Imperial College London

ProfessorCharlesBangham

Institute of Infection

Co-Director of the Institute of Infection
 
 
 
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Contact

 

+44 (0)20 7594 3730c.bangham Website

 
 
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Assistant

 

Ms Linda Hollick +44 (0)20 7594 3729

 
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Location

 

115Wright Fleming WingSt Mary's Campus

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Summary

 

Publications

Publication Type
Year
to

304 results found

Maher A, Aristodemou A, Giang N, Tanaka Y, Bangham C, Taylor G, Dominguez-Villar Met al., 2024, HTLV-1 induces an inflammatory CD4+CD8+ T cell population in HTLV-1-associated myelopathy, Journal of Clinical Investigation Insight, Vol: 9, ISSN: 0021-9738

Human T cell leukemia virus type 1 (HTLV-1) is a retrovirus with preferential CD4+ T cell tropism that causes a range of conditions spanning from asymptomatic infection to adult T-cell leukemia and HTLV-1-associated myelopathy (HAM), an inflammatory disease of the CNS. The mechanisms by which HTLV-1 induces HAM are poorly understood. By directly examining the ex vivo phenotype and function of T cells from asymptomatic carriers and patients with HAM, we show that patients with HAM have a higher frequency of CD4+CD8+ double positive (DP) T cells, which are infected with HTLV-1 at higher rates than CD4+ T cells. Displaying both helper and cytotoxic phenotypes, these DP T cells are highly pro-inflammatory and contain high frequencies of HTLV-1-specific cells. Mechanistically, we demonstrate that DP T cells arise by direct HTLV-1 infection of CD4+ and CD8+ T cells. High levels of CD49d and CXCR3 expression suggest that DP T cells possess the ability to migrate to the CNS, and when co-cultured with astrocytes, DP T cells induce proinflammatory astrocytes that express high levels of CXCL10, IFN-, and IL-6. These results demonstrate the potential of DP T cells to directly contribute to CNS pathology.

Journal article

Aristodemou AENR, Rueda D, Taylor GR, Bangham CRM, Green PLRet al., 2023, The transcriptome of HTLV-1-infected primary cells following reactivation reveals changes to host gene expression central to the proviral life cycle, PLOS PATHOGENS, Vol: 19, ISSN: 1553-7366

Journal article

Bangham CRM, 2023, HTLV-1 persistence and the oncogenesis of adult T-cell leukemia/lymphoma, BLOOD, Vol: 141, Pages: 2299-2306, ISSN: 0006-4971

Journal article

Prawiro C, Bunney TD, Kampyli C, Yaguchi H, Katan M, Bangham CRMet al., 2023, A frequent PLCγ1 mutation in adult T-cell leukemia/lymphoma determines functional properties of the malignant cells, BIOCHIMICA ET BIOPHYSICA ACTA-MOLECULAR BASIS OF DISEASE, Vol: 1869, ISSN: 0925-4439

Journal article

Aristodemou AEN, Rueda DS, Taylor GP, Bangham CRMet al., 2023, The transcriptome of HTLV-1-infected primary cells following reactivation reveals changes to host gene expression central to the proviral life cycle

<jats:title>Abstract</jats:title><jats:p>Infections by Human T cell Leukaemia Virus type 1 (HTLV-1) persist for the lifetime of the host by integrating into the genome of CD4<jats:sup>+</jats:sup>T cells. Proviral gene expression is core to proviral survival and the maintenance of the proviral load, through the pro-proliferative changes it induces in infected cells. Despite their role in HTLV-1 infection and a persistent cytotoxic T lymphocyte response raised against them, proviral transcripts from the sense-strand are rarely detected in fresh cells extracted from the peripheral blood, and have recently been found to be expressed intermittently by a small subset of cells at a given time.<jats:italic>Ex vivo</jats:italic>culture of infected cells prompts synchronised proviral expression in infected cells from peripheral blood, allowing the study of factors involved in reactivation in primary cells. Here, we used bulk RNA-seq to examine the host transcriptome over six days<jats:italic>in vitro</jats:italic>, following proviral reactivation in primary peripheral CD4<jats:sup>+</jats:sup>T cells isolated from subjects with non-malignant HTLV-1 infection. Infected cells displayed a conserved response to reactivation, characterised by discrete stages of gene expression, cell division and subsequently horizontal transmission of the virus. We observed widespread changes in Polycomb gene expression following reactivation, including an increase in PRC2 transcript levels and diverse changes in the expression of PRC1 components. We hypothesize that these transcriptional changes constitute a negative feedback loop that maintains proviral latency by re-deposition of H2AK119ub1 following the end of proviral expression. Using RNAi, we found that certain deubiquitinases,<jats:italic>BAP1</jats:italic>,<jats:italic>USP14</jats:italic>and<jats:italic>OTUD5</jats:italic>each promote pr

