{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"institution":[{"name":"bioRxiv"}],"indexed":{"date-parts":[[2026,4,5]],"date-time":"2026-04-05T07:26:32Z","timestamp":1775373992077,"version":"3.50.1"},"posted":{"date-parts":[[2023,10,20]]},"group-title":"Immunology","reference-count":69,"publisher":"openRxiv","license":[{"start":{"date-parts":[[2023,10,20]],"date-time":"2023-10-20T00:00:00Z","timestamp":1697760000000},"content-version":"vor","delay-in-days":0,"URL":"http:\/\/creativecommons.org\/licenses\/by-nc\/4.0\/"}],"content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":[],"accepted":{"date-parts":[[2025,3,4]]},"abstract":"<jats:title>Abstract<\/jats:title>\n                <jats:p>\n                  Pulmonary tuberculosis (PTB) represents 85% of the disease burden caused by\n                  <jats:italic>Mycobacterium tuberculosis<\/jats:italic>\n                  (Mtb) and promotes aerosol transmission infecting about a quarter of people globally. Most Mtb infections are effectively limited within primary granulomatous lesions. Containment failures lead to hematogenous spread and the formation of post-primary destructive PTB lesions. Factors that favor Mtb survival and replication in the lungs after hematogenous spread despite systemic immunity represent appealing targets for host-directed TB therapies, but are currently unknown. We developed a novel mouse model that mimics progression of chronic post-primary PTB in humans: wherein PTB lesions form after hematogenous spread from a remote primary lesion in immunocompetent but TB-susceptible B6.Sst1S mice. The B6.Sst1S mice developed PTB lesions featuring granulomatous pneumonia, bronchogenic expansion and broncho-occlusion closely resembling post-primary PTB in humans. Using spatial transcriptomic and fluorescent multiplexed immunochemistry, we demonstrated the expansion of myeloid cell populations with the appearance of alternatively activated macrophages, dissolution of initial lymphoid follicles, and accumulation of de-differentiated lung epithelial cells in the advanced PTB lesions. To determine whether lung parenchymal cells or lung oxygenation were necessary for the pulmonary TB progression, we implanted lung and spleen fragments subcutaneously to serve as potential targets for hematogenous spread. The lung (but not spleen) implants displayed characteristic organized granulomas with necrosis and Mtb replication demonstrating that deleterious interactions of aberrantly activated macrophages with the inflammation-injured lung resident cells, and possibly hypoxia, not oxygenation, are critical determinants of PTB progression in immunocompetent hosts. Necrotic TB lesions also developed in subcutaneous implants of human lung tissue in mice with human immune system after respiratory infection. These animal models may serve to further dissect the lung-specific mechanisms of host susceptibility to virulent Mtb and for testing therapeutic interventions targeting these mechanisms.