Quantitative label-free mass spectrometry analysis of formalin-fixed, paraffin-embedded tissue representing the invasive cutaneous malignant melanoma proteome

Abstract

Understanding the events at a protein level that govern the progression from melanoma in situ to invasive melanoma are important areas of current research to be developed. Recent advances in the analysis of formalin-fixed, paraffin-embedded tissue by proteomics, particularly using the filter-aided sample preparation protocol, has opened up the possibility of studying vast archives of clinical material and associated medical records. In the present study, quantitative protein profiling was performed using tandem mass spectrometry, and the proteome differences between melanoma in situ and invasive melanoma were compared. Biological pathway analyses revealed several signalling pathways differing between melanoma in situ and invasive melanoma, including metabolic pathways and the phosphoinositide 3-kinase-Akt signalling pathway. Selected proteins of interest (14–3-3ε and fatty acid synthase) were subsequently investigated using immunohistochemical analysis of tissue microarrays. Identifying the key proteins that play significant roles in the establishment of a more invasive phenotype in melanoma may ultimately aid diagnosis and treatment decisions.

Characterization of long noncoding RNA and messenger RNA signatures in melanoma tumorigenesis and metastasis

“…Pathway in cancer was the top enriched term in MM vs. N and MM vs. PM, suggesting that our differentially expressed mRNAs are correlated with cancer. According to the study by Dowling et al [ 71 ], metabolic pathways differed between melanoma in situ and invasive melanoma. Melanogenesis can be a pathogenic factor during melanoma progression.…”

Proteome Profiling of Primary Pancreatic Ductal Adenocarcinomas Undergoing Additive Chemoradiation Link ALDH1A1 to Early Local Recurrence and Chemoradiation Resistance

“…Coupled with label-free shotgun proteomics and immunohistochemistry, these FFPE tissues have been widely used to identify biomarkers and drug targets in different disease settings [22], [23], [24], [25]. Several recent reports highlight a limited correlation between mRNA levels and corresponding protein levels, thus arguing in favor of proteomic approaches [26], [27].…”

Biomarkers in Malignant Melanoma: Recent Trends and Critical Perspective

“…In contrast, a cluster of biomarkers for one disease would be a better diagnostic tool with much higher sensitivity, specificity, and clinical accuracy. Therefore, new investigations called "proteomic profiling" or "multimarker profiling" focus on the identification of multiple co-expressed biomarkers or signature biomarker patterns which allow early detection, staging, therapeutic monitoring, and prognostic predictions (7,(84)(85)(86)(87)(88). This approach can be adopted for both serum and tissue specimens.…”