Single-Cell Insights into Cellular Heterogeneity and Immune Dynamics in Cutaneous T-Cell Lymphoma
Authors: Childs Beth , Elghonaimy Eslam , Ramakrishnan Geethakumari Praveen , Aguilera Todd , Goff Heather W 
Published: December 2024

Single-cell RNA sequencing (scRNAseq) has revolutionized our understanding of cellular diversity, yet its full application in cutaneous T-cell lymphoma (CTCL) remains underexplored. Here, we utilize scRNAseq to characterize the intricate landscape of cell diversity and function in CTCL. Integrating 16,928 cells from UT Southwestern Dermatology patients with 83,610 cells from public datasets yielded a comprehensive analysis across 100,531 cells from blood samples of CTCL patients. Rigorous quality controls ensured robust data analysis, revealing nuanced immune profiles and dynamic behaviors of malignant T cells within the tumor microenvironment.
Our analysis identified thirteen distinct clusters of malignant T cells, each characterized by unique transcriptomic profiles. Differential expression analysis uncovered upregulated genes in malignant T cells, including AIRE, CXCL13, ANK1, TUSC3, PDLIM1, and EPHB6 (all p &lt; 0.001), collectively contributing to the ongoing quest for a comprehensive genetic signature of CTCL. All clusters positively expressed markers indicative of central/effector memory T cells (SELL, CCR7, TCF7).
Subsequently, these clusters were stratified into two groups of malignant cells, MTC1 and MTC2, based on distinct gene expression patterns and functional profiles. MTC1 exhibited upregulation of genes associated with metabolism (PFKL, GLUL), growth and proliferation (TUSC3, PDLIM1), and chemotaxis (CXCL13, EPHB6, AIRE). MTC2 exhibited a more activated phenotype, with upregulation of genes related to cytotoxicity and inflammation (NKG7, LAIR2, CCL5), immunomodulation (IFI44L, LAPTM5, KIR3DL1, KIR3DL2), and metabolic adaptation to stress (HACD1, IDI1).
Employing consensus estimates, we investigated interactions between these groups of malignant cells and tumor infiltrating lymphocytes (TILs). Both MTC1 and MTC2 had upregulated major histocompatibility complex class 1 (MHC1) interaction with Leukocyte Immunoglobulin-Like Receptors (LILRs) LILRB1 and LILRB2 on macrophages, monocytes, and neutrophils. Activation of these receptors transduce inhibitory signals that prevent phagocytosis, potentially fostering immune evasion. Additionally, both groups had upregulated interactions at Integrin Beta-2 (ITGB2) with S100A8 and S100A9 (S100A8/A9) ligands on monocytes and neutrophils. Prior literature suggests that the downstream effects of these two molecules could contribute to cancer metastasis and infiltration.
Notably, MTC2 demonstrated heightened interactions with TILs through killer cell immunoglobulin-like receptor KIR3DL2. Ligands on B cells, macrophages, monocytes, NK cells, and neutrophils comprise the major histocompatibility complex 1 (HLA-A, HLA-B, and B2M). KIR3DL2 is thought to inhibit immune response fostering immune evasion, contributing to diseases such as ankylosing spondylitis and atopic dermatitis (a clinical mimicker of CTCL) and protecting against T cell depletion in HIV. These interactions underscore potential targets for therapeutic intervention in CTCL.
In conclusion, this study unveils specific genetic and interactional landscapes of CTCL at the single-cell level, providing critical insights for diagnostic strategies and targeted therapies aimed at halting disease progression. Future directions will integrate immunohistochemical data to validate the alignment between protein expression and genetic findings.