\n                <\/jats:p>","DOI":"10.1101\/2023.10.17.562695","type":"posted-content","created":{"date-parts":[[2023,10,20]],"date-time":"2023-10-20T13:20:22Z","timestamp":1697808022000},"source":"Crossref","is-referenced-by-count":7,"title":["Aberrant macrophage activation and maladaptive lung repair promote tuberculosis progression uniquely in the lung"],"prefix":"10.64898","author":[{"ORCID":"https:\/\/orcid.org\/0000-0002-5793-1661","authenticated-orcid":false,"given":"Shivraj M.","family":"Yabaji","sequence":"first","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]},{"ORCID":"https:\/\/orcid.org\/0000-0001-5548-9315","authenticated-orcid":false,"given":"Suruchi","family":"Lata","sequence":"additional","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Anna E.","family":"Tseng","sequence":"additional","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-5441-3826","authenticated-orcid":false,"given":"Prasanna Babu","family":"Araveti","sequence":"additional","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Ming","family":"Lo","sequence":"additional","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]},{"ORCID":"https:\/\/orcid.org\/0000-0001-9810-4091","authenticated-orcid":false,"given":"Igor","family":"Gavrish","sequence":"additional","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Aoife K","family":"O\u2019Connell","sequence":"additional","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Hans P","family":"Gertje","sequence":"additional","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]},{"ORCID":"https:\/\/orcid.org\/0000-0001-7967-6254","authenticated-orcid":false,"given":"Anna C.","family":"Belkina","sequence":"additional","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Colleen E","family":"Thurman","sequence":"additional","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Hirofumi","family":"Kiyokawa","sequence":"additional","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Darrell","family":"Kotton","sequence":"additional","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]},{"ORCID":"https:\/\/orcid.org\/0000-0003-1093-2576","authenticated-orcid":false,"given":"Shumin","family":"Tan","sequence":"additional","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Janice J.","family":"Endsley","sequence":"additional","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-8734-4118","authenticated-orcid":false,"given":"William R","family":"Bishai","sequence":"additional","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]},{"ORCID":"https:\/\/orcid.org\/0000-0003-3873-9188","authenticated-orcid":false,"given":"Nicholas","family":"Crossland","sequence":"additional","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]},{"ORCID":"https:\/\/orcid.org\/0000-0003-4328-937X","authenticated-orcid":false,"given":"Lester","family":"Kobzik","sequence":"additional","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]},{"ORCID":"https:\/\/orcid.org\/0000-0001-6511-9246","authenticated-orcid":false,"given":"Igor","family":"Kramnik","sequence":"additional","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]}],"member":"54368","reference":[{"key":"2025030606500499000_2023.10.17.562695v2.1","unstructured":"WHO, Global Health TB Report. https:\/\/www.who.int\/tb\/publications\/global_report\/en\/, (2023)."},{"key":"2025030606500499000_2023.10.17.562695v2.2","doi-asserted-by":"crossref","first-page":"51","DOI":"10.1080\/21548331.1993.11442738","article-title":"Immunopathogenesis of pulmonary tuberculosis","volume":"28","year":"1993","journal-title":"Hosp Pract (Off Ed"},{"key":"2025030606500499000_2023.10.17.562695v2.3","unstructured":"3. A. R. Rich , The pathogenesis of tuberculosis (Thomas, Springfield, Ill.,, ed. 2d, 1951), pp. xxvii, 1028 p."