Abstract
In order to further our understanding of the physiological consequences of Helicobacter pylori infection , analysis of clinical tissue specimens is required. To this end, RNA is frequently isolated from stomach biopsies of H. pylori-infected patients and compared to samples from uninfected controls to monitor gene expression using molecular methods such as reverse-transcription real-time PCR, microarrays, and next-generation sequencing. The successful purification of sufficient quantities of high-quality RNA is essential for accurate and reproducible downstream analysis. This chapter describes the key steps for high-quality RNA purification from human tissue samples, including sample collection and storage, tissue disruption and lysis, RNA purification, and assessment of RNA yield and quality.
Access this chapter
Tax calculation will be finalised at checkout
Purchases are for personal use only
Similar content being viewed by others
References
IARC (1994) Shistosomes, liver flukes and Helicobacter pylori. In: IARC monographs on the evaluation of carcinogenic risks to humans, vol. 61. pp. 1–241
Correa P (1988) A human model of gastric carcinogenesis. Cancer Res 48:3554–3560
Smith SM, Moran AP, Duggan SP et al (2011) Tribbles 3: a novel regulator of TLR2-mediated signaling in response to helicobacter pylori lipopolysaccharide. J Immunol 186:2462–2471
Smith SM, Freeley M, Moynagh PN et al (2016) Differential modulation of Helicobacter pylori lipopolysaccharide-mediated TLR2 signaling by individual Pellino proteins. Helicobacter 22(1). https://doi.org/10.1111/hel.12325
Kameoka S, Kameyama T, Hayashi T et al (2016) Helicobacter pylori induces IL-1β protein through the inflammasome activation in differentiated macrophagic cells. Biomed Res 37:21–27
Tran LS, Chonwerawong M, Ferrero RL (2017) Regulation and functions of inflammasome-mediated cytokines in Helicobacter pylori infection. Microbes Infect 19:449–458
Kim DJ, Park JH, Franchi L et al (2013) The Cag pathogenicity island and interaction between TLR 2/NOD 2 and NLRP 3 regulate IL-1β production in Helicobacter pylori infected dendritic cells. Eur J Immunol 43:2650–2658
Mannick EE, Schurr JR, Zapata A et al (2004) Gene expression in gastric biopsies from patients infected with Helicobacter pylori. Scand J Gastroenterol 39:1192–1200
Nagashima H, Iwatani S, Cruz M et al (2015) Toll-like receptor 10 in Helicobacter pylori infection. J Infect Dis 212:1666–1676
Graham JE, Peek RM Jr, Krishna U et al (2002) Global analysis of Helicobacter pylori gene expression in human gastric mucosa. Gastroenterology 123:1637–1648
Hu Y, He C, Liu JP et al (2018) Analysis of key genes and signaling pathways involved in Helicobacter pylori-associated gastric cancer based on the Cancer Genome Atlas database and RNA sequencing data. Helicobacter 23:e12530
Galamb O, Sipos F, Molnar B et al (2007) Evaluation of malignant and benign gastric biopsy specimens by mRNA expression profile and multivariate statistical methods. Cytometry B Clin Cytom 72:299–309
Morales-Guerrero SE, Rivas-Ortiz CI, Ponce de Leon-Rosales S et al (2020) Translation of gastric disease progression at gene level expression. J Cancer 11:520–532
Qiagen RNeasy Mini kit handbook; 2019. https://www.qiagen.com/ie/resources/resourcedetail?id=14e7cf6e-521a-4cf7-8cbc-bf9f6fa33e24&lang=en. Accessed 18 Dec 2019
Smith SM, Murray DW (2012) An overview of microRNA methods: expression profiling and target identification. Methods Mol Biol (Clifton, NJ) 823:119–138
Desjardins P, Conklin D (2010) NanoDrop microvolume quantitation of nucleic acids. J Vis Exp 45:2565
Smith SM, Murray DW (2014) MicroRNA profiling: an overview of current technologies and applications. In: Simo C (ed) Applications of advanced omics: from genes to metabolites. Elsevier, Oxford, UK, pp 23–46
Acknowledgments
Acknowledgements Support is acknowledged from the Health Research Board and a Trinity College Dublin Provost PhD Award.
Author information
Authors and Affiliations
Corresponding author
Editor information
Editors and Affiliations
Rights and permissions
Copyright information
© 2021 Springer Science+Business Media, LLC, part of Springer Nature
About this protocol
Cite this protocol
FitzGerald, R., Devapal, M., Hickey, J.J., McNamara, D., Kelleher, D., Smith, S.M. (2021). Purification of Total RNA from Stomach Tissue Biopsies. In: Smith, S.M. (eds) Helicobacter Pylori. Methods in Molecular Biology, vol 2283. Humana, New York, NY. https://doi.org/10.1007/978-1-0716-1302-3_7
Download citation
DOI: https://doi.org/10.1007/978-1-0716-1302-3_7
Published:
Publisher Name: Humana, New York, NY
Print ISBN: 978-1-0716-1301-6
Online ISBN: 978-1-0716-1302-3
eBook Packages: Springer Protocols