Journal article

Ramanayake S, Moulding D, Tanaka YR, Singh AR, Bangham CRMRet al., 2022, Dynamics and consequences of the HTLV-1 proviral plus-strand burst, PLOS PATHOGENS, Vol: 18, ISSN: 1553-7366

Journal article

Schnell AP, Kohrt S, Aristodemou A, Taylor GP, Bangham CRM, Thoma-Kress AKet al., 2022, HDAC inhibitors Panobinostat and Romidepsin enhance <i>tax</i> transcription in HTLV-1-infected cell lines and freshly isolated patients' T-cells, FRONTIERS IN IMMUNOLOGY, Vol: 13, ISSN: 1664-3224

Journal article

Ramanayake S, Moulding DA, Tanaka Y, Singh A, Bangham CRMet al., 2022, Dynamics and consequences of the HTLV-1 proviral plus-strand burst

<jats:title>Abstract</jats:title><jats:p>Expression of the transcriptional transactivator protein Tax, encoded on the proviral plus-strand of human T-cell leukaemia virus type 1 (HTLV-1), is crucial for the replication of the virus, but Tax-expressing cells are rarely detected in fresh blood <jats:italic>ex vivo</jats:italic>. The dynamics and consequences of the proviral plus-strand transcriptional burst remain insufficiently characterised. We combined time-lapse live-cell imaging, single-cell tracking and mathematical modelling to study the dynamics of Tax expression at single-cell resolution in two naturally-infected T-cell clones transduced with a short-lived enhanced green fluorescent protein (d2EGFP) Tax reporter system. Five different patterns of Tax expression were observed during the 30-hour observation period; the distribution of these patterns differed between the two clones. The mean duration of Tax expression in the two clones was 94 and 417 hours respectively, estimated from mathematical modelling of the experimental data. Tax expression was associated with decreased proliferation, increased apoptosis, enhanced activation of the DNA damage response pathways, and slower cell-cycle progression. Longer-term follow-up (14 days) revealed an increase in the proportion of proliferating cells and a decrease in the fraction of apoptotic cells as the cells ceased Tax expression, resulting in a greater net expansion of the initially Tax-positive population. Time-lapse live-cell imaging showed enhanced cell-to-cell adhesion among Tax-expressing cells, and decreased cell motility of Tax-expressing cells at the single-cell level. The results demonstrate the within-clone and between-clone heterogeneity in the dynamics and patterns of HTLV-1 plus-strand transcriptional bursts and the balance of positive and negative consequences of the burst for the host cell.</jats:p><jats:sec><jats:title>Author Summary</jats:title&g

Journal article

Kiik H, Ramanayake S, Miura M, Tanaka Y, Melamed A, Bangham CRMet al., 2022, Time-course of host cell transcription during the HTLV-1 transcriptional burst, PLoS Pathogens, Vol: 18, ISSN: 1553-7366

The human T-cell leukemia virus type 1 (HTLV-1) transactivator protein Tax has pleiotropic functions in the host cell affecting cell-cycle regulation, DNA damage response pathways and apoptosis. These actions of Tax have been implicated in the persistence and pathogenesis of HTLV-1-infected cells. It is now known that tax expression occurs in transcriptional bursts of the proviral plus-strand, but the effects of the burst on host transcription are not fully understood. We carried out RNA sequencing of two naturally-infected T-cell clones transduced with a Tax-responsive Timer protein, which undergoes a time-dependent shift in fluorescence emission, to study transcriptional changes during successive phases of the HTLV-1 plus-strand burst. We found that the transcriptional regulation of genes involved in the NF-κB pathway, cell-cycle regulation, DNA damage response and apoptosis inhibition were immediate effects accompanying the plus-strand burst, and are limited to the duration of the burst. The results distinguish between the immediate and delayed effects of HTLV-1 reactivation on host transcription, and between clone-specific effects and those observed in both clones. The major transcriptional changes in the infected host T-cells observed here, including NF-κB, are transient, suggesting that these pathways are not persistently activated at high levels in HTLV-1-infected cells. The two clones diverged strongly in their expression of genes regulating the cell cycle. Up-regulation of senescence markers was a delayed effect of the proviral plus-strand burst and the up-regulation of some pro-apoptotic genes outlasted the burst. We found that activation of the aryl hydrocarbon receptor (AhR) pathway enhanced and prolonged the proviral burst, but did not increase the rate of reactivation. Our results also suggest that sustained plus-strand expression is detrimental to the survival of infected cells.