},{"key":"2025030606500499000_2023.10.17.562695v2.4","doi-asserted-by":"publisher","DOI":"10.1146\/annurev-immunol-093019-125148"},{"key":"2025030606500499000_2023.10.17.562695v2.5","doi-asserted-by":"publisher","DOI":"10.1016\/j.chom.2018.06.004."},{"key":"2025030606500499000_2023.10.17.562695v2.6","doi-asserted-by":"crossref","unstructured":"M. Pai , M. A. Behr , D. Dowdy , K. Dheda , M. Divangahi , C. C. Boehme , A. Ginsberg , S. Swaminathan , M. Spigelman , H. Getahun , D. Menzies , M. Raviglione , Tuberculosis. Nat Rev Dis Primers 2, 16076 (2016).","DOI":"10.1038\/nrdp.2016.76"},{"key":"2025030606500499000_2023.10.17.562695v2.7","doi-asserted-by":"publisher","DOI":"10.1016\/j.mib.2017.11.021"},{"key":"2025030606500499000_2023.10.17.562695v2.8","doi-asserted-by":"crossref","unstructured":"P. K. Drain , K. L. Bajema , D. Dowdy , K. Dheda , K. Naidoo , S. G. Schumacher , S. Ma , E. Meermeier , D. M. Lewinsohn , D. R. Sherman , Incipient and Subclinical Tuberculosis: a Clinical Review of Early Stages and Progression of Infection. Clin Microbiol Rev 31, (2018).","DOI":"10.1128\/CMR.00021-18"},{"key":"2025030606500499000_2023.10.17.562695v2.9","doi-asserted-by":"publisher","DOI":"10.1164\/rccm.202011-4239PP"},{"key":"2025030606500499000_2023.10.17.562695v2.10","doi-asserted-by":"crossref","unstructured":"S. Verver , R. M. Warren , N. Beyers , M. Richardson , G. D. v. d. Spuy , M. W. Borgdorff , D. A. Enarson , M. A. Behr , P. D. v. Helden , Rate of reinfection tuberculosis after successful treatment is higher than rate of new tuberculosis. Am J Respir Crit Care Med 171, 1430 - 1435 (2005).","DOI":"10.1164\/rccm.200409-1200OC"},{"key":"2025030606500499000_2023.10.17.562695v2.11","doi-asserted-by":"publisher","DOI":"10.1016\/0962-8479(94)90002-7"},{"key":"2025030606500499000_2023.10.17.562695v2.12","doi-asserted-by":"publisher","DOI":"10.1016\/S1472-9792(02)00079-3"},{"key":"2025030606500499000_2023.10.17.562695v2.13","first-page":"157","article-title":"Pathogenesis of experimental tuberculosis in animal models","volume":"215","year":"1996","journal-title":"Curr Top Microbiol Immunol"},{"key":"2025030606500499000_2023.10.17.562695v2.14","doi-asserted-by":"crossref","unstructured":"M. G. Moule , J. D. Cirillo , Mycobacterium tuberculosis Dissemination Plays a Critical Role in Pathogenesis. Frontiers in Cellular and Infection Microbiology 10, 492 (2020).","DOI":"10.3389\/fcimb.2020.00065"},{"key":"2025030606500499000_2023.10.17.562695v2.15","doi-asserted-by":"publisher","DOI":"10.1146\/annurev.immunol.22.012703.104635"},{"key":"2025030606500499000_2023.10.17.562695v2.16","first-page":"933","article-title":"High-sensitivity, Bacteriophage-based Assay Identifies Low-level Mycobacterium tuberculosis Bacteremia in Immunocompetent Patients With Active and Incipient Tuberculosis","volume":"70","year":"2019","journal-title":"Clin. Infect. Dis"},{"key":"2025030606500499000_2023.10.17.562695v2.17","doi-asserted-by":"crossref","unstructured":"R. L. Hunter , The Pathogenesis of Tuberculosis: The Early Infiltrate of Post-primary (Adult Pulmonary) Tuberculosis: A Distinct Disease Entity. Front Immunol 9, 2108 (2018).","DOI":"10.3389\/fimmu.2018.02108"},{"key":"2025030606500499000_2023.10.17.562695v2.18","doi-asserted-by":"publisher","DOI":"10.1016\/j.tube.2011.03.007"},{"key":"2025030606500499000_2023.10.17.562695v2.19","doi-asserted-by":"crossref","unstructured":"R. L. Hunter , The Pathogenesis of Tuberculosis\u2013The Koch Phenomenon Reinstated. Pathogens 9, 813 (2020).","DOI":"10.3390\/pathogens9100813"},{"key":"2025030606500499000_2023.10.17.562695v2.20","doi-asserted-by":"publisher","DOI":"10.1164\/rccm.202101-0032OC"},{"key":"2025030606500499000_2023.10.17.562695v2.21","doi-asserted-by":"publisher","DOI":"10.1073\/pnas.2211045119"},{"key":"2025030606500499000_2023.10.17.562695v2.22","doi-asserted-by":"publisher","DOI":"10.4049\/jimmunol.179.10.6919"},{"key":"2025030606500499000_2023.10.17.562695v2.23","doi-asserted-by":"publisher","DOI":"10.1016\/j.chom.2017.06.004"},{"key":"2025030606500499000_2023.10.17.562695v2.24","doi-asserted-by":"publisher","DOI":"10.1016\/j.smim.2014.09.003"},{"key":"2025030606500499000_2023.10.17.562695v2.25","doi-asserted-by":"crossref","unstructured":"K. D. Kauffman , M. A. Sallin , S. Sakai , O. Kamenyeva , J. Kabat , D. Weiner , M. Sutphin , D. Schimel , L. Via , C. E. Barry , 3rd, T. Wilder-Kofie , I. Moore , R. Moore , D. L. Barber , Defective positioning in granulomas but not lung-homing limits CD4 T-cell interactions with Mycobacterium tuberculosis-infected macrophages in rhesus macaques. Mucosal Immunol 11, 462-473 (2018).","DOI":"10.1038\/mi.2017.60"},{"key":"2025030606500499000_2023.10.17.562695v2.26","first-page":"550","article-title":"Moving tuberculosis vaccines from theory to practice","volume":"19","year":"2019","journal-title":"Nature Publishing Group"},{"key":"2025030606500499000_2023.10.17.562695v2.27","doi-asserted-by":"publisher","DOI":"10.1038\/ng.590"},{"key":"2025030606500499000_2023.10.17.562695v2.28","doi-asserted-by":"publisher","DOI":"10.1038\/s41591-022-02123-4"},{"key":"2025030606500499000_2023.10.17.562695v2.29","doi-asserted-by":"publisher","DOI":"10.1016\/j.immuni.2009.10.007"},{"key":"2025030606500499000_2023.10.17.562695v2.30","doi-asserted-by":"crossref","unstructured":"H. P. Gideon , T. K. Hughes , C. N. Tzouanas , M. H. Wadsworth , A. A. Tu , T. M. Gierahn , J. M. Peters , F. F. Hopkins , J.-R. Wei , C. Kummerlowe , N. L. Grant , K. Nargan , J. Y. Phuah , H. J. Borish , P. Maiello , A. G. White , C. G. Winchell , S. K. Nyquist , S. K. C. Ganchua , A. Myers , K. V. Patel , C. L. Ameel , C. T. Cochran , S. Ibrahim , J. A. Tomko , L. J. Frye , J. M. Rosenberg , A. Shih , M. Chao , E. Klein , C. A. Scanga , J. Ordovas-Montanes , B. Berger , J. T. Mattila , R. Madansein , J. C. Love , P. L. Lin , A. Leslie , S. M. Behar , B. Bryson , J. L. Flynn , S. M. Fortune , A. K. Shalek , Multimodal profiling of lung granulomas in macaques reveals cellular correlates of tuberculosis control. Immunity, (2022).","DOI":"10.1016\/j.immuni.2022.04.004"},{"key":"2025030606500499000_2023.10.17.562695v2.31","doi-asserted-by":"crossref","unstructured":"H. E. Volkman , T. C. Pozos , J. Zheng , J. M. Davis , J. F. Rawls , L. Ramakrishnan , Tuberculous granuloma induction via interaction of a bacterial secreted protein with host epithelium. Science 327, 466\u2013469.","DOI":"10.1126\/science.1179663"},{"key":"2025030606500499000_2023.10.17.562695v2.32","doi-asserted-by":"publisher","DOI":"10.1136\/thoraxjnl-2021-217997"},{"key":"2025030606500499000_2023.10.17.562695v2.33","doi-asserted-by":"crossref","unstructured":"S. T. Reece , C. Loddenkemper , D. J. Askew , U. Zedler , S. Schommer-Leitner , M. Stein , F. A. Mir , A. Dorhoi , H.