Year: 2022
Type: preprint
Abstract: This protocol outlines the NanoString GeoMx DSP protein assay that was applied in the Human Tumor Atlas Network (HTAN) Tissue MicroArrary (TMA) -TransNetwork Project (TNP). The TMA-TNP evaluates various characterization and analytics methodologies on a large array of breast tumor samples representing a broad spectrum of disease state and subtype. A commercially available anonymized breast tumor TMA was purchased and serial sections were distributed. Participating HTAN Centers characterized the FFPE specimens using various imaging platforms and generated a spatially resolved cell type/state census using each center’s method of choice. Data was recorded in a common repository to enable joint analysis. The protocol that immediately precedes this one for TMA-TNP Phase 3 (when this NanoString GeoMx DSP protein assay protocol was first tested) can be found at: dx.doi.org/10.17504/protocols.io.6qpvr6992vmk/v1. It describes FFPE block serial sectioning, slide processing and TMA sample distribution. In this protocol, the DSP protein assay was performed with the following human marker panels: Immune cell profiling core, Immune activation status, Immune-Oncology (IO) Drug target, Cell death, Pan-tumor, MAPK and PI3K/AKT panels including OHSU custom panel (Cell cycle and DNA damage). A total of 87 protein targets were evaluated in the TMA samples. Three compartments (Immune, Tumor and Stroma) in each TMA core were analyzed to determine cell-to-cell interactions in the tissues.
Language: English
Subfield: Molecular Biology
Domain: Life Sciences
Open Access status: green
OpenAlex ID: W4283265457