Plasma proteome analysis in HTLV-1-associated myelopathy/tropical spastic paraparesis

Repeated Decision Stumping Distils Simple Rules from Single-Cell Data

Single-cell data afford unprecedented insights into molecular processes. But the complexity and size of these data sets have proved challenging and given rise to a large armory of statistical and machine learning approaches. The majority of approaches focuses on either describing features of these data, or making predictions and classifying unlabeled samples. In this study, we introduce repeated decision stumping (ReDX) as a method to distill simple models from single-cell data. We develop decision trees of depth one-hence "stumps"-to identify in an inductive manner, gene products involved in driving cell fate transitions, and in applications to published data we are able to discover the key players involved in these processes in an unbiased manner without prior knowledge. Our algorithm is deliberately targeting the simplest possible candidate hypotheses that can be extracted from complex high-dimensional data. There are three reasons for this: (1) the predictions become straightforwardly testable hypotheses; (2) the identified candidates form the basis for further mechanistic model development, for example, for engineering and synthetic biology interventions; and (3) this approach complements existing descriptive modeling approaches and frameworks. The approach is computationally efficient, has remarkable predictive power, including in simulation studies where the ground truth is known, and yields robust and statistically stable predictors; the same set of candidates is generated by applying the algorithm to different subsamples of experimental data.

Refining the risk of HTLV-1-associated myelopathy in people living with HTLV-1: identification of a HAM-like phenotype in a proportion of asymptomatic carriers

Up to 3.8% of human T-lymphotropic virus type-1 (HTLV-1)-infected asymptomatic carriers (AC) eventually develop HTLV-1-associated myelopathy (HAM). HAM occurs in patients with high (> 1%) HTLV proviral load (PVL). However, this cut-off includes more than 50% of ACs and therefore the risk needs to be refined. As HAM is additionally characterised by an inflammatory response to HTLV-1, markers of T cell activation (TCA), β₂-microglobulin (β₂M) and neuronal damage were accessed for the identification of ACs at high risk of HAM. Retrospective analysis of cross-sectional and longitudinal routine clinical data examining differences in TCA (CD4/CD25, CD4/HLA-DR, CD8/CD25 & CD8/HLA-DR), β₂M and neurofilament light (NfL) in plasma in ACs with high or low PVL and patients with HAM. Comparison between 74 low PVL ACs, 84 high PVL ACs and 58 patients with HAM revealed a significant, stepwise, increase in TCA and β₂M. Construction of receiver operating characteristic (ROC) curves for each of these blood tests generated a profile that correctly identifies 88% of patients with HAM along with 6% of ACs. The 10 ACs with this 'HAM-like' profile had increased levels of NfL in plasma and two developed myelopathy during follow-up, compared to none of the 148 without this viral-immune-phenotype. A viral-immuno-phenotype resembling that seen in patients with HAM identifies asymptomatic carriers who are at increased risk of developing HAM and have markers of subclinical neuronal damage.

HTLV-1-associated myelopathy/tropical spastic paraparesis

Human T-lymphotropic virus 1 (HTLV-1)-associated myelopathy/tropical spastic paraparesis (HAM/TSP) is a progressive disease of the CNS that causes weakness or paralysis of the legs, lower back pain and urinary symptoms. HAM/TSP was first described in Jamaica in the nineteenth century, but the aetiology of the condition, infection with the retrovirus HTLV-1, was only identified in the 1980s. HAM/TSP causes chronic disability and, accordingly, imposes a substantial health burden in areas where HTLV-1 infection is endemic. Since the discovery of the cause of HAM/TSP, considerable advances have been made in the understanding of the virology, immunology, cell biology and pathology of HTLV-1 infection and its associated diseases. However, progress has been limited by the lack of accurate animal models of the disease. Moreover, the treatment of HAM/TSP remains highly unsatisfactory: antiretroviral drugs have little impact on the infection and, although potential disease-modifying therapies are widely used, their value is unproved. At present, clinical management is focused on symptomatic treatment and counselling. Here, we summarize current knowledge on the epidemiology, pathogenesis and treatment of HAM/TSP and identify areas in which further research is needed. For an illustrated summary of this Primer, visit: http://go.nature.com/tjZCFM.

