Cellular Profiling Identifies Targetable T Cell Phenotypes in Lymphocytic Variant Hypereosinophilic Syndrome

Lymphocytic variant hypereosinophilic syndrome (LHES) is driven by aberrant Th2‑skewed lymphocyte clones that promote tissue eosinophilia. We performed multimodal single‑cell RNA‑sequencing (scRNA‑seq), cell‑surface protein (ADT) profiling, and paired αβ‑TCR sequencing on peripheral‑blood mononuclear cells (PBMCs) from two clinically characterized LHES patients and one idiopathic HES control. One LHES patient was sequenced at two timepoints, pre-JAK inhibitor treatment and post-JAK inhibitor treatment. Single‑cell regulatory‑network inference (SCENIC), CellChat ligand–receptor modelling, and scRNA variant calling were integrated with flow‑cytometric validation and 5,000× amplicon sequencing. Two clonally expanded CD3‑CD4⁺ central‑/effector‑memory T‑cell clusters were observed exclusively in LHES. These cells showed Th2‑associated regulons (GATA3, BATF, MAF), high expression of CCR4, CD52, PTGDR2 and IL13, and down‑regulation of CD247 (CD3ζ), a mechanism experimentally confirmed to abolish surface CD3/TCR. Autocrine IL‑7 signaling, predicted by CellChat, provides an antigen‑independent proliferative cue. Therapeutically actionable targets (CCR4, CD52, IL‑5, IL‑7, TNF) were prioritized; one refractory patient achieved complete clinical and cytologic remission after mogamulizumab (anti‑CCR4) therapy. Longitudinal sequencing revealed clonal evolution with acquisition of a STAT3 p.G618R mutation under JAK‑inhibition, highlighting a resistance mechanism. Raw scRNA‑seq (5′ cDNA, VDJ, ADT) data, and sample‑level metadata will be distributed through dbGaP. These resources provide the first high‑resolution immune atlas of LHES and a framework for rational, precision immunotherapy in eosinophilic disorders.]]>
FSM library level 3README for dbGaP pooled single-cell submissionInclusion Absolute eosinophil count (AEC) > 1.5 × 10⁹ L⁻¹ for > 6 months Tissue damage attributable to eosinophils (all patients had eosinophilic skin lesions) Circulating abnormal T‑cell population by flow cytometry (CD3‑CD4⁺) Exclusion of all secondary causes of eosinophilia Informed consent for genomic studies Exclusion Absence of aberrant T‑cell clone (for LHES cohort) Unwillingness or inability to provide consent Active systemic infection at time of phlebotomy Concomitant hematological malignancy other than LHES/iHES]]>
2021‑2023: Patient identification, longitudinal clinical follow‑up and initial flow cytometry (Northwestern University) Jul 2024: JAK‑inhibitor resistance case emerged; STAT3 G618R captured by amplicon‑seq ]]>