Development and validation of a noninvasive 2-gene molecular assay for cutaneous melanoma

High-throughput lipidomic profiles sampled with electroporation-based biopsy differentiate healthy skin, cutaneous squamous cell carcinoma, and basal cell carcinoma

BACKGROUND

The incidence rates of cutaneous squamous cell carcinoma (cSCC) and basal cell carcinoma (BCC) skin cancers are rising, while the current diagnostic process is time-consuming. We describe the development of a novel approach to high-throughput sampling of tissue lipids using electroporation-based biopsy, termed e-biopsy. We report on the ability of the e-biopsy technique to harvest large amounts of lipids from human skin samples.

MATERIALS AND METHODS

Here, 168 lipids were reliably identified from 12 patients providing a total of 13 samples. The extracted lipids were profiled with ultra-performance liquid chromatography and tandem mass spectrometry (UPLC-MS-MS) providing cSCC, BCC, and healthy skin lipidomic profiles.

RESULTS

Comparative analysis identified 27 differentially expressed lipids (p < 0.05). The general profile trend is low diglycerides in both cSCC and BCC, high phospholipids in BCC, and high lyso-phospholipids in cSCC compared to healthy skin tissue samples.

CONCLUSION

The results contribute to the growing body of knowledge that can potentially lead to novel insights into these skin cancers and demonstrate the potential of the e-biopsy technique for the analysis of lipidomic profiles of human skin tissues.

A signature of seven hypoxia-related lncRNAs is a potential biomarker for predicting the prognosis of melanoma

Melanoma is the most aggressive type of skin cancer and has a high mortality rate once metastasis occurs. Hypoxia is a universal characteristic of the microenvironment of cancer and a driver of melanoma progression. In recent years, long noncoding RNAs (lncRNAs) have attracted widespread attention in oncology research. In this study, screening was performed and revealed seven hypoxia-related lncRNAs AC008687.3, AC009495.1, AC245128.3, AL512363.1, LINC00518, LINC02416 and MCCC1-AS1 as predictive biomarkers. A predictive risk model was constructed via univariate Cox regression analysis, least absolute shrinkage and selection operator (LASSO), and multivariate Cox regression analyses. Patients were grouped according to the model risk score, and Kaplan-Meier analysis was performed to compare survival between groups. Functional and pathway enrichment analyses were performed to compare gene set enrichment between groups. Moreover, a nomogram was constructed with the risk score as a variable. In both the training and validation sets, patients in the low-risk group had better overall survival than did those in the high-risk group (P<0.001). The 3-, 5- and 10-year area under the curve (AUC) values for the nomogram model were 0.821, 0.795 and 0.820, respectively. Analyses of immune checkpoints, immunotherapy response, drug sensitivity, and mutation landscape were also performed. The results suggested that the low-risk group had a better response to immunotherapeutic. In addition, the nomogram can effectively predict the prognosis and immunotherapy response of melanoma patients. The signature of seven hypoxia-related lncRNAs showed great potential value as an immunotherapy response biomarker, and these lncRNAs might be treatment targets for melanoma patients.

Artificial intelligence and skin cancer

Artificial intelligence is poised to rapidly reshape many fields, including that of skin cancer screening and diagnosis, both as a disruptive and assistive technology. Together with the collection and availability of large medical data sets, artificial intelligence will become a powerful tool that can be leveraged by physicians in their diagnoses and treatment plans for patients. This comprehensive review focuses on current progress toward AI applications for patients, primary care providers, dermatologists, and dermatopathologists, explores the diverse applications of image and molecular processing for skin cancer, and highlights AI's potential for patient self-screening and improving diagnostic accuracy for non-dermatologists. We additionally delve into the challenges and barriers to clinical implementation, paths forward for implementation and areas of active research.

The Use of Gene Expression Profiling and Biomarkers in Melanoma Diagnosis and Predicting Recurrence: Implications for Surveillance and Treatment

Cutaneous melanoma is becoming more prevalent in the United States and has the highest mortality among cutaneous malignancies. The majority of melanomas are diagnosed at an early stage and, as such, survival is generally favorable. However, there remains prognostic uncertainty among subsets of early- and intermediate-stage melanoma patients, some of whom go on to develop advanced disease while others remain disease-free. Melanoma gene expression profiling (GEP) has evolved with the notion to help bridge this gap and identify higher- or lower-risk patients to better tailor treatment and surveillance protocols. These tests seek to prognosticate melanomas independently of established AJCC 8 cancer staging and clinicopathologic features (sex, age, primary tumor location, thickness, ulceration, mitotic rate, lymphovascular invasion, microsatellites, and/or SLNB status). While there is a significant opportunity to improve the accuracy of melanoma prognostication and diagnosis, it is equally important to understand the current landscape of molecular profiling for melanoma treatment. Society guidelines currently do not recommend molecular testing outside of clinical trials for melanoma clinical decision making, citing insufficient high-quality evidence guiding indications for the testing and interpretation of results. The goal of this chapter is to review the available literature for GEP testing for melanoma diagnosis and prognostication and understand their place in current treatment paradigms.

Mind the Gap: A Questionnaire on the Distance between Diagnostic Advances and Clinical Practice in Skin Cancer Treatment

Background and Objectives: Significant progress has been made in skin cancer diagnosis, with a surge in available technologies in recent years. Despite this, the practical application and integration of these technologies in dermatology and plastic surgery remain uneven. Materials and Methods: A comprehensive 20-question survey was designed and distributed using online survey administration software (Google Forms, 2018, Google, Mountain View, CA, USA) from June 2023 to September 2023. The survey aimed to assess the knowledge and utilization of dermatologic diagnostic advancements among plastic surgeons in various European countries. Results: Data were obtained from 29 plastic surgeons across nine European countries, revealing a notable gap between diagnostic technologies and their routine use in surgical practice. The gap for some technologies was both cognitive and applicative; for electrical impedance spectroscopy (EIS) and multispectral imaging, only 6.9% of the sample knew of the technologies and no surgeons in the sample used them. In the case of other technologies, such as high-frequency ultrasound (HFUS), 72.4% of the sample knew about them but only 34.5% used them, highlighting a more significant application problem. Conclusions: Spotlighting this discrepancy provides a valuable foundation for initiating collaborative efforts between units and facilitating knowledge exchange among diverse specialists. This, in turn, contributes to advancing clinical practice by integrating the innovative opportunities presented by ongoing research.

A noninvasive method for whole-genome skin methylome profiling

BACKGROUND

Ageing, disease and malignant transformation of the skin are associated with changes in DNA methylation. So far, mostly invasive methodologies such as biopsies have been applied in collecting DNA methylation signatures. Tape stripping offers a noninvasive option for skin diagnostics. It enables the easy but robust capture of biologic material in large numbers of participants without the need for specialized medical personnel.

