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Amyloidóza lehkých řetězců imunoglobulinů (AL amyloidosis – ALA) je monoklonální gamapatie charakteristická přítomností aberantních plazmatických buněk produkujících amyloidogenní lehké řetězce imunoglobulinů. To vede k tvorbě amyloidních fibril v cílových orgánech a tkáních, především v srdci a ledvinách, což způsobuje jejich dysfunkci. Jelikož tvorba amyloidních depozit je nezvratný proces, je kladeno velké úsilí k nalezení biomarkeru, který by odlišil ALA od ostatních monoklonálních gamapatií v časném stadiu onemocnění, kdy amyloidní depozita ještě nemají fatální následky. Vysoce výkonné technologie přinášejí nové možnosti v rámci moderního výzkumu nádorů, jelikož umožňují studovat nemoc v rámci jeho komplexnosti. Moderní metody, jako jsou sekvenování nové generace, genové expresní profilování a profilování cirkulujících mikroRNA u aberantních buněk ALA pacientů a příbuzných onemocnění patří mezi nové přístupy využívané ke studiu aberantních plazmatických buněk amyloidózy lehkých řetězců a jiných příbuzných onemocnění. Zatímco obecně známé mutace u pacientů s mnohočetným myelomem (KRAS, NRAS, MYC, TP53) nebyly u ALA pacientů nalezeny, počet mutovaných genů u jednotlivých diagnóz není rozdílný. Transkriptom ALA pacientů se jeví být podobnější pacientům s monoklonální gamapatií nejasného významu, a zároveň exprese cirkulujících mikroRNA, pro které je známá korelace s poškozením srdce je zvýšená právě u ALA pacientů, u nichž je poškození srdce typickým projevem.
Immunoglobulin light chain amyloidosis (AL amyloidosis – ALA) is a monoclonal gammopathy characterized by presence of aberrant plasma cells producing amyloidogenic immunoglobulin light chains. This leads to formation of amyloid fibrils in various organs and tissues, mainly in heart and kidney, and causes their dysfunction. As amyloid depositing in target organs is irreversible, there is a big effort to identify biomarker that could help to distinguish ALA from other monoclonal gammopathies in the early stages of disease, when amyloid deposits are not fatal yet. High throughput technologies bring new opportunities to modern cancer research as they enable to study disease within its complexity. Sophisticated methods such as next generation sequencing, gene expression profiling and circulating microRNA profiling are new approaches to study aberrant plasma cells from patients with light chain amyloidosis and related diseases. While generally known mutation in multiple myeloma patients (KRAS, NRAS, MYC, TP53) were not found in ALA, number of mutated genes is comparable. Transcriptome of ALA patients proves to be more similar to monoclonal gammopathy of undetermined significance patients, moreover level of circulating microRNA, that are known to correlate with heart damage, is increased in ALA patients, where heart damage in ALA typical symptom.
