The Genomic Landscape of Melanoma and Its Therapeutic Implications

Photocarcinogenesis of the skin: Current status and future trends

Solar radiation is essential for life on Earth but is also a major contributor to skin carcinogenesis. Solar radiation, particularly ultraviolet (UV) B (280-320 nm) and UVA (320-400 nm), induces photocarcinogenesis via various pathways. UV light can directly cause DNA damage, resulting in genetic mutations if not repaired correctly. UV light can also induce photocarcinogenesis by generating reactive oxygen species, inducing immunosuppression and inflammation. Recently, visible light (400-760 nm) has been shown to contribute to photocarcinogenesis by activating oxidative pathways. In addition to the irradiation dose (fluence, J/m2), UVB irradiance (W/m2) is also considered a factor influencing photocarcinogenesis. In this review, we summarize the mechanisms of photocarcinogenesis and provide strategies to prevent skin cancer.

Mini review on skin biopsy: traditional and modern techniques

The incidence of skin cancer continues to rise due to increased sun exposure and tanning habits, requiring early detection and treatment for favorable outcomes. Skin biopsy is an important diagnostic tool in dermatology and pathology, as it provides a valuable understanding of various skin diseases. Proper handling of skin biopsy specimens is vital to ensure accurate histopathological assessment. Still, the use of light microscopy and immunofluorescence provides a comprehensive approach to evaluating skin biopsy specimens, with each contributing unique information to aid in accurate diagnosis and management. This review highlights the evolution of skin biopsy practices, from traditional techniques to advanced methods incorporating artificial intelligence (AI) and convolutional neural networks. AI technologies enhance diagnostic accuracy and efficiency, aiding in the rapid analysis of skin lesions and biopsies. Despite challenges such as the need for extensively annotated datasets and ethical considerations, AI shows promise in dermatological diagnostics. The future of skin biopsy lies in minimally invasive techniques, liquid biopsies, and integrated pharmacogenomics for personalized medicine.

Predicting BRAF Mutations in Cutaneous Melanoma Patients Using Neural Network Analysis

Point mutations at codon 600 of the BRAF oncogene are the most common alterations in cutaneous melanoma (CM). Assessment of BRAF status allows to personalize patient management, though the affordability of molecular testing is limited in some countries. This study aimed to develop a model for predicting alteration in BRAF based on routinely available clinical and histological data. Methods: For identifying the key factors associated with point mutations in BRAF, 2041 patients with CM were recruited in the study. The presence of BRAF mutations was an endpoint. The variables included demographic data (gender and age), anatomic location, stage, histological subtype, number of mitosis, and also such features as ulceration, Clark level, Breslow thickness, infiltration by lymphocytes, invasiveness, regression, microsatellites, and association with nevi. Results: A relatively high rate of BRAF mutation was revealed in the Ukrainian cohort of patients with CM. BRAF-mutant melanoma was associated with younger age and location of nonsun-exposed skin. Besides, sex-specific differences were found between CM of various anatomic distributions and the frequency of distinct BRAF mutation subtypes. A minimal set of variables linked to BRAF mutations, defined by the genetic input selection algorithm, included patient age, primary tumor location, histological type, lymphovascular invasion, ulceration, and association with nevi. To encounter nonlinear links, neural network modeling was applied resulting in a multilayer perceptron (MLP) with one hidden layer. Its architecture included four neurons with a logistic activation function. The AUROCMLP6 of the MLP model comprised 0.79 (95% CІ: 0.74-0.84). Under the optimal threshold, the model demonstrated the following parameters: sensitivity: 89.4% (95% CІ: 84.5%-93.1%), specificity: 50.7% (95% CІ: 42.2%-59.1%), positive predictive value: 73.1% (95% CІ: 69.6%-76.3%), and negative predictive value: 76.0% (95% CІ: 67.6%-82.8%). The developed MLP model enables the prediction of the mutation in BRAF oncogene in CM, alleviating decisions on personalized management of patients with CM. In conclusion, the developed MLP model, which relies on the assessment of 6 variables, can predict the BRAF mutation status in patients with CM, supporting decisions on patient management.