OBJECTIVES

To design and validate a methodology for noninvasive skin sample collection using tape stripping for subsequent DNA -methylation analysis.

METHODS

A total of 175 participants were recruited and provided tape-stripping samples from a sun-exposed area; 92 provided matched tape-stripping samples from a sun-protected area, and an additional 5 provided matched skin-shave biopsies from the same area. Using -enzymatic conversion and whole-genome Illumina sequencing, we generated genome-wide DNA methylation profiles that were used to evaluate the feasibility of noninvasive data acquisition, to compare with established sampling approaches and to investigate biomarker identification for age and ultraviolet (UV) exposure.

RESULTS

We found that tape-stripping samples showed strong concordance in their global DNA methylation landscapes to those of conventional invasive biopsies. Moreover, we showed sample reproducibility and consistent global methylation profiles in skin tape-stripping samples collected from different areas of the body. Using matched samples from sun-protected and sun-exposed areas of the body we were able to validate the capacity of our method to capture the effects of environmental changes and ageing in a cohort covering various ages, ethnicities and skin types. We found DNA methylation changes on the skin resulting from UV exposure and identified significant age-related hypermethylation of CpG islands, with a pronounced peak effect at 50-55 years of age, including methylation changes in well-described markers of ageing.

CONCLUSIONS

These data demonstrate the feasibility of using tape stripping combined with whole-genome sequencing as a noninvasive approach to measuring DNA methylation changes in the skin. In addition, they outline a viable experimental framework for the use of skin tape stripping, particularly when it is performed in large cohorts of patients to identify biomarkers of skin ageing, UV damage and, possibly, to track treatment response to therapeutic interventions.

RNA analysis of tape strips to rule out melanoma in lesions clinically assessed as cutaneous malignant melanoma: A diagnostic study

BACKGROUND

Distinguishing cutaneous malignant melanoma (CMM) from nevi can be clinically challenging. Suspicious lesions are therefore excised, resulting in many benign lesions being removed surgically to find 1 CMM. It has been proposed to use tape strip derived ribonucleic acid (RNA) to distinguish CMM from nevi.

OBJECTIVE

To develop this technique further and validate if RNA profiles can rule out CMM in clinically suspicious lesions with 100% sensitivity.

METHODS

Before surgical excision, 200 lesions clinically assessed as CMM were tape stripped. Expression levels of 11 genes on the tapes were investigated by RNA measurement and used in a rule-out test.

RESULTS

Histopathology showed that 73 CMMs and 127 non-CMMs were included. Our test correctly identified all CMMs (100% sensitivity) based on the expression levels of 2 oncogenes, PRAME and KIT, relative to a housekeeping gene. Patient age and sample storage time were also significant. Simultaneously, our test correctly excluded CMM in 32% of non-CMM lesions (32% specificity).

LIMITATIONS

Our sample contained a very high proportion of CMMs, perhaps due to inclusion during COVID-19 shutdown. Validation in a separate trial must be performed.

CONCLUSION

Our results demonstrate that the technique can reduce removal of benign lesions by one-third without overlooking any CMMs.

The Role of Biomarkers in the Diagnosis and Prognosis of Different Stages of Melanoma

Melanoma is a skin cancer arising from melanocytes, the cells responsible for synthesizing melanin pigment, which gives the skin its color. Early diagnosis and treatment of melanoma increase survival rates. Clinical examination and biopsy are the primary tools used to diagnose melanoma. However, distinguishing between pre-malignant melanocytic lesions and early invasive melanoma histopathologically remains challenging. Therefore, additional modalities such as a detailed clinical history, imaging, genetic testing, and biomarkers have been applied to diagnose melanoma. This review discusses the current trends in biomarker advancements over the last 10 years to assist in the early detection and diagnosis of melanoma. Biomarkers such as melanoma-associated antigens (MAAs), S100B, microRNAs (miRNAs), and circulating tumor cells (CTCs) have the potential to aid in the detection, diagnosis, and prognosis of melanoma. However, the application of biomarkers in the diagnosis of melanoma is still evolving.

Dermoscopic features associated with 3-GEP PLA: LINC00518, PRAME, and TERT expression in suspicious pigmented lesions

Utilization of dermoscopy and novel molecular triage technologies augments visual triage of pigmented skin lesions, promoting early detection of melanoma. One emerging in vivo genomic test, 3-GEP pigmented lesion assay (3-GEP PLA) aids in pigmented lesion triage by noninvasively detecting the presence of three genes associated with melanoma: LINC00518, PRAME, and TERT. The purpose of our retrospective case-control study was to identify dermoscopic features uniquely associated with the presence of LINC00518, PRAME, or TERT in the stratum corneum as determined by 3-GEP PLA testing. Images of suspicious pigmented lesions that had undergone 3-GEP PLA testing and received a definitive positive or negative result (n = 393) were evaluated for the presence of specific clinical and dermoscopic features associated with melanoma. We found that asymmetry of color was a significant predictor for PRAME expression (Odds Ratio (OR) 5.5, 95% Confidence Interval (CI) 1.6-34.5, p = 0.004), blue color and negative pigment network were significant predictors for LINC00518 expression (adjusted OR 2.7, 95% CI 1.2-5.5, p = 0.014 and adjusted OR 5.4, 95% CI 1.6-16.9, p = 0.010, respectively), and atypical polymorphous vessels present in a pigmented skin lesion were a significant predictor for TERT promoter mutations (OR 5.8, 95% CI 1.3-23.4, p = 0.022). The results presented suggest a hierarchy in the significance of these dermoscopic features and may help guide evaluation and management of pigmented skin lesions.

Systematic Review on the Metabolic Interest of Glucosinolates and Their Bioactive Derivatives for Human Health

In the last decade, most of the evidence on the clinical benefits of including cruciferous foods in the diet has been focused on the content of glucosinolates (GSL) and their corresponding isothiocyanates (ITC), and mercapturic acid pathway metabolites, based on their capacity to modulate clinical, biochemical, and molecular parameters. The present systematic review summarizes findings of human studies regarding the metabolism and bioavailability of GSL and ITC, providing a comprehensive analysis that will help guide future research studies and facilitate the consultation of the latest advances in this booming and less profusely researched area of GSL for food and health. The literature search was carried out in Scopus, PubMed and the Web of Science, under the criteria of including publications centered on human subjects and the use of Brassicaceae foods in different formulations (including extracts, beverages, and tablets), as significant sources of bioactive compounds, in different types of subjects, and against certain diseases. Twenty-eight human intervention studies met inclusion criteria, which were classified into three groups depending on the dietary source. This review summarizes recent studies that provided interesting contributions, but also uncovered the many potential venues for future research on the benefits of consuming cruciferous foods in our health and well-being. The research will continue to support the inclusion of GSL-rich foods and products for multiple preventive and active programs in nutrition and well-being.

