Multimodal single cell analysis of molecular profiles of paired tissues of cutaneous T cell lymphoma

Cutaneous T cell lymphoma (CTCL) is a heterogeneous group of mature T cell neoplasms characterized by the accumulation of clonal malignant CD4+ T cells in the skin. The most common variant of CTCL, Mycosis Fungoides, is confined to the skin in early stages but can be accompanied by extracutaneous dissemination of malignant T cells to the blood and lymph nodes in advanced stages of disease. Sézary Syndrome, a leukemic form of disease is characterized by significant blood involvement. Little is known about the transcriptional and genomic relationship between skin and blood residing malignant T cells in CTCL. In the present study we interrogate multiple modalities of information in single cells from matched skin and blood samples of patients with leukemic disease and healthy controls within a single workflow. By employing expanded CRISPR-compatible cellular indexing of transcriptomes and epitopes by sequencing (ECCITE-seq), we sought to compare the molecular profile of malignant clones residing in the skin and circulation of these patients across gene and protein expression modalities. We apply inferred CNV and phylogenetic analysis to examine sub-clonal heterogeneity to gain insights into the evolution and the relationship of malignant clones across tissues. Our data reveals clonal evolution at a transcriptional and genetic level within the malignant populations of individual patients. We highlight highly consistent transcriptional signatures delineating skin-derived and blood-derived malignant T cells. Analysis of these two populations suggests that environmental cues, along with genetic aberrations, contribute to transcriptional profiles of malignant T cells. ECCITE-seq gene expression, antibody derived tag, and TCR clonotype profiles of matched skin and blood from 5 Sézary syndrome (SS) and leukemic Mycosis Fungoides (MF) patients and a healthy control. We also include ECCITE-seq profiles from 2 additional SS patients. >>>Submitter states that raw data will be made available at dbGaP due to patient privacy concerns<<<

皮肤T细胞淋巴瘤（cutaneous T cell lymphoma, CTCL）是一组异质性成熟T细胞肿瘤，以克隆性恶性CD4+ T细胞在皮肤中聚集为核心特征。CTCL最常见的亚型为蕈样肉芽肿（Mycosis Fungoides, MF），疾病早期仅局限于皮肤；至疾病晚期，恶性T细胞可播散至皮肤以外的血液与淋巴结。塞扎里综合征（Sézary Syndrome, SS）属于白血病型CTCL，以显著的血液受累为典型表现。目前学界对CTCL患者皮肤与血液中恶性T细胞的转录组与基因组关联机制尚缺乏深入认知。
本研究通过单一实验流程，对白血病型CTCL患者与健康对照的配对皮肤、血液样本中的单细胞开展多组学信息解析。研究采用扩增型CRISPR兼容转录组与表位细胞索引测序（expanded CRISPR-compatible cellular indexing of transcriptomes and epitopes by sequencing, ECCITE-seq），旨在从基因与蛋白表达两个维度，对比此类患者皮肤与循环系统中恶性克隆的分子特征。本研究通过推断拷贝数变异（copy number variation, CNV）与系统发育分析，解析亚克隆异质性，以深入探究恶性克隆在不同组织中的演化过程与相互关联。
本研究数据揭示了单个患者恶性群体在转录组与遗传层面的克隆演化特征；同时鉴定出可清晰区分皮肤来源与血液来源恶性T细胞的高度保守转录特征。对两类群体的分析表明，环境信号与遗传畸变共同塑造了恶性T细胞的转录组表型。
本数据集包含5例塞扎里综合征（Sézary Syndrome, SS）与白血病型蕈样肉芽肿患者的配对皮肤、血液样本的ECCITE-seq基因表达、抗体标签及T细胞受体（TCR）克隆型谱数据，以及1例健康对照的对应信息；此外还纳入了额外2例SS患者的ECCITE-seq谱数据。数据集提交者说明，受限于患者隐私保护要求，原始数据将在dbGaP数据库中公开。