Braf-Mutant Melanomas: Biology and Therapy

The incidence of melanoma, the most lethal form of skin cancer, has increased mainly due to ultraviolet exposure. The molecular characterization of melanomas has shown a high mutational burden led to the identification of some recurrent genetic alterations. BRAF gene is mutated in 40-50% of melanomas and its role in melanoma development is paramount. BRAF mutations confer constitutive activation of MAPK signalling. The large majority (about 90%) of BRAF mutations occur at amino acid 600; the majority are BRAFV600E mutations and less frequently BRAFv600K, V600D and V600M. The introduction of drugs that directly target BRAF-mutant protein (BRAF inhibitors) and of agents that stimulate immune response through targeting of immune check inhibitor consistently improved the survival of melanoma BRAFV600-mutant patients with unresectable/metastatic disease. In parallel, studies in melanoma stage II-III patients with resectable disease have shown that adjuvant therapy with ICIs and/or targeted therapy improves PFS and RFS, but not OS compared to placebo; however, neoadjuvant therapy plus adjuvant therapy improved therapeutic response compared to adjuvant therapy alone.

An Extremely Rare Case of Primary Malignant Melanoma of the Kidney

Malignant melanoma (MM) is a tumor that usually occurs in the skin, but this malignant tumor can also develop in extracutaneous tissues, including urogenital tissues. In regard to MM occurring in urogenital tissues, bladder origin is common but renal primary MM is extremely rare. In the Department of Emergency and Urology at Gifu Municipal Hospital, a tumor of the right kidney was detected in a computed tomography scan to determine the cause of severe pain in the lower extremities of a 45-year-old Japanese woman. With the clinical diagnosis of renal cell carcinoma, resection of the right kidney was performed under laparoscopy. The cut surface of the tumor encapsulated by a thick fibrous capsule was dark brown, and the tumor cells with large nuclei, large nucleoli, acidophil cytoplasm, and numerous melanin granules showed papillary, solid, or alveolar growth. Immunohistochemically, the tumor cells were positive for Melan A and human melanoma black 45 (HMG45) but negative for transcription factor E3 (TFE3), transcription factor EB (TFEB), cytokeratin 7 (CK7), carbonic anhydrase 9 (CA9), and AEl/AE3. We conducted careful and detailed examinations, including an association of the patient's medical history, but there were no indications for tumors, particularly MM, in any organs. Therefore, she was ultimately diagnosed with primary kidney MM.

Advances in Personalized Oncology

Advances in next-generation sequencing (NGS) have catalyzed a paradigm shift in cancer treatment, steering the focus from conventional, organ-specific protocols to precision medicine. Emerging targeted therapies offer a cutting-edge approach to cancer treatment, while companion diagnostics play an essential role in aligning therapeutic choices with specific molecular changes identified through NGS. Despite these advances, interpreting the clinical implications of a rapidly expanding catalog of genetic mutations remains a challenge. The selection of therapies in the presence of multiple mutations requires careful clinical judgment, supported by quality-centric genomic testing that emphasizes actionable mutations. Molecular tumor boards can play an increasing role in assimilating genomic data into clinical trials, thereby refining personalized treatment approaches and improving patient outcomes.

Resolving Discrepancies in Idylla BRAF Mutational Assay Results Using Targeted Next-Generation Sequencing

BRAF mutation identification is important for the diagnosis and treatment of several tumor types, both solid and hematologic. Rapid identification of BRAF mutations is required to determine eligibility for targeted BRAF inhibitor therapy. The Idylla BRAF mutation assay is a rapid, multiplex allele-specific PCR test designed to detect the most common oncogenic BRAF V600 mutations in formalin-fixed paraffin-embedded (FFPE) tissue samples. Here, we describe the validation of the Idylla BRAF mutation assay in our laboratory. During routine clinical practice, we noticed cases in which BRAF V600 mutations were identified with unusual amplification curves, with three cases displaying a delayed amplification within a double amplification pattern and two false-positive calls. We therefore initiated a quality improvement effort to systematically and retrospectively evaluate next-generation sequencing (NGS)-tested cases with BRAF mutations identified within five amino acids of BRAF codon V600 and did not identify additional false-positive cases. We hypothesize that late amplification in a double amplification pattern may represent non-specific amplification, whereas cases displaying single delayed amplification curves may stem from the presence of either non-V600 variants, very low-level V600 variants, cytosine deamination artifacts, and/or non-specific amplification by an allele-specific PCR primer. Regardless, we recommend that Idylla BRAF cases with non-classical amplification curves undergo reflex NGS testing. These findings are likely relevant for other Idylla assays interrogating hotspot mutations in genes such as EGFR, IDH1/2, KRAS, and NRAS.