Detection of cutaneous malignant melanoma by tape stripping of pigmented skin lesions - A systematic review

BACKGROUND

Cutaneous malignant melanoma (MM) is potentially aggressive, and numerous clinically suspicious pigmented skin lesions are excised, causing unnecessary mutilation for patients at high healthcare costs, but without histopathological evidence of MM. The high number of excisions may be lowered by using more accurate diagnostics. Tape stripping (TS) of clinically suspicious lesions is a non-invasive diagnostic test of MM that can potentially lower the number needed to biopsy/excise.

MATERIALS AND METHODS

The aim is to determine the diagnostic accuracy of TS in detecting MM in clinically suspicious pigmented skin lesions. This systematic review following PRISMA guidelines searched PubMed, Web of Science, and Embase (September 2022) using melanoma combined with tape stripping, adhesive patch(es), pigmented lesion assay, or epidermal genetic information retrieval.

RESULTS

Ten studies were included. Sensitivity ranged from 68.8% (95% confidence interval [CI] 51.5, 82.1) to 100% (95% CI 91.0, 100). Specificity ranged from 69.1% (95% CI 63.8, 74.0) to 100% (95% CI 78.5, 100). A pooled analysis of five studies testing the RNA markers LINC00518 and PRAME found a sensitivity of 86.9% (95% CI 81.7, 90.8) and a specificity of 82.4% (95% CI 80.8, 83.9).

CONCLUSION

Overall quality of studies was low, and the reliability of sensitivity and specificity is questionable. However, TS may supplement well-established diagnostic methods as pooled analysis of five studies indicates a moderate sensitivity. Future studies are needed to obtain more reliable data as independent studies with no conflict of interest.

New Technologies in Diagnosis and Prognosis of Melanocytic Lesions

Analysis of morphological characteristics for the diagnosis of melanoma remains a challenge. New technologies for the diagnosis and prognosis of melanocytic lesions have been emerging to ensure earlier and more accurate detection. In this article, we review multiple technologies that improve melanoma diagnostic accuracy such as electrical impedance spectroscopy, pigmented lesion assay, reflectance confocal microscopy, and gene expression profile tests.

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.

Molecular Skin Cancer Diagnosis: Promise and Limitations

Skin cancer is a significant and increasing global health burden. Although the current diagnostic workflow is robust and able to provide clinically actionable results, it is subject to notable limitations. The training and expertise required for accurate diagnoses using conventional skin cancer diagnostics are significant, and patient access to this workflow can be limited by geographic location or unforeseen events, such as coronavirus disease 2019 (COVID-19). Molecular biomarkers have transformed diagnostics and treatment delivery in oncology. With rapid advancements in molecular biology techniques, understanding of the underlying molecular mechanism of cancer pathologies has deepened, yielding biomarkers that can be used to monitor the course of malignant diseases. Herein, commercially available, clinically validated, and emerging skin cancer molecular biomarkers are reviewed. The qualities of an ideal molecular biomarker are defined. The potential benefits and limitations of applying molecular biomarker testing over the course of skin cancer from susceptibility to treatment are explored, with a view to outlining a future model of molecular biomarker skin cancer diagnostics.

Dysplastic nevus part II: Dysplastic nevi: Molecular/genetic profiles and management

Dermatologists frequently see patients with clinically atypical nevi and dermatopathologists interpret histologically dysplastic nevi on a near-daily basis, but there is great variability in the definition and management of such lesions. This part of the CME review focuses on information published since the previous comprehensive review (2012), with emphasis on molecular and genetic attributes of histologically dysplastic nevi and clinical management.

Long non-coding RNAs and melanoma: From diagnosis to therapy

Although extremely rare, malignant melanoma is the deadliest type of skin malignancy with the inherent capability to invade other organs and metastasize to distant tissues. In 2021, it was estimated that approximately 106,110 patients may have received the diagnosis of melanoma, with a mortality rate of 7180. Surgery remains the common choice for treatment in patients with melanoma. Despite many advances in the treatment of melanoma, some patients, such as those who have received cytotoxic chemotherapeutic and immunotherapic agents, a significant number of patients may show inadequate treatment response following initiating these treatments. Non-coding RNAs, including lncRNAs, have become recently popular and attracted the attention of many researchers to make new insights into the pathogenesis of many diseases, particularly malignancies. LncRNAs have been thoroughly investigated in multiple cancers such as melanoma and have been shown to play a major role in regulating various physiological and pathological cellular processes. Considering their core regulatory function, these non-coding RNAs may be appropriate candidates for melanoma patients' diagnosis, prognosis, and treatment. In this review, we will cover all the current literature available for lncRNAs in melanoma and will discuss their potential benefits as diagnostic and/or prognostic markers or potent therapeutic targets in the treatment of melanoma patients.

Combining fiber optical tweezers and Raman spectroscopy for rapid identification of melanoma

Cutaneous melanoma is a skin tumor with a high degree of malignancy and fatality rate, the incidence of which has increased in recent years. Therefore, a rapid and sensitive diagnostic technique of melanoma cells is urgently needed. In this paper, we present a new approach using fiber optical tweezers to manipulate melanoma cells to measure their Raman spectra. Then, combined with Principal Component Analysis and Support Vector Machines (PCA-SVM) classification model, to achieve the classification of common mutant, wild-type and drug-resistant melanoma cells. A total of 150 Raman spectra of 30 cells were collected from mutant, wild-type and drug-resistant melanoma cell lines, and the classification accuracy was 92%, 94%, 97.5%, respectively. These results suggest that the study of tumor cells based on fiber optical tweezers and Raman spectroscopy is a promising method for early and rapid identification and diagnosis of tumor cells.

Potential Limitations in the Clinical Adoption of 3-GEP Pigmented Lesion Assay for Melanoma Triage by Dermatologists and Advanced Practice Practitioners

Background A pigmented lesion assay (PLA) is used to non-invasively detect the presence of three genes associated with melanoma (LINC00518, PRAME, and TERT) using adhesive patch testing and has the potential to reduce unnecessary biopsies. However, few studies have evaluated the clinical applicability of PLA testing and its potential limitations in real-world practice. We aim to identify possible barriers that inhibit the clinical utility of PLA testing by dermatologists. Methods Retrospective case-control study analyzing the PLA testing by two pigmented-lesion specialists that underwent PLA testing as part of clinical management. Data was collected from April 2021 to April 2022 from an academic tertiary-level center. Results The total cohort consists of 472 lesions. Genetic analysis failure for LINC00518 and PRAME occurred in 12.5% of cases and in 70.9% of cases for TERT. In 38.5% of cases, PLA results were discrepant with histopathology. The additional time associated with PLA use independent from the patient's visit was 15 min on average. Conclusion The high proportion of non-actionable results and discrepant cases highlights potential barriers to the widespread adoption of PLA testing. The high proportion of genetic analysis failure seen for TERT and limited influence on the proposed risk suggests TERT does not offer significant clinical value.

