Studying the role of skin pathobionts in cutaneous t cell lymphoma

The National Institute of Allergy and Infectious Diseases awarded New York University $218,728 on December 22, 2025, under the Allergy and Infectious Diseases Research program (CFDA 93.855) to study the role of skin pathobionts in cutaneous T cell lymphoma.

The research investigates whether Staphylococcus aureus colonization contributes to cutaneous T cell lymphoma (CTCL) progression. The study addresses three primary questions: whether S. aureus is enriched in CTCL patient skin microbiomes and what strains and virulence factors are present; whether S. aureus contributes to CTCL progression in vivo; and whether in vivo CTCL progression is mediated by an antigen-specific skin response. The project will collect and analyze skin samples from over 200 CTCL patients, including 102 previously collected samples from collaborating clinicians and an additional 100 samples to be gathered through IRB-approved human studies spanning multiple institutions. Microbial analysis will employ 16S sequencing and single-cell surface expression profiling to characterize S. aureus proportions, genetic characteristics, and the relationship between skin microbiome composition and malignant T cell activation.

Performance occurs at New York University in New York, New York, with a period of performance from December 22, 2025, through August 31, 2028.

Abstract

Cutaneous t cell lymphoma (ctcl) involves dermal expansion and accumulation of malignant CD4+ t cells. While putative triggers ranging from chemical exposures to microbial elements have been suggested, the etiology of ctcl is unknown. However, studies have observed increased skin colonization with s. Aureus in ctcl patients compared to healthy controls, and a small trial documented disease regression in response to aggressive antibiotic treatment that eradicated s. Aureus colonization. These findings suggest that s. Aureus colonization may play a role in the progression of ctcl, although no unifying mechanism for this relationship has been uncovered to date. There are major gaps in our knowledge, which will be addressed by the experiments in this proposal: 1) is s. Aureus indeed enriched in ctcl patient skin microbiomes, and what strain(s) and virulence factor(s) are found in patient samples? And how does the presence of s. Aureus impact malignant cell features in ctcl patient samples? 2) is s. Aureus contributing to ctcl progression in vivo? 3) and is in vivo ctcl progression mediated by an antigen-specific response in the skin? Prior studies have been limited by low patient numbers, as ctcl is a rare disease, and a lack of comprehensive integration of 16S sequencing, microbial molecular genetics, and malignant cell characteristics. This study will overcome these limitations through sample collection of over 200 ctcl patients for analysis, including 102 previously collected samples from collaborating clinicians, and an additional 100 ctcl samples to be collected through our active, IRB-approved human studies spanning multiple institutions. Microbial analysis will reveal the proportions of, and genetic characteristics of, s. Aureus in the ctcl microbiome, and the relationship between the skin microbiome and human malignant t cell activation, as determined by single- cell surface expression and transcriptomics (aim 1). In vivo mouse models of ctcl subjected to s. Aureus colonization will allow study of skin-resident immune responses to s. Aureus, and its mechanistic relationship to disease progression (aim 2). And finally, sophisticated in vivo models of ctcl will be used to determine if topical antigenic stimulation is sufficient and necessary to drive disease progression in the skin (aim 3).