Nikitina D, Lehr K, Vilchez-Vargas R, Jonaitis LV, Urba M, Kupcinskas J, Skieceviciene J, Link A. Comparison of genomic and transcriptional microbiome analysis in gastric cancer patients and healthy individuals. World J Gastroenterol 2023; 29(7): 1202-1218 [PMID: 36926663 DOI: 10.3748/wjg.v29.i7.1202]
Corresponding Author of This Article
Jurgita Skieceviciene, PhD, Professor, Senior Researcher, Institute for Digestive Research, Lithuanian University of Health Sciences, Eivenių g. 4, Kaunas 44307, Lithuania. jurgita.skieceviciene@lsmu.lt
Research Domain of This Article
Gastroenterology & Hepatology
Article-Type of This Article
Case Control Study
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Nikitina D, Lehr K, Vilchez-Vargas R, Jonaitis LV, Urba M, Kupcinskas J, Skieceviciene J, Link A. Comparison of genomic and transcriptional microbiome analysis in gastric cancer patients and healthy individuals. World J Gastroenterol 2023; 29(7): 1202-1218 [PMID: 36926663 DOI: 10.3748/wjg.v29.i7.1202]
World J Gastroenterol. Feb 21, 2023; 29(7): 1202-1218 Published online Feb 21, 2023. doi: 10.3748/wjg.v29.i7.1202
Comparison of genomic and transcriptional microbiome analysis in gastric cancer patients and healthy individuals
Darja Nikitina, Konrad Lehr, Ramiro Vilchez-Vargas, Laimas Virginijus Jonaitis, Mindaugas Urba, Juozas Kupcinskas, Jurgita Skieceviciene, Alexander Link
Darja Nikitina, Juozas Kupcinskas, Jurgita Skieceviciene, Institute for Digestive Research, Lithuanian University of Health Sciences, Kaunas 44307, Lithuania
Konrad Lehr, Ramiro Vilchez-Vargas, Alexander Link, Department of Gastroenterology, Hepatology and Infectious Diseases, Otto-von-Guericke University Hospital, Magdeburg 39120, Germany
Laimas Virginijus Jonaitis, Mindaugas Urba, Juozas Kupcinskas, Department of Gastroenterology, Lithuanian University of Health Sciences, Kaunas 44307, Lithuania
Author contributions: Vilchez-Vargas R, Link A, Lehr K, Kupcinskas J, Skieceviciene J and Nikitina D contributed to the study design, analysis, and interpretation of the data; Nikitina D, Link A, and Skieceviciene J drafted the manuscript; Skieceviciene J, Kupcinskas J, Vilchez-Vargas R and Link A supervised the study procedures and revised the manuscript; Nikitina D, Lehr K, and Vilchez-Vargas R performed bioinformatic and statistical analyses; Urba M and Jonaitis LV obtained participant’s samples and provided clinical data; Skieceviciene J and Link A have contributed equally to this work and share last authorship; and all authors read and approved the final version of the manuscript.
Supported bythe MULTIOMICS project that has received funding from European Social Fund (No. 09.3.3-LMT-K-712-01 0130) under grant agreement with the Research Council of Lithuania; and the “LiLife” project as part of the “Autonomy in old Age” research group (No. ZS/2018/11/95324) under grant agreement with European Commission through the “European Funds for Regional development”.
Institutional review board statement: The study was approved by the Kaunas Regional Biomedical Research Ethics Committee.
Informed consent statement: All study participants provided informed consent prior to study enrollment.
Conflict-of-interest statement: All the authors report no relevant conflicts of interest for this article.
Data sharing statement: Technical appendix, statistical code, and dataset available from the corresponding author at jurgita.skieceviciene@lsmuni.lt.
STROBE statement: The authors have read the STROBE Statement-checklist of items, and the manuscript was prepared and revised according to the STROBE Statement-checklist of items.
Corresponding author: Jurgita Skieceviciene, PhD, Professor, Senior Researcher, Institute for Digestive Research, Lithuanian University of Health Sciences, Eivenių g. 4, Kaunas 44307, Lithuania. jurgita.skieceviciene@lsmu.lt
Received: October 27, 2022 Peer-review started: October 27, 2022 First decision: November 14, 2022 Revised: November 19, 2022 Accepted: December 21, 2022 Article in press: December 21, 2022 Published online: February 21, 2023 Processing time: 116 Days and 18.3 Hours
Abstract
BACKGROUND
Helicobacter pylori and the stomach microbiome play a crucial role in gastric carcinogenesis, and detailed characterization of the microbiome is necessary for a better understanding of the pathophysiology of the disease. There are two common modalities for microbiome analysis: DNA (16S rRNA gene) and RNA (16S rRNA transcript) sequencing. The implications from the use of one or another sequencing approach on the characterization and comparability of the mucosal microbiome in gastric cancer (GC) are poorly studied.
AIM
To characterize the microbiota of GC using 16S rRNA gene and its transcript and determine difference in the bacterial composition.
METHODS
In this study, 316 DNA and RNA samples extracted from 105 individual stomach biopsies were included. The study cohort consisted of 29 healthy control individuals and 76 patients with GC. Gastric tissue biopsy samples were collected from damaged mucosa and healthy mucosa at least 5 cm from the tumor tissue. From the controls, healthy stomach mucosa biopsies were collected. From all biopsies RNA and DNA were extracted. RNA was reverse transcribed into cDNA. V1-V2 region of bacterial 16S rRNA gene from all samples were amplified and sequenced on an Illumina MiSeq platform. Bray-Curtis algorithm was used to construct sample-similarity matrices abundances of taxonomic ranks in each sample type. For significant differences between groups permutational multivariate analysis of variance and Mann-Whitney test followed by false-discovery rate test were used.
RESULTS
Microbial analysis revealed that only a portion of phylotypes (18%-30%) overlapped between microbial profiles obtained from DNA and RNA samples. Detailed analysis revealed differences between GC and controls depending on the chosen modality, identifying 17 genera at the DNA level and 27 genera at the RNA level. Ten of those bacteria were found to be different from the control group at both levels. The key taxa showed congruent results in various tests used; however, differences in 7 bacteria taxa were found uniquely only at the DNA level, and 17 uniquely only at the RNA level. Furthermore, RNA sequencing was more sensitive for detecting differences in bacterial richness, as well as differences in the relative abundance of Reyranella and Sediminibacterium according to the type of GC. In each study group (control, tumor, and tumor adjacent) were found differences between DNA and RNA bacterial profiles.
CONCLUSION
Comprehensive microbial study provides evidence for the effect of choice of sequencing modality on the microbiota profile, as well as on the identified differences between case and control.
Core Tip: In this study, we aimed to characterize the microbiota of gastric cancer (GC) on two levels: 16S rRNA gene and its transcript. Our study showed that only a small portion of bacterial sequences overlapped using those two approaches. Moreover, our study revealed that obtained results comparing the case group with the controls depend on the chosen modality. We also showed that Reyranella and Sediminibacterium was associated with the Lauren classification and RNA level was more sensitive to detect low abundant bacteria. This study provides novel insights into microbiome study as well as new founding related to complex GC pathogenesis.
