AI-Assisted High-Throughput Tissue Microarray Workflow

• Published in: Methods and protocols 2024-11, Vol.7 (6), p.96
• Main Authors: Kurowski, Konrad, Timme, Sylvia, Föll, Melanie Christine, Backhaus, Clara, Holzner, Philipp Anton, Bengsch, Bertram, Schilling, Oliver, Werner, Martin, Bronsert, Peter
• Format: Article
• Language: English
• ISSN: 2409-9279; 2409-9279
• DOI: 10.3390/mps7060096

Immunohistochemical (IHC) studies of formalin-fixed paraffin-embedded (FFPE) samples are a gold standard in oncology for tumor characterization, and the identification of prognostic and predictive markers. However, despite the abundance of archived FFPE samples, their research use is limited due to the labor-intensive nature of IHC on large cohorts. This study aimed to create a high-throughput workflow using modern technologies to facilitate IHC biomarker studies on large patient groups. Semiautomatic constructed tissue microarrays (TMAs) were created for two tumor patient cohorts and IHC stained for seven antibodies (ABs). AB expression in the tumor and surrounding stroma was quantified using the AI-supported image analysis software QuPath. The data were correlated with clinicopathological information using an R-script, all results were automatically compiled into formatted reports. By minimizing labor time to 7.7%—compared to whole-slide studies—the established workflow significantly reduced human and material resource consumption. It successfully correlated AB expression with overall patient survival and additional clinicopathological data, providing publication-ready figures and tables. The AI-assisted high-throughput TMA workflow, validated on two patient cohorts, streamlines modern histopathological research by offering cost and time efficiency compared to traditional whole-slide studies. It maintains research quality and preserves patient tissue while significantly reducing material and human resources, making it ideal for high-throughput research centers and collaborations.