Molecular Frontiers in Melanoma: Pathogenesis, Diagnosis, and Therapeutic Advances

Melanoma, a highly aggressive skin cancer, is characterized by rapid progression and high mortality. Recent advances in molecular pathogenesis have shed light on genetic and epigenetic changes that drive melanoma development. This review provides an overview of these developments, focusing on molecular mechanisms in melanoma genesis. It highlights how mutations, particularly in the BRAF, NRAS, c-KIT, and GNAQ/GNA11 genes, affect critical signaling pathways. The evolution of diagnostic techniques, such as genomics, transcriptomics, liquid biopsies, and molecular biomarkers for early detection and prognosis, is also discussed. The therapeutic landscape has transformed with targeted therapies and immunotherapies, improving patient outcomes. This paper examines the efficacy, challenges, and prospects of these treatments, including recent clinical trials and emerging strategies. The potential of novel treatment strategies, including neoantigen vaccines, adoptive cell transfer, microbiome interactions, and nanoparticle-based combination therapy, is explored. These advances emphasize the challenges of therapy resistance and the importance of personalized medicine. This review underlines the necessity for evidence-based therapy selection in managing the increasing global incidence of melanoma.

Recent advancements in the diagnosis and treatment of acral melanoma

Acral melanoma (AM) is the most common histologic subtype of melanoma in dark-skinned patients and is associated with a worse prognosis and a high mortality rate, largely due to the inconspicuous nature of early-stage lesions, which can lead to late diagnosis. Because of the overlapping clinical and histopathological features of AM with other forms of cutaneous melanomas, early detection of AM requires a multidisciplinary approach that integrates various diagnostic modalities, including clinical examination, dermoscopy, histopathology, molecular testing, radiological imaging, and blood tests. While surgery is the preferred method of treatment for AM, other therapeutic options may be employed based on the stage and underlying etiology of the disease. Immune checkpoint inhibitors, molecular targeted therapy, radiotherapy, chemotherapy, and oncolytic virotherapy represent promising advanced treatment options for AM. In this review, we provide an overview of the latest advancements in diagnostic and therapeutic methods for AM, highlighting the importance of early detection and the prompt, individualized management of this challenging disease.

Refining mutanome-based individualised immunotherapy of melanoma using artificial intelligence

Using the particular nature of melanoma mutanomes to develop medicines that activate the immune system against specific mutations is a game changer in immunotherapy individualisation. It offers a viable solution to the recent rise in resistance to accessible immunotherapy alternatives, with some patients demonstrating innate resistance to these drugs despite past sensitisation to these agents. However, various obstacles stand in the way of this method, most notably the practicality of sequencing each patient's mutanome, selecting immunotherapy targets, and manufacturing specific medications on a large scale. With the robustness and advancement in research techniques, artificial intelligence (AI) is a potential tool that can help refine the mutanome-based immunotherapy for melanoma. Mutanome-based techniques are being employed in the development of immune-stimulating vaccines, improving current options such as adoptive cell treatment, and simplifying immunotherapy responses. Although the use of AI in these approaches is limited by data paucity, cost implications, flaws in AI inference capabilities, and the incapacity of AI to apply data to a broad population, its potential for improving immunotherapy is limitless. Thus, in-depth research on how AI might help the individualisation of immunotherapy utilising knowledge of mutanomes is critical, and this should be at the forefront of melanoma management.

Validity of Xiphophorus fish as models for human disease

Platyfish and swordtails of the genus Xiphophorus provide a well-established model for melanoma research and have become well known for this feature. Recently, modelling approaches for other human diseases in Xiphophorus have been developed or are emerging. This Review provides a comprehensive summary of these models and discusses how findings from basic biological and molecular studies and their translation to medical research demonstrate that Xiphophorus models have face, construct and predictive validity for studying a broad array of human diseases. These models can thus improve our understanding of disease mechanisms to benefit patients.

Clinical research progress on BRAF V600E-mutant advanced colorectal cancer

Colorectal cancer is one of the malignant tumors that pose a serious threat to human health. A particularly bad prognosis might be expected for colorectal tumors with the unique molecular subtype BRAF V600E mutation. With the development of precision therapy, the advent of molecularly targeted therapies and immune checkpoint inhibitors has improved the outcome of intermediate to advanced colorectal cancer. However, the duration of drug benefit is usually short, and overall survival and progression-free survival remain suboptimal. Therefore, investigators are exploring more rational, safe, and effective drug combination regimens through clinical trials to provide longer survival for patients with such genetic mutations with metastatic colorectal cancer (mCRC). This article reviews the progress of clinical research on molecularly targeted drugs, immune checkpoint inhibitors, first-line chemotherapeutic agents, and different combination therapy regimens (including different targeted drug combinations, immune combination targeting, and chemotherapy combination targeting) for colorectal cancer patients with BRAF V600E mutation, which provides a reference for further in-depth clinical exploration of the treatment of colorectal cancer patients with BRAF V600E mutation.

