Spa-RQ : an Image Analysis Tool to Visualise and Quantify Spatial Phenotypes Applied to Non-Small Cell Lung Cancer

Show full item record



Permalink

http://hdl.handle.net/10138/308110

Citation

Bao , J , Walliander , M , Kovacs , F , Nagaraj , A S , Hemmes , A , Sarhadi , V K , Knuutila , S , Lundin , J , Horvath , P & Verschuren , E W 2019 , ' Spa-RQ : an Image Analysis Tool to Visualise and Quantify Spatial Phenotypes Applied to Non-Small Cell Lung Cancer ' , Scientific Reports , vol. 9 , 17613 . https://doi.org/10.1038/s41598-019-54038-9

Title: Spa-RQ : an Image Analysis Tool to Visualise and Quantify Spatial Phenotypes Applied to Non-Small Cell Lung Cancer
Author: Bao, Jie; Walliander, Margarita; Kovacs, Ferenc; Nagaraj, Ashwini S.; Hemmes, Annabrita; Sarhadi, Virinder Kaur; Knuutila, Sakari; Lundin, Johan; Horvath, Peter; Verschuren, Emmy W.
Contributor organization: Institute for Molecular Medicine Finland
Lung Cancer Model Systems
Helsinki Institute of Life Science HiLIFE
University of Helsinki
Research Program in Systems Oncology
HUS Abdominal Center
Department of Pathology
Medicum
University Management
Johan Edvard Lundin / Principal Investigator
Research Group Verschuren Emmy
Date: 2019-11-26
Language: eng
Number of pages: 11
Belongs to series: Scientific Reports
ISSN: 2045-2322
DOI: https://doi.org/10.1038/s41598-019-54038-9
URI: http://hdl.handle.net/10138/308110
Abstract: To facilitate analysis of spatial tissue phenotypes, we created an open-source tool package named 'Spa-RQ' for 'Spatial tissue analysis: image Registration & Quantification'. Spa-RQ contains software for image registration (Spa-R) and quantitative analysis of DAB staining overlap (Spa-Q). It provides an easy-to-implement workflow for serial sectioning and staining as an alternative to multiplexed techniques. To demonstrate Spa-RQ's applicability, we analysed the spatial aspects of oncogenic KRAS-related signalling activities in non-small cell lung cancer (NSCLC). Using Spa-R in conjunction with ImageJ/Fiji, we first performed annotation-guided tumour-by-tumour phenotyping using multiple signalling markers. This analysis showed histopathology-selective activation of PI3K/AKT and MAPK signalling in Kras mutant murine tumours, as well as high p38MAPK stress signalling in p53 null murine NSCLC. Subsequently, Spa-RQ was applied to measure the co-activation of MAPK, AKT, and their mutual effector mTOR pathway in individual tumours. Both murine and clinical NSCLC samples could be stratified into 'MAPK/mTOR', 'AKT/mTOR', and 'Null' signature subclasses, suggesting mutually exclusive MAPK and AKT signalling activities. Spa-RQ thus provides a robust and easy to use tool that can be employed to identify spatially-distributed tissue phenotypes.
Subject: TUMOR EVOLUTION
HETEROGENEITY
MICROENVIRONMENT
TRACKING
PLATFORM
THERAPY
PATHWAY
ORIGIN
DRIVEN
KRAS
3111 Biomedicine
1182 Biochemistry, cell and molecular biology
3122 Cancers
Peer reviewed: Yes
Rights: cc_by
Usage restriction: openAccess
Self-archived version: publishedVersion


Files in this item

Total number of downloads: Loading...

Files Size Format View
s41598_019_54038_9.pdf 3.042Mb PDF View/Open

This item appears in the following Collection(s)

Show full item record