{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,6,16]],"date-time":"2026-06-16T23:00:10Z","timestamp":1781650810794,"version":"3.54.5"},"reference-count":104,"publisher":"Springer Science and Business Media LLC","issue":"1","license":[{"start":{"date-parts":[[2026,4,23]],"date-time":"2026-04-23T00:00:00Z","timestamp":1776902400000},"content-version":"tdm","delay-in-days":0,"URL":"https:\/\/creativecommons.org\/licenses\/by\/4.0"},{"start":{"date-parts":[[2026,6,5]],"date-time":"2026-06-05T00:00:00Z","timestamp":1780617600000},"content-version":"vor","delay-in-days":43,"URL":"https:\/\/creativecommons.org\/licenses\/by\/4.0"}],"funder":[{"DOI":"10.13039\/501100003130","name":"Fonds Wetenschappelijk Onderzoek","doi-asserted-by":"publisher","award":["G0A0621N"],"award-info":[{"award-number":["G0A0621N"]}],"id":[{"id":"10.13039\/501100003130","id-type":"DOI","asserted-by":"publisher"}]}],"content-domain":{"domain":["link.springer.com"],"crossmark-restriction":false},"short-container-title":["Mol Med"],"abstract":"<jats:title>Abstract<\/jats:title>\n                  <jats:sec>\n                    <jats:title>Background<\/jats:title>\n                    <jats:p>Human T-lymphotropic virus type 1 (HTLV-1) infects up to ten million people worldwide and is associated with inflammatory diseases, including HTLV-1-associated myelopathy\/tropical spastic paraparesis (HAM\/TSP). Individuals with HAM\/TSP are prone to pulmonary complications such as bronchiectasis, characterized by sustained mononuclear cell infiltration and elevated inflammatory mediators in bronchoalveolar lavage fluid. However, the epithelial mechanisms linking HTLV-1 exposure to lung inflammation remain poorly defined.<\/jats:p>\n                  <\/jats:sec>\n                  <jats:sec>\n                    <jats:title>Methods<\/jats:title>\n                    <jats:p>\n                      To study epithelial signaling in response to HTLV-1 exposure, human alveolar epithelial A549 cells were co-cultured with HTLV-1-infected (MT-2 or MT-4 cells) T cells\/supernatants or uninfected (Jurkat) T cells. Transcriptomic changes were assessed by RNA sequencing and pathway enrichment analyses, with key mediators validated by RT-qPCR. NF-\u03baB dependency was evaluated using CRISPR\/Cas9-mediated knockout of NF-\u03baB RelA\/p65. Functional consequences of epithelial activation were assessed using monocyte chemotaxis and differentiation assays in THP-1 cells and primary human monocytes.\n                      <jats:italic>In vivo<\/jats:italic>\n                      relevance was examined through integrative cross-omics analyses combining our own and publicly available bulk and single-cell transcriptomics, epigenomics, viral interactomics, and multi-ancestry genome-wide association studies (GWAS).\n                    <\/jats:p>\n                  <\/jats:sec>\n                  <jats:sec>\n                    <jats:title>Results<\/jats:title>\n                    <jats:p>\n                      HTLV-1 exposure induced a robust epithelial antiviral and inflammatory transcriptional program in A549 cells, predominantly regulated by NF-\u03baB signaling. Among the most strongly upregulated genes in A549 MT-2 co-cultures were the monocyte chemoattractant\n                      <jats:italic>MCP-1<\/jats:italic>\n                      \/\n                      <jats:italic>CCL2<\/jats:italic>\n                      and the macrophage differentiation factor\n                      <jats:italic>CSF1<\/jats:italic>\n                      , as confirmed by RT-qPCR. CRISPR\/Cas9-mediated knockout of NF-\u03baB RelA\/p65 demonstrated that CSF-1 induction is mechanistically dependent on NF-\u03baB activation. Supernatants from HTLV-1-exposed epithelial cells promoted monocyte chemotaxis and macrophage differentiation in THP-1 cells and primary human monocytes. Transcriptomic data of people living with HTLV-1, HAM\/TSP patients and idiopathic pulmonary fibrosis patients confirm\n                      <jats:italic>in vivo<\/jats:italic>\n                      expression of the\n                      <jats:italic>in vitro<\/jats:italic>\n                      gene signature, whereas single cell RNA-seq identified a unique myeloid subset in human lung, characterized by co-expression of\n                      <jats:italic>CCL2\/ISG15\/CXCL10.<\/jats:italic>\n                      Finally, GWAS analyses revealed ancestry-specific associations (\n                      <jats:italic>CCL2<\/jats:italic>\n                      for European and\n                      <jats:italic>CSF1<\/jats:italic>\n                      for African ancestry).\n                    <\/jats:p>\n                  <\/jats:sec>\n                  <jats:sec>\n                    <jats:title>Conclusions<\/jats:title>\n                    <jats:p>\n                      We report an\n                      <jats:italic>in vitro<\/jats:italic>\n                      co-culture model that recapitulates HTLV-1-triggered lung inflammation through RelA\/NF-kB-dependent release of pro-inflammatory cytokines and chemokines resulting in monocyte chemotaxis, activation and differentiation. This epithelial-myeloid inflammatory axis provides a relevant\n                      <jats:italic>in vitro<\/jats:italic>\n                      model that recapitulates\n                      <jats:italic>in vivo<\/jats:italic>\n                      HTLV-1-associated lung pathology.\n                    <\/jats:p>\n                  <\/jats:sec>","DOI":"10.1186\/s10020-026-01482-9","type":"journal-article","created":{"date-parts":[[2026,4,23]],"date-time":"2026-04-23T06:57:41Z","timestamp":1776927461000},"update-policy":"https:\/\/doi.org\/10.1007\/springer_crossmark_policy","source":"Crossref","is-referenced-by-count":0,"title":["Integrated in vitro and multi-cohort cross-omics analysis of HTLV-1-associated lung pathology reveals a RelA-dependent mechanism for monocyte recruitment and differentiation"],"prefix":"10.1186","volume":"32","author":[{"given":"Cl\u00e9ment J. F.","family":"Heymann","sequence":"first","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Mieke","family":"Gouwy","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Robin","family":"Hermans","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Jean-Claude","family":"Twizere","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Tatiane","family":"Assone","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Jorge","family":"Casseb","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Isaac","family":"Racine","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Isabelle","family":"Cleynen","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Edward L.","family":"Murphy","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Roberta","family":"Bruhn","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Dominique","family":"Schols","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Evelien","family":"Vanderlinden","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Johan","family":"Van