Scenario description
In this scenario RNA can be expressed in a particular subcellular compartment, eg. nuclei or cytoplasm, and the expression level within that particular subcellular compartment could be of importance (Figures 9 and 10).
Figure 9. Subcellular expression of GAS5 in breast cancer using the RNAscope ® 2.5 HD BROWN assay. GAS5 is detected in both the nucleus (arrow) and cytoplasm (arrow head).
Figure 10. Subcellular expression of MALAT1 in lung cancer using the RNAscope ® 2.5 HD BROWN assay. MALAT1 is detected primarily in the nucleus.
Analysis guidelines
In the scenario that a biomarker or target is expressed in a specific subcellular compartment data analysis can be challenging due to 2D representation (the image) of a 3 dimensional structure (the tissue). However, a qualitative analysis of the relative expression within each compartment could be informative and methodologies #1 and #2 can be applied for quantification. Furthermore, percentage positive cells can be assessed based on number of cells with ≥1 dot/cell.
