Transcriptome and Somatic Mutation Associated with Non-Malignant Human T Lymphotropic Virus Type 1 Infection and Adult T-Cell Leukemia/Lymphoma
Authors: Kagdi Huseini Hatimbhai , Taylor Graham Phillip 
Published: October 2019

Abstract
Aggressive Adult T-cell leukemia/lymphoma (ATL), a human T lymphotropic virus type 1 (HTLV-1) -associated disease, has a poor prognosis. There is an urgent need for effective prevention and treatment. A large number of genomic aberrations including hundreds of somatic mutations and copy number changes are typically observed in ATL tumours, with certain genes, PLCG1, PRKCB, CCR4, CARD11, STAT3, TP53, VAV1, TBL1XR1, NOTCH1, GATA3 and IRF4 mutated in over 10% of cases(1). CD4+CCR4+CD26-CD7- is the dominant immunophenotype of lymphocytes in patients with ATL (ATL cells) but infected cells with similar immunophenotype ('ATL-like' cells) are also present in patients with non-malignant HTLV-1 infection(2, 3). Aggressive ATL develops in patients with non-malignant HTLV-1 (asymptomatic carriers (AC) and patients with HTLV-1 associated myelopathy (HAM)) over decades with evolution from high proviral load (PVL) and non-dominant clonal growth through emergence of dominant clones and indolent to aggressive ATL. HTLV-1 infected clones have been shown to have cells with mixed immunophenotype. The aim was to investigate specific genomic aberration associated with non-malignant HTLV-1 infection, dominant clonal growth and ATL.
RNA sequencing followed by differential gene expression and mutational analysis of HTLV-1 and human genes was performed on sorted CD4+CCR4+CD26-CD7- cells from nine patients with ATL (four with indolent, four with aggressive ATL and one with indolent to aggressive transformation; ATL cells); and 18 patients with high PVL non-malignant HTLV-1 infection (three with dominant clones and 15 with non-dominant clones, 'ATL-like' infected cells). Seven antisense transcript of HTLV-1 genome was detected. A spliced antisense transcript spanning the whole HTLV-1 genome was detected in all samples whilst two novel transcripts were detected in > 2 samples. There was no significant difference in viral transcriptome expression between ATL and 'ATL-like' cells. A total of 13637 including 7952 well annotated human genes were detected within which 400 genes were significantly differentially expressed ( > 2 fold change and false discover rate < 0.1) between ATL and 'ATL-like' cells as shown in figure 1. Small nuclear RNA and endothelial cancer associated genes were upregulated in patients with ATL whilst T-cell, inflammatory, apoptosis and proliferation related genes were upregulated in patients with non-malignant HTLV-1 infection respectively. Principle component analysis did not showed any significant cluster but hierarchical analysis using differentially expressed genes showed clustering of ATL cells from patient with aggressive ATL, indolent ATL and 'ATL-like' cells from patients with non-malignant HTLV-1 infection (AC and HAM) of ATL as shown in figure 2. One out of three patient with high PVL non-malignant HTLV-1 infection and dominant clones (HKU) clustered with ATL and this patient progressed to ATL 12 months from sample data. Hallmark pathway analysis showed upregulation cluster in 'ATL-like' cells with only metabolism associated pathways clustered in ATL cells as shown in table 1. Expression of all recurrently mutated genes was detected and mutation analysis is currently underway.
In summary, there is a major overlap of infected cell transcriptome in patient with non-malignant HTLV-1 infection and ATL. ATL cells have downregulation of T-cell, inflammatory, apoptosis and proliferation related genes compared to 'ATL-like' infected cells whilst upregulation of small nuclear RNAs. Transcriptome analysis in patient with high PVL non-malignant HTLV-1 infection might help in further prognostication in malignant risk.Kataoka K, Nagata Y, Kitanaka A, Shiraishi Y, Shimamura T, Yasunaga J, et al. Integrated molecular analysis of adult T cell leukemia/lymphoma. Nature genetics. 2015;47(11):1304-15.Kagdi H, Demontis MA, Ramos JC, Taylor GP. Switching and loss of cellular cytokine producing capacity characterize in vivo viral infection and malignant transformation in human T- lymphotropic virus type 1 infection. PLoS pathogens. 2018;14(2):e1006861.Kagdi HH, Demontis MA, Fields PA, Ramos JC, Bangham CR, Taylor GP. Risk stratification of adult T-cell leukemia/lymphoma using immunophenotyping. Cancer medicine. 2017;6(1):298-309.

Disclosures
No relevant conflicts of interest to declare.