LC/MS-Based Quantitative Proteomic Analysis of Paraffin-Embedded Archival Melanomas Reveals Potential Proteomic Biomarkers Associated with Metastasis

Abstract

BackgroundMelanoma metastasis status is highly associated with the overall survival of patients; yet, little is known about proteomic changes during melanoma tumor progression. To better understand the changes in protein expression involved in melanoma progression and metastasis, and to identify potential biomarkers, we conducted a global quantitative proteomic analysis on archival metastatic and primary melanomas.Methodology and FindingsA total of 16 metastatic and 8 primary cutaneous melanomas were assessed. Proteins were extracted from laser captured microdissected formalin fixed paraffin-embedded archival tissues by liquefying tissue cells. These preparations were analyzed by a LC/MS-based label-free protein quantification method. More than 1500 proteins were identified in the tissue lysates with a peptide ID confidence level of >75%. This approach identified 120 significant changes in protein levels. These proteins were identified from multiple peptides with high confidence identification and were expressed at significantly different levels in metastases as compared with primary melanomas (q-Value<0.05).Conclusions and SignificanceThe differentially expressed proteins were classified by biological process or mapped into biological system networks, and several proteins were implicated by these analyses as cancer- or metastasis-related. These proteins represent potential biomarkers for tumor progression. The study successfully identified proteins that are differentially expressed in formalin fixed paraffin-embedded specimens of metastatic and primary melanoma.

In Silico Analysis Validates Proteomic Findings of Formalin-fixed Paraffin Embedded Cutaneous Squamous Cell Carcinoma Tissue

“…We identified over 1,310 unique protein species across FFPE tissues from five patients. This number is comparable to those observed in global, whole-tissue proteomic studies in other tumor samples using similar methodologies (46)(47)(48)(49). In addition, the peptide sequence coverage of up to 88% was a reflection of sufficient protein digestion and reliable protein identification in our study (50).…”

Quantitative Proteomic Analysis in Metastatic Renal Cell Carcinoma Reveals a Unique Set of Proteins with Potential Prognostic Significance

“…These include fructose-bisphosphate aldolase A, glucose-6-phosphate isomerase, glyceraldehyde-3-phosphate dehydrogenase, pyruvate kinase M1/ M2, and triosephosphate isomerase. Interestingly, proteins involved in the glycolytic pathway have also been reported to be involved in the metastasis of other cancers such as melanoma (54,55).…”

Photosensitizers Imprinting Intracellular Signaling Pathways in Dermato-Oncology Therapy

“…Referring strictly to cutaneous cancers, ESI-LC-MS was used for investigating in paraffin-embedded metastatic melanomas for comparative proteomic study [101]. This method quantifies peptide spectra that have been sequenced by the MS and can be used for biomarkers discovery through comparing the peak intensities derived from multiple LC-MS data set [102].…”