-J. Mollenkopf , G. A. Silverman , S. H. E. Kaufmann , Serine protease activity contributes to control of Mycobacterium tuberculosis in hypoxic lung granulomas in mice. The Journal of clinical investigation 120, 3365 - 3376 (2010).","DOI":"10.1172\/JCI42796"},{"key":"2025030606500499000_2023.10.17.562695v2.34","doi-asserted-by":"publisher","DOI":"10.1371\/journal.ppat.1008655"},{"key":"2025030606500499000_2023.10.17.562695v2.35","doi-asserted-by":"publisher","DOI":"10.1038\/s41598-017-00643-5"},{"key":"2025030606500499000_2023.10.17.562695v2.36","doi-asserted-by":"publisher","DOI":"10.1371\/journal.pone.0158849"},{"key":"2025030606500499000_2023.10.17.562695v2.37","doi-asserted-by":"publisher","DOI":"10.1073\/pnas.150227197"},{"key":"2025030606500499000_2023.10.17.562695v2.38","doi-asserted-by":"publisher","DOI":"10.2353\/ajpath.2009.081075"},{"key":"2025030606500499000_2023.10.17.562695v2.39","doi-asserted-by":"crossref","unstructured":"B. Bhattacharya , S. Xiao , S. Chatterjee , M. Urbanowski , A. Ordonez , E. A. Ihms , G. Agrahari , S. Lun , R. Berland , A. Pichugin , Y. Gao , J. Connor , A. R. Ivanov , B. S. Yan , L. Kobzik , B. B. Koo , S. Jain , W. Bishai , I. Kramnik , The integrated stress response mediates necrosis in murine Mycobacterium tuberculosis granulomas. J Clin Invest 131, (2021).","DOI":"10.1172\/JCI130319"},{"key":"2025030606500499000_2023.10.17.562695v2.40","doi-asserted-by":"publisher","DOI":"10.1038\/nature03419"},{"key":"2025030606500499000_2023.10.17.562695v2.41","doi-asserted-by":"crossref","unstructured":"S. M. Riaz , K. Hanevik , L. Helgeland , L. Sviland , R. L. Hunter , T. Mustafa , Novel Insights into the Pathogenesis of Human Post-Primary Tuberculosis from Archival Material of the Pre-Antibiotic Era, 1931\u20131947. Pathogens 12, 1426 (2023).","DOI":"10.3390\/pathogens12121426"},{"key":"2025030606500499000_2023.10.17.562695v2.42","doi-asserted-by":"publisher","DOI":"10.1016\/j.jim.2007.08.004"},{"key":"2025030606500499000_2023.10.17.562695v2.43","first-page":"173","article-title":"Regulation of T-cell proliferative responses by cells from solid lung tissue of M. tuberculosis-infected mice","volume":"73","year":"1991","journal-title":"Immunology"},{"key":"2025030606500499000_2023.10.17.562695v2.44","doi-asserted-by":"publisher","DOI":"10.1371\/journal.ppat.1010459"},{"key":"2025030606500499000_2023.10.17.562695v2.45","doi-asserted-by":"publisher","DOI":"10.1093\/nar\/gkw377"},{"key":"2025030606500499000_2023.10.17.562695v2.46","doi-asserted-by":"crossref","unstructured":"C. Li , A. Menoret , C. Farragher , Z. Ouyang , C. Bonin , P. Holvoet , A. T. Vella , B. Zhou , Single cell transcriptomics based-MacSpectrum reveals novel macrophage activation signatures in diseases. JCI Insight 5, (2019).","DOI":"10.1172\/jci.insight.126453"},{"key":"2025030606500499000_2023.10.17.562695v2.47","doi-asserted-by":"publisher","DOI":"10.1016\/j.stem.2019.12.014"},{"key":"2025030606500499000_2023.10.17.562695v2.48","doi-asserted-by":"publisher","DOI":"10.1084\/jem.20180325"},{"key":"2025030606500499000_2023.10.17.562695v2.49","doi-asserted-by":"crossref","unstructured":"S. Lata , S. M. Yabaji , A. K. O\u2019Connell , H. P. Gertje , M. T. Kirber , N. A. Crossland , I. Kramnik , Protocol for 3D multiplexed fluorescent imaging of pulmonary TB lesions using Opal-TSA dyes for signal amplification. STAR Protoc. 