Weyenbergh","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]}],"member":"297","published-online":{"date-parts":[[2026,4,23]]},"reference":[{"key":"1482_CR1","doi-asserted-by":"publisher","first-page":"D322","DOI":"10.1093\/nar\/gkl799","volume":"35","author":"G Alterovitz","year":"2007","unstructured":"Alterovitz G, Xiang M, Mohan M, Ramoni MF. GO PaD: the gene ontology partition database. Nucleic Acids Res. 2007;35:D322-327. https:\/\/doi.org\/10.1093\/nar\/gkl799.","journal-title":"Nucleic Acids Res"},{"key":"1482_CR2","doi-asserted-by":"publisher","first-page":"1128","DOI":"10.1038\/s41591-018-0090-y","volume":"24","author":"V Anathy","year":"2018","unstructured":"Anathy V, Lahue KG, Chapman DG, Chia SB, Casey DT, Aboushousha R, et al. Reducing protein oxidation reverses lung fibrosis. Nat Med. 2018;24:1128\u201335. https:\/\/doi.org\/10.1038\/s41591-018-0090-y.","journal-title":"Nat Med"},{"key":"1482_CR3","doi-asserted-by":"publisher","first-page":"293","DOI":"10.1186\/s12974-022-02658-w","volume":"19","author":"T Assone","year":"2022","unstructured":"Assone T, Menezes SM, de Toledo Gon\u00e7alves F, Folgosi VA, da Silva Prates G, Dierckx T, et al. Systemic cytokines and GlycA discriminate disease status and predict corticosteroid response in HTLV-1-associated neuroinflammation. J Neuroinflammation. 2022;19:293. https:\/\/doi.org\/10.1186\/s12974-022-02658-w.","journal-title":"J Neuroinflammation"},{"key":"1482_CR4","doi-asserted-by":"publisher","first-page":"1416476","DOI":"10.3389\/fimmu.2024.1416476","volume":"15","author":"T Assone","year":"2024","unstructured":"Assone T, Menezes SM, Gon\u00e7alves FT, Folgosi VA, Braz M, Smid J, et al. IL-10 predicts incident neuroinflammatory disease and proviral load dynamics in a large Brazilian cohort of people living with human T-lymphotropic virus type 1. Front Immunol. 2024;15:1416476. https:\/\/doi.org\/10.3389\/fimmu.2024.1416476.","journal-title":"Front Immunol"},{"key":"1482_CR5","doi-asserted-by":"publisher","first-page":"11","DOI":"10.1016\/j.cytogfr.2018.10.003","volume":"44","author":"N Au-Yeung","year":"2018","unstructured":"Au-Yeung N, Horvath CM. Transcriptional and chromatin regulation in interferon and innate antiviral gene expression. Cytokine Growth Factor Rev. 2018;44:11\u20137. https:\/\/doi.org\/10.1016\/j.cytogfr.2018.10.003.","journal-title":"Cytokine Growth Factor Rev"},{"key":"1482_CR6","doi-asserted-by":"publisher","first-page":"4064","DOI":"10.4049\/jimmunol.163.7.4064","volume":"163","author":"N Azimi","year":"1999","unstructured":"Azimi N, Jacobson S, Leist T, Waldmann TA. Involvement of IL-15 in the pathogenesis of human T lymphotropic virus type I-associated myelopathy\/tropical spastic paraparesis: implications for therapy with a monoclonal antibody directed to the IL-2\/15R beta receptor. J Immunol. 1999;163:4064\u201372.","journal-title":"J Immunol"},{"key":"1482_CR7","doi-asserted-by":"publisher","first-page":"2114","DOI":"10.1093\/bioinformatics\/btu170","volume":"30","author":"AM Bolger","year":"2014","unstructured":"Bolger AM, Lohse M, Usadel B. Trimmomatic: a flexible trimmer for Illumina sequence data. Bioinformatics. 2014;30:2114\u201320. https:\/\/doi.org\/10.1093\/bioinformatics\/btu170.","journal-title":"Bioinformatics"},{"key":"1482_CR8","doi-asserted-by":"publisher","first-page":"769214","DOI":"10.1155\/2013\/769214","volume":"2013","author":"CE Boorsma","year":"2013","unstructured":"Boorsma CE, Draijer C, Melgert BN. Macrophage heterogeneity in respiratory diseases. Mediators Inflamm. 2013;2013:769214. https:\/\/doi.org\/10.1155\/2013\/769214.","journal-title":"Mediators Inflamm"},{"key":"1482_CR9","doi-asserted-by":"publisher","first-page":"2195","DOI":"10.1128\/jvi.02735-15","volume":"90","author":"MF de Castro-Amarante","year":"2015","unstructured":"de Castro-Amarante MF, Pise-Masison CA, McKinnon K, Washington Parks R, Galli V, Omsland M, et al. Human T cell leukemia virus type 1 infection of the three monocyte subsets contributes to viral burden in humans. J Virol. 2015;90:2195\u2013207. https:\/\/doi.org\/10.1128\/jvi.02735-15.","journal-title":"J Virol"},{"key":"1482_CR10","doi-asserted-by":"publisher","first-page":"153","DOI":"10.1186\/s12931-018-0857-1","volume":"19","author":"MJ Cecchini","year":"2018","unstructured":"Cecchini MJ, Hosein K, Howlett CJ, Joseph M, Mura M. Comprehensive gene expression profiling identifies distinct and overlapping transcriptional profiles in non-specific interstitial pneumonia and idiopathic pulmonary fibrosis. Respir Res. 2018;19:153. https:\/\/doi.org\/10.1186\/s12931-018-0857-1.","journal-title":"Respir Res"},{"key":"1482_CR11","doi-asserted-by":"publisher","unstructured":"Chen YC, Lai YS, Hsuuw YD, Chang KT. Withholding of M-CSF supplement reprograms macrophages to M2-like via endogenous CSF-1 activation. Int J Mol Sci 2021;22. https:\/\/doi.org\/10.3390\/ijms22073532.","DOI":"10.3390\/ijms22073532"},{"key":"1482_CR12","doi-asserted-by":"publisher","first-page":"625","DOI":"10.7326\/0003-4819-109-8-625","volume":"109","author":"LJ Couderc","year":"1988","unstructured":"Couderc LJ, Caubarrere I, Venet A, Magdeleine J, Jouanelle A, Danon F, et al. Bronchoalveolar lymphocytosis in patients with tropical spastic paraparesis associated with human T-cell lymphotropic virus type 1 (HTLV-1). Clinical, immunologic, and cytologic studies. Ann Intern Med. 1988;109:625\u20138. https:\/\/doi.org\/10.7326\/0003-4819-109-8-625.","journal-title":"Ann Intern Med"},{"key":"1482_CR13","doi-asserted-by":"publisher","first-page":"8277","DOI":"10.1128\/jvi.74.18.8277-8285.2000","volume":"74","author":"S Datta","year":"2000","unstructured":"Datta S, Kothari NH, Fan H. In vivo genomic footprinting of the human T-cell leukemia virus type 1 (HTLV-1) long terminal repeat enhancer sequences in HTLV-1-infected human T-cell lines with different levels of Tax I activity. J Virol. 2000;74:8277\u201385. https:\/\/doi.org\/10.1128\/jvi.74.18.8277-8285.2000.","journal-title":"J Virol"},{"key":"1482_CR14","doi-asserted-by":"publisher","first-page":"48","DOI":"10.1136\/thoraxjnl-2013-204596","volume":"70","author":"DJ DePianto","year":"2015","unstructured":"DePianto DJ, Chandriani S, Abbas AR, Jia G, N\u2019Diaye EN, Caplazi P, et al. Heterogeneous gene expression signatures correspond to distinct lung pathologies and biomarkers of disease severity in idiopathic pulmonary fibrosis. Thorax. 