Abstract Mycosis fungoides (MF) and Sézary syndrome (SS) are the most common subtypes of cutaneous T-cell lymphoma (CTCL). MF is primarily a benign disease often confined to skin. MF, in about 10% of cases, can progress to SS or transform to large-cell histology. SS, the leukemic variant of CTCL, is defined as erythroderma on ≥ 80% of the skin plus ≥1000/μL circulating malignant T-cells. SS is very aggressive with a median overall survival of only 2-5 years. So far, effective treatment options for CTCLs are still very limited and the underlying genetic basis remains incompletely characterized. Here, we performed integrated genomic analyses of 105 patients with de novo or transformed SS, using whole-exome, targeted exon, transcriptome sequencing and SNP array. Frequent somatic alterations were identified in TP53, CARD11, CCR4, PLCG1, TNFRSF1B, CDKN2A, ARID1A, RPS6KA1 and ZEB1. Activating CCR4 and CARD11 mutations were detected in nearly one third of patients. CCR4 is important for T-cell migration into the skin. All CCR4 mutations were either nonsense or frameshift and located at the C-terminus. CARD11 is required for T cell receptor (TCR)-mediated activation of NF-κB signaling. About half of the CARD11 mutations were located in the domain previously reported in diffuse large B cell lymphoma (DLBCL). The remaining mutations were located at a highly conserved new hotspot. As was previously suggested in DLBCL, therapies targeting CARD11 signaling could benefit SS patients. PLCG1 is a key modulator of TCR signaling. In addition to the recently reported S345F hotspot mutation, we identified a new hotspot located in the C-terminal of the protein. The mutation frequency of the new hotspot was significantly higher in patients with prior history of MF, suggesting the possibility that PLCG1 may play a role in transformation of MF to SS. Focal deletion of ZEB1 was observed in over half of the patients. ZEB1 is suggested to be critical for early T-cell development. ZEB1 downregulation contributes to resistance to TGF-β1-mediated growth suppression in adult T-cell leukemia/lymphoma derived cell lines. Loss of ZEB1 may play a similar role in SS pathogenesis. IL32 and IL2RG were strongly upregulated in nearly all patients. IL32 protein expression is correlated with the mRNA expression and the density of Sézary cells in patients’ blood. IL32 accelerates the proliferation of CTCL cell lines through mitogen-activated protein kinase and NF-κB-mediated signaling. IL32 could become a target that is specific to SS patients. Surprisingly, the UVB mutation signature was detected in most of the cases, indicating that the malignant clonal population arose from a cell that spent significant time in the superficial layers of the skin and challenging the view that SS originated from the circulating memory T-cell rather than those resident in the skin. Our results showed profound disruption of key T-cell signaling in SS patients and suggested potential targets for novel therapies. Citation Format: Linghua Wang, Xiao Ni, Kyle R. Covington, Liu Xi, David A. Wheeler, Madeleine Duvic. Molecular pathogenesis of an advanced cutaneous T-cell lymphoma. [abstract]. In: Proceedings of the 107th Annual Meeting of the American Association for Cancer Research; 2016 Apr 16-20; New Orleans, LA. Philadelphia (PA): AACR; Cancer Res 2016;76(14 Suppl):Abstract nr 124.