Journal article

Halawa S, Pullamsetti SS, Bangham CRM, Stenmark KR, Dorfmuller P, Frid MG, Butrous G, Morrell NW, de Jesus Perez VA, Stuart DI, O'Gallagher K, Shah AM, Aguib Y, Yacoub MHet al., 2022, Potential long-term effects of SARS-CoV-2 infection on the pulmonary vasculature: a global perspective, NATURE REVIEWS CARDIOLOGY, Vol: 19, Pages: 314-331, ISSN: 1759-5002

Journal article

Melamed A, Fitzgerald T, Wang Y, Ma J, Birney E, Bangham Cet al., 2022, Selective clonal persistence of human retroviruses in vivo: radial chromatin organization, integration site and host transcription, Science Advances, Vol: 8, ISSN: 2375-2548

The human retroviruses HTLV-1 and HIV-1 persist in vivo as a reservoir of latently infected T-cell clones. It is poorly understood what determines which clones survive in the reservoir. We compared >160,000 HTLV-1 integration sites (>40,000 HIV-1 sites) from T-cells isolated ex vivo from naturally-infected subjects with >230,000 HTLV-1 integration sites (>65,000 HIV-1 sites) from in vitro infection, to identify genomic features that determineselective clonal survival. Three statistically independent factors together explained >40% of the observed variance in HTLV-1 clonal survival in vivo: the radial intranuclear position of the provirus, its genomic distance from the centromere, and the intensity of local host genome transcription. The radial intranuclear position of the provirus and its distance from the centromere also explained ~7% of clonal persistence of HIV-1 in vivo. Selection for theintranuclear and intrachromosomal location of the provirus, and host transcription intensity, favours clonal persistence of human retroviruses in vivo.

Journal article

Mentzer AJ, Brenner N, Allen N, Littlejohns TJ, Chong AY, Cortes A, Almond R, Hill M, Sheard S, McVean G, Collins R, Hill AVS, Waterboer Tet al., 2022, Identification of host-pathogen-disease relationships using a scalable multiplex serology platform in UK Biobank, NATURE COMMUNICATIONS, Vol: 13

Journal article

Bangham CRM, 2022, Adult T-cell leukemia: genomic analysis <i>Comment</i>, BLOOD, Vol: 139, Pages: 953-954, ISSN: 0006-4971

Journal article

Katsuya H, Cook LBM, Rowan AG, Melamed A, Turpin J, Ito J, Islam S, Miyazato P, Tan BJY, Matsuo M, Miyakawa T, Nakata H, Matsushita S, Taylor GP, Bangham CRM, Kimura S, Satou Yet al., 2022, Clonality of HIV-1- and HTLV-1-Infected Cells in Naturally Coinfected Individuals (vol 225, pg 317, 2021), JOURNAL OF INFECTIOUS DISEASES, Vol: 225, Pages: 359-359, ISSN: 0022-1899

Journal article

Katsuya H, Cook LBM, Rowan AG, Melamed A, Turpin J, Ito J, Islam S, Miyazato P, Jek Yang Tan B, Matsuo M, Miyakawa T, Nakata H, Matsushita S, Taylor GP, Bangham CRM, Kimura S, Satou Yet al., 2022, Clonality of HIV-1 and HTLV-1 infected cells in naturally coinfected individuals, Journal of Infectious Diseases, Vol: 225, Pages: 317-326, ISSN: 0022-1899

