Genomic and Single-Cell Landscape Reveals Novel Drivers and Therapeutic Vulnerabilities of Transformed Cutaneous T-cell Lymphoma

ABSTRACT

Cutaneous T-cell lymphoma (CTCL) is a rare cancer of skin-homing T cells. A subgroup of patients develops large cell transformation with rapid progression to an aggressive lymphoma. Here, we investigated the transformed CTCL (tCTCL) tumor ecosystem using integrative multiomics spanning whole-exome sequencing (WES), single-cell RNA sequencing, and immune profiling in a unique cohort of 56 patients. WES of 70 skin biopsies showed high tumor mutation burden, UV signatures that are prognostic for survival, exome-based driver events, and most recurrently mutated pathways in tCTCL. Single-cell profiling of 16 tCTCL skin biopsies identified a core oncogenic program with metabolic reprogramming toward oxidative phosphorylation (OXPHOS), cellular plasticity, upregulation of MYC and E2F activities, and downregulation of MHC I suggestive of immune escape. Pharmacologic perturbation using OXPHOS and MYC inhibitors demonstrated potent antitumor activities, whereas immune profiling provided in situ evidence of intercellular communications between malignant T cells expressing macrophage migration inhibitory factor and macrophages and B cells expressing CD74.

SIGNIFICANCE

Our study contributes a key resource to the community with the largest collection of tCTCL biopsies that are difficult to obtain. The multiomics data herein provide the first comprehensive compendium of genomic alterations in tCTCL and identify potential prognostic signatures and novel therapeutic targets for an incurable T-cell lymphoma. This article is highlighted in the In This Issue feature, p. 1171.

Clinical characteristics and prognostic factors of 70 patients with Sézary syndrome: a single-institutional experience at Moffitt cancer center

Sézary syndrome (SS) is a rare and aggressive leukemic variant of cutaneous T-cell lymphoma, with a median overall survival (OS) rate of 2-4 years. Few studies have described the clinical outcome of SS patients since 2012. We retrospectively analyzed 70 patients diagnosed with SS treated at a high-volume tertiary cancer center between 2000 and 2018. Overall survival at 1 and 5 years was 84.1% and 50.7%, respectively. Univariate analyses identified older age (>65 years) and male sex as poor prognostic factors. Five patients presented with circulating large granular lymphocytic proliferation and had a favorable prognosis. Targeted therapies were effective in treating refractory/relapsed SS patients with a durable response. Therapeutic advancements and the comprehensive treatments used in a multidisciplinary clinic improved OS rates.

Assessment of lifetime patterns of dairy food intake and physical activity

Patterns of nutrition and exercise throughout the life span may account for differences in health problems of aging. The purpose of this study was to develop and validate a simple life span history questionnaire of dairy food intake and to assess recalled levels of leisure time physical activity over the life span. Volunteers, 98 women and 49 men, completed two nutritional surveys (Criterion Questionnaire, ¿CRIQ¿ and Diary Food Index, ¿INDX¿) and a physical activity questionnaire (P-ACTQ) in a test re-test design. The INDX and P-ACTQ consisted of a one to four scale (low to high intake). Dairy food intake averaged 1.4 to 2.3 servings per day with no significant differences in current dairy food intake between decade age categories. When compared to their own recalled 20's decade, dairy food intake declined slightly with age, except for the 80-89 age group which showed an increased intake. Test retest reliability for the INDX was r = 0.64. Validity of the INDX compared to the CRIQ was r = 0.64. All groups showed a decrease in physical activity levels across the life span. The Dairy Food Index holds promise as a simple "global" assessment of dairy food intake for the study of lifetime trends in advancing our understanding of the role of lifetime habits in chronic "lifestyle" diseases.