An update on methods for detection of prognostic and predictive biomarkers in melanoma

The approval of immunotherapy for stage II-IV melanoma has underscored the need for improved immune-based predictive and prognostic biomarkers. For resectable stage II-III patients, adjuvant immunotherapy has proven clinical benefit, yet many patients experience significant adverse events and may not require therapy. In the metastatic setting, single agent immunotherapy cures many patients but, in some cases, more intensive combination therapies against specific molecular targets are required. Therefore, the establishment of additional biomarkers to determine a patient's disease outcome (i.e., prognostic) or response to treatment (i.e., predictive) is of utmost importance. Multiple methods ranging from gene expression profiling of bulk tissue, to spatial transcriptomics of single cells and artificial intelligence-based image analysis have been utilized to better characterize the immune microenvironment in melanoma to provide novel predictive and prognostic biomarkers. In this review, we will highlight the different techniques currently under investigation for the detection of prognostic and predictive immune biomarkers in melanoma.

Cerebrospinal fluid circulating tumour DNA genotyping and survival analysis in lung adenocarcinoma with leptomeningeal metastases

PURPOSE

The prognosis of patients with leptomeningeal metastasis (LM) remains poor. Circulating tumour DNA (ctDNA) has been proven to be abundantly present in cerebrospinal fluid (CSF); hence, its clinical implication as a biomarker needs to be further verified.

METHODS

We conducted a retrospective study of 35 lung adenocarcinoma (LUAD) patients with LM, and matched CSF and plasma samples were collected from all patients. All paired samples underwent next-generation sequencing (NGS) of 139 lung cancer-associated genes. The clinical characteristics and genetic profiling of LM were analysed in association with survival prognosis.

RESULTS

LM showed genetic heterogeneity, in which CSF had a higher detection rate of ctDNA (P = 0.003), a higher median mutation count (P < 0.0001), a higher frequency of driver mutations (P < 0.01), and more copy number variation (CNV) alterations (P < 0.001) than plasma. The mutation frequencies of the EGFR, TP53, CDKN2A, MYC and CDKN2B genes were easier to detect in CSF than in LUAD tissue (P < 0.05), possibly reflecting the underlying mechanism of LM metastasis. CSF ctDNA is helpful for analysing the mechanism of EGFR-TKI resistance. In cohort 1, which comprised patients who received 1/2 EGFR-TKIs before the diagnosis of LM, TP53 and CDKN2A were the most common EGFR-independent resistant mutations. In cohort 2, comprising those who progressed after osimertinib and developed LM, 7 patients (43.75%) had EGFR CNV detected in CSF but not plasma. Furthermore, patient characteristics and various genes were included for interactive survival analysis. Patients with EGFR-mutated LUAD (P = 0.042) had a higher median OS, and CSF ctDNA mutation with TERT (P = 0.013) indicated a lower median OS. Last, we reported an LM case in which CSF ctDNA dynamic changes were well correlated with clinical treatment.

CONCLUSIONS

CSF ctDNA could provide a more comprehensive genetic landscape of LM, indicating the potential metastasis-related and EGFR-TKI resistance mechanisms of LM patients. In addition, genotyping of CSF combined with clinical outcomes can predict the prognosis of LUAD patients with LM.

Incidence of BRAF mutations in cutaneous melanoma: histopathological and molecular analysis of a Ukrainian population

Aim

This study aimed to investigate the incidence of BRAF mutation in cutaneous melanoma in the Ukrainian population with respect to clinical and histopathological data.

Materials & methods

This single-center retrospective cohort study enrolled 299 primary CM with known BRAF status assessed by RT-PCR.

Results

The overall BRAF mutation rate was 56.5% in CM and demonstrated a link with the younger age (p < 0.001), anatomical site (p < 0.001) and histological type of CM (p = 0.022). BRAF-positive CM possessed a slightly higher mitotic rate (p = 0.015) and Breslow thickness (p = 0.028) but did not relate to tumor-infiltrating lymphocytes.

Conclusion

The high rate of BRAF mutations in CM patients in the Ukrainian cohort was associated with superficial spreading histology, higher depth of invasion and proliferation.