Detection of cutaneous malignant melanoma using RNA sampled by tape strips: A study protocol

Background

Cutaneous malignant melanoma (CMM) is curable if detected in its early stages. However, the clinical recognition of CMM is challenging. An American research group has shown promising results in detecting CMM based on RNA profiles sampled from suspicious lesions with tape strips. We aim to further develop this technique and validate if RNA profiles sampled with tape strips can detect CMM.

Methods

This prospective cohort study will include approximately 200 lesions clinically suspected of CMM requiring surgical removal. Tape stripping of the lesions will be performed just before surgical excision. Subsequently, RNA on the tape strips is analyzed using quantitative real-time polymerase chain reaction with TaqMan technology. The results are combined into a binary outcome where positive indicates CMM and negative indicates no CMM. The histopathological diagnosis of the lesions will be used as the gold standard. The main outcome is the results of the RNA test and the histopathological diagnosis, which, combined, provide the sensitivity and specificity of the test.

Discussion

The accuracy of the clinical examination in CMM diagnostics is limited. This clinical trial will explore the ability to use RNA analysis to improve the management of suspicious lesions by enhancing early diagnostic accuracy. Hopefully, it can reduce the number of benign lesions being surgically removed to rule out CMM and decrease patient morbidity.

Trial registration

The project was approved by The Committee on Health Research Ethics of the Capital Region of Denmark (H-15010559) and registered at the Danish Data Protection Agency (BFH-2015-065).

Acral Amelanotic Melanoma Mimicking a Foot Ulcer

Acral amelanotic melanoma can be difficult to diagnose and is often clinically aggressive. The present report describes a case of an acral amelanotic melanoma presenting as a non-healing wound after mimicking a plantar wart for two years. The decision to biopsy a borderline-suspicious lesion on the lower extremity in an elderly individual must be weighed carefully, as lower extremity biopsy carries a risk of poor wound healing and other complications. We discuss clinical and epidemiologic features that can assist in deciding when to perform a biopsy in this setting and can improve the early detection of acral amelanotic melanoma.

LINC00518 Promotes Cell Malignant Behaviors via Influencing EIF4A3-Mediated mRNA Stability of MITF in Melanoma

Melanoma has become the most severe sort of skin cancer, deriving from the pigment-producing melanocytes. Existing research has validated that long noncoding RNAs (lncRNAs) have critical function in the progression of cancers. LINC00518 has been studied in cutaneous melanoma; however, the molecular mechanism of LINC00518 in melanoma needs in-depth investigation. In our study, LINC00518 was revealed to be upregulated in melanoma tissues and cells, and melanoma patients in high LINC00518 expression group had poorer prognosis as depicted in GEPIA database. Functional assays revealed that LINC00518 depletion inhibited cell proliferation, migration, invasion, and epithelial-mesenchymal transition (EMT). Furthermore, MITF was confirmed to be upregulated in melanoma tissues and cells, and melanoma patients in high MITF expression group had poorer prognosis as displayed in GEPIA database. MITF expression was positively connected to LINC00518 expression. Additionally, results of mechanism assays uncovered EIF4A3 could bind with LINC00518 and MITF, and LINC00518 recruited EIF4A3 to stabilize MITF mRNA. Finally, it was demonstrated that upregulation of MITF could partially abrogate the inhibitory impact of LINC00518 knockdown on melanoma cell malignant behaviors. To summarize, LINC00518 promotes the malignant processes of melanoma cells through targeting EIF4A3/MITF axis, which might provide novel potential biomarkers for melanoma prognosis.

Classification of skin cancer using convolutional neural networks analysis of Raman spectra

BACKGROUND AND OBJECTIVE

Skin cancer is the most common malignancy in whites accounting for about one third of all cancers diagnosed per year. Portable Raman spectroscopy setups for skin cancer "optical biopsy" are utilized to detect tumors based on their spectral features caused by the comparative presence of different chemical components. However, low signal-to-noise ratio in such systems may prevent accurate tumors classification. Thus, there is a challenge to develop methods for efficient skin tumors classification.

METHODS

We compare the performance of convolutional neural networks and the projection on latent structures with discriminant analysis for discriminating skin cancer using the analysis of Raman spectra with a high autofluorescence background stimulated by a 785 nm laser. We have registered the spectra of 617 cases of skin neoplasms (615 patients, 70 melanomas, 122 basal cell carcinomas, 12 squamous cell carcinomas and 413 benign tumors) in vivo with a portable Raman setup and created classification models both for convolutional neural networks and projection on latent structures approaches. To check the classification models stability, a 10-fold cross-validation was performed for all created models. To avoid models overfitting, the data was divided into a training set (80% of spectral dataset) and a test set (20% of spectral dataset).

RESULTS

The results for different classification tasks demonstrate that the convolutional neural networks significantly (p<0.01) outperforms the projection on latent structures. For the convolutional neural networks implementation we obtained ROC AUCs of 0.96 (0.94 - 0.97; 95% CI), 0.90 (0.85-0.94; 95% CI), and 0.92 (0.87 - 0.97; 95% CI) for classifying a) malignant vs benign tumors, b) melanomas vs pigmented tumors and c) melanomas vs seborrheic keratosis respectively.

CONCLUSIONS

The performance of the convolutional neural networks classification of skin tumors based on Raman spectra analysis is higher or comparable to the accuracy provided by trained dermatologists. The increased accuracy with the convolutional neural networks implementation is due to a more precise accounting of low intensity Raman bands in the intense autofluorescence background. The achieved high performance of skin tumors classifications with convolutional neural networks analysis opens a possibility for wide implementation of Raman setups in clinical setting.

High-Plex Spatial RNA Profiling Reveals Cell Type‒Specific Biomarker Expression during Melanoma Development

Early diagnosis of melanoma is critical for improved survival. However, the biomarkers of early melanoma evolution and their origin within the tumor and its microenvironment, including the keratinocytes, are poorly defined. To address this, we used spatial transcript profiling that maintains the morphological tumor context to measure the expression of >1,000 RNAs in situ in patient-derived formalin-fixed, paraffin-embedded tissue sections in primary melanoma and melanocytic nevi. We profiled 134 regions of interest (each 200 μm in diameter) enriched in melanocytes, neighboring keratinocytes, or immune cells. This approach captured distinct expression patterns across cell types and tumor types during melanoma development. Unexpectedly, we discovered that S100A8 is expressed by keratinocytes within the tumor microenvironment during melanoma growth. Immunohistochemistry of 252 tumors showed prominent keratinocyte-derived S100A8 expression in melanoma but not in benign tumors and confirmed the same pattern for S100A8's binding partner S100A9, suggesting that injury to the epidermis may be an early and readily detectable indicator of melanoma development. Together, our results establish a framework for high-plex, spatial, and cell type‒specific resolution of gene expression in archival tissue applicable to the development of biomarkers and characterization of tumor microenvironment interactions in tumor evolution.

