2024
Prior knowledge-guided vision-transformer-based unsupervised domain adaptation for intubation prediction in lung disease at one week
Yang J, Henao J, Dvornek N, He J, Bower D, Depotter A, Bajercius H, de Mortanges A, You C, Gange C, Ledda R, Silva M, Dela Cruz C, Hautz W, Bonel H, Reyes M, Staib L, Poellinger A, Duncan J. Prior knowledge-guided vision-transformer-based unsupervised domain adaptation for intubation prediction in lung disease at one week. Computerized Medical Imaging And Graphics 2024, 118: 102442. DOI: 10.1016/j.compmedimag.2024.102442.Peer-Reviewed Original ResearchUnsupervised domain adaptationSpatial prior informationDomain adaptationLabeled dataData-driven approachUnsupervised domain adaptation modelMedical image analysis tasksImage analysis tasksTransformer-based modelsMedical image analysisPrior informationOutcome prediction tasksAdversarial trainingDistribution alignmentDomain shiftAttention headsClass tokenPoor generalizationAnalysis tasksTarget domainPrediction taskData distributionKnowledge-guidedLocal weightsMedical imagesContext‐specific anti‐inflammatory roles of type III interferon signaling in the lung in nonviral injuries
Feng J, Kim J, Wang V, Chang D, Liu H, Bain W, Robinson K, Jie Z, Kotenko S, Dela Cruz C, Sharma L. Context‐specific anti‐inflammatory roles of type III interferon signaling in the lung in nonviral injuries. Physiological Reports 2024, 12: e70104. PMID: 39455422, PMCID: PMC11511623, DOI: 10.14814/phy2.70104.Peer-Reviewed Original ResearchConceptsIII interferon signalingType III interferon signalingLung injuryInterferon signalingBleomycin-induced weight lossInflammatory responseModel of lung injuryBacterial pathogen Pseudomonas aeruginosaAcute lung injuryPathogen Pseudomonas aeruginosaBacterial endotoxin LPSChemotherapeutic agent bleomycinType III interferonsAnti-inflammatory roleIncreased inflammatory signalingLate time pointsBleomycin modelKnockout miceEndotoxin LPSIII interferonsAntiviral cytokinesDay 3Inflammatory signalingEarly injuryImpaired recoverySingle-Cell Profiling Reveals Immune Aberrations in Progressive Idiopathic Pulmonary Fibrosis.
Unterman A, Zhao A, Neumark N, Schupp J, Ahangari F, Cosme C, Sharma P, Flint J, Stein Y, Ryu C, Ishikawa G, Sumida T, Gomez J, Herazo-Maya J, Dela Cruz C, Herzog E, Kaminski N. Single-Cell Profiling Reveals Immune Aberrations in Progressive Idiopathic Pulmonary Fibrosis. American Journal Of Respiratory And Critical Care Medicine 2024, 210: 484-496. PMID: 38717443, PMCID: PMC11351796, DOI: 10.1164/rccm.202306-0979oc.Peer-Reviewed Original ResearchStable idiopathic pulmonary fibrosisIdiopathic pulmonary fibrosisPeripheral blood mononuclear cellsProgressive idiopathic pulmonary fibrosisPeripheral immune systemT cellsPulmonary fibrosisCohort of IPF patientsAssociated with decreased survivalIdiopathic pulmonary fibrosis patientsPeripheral blood mononuclear cell samplesPeripheral blood cell populationsImmune systemFraction of TregsRegulatory T cellsBlood mononuclear cellsBlood cell populationsFlow cytometry analysisImmune aberrationsIPF patientsTregsMononuclear cellsSingle-cell RNA sequencingLung homogenatesMonocyte chemoattractantThe protein disulfide isomerase A3 and osteopontin axis promotes influenza‐induced lung remodelling