A plasma diagnostic model of human T-cell leukemia virus-1 associated myelopathy

OBJECTIVE

Human T-cell leukemia virus-1 (HTLV-1) associated myelopathy/tropic spastic paraparesis (HAM/TSP) is induced by chronic inflammation in spinal cord due to HTLV-1 infection. Cerebrospinal fluid (CSF) neopterin or proviral load are clinically measured as disease grading biomarkers, however, they are not exactly specific to HAM/TSP. Therefore, we aimed to identify HAM/TSP-specific biomarker molecules and establish a novel less-invasive plasma diagnostic model for HAM/TSP.

METHODS

Proteome-wide quantitative profiling of CSFs from six asymptomatic HTLV-1 carriers (AC) and 51 HAM/TSP patients was performed. Fourteen severity grade biomarker proteins were further examined plasma enzyme-linked immunosorbent assay (ELISA) assays (n = 71). Finally, we constructed three-factor logistic regression model and evaluated the diagnostic power using 105 plasma samples.

RESULTS

Quantitative analysis for 1871 nonredundant CSF proteins identified from 57 individuals defined 14 CSF proteins showing significant correlation with Osame's motor disability score (OMDS). Subsequent ELISA experiments using 71 plasma specimens confirmed secreted protein acidic and rich in cysteine (SPARC) and vascular cell adhesion molecule-1 (VCAM-1) demonstrated the same correlations in plasma (R = -0.373 and R = 0.431, respectively). In this training set, we constructed a HAM/TSP diagnostic model using SPARC, VCAM1, and viral load. Sensitivity and specificity to diagnose HAM/TSP patients from AC (AC vs. OMDS 1-11) were 85.3% and 81.1%, respectively. Importantly, this model could be also useful for determination of therapeutic intervention point (OMDS 1-3 + AC vs. OMDS 4-11), exhibiting 80.0% sensitivity and 82.9% specificity.

INTERPRETATION

We propose a novel less-invasive diagnostic model for early detection and clinical stratification of HAM/TSP.

Human T-cell leukemia/lymphoma virus type 1 p30, but not p12/p8, counteracts toll-like receptor 3 (TLR3) and TLR4 signaling in human monocytes and dendritic cells

The human T-cell leukemia/lymphoma virus type 1 (HTLV-1) p30 protein, essential for virus infectivity in vivo, is required for efficient infection of human dendritic cells (DCs) but not B and T cells in vitro. We used a human monocytic cell line, THP-1, and dendritic cells to study the mechanism of p30 and p12/p8 requirements in these cell types. p30 inhibited the expression of interferon (IFN)-responsive genes (ISG) following stimulation by lipopolysaccharide (LPS) of Toll-like receptor 4 (TLR4) and by poly(I·C) of TLR3 but not of TLR7/8 with imiquimod. Results with THP-1 mirrored those for ex vivo human primary monocytes and monocyte-derived dendritic cells (Mo-mDC). The effect of p30 on TLR signaling was also demonstrated by ablating its expression within a molecular clone of HTLV-1. HTLV-1 infection of monocytes inhibited TLR3- and TLR4-induced ISG expression by 50 to 90% depending on the genes, whereas the isogenic clone p30 knockout virus was less effective at inhibiting TLR3 and TRL4 signaling and displayed lower infectivity. Viral expression and inhibition of ISG transcription was, however, rescued by restoration of p30 expression. A chromatin immunoprecipitation assay demonstrated that p30 inhibits initiation and elongation of PU.1-dependent transcription of IFN-α1, IFN-β, and TLR4 genes upon TLR stimulation. In contrast, experiments conducted with p12/p8 did not demonstrate an effect on ISG expression. These results provide a mechanistic explanation of the requirement of p30 for HTLV-1 infectivity in vivo, suggest that dampening interferon responses in monocytes and DCs is specific for p30, and represent an essential early step for permissive HTLV-1 infection and persistence.