BACKGROUND: Coinfection with HIV-1 and HTLV-1 diminishes the value of the CD4 + T-cell count in diagnosing AIDS, and increases the rate of HTLV-1-associated myelopathy. It remains elusive how HIV-1/HTLV-1 coinfection is related to such clinical characteristics. Here, we investigated the mutual effect of HIV-1/HTLV-1 coinfection on their integration sites (ISs) and the clonal expansion. METHODS: We extracted DNA from longitudinal peripheral blood samples from 7 HIV-1/HTLV-1 coinfected individuals, and from 12 HIV-1 and 13 HTLV-1 mono-infected individuals. The proviral loads (PVL) were quantified using real-time PCR. Viral ISs and clonality were quantified by ligation-mediated PCR followed by high-throughput sequencing. RESULTS: The PVL of both HIV-1 and HTLV-1 in coinfected individuals was significantly higher than that of the respective virus in mono-infected individuals. The degree of oligoclonality of both HIV-1- and HTLV-1-infected cells in co-infected individuals was also greater than that in mono-infected subjects. The ISs of HIV-1 in cases of coinfection were more frequently located in intergenic regions and transcriptionally silent regions, compared with HIV-1 mono-infected individuals. CONCLUSION: HIV-1/HTLV-1 coinfection makes an impact on the distribution of viral ISs and the clonality of virus-infected cells and thus may alter the risks of both HTLV-1- and HIV-1-associated disease.

Journal article

Melamed A, Fitzgerald TW, Wang Y, Ma J, Birney E, Bangham CRMet al., 2021, Selective clonal persistence of human retroviruses in vivo: radial chromatin organization, integration site and host transcription

<jats:title>Abstract</jats:title><jats:p>The human retroviruses HTLV-1 and HIV-1 persist in vivo, despite the host immune response and antiretroviral therapy, as a reservoir of latently infected T-cell clones. It is poorly understood what determines which clones survive in the reservoir and which are lost. We compared &gt;160,000 HTLV-1 integration sites from T-cells isolated ex vivo from naturally-infected subjects with &gt;230,000 integration sites from in vitro infection, to identify the genomic features that determine selective clonal survival. Three factors explained &gt;40% of the observed variance in clone survival of HTLV-1 in vivo: the radial intranuclear position of the provirus, its absolute genomic distance from the centromere, and the intensity of host genome transcription flanking the provirus. The radial intranuclear position of the provirus and its distance from the centromere also explained ~7% of clonal persistence of HIV-1 in vivo. Selection for transcriptionally repressive nuclear compartments favours clonal persistence of human retroviruses in vivo.</jats:p>

Working paper

Izaki M, Yasunaga J-I, Nosaka K, Sugata K, Utsunomiya H, Suehiro Y, Shichijo T, Yamada A, Sugawara Y, Hibi T, Inomata Y, Akari H, Melamed A, Bangham C, Matsuoka Met al., 2021, <i>In vivo</i> dynamics and adaptation of HTLV-1-infected clones under different clinical conditions, PLOS PATHOGENS, Vol: 17, ISSN: 1553-7366

Journal article

Laydon DJ, Sunkara V, Boelen L, Bangham CRM, Asquith Bet al., 2020, The relative contributions of infectious and mitotic spread to HTLV-1 persistence, PLoS Computational Biology, Vol: 16, ISSN: 1553-734X

Human T-lymphotropic virus type-1 (HTLV-1) persists within hosts via infectious spread (de novo infection) and mitotic spread (infected cell proliferation), creating a population structure of multiple clones (infected cell populations with identical genomic proviral integration sites). The relative contributions of infectious and mitotic spread to HTLV-1 persistence are unknown, and will determine the efficacy of different approaches to treatment. The prevailing view is that infectious spread is negligible in HTLV-1 persistence beyond early infection. However, in light of recent high-throughput data on the abundance of HTLV-1 clones, and recent estimates of HTLV-1 clonal diversity that are substantially higher than previously thought (typically between 104 and 105 HTLV-1+ T cell clones in the body of an asymptomatic carrier or patient with HTLV-1-associated myelopathy/tropical spastic paraparesis), ongoing infectious spread during chronic infection remains possible. We estimate the ratio of infectious to mitotic spread using a hybrid model of deterministic and stochastic processes, fitted to previously published HTLV-1 clonal diversity estimates. We investigate the robustness of our estimates using three alternative estimators. We find that, contrary to previous belief, infectious spread persists during chronic infection, even after HTLV-1 proviral load has reached its set point, and we estimate that between 100 and 200 new HTLV-1 clones are created and killed every day. We find broad agreement between all estimators. The risk of HTLV-1-associated malignancy and inflammatory disease is strongly correlated with proviral load, which in turn is correlated with the number of HTLV-1-infected clones, which are created by de novo infection. Our results therefore imply that suppression of de novo infection may reduce the risk of malignant transformation.

