Comprehensive Antiretroviral Restriction Factor Profiling Reveals the Evolutionary Imprint of the ex Vivo and in Vivo IFN-β Response in HTLV-1-Associated Neuroinflammation

Abstract

HTLV-1-Associated Myelopathy (HAM/TSP) is a progressive neuroinflammatory disorder for which no disease-modifying treatment exists. Modest clinical benefit from type I interferons (IFN-α/β) in HAM/TSP contrasts with its recently identified IFN-inducible gene signature. In addition, IFN-α treatment in vivo decreases proviral load and immune activation in HAM/TSP, whereas IFN-β therapy decreases tax mRNA and lymphoproliferation. We hypothesize this “IFN paradox” in HAM/TSP might be explained by both cell type- and gene-specific effects of type I IFN in HTLV-1-associated pathogenesis. Therefore, we analyzed ex vivo transcriptomes of CD4+ T cells, PBMCs and whole blood in healthy controls, HTLV-1-infected individuals, and HAM/TSP patients. First, we used a targeted approach, simultaneously quantifying HTLV-1 mRNA (HBZ, Tax), proviral load and 42 host genes with known antiretroviral (anti-HIV) activity in purified CD4+ T cells. This revealed two major clusters (“antiviral/protective” vs. “proviral/deleterious”), as evidenced by significant negative (TRIM5/TRIM22/BST2) vs. positive correlation (ISG15/PAF1/CDKN1A) with HTLV-1 viral markers and clinical status. Surprisingly, we found a significant inversion of antiretroviral activity of host restriction factors, as evidenced by opposite correlation to in vivo HIV-1 vs. HTLV-1 RNA levels. The anti-HTLV-1 effect of antiviral cluster genes was significantly correlated to their adaptive chimp/human evolution score, for both Tax mRNA and PVL. Six genes of the proposed antiviral cluster underwent lentivirus-driven purifying selection during primate evolution (TRIM5/TRIM22/BST2/APOBEC3F-G-H), underscoring the cross-retroviral evolutionary imprint. Secondly, we examined the genome-wide type I IFN response in HAM/TSP patients, following short-term ex vivo culture of PBMCs with either IFN-α or IFN-β. Microarray analysis evidenced 12 antiretroviral genes (including TRIM5α/TRIM22/BST2) were significantly up-regulated by IFN-β, but not IFN-α, in HAM/TSP. This was paralleled by a significant decrease in lymphoproliferation by IFN-β, but not IFN-α treatment. Finally, using published ex vivo whole blood transcriptomic data of independent cohorts, we validated the significant positive correlation between TRIM5, TRIM22, and BST2 in HTLV-1-infected individuals and HAM/TSP patients, which was independent of the HAM/TSP disease signature. In conclusion, our results provide ex vivo mechanistic evidence for the observed immunovirological effect of in vivo IFN-β treatment in HAM/TSP, reconcile an apparent IFN paradox in HTLV-1 research and identify biomarkers/targets for a precision medicine approach.

An Antiviral Process Targeting HTLV-1: The Complex Relationship between HTLV-1 and Nonsense-mediated mRNA Decay

“…Other members of the TRIM family, such as TRIM19/PML, were found to be negatively correlated with HTLV-1 Tax mRNA expression levels [17]. In line with previous work showing that TRIM19/PML interferes with HTLV-1 replication via Tax proteosomal degradation in ATL patients [18], all these data reinforce the potential involvement of the TRIM family in the early restriction of HTLV-1 replication.…”

“…In a cohort of 60 ATL patients, in whom the authors observed loss-of-expression mutations in several viral genes, including Tax, the HBZ oncogene remained intact [27]. Consistently, Leal et al [17] pointed to a large "antiviral cluster", a negative correlation between different members of the APOBEC3 family and Tax mRNA levels, as having greater impact than PVLs, clinical status or HAM/TSP parameters. Interestingly, an increase in h3AB, but not h3AG, was recently reported in HTLV-1-infected humanized mice exhibiting ATL-like features [28], a finding in line with that of another integrated molecular analysis showing increased h3AB expression in large ATL and AC cohorts [29].…”

Regulation of Expression and Latency in BLV and HTLV

“…HDACi used alone can be used to induce expression of BLV and HTLV-1 and reduce proviral loads [ 37 , 38 , 78 ]. However, the effect is only transient in HAM/TSP patients [ 40 ], and may be related to temporal fluctuations in viral RNA and response to immune control mechanisms in these patients [ 250 , 251 , 252 ]. Improved therapies include VPA combinations with zidovudine (AZT) or cytokines (IFNα) [ 253 , 254 , 255 ].…”

The Complex Relationship between HTLV-1 and Nonsense-Mediated mRNA Decay (NMD)

“…- [13] Negative correlation between members of APOBEC3 family and Tax mRNA levels. + [14] In [28] No effect on HTLV-1 and Tax expression in macrophages and cycling CD4+ T cells.…”

“…Regarding TRIM Family implication, all data reinforce the potential involvement of the TRIM family in the early restriction of HTLV-1 replication. The majority of the data are obtained by whole exome sequencing analysis [13] or microarray analysis of CD4+ T Cells [14] in HAM/TSP cohorts of patients. Consistently with the fact that HTLV-1 mainly replicates by clonal expansion and the fact that virions are poorly infective, the involvement of APOBEC family, as well as BST2/Tetherin, remains uncertain.…”