Targeted deep sequencing reveals clonal and subclonal mutational signatures in Adult T-cell leukemia/lymphoma and defines an unfavorable indolent subtype

Abstract

Adult T-cell leukemia/lymphoma (ATL) carries a poor prognosis even in indolent subtypes. We performed targeted deep sequencing combined with mapping of HTLV-1 proviral integration sites of 61 ATL patients of African and Caribbean origin. This revealed mutations mainly affecting TCR/NF-kB (74%), T-cell trafficking (46%), immune escape (29%), and cell cycle (26%) related pathways, consistent with the genomic landscape previously reported in a large Japanese cohort. To examine the evolution of mutational signatures upon disease progression while tracking the viral integration architecture of the malignant clone, we carried out a longitudinal study of patients who either relapsed or progressed from an indolent to an aggressive subtype. Serial analysis of relapsing patients identified several patterns of clonal evolution. In progressing patients, the longitudinal study revealed NF-kB/NFAT mutations at progression that were present at a subclonal level at diagnosis (allelic frequency < 5%). Moreover, the presence in indolent subtypes of mutations affecting the TCR/NF-kB pathway, whether clonal or subclonal, was associated with significantly shorter time to progression and overall survival. Our observations reveal the clonal dynamics of ATL mutational signatures at relapse and during progression. Our study defines a new subgroup of indolent ATLs characterized by a mutational signature at high risk of transformation.

The HTLV-1 viral oncoproteins Tax and HBZ reprogram the cellular mRNA splicing landscape

“…In the second cohort, referred to as the “Afro-Caribbean cohort”, we analyzed 29 ATLLs, 5 HTLV-1 asymptomatic carriers and 4 CD4+ T-cell samples from uninfected healthy individuals [ 8 , 55 , 56 ]. Using rMATS v4.1.1 [ 46 ], we identified 2826 ASEs in HTLV-1 carriers and 4172 ASEs in ATLL patients ( Fig 6A ).…”

“…Our data suggest that both viral proteins interfere almost equally with all steps of mRNA life, including splicing processes, to reprogram the host cell transcriptome. Second, we used a Jurkat T-cell line model to identify potential Tax and HBZ splicing targets, which were validated in primary cells isolated from two independent cohorts of HTLV-1 asymptomatic carriers and ATLL patients [ 6 , 8 , 55 , 56 ]. These two cohorts are unbalanced in the number of control samples (purified CD4+ T-cells) from healthy individuals compared to HTLV-1 positive samples, and their genetic and epidemiological heterogeneity could affect our results.…”

Germinal epimutation of Fragile Histidine Triad (FHIT) gene is associated with progression to acute and chronic adult T-cell leukemia diseases

“…12 Laboratory of Virus Control, Institute for Frontier Life and Medical Sciences, Kyoto University, Kyoto, Japan. 13 Department of Hematology, Rheumatology, and Infectious Disease, Graduate School of Medical Sciences, Faculty of Life Sciences, Kumamoto University, Kumamoto, Japan. 14 Department of Hematology/Oncology, IMSUT Hospital, The Institute of Medical Science, The University of Tokyo, Tokyo, Japan.…”

“…High plasma levels of soluble tumor necrosis factor receptor 2 (sTNFR2) have been found in acute ATL, and could be used for diagnostic purposes [11]. A group of driver mutations (PLCG1, PRKCB, CCR4, TP53, and NOTCH1) have also been found in clonally expanded asymptomatic carrier patient cells of Afro-Caribbean lineage with high proviral loads that went on to develop aggressive ATL [12]; while sub-clonal mutations in the NF-κB/NFAT pathway have been found in the same geographical region of patients that relapsed or progressed from an indolent to aggressive ATL [13]. The mutational and transcriptional landscape of ATL patients from North America (which are predominately of Caribbean origin) also displayed similar mutations with a higher epigenetic mutational rates in EP300 [14].…”

An Improved Sequencing-Based Bioinformatics Pipeline to Track the Distribution and Clonal Architecture of Proviral Integration Sites

“…In a longitudinal study of adult T-cell leukemia (ATL) patients, we demonstrated that the optimized NGS mapping protocol applied to HTLV-1 outperformed other currently available methods, enabling the detection of patients refractory to first-line therapy and providing a better estimation of response to therapy (Artesi et al, 2017). We have then applied this method to samples collected from HTLV-1-and BLV-infected individuals of human, ovine, and bovine origin as well as HTLV-1 infected humanized mice, reflecting both basic and clinical settings (Artesi et al, 2017;Percher et al, 2017;Rosewick et al, 2017;Pérès et al, 2018;Galli et al, 2019;Marçais et al, 2020). This generated an unprecedented volume of raw sequencing data.…”