Journal article

Rowan AG, Dillon R, Witkover A, Melamed A, Demontis M-A, Gillet NA, Mun LJ, Bangham CRM, Cook LB, Fields PA, Taylor GPet al., 2020, Evolution of retrovirus-infected premalignant T-cell clones prior to Adult T-cell leukemia/lymphoma diagnosis, Blood, Vol: 135, Pages: 2023-2032, ISSN: 0006-4971

Adult T cell leukemia/lymphoma (ATL) is an aggressive hematological malignancy caused by Human T-cell leukemia virus type-1 (HTLV-1). ATL is preceded by decades of chronic HTLV-1 infection, and the tumors carry both somatic mutations and proviral DNA integrated into the tumor genome. In order to gain insight into the oncogenic process, we used targeted sequencing to track the evolution of the malignant clone in six individuals, 2-10 years before the diagnosis of ATL. Clones of premalignant HTLV-1-infected cells bearing known driver mutations were detected in the blood up to 10 years before individuals developed acute and lymphoma subtype ATL. Six months before diagnosis, the total number and variant allele fraction of mutations increased in the blood. Peripheral blood mononuclear cells from premalignant cases (1 year pre-diagnosis) had significantly higher mutational burden in genes frequently mutated in ATL than did high risk, age-matched HTLV-1-carriers who remained ATL-free after a median of 10 years of follow up. These data show that HTLV-1-infected T cell clones carrying key oncogenic driver mutations can be detected in cases of ATL years before the onset of symptoms. Early detection of such mutations may enable earlier and more effective intervention to prevent the development of ATL.

Journal article

Marcais A, Cook L, Witkover A, Asnafi V, Avettand-Fenoel V, Delarue R, Cheminant M, Sibon D, Frenzel L, de The H, Bangham CRM, Bazarbachi A, Hermine O, Suarez Fet al., 2020, Arsenic trioxide (As2O3) as a maintenance therapy for adult T cell leukemia/lymphoma, Retrovirology, Vol: 17, Pages: 1-5, ISSN: 1742-4690

BackgroundAdult T-cell leukemia-lymphoma (ATL) is an aggressive mature lymphoid proliferation associated with poor prognosis. Standard of care includes chemotherapy and/or the combination of zidovudine and interferon-alpha. However, most patients experience relapse less than 6 months after diagnosis. Allogeneic stem cell transplantation is the only curative treatment, but is only feasible in a minority of cases. We previously showed in a mouse model that Arsenic trioxide (As2O3) targets ATL leukemia initiating cells.ResultsAs2O3 consolidation was given in 9 patients with ATL (lymphoma n = 4; acute n = 2; and indolent n = 3), who were in complete (n = 4) and partial (n = 3) remission, in stable (n = 1) and in progressive (n = 1) disease. Patients received up to 8 weeks of As2O3 at the dose of 0.15 mg/kg/day intravenously in combination with zidovudine and interferon-alpha. One patient in progression died rapidly. Of the remaining eight patients, three with indolent ATL subtype showed overall survivals of 48, 53 and 97 months, and duration of response to As2O3 of 22, 25 and 73 months. The other 5 patients with aggressive ATL subtype had median OS of 36 months and a median duration of response of 10 months. Side effects were mostly hematological and cutaneous (one grade 3) and reversible with dose reduction of AZT/IFN and/or As2O3 discontinuation. The virus integration analysis revealed the regression of the predominant malignant clone in one patient with a chronic subtype.ConclusionThese results suggest that consolidation with As2O3 could be an option for patients with ATL in response after induction therapy and who are not eligible for allogeneic stem cell transplantation.

Journal article

Araujo A, Bangham CRM, Casseb J, Gotuzzo E, Jacobson S, Martin F, Oliviera AP, Puccioni-Sohler M, Taylor GP, Yamano Yet al., 2020, The management of HAM/TSP: Systematic review and consensus-based recommendations 2019, Neurology: Clinical Practice, Vol: 11, Pages: 49-56, ISSN: 2163-0402

Purpose of Review: To provide an evidence-based approach to the use of therapies that are prescribed to improve the natural history of HTLV-1-associated myelopathy/tropical spastic paraparesis (HAM/TSP) – a rare disease.Recent Findings: All 41 articles on the clinical outcome of disease-modifying therapy for HAM/TSP were included in a systematic review by members of the International Retrovirology Association; we report here the consensus assessment and recommendations. The quality of available evidence is low, being based for the most part on observational studies, with only one double-masked placebo-controlled randomised trial. Summary: There is evidence to support the use of both high-dose pulsed methyl prednisolone for induction and low-dose (5mg) oral prednisolone as maintenance therapy for progressive disease. There is no evidence to support the use of antiretroviral therapy. There is insufficient evidence to support the use of interferon-α as a first-line therapy.