- MeSH
- amyloidóza * diagnóza krev patologie MeSH
- genom genetika MeSH
- interpretace statistických dat MeSH
- lidé MeSH
- mikro RNA analýza fyziologie MeSH
- paraproteinemie klasifikace patologie MeSH
- plazmatické buňky * fyziologie MeSH
- průtoková cytometrie MeSH
- transkriptom fyziologie genetika MeSH
- Check Tag
- lidé MeSH
BACKGROUND: Gynodioecious species exist in two sexes - male-sterile females and hermaphrodites. Male sterility in higher plants often results from mitonuclear interaction between the CMS (cytoplasmic male sterility) gene(s) encoded by mitochondrial genome and by nuclear-encoded restorer genes. Mitochondrial and nuclear-encoded transcriptomes in females and hermaphrodites are intensively studied, but little is known about sex-specific gene expression in plastids. We have compared plastid transcriptomes between females and hermaphrodites in two haplotypes of a gynodioecious species Silene vulgaris with known CMS candidate genes. RESULTS: We generated complete plastid genome sequences from five haplotypes S. vulgaris including the haplotypes KRA and KOV, for which complete mitochondrial genome sequences were already published. We constructed a phylogenetic tree based on plastid sequences of S. vulgaris. Whereas lowland S. vulgaris haplotypes including KRA and KOV clustered together, the accessions from high European mountains diverged early in the phylogram. S. vulgaris belongs among Silene species with slowly evolving plastid genomes, but we still detected 212 substitutions and 112 indels between two accessions of this species. We estimated elevated Ka/Ks in the ndhF gene, which may reflect the adaptation of S. vulgaris to high altitudes, or relaxed selection. We compared depth of coverage and editing rates between female and hermaphrodite plastid transcriptomes and found no significant differences between the two sexes. We identified 51 unique C to U editing sites in the plastid genomes of S. vulgaris, 38 of them in protein coding regions, 2 in introns, and 11 in intergenic regions. The editing site in the psbZ gene was edited only in one of two plastid genomes under study. CONCLUSIONS: We revealed no significant differences between the sexes in plastid transcriptomes of two haplotypes of S. vulgaris. It suggests that gene expression of plastid genes is not affected by CMS in flower buds of S. vulgaris, although both sexes may still differ in plastid gene expression in specific tissues. We revealed the difference between the plastid transcriptomes of two S. vulgaris haplotypes in editing rate and in the coverage of several antisense transcripts. Our results document the variation in plastid genomes and transcriptomes in S. vulgaris.
- MeSH
- genom plastidový genetika MeSH
- Silene genetika metabolismus MeSH
- transkriptom genetika MeSH
- Publikační typ
- časopisecké články MeSH
Sekvenování nové generace, nazývané také masivně paralelní sekvenování (MPS), je v současnosti nejrychleji se rozvíjející metodou molekulární genetiky, která přinese zlom v oblasti personalizované medicíny. V tomto přehledu stručně popisujeme hlavní typy MPS, kterými jsou celogenomová a exomová sekvenace, sekvenace transkriptomu a amplikonové sekvenování. Dále je uveden souhrn výhod, nevýhod a možných aplikací technologií nabízených v současnosti v České republice.
Next generation or massive parallel sequencing (MPS) is a rapidly advancing method in molecular genetics that will bring significant changes in the personalized medicine field. In this review we briefly describe major types of MPS, including whole-genome, -exome, -transcriptome and amplicon sequencing. We also present an overview of the advantages, drawbacks and possible applications of sequencing technologies available in the Czech Republic.
- Klíčová slova
- masivně paralelní sekvenování, amplikonové sekvenování, sekvenování nové generace,
- MeSH
- exom MeSH
- lidé MeSH
- sekvenční analýza DNA * ekonomika přístrojové vybavení trendy MeSH
- sekvenční analýza RNA metody MeSH
- transkriptom MeSH
- vysoce účinné nukleotidové sekvenování * ekonomika metody přístrojové vybavení MeSH
- Check Tag
- lidé MeSH
- Publikační typ
- práce podpořená grantem MeSH
- přehledy MeSH
Viroids are small non-capsidated, single-stranded, covalently-closed circular noncoding RNA replicons of 239-401 nucleotides that exploit host factors for their replication, and some cause disease in several economically important crop plants, while others appear to be benign. The proposed mechanisms of viroid pathogenesis include direct interaction of the genomic viroid RNA with host factors and post-transcriptional or transcriptional gene silencing via viroid-derived small RNAs (vd-sRNAs) generated by the host defensive machinery. Humulus lupulus (hop) plants are hosts to several viroids among which Hop latent viroid (HLVd) and Citrus bark cracking viroid (CBCVd) are attractive model systems for the study of viroid-host interactions due to the symptomless infection of the former and severe symptoms induced by the latter in this indicator host. To better understand their interactions with hop plant, a comparative transcriptomic analysis based on RNA sequencing (RNA-seq) was performed to reveal the transcriptional alterations induced as a result of single HLVd and CBCVd infection in hop. Additionally, the effect of HLVd on the aggressiveness of CBCVd that underlies severe stunting in hop in a mixed infection was studied by transcriptomic analysis. Our analysis revealed that CBCVd infection resulted in dynamic changes in the activity of genes as compared to single HLVd infection and their mixed infection. The differentially expressed genes that are involved in defense, phytohormone signaling, photosynthesis and chloroplasts, RNA regulation, processing and binding; protein metabolism and modification; and other mechanisms were more modulated in the CBCVd infection of hop. Nevertheless, Gene Ontology (GO) classification and pathway enrichment analysis showed that the expression of genes involved in the proteolysis mechanism is more active in a mixed infection as compared to a single one, suggesting co-infecting viroids may result in interference with host factors more prominently. Collectively, our results provide a deep transcriptome of hop and insight into complex single HLVd, CBCVd, and their coinfection in hop-plant interactions.
