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

• Published in: Scientific reports Vol. 9; no. 1; pp. 17613 - 11
• Main Authors: Bao, Jie, Walliander, Margarita, Kovács, Ferenc, Nagaraj, Ashwini S., Hemmes, Annabrita, Sarhadi, Virinder Kaur, Knuutila, Sakari, Lundin, Johan, Horvath, Peter, Verschuren, Emmy W.
• Format: Journal Article
• Language: English
• Published: London Nature Publishing Group UK 26-11-2019; Nature Publishing Group
• Subjects: 1-Phosphatidylinositol 3-kinase; 13/51; 14/105; 3,3'-Diaminobenzidine; 631/67/1612/1350; 631/67/2329; 64/110; 96/1; 96/63; AKT protein; Biomarkers, Tumor; Carcinoma, Non-Small-Cell Lung - chemistry; Carcinoma, Non-Small-Cell Lung - pathology; Genes, ras; Hematoxylin; Histopathology; Humanities and Social Sciences; Humans; Image processing; Image Processing, Computer-Assisted - methods; Immunoenzyme Techniques; Lung cancer; Lung Neoplasms - chemistry; Lung Neoplasms - pathology; MAP kinase; MAP Kinase Signaling System; Medicin och hälsovetenskap; Mitogen-Activated Protein Kinase Kinases - analysis; multidisciplinary; Neoplasm Proteins - analysis; Non-small cell lung carcinoma; p53 Protein; Phenotype; Phenotypes; Phenotyping; Phosphoproteins - analysis; Proof of Concept Study; Proto-Oncogene Proteins c-akt - analysis; Science; Science (multidisciplinary); Sectioning; Signal Transduction; Small cell lung carcinoma; Software; Spatial analysis; Staining and Labeling - methods; Tissue analysis; TOR protein; TOR Serine-Threonine Kinases - analysis; Tumors
• ISSN: 2045-2322; 2045-2322
• DOI: 10.1038/s41598-019-54038-9

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.