Proteomic Findings in Melanoma

Genomic and proteomic findings in early melanoma and opportunities for early diagnosis

Overdiagnosis of early melanoma is a significant problem. Due to subtle unique and overlapping clinical and histological criteria between pigmented lesions and the risk of mortality from melanoma, some benign pigmented lesions are diagnosed as melanoma. Although histopathology is the gold standard to diagnose melanoma, there is a demand to find alternatives that are more accurate and cost-effective. In the current "omics" era, there is gaining interest in biomarkers to help diagnose melanoma early and to further understand the mechanisms driving tumor progression. Genomic investigations have attempted to differentiate malignant melanoma from benign pigmented lesions. However, genetic biomarkers of early melanoma diagnosis have not yet proven their value in the clinical setting. Protein biomarkers may be more promising since they directly influence tissue phenotype, a result of by-products of genomic mutations, posttranslational modifications and environmental factors. Uncovering relevant protein biomarkers could increase confidence in their use as diagnostic signatures. Currently, proteomic investigations of melanoma progression from pigmented lesions are limited. Studies have previously characterised the melanoma proteome from cultured cell lines and clinical samples such as serum and tissue. This has been useful in understanding how melanoma progresses into metastasis and development of resistance to adjuvant therapies. Currently, most studies focus on metastatic melanoma to find potential drug therapy targets, prognostic factors and markers of resistance. This paper reviews recent advancements in the genomics and proteomic fields and reports potential avenues, which could help identify and differentiate melanoma from benign pigmented lesions and prevent the progression of melanoma.

Inhibition of bone morphogenetic proteins signaling suppresses metastasis melanoma: a proteomics approach

BACKGROUND

Bone morphogenetic proteins (BMPs) are members of the transforming growth factor-β superfamily, known to promote the tumor invasion and metastasis. There are continual progresses in understanding the role of BMP signaling pathways in carcinogenesis. However, the biological significance of BMPs in human melanoma has received very little attention. The study aimed to explore the effect of BMP inhibition on melanoma treated with LDN193189 (BMP inhibitor) using a quantitative proteomics approach in a melanoma xenograft model.

MATERIALS AND METHODS

Melanoma tumor was induced in C57BL6 mice and treated intraperitoneally with LDN193189 for ten consecutive days. Post-treatment, tumors were collected, and comparative proteomics was performed using a high-resolution Orbitrap Fusion Tribrid mass spectrometer.

RESULTS

Treatment of melanoma with LDN193189 at 3 mg/kg body weight twice daily showed a significant decrease in the growth rate of the tumor compared to the other doses tested. Quantitative proteomic profiling identified 3231 proteins. Bioinformatics analysis of the 131 differentially expressed proteins selected by their relative abundance revealed that LDN193189 induces alterations in the cellular and metabolic process and the proteins that are involved in protein binding and catalytic activity in melanoma.

CONCLUSIONS

Down-regulation of metallothionein (MT) 1 and MT2, emerging proteins for their role in tumor formation, progression, and drug resistance and transcription factor EB that plays a crucial role in the regulation of basic cellular processes, such as lysosomal biogenesis and autophagy, were identified upon inhibition of the BMP pathway in melanoma, suggesting their roles in melanoma growth. Understanding the role of these proteins will provide new directions for treating cancer.

Proteogenomic analysis of melanoma brain metastases from distinct anatomical sites identifies pathways of metastatic progression

Melanoma brain metastases (MBM) portend a grim prognosis and can occur in up to 40% of melanoma patients. Genomic characterization of brain metastases has been previously carried out to identify potential mutational drivers. However, to date a comprehensive multi-omics approach has yet to be used to analyze brain metastases. In this case report, we present an unbiased proteogenomics analyses of a patient's primary skin cancer and three brain metastases from distinct anatomic locations. We performed molecular profiling comprised of a targeted DNA panel and full transcriptome as well as proteomics using mass spectrometry. Phylogeny demonstrated that all MBMs shared a SMARCA4 mutation and deletion of 12q. Proteogenomics identified multiple pathways upregulated in the MBMs compared to the primary tumor. The protein, PIK3CG, was present in many of these pathways and had increased gene expression in metastatic melanoma tissue from the cancer genome atlas data. Proteomics demonstrated PIK3CG levels were significantly increased in all 3 MBMs and this finding was further validated by immunohistochemistry. In summary, this case report highlights the potential role of proteogenomics in identifying pathways involved in metastatic tumor progression. Furthermore, our multi-omics approach can be considered to aid in precision oncology efforts and provide avenues for therapeutic innovation.

Clinical Implications of Primary Cilia in Skin Cancer

The primary cilium is a cell surface organelle that is an important component of cellular biology. While it was once believed to be a vestigial structure without biologic function, it is now known to have essential roles in critical cellular signaling pathways such as Hedgehog (HH) and Wnt. The HH and Wnt pathways are involved in pathogenesis of basal cell carcinoma and melanoma, respectively, and this knowledge is now beginning to inform therapeutic and diagnostic options for patients. The purpose of this review is to familiarize clinicians with primary cilia biology and how this complex cellular organelle has started to translate into clinical care.

Improving clinical diagnosis of early-stage cutaneous melanoma based on Raman spectroscopy

Background

Clinical diagnosis of early melanoma (Breslow thickness less than 0.8 mm) is crucial to disease-free survival. However, it is subjective and can be exceedingly difficult, leading to missed melanomas, or unnecessary excision of benign pigmented skin lesions. An objective technique is needed to improve the diagnosis of early melanoma.

Methods

We have developed a method to improve diagnosis of (thin) melanoma, based on Raman spectroscopy. In an ex vivo study in a tertiary referral (pigmented lesions) centre, high-wavenumber Raman spectra were collected from 174 freshly excised melanocytic lesions suspicious for melanoma. Measurements were performed on multiple locations within the lesions. A diagnostic model was developed and validated on an independent data set of 96 lesions.

Results

Approximately 60% of the melanomas included in this study were melanomas in situ. The invasive melanomas had an average Breslow thickness of 0.89 mm. The diagnostic model correctly classified all melanomas (including in situ) with a specificity of 43.8%, and showed a potential improvement of the number needed to treat from 6.0 to 2.7, at a sensitivity of 100%.

Conclusion

This work signifies an important step towards accurate and objective clinical diagnosis of melanoma and in particular melanoma with Breslow thickness <0.8 mm.

Mass spectrometry-assisted gel-based proteomics in cancer biomarker discovery: approaches and application

There is a critical need for the discovery of novel biomarkers for early detection and targeted therapy of cancer, a major cause of deaths worldwide. In this respect, proteomic technologies, such as mass spectrometry (MS), enable the identification of pathologically significant proteins in various types of samples. MS is capable of high-throughput profiling of complex biological samples including blood, tissues, urine, milk, and cells. MS-assisted proteomics has contributed to the development of cancer biomarkers that may form the foundation for new clinical tests. It can also aid in elucidating the molecular mechanisms underlying cancer. In this review, we discuss MS principles and instrumentation as well as approaches in MS-based proteomics, which have been employed in the development of potential biomarkers. Furthermore, the challenges in validation of MS biomarkers for their use in clinical practice are also reviewed.