- MeSH
- Humulus genetika virologie MeSH
- nemoci rostlin genetika virologie MeSH
- transkriptom * MeSH
- viroidy patogenita MeSH
- Publikační typ
- časopisecké články MeSH
- MeSH
- epigeneze genetická * MeSH
- RNA genetika metabolismus MeSH
- transkriptom * MeSH
- Publikační typ
- časopisecké články MeSH
Few invertebrates can survive cryopreservation in liquid nitrogen, and the mechanisms by which some species do survive are underexplored, despite high application potential. Here, we turn to the drosophilid Chymomyza costata to strengthen our fundamental understanding of extreme freeze tolerance and gain insights about potential avenues for cryopreservation of biological materials. We first use RNAseq to generate transcriptomes of three C. costata larval phenotypic variants: those warm-acclimated in early or late diapause (weak capacity to survive cryopreservation), and those undergoing cold acclimation after diapause entry (extremely freeze tolerant, surviving cryopreservation). We identify mRNA transcripts representing genes and processes that accompany the physiological transition to extreme freeze tolerance and relate cryopreservation survival to the transcriptional profiles of select candidate genes using extended sampling of phenotypic variants. Enhanced capacity for protein folding, refolding and processing appears to be a central theme of extreme freeze tolerance and may allow cold-acclimated larvae to repair or eliminate proteins damaged by freezing (thus mitigating the toxicity of denatured proteins, endoplasmic reticulum stress and subsequent apoptosis). We also find a number of candidate genes (including both known and potentially novel, unannotated sequences) whose expression profiles tightly mirror the change in extreme freeze tolerance status among phenotypic variants.
- MeSH
- aklimatizace genetika MeSH
- Drosophilidae genetika MeSH
- hmyz genetika MeSH
- transkriptom MeSH
- zmrazování * MeSH
- zvířata MeSH
- Check Tag
- zvířata MeSH
- Publikační typ
- časopisecké články MeSH
- práce podpořená grantem MeSH
Molecular methods for the analysis of biomolecules have undergone rapid technological development in the last decade. The advent of next-generation sequencing methods and improvements in instrumental resolution enabled the analysis of complex transcriptome, proteome and metabolome data, as well as a detailed annotation of microbial genomes. The mechanisms of decomposition by model fungi have been described in unprecedented detail by the combination of genome sequencing, transcriptomics and proteomics. The increasing number of available genomes for fungi and bacteria shows that the genetic potential for decomposition of organic matter is widespread among taxonomically diverse microbial taxa, while expression studies document the importance of the regulation of expression in decomposition efficiency. Importantly, high-throughput methods of nucleic acid analysis used for the analysis of metagenomes and metatranscriptomes indicate the high diversity of decomposer communities in natural habitats and their taxonomic composition. Today, the metaproteomics of natural habitats is of interest. In combination with advanced analytical techniques to explore the products of decomposition and the accumulation of information on the genomes of environmentally relevant microorganisms, advanced methods in microbial ecophysiology should increase our understanding of the complex processes of organic matter transformation.