Tape Stripping: Investigational, Diagnostic and Therapeutic Uses in Dermatology

Adhesive tape has been used in the scientific study of human skin for over 90 years. Using the tape stripping method in dermatology has aided in the research and diagnose of different skin diseases. Basic science, identification, and therapeutic interventions in skin diseases such as psoriasis, atopic dermatitis, non-melanoma skin cancer, and melanoma have been studied using this technique. Among many promising applications that will be discussed throughout this paper, the Pigmented Lesion Assay (PLA) will be discussed in depth in relation to melanoma. This product carries considerable and significant research towards early detection of melanoma. Tape stripping is unique and advantageous in its ability to provide a non-surgical approach to evaluating the human epidermis. The cellular and molecular components of the skin are used to diagnose different skin conditions without invasive skin biopsy.

Immunohistochemistry for Preferentially Expressed Antigen in Melanoma in the Differential Diagnosis of Melanocytic Lesions of the Nail Apparatus

ABSTRACT

Nail unit melanocytic lesions present a unique set of diagnostic challenges because of the unfamiliarity with clinical assessment and the lack of experience with histologic examination. Because the first surgical specimen received in the pathology laboratory is typically small, sometimes suboptimal biopsy, the distinction between melanoma and its histologic mimics can be difficult. For this reason, there has been a continued interest in the development of ancillary markers that may assist in the differential diagnosis of nail unit melanocytic lesions. Upregulation of preferentially expressed antigen in melanoma (PRAME) has been reported to be a common event in melanomas, and PRAME immunohistochemistry has been shown to be helpful in evaluating various melanocytic neoplasms. In this study, we evaluated PRAME protein expression in a series of nail unit melanocytic lesions. Twenty-five nail unit melanomas (including small biopsy and amputation specimens) and 32 control benign melanocytic lesions were retrospectively retrieved. Nuclear PRAME staining was scored as percentage and intensity labeling. All melanoma cases showed the nuclear expression of PRAME, which was usually diffuse and strong. In specimens where the neoplastic cells are limited in number, the staining was restricted to the tumor cells, corresponding to the initial H&E impression. All control cases were negative for PRAME expression. PRAME expression is helpful in distinguishing between melanomas and other nail unit melanocytic lesions. This antibody also proved to be diagnostically valuable in detecting melanoma cells in small specimens with minimal disease.

Role of Biomarkers in the Integrated Management of Melanoma

Melanoma, which is an aggressive skin cancer, is currently the fifth and seventh most common cancer in men and women, respectively. The American Cancer Society reported that approximately 106,110 new cases of melanoma were diagnosed in the United States in 2021, with 7,180 people dying from the disease. This information could facilitate the early detection of possible metastatic lesions and the development of novel therapeutic techniques for melanoma. Additionally, early detection of malignant melanoma remains an objective of melanoma research. Recently, melanoma treatment has substantially improved, given the availability of targeted treatments and immunotherapy. These developments have highlighted the significance of identifying biomarkers for prognosis and predicting therapy response. Biomarkers included tissue protein expression, circulating DNA detection, and genetic alterations in cancer cells. Improved diagnostic and prognostic biomarkers are becoming increasingly relevant in melanoma treatment, with the development of newer and more targeted treatments. Here, the author discusses the aspects of biomarkers in the real-time management of patients with melanoma.

Shared Gene Expression and Immune Pathway Changes Associated with Progression from Nevi to Melanoma

Simple Summary

Melanoma is a deadly skin cancer, and the incidence of melanoma is rising. Chemoprevention, using small molecule drugs to prevent the development of cancer, is a key strategy that could reduce the burden of melanoma on society. The long-term goal of our study is to develop a gene signature biomarker of progression from nevi to melanoma. We found that a small number of genes can distinguish nevi from melanoma and identified shared genes and immune-related pathways that are associated with progression from nevi to melanoma across independent datasets. This study demonstrates (1) a novel approach to aid melanoma chemoprevention trials by using a gene signature as a surrogate endpoint and (2) the feasibility of determining a gene signature biomarker of melanoma progression.

Abstract

There is a need to identify molecular biomarkers of melanoma progression to assist the development of chemoprevention strategies to lower melanoma incidence. Using datasets containing gene expression for dysplastic nevi and melanoma or melanoma arising in a nevus, we performed differential gene expression analysis and regularized regression models to identify genes and pathways that were associated with progression from nevi to melanoma. A small number of genes distinguished nevi from melanoma. Differential expression of seven genes was identified between nevi and melanoma in three independent datasets. C1QB, CXCL9, CXCL10, DFNA5 (GSDME), FCGR1B, and PRAME were increased in melanoma, and SCGB1D2 was decreased in melanoma, compared to dysplastic nevi or nevi that progressed to melanoma. Further supporting an association with melanomagenesis, these genes demonstrated a linear change in expression from benign nevi to dysplastic nevi to radial growth phase melanoma to vertical growth phase melanoma. The genes associated with melanoma progression showed significant enrichment of multiple pathways related to the immune system. This study demonstrates (1) a novel application of bioinformatic approaches to aid clinical trials of melanoma chemoprevention and (2) the feasibility of determining a gene signature biomarker of melanomagenesis.

Correlation of FISH and PRAME Immunohistochemistry in Ambiguous Superficial Cutaneous Melanocytic Proliferations

ABSTRACT

Preferentially expressed antigen in melanoma (PRAME) is a tumor-associated repressor of retinoic acid signaling which is expressed in melanoma and has emerged as a potential biomarker for malignant behavior in melanocytic neoplasms. Although ancillary molecular techniques such as fluorescence in situ hybridization (FISH) are established techniques in the diagnosis of problematic cutaneous melanocytic proliferations, they are expensive, time-consuming, and require appropriate infrastructure, which places them out of reach of some laboratories. The advent of readily available commercial antibodies to PRAME has the potential to provide a more accessible alternative. The aim of this study was to determine whether immunohistochemistry for PRAME could serve as a surrogate for FISH analysis in a subgroup of challenging superficial melanocytic proliferations. Cases which had previously been submitted for FISH analysis were stained for PRAME and interpreted by a panel of at least 3 dermatopathologists is a blinded fashion. Of a study set of 55 cases, 42 (76%) showed a pattern of PRAME immunostaining which was concordant with the cytogenetic interpretation, with an unweighted kappa of 0.42 (representing mild-to-moderate agreement). Thus, although there was a correlation between positive immunohistochemistry for PRAME and abnormal findings on FISH analysis, in our view, the concordance was not sufficient to enable PRAME immunohistochemistry to act as a surrogate for FISH testing. Our findings reiterate the principle that interpretation of problematic superficial melanocytic proliferations requires a synthesis of all the available data, including clinical scenario, morphological features, immunohistochemistry, and ancillary molecular investigations.

