Single-Cell profiling reveals targetable malignant T-cell subtypes and immune evasion pathways in Sezary Syndrome

BackgroundSezary syndrome (SS) is a rare and aggressive leukemic variant of cutaneous T-cell lymphoma (CTCL) with limited therapeutic options and a median survival of fewer than five years. Despite advances in how single-cell RNA sequencing (scRNA-seq) has improved the understanding and treatment of other cancer types, such insights in SS remain limited. The drivers of disease progression and immunologic dysfunction are incompletely defined, underscoring the need to characterize both malignant T cells (MTCs) and their interactions with surrounding immune populations. ObjectivesTo systematically characterize malignant and non-malignant immune cells in CTCL, identify distinct malignant T-cell subtypes, and uncover transcriptional programs and immune evasion pathways with therapeutic relevance. MethodsWe analyzed scRNA-seq data on peripheral blood mononuclear cells (PBMCs) from 22 SS patients and 7 healthy controls. MTC subtypes were identified using a combination of transcriptional profiling, copy number variation (CNV) analysis, and T-cell receptor (TCR) clonotyping. CITE-seq was utilized on a subset of samples to correlate genetic findings with surface protein expression. ResultsWe identified three MTC subtypes: (1) MTC central memory (CM), a Th2-skewed CM phenotype that constituted the dominant malignant population; (2) MTC effector/effector-memory (E/EM), a subset enriched in Th1-associated genes; and (3) MTC regulatory (Reg), a regulatory-like, exhausted phenotype, along with shared and subtype-specific gene signatures. The predominance of MTC CM suggests a stable malignant state, while relative rarity of MTC E/EM and MTC Reg may reflect treatment effects or disease progression. In addition to KIR3DL2, we identified KIR2DL3 and KIR3DL1 as upregulated immune-evasive receptors on MTCs and surrounding cells. Tensor factorization of ligand-receptor interactions revealed pro-inflammatory yet immunosuppressive signaling in myeloid cells converging on STAT3 activation. ConclusionsThis study defines three transcriptionally and functionally distinct MTC subtypes in SS, highlighting subtype-specific vulnerabilities that may inform personalized treatment strategies. Our findings suggest that targeting not only MTCs but also KIR-family receptor signaling and JAK-STAT activation in the immune microenvironment may have therapeutic implications. The identification of novel immunosuppressive pathways and cell survival mechanisms opens avenues for tailored interventions - including widespread KIR inhibition, repurposing JAK inhibitors, and other novel therapies - to improve patient outcomes in SS. Contributor StatementB.A. Childs conducted the conceptualization (equal), data curation (equal), formal analysis (lead), investigation (lead), methodology (equal), validation (equal), visualization (equal), writing - original draft (lead), writing - review & editing (supporting). E. Elghonaimy provided conceptualization (equal), data curation (equal), formal analysis (equal), investigation (equal), methodology (equal), resources (equal), supervision (equal), validation (equal), visualization (equal), writing - original draft (supporting), and writing - review & editing (supporting). P. R. Geethakumari provided data curation (supporting), investigation (supporting), resources (supporting), writing - review & editing (supporting). K. Kumar contributed conceptualization (supporting), data curation (supporting), resources (supporting), and writing - review & editing (supporting). J. F. Merola provided conceptualization (supporting), investigation (supporting), resources (supporting), writing - review & editing (supporting). H.W. Goff contributed conceptualization (equal), data curation (equal), formal analysis (supporting), funding acquisition (lead), investigation (supporting), methodology (supporting), resources (supporting), supervision (equal), visualization (equal), writing - review & editing (equal). T. A. Aguilera provided conceptualization of the project (equal), data curation (equal), formal analysis (equal), funding acquisition (equal), investigation (equal), methodology (equal), project administration (equal), resources (lead), supervision (lead), visualization (supporting), writing - original draft (supporting), writing - review & editing (equal). T.A. Aguilera is the guarantor and accepts full responsibility for the overall content, had access to all the data, and controlled the decision to publish. Bulleted StatementsO_ST_ABSWhat is already known about this topic?C_ST_ABSO_LISezary syndrome is a rare, aggressive CTCL subtype associated with poor survival; a minority of patients achieve long-term remission with allogeneic stem cell transplant. C_LIO_LIKIR3DL2 is an investigational target with ongoing trials (e.g., lacutamab, anti-KIR3DL2 agent). C_LIO_LIJAK inhibitors have shown mixed effects, with anecdotal benefit and potential harm. C_LIO_LIThe heterogeneous biology of Sezary cells remains poorly characterized, limiting diagnostic and therapeutic advancement. C_LI What does this study add?O_LIWe define three distinct malignant T-cell subtypes in Sezary syndrome, each with clinical and therapeutic implications, and a unifying genetic signature. C_LIO_LIIn addition to KIR3DL2, a known CTCL marker, we identify KIR2DL3 and KIR3DL1, inhibitory receptors implicated in viral and autoimmune regulation, as additional immune evasion mechanisms. C_LIO_LIJAK/STAT activation in neighboring myeloid cells may be driven by Sezary cell signaling through S100A8, S100A9, CD74, IL-10, and TNF, a potentially targetable axis. C_LI What is the translational message?O_LIThe predominance of a central memory-like malignant phenotype, alongside other distinct subsets reveal an opportunity for subtype-guided treatment strategies. C_LIO_LIOptimal therapeutic targeting may include both malignant T cells and interacting immune cells. C_LIO_LIOur findings identify targets that may be actionable, including KIR-family receptors and STAT3-related signaling. C_LIO_LIInsights from other T-cell disorders may guide repurposing of existing therapies to improve outcomes. C_LI Lay Summary: How Sezay Syndrome, a Type of Skin Lymphoma, Impacts the Immune SystemSezary syndrome (SS) is a rare and aggressive form of skin cancer that starts in the blood. It is a type of cutaneous T-cell lymphoma (CTCL), where cancerous T cells (a kind of white blood cell) spread from the bloodstream to the skin. SS mainly affects adults and has limited treatment options, with most people living less than five years after diagnosis. This study, based in the United States, aimed to understand how cancerous T cells behave in SS and how they interact with other immune cells. We used a method called single-cell RNA sequencing to examine over 100,000 individual immune cells from the blood of 22 patients with SS and 7 healthy individuals. This allowed us to see which genes were active in each cell. We found that the cancerous T cells in SS are not all the same. Instead, they fall into three distinct groups: one resembled central memory T cells that typically live in the blood, one looked more aggressive and inflammatory, and one resembled exhausted regulatory immune cells. We also discovered that cancer cells and surrounding immune cells expressed molecules called KIRs, which may help them avoid being attacked. Other immune cells released signals that turned on a pathway called JAK-STAT, which may further protect the cancer. These findings reveal new ways that SS protects itself and avoids the immune system. Understanding these escape routes may help guide future treatments, including drug combinations that block these signals and improve patient outcomes. Abbreviated AbstractSingle-cell RNA and protein profiling of Sezary syndrome reveals three distinct malignant T-cell subtypes and uncovers convergent immunosuppressive signaling through KIR-family receptors and STAT3 activation. These findings expose targetable pathways driving immune evasion and offer a foundation for more personalized therapeutic strategies in this aggressive form of cutaneous T-cell lymphoma.