Kumar A, Mark Z, Carbajal M, DeLima D, Chamberlain N, Walzer J, Ruban M, Chandrasekaran R, Daphtary N, Aliyeva M, Poynter M, Janssen‐Heininger Y, Bates J, Alcorn J, Britto C, Dela Cruz C, Jegga A, Anathy V. The protein disulfide isomerase A3 and osteopontin axis promotes influenza‐induced lung remodelling. British Journal Of Pharmacology 2024, 181: 4610-4627. PMID: 39118388, DOI: 10.1111/bph.16511.Peer-Reviewed Original ResearchProtein disulfide isomerase A3Secreted phosphoprotein 1Lung fibrosisLung remodelingFibrotic remodelingViral infectionAssociated with pulmonary fibrosisInfluenza-infected patientsMacrophage colony-stimulating factorFibrotic lung remodelingSPP1 expressionRespiratory viral infectionsImproved oxygen saturationColony-stimulating factorLung fibrotic remodelingDebilitating clinical sequelaeIAV infectionFibrotic sequelaeClinical sequelaeTherapeutic optionsPulmonary fibrosisRetrospective analysisNeutralizing antibodiesCell culture modelHealthy controlsLongitudinal multicompartment characterization of host-microbiota interactions in patients with acute respiratory failure
Kitsios G, Sayed K, Fitch A, Yang H, Britton N, Shah F, Bain W, Evankovich J, Qin S, Wang X, Li K, Patel A, Zhang Y, Radder J, Dela Cruz C, Okin D, Huang C, Van Tyne D, Benos P, Methé B, Lai P, Morris A, McVerry B. Longitudinal multicompartment characterization of host-microbiota interactions in patients with acute respiratory failure. Nature Communications 2024, 15: 4708. PMID: 38830853, PMCID: PMC11148165, DOI: 10.1038/s41467-024-48819-8.Peer-Reviewed Original ResearchConceptsAcute respiratory failureRespiratory failureCohort of COVID-19 patientsLung microbiotaMechanically ventilated patientsChronic obstructive pulmonary diseaseIllumina amplicon sequencingDNA sequencing technologiesHost-microbiota interactionsObstructive pulmonary diseaseCOVID-19 patientsAssociated with specific patternsAntibiotic exposureClinical factorsNanopore metagenomicsPredicting survivalPrecision medicine interventionsPrognostic biomarkerSequencing technologiesAmplicon sequencingPulmonary diseaseGut microbiotaCritical illnessMicrobial diversityHuman microbiomeClinical features and multiomics profiles indicate coagulation and platelet dysfunction in COVID-19 viral sepsis
Xiao Z, Lin M, Song N, Wu X, Hou J, Wang L, Tian X, An C, Dela Cruz C, Sharma L, Chang D. Clinical features and multiomics profiles indicate coagulation and platelet dysfunction in COVID-19 viral sepsis. IScience 2024, 27: 110110. PMID: 38974472, PMCID: PMC11225851, DOI: 10.1016/j.isci.2024.110110.Peer-Reviewed Original ResearchViral sepsisCausative agent of sepsisAgent of sepsisCases of sepsisSusceptibility to secondary bacterial infectionsNon-sepsis patientsSecondary bacterial infectionPlatelet activation pathwaysMetabolomic characteristicsPlatelet dysfunctionSepsis phenotypesClinical featuresSystemic disease phenotypeSepsis patientsSepsisCOVID-19 pathologyBacterial infectionsProteomic signatureDisease phenotypeComplement proteinsBacterial pathogensProteomic dataActivation pathwayFunctional consequencesPathway proteinsLung Epithelium Releases Growth Differentiation Factor 15 in Response to Pathogen-mediated Injury