2015;70:48\u201356. https:\/\/doi.org\/10.1136\/thoraxjnl-2013-204596.","journal-title":"Thorax"},{"key":"1482_CR15","doi-asserted-by":"publisher","first-page":"162","DOI":"10.1093\/infdis\/160.1.162","volume":"160","author":"C Desgranges","year":"1989","unstructured":"Desgranges C, Bechet JM, Couderc LJ, Caubarrere I, Vernant JC. Detection of HTLV-1 DNA by polymerase chain reaction in alveolar lymphocytes of patients with tropical spastic paraparesis. J Infect Dis. 1989;160:162\u20133. https:\/\/doi.org\/10.1093\/infdis\/160.1.162.","journal-title":"J Infect Dis"},{"key":"1482_CR16","doi-asserted-by":"publisher","first-page":"e0261864","DOI":"10.1371\/journal.pone.0261864","volume":"16","author":"ARN Dias","year":"2021","unstructured":"Dias ARN, Vieira WB, Normando VMF, Franco K, Falc\u00e3o ASC, de Sousa RCM, et al. Computed tomography with 6-year follow-up demonstrates the evolution of HTLV-1 related lung injuries: a cohort study. PLoS One. 2021;16:e0261864. https:\/\/doi.org\/10.1371\/journal.pone.0261864.","journal-title":"PLoS One"},{"key":"1482_CR17","doi-asserted-by":"publisher","first-page":"914498","DOI":"10.3389\/fimmu.2022.914498","volume":"13","author":"RN Dias \u00c1","year":"2022","unstructured":"Dias \u00c1 RN, Falc\u00e3o LFM, Quaresma JAS. An overview of human T-lymphotropic virus type 1 lung injury. Front Immunol. 2022;13:914498. https:\/\/doi.org\/10.3389\/fimmu.2022.914498.","journal-title":"Front Immunol"},{"key":"1482_CR18","doi-asserted-by":"publisher","first-page":"57","DOI":"10.1038\/nature11247","volume":"489","author":"Consortium, E.P.","year":"2012","unstructured":"Consortium, E.P. An integrated encyclopedia of DNA elements in the human genome. Nature. 2012;489:57\u201374. https:\/\/doi.org\/10.1038\/nature11247.","journal-title":"Nature"},{"key":"1482_CR19","doi-asserted-by":"publisher","first-page":"1","DOI":"10.1186\/s12977-020-00543-z","volume":"18","author":"L Einsiedel","year":"2021","unstructured":"Einsiedel L, Chiong F, Jersmann H, Taylor GP. Human T-cell leukaemia virus type 1 associated pulmonary disease: clinical and pathological features of an under-recognised complication of HTLV-1 infection. Retrovirology. 2021;18:1. https:\/\/doi.org\/10.1186\/s12977-020-00543-z.","journal-title":"Retrovirology"},{"key":"1482_CR20","doi-asserted-by":"publisher","first-page":"43","DOI":"10.1093\/cid\/cir766","volume":"54","author":"L Einsiedel","year":"2012","unstructured":"Einsiedel L, Fernandes L, Spelman T, Steinfort D, Gotuzzo E. Bronchiectasis is associated with human T-lymphotropic virus 1 infection in an Indigenous Australian population. Clin Infect Dis. 2012;54:43\u201350. https:\/\/doi.org\/10.1093\/cid\/cir766.","journal-title":"Clin Infect Dis"},{"key":"1482_CR21","doi-asserted-by":"publisher","first-page":"2400","DOI":"10.1182\/blood-2008-02-138529","volume":"112","author":"Y Enose-Akahata","year":"2008","unstructured":"Enose-Akahata Y, Oh U, Grant C, Jacobson S. Retrovirally induced CTL degranulation mediated by IL-15 expression and infection of mononuclear phagocytes in patients with HTLV-I-associated neurologic disease. Blood. 2008;112:2400\u201310. https:\/\/doi.org\/10.1182\/blood-2008-02-138529.","journal-title":"Blood"},{"key":"1482_CR22","doi-asserted-by":"publisher","first-page":"1383","DOI":"10.1002\/acn3.50820","volume":"6","author":"Y Enose-Akahata","year":"2019","unstructured":"Enose-Akahata Y, Oh U, Ohayon J, Billioux BJ, Massoud R, Bryant BR, et al. Clinical trial of a humanized anti-IL-2\/IL-15 receptor \u03b2 chain in HAM\/TSP. Ann Clin Transl Neurol. 2019;6:1383\u201394. https:\/\/doi.org\/10.1002\/acn3.50820.","journal-title":"Ann Clin Transl Neurol"},{"key":"1482_CR23","doi-asserted-by":"publisher","first-page":"eadk5041","DOI":"10.1126\/sciimmunol.adk5041","volume":"10","author":"A Farhat","year":"2025","unstructured":"Farhat A, Radhouani M, Deckert F, Zahalka S, Pimenov L, Fokina A, et al. An aging bone marrow exacerbates lung fibrosis by fueling profibrotic macrophage persistence. Sci Immunol. 2025;10:eadk5041. https:\/\/doi.org\/10.1126\/sciimmunol.adk5041.","journal-title":"Sci Immunol"},{"key":"1482_CR24","doi-asserted-by":"publisher","first-page":"5245","DOI":"10.4049\/jimmunol.178.8.5245","volume":"178","author":"AJ Fleetwood","year":"2007","unstructured":"Fleetwood AJ, Lawrence T, Hamilton JA, Cook AD. Granulocyte-macrophage colony-stimulating factor (CSF) and macrophage CSF-dependent macrophage phenotypes display differences in cytokine profiles and transcription factor activities: implications for CSF blockade in inflammation. J Immunol. 2007;178:5245\u201352. https:\/\/doi.org\/10.4049\/jimmunol.178.8.5245.","journal-title":"J Immunol"},{"key":"1482_CR25","doi-asserted-by":"publisher","unstructured":"Franz\u00e9n O, Gan LM, Bj\u00f6rkegren JLM. PanglaoDB: a web server for exploration of mouse and human single-cell RNA sequencing data. Database (Oxford) 2019. https:\/\/doi.org\/10.1093\/database\/baz046.","DOI":"10.1093\/database\/baz046"},{"key":"1482_CR26","doi-asserted-by":"publisher","first-page":"388","DOI":"10.3389\/fmicb.2012.00388","volume":"3","author":"A Gessain","year":"2012","unstructured":"Gessain A, Cassar O. Epidemiological aspects and world distribution of HTLV-1 infection. Front Microbiol. 2012;3:388. https:\/\/doi.org\/10.3389\/fmicb.2012.00388.","journal-title":"Front Microbiol"},{"key":"1482_CR27","doi-asserted-by":"publisher","first-page":"407","DOI":"10.1016\/s0140-6736(85)92734-5","volume":"2","author":"A Gessain","year":"1985","unstructured":"Gessain A, Barin F, Vernant JC, Gout O, Maurs L, Calender A, et al. Antibodies to human T-lymphotropic virus type-I in patients with tropical spastic paraparesis. Lancet. 1985;2:407\u201310. https:\/\/doi.org\/10.1016\/s0140-6736(85)92734-5.","journal-title":"Lancet"},{"key":"1482_CR28","doi-asserted-by":"publisher","first-page":"569","DOI":"10.1164\/rccm.201010-1719OC","volume":"184","author":"MA Gibbons","year":"2011","unstructured":"Gibbons MA, MacKinnon AC, Ramachandran P, Dhaliwal K, Duffin R, Phythian-Adams AT, et al. Ly6Chi monocytes direct alternatively activated profibrotic macrophage regulation of lung fibrosis. Am J Respir Crit Care Med. 2011;184:569\u201381. https:\/\/doi.org\/10.1164\/rccm.201010-1719OC.","journal-title":"Am J Respir Crit Care Med"},{"key":"1482_CR29","doi-asserted-by":"publisher","first-page":"485","DOI":"10.1124\/mol.108.045146","volume":"74","author":"M Gouwy","year":"2008","unstructured":"Gouwy M, Struyf S, Noppen S, Schutyser E, Springael JY, Parmentier M, et al. Synergy between coproduced CC and CXC chemokines in monocyte chemotaxis through receptor-mediated events. Mol Pharmacol. 2008;74:485\u201395. https:\/\/doi.org\/10.1124\/mol.108.045146.","journal-title":"Mol Pharmacol"},{"key":"1482_CR30","doi-asserted-by":"publisher","first-page":"D380","DOI":"10.1093\/nar\/gkx1013","volume":"46","author":"H Han","year":"2018","unstructured":"Han H, Cho JW, Lee S, Yun A, Kim H, Bae D, et al. TRRUST v2: an expanded reference database of human and mouse transcriptional regulatory interactions. Nucleic Acids Res. 2018;46:D380-d386. https:\/\/doi.org\/10.1093\/nar\/gkx1013.","journal-title":"Nucleic Acids Res"},{"key":"1482_CR31","doi-asserted-by":"publisher","first-page":"686","DOI":"10.1038\/nri3739","volume":"14","author":"MJ Holtzman","year":"2014","unstructured":"Holtzman MJ, Byers DE, Alexander-Brett J, Wang X. The role of airway epithelial cells and innate immune cells in chronic respiratory disease. Nat Rev Immunol. 