LCK and HOMER1 gene expression-based classifier distinguishes early mycosis fungoides from eczema and psoriasis

Abstract Mycosis fungoides (MF) is a rare cutaneous T cell lymphoma that, in its early stages, can closely mimic eczema and psoriasis in both clinical appearance and histopathologic features, leading to frequent misdiagnosis, inappropriate treatment, and delayed care. Reliable adjunctive biomarkers are lacking, underscoring the need for improved diagnostic strategies. We developed a biomarker discovery framework based on bulk RNA sequencing of skin biopsies (19 MF, 112 psoriasis, 105 eczema), which identified seven candidate diagnostic genes. RT-PCR analysis in FFPE tissue specimens from 65 MF and 101 eczema/psoriasis samples verified LCK and HOMER1 as robust discriminator genes. A logistic regression model based on LCK and HOMER1 gene expression differentiated MF from psoriasis and eczema with 91% sensitivity and 94% specificity. Independent validation on 7 additional international cohorts (MF n=58, eczema/psoriasis n=55) confirmed robust performance. Spatial and single-cell transcriptomic analyses revealed biological underpinnings of classifier accuracy: LCK was enriched in malignant and specific T cell subsets in MF, whereas HOMER1 was confined to keratinocytes in eczema and psoriasis but nearly absent in MF. Case studies demonstrated that the classifier identified MF in routine biopsies earlier than histopathology. This molecular diagnostic approach enables earlier and more reliable distinction of MF from common inflammatory dermatoses, offering a clinically applicable tool to reduce diagnostic uncertainty, accelerate appropriate treatment, and might improve patient outcomes. One Sentence Summary A two-gene classifier reliably distinguishes mycosis fungoides from eczema and psoriasis, enabling early and accurate diagnosis. Competing Interest Statement NGS, SE and KE are founders and shareholders of Dermagnostix GmbH and Dermagnostix R#x0026;D GmbH Funding Statement European Research council (ERC) (IMCIS, 676858); Swiss National Science Foundation (SNF 320030-232320 to EG), Helmholtz Association (W2_W3-077; VH-NG-923) 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 study was approved by the local ethical committees (University of Freiburg, 25-1087-S1-AV; Technical University Munich, 166/21; University Hospital Pilsen, 123/25; University of Lausanne, CER-VD 2021-00878; University of Goettingen, 6/5/25 Ue). 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 All data produced in the present study are available upon reasonable request to the authors. The code can be found here: https://github.com/MendenLab/SAFARI