Towards automatic protein co-expression quantification in immunohistochemical TMA slides

• 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.

Subject headings

TEKNIK OCH TEKNOLOGIER  -- Medicinteknik -- Medicinsk bildbehandling (hsv//swe)

ENGINEERING AND TECHNOLOGY  -- Medical Engineering -- Medical Image Processing (hsv//eng)

MEDICIN OCH HÄLSOVETENSKAP  -- Klinisk medicin -- Cancer och onkologi (hsv//swe)

MEDICAL AND HEALTH SCIENCES  -- Clinical Medicine -- Cancer and Oncology (hsv//eng)

Keyword

Co-expression

computational pathology

gastric cancer

image analysis

immunohistochemistry

protein

registration

Computerized Image Processing

Datoriserad bildbehandling

Publication and Content Type

ref (subject category)

art (subject category)