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.

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.

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).

Dermatologic Disease-Directed Targeted Therapy (D3T2): The Application of Biomarker-Based Precision Medicine for the Personalized Treatment of Skin Conditions-Precision Dermatology

Precision dermatology uses individualized dermatologic disease-directed targeted therapy (D³T²) for the management of dermatoses and for the evaluation and therapy of cutaneous malignancies. Personalized/precision strategies are based on biomarkers that are most frequently derived from tissue transcriptomic expression or genomic sequencing or from circulating cytokines. For instance, the pathologic diagnosis of a pigmented lesion and determining the prognosis of a malignant melanocytic neoplasm can be enhanced by genomic/transcriptomic analysis. In addition to biopsy, innovative techniques have been developed for obtaining transcriptomes in skin conditions; as an example, patches can be applied to a psoriasis plaque for a few minutes to capture the epidermis/upper dermis transcriptome. Atopic dermatitis and prurigo nodularis may also be candidate conditions for precision dermatology. Precision dermatology has a role in managing melanoma and nonmelanoma skin cancers and rare cutaneous tumors-such as perivascular epithelioid cell tumor (PEComa)-that can originate in or metastasize to the skin. For instance, advanced/metastatic basal cell carcinomas can be treated with Hedgehog inhibitors (vismodegib and sonidegib) targeting the smoothened (SMO) or patched 1 (PTCH1) gene alterations that are a hallmark of these cancers and activate the Hedgehog pathway. Advanced/metastatic basal and cutaneous squamous cell cancers often have a high tumor mutational burden (which predicts immunotherapy response); immune checkpoint blockade with cemiplimab, a programmed cell death protein 1 (PD1) inhibitor, is now approved for these malignancies. Gene expression profiling of primary cutaneous squamous cell carcinoma can identify those individuals at high risk for subsequent metastases. In the realm of rare neoplasms, PEComas-which can originate in the skin, albeit uncommonly-have tuberous sclerosis complex 1 (TSC1)/tuberous sclerosis complex 2 (TSC2) gene alterations, which activate mammalian target of rapamycin (mTOR) signaling, and can be suppressed by nab-sirolimus, now approved for this condition. In summary, precision dermatologic techniques/strategies are an important emerging approach for evaluation and management of skin disorders and cutaneous neoplasms, and may serve as a paradigm for the application of precision medicine beyond dermatology.

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.

Melanoma: How and When to Consider Clinical Diagnostic Technologies

In response to rising rates of melanoma worldwide, novel non-invasive melanoma detection techniques are emerging to facilitate the early detection of melanoma and decrease unnecessary biopsies of benign pigmented lesions. Because they often report similar study findings, it may be difficult to determine how best to incorporate these technologies into clinical practice based on their supporting studies alone. As an expansion of the recent article by Fried et al.¹, which reviewed the clinical data supporting these non-invasive melanoma detection techniques, the first article in this continuing medical education series provides practical advice on how and when to use various non-invasive melanoma detection techniques into clinical practice.

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.

Tape strips in dermatology research

Tape strips have been used widely in dermatology research as a minimally invasive method to sample the epidermis, avoiding the need for skin biopsies. Most research has focused on epidermal pathology, such as atopic eczema, but there is increasing research into the use of tape strips in other dermatoses, such as skin cancer, and the microbiome. This review summarizes the technique of tape stripping, and discusses which dermatoses have been studied by tape stripping and alternative minimally invasive sampling methods. We review the number of tape strips needed from each patient and the components of the epidermis that can be obtained by tape stripping. With a focus on protein and RNA extraction, we address the techniques used to process tape strips. There is no optimal protocol to extract protein, as this depends on the abundance of the protein studied, its level of expression in the epidermis and its solubility. Many variables can alter the amount of protein obtained from tape strips, which must be standardized to ensure consistency between samples. No study has compared different RNA extraction techniques, but our own experience is that RNA yield is optimized by using 20 tape strips and the use of a cell scraper.

Technological advances for the detection of melanoma: Advances in molecular techniques

The growth of molecular technologies analyzing skin cells and inherited genetic variations has the potential to address current gaps in both diagnostic accuracy and prognostication in patients with melanoma or in individuals who are at risk for developing melanoma. In the second article in this continuing medical education series, novel molecular technologies are reviewed. These have been developed as adjunct tools for melanoma management and include the Pigmented Lesion Assay, myPath Melanoma, and DecisionDx-Melanoma tests, and genetic testing in patients with a strong familial melanoma history. These tests are commercially available and marketed as ancillary tools for clinical decision-making, diagnosis, and prognosis. We review fundamental principles behind each test, discuss peer-reviewed literature assessing their performance, and highlight the utility and limitations of each assay. The goal of this article is to provide a comprehensive, evidence-based foundation for clinicians regarding the management of patients with difficult pigmented lesions.