Soluble IL-2 receptor and beta-2 microglobulin as possible serologic markers of neurologic disease in HTLV-1 infection

The human T-cell leukemia virus (HTLV-1) is the causative agent of a variety of neurologic diseases, including HTLV-1 Associated Myelopathy (HAM/TSP) and overactive bladder. Investigation of immune markers such as soluble interleukin-2 receptor (sIL-2R) and beta-2 microglobulin (B2M) has shown some promising results in distinguishing patients with neurologic disease from those with carrier status. The objective of the present study was to determine if plasma levels of sIL-2R and B2M are markers of neurologic disease in individuals infected with HTLV-1. The present study was divided into two parts. A cross-sectional study and a nested case control study. In the cross-sectional study, HAM/TSP patients had higher plasma levels of B2M and sIL-2R than patients with overactive bladder and HTLV-1 carriers (P < 0.01 for all comparisons). For the nested case control study, the sIL-2 receptor test was able to distinguish patients with HAM/TSP from patients in the combined group of carriers and patients with overactive bladder with a sensitivity of 75.8% and false positive rate of 25.4%. Plasma levels of these markers did not change with the development of HAM/TSP and overactive bladder in HTLV-1 carrier patients. The present study has shown the importance of sIL-2 receptor in helping identifying HAM/TSP. However, the levels of these makers did not change significantly with the development of neurologic disease.

Balancing the robustness and predictive performance of biomarkers

Recent studies have highlighted the importance of assessing the robustness of putative biomarkers identified from experimental data. This has given rise to the concept of stable biomarkers, which are ones that are consistently identified regardless of small perturbations to the data. Since stability is not by itself a useful objective, we present a number of strategies that combine assessments of stability and predictive performance in order to identify biomarkers that are both robust and diagnostically useful. Moreover, by wrapping these strategies around logistic regression classifiers regularized by the elastic net penalty, we are able to assess the effects of correlations between biomarkers upon their perceived stability. We use a synthetic example to illustrate the properties of our proposed strategies. In this example, we find that: (i) assessments of stability can help to reduce the number of false-positive biomarkers, although potentially at the cost of missing some true positives; (ii) combining assessments of stability with assessments of predictive performance can improve the true positive rate; and (iii) correlations between biomarkers can have adverse effects on their stability and hence must be carefully taken into account when undertaking biomarker discovery. We then apply our strategies in a proteomics context to identify a number of robust candidate biomarkers for the human disease HTLV1-associated myelopathy/tropical spastic paraparesis (HAM/TSP).

Preapoptotic protease calpain-2 is frequently suppressed in adult T-cell leukemia

Adult T-cell leukemia (ATL) is one of the most aggressive hematologic malignancies caused by human T-lymphotropic virus type 1 (HTLV-1) infection. The prognosis of ATL is extremely poor; however, effective strategies for diagnosis and treatment have not been established. To identify novel therapeutic targets and diagnostic markers for ATL, we employed focused proteomic profiling of the CD4(+)CD25(+)CCR4(+) T-cell subpopulation in which HTLV-1-infected cells were enriched. Comprehensive quantification of 14 064 peptides and subsequent 2-step statistical analysis using 29 cases (6 uninfected controls, 5 asymptomatic carriers, 9 HTLV-1-associated myelopathy/tropical spastic paraparesis patients, 9 ATL patients) identified 91 peptide determinants that statistically classified 4 clinical groups with an accuracy rate of 92.2% by cross-validation test. Among the identified 17 classifier proteins, α-II spectrin was drastically accumulated in infected T cells derived from ATL patients, whereas its digestive protease calpain-2 (CAN2) was significantly downregulated. Further cell cycle analysis and cell growth assay revealed that rescue of CAN2 activity by overexpressing constitutively active CAN2 (Δ(19)CAN2) could induce remarkable cell death on ATL cells accompanied by reduction of α-II spectrin. These results support that proteomic profiling of HTLV-1-infected T cells could provide potential diagnostic biomarkers and an attractive resource of therapeutic targets for ATL.

The Impact of Immune Response on HTLV-I in HTLV-I-Associated Myelopathy/Tropical Spastic Paraparesis (HAM/TSP)

Human T lymphotropic virus type I (HTLV-I) is a retrovirus which is associated with adult T cells leukaemia (ATL) and HTLV-I-associated myelopathy/tropical spastic paraparesis (HAM/TSP) in a minority of HTLV-I-infected individuals. It is not clear why a minority of HTLV-I-infected individuals develop HAM/TSP and majority remains lifelong carriers. It seems that the interaction between the virus and the immune response plays an important role in HTLV-I-associated diseases. Although the role of the immune response in HTLV-I pathogenesis is not fully understood, however it seems that the efficacy of the immune response which is involved in controlling or limiting of viral persistence determines the outcome of HTLV-I-associated diseases. Here we discuss the role of innate and adaptive immune response and also the risk factors contribute to the observed differences between HAM/TSP patients and asymptomatic HTLV-I carriers.

