Portal de investigação
Towards Automatic Protein Co-Expression Quantification in Immunohistochemical TMA Slides
Data de publicação:
Autores da FMUP
Participantes de fora da FMUP
- Solorzano, L
- Pereira, C
- Martins, D
- Almeida, R.
- Almeida, GM
- Wahlby, C
Unidades de investigação
Abstract
Immunohistochemical (IHC) analysis of tissue biopsies is currently used for clinical screening of solid cancers to assess protein expression. The large amount of image data produced from these tissue samples requires specialized computational pathology methods to perform integrative analysis. Even though proteins are traditionally studied independently, the study of protein co-expression may offer new insights towards patients' clinical and therapeutic decisions. To explore protein co-expression, we constructed a modular image analysis pipeline to spatially align tissue microarray (TMA) image slides, evaluate alignment quality, define tumor regions, and ultimately quantify protein expression, before and after tumor segmentation. The pipeline was built with open-source tools that can manage gigapixel slides. To evaluate the consensus between pathologist and computer, we characterized a cohort of 142 gastric cancer (GC) cases regarding the extent of E-cadherin and CD44v6 expression. We performed IHC analysis in consecutive TMA slides and compared the automated quantification with the pathologists' manual assessment. Our results show that automated quantification within tumor regions improves agreement with the pathologists' classification. A co-expression map was created to identify the cores co-expressing both proteins. The proposed pipeline provides not only computational tools forwarding current pathology practices to explore co-expression, but also a framework for merging data and transferring information in learning-based approaches to pathology.
Dados da publicação
- ISSN/ISSNe:
- 2168-2208, 2168-2194
- Tipo:
- Article
- Páginas:
- 393-402
- Link para outro recurso:
- www.scopus.com
IEEE Journal of Biomedical and Health Informatics Institute of Electrical and Electronics Engineers Inc.
Citações Recebidas na Web of Science: 3
Citações Recebidas na Scopus: 6
Documentos
- Não há documentos
Filiações
Keywords
- Co-expression; computational pathology; gastric cancer; image analysis; immunohistochemistry; protein; registration
Financiamento
Proyectos asociados
Gastric Cancer Morphological, Immunophenotypic and molecular heterogeneity
Investigador Principal: Maria de Fátima Machado Henriques Carneiro
Estudo Clínico Académico . 2020
Citar a publicação
Solorzano L,Pereira C,Martins D,Almeida R,Carneiro F,Almeida GM,Oliveira C,Wahlby C. Towards Automatic Protein Co-Expression Quantification in Immunohistochemical TMA Slides. IEEE J. Biomedical Health Informat. 2021. 25. (2):p. 393-402. IF:7,021. (1).
