Transcriptome sequencing in Sézary syndrome identifies Sézary cell and mycosis fungoides-associated lncRNAs and novel transcripts

• Published in: Blood Vol. 120; no. 16; pp. 3288 - 3297
• Main Authors: Lee, Carolyn S., Ungewickell, Alexander, Bhaduri, Aparna, Qu, Kun, Webster, Dan E., Armstrong, Randall, Weng, Wen-Kai, Aros, Cody J., Mah, Angela, Chen, Richard O., Lin, Meihong, Sundram, Uma, Chang, Howard Y., Kretz, Markus, Kim, Youn H., Khavari, Paul A.
• Format: Journal Article
• Language: English
• Published: Washington, DC Elsevier Inc 18-10-2012; Americain Society of Hematology; American Society of Hematology
• Subjects: Biological and medical sciences; Biomarkers, Tumor - genetics; Flow Cytometry; Gene Expression Profiling; Hematologic and hematopoietic diseases; Humans; Leukemias. Malignant lymphomas. Malignant reticulosis. Myelofibrosis; Lymphoid Neoplasia; Medical sciences; Mycosis Fungoides - genetics; Mycosis Fungoides - pathology; Oligonucleotide Array Sequence Analysis; Prognosis; Real-Time Polymerase Chain Reaction; Reverse Transcriptase Polymerase Chain Reaction; RNA, Long Noncoding - genetics; RNA, Messenger - genetics; Sezary Syndrome - genetics; Sezary Syndrome - pathology; Skin Neoplasms - genetics; Skin Neoplasms - pathology; Tumor Cells, Cultured; Cutaneous T cell lymphoma; Skin disease; Sezary cell; Hematology; T cell neoplasm; Transcriptome; Mycosis fungoides; Malignant hemopathy; Lymphoid neoplasm; Non Hodgkin lymphoma; Peripheral T cell lymphoma; Chronic; Cutaneous hematologic disease; Messenger RNA; Gene; Sezary syndrome; Lymphoproliferative syndrome; Sequencing; Cancer
• ISSN: 0006-4971; 1528-0020; 1528-0020
• DOI: 10.1182/blood-2012-04-423061

Sézary syndrome (SS) is an aggressive cutaneous T-cell lymphoma (CTCL) of unknown etiology in which malignant cells circulate in the peripheral blood. To identify viral elements, gene fusions, and gene expression patterns associated with this lymphoma, flow cytometry was used to obtain matched pure populations of malignant Sézary cells (SCs) versus nonmalignant CD4+ T cells from 3 patients for whole transcriptome, paired-end sequencing with an average depth of 112 million reads per sample. Pathway analysis of differentially expressed genes identified mis-regulation of PI3K/Akt, TGFβ, and NF-κB pathways as well as T-cell receptor signaling. Bioinformatic analysis did not detect either nonhuman transcripts to support a viral etiology of SS or recurrently expressed gene fusions, but it did identify 21 SC-associated annotated long noncoding RNAs (lncRNAs). Transcriptome assembly by multiple algorithms identified 13 differentially expressed unannotated transcripts termed Sézary cell-associated transcripts (SeCATs) that include 12 predicted lncRNAs and a novel transcript with coding potential. High-throughput sequencing targeting the 3′ end of polyadenylated transcripts in archived tumors from 24 additional patients with tumor-stage CTCL confirmed the differential expression of SC-associated lncRNAs and SeCATs in CTCL. Our findings characterize the SS transcriptome and support recent reports that implicate lncRNA dysregulation in human malignancies.