2014;14:686\u201398. https:\/\/doi.org\/10.1038\/nri3739.","journal-title":"Nat Rev Immunol"},{"key":"1482_CR32","doi-asserted-by":"publisher","first-page":"258","DOI":"10.1186\/s12879-015-1002-0","volume":"15","author":"S Honarbakhsh","year":"2015","unstructured":"Honarbakhsh S, Taylor GP. High prevalence of bronchiectasis is linked to HTLV-1-associated inflammatory disease. BMC Infect Dis. 2015;15:258. https:\/\/doi.org\/10.1186\/s12879-015-1002-0.","journal-title":"BMC Infect Dis"},{"key":"1482_CR33","unstructured":"Menezes S. Identification of novel biomarkers and therapeutic targets in HTLV-1 associated neuroinflammation (HAM\/TSP): A target gene and cell-specific study of interferon response 2018. https:\/\/lirias.kuleuven.be\/handle\/123456789\/631004."},{"key":"1482_CR34","doi-asserted-by":"publisher","first-page":"470","DOI":"10.1016\/j.it.2011.05.001","volume":"32","author":"MA Ingersoll","year":"2011","unstructured":"Ingersoll MA, Platt AM, Potteaux S, Randolph GJ. Monocyte trafficking in acute and chronic inflammation. Trends Immunol. 2011;32:470\u20137. https:\/\/doi.org\/10.1016\/j.it.2011.05.001.","journal-title":"Trends Immunol"},{"key":"1482_CR35","doi-asserted-by":"publisher","first-page":"51","DOI":"10.1016\/j.cellimm.2013.01.010","volume":"281","author":"M Jaguin","year":"2013","unstructured":"Jaguin M, Houlbert N, Fardel O, Lecureur V. Polarization profiles of human M-CSF-generated macrophages and comparison of M1-markers in classically activated macrophages from GM-CSF and M-CSF origin. Cell Immunol. 2013;281:51\u201361. https:\/\/doi.org\/10.1016\/j.cellimm.2013.01.010.","journal-title":"Cell Immunol"},{"key":"1482_CR36","doi-asserted-by":"publisher","unstructured":"Joshi N, Watanabe S, Verma R, Jablonski RP, Chen CI, Cheresh P, Markov NS, Reyfman PA, McQuattie-Pimentel AC, Sichizya L. A spatially restricted fibrotic niche in pulmonary fibrosis is sustained by M-CSF\/M-CSFR signalling in monocyte-derived alveolar macrophages. Eur Respir J 2020;55 https:\/\/doi.org\/10.1183\/13993003.00646-2019","DOI":"10.1183\/13993003.00646-2019"},{"key":"1482_CR37","doi-asserted-by":"publisher","first-page":"12673","DOI":"10.1074\/jbc.M116.721217","volume":"291","author":"V Kadiyala","year":"2016","unstructured":"Kadiyala V, Sasse SK, Altonsy MO, Berman R, Chu HW, Phang TL, et al. Cistrome-based cooperation between airway epithelial glucocorticoid receptor and NF-\u03baB orchestrates anti-inflammatory effects. J Biol Chem. 2016;291:12673\u201387. https:\/\/doi.org\/10.1074\/jbc.M116.721217.","journal-title":"J Biol Chem"},{"key":"1482_CR38","doi-asserted-by":"publisher","first-page":"60","DOI":"10.1016\/s0140-6736(21)02442-9","volume":"399","author":"K Kamoi","year":"2022","unstructured":"Kamoi K, Uchimaru K, Tojo A, Watanabe T, Ohno-Matsui K. HTLV-1 uveitis and Graves\u2019 disease presenting with sudden onset of blurred vision. Lancet. 2022;399:60. https:\/\/doi.org\/10.1016\/s0140-6736(21)02442-9.","journal-title":"Lancet"},{"key":"1482_CR39","doi-asserted-by":"publisher","first-page":"D353","DOI":"10.1093\/nar\/gkw1092","volume":"45","author":"M Kanehisa","year":"2017","unstructured":"Kanehisa M, Furumichi M, Tanabe M, Sato Y, Morishima K. KEGG: new perspectives on genomes, pathways, diseases and drugs. Nucleic Acids Res. 2017;45:D353-d361. https:\/\/doi.org\/10.1093\/nar\/gkw1092.","journal-title":"Nucleic Acids Res"},{"key":"1482_CR40","doi-asserted-by":"publisher","first-page":"138","DOI":"10.1002\/jmv.1890380212","volume":"38","author":"H Kawai","year":"1992","unstructured":"Kawai H, Inui T, Kashiwagi S, Tsuchihashi T, Masuda K, Kondo A, et al. HTLV-I infection in patients with autoimmune thyroiditis (Hashimoto\u2019s thyroiditis). J Med Virol. 1992;38:138\u201341. https:\/\/doi.org\/10.1002\/jmv.1890380212.","journal-title":"J Med Virol"},{"key":"1482_CR41","doi-asserted-by":"publisher","first-page":"85","DOI":"10.1007\/bf00270582","volume":"73","author":"H Kawai","year":"1995","unstructured":"Kawai H, Yokoi K, Akaike M, Kunishige M, Abe M, Tanouchi Y, et al. Graves\u2019 disease in HTLV-I carriers. J Mol Med (Berl). 1995;73:85\u20138. https:\/\/doi.org\/10.1007\/bf00270582.","journal-title":"J Mol Med (Berl)"},{"key":"1482_CR42","doi-asserted-by":"publisher","first-page":"907","DOI":"10.1038\/s41587-019-0201-4","volume":"37","author":"D Kim","year":"2019","unstructured":"Kim D, Paggi JM, Park C, Bennett C, Salzberg SL. Graph-based genome alignment and genotyping with HISAT2 and HISAT-genotype. Nat Biotechnol. 2019;37:907\u201315. https:\/\/doi.org\/10.1038\/s41587-019-0201-4.","journal-title":"Nat Biotechnol"},{"key":"1482_CR43","doi-asserted-by":"publisher","first-page":"924","DOI":"10.1186\/s12864-015-2170-4","volume":"16","author":"S Kim","year":"2015","unstructured":"Kim S, Herazo-Maya JD, Kang DD, Juan-Guardela BM, Tedrow J, Martinez FJ, et al. Integrative phenotyping framework (iPF): integrative clustering of multiple omics data identifies novel lung disease subphenotypes. BMC Genomics. 2015;16:924. https:\/\/doi.org\/10.1186\/s12864-015-2170-4.","journal-title":"BMC Genomics"},{"key":"1482_CR44","doi-asserted-by":"publisher","first-page":"281","DOI":"10.18926\/amo\/31916","volume":"40","author":"I Kimura","year":"1986","unstructured":"Kimura I, Tsubota T, Tada S, Sogawa J. Presence of antibodies against adult T cell leukemia antigen in the patients with chronic respiratory diseases. Acta Med Okayama. 1986;40:281\u20134. https:\/\/doi.org\/10.18926\/amo\/31916.","journal-title":"Acta Med Okayama"},{"key":"1482_CR45","doi-asserted-by":"publisher","first-page":"74","DOI":"10.1164\/rccm.202003-0669OC","volume":"204","author":"M Kreuter","year":"2021","unstructured":"Kreuter M, Lee JS, Tzouvelekis A, Oldham JM, Molyneaux PL, Weycker D, et al. Monocyte count as a prognostic biomarker in patients with idiopathic pulmonary fibrosis. Am J Respir Crit Care Med. 2021;204:74\u201381. https:\/\/doi.org\/10.1164\/rccm.202003-0669OC.","journal-title":"Am J Respir Crit Care Med"},{"key":"1482_CR46","doi-asserted-by":"publisher","first-page":"W90","DOI":"10.1093\/nar\/gkw377","volume":"44","author":"MV Kuleshov","year":"2016","unstructured":"Kuleshov MV, Jones MR, Rouillard AD, Fernandez NF, Duan Q, Wang Z, et al. Enrichr: a comprehensive gene set enrichment analysis web server 2016 update. Nucleic Acids Res. 2016;44:W90-97. https:\/\/doi.org\/10.1093\/nar\/gkw377.","journal-title":"Nucleic Acids Res"},{"key":"1482_CR47","doi-asserted-by":"publisher","first-page":"1557","DOI":"10.1086\/508899","volume":"194","author":"N Kwaan","year":"2006","unstructured":"Kwaan N, Lee TH, Chafets DM, Nass C, Newman B, Smith J, et al. Long-term variations in human T lymphotropic virus (HTLV)-I and HTLV-II proviral loads and association with clinical data. J Infect Dis. 2006;194:1557\u201364. https:\/\/doi.org\/10.1086\/508899.","journal-title":"J Infect Dis"},{"key":"1482_CR48","doi-asserted-by":"publisher","first-page":"1366","DOI":"10.1038\/s41467-018-03751-6","volume":"9","author":"A Lachmann","year":"2018","unstructured":"Lachmann A, Torre D, Keenan AB, Jagodnik KM, Lee HJ, Wang L, et al. Massive mining of publicly available RNA-seq data from human and mouse. Nat Commun. 