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

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.

• Authors: Jie Bao, Margarita Walliander, Ferenc Kovács, Ashwini S Nagaraj, Annabrita Hemmes, Virinder Kaur Sarhadi, Sakari Knuutila, Johan Lundin, Peter Horvath, Emmy W Verschuren
• Journal: Scientific reports (Sci Rep) Vol. 9 Issue 1 Pg. 17613 (11 26 2019) ISSN: 2045-2322 [Electronic] England
• PMID: 31772293 (Publication Type: Journal Article, Research Support, Non-U.S. Gov't)

Chemical References

• Biomarkers, Tumor
• Neoplasm Proteins
• Phosphoproteins
• 3,3'-Diaminobenzidine
• mTOR protein, mouse
• Akt1 protein, mouse
• Proto-Oncogene Proteins c-akt
• TOR Serine-Threonine Kinases
• Mitogen-Activated Protein Kinase Kinases
• Hematoxylin

Topics

• 3,3'-Diaminobenzidine
• Biomarkers, Tumor
• Carcinoma, Non-Small-Cell Lung (chemistry, pathology)
• Genes, ras
• Hematoxylin
• Humans
• Image Processing, Computer-Assisted (methods)
• Immunoenzyme Techniques
• Lung Neoplasms (chemistry, pathology)
• MAP Kinase Signaling System
• Mitogen-Activated Protein Kinase Kinases (analysis)
• Neoplasm Proteins (analysis)
• Phenotype
• Phosphoproteins (analysis)
• Proof of Concept Study
• Proto-Oncogene Proteins c-akt (analysis)
• Signal Transduction
• Software
• Staining and Labeling (methods)
• TOR Serine-Threonine Kinases (analysis)