Development of a new high-yield integration site assay reveals disease-specific patterns across HTLV-1-associated pathologies
Résumé
Human T lymphotropic virus type 1 (HTLV-1) chronic infection is maintained through mitotic proliferation of the infected CD4+ T cells, where the viral genome is integrated as a provirus in its host genome. HTLV-1 integration sites (ISs) have a part in HTLV-1-associated pathologies, with distinct IS patterns associated with malignant proliferation or inflammatory diseases. However, IS determination remains challenging because most assays rely on complex biological and biocomputing protocols. We present an IS assay that solely relies on PCR and Sanger sequencing, which allowed HTLV-1 IS determination in four patients with various HTLV-1-associated pathologies. We adapted an IS assay derived from a panhandle PCR, with several modifications to increase yield. Absence of bias regarding IS retrieval was confirmed using TCRγ clonality. IS analysis was performed in four HTLV-1-positive patients: two with polymyositis, one with adult T-cell leukemia/lymphoma (ATLL), and one with HTLV-1-associated myelopathy (HAM). Overall yield was around 20%, with a mean sequence length downstream the IS of 336 ± 230 bp (range, 44-1,024 bp). There was no major bias in clonal determination, as IS results matched clonality assessed using a TCRγ assay. The IS assay revealed distinct clonal patterns depending on HTLV-1 pathology: dominated by a large clone for ATLL, oligo-or polyclonal for polymyositis and polyclonal for HAM. As a conclusion, we present an easy-to-implement integration site assay for HTLV-1 that allows a relatively unbiased IS analysis regarding clonal populations. This assay could be useful to further explore IS involvement in HTLV-1 associated pathologies.
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