2018;9:1366. https:\/\/doi.org\/10.1038\/s41467-018-03751-6.","journal-title":"Nat Commun"},{"key":"1482_CR49","doi-asserted-by":"publisher","first-page":"985","DOI":"10.3389\/fmicb.2018.00985","volume":"9","author":"FE Leal","year":"2018","unstructured":"Leal FE, Menezes SM, Costa EAS, Brailey PM, Gama L, Segurado AC, et al. Comprehensive antiretroviral restriction factor profiling reveals the evolutionary imprint of the ex vivo and in vivo IFN-\u03b2 response in HTLV-1-associated neuroinflammation. Front Microbiol. 2018;9:985. https:\/\/doi.org\/10.3389\/fmicb.2018.00985.","journal-title":"Front Microbiol"},{"key":"1482_CR50","doi-asserted-by":"publisher","first-page":"e0007821","DOI":"10.1128\/cmr.00078-21","volume":"35","author":"N Legrand","year":"2022","unstructured":"Legrand N, McGregor S, Bull R, Bajis S, Valencia BM, Ronnachit A, et al. Clinical and public health implications of human T-lymphotropic virus type 1 infection. Clin Microbiol Rev. 2022;35:e0007821. https:\/\/doi.org\/10.1128\/cmr.00078-21.","journal-title":"Clin Microbiol Rev"},{"key":"1482_CR51","doi-asserted-by":"publisher","first-page":"e47","DOI":"10.1093\/nar\/gkz114","volume":"47","author":"Y Liao","year":"2019","unstructured":"Liao Y, Smyth GK, Shi W. The R package Rsubread is easier, faster, cheaper and better for alignment and quantification of RNA sequencing reads. Nucleic Acids Res. 2019;47:e47. https:\/\/doi.org\/10.1093\/nar\/gkz114.","journal-title":"Nucleic Acids Res"},{"key":"1482_CR52","doi-asserted-by":"publisher","first-page":"550","DOI":"10.1186\/s13059-014-0550-8","volume":"15","author":"MI Love","year":"2014","unstructured":"Love MI, Huber W, Anders S. Moderated estimation of fold change and dispersion for RNA-seq data with DESeq2. Genome Biol. 2014;15:550. https:\/\/doi.org\/10.1186\/s13059-014-0550-8.","journal-title":"Genome Biol"},{"key":"1482_CR53","doi-asserted-by":"publisher","first-page":"e57912","DOI":"10.15252\/embr.202357912","volume":"24","author":"VG Magalh\u00e3es","year":"2023","unstructured":"Magalh\u00e3es VG, Lukassen S, Drechsler M, Loske J, Burkart SS, W\u00fcst S, et al. Immune-epithelial cell cross-talk enhances antiviral responsiveness to SARS-CoV-2 in children. EMBO Rep. 2023;24:e57912. https:\/\/doi.org\/10.15252\/embr.202357912.","journal-title":"EMBO Rep"},{"key":"1482_CR54","doi-asserted-by":"publisher","first-page":"166","DOI":"10.1056\/NEJMra0905980","volume":"363","author":"TA Manolio","year":"2010","unstructured":"Manolio TA. Genomewide association studies and assessment of the risk of disease. N Engl J Med. 2010;363:166\u201376. https:\/\/doi.org\/10.1056\/NEJMra0905980.","journal-title":"N Engl J Med"},{"key":"1482_CR55","doi-asserted-by":"publisher","first-page":"2602","DOI":"10.4049\/jimmunol.166.4.2602","volume":"166","author":"JM Mariner","year":"2001","unstructured":"Mariner JM, Lantz V, Waldmann TA, Azimi N. Human T cell lymphotropic virus type I Tax activates IL-15R alpha gene expression through an NF-kappa B site. J Immunol. 2001;166:2602\u20139. https:\/\/doi.org\/10.4049\/jimmunol.166.4.2602.","journal-title":"J Immunol"},{"key":"1482_CR56","doi-asserted-by":"publisher","first-page":"397","DOI":"10.1046\/j.1365-2249.2003.02240.x","volume":"133","author":"W Matsuyama","year":"2003","unstructured":"Matsuyama W, Kawabata M, Mizoguchi A, Iwami F, Wakimoto J, Osame M. Influence of human T lymphotrophic virus type I on cryptogenic fibrosing alveolitis - HTLV-I associated fibrosing alveolitis: proposal of a new clinical entity. Clin Exp Immunol. 2003;133:397\u2013403. https:\/\/doi.org\/10.1046\/j.1365-2249.2003.02240.x.","journal-title":"Clin Exp Immunol"},{"key":"1482_CR57","doi-asserted-by":"publisher","first-page":"97","DOI":"10.3389\/fimmu.2017.00097","volume":"8","author":"SM Menezes","year":"2017","unstructured":"Menezes SM, Leal FE, Dierckx T, Khouri R, Decanine D, Silva-Santos G, et al. A Fas(hi) lymphoproliferative phenotype reveals non-apoptotic Fas signaling in HTLV-1-associated neuroinflammation. Front Immunol. 2017;8:97. https:\/\/doi.org\/10.3389\/fimmu.2017.00097.","journal-title":"Front Immunol"},{"key":"1482_CR58","doi-asserted-by":"publisher","first-page":"18","DOI":"10.1186\/1742-2094-11-18","volume":"11","author":"SM Menezes","year":"2014","unstructured":"Menezes SM, Decanine D, Brassat D, Khouri R, Schnitman SV, Kruschewsky R, et al. CD80+ and CD86+ B cells as biomarkers and possible therapeutic targets in HTLV-1 associated myelopathy\/tropical spastic paraparesis and multiple sclerosis. J Neuroinflammation. 2014;11:18. https:\/\/doi.org\/10.1186\/1742-2094-11-18.","journal-title":"J Neuroinflammation"},{"key":"1482_CR59","doi-asserted-by":"publisher","first-page":"1039","DOI":"10.1002\/eji.202048793","volume":"51","author":"I Meyts","year":"2021","unstructured":"Meyts I, Casanova JL. Viral infections in humans and mice with genetic deficiencies of the type I IFN response pathway. Eur J Immunol. 2021;51:1039\u201361. https:\/\/doi.org\/10.1002\/eji.202048793.","journal-title":"Eur J Immunol"},{"key":"1482_CR60","doi-asserted-by":"publisher","first-page":"2044","DOI":"10.1158\/1078-0432.Ccr-12-3603","volume":"20","author":"A Mishra","year":"2014","unstructured":"Mishra A, Sullivan L, Caligiuri MA. Molecular pathways: interleukin-15 signaling in health and in cancer. Clin Cancer Res. 2014;20:2044\u201350. https:\/\/doi.org\/10.1158\/1078-0432.Ccr-12-3603.","journal-title":"Clin Cancer Res"},{"key":"1482_CR61","doi-asserted-by":"publisher","first-page":"149","DOI":"10.1136\/bjo.78.2.149","volume":"78","author":"M Mochizuki","year":"1994","unstructured":"Mochizuki M, Tajima K, Watanabe T, Yamaguchi K. Human T lymphotropic virus type 1 uveitis. Br J Ophthalmol. 1994;78:149\u201354. https:\/\/doi.org\/10.1136\/bjo.78.2.149.","journal-title":"Br J Ophthalmol"},{"key":"1482_CR62","doi-asserted-by":"publisher","first-page":"373","DOI":"10.1136\/bjophthalmol-2017-310658","volume":"102","author":"K Nakao","year":"2018","unstructured":"Nakao K, Abematsu N, Sakamoto T. Systemic diseases in patients with HTLV-1-associated uveitis. Br J Ophthalmol. 