The importance of ubiquitination and sumoylation on the transforming activity of HTLV Tax-1 and Tax-2

Human T-cell Leukemia Virus type 1 (HTLV-1) and 2 (HTLV-2) are two closely related human retroviruses. HTLV-1 is associated with an aggressive Adult T-cell Leukemia (ATL) while there is no evidence for an association of HTLV-2 with any human malignancies. The two viruses encode transactivator proteins, Tax-1 and Tax-2 respectively. In ATL, Tax-1 is thought to play a central role in the transformation of a normal T-cell into a leukemic cell; however, it has not been entirely clear how post-translational modifications of Tax-1 influence its transforming activity. Here, we discuss three recent papers that report on the ubiquitination and sumoylation of Tax-1 and Tax-2. We comment on their divergent findings implicating the importance (or lack of importance) of these modifications and other events on Tax activation of NF-κB as related to cellular transformation.

Ciclosporin A proof of concept study in patients with active, progressive HTLV-1 associated myelopathy/tropical spastic paraparesis

Introduction

Patients with HTLV-1-associated myelopathy/tropical spastic paraparesis (HAM/TSP) become progressively impaired, with chronic pain, immobility and bladder, bowel and sexual dysfunction. Tested antiretroviral therapies have not been effective and most patients are offered a short course of corticosteroids or interferon-α, physiotherapy and symptomatic management. Pathogenesis studies implicate activated T-lymphocytes and cytokines in tissue damage. We therefore tested the hypothesis that inhibition of T-cell activation with ciclosporin A would be safe and clinically beneficial in patients with early and/or clinically progressing HAM/TSP.

Materials and Methods

Open label, proof of concept, pilot study of 48 weeks therapy with the calcineurin antagonist, ciclosporin A (CsA), in seven patients with ‘early’ (<two years) or ‘progressive’ (>50% deterioration in timed walk during the preceding three months) HAM/TSP. Primary outcomes were incidence of clinical failure at 48 weeks and time to clinical failure.

Results

All patients completed 72 weeks study participation and five showed objective evidence of clinical improvement after 3 months treatment with CsA. Two patients exhibited clinical failure over 6.4 person-years of follow-up to week 48. One patient had a >2 point deterioration in IPEC (Insituto de Pesquisa Clinica Evandro Chagas) disability score at weeks 8 and 12, and then stopped treatment. The other stopped treatment at week 4 because of headache and tremor and deterioration in timed walk, which occurred at week 45. Overall pain, mobility, spasticity and bladder function improved by 48 weeks. Two patients recommenced CsA during follow-up due to relapse.

Conclusions

These data provide initial evidence that treatment with CsA is safe and may partially reverse the clinical deterioration seen in patients with early/progressive HAM/TSP. This trial supports further investigation of this agent's safety and effectiveness in larger, randomised controlled studies in carefully selected patients with disease progression.

HTLV-1 is a retrovirus transmitted through body fluids that is commonly seen in the West Indies, South America and Southern Japan but rarely in the UK. Although most patients remain healthy carriers, HTLV-1 causes serious conditions such as adult T cell leukaemia/lymphoma (ATLL) and HTLV-1-associated myelopathy/Tropical Spastic Paraparesis (HAM/TSP). The infection which is life-long cannot be eradicated and treatments for the associated diseases are limited. We report the encouraging findings of the first UK Medical Research Council funded treatment study for patients with early and/or deteriorating HAM/TSP. Treatment with ciclosporin A, a drug commonly used to dampen the immune system in transplant patients, was investigated. Symptoms and signs of disease, particularly low back pain and muscle stiffness, improved by week 24 and in some patients this improvement persisted after the 48 weeks of treatment, at least to the end of the study at week 72. Most striking was the finding that the amount of HTLV-1 in the fluid around the spinal cord, called cerebrospinal fluid, was reduced during treatment. These findings justify the further study of ciclosporin A in patients with HAM/TSP.