We have published 2 papers using double indirect immunofluorescence on paraffin sections of stratified squamous epithelium, where protein expression changes as the cells differentiate. It is a good technique for defining cells unique to adjacent tissues as well (e.g. dermis and epidermis). Antigen retrieval using citrate buffer and an autoclave do a great job of removing wax so the tissues can be immunostained. Here are the two citations, old but still relevant:
Phenotypic plasticity in normal breast derived epithelial cells - PubMed (nih.gov) DOI: 10.1186/1471-2121-15-20
H-ras expression in immortalized keratinocytes produces an invasive epithelium in cultured skin equivalents - PubMed (nih.gov)
Article H-Ras Expression in Immortalized Keratinocytes Produces an I...