysregulation of focal adhesion on axon guidance and neuronal circuits could underpin mechanisms of response to lithium, as well as underlying BD. It also highlights the power of integrative multi-omics analysis of transcriptomic and genomic profiling to gain molecular insights into lithium response in BD.
- MeSH
- antimanika farmakologie terapeutické užití MeSH
- bipolární porucha * farmakoterapie genetika MeSH
- celogenomová asociační studie * metody MeSH
- farmakogenetika metody MeSH
- fokální adheze * účinky léků genetika MeSH
- genomika metody MeSH
- genové regulační sítě * účinky léků genetika MeSH
- indukované pluripotentní kmenové buňky účinky léků metabolismus MeSH
- lidé MeSH
- lithium * farmakologie terapeutické užití MeSH
- multiomika MeSH
- neurony metabolismus účinky léků MeSH
- sloučeniny lithia farmakologie terapeutické užití MeSH
- stanovení celkové genové exprese metody MeSH
- transkriptom * genetika účinky léků MeSH
- Check Tag
- lidé MeSH
- mužské pohlaví MeSH
- ženské pohlaví MeSH
- Publikační typ
- časopisecké články MeSH
- práce podpořená grantem MeSH
- Research Support, N.I.H., Extramural MeSH
- Klíčová slova
- test MammaPrint,
- MeSH
- diagnostické techniky molekulární metody přístrojové vybavení MeSH
- fixace tkání MeSH
- genetické testování * metody přístrojové vybavení MeSH
- klinické laboratoře organizace a řízení zákonodárství a právo MeSH
- klinické zkoušky, fáze III jako téma MeSH
- lidé MeSH
- metody pro přípravu analytických vzorků MeSH
- nádory prsu * diagnóza genetika MeSH
- staging nádorů MeSH
- stanovení celkové genové exprese metody MeSH
- Check Tag
- lidé MeSH
- ženské pohlaví MeSH
- Publikační typ
- novinové články MeSH
Východiska: Dlaždicobuněčný karcinom ústní dutiny (oral squamous cell carcinoma – OSCC) je jedným z nejběžnějších nádorů ze skupin dlaždicobuněčných karcinomů hlavy a krku. Zvyšující se výskyt karcinomů ústní dutiny a jejich zjištění v pokročilých stadiích je celosvětovým zdravotním problémem. Stále více údajů svědčí o tom, že při růstu a progresi zhoubných nádorů hrají důležitou roli microRNA (miRNAs), zatímco o významu miR-7113-3p and miR-6721-5p v OSCC nejsou k dispozici žádné informace. Tento článek pojednává o zkoumání exprese MAP2K1, miR-7113-3p a miR-6721-5p pro možné biologické funkce při rozvoji dlaždicobuněčného karcinomu ústní dutiny. Materiál a metody: Pomocí kvantitativní polymerázové řetězové reakce v reálném čase jsme stanovili expresi mRNA u MAP2K1, miR-7113-3p a miR-6721-5p v čerstvě zmražených tkáních OSCC a v čerstvě zmražených přilehlých normálních tkáních 30 pacientů a zkoumali jsme jejich vztah ke klinickým parametrům. Výsledky: Exprese MAP2K1 v nádorové tkáni byla oproti normálním tkáním významně vyšší, zatímco exprese miR-7113-3p a miR-6721-5p byla významně nižší. Také byla pozorována statistická korelace p = 0,04 mezi zvýšenou expresí MAP2K1 a perineurální invazí. Navíc jsme zaznamenali, že mezi down-regulací miR-7113-3p a zvýšenou expresí MAP2K1 je pozitivní korelace (p = 0,0218) a mezi down-regulací miR-6721-5p a zvýšenou expresí MAP2K1 je negativní korelace (p = 0,7771). Závěr: Z těchto nálezů vyplývá, že u pacientů s OSCC mohou miR-7113-3p a miR-6721-5p sloužit jako prospektivní biomarkery, které by v budoucnu mohly být využívány k detekci OSCC v časném stadiu. Zvýšená exprese MAP2K1 je spojena s rozvojem OSCC a perineurální invazí.
