Proteomics and single-cell transcriptomics identify LRP1 as a diagnostic biomarker for atypical fibroxanthoma and pleomorphic dermal sarcoma

Atypical fibroxanthoma (AFX) and pleomorphic dermal sarcoma (PDS) are cutaneous neoplasms that fall along a spectrum. PDS is more aggressive than AFX with higher rates of local and distant metastases. Diagnostic biomarkers for AFX and PDS are lacking and therefore these tumors are diagnosed only after excluding other dermal spindle cell neoplasms, including cutaneous leiomyosarcoma (cLMS), spindle cell melanoma (SCM), and sarcomatoid squamous cell carcinoma (sSCC). To identify clinically valuable biomarkers, we contrast the tumors within the diagnostic differential using single-cell RNA sequencing and bulk proteomic data. Gene Ontology (GO) analysis of transcripts and proteins enriched in AFX/PDS identified multiple shared pathways associated with cell adherence and the extracellular matrix. We identify that LRP1, LTBP2, and NAV1 are all enriched in AFX/PDS over other tumors in the differential at both the level of mRNA and protein. IHC reveals that LRP1 is 90% sensitive and 73% specific for AFX/PDS in a cohort of AFX, PDS, cLMS, SCM, and sSCC. This outperforms published data for CD10, which is currently used clinically (sensitivity 83.5% and specificity 50%). When used in conjunction with LTBP2, specificity for AFX/PDS within the differential rises from 73% to 93%. These findings suggest that LRP1, particularly if evaluated in conjunction with existing stains, can improve diagnostic accuracy for AFX and PDS.