AUTHOR=Srinivas Nalini , Peiffer Lukas , Horny Kai , Lei Kuan Cheok , Buus Terkild B. , Kubat Linda , Luo Meng , Yin Menghong , Spassova Ivelina , Sucker Antje , Farahpour Farnoush , Kehrmann Jan , Ugurel Selma , Livingstone Elisabeth , Gambichler Thilo , Ødum Niels , Becker Jürgen C. 

TITLE=Single-cell RNA and T-cell receptor sequencing unveil mycosis fungoides heterogeneity and a possible gene signature

JOURNAL=Frontiers in Oncology

VOLUME=14

YEAR=2024

URL=https://www.frontiersin.org/journals/oncology/articles/10.3389/fonc.2024.1408614

DOI=10.3389/fonc.2024.1408614

ISSN=2234-943X

ABSTRACT=<sec><title>Background</title><p>Mycosis fungoides (MF) is the most common subtype of cutaneous T-cell lymphoma (CTCL). Comprehensive analysis of MF cells <italic>in situ</italic> and <italic>ex vivo</italic> is complicated by the fact that is challenging to distinguish malignant from reactive T cells with certainty.</p></sec><sec><title>Methods</title><p>To overcome this limitation, we performed combined single-cell RNA (scRNAseq) and T-cell receptor TCR sequencing (scTCRseq) of skin lesions of cutaneous MF lesions from 12 patients. A sufficient quantity of living T cells was obtained from 9 patients, but 2 had to be excluded due to unclear diagnoses (coexisting CLL or revision to a fixed toxic drug eruption).</p></sec><sec><title>Results</title><p>From the remaining patients we established single-cell mRNA expression profiles and the corresponding TCR repertoire of 18,630 T cells. TCR clonality unequivocally identified 13,592 malignant T cells. Reactive T cells of all patients clustered together, while malignant cells of each patient formed a unique cluster expressing genes typical of naive/memory, such as <italic>CD27, CCR7</italic> and <italic>IL7R</italic>, or cytotoxic T cells, e.g., <italic>GZMA, NKG7</italic> and <italic>GNLY</italic>. Genes encoding classic CTCL markers were not detected in all clusters, consistent with the fact that mRNA expression does not correlate linearly with protein expression. Nevertheless, we successfully pinpointed distinctive gene signatures differentiating reactive malignant from malignant T cells: keratins (<italic>KRT81</italic>, <italic>KRT86</italic>), galectins (<italic>LGALS1</italic>, <italic>LGALS3</italic>) and S100 genes (<italic>S100A4</italic>, <italic>S100A6</italic>) being overexpressed in malignant cells.</p></sec><sec><title>Conclusions</title><p>Combined scRNAseq and scTCRseq not only allows unambiguous identification of MF cells, but also revealed marked heterogeneity between and within patients with unexpected functional phenotypes. While the correlation between mRNA and protein abundance was limited with respect to established MF markers, we were able to identify a single-cell gene expression signature that distinguishes malignant from reactive T cells.</p></sec>