The microenvironment of ulcerated acral melanoma is characterised by an inflammatory milieu and an enhanced humoral immune response

Abstract Acral melanoma (AM) is a distinct and understudied subtype of melanoma that is reported to represent the majority of melanoma diagnoses in various Latin American, African and Asian countries. Patients with ulcerated AM diagnoses face a worse prognosis and increased risk of recurrence. While tumour ulceration has been shown to influence therapy response in cutaneous melanoma patients, the clinical and molecular traits of AM tumours remain poorly understood. In this study, we performed transcriptomic profiling of 59 AM samples and proteomic analysis of 45 AM samples from patients with extensively annotated clinical information. Our analysis revealed immunological differences in ulcerated tumours, including a significant upregulation of processes related to humoral immunity and markers for macrophages/monocytes, alongside a downregulation of keratins, epidermis-associated processes and cell adhesion. Notably, ulcerated tumours exhibited disruption of tight junctions and desmosomes, potentially explaining their compromised tissue integrity. We identified a significant increase of plasma cells, M0 macrophages and eosinophils within the ulcerated tumour microenvironment, suggesting that inflammation and infection might accompany these lesions. Moreover, fibronectin, CD8, PD-1, CD14 and CD68 protein levels were useful in distinguishing between ulcerated and non-ulcerated samples using a random forest classifier. These findings indicate that persistent inflammation and dysregulated immune responses characterise ulcerated AM, potentially offering new avenues for targeted therapeutic interventions in this aggressive melanoma subtype. Competing Interest Statement JSR reports in the last 3 years funding from GSK and Pfizer & fees/honoraria from Travere Therapeutics, Stadapharm, Astex, Owkin, Pfizer, Grunenthal, Tempus and Moderna. All other authors report no conflict of interest. Funding Statement Work included in this paper has been funded by Wellcome Trust (204562/Z/16/Z and 227228/Z/23/Z to C.D.R.-E.), the Melanoma Research Alliance (Pilot Award #825924, to C.D.R.-E.), the Mexican National Council of Humanities, Science and Technology (CONAHCYT, FOSISS A3-S-31603, to C.D.R.-E.), Programa de Apoyo a Proyectos de Investigacion e Innovacion Tecnologica (PAPIIT UNAM) (IN209422 to C.D.R.-E.), and the Wellcome Sanger Institute through an International Fellowship. This project was also supported by the MRC Dermatlas project; MR/V000292/1. M.E.V.-C. is a doctoral student from the Programa de Doctorado en Ciencias Biomedicas, Universidad Autonoma de Mexico (UNAM) and has received a CONAHCYT fellowship with number 521002192. The funders had no role in the study design, data analysis, or preparation of the manuscript. Author Declarations I confirm all relevant ethical guidelines have been followed, and any necessary IRB and/or ethics committee approvals have been obtained. Yes The details of the IRB/oversight body that provided approval or exemption for the research described are given below: The protocol for sample collection was approved by the Mexican National Cancer Institute's (Instituto Nacional de Cancerologia, INCan, Mexico) Ethics and Research committees (017/041/PBI;CEI/1209/17) and the United Kingdom's National Health Service (NHS, UK) (18/EE/00076). All patients signed informed consent. I confirm that all necessary patient/participant consent has been obtained and the appropriate institutional forms have been archived, and that any patient/participant/sample identifiers included were not known to anyone (e.g., hospital staff, patients or participants themselves) outside the research group so cannot be used to identify individuals. Yes I understand that all clinical trials and any other prospective interventional studies must be registered with an ICMJE-approved registry, such as ClinicalTrials.gov. I confirm that any such study reported in the manuscript has been registered and the trial registration ID is provided (note: if posting a prospective study registered retrospectively, please provide a statement in the trial ID field explaining why the study was not registered in advance). Yes I have followed all appropriate research reporting guidelines, such as any relevant EQUATOR Network research reporting checklist(s) and other pertinent material, if applicable. Yes Data Availability Sequencing data are available at the European Genome-Phenome Archive (EGA) under ENA accession number EGAS00001003758. Protein data and code is available at https://github.com/CGBio-Lab/Ulceration_Acral_Melanoma.