Journal article

Lewin A, Hamilton S, Witkover A, Langford P, Nicholas R, Chataway J, Bangham CRMet al., 2019, Free serum haemoglobin is associated with brain atrophy in secondary progressive multiple sclerosis [version 2; peer review: 3 approved], Wellcome Open Research, Vol: 1, ISSN: 2398-502X

Background: A major cause of disability in secondary progressive multiple sclerosis (SPMS) is progressive brain atrophy, whose pathogenesis is not fully understood. The objective of this study was to identify protein biomarkers of brain atrophy in SPMS. Methods: We used surface-enhanced laser desorption-ionization time-of-flight mass spectrometry to carry out an unbiased search for serum proteins whose concentration correlated with the rate of brain atrophy, measured by serial MRI scans over a 2-year period in a well-characterized cohort of 140 patients with SPMS. Protein species were identified by liquid chromatography-electrospray ionization tandem mass spectrometry. Results: There was a significant (p<0.004) correlation between the rate of brain atrophy and a rise in the concentration of proteins at 15.1 kDa and 15.9 kDa in the serum. Tandem mass spectrometry identified these proteins as alpha-haemoglobin and beta-haemoglobin, respectively. The abnormal concentration of free serum haemoglobin was confirmed by ELISA (p<0.001). The serum lactate dehydrogenase activity was also highly significantly raised (p<10-12) in patients with secondary progressive multiple sclerosis. Conclusions: The results are consistent with the following hypothesis. In progressive multiple sclerosis, low-grade chronic intravascular haemolysis releases haemoglobin into the serum; the haemoglobin is subsequently translocated into the central nervous system (CNS) across the damaged blood-brain barrier. In the CNS, the haemoglobin and its breakdown products, including haem and iron, contribute to the neurodegeneration and consequent brain atrophy seen in progressive disease. We postulate that haemoglobin is a source of the iron whose deposition along blood vessels in multiple sclerosis plaques is associated with neurodegeneration. If so, then chelators of haemoglobin, rather than chelators of free serum iron, may be effective in preventing this neurodegeneration.

Journal article

Cook L, Demontis MA, Sagawe S, Witkover A, Melamed A, Turpin J, Dillon R, Haddow J, Marks A, Bangham C, Fields P, Taylor G, Rowan Aet al., 2019, Molecular remissions are observed in chronic adult T cell leukemia/lymphoma in patients treated with mogamulizumab, Haematologica, Vol: 104, Pages: e566-e569, ISSN: 0390-6078

Journal article

Miura M, Dey S, Ramanayake S, Singh A, Rueda DS, Bangham CRMet al., 2019, Kinetics of HTLV-1 reactivation from latency quantified by single-molecule RNA FISH and stochastic modelling, PLoS Pathogens, Vol: 15, ISSN: 1553-7366

The human T cell leukemia virus HTLV-1 establishes a persistent infection in vivo in which the viral sense-strand transcription is usually silent at a given time in each cell. However, cellular stress responses trigger the reactivation of HTLV-1, enabling the virus to transmit to a new host cell. Using single-molecule RNA FISH, we measured the kinetics of the HTLV-1 transcriptional reactivation in peripheral blood mononuclear cells (PBMCs) isolated from HTLV-1+ individuals. The abundance of the HTLV-1 sense and antisense transcripts was quantified hourly during incubation of the HTLV-1-infected PBMCs ex vivo. We found that, in each cell, the sense-strand transcription occurs in two distinct phases: the initial low-rate transcription is followed by a phase of rapid transcription. The onset of transcription peaked between 1 and 3 hours after the start of in vitro incubation. The variance in the transcription intensity was similar in polyclonal HTLV-1+ PBMCs (with tens of thousands of distinct provirus insertion sites), and in samples with a single dominant HTLV-1+ clone. A stochastic simulation model was developed to estimate the parameters of HTLV-1 proviral transcription kinetics. In PBMCs from a leukemic subject with one dominant T-cell clone, the model indicated that the average duration of HTLV-1 sense-strand activation by Tax (i.e. the rapid transcription) was less than one hour. HTLV-1 antisense transcription was stable during reactivation of the sense-strand. The antisense transcript HBZ was produced at an average rate of ~0.1 molecules per hour per HTLV-1+ cell; however, between 20% and 70% of HTLV-1-infected cells were HBZ-negative at a given time, the percentage depending on the individual subject. HTLV-1-infected cells are exposed to a range of stresses when they are drawn from the host, which initiate the viral reactivation. We conclude that whereas antisense-strand transcription is stable throughout the stress response, the HTLV-1 sense-strand reactivati