Impact of Next-generation Sequencing on Interobserver Agreement and Diagnosis of Spitzoid Neoplasms

Atypical Spitzoid melanocytic tumors are diagnostically challenging. Many studies have suggested various genomic markers to improve classification and prognostication. We aimed to assess whether next-generation sequencing studies using the Tempus xO assay assessing mutations in 1711 cancer-related genes and performing whole transcriptome mRNA sequencing for structural alterations could improve diagnostic agreement and accuracy in assessing neoplasms with Spitzoid histologic features. Twenty expert pathologists were asked to review 70 consultation level cases with Spitzoid features, once with limited clinical information and again with additional genomic information. There was an improvement in overall agreement with additional genomic information. Most significantly, there was increase in agreement of the diagnosis of conventional melanoma from moderate (κ=0.470, SE=0.0105) to substantial (κ=0.645, SE=0.0143) as measured by an average Cohen κ. Clinical follow-up was available in all 70 cases which substantiated that the improved agreement was clinically significant. Among 3 patients with distant metastatic disease, there was a highly significant increase in diagnostic recognition of the cases as conventional melanoma with genomics (P<0.005). In one case, none of 20 pathologists recognized a tumor with BRAF and TERT promoter mutations associated with fatal outcome as a conventional melanoma when only limited clinical information was provided, whereas 60% of pathologists correctly diagnosed this case when genomic information was also available. There was also a significant improvement in agreement of which lesions should be classified in the Spitz category/WHO Pathway from an average Cohen κ of 0.360 (SE=0.00921) to 0.607 (SE=0.0232) with genomics.

Sensitive Immunofluorescent Detection of the PRAME Antigen Using a Practical Antibody Conjugation Approach

Bioconjugation of antibodies with various payloads has diverse applications across various fields, including drug delivery and targeted imaging techniques. Fluorescent immunoconjugates provide a promising tool for cancer diagnostics due to their high brightness, specificity, stability and target affinity. Fluorescent antibodies are widely used in flow cytometry for fast and sensitive identification and collection of cells expressing the target surface antigen. Nonetheless, current approaches to fluorescent labeling of antibodies most often use random modification, along with a few rather sophisticated site-specific techniques. The aim of our work was to develop a procedure for fluorescent labeling of immunoglobulin G via periodate oxidation of antibody glycans, followed by oxime ligation with fluorescent oxyamines. Here, we report a novel technique based on an in situ oxime ligation of ethoxyethylidene-protected aminooxy compounds with oxidized antibody glycans. The approach is suitable for easy modification of any immunoglobulin G, while ensuring that antigen-binding domains remain intact, thus revealing various possibilities for fluorescent probe design. The technique was used to label an antibody to PRAME, a cancer-testis protein overexpressed in a number of cancers. A 6H8 monoclonal antibody to the PRAME protein was directly modified with protected-oxyamine derivatives of fluorescein-type dyes (FAM, Alexa488, BDP-FL); the stoichiometry of the resulting conjugates was characterized spectroscopically. The immunofluorescent conjugates obtained were applied to the analysis of bone marrow samples from patients with oncohematological diseases and demonstrated high efficiency in flow cytometry quantification. The approach can be applied for the development of various immunofluorescent probes for detection of diagnostic and prognostic markers, which can be useful in anticancer therapy.

Emerging Minimally Invasive Technologies for the Detection of Skin Cancer

With the increasing incidence of skin cancer, many noninvasive technologies to detect its presence have been developed. This review focuses on reflectance confocal microscopy (RCM), optical coherence tomography (OCT), high-frequency ultrasound (HFUS), electrical impedance spectroscopy (EIS), pigmented lesion assay (PLA), and Raman spectroscopy (RS) and discusses the basic principle, clinical applications, advantages, and disadvantages of each technology. RCM provides high cellular resolution and has high sensitivity and specificity for the diagnosis of skin cancer. OCT provides lower resolution than RCM, although its evaluable depth is deeper than that of RCM. RCM and OCT may be useful in reducing the number of unnecessary biopsies, evaluating the tumor margin, and monitoring treatment response. HFUS can be mainly used to delineate tumor depths or margins and monitor the treatment response. EIS provides high sensitivity but low specificity for the diagnosis of skin malignancies. PLA, which is based on the genetic information of lesions, is applicable for the detection of melanoma with high sensitivity and moderate-to-high specificity. RS showed high accuracy for the diagnosis of skin cancer, although more clinical studies are required. Advances in these technologies for the diagnosis of skin cancer can lead to the realization of optimized and individualized treatments.

Pigmented Lesion Assay for Suspected Melanoma Lesions: A Health Technology Assessment

BACKGROUND

Early detection of melanoma is key, as survival rates are substantially better when the cancer is detected in its early stages. Currently, the standard of care is to biopsy any lesion suspected of melanoma for diagnostic confirmation by histopathology. As a result, most people who undergo biopsy receive negative melanoma results. If effective, a non-invasive alternative, such as pigmented lesion assay, could minimize the number of unnecessary biopsies performed. We conducted a health technology assessment of pigmented lesion assay for people with suspected melanoma lesions, which included an evaluation of diagnostic accuracy, clinical utility, the budget impact of publicly funding pigmented lesion assay, and the preferences and values of people who have undergone biopsy for suspected melanoma.

METHODS

We performed a systematic literature search of the clinical evidence. We assessed the risk of bias of each included study using the Quality Assessment of Diagnostic Accuracy Studies-2 (QUADAS-2) and the Risk of Bias Assessment Tool for Non-randomized Studies (RoBANS). We assessed the quality of the body of evidence according to the Grading of Recommendations Assessment, Development, and Evaluation (GRADE) Working Group criteria. We performed a systematic literature search of the economic evidence. We also analyzed the budget impact of publicly funding pigmented lesion assay in adults with suspected melanoma in Ontario. To contextualize the potential value of pigmented lesion assay, we spoke with people who had undergone skin biopsy for melanoma. We also used the qualitative research synthesis from a report by the Canadian Agency for Drugs and Technologies in Health to provide context for the preferences and values of those with suspected melanoma.

RESULTS

We included seven studies in the clinical evidence review. Pigmented lesion assay has a sensitivity of 79% (95% confidence interval [CI] 58%-93%) and a specificity of 80% (95% CI 73%-85%; GRADE: Low). We found one published cost-effectiveness study with potentially serious limitations. Therefore, the cost-effectiveness of pigmented lesion assay compared with the standard care pathway is currently uncertain. Assuming a very low uptake, we estimated that the budget impact of publicly funding pigmented lesion assay in Ontario over the next 5 years is about $3.44 million if the test is used exclusively by primary care providers, or about $2.56 million if it is used exclusively by specialists. The people with whom we spoke who had experienced biopsy for suspected melanoma responded positively to the potential benefits of pigmented lesion assay, emphasizing its ease-of-use, potential increase in early detection of melanoma, and reduction in physical and emotional burden of unnecessary biopsies. Participants also felt that the accuracy of this tool was essential to ensure minimal false negatives.