Background: Oral squamous cell carcinoma (OSCC) is one of the most common cancers in the head and neck squamous cell cancer group. The increasing frequency of oral carcinomas and their late-stage appearance is a major worldwide health concern. MicroRNAs (miRNAs) appear to play an important role in cancer growth and progression, according to growing data, whereas no information is available regarding miR-7113-3p and miR-6721-5p involvement in OSCC. In this article, the expression of MAP2K1, miR-7113-3p, and miR-6721-5p was examined for possible biological functions in the advancement of oral squamous cell carcinoma. Material and methods: We used quantitative real-time PCR (to examine the mRNA expression of MAP2K1, miR-7113-3p, and miR-6721-5p in fresh frozen OSCC tissues and adjacent normal fresh frozen tissues from 30 patients, and we investigated their relationship with clinical parameters. Results: MAP2K1 expression was found to be dramatically increased in tumor tissues than in normal tissues, whereas miR7113-3p and miR-6721-5p expression was significantly decreased. Furthermore, a statistical correlation of P = 0.04 was also observed between increased MAP2K1 expression and perineural invasion. Additionally, we noted that the downregulation of miR-7113-3p appears to correlate positively with overexpression of MAP2K1 (P = 0.0218), and a negative correlation was observed between downregulation of miR-6721-5p and overexpression of MAP2K1 (P = 0.7771). Conclusion: Based on these findings, miR-7113-3p and miR-6721-5p might be prospective biomarkers for OSCC patients, and could be utilized to detect OSCC at an early stage for future diagnosis. MAP2K1 overexpression has been linked to the development of OSCC and perineural invasion.
- Klíčová slova
- miR-7113-3p, miR-6721-5p,
- MeSH
- dlaždicobuněčné karcinomy hlavy a krku * diagnostické zobrazování genetika MeSH
- kvantitativní polymerázová řetězová reakce metody MeSH
- lidé MeSH
- MAP kinasa-kinasa 1 genetika MeSH
- nádorové biomarkery analýza MeSH
- stanovení celkové genové exprese klasifikace metody MeSH
- Check Tag
- lidé MeSH
- Publikační typ
- klinická studie MeSH
Heterogeneity of colorectal carcinoma (CRC) represents a major hurdle towards personalized medicine. Efforts based on whole tumor profiling demonstrated that the CRC molecular subtypes were associated with specific tumor morphological patterns representing tumor subregions. We hypothesize that whole-tumor molecular descriptors depend on the morphological heterogeneity with significant impact on current molecular predictors. We investigated intra-tumor heterogeneity by morphology-guided transcriptomics to better understand the links between gene expression and tumor morphology represented by six morphological patterns (morphotypes): complex tubular, desmoplastic, mucinous, papillary, serrated, and solid/trabecular. Whole-transcriptome profiling by microarrays of 202 tumor regions (morphotypes, tumor-adjacent normal tissue, supportive stroma, and matched whole tumors) from 111 stage II-IV CRCs identified morphotype-specific gene expression profiles and molecular programs and differences in their cellular buildup. The proportion of cell types (fibroblasts, epithelial and immune cells) and differentiation of epithelial cells were the main drivers of the observed disparities with activation of EMT and TNF-α signaling in contrast to MYC and E2F targets signaling, defining major gradients of changes at molecular level. Several gene expression-based (including single-cell) classifiers, prognostic and predictive signatures were examined to study their behavior across morphotypes. Most exhibited important morphotype-dependent variability within same tumor sections, with regional predictions often contradicting the whole-tumor classification. The results show that morphotype-based tumor sampling allows the detection of molecular features that would otherwise be distilled in whole tumor profile, while maintaining histopathology context for their interpretation. This represents a practical approach at improving the reproducibility of expression profiling and, by consequence, of gene-based classifiers.
