16S rRNA amplicon sequencing or, more recently, metatranscriptomic analysis are currently the only preferred methods for microbial profiling of samples containing a predominant ratio of human to bacterial DNA. However, due to the off-target amplification of human DNA, current protocols are inadequate for bioptic samples. Here we present an efficient, reliable, and affordable method for the bacteriome analysis of clinical samples human DNA content predominates. We determined the microbiota profile in a total of 40 human biopsies of the esophagus, stomach, and duodenum using 16S rRNA amplicon sequencing with the widely used 515F-806R (V4) primers targeting the V4 region, 68F-338R primers and a modified set of 68F-338R (V1-V2M) primers targeting the V1-V2 region. With the V4 primers, on average 70% of amplicon sequence variants (ASV) mapped to the human genome. On the other hand, this off-target amplification was absent when using the V1-V2M primers. Moreover, the V1-V2M primers provided significantly higher taxonomic richness and reproducibility of analysis compared to the V4 primers. We conclude that the V1-V2M 16S rRNA sequencing method is reliable, cost-effective, and applicable for low-bacterial abundant human samples in medical research.
- MeSH
- biopsie MeSH
- gastrointestinální trakt MeSH
- geny rRNA MeSH
- lidé MeSH
- mikrobiota * genetika MeSH
- reprodukovatelnost výsledků MeSH
- RNA ribozomální 16S genetika MeSH
- sekvenční analýza DNA metody MeSH
- vysoce účinné nukleotidové sekvenování metody MeSH
- Check Tag
- lidé MeSH
- Publikační typ
- časopisecké články MeSH
- práce podpořená grantem MeSH
The epidermal growth factor (EGF) and its receptor (EGFR) gene-gene interactions were shown to increase the susceptibility to esophageal cancer. However, the role of the EGF/EGFR pathway in the development of gastroesophageal reflux disease (GERD) and its complications (reflux esophagitis (RE), Barrett's esophagus (BE), and esophageal adenocarcinoma (EAC)) remains unclear. This association study is aimed at investigating functional EGF and EGFR gene polymorphisms, their mRNA expression in esophageal tissues, and EGF plasma levels in relation to RE, BE, and EAC development in the Central European population. 301 patients with RE/BE/EAC (cases) as well as 98 patients with nonerosive reflux disease (NERD) and 8 healthy individuals (controls) were genotyped for +61 A>G EGF (rs4444903) and +142285 G>A EGFR (rs2227983) polymorphisms using the TaqMan quantitative polymerase chain reaction (qPCR). In random subgroups, the EGF and EGFR mRNA expressions were analyzed by reverse transcription qPCR in esophageal tissue with and without endoscopically visible pathological changes; and the EGF plasma levels were determined by enzyme-linked immunosorbent assay. None of the genotyped SNPs nor EGF-EGFR genotype interactions were associated with RE, BE, or EAC development (p > 0.05). Moreover, mRNA expression of neither EGF nor EGFR differed between samples of the esophageal tissue with and without endoscopically visible pathology (p > 0.05) nor between samples from patients with different diagnoses, i.e., RE, BE, or EAC (p > 0.05). Nevertheless, the lower EGF mRNA expression in carriers of combined genotypes AA +61 EGF (rs4444903) and GG +142285 EGFR (rs2227983; p < 0.05) suggests a possible direct/indirect effect of EGF-EGFR gene interactions on EGF gene expression. In conclusion, EGF and EGFR gene variants and their mRNA/protein expression were not associated with RE, BE or EAC development in the Central European population.
- MeSH
- adenokarcinom * patologie MeSH
- Barrettův syndrom * metabolismus MeSH
- epidermální růstový faktor genetika MeSH
- erbB receptory genetika metabolismus MeSH
- gastroezofageální reflux * genetika MeSH
- jednonukleotidový polymorfismus MeSH
- lidé MeSH
- messenger RNA MeSH
- nádory jícnu * patologie MeSH
- peptická ezofagitida * genetika MeSH
- studie případů a kontrol MeSH
- transportní proteiny genetika MeSH
- Check Tag
- lidé MeSH
- Publikační typ
- časopisecké články MeSH
Refluxní choroba jícnu (gastroesophageal reflux disease – GERD) je multifaktoriální onemocnění, na kterém se mimo jiné podílí i genetická predispozice jedince. Při diagnostice GERD a jejich komplikací, jako je Barrettův jícen (Barrett‘s esophagus – BE) a adenokarcinom jícnu (esophageal adenocarcinoma – EAC), jsou standardně využívány endoskopické metody a histologické vyšetření. Pro screening BE u osob se zvýšeným rizikem vzniku tohoto onemocnění i při sledování rozvoje dysplazie BE by vzorky jícnové sliznice mohly být odebrány pomocí novodobých neendoskopických postupů, kterými lze minimalizovat invazivnost zákroku a zlepšit compliance a adherenci pacientů k léčbě. Neendoskopicky odebraný vzorek sliznice jícnu je možné stejně jako vzorek získaný endoskopickou biopsií analyzovat jak imunohistochemickým vyšetřením, tak provést molekulárně biologickou analýzu na specifické biomarkery. Markery jako caudal type homeobox 2 (CDX2) a protein p53 již našly své uplatnění v diagnostice GERD, a proto se výzkum v posledních letech zaměřuje na identifikaci dalších biomarkerů, pomocí kterých by bylo možné spolehlivě predikovat vznik a rozvoj BE nebo EAC. Tento přehledový článek shrnuje informace o moderních neendoskopických metodách odběru vzorků sliznice jícnu a o biomarkerech, které byly v souvislosti s predikcí a diagnostikou BE a EAC studovány v neendoskopicky odebrané tkáni a mají potenciál pro využití v klinické praxi.
Gastroesophageal reflux disease (GERD) is a multifactorial disease; an individual´s genetic predisposition may contribute to the development of this disorder. Endoscopic methods and histological examination are commonly used to diagnose GERD and its complications such as Barrett's esophagus (BE) and esophageal adenocarcinoma (EAC). For BE screening in high-risk individuals as well as monitoring the development of BE dysplasia, esophageal mucosa samples could be taken using modern non-endoscopic procedures to minimize invasiveness of the procedure and improve patient adherence and compliance with a treatment. Esophageal mucosa samples taken by non-endoscopic or endoscopic biopsy can be analyzed both by immunohistochemistry and molecular biology analysis for specific biomarkers. Markers such as caudal type homeobox 2 (CDX2) and protein p53 have found their use in GERD diagnosis, and therefore research in recent years has focused on identifying other biomarkers that could reliably predict the development and progression of BE or EAC. This review article summarizes information on modern non-endoscopic methods of sampling from the esophagus mucosa and biomarkers, which have been studied in connection with the prediction and diagnosis of BE and EAC and have a potential for the use in clinical practice.
- MeSH
- Barrettův syndrom * diagnóza MeSH
- biologické markery MeSH
- lidé MeSH
- mikro RNA MeSH
- nádory jícnu * diagnóza MeSH
- Check Tag
- lidé MeSH
- Publikační typ
- práce podpořená grantem MeSH
- přehledy MeSH