Journal article

Laydon DJ, Sunkara V, Boelen L, Bangham CRM, Asquith Bet al., 2019, The relative contributions of infectious and mitotic spread to HTLV-1 persistence

<jats:title>Abstract</jats:title><jats:p>Human T-lymphotropic virus type-1 (HTLV-1) persists within hosts via infectious spread (<jats:italic>de novo</jats:italic>infection) and mitotic spread (infected cell proliferation), creating a population structure of multiple clones (infected cell populations with identical genomic proviral integration sites). The relative contributions of infectious and mitotic spread to HTLV-1 persistence are unknown, and will determine the efficacy of different approaches to treatment.</jats:p><jats:p>The prevailing view is that infectious spread is negligible in HTLV-1 proviral load maintenance beyond early infection. However, in light of recent high-throughput data on the abundance of HTLV-1 clones, and recent estimates of HTLV-1 clonal diversity that are substantially higher than previously thought (typically between 10<jats:sup>4</jats:sup>and 10<jats:sup>5</jats:sup>HTLV-1<jats:sup>+</jats:sup>T cell clones in the body of an asymptomatic carrier or patient with HAM/TSP), ongoing infectious spread during chronic infection remains possible.</jats:p><jats:p>We estimate the ratio of infectious to mitotic spread using a hybrid model of deterministic and stochastic processes, fitted to previously published HTLV-1 clonal diversity estimates. We investigate the robustness of our estimates using two alternative methods. We find that, contrary to previous belief, infectious spread persists during chronic infection, even after HTLV-1 proviral load has reached its set point, and we estimate that between 100 and 200 new HTLV-1 clones are created and killed every day. We find broad agreement between all three methods.</jats:p><jats:p>The risk of HTLV-1-associated malignancy and inflammatory disease is strongly correlated with proviral load, which in turn is correlated with the number of HTLV-1-infected clones, which are created by de novo infectio

Working paper

Bangham CRM, Miura M, Kulkarni A, Matsuoka Met al., 2019, Regulation of Latency in the Human T Cell Leukemia Virus, HTLV-1., Annu Rev Virol

The human T cell leukemia virus persists in vivo in 103 to 106 clones of T lymphocytes that appear to survive for the lifetime of the host. The plus strand of the provirus is typically transcriptionally silent in freshly isolated lymphocytes, but the strong, persistently activated cytotoxic T lymphocyte (CTL) response to the viral antigens indicates that the virus is not constantly latent in vivo. There is now evidence that the plus strand is transcribed in intense intermittent bursts that are triggered by cellular stress, modulated by hypoxia and glycolysis, and inhibited by polycomb repressive complex 1 (PRC1). The minus-strand gene hbz is transcribed at a lower, more constant level but is silent in a proportion of infected cells at a given time. Viral genes in the sense and antisense strands of the provirus play different respective roles in latency and de novo infection: Expression of the plus-strand gene tax is essential for de novo infection, whereas hbz appears to facilitate survival of the infected T cell clone in vivo. Expected final online publication date for the Annual Review of Virology Volume 6 is September 30, 2019. Please see http://www.annualreviews.org/page/journal/pubdates for revised estimates.

Journal article

Cook L, Demontis MA, Sagawe S, Witkover A, Melamed A, Turpin J, Haddow J, Wolf S, Marks S, Bangham C, Fields P, Taylor G, Rowan Aet al., 2019, Molecular remissions are observed in chronic adult T-cell leukaemia/lymphoma in patients treated with mogamulizumab, BRITISH JOURNAL OF HAEMATOLOGY, Vol: 185, Pages: 172-173, ISSN: 0007-1048

Journal article

Turpin J, Yurick D, Khoury G, Pham H, Locarnini S, Melamed A, Witkover A, Wilson K, Purcell D, Bangham CRM, Einsiedel Let al., 2019, Impact of Hepatitis B virus coinfection on human T-lymphotropic virus type 1 clonality in an indigenous population of central Australia, Journal of Infectious Diseases, Vol: 219, Pages: 562-567, ISSN: 0022-1899

The prevalence of human T-cell lymphotropic virus type 1 (HTLV-1) and hepatitis B virus (HBV) coinfection is high in certain Indigenous Australian populations, but its impact on HTLV-1 has not been described. We compared 2 groups of Indigenous adults infected with HTLV-1, either alone or coinfected with HBV. The 2 groups had a similar HTLV-1 proviral load, but there was a significant increase in clonal expansion of HTLV-1–infected lymphocytes in coinfected asymptomatic individuals. The degree of clonal expansion was correlated with the titer of HBV surface antigen. We conclude that HTLV-1/HBV coinfection may predispose to HTLV-1–associated malignant disease.

