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Proteomic and Molecular Changes in Cutaneous Melanoma Metastasis


Using mass spectrometry, researchers examined novel changes to gather updated metastasis information.

Metastasis of primary cutaneous melanomas involves an abundance of proteins and molecular changes.


In a study,1 researchers sought to obtain up-to-date information about changes in the metastatic melanoma progression journey, particularly to varying regions, and even organs of the body, in order to improve patient treatment response and survival rates.

Researchers first obtained formalin-fixed and paraffin-embedded (FFPE) samples of human primary melanoma (n=21), regional lymph node metastatic melanoma (n=19), and distant organ metastatic melanoma (n=20). A dermatopathologist examined clinical notes and haematoxylin and eosin (H&E) stained lesion sections to confirm the lesion’s exact diagnosis.

Furthermore, researchers collected lymph node samples from patient participants who had not previously received treatment, as well as 4 patients whose melanoma had progressed while being treated (with dabrafenib, pembrolizumab, or trametinib). Researchers also evaluated patients’ demographic information and certain disease-specific data, including tumour stage, Breslow thickness, mitotic count, presence or lack of ulceration, and Clark level.

All FFPE melanoma samples were prepared via oven drying, dewaxing in xylene, rehydrating in ethanol, alkylation, tryptic digestion, and vacuum concentration before mass spectrometry evaluation. Then, researchers conducted a liquid chromatography–tandem mass spectrometry (LC-MS/MS) analysis followed by a data analysis.

As a result, researchers made note of several proteome changes between primary and metastatic melanomas.

“Differential abundance analysis identified that a total of 72 (19 increased and 53 decreased) and 453 (213 increased and 240 decreased) protein groups were significantly changed between the LN [lymph node] and distant organ metastatic melanomas compared to the primary lesions, respectively,” study authors wrote. “Of these, 55 protein groups were commonly found as differentially abundant in the LN and distant organ metastatic melanomas. In addition, 181 protein groups (75 increased and 106 decreased) were significantly changed in the distant organ metastatic melanomas compared to the LN metastatic cohort."

They also conducted an in silico proteomic data assessment and validation, wherein they found that differentially abundant proteins in the lymph node metastatic melanoma and the distant organ metastatic melanoma samples showed that melanoma and other related skin diseases were among the most significantly enriched disease perturbations.

Through imaging, researchers found that tissue expression of L1CAM was decreased, TPMO was increased in both lymph node metastasis and primary melanoma, PPP2R5A was increased, and CDKAN2A and TOP1 decreased in distant organ metastasis and primary melanoma across multiple data sets.

Researchers had also performed a classification analysis and an analysis of molecular pathways, biofunction, and upstream regulators.

Highly-abundant proteins in the metastatic melanoma samples include GYPA, ADD2, EPB42, STAB2, GFAP, RUFY3, and AGR2.

“This led to the identification of 4631 protein groups, of which 525 were differentially abundant between the LN and distant organ metastatic melanomas compared to the primary lesions,” study authors wrote. “From our study, it appeared that changes in metastatic melanoma are manifested mainly as a reduction in the abundance of proteins compared to the primary lesions, that is, (53 decreased vs. 19 increased in LN metastasis: 240 decreased vs. 213 increased in distant metastasis). While it is out of the scope of this study to explain this reduction in protein abundance, previous transcriptomic study data (GEO GSE46517) deposited in the GEO database had reported similar findings.”


  1. Azimi A, Patrick E, Teh R, Kim J, Fernandez‐Penas P. Proteomic profiling of cutaneous melanoma explains the aggressiveness of distant organ metastasis. Exp Dermatol. 2023. doi:10.1111/exd.14814
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