2018;102:373\u20136. https:\/\/doi.org\/10.1136\/bjophthalmol-2017-310658.","journal-title":"Br J Ophthalmol"},{"key":"1482_CR63","doi-asserted-by":"publisher","first-page":"2599","DOI":"10.2169\/internalmedicine.52.0845","volume":"52","author":"Y Nakayama","year":"2013","unstructured":"Nakayama Y, Yamazato Y, Tamayose M, Atsumi E, Yara S, Higa F, et al. Increased expression of HBZ and Foxp3 mRNA in bronchoalveolar lavage cells taken from human T-lymphotropic virus type 1-associated lung disorder patients. Intern Med. 2013;52:2599\u2013609. https:\/\/doi.org\/10.2169\/internalmedicine.52.0845.","journal-title":"Intern Med"},{"key":"1482_CR64","doi-asserted-by":"publisher","first-page":"1750","DOI":"10.1099\/jmm.0.033456-0","volume":"60","author":"Y Nakayama","year":"2011","unstructured":"Nakayama Y, Ishikawa C, Tamaki K, Senba M, Fujita J, Mori N. Interleukin-1 alpha produced by human T-cell leukaemia virus type I-infected T cells induces intercellular adhesion molecule-1 expression on lung epithelial cells. J Med Microbiol. 2011;60:1750\u201361. https:\/\/doi.org\/10.1099\/jmm.0.033456-0.","journal-title":"J Med Microbiol"},{"key":"1482_CR65","doi-asserted-by":"publisher","first-page":"1016","DOI":"10.1182\/blood-2008-03-136770","volume":"114","author":"M Nejmeddine","year":"2009","unstructured":"Nejmeddine M, Negi VS, Mukherjee S, Tanaka Y, Orth K, Taylor GP, et al. HTLV-1-Tax and ICAM-1 act on T-cell signal pathways to polarize the microtubule-organizing center at the virological synapse. Blood. 2009;114:1016\u201325. https:\/\/doi.org\/10.1182\/blood-2008-03-136770.","journal-title":"Blood"},{"key":"1482_CR66","doi-asserted-by":"publisher","first-page":"773","DOI":"10.1038\/s41587-019-0114-2","volume":"37","author":"AM Newman","year":"2019","unstructured":"Newman AM, Steen CB, Liu CL, Gentles AJ, Chaudhuri AA, Scherer F, et al. Determining cell type abundance and expression from bulk tissues with digital cytometry. Nat Biotechnol. 2019;37:773\u201382. https:\/\/doi.org\/10.1038\/s41587-019-0114-2.","journal-title":"Nat Biotechnol"},{"key":"1482_CR67","doi-asserted-by":"publisher","first-page":"117979","DOI":"10.1016\/j.lfs.2020.117979","volume":"256","author":"VMFP Normando","year":"2020","unstructured":"Normando VMFP, Dias \u00c1 RNM, da Silva AL, da Silva Pinto DP, de Souza Santos MCP, Rodrigues CLL, et al. HTLV-I induces lesions in the pulmonary system: a systematic review. Life Sci. 2020;256:117979. https:\/\/doi.org\/10.1016\/j.lfs.2020.117979.","journal-title":"Life Sci"},{"key":"1482_CR68","doi-asserted-by":"publisher","first-page":"11118","DOI":"10.1038\/s41598-018-29391-w","volume":"8","author":"M Omsland","year":"2018","unstructured":"Omsland M, Pise-Masison C, Fujikawa D, Galli V, Fenizia C, Parks RW, et al. Inhibition of Tunneling Nanotube (TNT) formation and Human T-cell Leukemia Virus Type 1 (HTLV-1) transmission by cytarabine. Sci Rep. 2018;8:11118. https:\/\/doi.org\/10.1038\/s41598-018-29391-w.","journal-title":"Sci Rep"},{"key":"1482_CR69","doi-asserted-by":"publisher","first-page":"4056","DOI":"10.1096\/fj.201600373R","volume":"30","author":"X Peng","year":"2016","unstructured":"Peng X, Moore M, Mathur A, Zhou Y, Sun H, Gan Y, et al. Plexin C1 deficiency permits synaptotagmin 7-mediated macrophage migration and enhances mammalian lung fibrosis. FASEB J. 2016;30:4056\u201370. https:\/\/doi.org\/10.1096\/fj.201600373R.","journal-title":"FASEB J"},{"key":"1482_CR70","doi-asserted-by":"publisher","first-page":"631235","DOI":"10.3389\/fimmu.2021.631235","volume":"12","author":"T Plant\u00e9-Bordeneuve","year":"2021","unstructured":"Plant\u00e9-Bordeneuve T, Pilette C, Froidure A. The epithelial-immune crosstalk in pulmonary fibrosis. Front Immunol. 2021;12:631235. https:\/\/doi.org\/10.3389\/fimmu.2021.631235.","journal-title":"Front Immunol"},{"key":"1482_CR71","doi-asserted-by":"publisher","first-page":"622","DOI":"10.1164\/rccm.201712-2551OC","volume":"199","author":"A Prasse","year":"2019","unstructured":"Prasse A, Binder H, Schupp JC, Kayser G, Bargagli E, Jaeger B, et al. BAL cell gene expression is indicative of outcome and airway basal cell involvement in idiopathic pulmonary fibrosis. Am J Respir Crit Care Med. 2019;199:622\u201330. https:\/\/doi.org\/10.1164\/rccm.201712-2551OC.","journal-title":"Am J Respir Crit Care Med"},{"key":"1482_CR72","doi-asserted-by":"publisher","first-page":"e47","DOI":"10.1093\/nar\/gkv007","volume":"43","author":"ME Ritchie","year":"2015","unstructured":"Ritchie ME, Phipson B, Wu D, Hu Y, Law CW, Shi W, et al. Limma powers differential expression analyses for RNA-sequencing and microarray studies. Nucleic Acids Res. 2015;43:e47. https:\/\/doi.org\/10.1093\/nar\/gkv007.","journal-title":"Nucleic Acids Res"},{"key":"1482_CR73","doi-asserted-by":"publisher","first-page":"8470","DOI":"10.1038\/s41467-025-63325-1","volume":"16","author":"S Sarkis","year":"2025","unstructured":"Sarkis S, Gutowska A, Rahman MA, Schifanella L, Goldfarbmuren KC, Bissa M, et al. High expression of Rex-orf-I and HBZ mRNAs and bronchiectasis in lung of HTLV-1A\/C infected macaques. Nat Commun. 2025;16:8470. https:\/\/doi.org\/10.1038\/s41467-025-63325-1.","journal-title":"Nat Commun"},{"key":"1482_CR74","doi-asserted-by":"publisher","first-page":"497","DOI":"10.1016\/s2213-2600(18)30508-3","volume":"7","author":"MKD Scott","year":"2019","unstructured":"Scott MKD, Quinn K, Li Q, Carroll R, Warsinske H, Vallania F, et al. Increased monocyte count as a cellular biomarker for poor outcomes in fibrotic diseases: a retrospective, multicentre cohort study. Lancet Respir Med. 2019;7:497\u2013508. https:\/\/doi.org\/10.1016\/s2213-2600(18)30508-3.","journal-title":"Lancet Respir Med"},{"key":"1482_CR75","doi-asserted-by":"publisher","first-page":"762","DOI":"10.1038\/nri3070","volume":"11","author":"C Shi","year":"2011","unstructured":"Shi C, Pamer EG. Monocyte recruitment during infection and inflammation. Nat Rev Immunol. 2011;11:762\u201374. https:\/\/doi.org\/10.1038\/nri3070.","journal-title":"Nat Rev Immunol"},{"key":"1482_CR76","doi-asserted-by":"publisher","first-page":"1563","DOI":"10.1038\/s41591-023-02327-2","volume":"29","author":"L Sikkema","year":"2023","unstructured":"Sikkema L, Ram\u00edrez-Su\u00e1stegui C, Strobl DC, Gillett TE, Zappia L, Madissoon E, et al. An integrated cell atlas of the lung in health and disease. Nat Med. 2023;29:1563\u201377. https:\/\/doi.org\/10.1038\/s41591-023-02327-2.","journal-title":"Nat Med"},{"key":"1482_CR77","doi-asserted-by":"publisher","unstructured":"Da Silva SJ, Cabral-Castro MJ, Faria LC, Rosadas C, de Ara\u00fajo MFL, Dutra ACS, Yamano Y, Taylor G, Puccioni-Sohler M. CXCL-10 in cerebrospinal fluid detects neuroinflammation in HTLV-1-Associated myelopathy with high accuracy. Viruses 2025;17. https:\/\/doi.org\/10.3390\/v17010089","DOI":"10.3390\/v17010089"},{"key":"1482_CR78","doi-asserted-by":"publisher","first-page":"24","DOI":"10.1186\/s12865-024-00670-8","volume":"26","author":"S de Souza","year":"2025","unstructured":"de Souza S, Melo GA, Cal\u00f4ba C, Campos MCS, Pimenta JV, Dutra FF, et al. HTLV-1-infected cells drive the differentiation of monocytes into macrophages in vitro. BMC Immunol. 