Shah F, Bahudhanapati H, Jiang M, Tabary M, van der Geest R, Tolman N, Kochin M, Xiong Z, Al-Yousif N, Sayed K, Benos P, Raffensperger K, Evankovich J, Neal M, Snyder M, Eickelberg O, Ray P, Dela Cruz C, Bon J, McVerry B, Straub A, Jurczak M, Suber T, Zhang Y, Chen K, Kitsios G, Lee J, Alder J, Bain W. Lung Epithelium Releases Growth Differentiation Factor 15 in Response to Pathogen-mediated Injury. American Journal Of Respiratory Cell And Molecular Biology 2024, 70: 379-391. PMID: 38301257, PMCID: PMC11109583, DOI: 10.1165/rcmb.2023-0429oc.Peer-Reviewed Original ResearchConceptsLung injuryPlasma levelsLung epitheliumGDF15 levelsAssociated with plasma levelsAcute respiratory distress syndromeGrowth differentiation factor 15Acute respiratory failureRespiratory distress syndromeWild-type miceLung cytokine levelsHuman lung epitheliumAcute lung injuryDifferentiation factor 15Levels of GDF15Critically ill humansPrognostic of mortalitySARS-CoV-2 infectionCirculating GDF15 levelsRespiratory tract levelRespiratory failureDistress syndromeCytokine profileStress cytokinesCytokine levelsAnti-inflammatory Roles of Type I Interferon Signaling in the Lung
Feng J, Liu Y, Kim J, Ahangari F, Kaminski N, Bain W, Jie Z, Dela Cruz C, Sharma L. Anti-inflammatory Roles of Type I Interferon Signaling in the Lung. 2024, a6230-a6230. DOI: 10.1164/ajrccm-conference.2024.209.1_meetingabstracts.a6230.Peer-Reviewed Original ResearchInitial and Residual Cardiovascular Damage Remaining at Day 30 in Community-acquired Pneumonia
Méndez Ocaña R, González-Jiménez P, Mengot N, España P, Uranga A, Almirall J, Boixeda R, Alonso R, Piqueras M, Martínez-Dolz L, Dela Cruz C, Menéndez R. Initial and Residual Cardiovascular Damage Remaining at Day 30 in Community-acquired Pneumonia. 2024, a6241-a6241. DOI: 10.1164/ajrccm-conference.2024.209.1_meetingabstracts.a6241.Peer-Reviewed Original ResearchInhibition of Protein Disulfide Isomerase A3 and Osteopontin Attenuates Influenza-induced Lung Fibrosis
Kumar A, Mark Z, Janssen-Heininger Y, Poynter M, Dela Cruz C, Britto-Leon C, Alcorn J, Jegga A, Anathy V. Inhibition of Protein Disulfide Isomerase A3 and Osteopontin Attenuates Influenza-induced Lung Fibrosis. 2024, a2819-a2819. DOI: 10.1164/ajrccm-conference.2024.209.1_meetingabstracts.a2819.Peer-Reviewed Original ResearchChitotriosidase Regulates Host Response to Influenza Lung Infection
Kim J, Amick A, Sharma L, Dela Cruz C. Chitotriosidase Regulates Host Response to Influenza Lung Infection. 2024, a4183-a4183. DOI: 10.1164/ajrccm-conference.2024.209.1_meetingabstracts.a4183.Peer-Reviewed Original ResearchRapid Metagenomic Sequencing (RaMSes) for Comprehensive Detection of Respiratory Pathogens in Patients With Hematologic Malignancy
Hensley M, Sayed K, Haidar G, Wang X, Benos P, Ito S, Im A, Geramita E, Dela Cruz C, Morris A, Kitsios G. Rapid Metagenomic Sequencing (RaMSes) for Comprehensive Detection of Respiratory Pathogens in Patients With Hematologic Malignancy. 2024, a2915-a2915. DOI: 10.1164/ajrccm-conference.2024.209.1_meetingabstracts.a2915.Peer-Reviewed Original ResearchSARS-CoV-2 Viremia Associates With Thrombosis and Mortality in the ACTIV-4a Trial
Zuchelkowski B, Nouraie M, Naqvi A, Qin S, Zhang Y, Dela Cruz C, Zhang L, Mcverry B, Morris A, Neal M, Seheult J, Kitsios G, Mellors J, Kim P, Jacobs J, Bain W. SARS-CoV-2 Viremia Associates With Thrombosis and Mortality in the ACTIV-4a Trial. 2024, a5011-a5011. DOI: 10.1164/ajrccm-conference.2024.209.1_meetingabstracts.a5011.Peer-Reviewed Original ResearchCirculating Glucagon-Like Peptide 1 Predicts Mortality in Critically Ill Patients With Acute Respiratory Failure