CONCLUSIONS

There is uncertainty because of the low-quality evidence for the diagnostic accuracy of pigmented lesion assay. The cost-effectiveness of pigmented lesion assay compared with standard care is also uncertain. We estimated that publicly funding pigmented lesion assay in Ontario over the next 5 years would result in additional costs of $3.44 million (if used exclusively by primary care providers) or $2.56 million (if used exclusively by specialists). For people who had experienced biopsy for suspected melanoma, it was felt that pigmented lesion assay could represent an effective tool to increase early detection and avoid unnecessary biopsies, if the tool was accurate.

Molecular Biomarkers for Melanoma Screening, Diagnosis and Prognosis: Current State and Future Prospects

Despite significant progress in the development of treatment options, melanoma remains a leading cause of death due to skin cancer. Advances in our understanding of the genetic, transcriptomic, and morphologic spectrum of benign and malignant melanocytic neoplasia have enabled the field to propose biomarkers with potential diagnostic, prognostic, and predictive value. While these proposed biomarkers have the potential to improve clinical decision making at multiple critical intervention points, most remain unvalidated. Clinical validation of even the most commonly assessed biomarkers will require substantial resources, including limited clinical specimens. It is therefore important to consider the properties that constitute a relevant and clinically-useful biomarker-based test prior to engaging in large validation studies. In this review article we adapt an established framework for determining minimally-useful biomarker test characteristics, and apply this framework to a discussion of currently used and proposed biomarkers designed to aid melanoma detection, staging, prognosis, and choice of treatment.

RNA tape sampling in cutaneous lupus erythematosus discriminates affected from unaffected and healthy volunteer skin

Objective

Punch biopsy, a standard diagnostic procedure for patients with cutaneous lupus erythematosus (CLE) carries an infection risk, is invasive, uncomfortable and potentially scarring, and impedes patient recruitment in clinical trials. Non-invasive tape sampling is an alternative that could enable serial evaluation of specific lesions. This cross-sectional pilot research study evaluated the use of a non-invasive adhesive tape device to collect messenger RNA (mRNA) from the skin surface of participants with CLE and healthy volunteers (HVs) and investigated its feasibility to detect biologically meaningful differences between samples collected from participants with CLE and samples from HVs.

Methods

Affected and unaffected skin tape samples and simultaneous punch biopsies were collected from 10 participants with CLE. Unaffected skin tape and punch biopsies were collected from 10 HVs. Paired samples were tested using quantitative PCR for a candidate immune gene panel and semi-quantitative immunohistochemistry for hallmark CLE proteins.

Results

mRNA collected using the tape device was of sufficient quality for amplification of 94 candidate immune genes. Among these, we found an interferon (IFN)-dominant gene cluster that differentiated CLE-affected from HV (23-fold change; p<0.001) and CLE-unaffected skin (sevenfold change; p=0.002), respectively. We found a CLE-associated gene cluster that differentiated CLE-affected from HV (fourfold change; p=0.005) and CLE-unaffected skin (fourfold change; p=0.012), respectively. Spearman’s correlation between per cent area myxovirus 1 protein immunoreactivity and IFN-dominant mRNA gene cluster expression was highly significant (dermis, rho=0.86, p<0.001). In total, skin tape-derived RNA expression comprising both IFN-dominant and CLE-associated gene clusters correlated with per cent area immunoreactivity of some hallmark CLE-associated proteins in punch biopsies from the same lesions.

Conclusions

A non-invasive tape RNA collection technique is a potential tool for repeated skin biomarker measures throughout a clinical trial.

Long noncoding RNA LINC00518 induces radioresistance by regulating glycolysis through an miR-33a-3p/HIF-1α negative feedback loop in melanoma

The long noncoding RNA, LINC00518, is highly expressed in various types of cancers and is involved in cancer progression. Although LINC00518 promotes the metastasis of cutaneous malignant melanoma (CMM), the mechanism underlaying its effects on CMM radiosensitivity remains unclear. In this study, LINC00518 expression was significantly upregulated in CMM samples, and LINC00518 levels were associated with poor prognosis of patients with CMM. Knockdown of LINC00518 in CMM cells significantly inhibited cell invasion, migration, proliferation, and clonogenicity. LINC00518-mediated invasion, migration, proliferation, and clonogenicity were negatively regulated by the microRNA, miR-33a-3p, in vitro, which increased sensitivity to radiotherapy via inhibition of the hypoxia-inducible factor 1α (HIF-1α)/lactate dehydrogenase A glycolysis axis. Additionally, HIF-1α recognized the miR-33a-3p promoter region and recruited histone deacetylase 2, which decreased the expression of miR-33a-3p and formed an LINC00518/miR-33a-3p/HIF-1α negative feedback loop. Furthermore, signaling with initially activated glycolysis and radioresistance in CMM cells was impaired by Santacruzamate A, a histone deacetylase inhibitor, and 2-deoxy-D-glucose, a glycolytic inhibitor. Lastly, knockdown of LINC00518 expression sensitized CMM cancer cells to radiotherapy in an in vivo subcutaneously implanted tumor model. In conclusion, LINC00518 was confirmed to be an oncogene in CMM, which induces radioresistance by regulating glycolysis through an miR-33a-3p/HIF-1α negative feedback loop. Our study, may provide a potential strategy to improve the treatment outcome of radiotherapy in CMM.

In vivo diagnosis of skin cancer with a portable Raman spectroscopic device

In this study, we performed in vivo diagnosis of skin cancer based on implementation of a portable low-cost spectroscopy setup combining analysis of Raman and autofluorescence spectra in the near-infrared region (800-915 nm). We studied 617 cases of skin neoplasms (615 patients, 70 melanomas, 122 basal cell carcinomas, 12 squamous cell carcinomas and 413 benign tumors) in vivo with a portable setup. The studies considered the patients examined by GPs in local clinics and directed to a specialized Oncology Dispensary with suspected skin cancer. Each sample was histologically examined after excisional biopsy. The spectra were classified with a projection on latent structures and discriminant analysis. To check the classification models stability, a 10-fold cross-validation was performed. We obtained ROC AUCs of 0.75 (0.71-0.79; 95% CI), 0.69 (0.63-0.76; 95% CI) and 0.81 (0.74-0.87; 95% CI) for classification of a) malignant and benign tumors, b) melanomas and pigmented tumors and c) melanomas and seborrhoeic keratosis, respectively. The positive and negative predictive values ranged from 20% to 52% and from 73% to 99%, respectively. The biopsy ratio varied from 0.92:1 to 4.08:1 (at sensitivity levels from 90% to 99%). The accuracy of automatic analysis with the proposed system is higher than the accuracy of GPs and trainees, and is comparable or less to the accuracy of trained dermatologists. The proposed approach may be combined with other optical techniques of skin lesion analysis, such as dermoscopy- and spectroscopy-based computer-assisted diagnosis systems to increase accuracy of neoplasms classification.