Journal article

Miura M, Miyazato P, Satou Y, Tanaka Y, Bangham CRMet al., 2018, Epigenetic changes around the pX region and spontaneous HTLV-1 transcription are CTCF-independent [version 2; approved 2], Wellcome Open Research, Vol: 3, ISSN: 2398-502X

Background: The human retrovirus HTLV-1 inserts the viral complementary DNA of 9 kb into the host genome. Both plus- and minus-strands of the provirus are transcribed, respectively from the 5' and 3' long terminal repeats (LTR). Plus-strand expression is rapid and intense once activated, whereas the minus-strand is transcribed at a lower, more constant level. To identify how HTLV-1 transcription is regulated, we investigated the epigenetic modifications associated with the onset of spontaneous plus-strand expression and the potential impact of the host factor CTCF. Methods: Patient-derived peripheral blood mononuclear cells (PBMCs) and in vitro HTLV-1-infected T cell clones were examined. Cells were stained for the plus-strand-encoded viral protein Tax, and sorted into Tax + and Tax - populations. Chromatin immunoprecipitation and methylated DNA immunoprecipitation were performed to identify epigenetic modifications in the provirus. Bisulfite-treated DNA fragments from the HTLV-1 LTRs were sequenced. Single-molecule RNA-FISH was performed, targeting HTLV-1 transcripts, for the estimation of transcription kinetics. The CRISPR/Cas9 technique was applied to alter the CTCF-binding site in the provirus, to test the impact of CTCF on the epigenetic modifications. Results: Changes in the histone modifications H3K4me3, H3K9Ac and H3K27Ac were strongly correlated with plus-strand expression. DNA in the body of the provirus was largely methylated except for the pX and 3' LTR regions, regardless of Tax expression. The plus-strand promoter was hypomethylated when Tax was expressed. Removal of CTCF had no discernible impact on the viral transcription or epigenetic modifications. Conclusions: The histone modifications H3K4me3, H3K9Ac and H3K27Ac are highly dynamic in the HTLV-1 provirus: they show rapid change with the onset of Tax expression, and are reversible. The HTLV-1 provirus has an intrinsic pattern of epigenetic modifications that is independent of both the provirus inse

Journal article

Bangham CRM, Taylor GP, Klose RJ, Schofield CJ, Kulkarni Aet al., 2018, Histone H2A mono-ubiquitylation and p38-MAP Kinases regulate immediate-early gene-like reactivation of latent retrovirus HTLV-1, Journal of Clinical Investigation, Vol: 3, ISSN: 0021-9738

It is not understood how the human T cell leukemia virus human T-lymphotropic virus-1 (HTLV-1), a retrovirus, regulates the in vivo balance between transcriptional latency and reactivation. The HTLV-1 proviral plus-strand is typically transcriptionally silent in freshly isolated peripheral blood mononuclear cells from infected individuals, but after short-term ex vivo culture, there is a strong, spontaneous burst of proviral plus-strand transcription. Here, we demonstrate that proviral reactivation in freshly isolated, naturally infected primary CD4+ T cells has 3 key attributes characteristic of an immediate-early gene. Plus-strand transcription is p38-MAPK dependent and is not inhibited by protein synthesis inhibitors. Ubiquitylation of histone H2A (H2AK119ub1), a signature of polycomb repressive complex-1 (PRC1), is enriched at the latent HTLV-1 provirus, and immediate-early proviral reactivation is associated with rapid deubiquitylation of H2A at the provirus. Inhibition of deubiquitylation by the deubiquitinase (DUB) inhibitor PR619 reverses H2AK119ub1 depletion and strongly inhibits plus-strand transcription. We conclude that the HTLV-1 proviral plus-strand is regulated with characteristics of a cellular immediate-early gene, with a PRC1-dependent bivalent promoter sensitive to p38-MAPK signaling. Finally, we compare the epigenetic signatures of p38-MAPK inhibition, DUB inhibition, and glucose deprivation at the HTLV-1 provirus, and we show that these pathways act as independent checkpoints regulating proviral reactivation from latency.

Journal article

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