2025;26:24. https:\/\/doi.org\/10.1186\/s12865-024-00670-8.","journal-title":"BMC Immunol"},{"key":"1482_CR79","doi-asserted-by":"publisher","first-page":"574","DOI":"10.1016\/j.rmed.2007.11.007","volume":"102","author":"DP Steinfort","year":"2008","unstructured":"Steinfort DP, Brady S, Weisinger HS, Einsiedel L. Bronchiectasis in Central Australia: a young face to an old disease. Respir Med. 2008;102:574\u20138. https:\/\/doi.org\/10.1016\/j.rmed.2007.11.007.","journal-title":"Respir Med"},{"key":"1482_CR80","doi-asserted-by":"publisher","first-page":"27","DOI":"10.1111\/j.1440-1827.1994.tb02582.x","volume":"44","author":"K Sueyoshi","year":"1994","unstructured":"Sueyoshi K, Goto M, Johnosono M, Sato E, Shibata D. Anatomical distribution of HTLV-I proviral sequence in an autopsy case of HTLV-I associated myelopathy: a polymerase chain reaction study. Pathol Int. 1994;44:27\u201333. https:\/\/doi.org\/10.1111\/j.1440-1827.1994.tb02582.x.","journal-title":"Pathol Int"},{"key":"1482_CR81","doi-asserted-by":"publisher","first-page":"1220","DOI":"10.1016\/s0140-6736(87)91362-6","volume":"2","author":"M Sugimoto","year":"1987","unstructured":"Sugimoto M, Nakashima H, Watanabe S, Uyama E, Tanaka F, Ando M, et al. T-lymphocyte alveolitis in HTLV-I-associated myelopathy. Lancet. 1987;2:1220. https:\/\/doi.org\/10.1016\/s0140-6736(87)91362-6.","journal-title":"Lancet"},{"key":"1482_CR82","doi-asserted-by":"publisher","first-page":"D607","DOI":"10.1093\/nar\/gky1131","volume":"47","author":"D Szklarczyk","year":"2019","unstructured":"Szklarczyk D, Gable AL, Lyon D, Junge A, Wyder S, Huerta-Cepas J, et al. STRING v11: protein-protein association networks with increased coverage, supporting functional discovery in genome-wide experimental datasets. Nucleic Acids Res. 2019;47:D607-d613. https:\/\/doi.org\/10.1093\/nar\/gky1131.","journal-title":"Nucleic Acids Res"},{"key":"1482_CR83","doi-asserted-by":"publisher","first-page":"2110","DOI":"10.3389\/fmicb.2019.02110","volume":"10","author":"K Tamaki","year":"2019","unstructured":"Tamaki K, Sato T, Tsugawa J, Fujioka S, Yagishita N, Araya N, et al. Cerebrospinal fluid CXCL10 as a candidate surrogate marker for HTLV-1-associated myelopathy\/tropical spastic paraparesis. Front Microbiol. 2019;10:2110. https:\/\/doi.org\/10.3389\/fmicb.2019.02110.","journal-title":"Front Microbiol"},{"key":"1482_CR84","doi-asserted-by":"publisher","first-page":"1392","DOI":"10.1164\/rccm.201509-1865OC","volume":"194","author":"J Tan","year":"2016","unstructured":"Tan J, Tedrow JR, Dutta JA, Juan-Guardela B, Nouraie M, Chu Y, et al. Expression of RXFP1 is decreased in idiopathic pulmonary fibrosis. Implications for relaxin-based therapies. Am J Respir Crit Care Med. 2016;194:1392\u2013402. https:\/\/doi.org\/10.1164\/rccm.201509-1865OC.","journal-title":"Am J Respir Crit Care Med"},{"key":"1482_CR85","doi-asserted-by":"publisher","first-page":"676","DOI":"10.1165\/rcmb.2015-0012OC","volume":"53","author":"AA Tarique","year":"2015","unstructured":"Tarique AA, Logan J, Thomas E, Holt PG, Sly PD, Fantino E. Phenotypic, functional, and plasticity features of classical and alternatively activated human macrophages. Am J Respir Cell Mol Biol. 2015;53:676\u201388. https:\/\/doi.org\/10.1165\/rcmb.2015-0012OC.","journal-title":"Am J Respir Cell Mol Biol"},{"key":"1482_CR86","doi-asserted-by":"publisher","first-page":"e1002480","DOI":"10.1371\/journal.ppat.1002480","volume":"8","author":"S Tattermusch","year":"2012","unstructured":"Tattermusch S, Skinner JA, Chaussabel D, Banchereau J, Berry MP, McNab FW, et al. Systems biology approaches reveal a specific interferon-inducible signature in HTLV-1 associated myelopathy. PLoS Pathog. 2012;8:e1002480. https:\/\/doi.org\/10.1371\/journal.ppat.1002480.","journal-title":"PLoS Pathog"},{"key":"1482_CR87","doi-asserted-by":"publisher","first-page":"86","DOI":"10.1186\/1742-4690-5-86","volume":"5","author":"H Teruya","year":"2008","unstructured":"Teruya H, Tomita M, Senba M, Ishikawa C, Tamayose M, Miyazato A, et al. Human T-cell leukemia virus type I infects human lung epithelial cells and induces gene expression of cytokines, chemokines and cell adhesion molecules. Retrovirology. 2008;5:86. https:\/\/doi.org\/10.1186\/1742-4690-5-86.","journal-title":"Retrovirology"},{"key":"1482_CR88","doi-asserted-by":"publisher","unstructured":"Berglund G, Lennon CD, Badu P, Berglund JA, Pager CT. Transcriptomic signatures of zika virus infection in patients and a cell culture model. Microorganisms 2024;12 https:\/\/doi.org\/10.3390\/microorganisms12071499","DOI":"10.3390\/microorganisms12071499"},{"key":"1482_CR89","doi-asserted-by":"publisher","first-page":"e1009919","DOI":"10.1371\/journal.ppat.1009919","volume":"17","author":"C Vandermeulen","year":"2021","unstructured":"Vandermeulen C, O\u2019Grady T, Wayet J, Galvan B, Maseko S, Cherkaoui M, et al. The HTLV-1 viral oncoproteins Tax and HBZ reprogram the cellular mRNA splicing landscape. PLoS Pathog. 2021;17:e1009919. https:\/\/doi.org\/10.1371\/journal.ppat.1009919.","journal-title":"PLoS Pathog"},{"key":"1482_CR90","doi-asserted-by":"publisher","first-page":"177","DOI":"10.1016\/s0140-6736(88)92744-4","volume":"1","author":"JC Vernant","year":"1988","unstructured":"Vernant JC, Buisson G, Magdeleine J, De Thore J, Jouannelle A, Neisson-Vernant C, et al. T-lymphocyte alveolitis, tropical spastic paresis, and Sj\u00f6gren syndrome. Lancet. 1988;1:177. https:\/\/doi.org\/10.1016\/s0140-6736(88)92744-4.","journal-title":"Lancet"},{"key":"1482_CR91","doi-asserted-by":"publisher","first-page":"2619","DOI":"10.1172\/jci124615","volume":"129","author":"S Watanabe","year":"2019","unstructured":"Watanabe S, Alexander M, Misharin AV, Budinger GRS. The role of macrophages in the resolution of inflammation. J Clin Invest. 2019;129:2619\u201328. https:\/\/doi.org\/10.1172\/jci124615.","journal-title":"J Clin Invest"},{"key":"1482_CR92","doi-asserted-by":"publisher","first-page":"445","DOI":"10.1038\/nature12034","volume":"496","author":"TA Wynn","year":"2013","unstructured":"Wynn TA, Chawla A, Pollard JW. Macrophage biology in development, homeostasis and disease. Nature. 2013;496:445\u201355. https:\/\/doi.org\/10.1038\/nature12034.","journal-title":"Nature"},{"key":"1482_CR93","doi-asserted-by":"publisher","first-page":"130","DOI":"10.1007\/s12026-022-09330-8","volume":"71","author":"S Yadav","year":"2023","unstructured":"Yadav S, Priya A, Borade DR, Agrawal-Rajput R. Macrophage subsets and their role: co-relation with colony-stimulating factor-1 receptor and clinical relevance. Immunol Res. 2023;71:130\u201352. https:\/\/doi.org\/10.1007\/s12026-022-09330-8.","journal-title":"Immunol Res"},{"key":"1482_CR94","doi-asserted-by":"publisher","first-page":"107669","DOI":"10.1016\/j.pharmthera.2020.107669","volume":"218","author":"J Yamauchi","year":"2021","unstructured":"Yamauchi J, Araya N, Yagishita N, Sato T, Yamano Y. An update on human T-cell leukemia virus type I (HTLV-1)-associated myelopathy\/tropical spastic paraparesis (HAM\/TSP) focusing on clinical and laboratory biomarkers. Pharmacol Ther. 2021;218:107669. https:\/\/doi.org\/10.1016\/j.pharmthera.2020.107669.","journal-title":"Pharmacol Ther"},{"key":"1482_CR95","doi-asserted-by":"publisher","first-page":"321","DOI":"10.1136\/jnnp-2019-321955","volume":"91","author":"J Yamauchi","year":"2020","unstructured":"Yamauchi J, Sato T, Yagishita N, Araya N, Hasegawa D, Tsutsumi S, et al. Use of cerebrospinal fluid CXCL10 and neopterin as biomarkers in HTLV-1-associated myelopathy\/tropical spastic paraparesis treated with steroids. J Neurol Neurosurg Psychiatry. 