LncRNA LINC00518 Acts as an Oncogene in Uveal Melanoma by Regulating an RNA-Based Network

Simple Summary

Uveal melanoma (UM) is the most frequent primary tumor of the eye in adults. Although molecular alterations on protein-coding genes have been associated with the development of UM, the role of non-coding RNAs and their competitive endogenous networks remain poorly investigated. Starting from a computational analysis on UM expression dataset deposited in The Cancer Genome Atlas, we identified the long non-coding RNA LINC00518 as a potential oncogene. We then experimentally evaluated LINC00518 and its supposed RNA signaling in human biopsies and in vitro functional assays. The results obtained suggest that LINC00518, under potential transcriptional control by MITF, regulates an RNA–RNA network promoting cancer-related processes (i.e., cell proliferation and migration). These findings open the way to the characterization of the unknown RNA signaling associated with UM and pave the way to the exploitation of a potential target for RNA-based therapeutics.

Abstract

Uveal melanoma (UM) is the most common primary intraocular malignant tumor in adults; little is known about the contribution of non-coding RNAs (ncRNAs) to UM pathogenesis. Competitive endogenous RNA (ceRNA) networks based on RNA–RNA interactions regulate physiological and pathological processes. Through a combined approach of in silico and experimental biology, we investigated the expression of a set of long non-coding RNAs (lncRNAs) in patient biopsies, identifying LINC00518 as a potential oncogene in UM. The detection of LINC00518 dysregulation associated with several in vitro functional assays allowed us to investigate its ceRNA regulatory network and shed light on its potential involvement in cancer-related processes, such as epithelial to mesenchymal transition (EMT) and CoCl₂-induced hypoxia-like response. In vitro transient silencing of LINC00518 impaired cell proliferation and migration, and affected mRNA expression of LINGO2, NFIA, OTUD7B, SEC22C, and VAMP3. A “miRNA sponge” and “miRNA protector” model have been hypothesized for LINC00518-induced regulation of mRNAs. In vitro inhibition of MITF suggested its role as a potential activator of LINC00518 expression. Comprehensively, LINC00518 may be considered a new oncogene in UM and a potential target for RNA-based therapeutic approaches.

Identification of robust reference genes for studies of gene expression in FFPE melanoma samples and melanoma cell lines

Supplemental Digital Content is available in the text.

There is an urgent need for novel diagnostic melanoma biomarkers that can predict increased risk of metastasis at an early stage. Relative quantification of gene expression is the preferred method for quantitative validation of potential biomarkers. However, this approach relies on robust tissue-specific reference genes. In the melanoma field, this has been an obstacle due to lack of validated reference genes. Accordingly, we aimed to identify robust reference genes for normalization of gene expression in melanoma. The robustness of 24 candidate reference genes was evaluated across 80 formalin-fixed paraffin-embedded melanomas of different thickness, −/+ ulceration, −/+ reported cases of metastases and of different BRAF mutation status using quantitative real-time PCR. The expression of the same genes and their robustness as normalizers was furthermore evaluated across a number of melanoma cell lines. We show that housekeeping genes like GAPDH do not qualify as stand-alone normalizers of genes expression in melanoma. Instead, we have as the first identified a panel of robust reference genes for normalization of gene expression in melanoma tumors and cultured melanoma cells. We recommend using a geometric mean of the expression of CLTA, MRPL19 and ACTB for normalization of gene expression in melanomas and a geometric mean of the expression of CASC3 and RPS2 for normalization of gene expression in melanoma cell lines. Normalization, according to our recommendation will allow for quantitative validation of potential novel melanoma biomarkers by quantitative real-time PCR.

The critical roles of lncRNAs in the pathogenesis of melanoma

Long non-coding RNAs (lncRNAs) embrace a huge fraction of human transcripts and participate in the pathogenesis of human disorders especially malignant conditions. Malignant melanoma, as the most fatal type of cutaneous malignnacies, is associated with dysregulation of several lncRNAs including PVT1, H19, MALAT1, and CCAT1. Moreover, a portion of lncRNAs are exclusively expressed in melanoma cell lines. Expression levels of several lncRNAs are associated with TNM stage, tumor size and progression of melanoma. Thus, these lncRNAs are regarded as biomarkers for this malignancy. Peripheral transcript levels of a number of lncRNAs, such as PVT1, SNHG5 and SPRY4-IT1, could distinguish melanoma patients from unaffected persons with appropriate sensitivity and specificity values. Moreover, expression levels of numerous lncRNAs in tissue biopsies could differentiate malignant samples from benign samples. Based on the results of both cell line and in vivo studies, lncRNAs regulate critical pathways in the carcinogenesis of melanoma, such as the PI3K/Akt and NF-κB signaling pathways, and are involved in the modulation of response to chemotherapeutic agents. Here we review the existing information on the role of lncRNAs in malignant melanoma.

A Review of Noninvasive Techniques for Skin Cancer Detection in Dermatology

As a result of increasing melanoma incidence and challenges with clinical and histopathologic evaluation of pigmented lesions, noninvasive techniques to assist in the assessment of skin lesions are highly sought after. This review discusses the methods, benefits, and limitations of adhesive patch biopsy, electrical impedance spectroscopy (EIS), multispectral imaging, high-frequency ultrasonography (HFUS), optical coherence tomography (OCT), and reflectance confocal microscopy (RCM) in the detection of skin cancer. Adhesive patch biopsy provides improved sensitivity and specificity for the detection of melanoma without a trade-off of higher sensitivity for lower specificity seen in other diagnostic tools to aid in skin cancer detection, including EIS and multispectral imaging. EIS and multispectral imaging provide objective information based on computer-assisted diagnosis to assist in the decision to biopsy and/or excise an atypical melanocytic lesion. HFUS may be useful for the determination of skin tumor depth and identification of surgical borders, although further studies are necessary to determine its accuracy in the detection of skin cancer. OCT and RCM provide enhanced resolution of skin tissue and have been applied for improved accuracy in skin cancer diagnosis, as well as monitoring the response of nonsurgical treatments of skin cancers and the determination of tumor margins and recurrences. These novel approaches to skin cancer assessment offer opportunities to dermatologists, but are dependent on the individual dermatologist's comfort, knowledge, and desire to invest in training and implementation of noninvasive techniques. These noninvasive modalities may have a role in the complementary assessment of skin cancers, although histopathologic diagnosis remains the gold standard for the evaluation of skin cancer.