Retrovirus insertion site analysis of LGL leukemia patient genomes

Abstract

23Background: Large granular lymphocyte (LGL) leukemia is an uncommon cancer characterized 24 by a sustained clonal proliferation of LGL cells. Antibodies reactive to retroviruses have been 25 documented in the serum of patients with LGL leukemia. Culture or molecular approaches have 26 to date not been successful in identifying a retrovirus. 27 Methods: Because a retrovirus must integrate into the genome of an infected cell, we focused 28 our efforts on detecting a novel retrovirus integration site in the clonally expanded LGL cells. 29We present a new computational tool that uses long-insert mate pair sequence data to search the 30 genome of LGL leukemia cells for retrovirus integration sites. We also utilize recently published 31 methods to interrogate the status of polymorphic human endogenous retrovirus type K (HERV-K) 32 provirus in patient genomes. 33Results: While our analysis did not reveal any new retrovirus insertions in LGL genomes from 34LGL leukemia patients, we did identify four HERV-K provirus integration sites that are 35 polymorphic in the human population and absent from the human reference genome, hg19. To 36 determine if the prevalence of these or other polymorphic proviral HERV-Ks differed between 37LGL leukemia patients and the general population, we applied a recently developed approach 38 that reports all sites in the human genome occupied by a proviral HERV-K. Using the 1000 39 genomes project (KGP) data as a reference database for HERV-K proviral prevalence at each 40 polymorphic site, we show that there are significant differences in the number of polymorphic 41 HERV-Ks in the genomes of LGL leukemia patients of European origin compared to individuals 42 with European ancestry in the KGP data. 43 Conclusions:Our study confirms that the integration of a new infectious or endogenous 44 retrovirus does not cause the clonal expansion of LGL cells in LGL leukemia, although we do 45 3 not rule out that these cells could be responding to retroviral antigens produced in other cell 46 types. However, it is of interest that the burden of polymorphic proviral HERV-K is elevated in 47LGL leukemia patient genomes. Our research emphasizes the merits of comprehensive genomic 48 assessment of HERV-K in cancer samples and suggests that further analyses to determine 49 contributions of HERV-K to LGL leukemia are warranted. 50 Keywords: Large granular lymphocyte leukemia, retrovirus, HERV-K, genomic insertion, 51 visualization tool 52 53 Background 54 Large granular lymphocyte (LGL) leukemia is a rare, chronic, proliferative disorder of cytotoxic 55 T cells (approximately 85% of cases) and NK cells [1]. Diagnosis of this leukemia is based on a 56 sustained elevation of a clonally expanded T or NK cell population. LGL leukemia is reported 57 most frequently in patients from North America and Europe and up to half of patients also have 58 an autoimmune disorder, most frequently rheumatoid arthritis [2]. A small subset of patients 59 show clonal proliferation of CD4+ cells, which has been associated with Cy...