6, 103640 (2025).","DOI":"10.1016\/j.xpro.2025.103640"},{"key":"2025030606500499000_2023.10.17.562695v2.50","doi-asserted-by":"crossref","unstructured":"S. M. Yabaji , S. Lata , I. Gavrish , M. Lo , A. K. O Connell , H. P. Gertje , C. E. Thurman , N. A. Crossland , L. Kobzik , I. Kramnik , Protocol for Developing a Mouse Model of Post Primary Pulmonary Tuberculosis after Hematogenous Spread in Native Lungs and Lung Implants. bioRxiv, 2025.2002.2028.640830 (2025).","DOI":"10.1101\/2025.02.28.640830"},{"key":"2025030606500499000_2023.10.17.562695v2.51","doi-asserted-by":"crossref","unstructured":"E. Brownhill , S. M. Yabaji , V. Zhernovkov , O. S. Rukhlenko , K. Seidel , B. Bhattacharya , S. Chatterjee , H. A. Chen , N. Crossland , W. Bishai , B. N. Kholodenko , A. Gimelbrant , L. Kobzik , I. Kramnik , Maladaptive oxidative stress cascade drives type I interferon hyperactivity in TNF activated macrophages promoting necrosis in murine tuberculosis granulomas. bioRxiv, 2020.2012.2014.422743 (2020).","DOI":"10.1101\/2020.12.14.422743"},{"key":"2025030606500499000_2023.10.17.562695v2.52","doi-asserted-by":"publisher","DOI":"10.1016\/j.cell.2022.10.025"},{"key":"2025030606500499000_2023.10.17.562695v2.53","doi-asserted-by":"crossref","unstructured":"D. X. Ji , K. C. Witt , D. I. Kotov , S. R. Margolis , A. Louie , V. Chevee , K. J. Chen , M. M. Gaidt , H. S. Dhaliwal , A. Y. Lee , S. L. Nishimura , D. S. Zamboni , I. Kramnik , D. A. Portnoy , K. H. Darwin , R. E. Vance , Role of the transcriptional regulator SP140 in resistance to bacterial infections via repression of type I interferons. Elife 10, (2021).","DOI":"10.7554\/eLife.67290"},{"key":"2025030606500499000_2023.10.17.562695v2.54","doi-asserted-by":"publisher","DOI":"10.1016\/j.it.2020.04.007"},{"key":"2025030606500499000_2023.10.17.562695v2.55","doi-asserted-by":"crossref","unstructured":"S. Mehta , D. A. Cronkite , M. Basavappa , T. L. Saunders , F. Adiliaghdam , H. Amatullah , S. A. Morrison , J. D. Pagan , R. M. Anthony , P. Tonnerre , G. M. Lauer , J. C. Lee , S. Digumarthi , L. Pantano , S. J. H. Sui , F. Ji , R. Sadreyev , C. Zhou , A. C. Mullen , V. Kumar , Y. Li , C. Wijmenga , R. J. Xavier , T. K. Means , K. L. Jeffrey , Maintenance of macrophage transcriptional programs and intestinal homeostasis by epigenetic reader SP140. Sci Immunol 2, (2017).","DOI":"10.1126\/sciimmunol.aag3160"},{"key":"2025030606500499000_2023.10.17.562695v2.56","doi-asserted-by":"publisher","DOI":"10.1016\/j.stem.2020.03.009"},{"key":"2025030606500499000_2023.10.17.562695v2.57","doi-asserted-by":"crossref","unstructured":"A. E. Engler , A. B. Ysasi , R. M. F. Pihl , C. Villacorta-Martin , H. M. Heston , H. M. K. Richardson , B. R. Thapa , N. R. Moniz , A. C. Belkina , S. A. Mazzilli , J. R. Rock , Airway- Associated Macrophages in Homeostasis and Repair. Cell Reports 33, 108553 (2020).","DOI":"10.1016\/j.celrep.2020.108553"},{"key":"2025030606500499000_2023.10.17.562695v2.58","doi-asserted-by":"publisher","DOI":"10.1016\/j.cell.2019.02.028"},{"key":"2025030606500499000_2023.10.17.562695v2.59","doi-asserted-by":"publisher","DOI":"10.1002\/path.4399"},{"key":"2025030606500499000_2023.10.17.562695v2.60","doi-asserted-by":"publisher","DOI":"10.1038\/s41586-020-2424-4"},{"key":"2025030606500499000_2023.10.17.562695v2.61","doi-asserted-by":"publisher","DOI":"10.1038\/s41556-020-00591-9"},{"key":"2025030606500499000_2023.10.17.562695v2.62","doi-asserted-by":"crossref","unstructured":"D. L. Jones , M. P. Morley , X. Li , Y. Ying , G. Zhao , S. E. Schaefer , L. R. Rodriguez , F. L. Cardenas-Diaz , S. Li , S. Zhou , U. V. Chembazhi , M. Kim , C. Shen , A. Nottingham , S. M. Lin , E. Cantu , J. M. Diamond , M. C. Basil , A. E. Vaughan , E. E. Morrisey , An injury- induced mesenchymal-epithelial cell niche coordinates regenerative responses in the lung. Science 386, eado5561 (2024).","DOI":"10.1126\/science.ado5561"},{"key":"2025030606500499000_2023.10.17.562695v2.63","doi-asserted-by":"publisher","DOI":"10.1038\/s41586-023-06797-9"},{"key":"2025030606500499000_2023.10.17.562695v2.64","doi-asserted-by":"publisher","DOI":"10.1371\/journal.pone.0063331"},{"key":"2025030606500499000_2023.10.17.562695v2.65","doi-asserted-by":"crossref","unstructured":"O. Escaffre , T. B. Saito , T. L. Juelich , T. Ikegami , J. K. Smith , D. D. Perez , C. Atkins , C. B. Levine , M. B. Huante , R. J. Nusbaum , J. J. Endsley , A. N. Freiberg , B. Rockx , Contribution of Human Lung Parenchyma and Leukocyte Influx to Oxidative Stress and Immune System-Mediated Pathology following Nipah Virus Infection. J Virol 91, (2017).","DOI":"10.1128\/JVI.00275-17"},{"key":"2025030606500499000_2023.10.17.562695v2.66","doi-asserted-by":"publisher","DOI":"10.1073\/pnas.0808537105"},{"key":"2025030606500499000_2023.10.17.562695v2.67","doi-asserted-by":"crossref","unstructured":"S. X. Ge , E. W. Son , R. Yao , iDEP: an integrated web application for differential expression and pathway analysis of RNA-Seq data. BMC Bioinform. 19, 534 (2018).","DOI":"10.1186\/s12859-018-2486-6"},{"key":"2025030606500499000_2023.10.17.562695v2.68","doi-asserted-by":"publisher","DOI":"10.1002\/cpz1.90"},{"key":"2025030606500499000_2023.10.17.562695v2.69","doi-asserted-by":"crossref","unstructured":"R. J. Nusbaum , V. E. Calderon , M. B. Huante , P. Sutjita , S. Vijayakumar , K. L. Lancaster , R. L. Hunter , J. K. Actor , J. D. Cirillo , J. Aronson , B. B. Gelman , J. G. Lisinicchia , G. Valbuena , J. J. Endsley , Pulmonary Tuberculosis in Humanized Mice Infected with HIV-1. Sci Rep 6, 21522 (2016).","DOI":"10.1038\/srep21522"}],"container-title":[],"original-title":[],"link":[{"URL":"https:\/\/syndication.highwire.org\/content\/doi\/10.1101\/2023.10.17.562695","content-type":"unspecified","content-version":"vor","intended-application":"similarity-checking"}],"deposited":{"date-parts":[[2026,1,15]],"date-time":"2026-01-15T05:24:30Z","timestamp":1768454670000},"score":1,"resource":{"primary":{"URL":"http:\/\/biorxiv.org\/lookup\/doi\/10.1101\/2023.10.17.562695"}},"subtitle":[],"short-title":[],"issued":{"date-parts":[[2023,10,20]]},"references-count":69,"URL":"https:\/\/doi.org\/10.1101\/2023.10.17.562695","relation":{},"subject":[],"published":{"date-parts":[[2023,10,20]]},"subtype":"preprint"}}