2020;91:321\u20133. https:\/\/doi.org\/10.1136\/jnnp-2019-321955.","journal-title":"J Neurol Neurosurg Psychiatry"},{"key":"1482_CR96","doi-asserted-by":"publisher","first-page":"2283","DOI":"10.1378\/chest.124.6.2283","volume":"124","author":"Y Yamazato","year":"2003","unstructured":"Yamazato Y, Miyazato A, Kawakami K, Yara S, Kaneshima H, Saito A. High expression of p40(tax) and pro-inflammatory cytokines and chemokines in the lungs of human T-lymphotropic virus type 1-related bronchopulmonary disorders. Chest. 2003;124:2283\u201392. https:\/\/doi.org\/10.1378\/chest.124.6.2283.","journal-title":"Chest"},{"key":"1482_CR97","doi-asserted-by":"publisher","first-page":"1114","DOI":"10.1136\/thoraxjnl-2012-202943","volume":"68","author":"IV Yang","year":"2013","unstructured":"Yang IV, Coldren CD, Leach SM, Seibold MA, Murphy E, Lin J, et al. Expression of cilium-associated genes defines novel molecular subtypes of idiopathic pulmonary fibrosis. Thorax. 2013;68:1114\u201321. https:\/\/doi.org\/10.1136\/thoraxjnl-2012-202943.","journal-title":"Thorax"},{"key":"1482_CR98","doi-asserted-by":"publisher","first-page":"2534","DOI":"10.1073\/pnas.81.8.2534","volume":"81","author":"M Yoshida","year":"1984","unstructured":"Yoshida M, Seiki M, Yamaguchi K, Takatsuki K. Monoclonal integration of human T-cell leukemia provirus in all primary tumors of adult T-cell leukemia suggests causative role of human T-cell leukemia virus in the disease. Proc Natl Acad Sci U S A. 1984;81:2534\u20137. https:\/\/doi.org\/10.1073\/pnas.81.8.2534.","journal-title":"Proc Natl Acad Sci U S A"},{"key":"1482_CR99","doi-asserted-by":"publisher","first-page":"284","DOI":"10.1089\/omi.2011.0118","volume":"16","author":"G Yu","year":"2012","unstructured":"Yu G, Wang LG, Han Y, He QY. ClusterProfiler: an R package for comparing biological themes among gene clusters. Omics. 2012;16:284\u20137. https:\/\/doi.org\/10.1089\/omi.2011.0118.","journal-title":"Omics"},{"key":"1482_CR100","doi-asserted-by":"publisher","first-page":"39","DOI":"10.1038\/nm.4447","volume":"24","author":"G Yu","year":"2018","unstructured":"Yu G, Tzouvelekis A, Wang R, Herazo-Maya JD, Ibarra GH, Srivastava A, et al. Thyroid hormone inhibits lung fibrosis in mice by improving epithelial mitochondrial function. Nat Med. 2018;24:39\u201349. https:\/\/doi.org\/10.1038\/nm.4447.","journal-title":"Nat Med"},{"key":"1482_CR101","doi-asserted-by":"publisher","first-page":"421","DOI":"10.3389\/fmicb.2020.00421","volume":"11","author":"R Zargari","year":"2020","unstructured":"Zargari R, Mahdifar M, Mohammadi A, Vahidi Z, Hassanshahi G, Rafatpanah H. The role of chemokines in the pathogenesis of HTLV-1. Front Microbiol. 2020;11:421. https:\/\/doi.org\/10.3389\/fmicb.2020.00421.","journal-title":"Front Microbiol"},{"key":"1482_CR102","doi-asserted-by":"publisher","first-page":"955125","DOI":"10.3389\/fmed.2022.955125","volume":"9","author":"X Zhang","year":"2022","unstructured":"Zhang X, Ren Y, Xie B, Ye Q, Ban C, Zhang S, et al. Blood monocyte counts as a prognostic biomarker and predictor in Chinese patients with idiopathic pulmonary fibrosis. Front Med (Lausanne). 2022;9:955125. https:\/\/doi.org\/10.3389\/fmed.2022.955125.","journal-title":"Front Med (Lausanne)"},{"key":"1482_CR103","doi-asserted-by":"publisher","unstructured":"Wickham H. Ggplot2: elegant graphics for data analysis. Springer International Publishing 2016. https:\/\/doi.org\/10.1007\/978-3-319-24277-4.","DOI":"10.1007\/978-3-319-24277-4"},{"key":"1482_CR104","doi-asserted-by":"publisher","unstructured":"Van Weyenbergh J, Assone T, Racine I, Menezes S, Gon\u00e7alves F, Folgosi V, Marcusso R, Haziot M, Smid J, Dahy F, et al. Multi-cohort cross-omics analysis reveals disease mechanisms and therapeutic targets in HTLV-1-associated myelopathy, a neglected retroviral neuroinflammatory disorder. Res Sq 2025. https:\/\/doi.org\/10.21203\/rs.3.rs-5960764\/v1.","DOI":"10.21203\/rs.3.rs-5960764\/v1"}],"container-title":["Molecular Medicine"],"original-title":[],"language":"en","link":[{"URL":"https:\/\/link.springer.com\/article\/10.1186\/s10020-026-01482-9","content-type":"text\/html","content-version":"vor","intended-application":"text-mining"},{"URL":"https:\/\/link.springer.com\/content\/pdf\/10.1186\/s10020-026-01482-9.pdf","content-type":"application\/pdf","content-version":"vor","intended-application":"text-mining"},{"URL":"https:\/\/link.springer.com\/content\/pdf\/10.1186\/s10020-026-01482-9.pdf","content-type":"application\/pdf","content-version":"vor","intended-application":"similarity-checking"}],"deposited":{"date-parts":[[2026,6,16]],"date-time":"2026-06-16T22:36:28Z","timestamp":1781649388000},"score":1,"resource":{"primary":{"URL":"https:\/\/link.springer.com\/10.1186\/s10020-026-01482-9"}},"subtitle":[],"short-title":[],"issued":{"date-parts":[[2026,4,23]]},"references-count":104,"journal-issue":{"issue":"1","published-online":{"date-parts":[[2026,12]]}},"alternative-id":["1482"],"URL":"https:\/\/doi.org\/10.1186\/s10020-026-01482-9","relation":{},"ISSN":["1528-3658"],"issn-type":[{"value":"1528-3658","type":"electronic"}],"subject":[],"published":{"date-parts":[[2026,4,23]]},"assertion":[{"value":"8 January 2026","order":1,"name":"received","label":"Received","group":{"name":"ArticleHistory","label":"Article History"}},{"value":"8 April 2026","order":2,"name":"accepted","label":"Accepted","group":{"name":"ArticleHistory","label":"Article History"}},{"value":"23 April 2026","order":3,"name":"first_online","label":"First Online","group":{"name":"ArticleHistory","label":"Article History"}},{"order":1,"name":"Ethics","group":{"name":"EthicsHeading","label":"Declarations"}},{"value":"Monocytes were isolated from buffy coats of healthy donors obtained from the Red Cross Belgium according to KU Leuven agreement RKOV_19006.","order":2,"name":"Ethics","group":{"name":"EthicsHeading","label":"Ethics approval and consent to participate"}},{"value":"Not applicable.","order":3,"name":"Ethics","group":{"name":"EthicsHeading","label":"Consent for publication"}},{"value":"The authors declare no competing interests.","order":4,"name":"Ethics","group":{"name":"EthicsHeading","label":"Competing interests"}}],"article-number":"85"}}