Hansell C, Kitsios G, Bain W, Zhao Y, Suber T, Evankovich J, Morris A, Ray P, Ray A, Prendergast N, Hensley M, Petro N, Patel J, Nouraie S, Dela Cruz C, Mcverry B, Zhang Y, Shah F. Circulating Glucagon-Like Peptide 1 Predicts Mortality in Critically Ill Patients With Acute Respiratory Failure. 2024, a1109-a1109. DOI: 10.1164/ajrccm-conference.2024.209.1_meetingabstracts.a1109.Peer-Reviewed Original ResearchSingle Nucleotide Variation in CX3CL1 and Risk for Bacterial Pneumonia and ARDS
Inman K, Chernus J, Lee M, Zhao Y, Shah F, Mayr F, Sharma L, Bon J, Dela Cruz C, Alder J, Mcverry B, Strollo P, Zhang Y, Kitsios G, Feingold E, Bain W. Single Nucleotide Variation in CX3CL1 and Risk for Bacterial Pneumonia and ARDS. 2024, a7203-a7203. DOI: 10.1164/ajrccm-conference.2024.209.1_meetingabstracts.a7203.Peer-Reviewed Original ResearchStreamlined Nucleus Isolation Protocol for Cryopreserved Mouse Lung Captures Non-immune Cell Types by Single-nucleus RNA Sequencing
Tolman N, Tabary M, Sharma L, Dela Cruz C, Alder J, Lee J, Chen K, Bain W. Streamlined Nucleus Isolation Protocol for Cryopreserved Mouse Lung Captures Non-immune Cell Types by Single-nucleus RNA Sequencing. 2024, a3315-a3315. DOI: 10.1164/ajrccm-conference.2024.209.1_meetingabstracts.a3315.Peer-Reviewed Original ResearchIntranasal neomycin evokes broad-spectrum antiviral immunity in the upper respiratory tract
Mao T, Kim J, Peña-Hernández M, Valle G, Moriyama M, Luyten S, Ott I, Gomez-Calvo M, Gehlhausen J, Baker E, Israelow B, Slade M, Sharma L, Liu W, Ryu C, Korde A, Lee C, Monteiro V, Lucas C, Dong H, Yang Y, Initiative Y, Gopinath S, Wilen C, Palm N, Dela Cruz C, Iwasaki A, Vogels C, Hahn A, Chen N, Breban M, Koch T, Chaguza C, Tikhonova I, Castaldi C, Mane S, De Kumar B, Ferguson D, Kerantzas N, Peaper D, Landry M, Schulz W, Grubaugh N. Intranasal neomycin evokes broad-spectrum antiviral immunity in the upper respiratory tract. Proceedings Of The National Academy Of Sciences Of The United States Of America 2024, 121: e2319566121. PMID: 38648490, PMCID: PMC11067057, DOI: 10.1073/pnas.2319566121.Peer-Reviewed Original ResearchConceptsInterferon-stimulated genesRespiratory infectionsStrains of influenza A virusTreatment of respiratory viral infectionsRespiratory virus infectionsInfluenza A virusMouse model of COVID-19Respiratory viral infectionsNeomycin treatmentExpression of interferon-stimulated genesUpper respiratory infectionInterferon-stimulated gene expressionLower respiratory infectionsBroad spectrum of diseasesAdministration of neomycinRespiratory viral diseasesDisease to patientsUpper respiratory tractIntranasal deliveryCongenic miceIntranasal applicationNasal mucosaSevere acute respiratory syndrome coronavirus 2Acute respiratory syndrome coronavirus 2A virusHost-microbe multiomic profiling reveals age-dependent immune dysregulation associated with COVID-19 immunopathology
Phan H, Tsitsiklis A, Maguire C, Haddad E, Becker P, Kim-Schulze S, Lee B, Chen J, Hoch A, Pickering H, van Zalm P, Altman M, Augustine A, Calfee C, Bosinger S, Cairns C, Eckalbar W, Guan L, Jayavelu N, Kleinstein S, Krammer F, Maecker H, Ozonoff A, Peters B, Rouphael N, Montgomery R, Reed E, Schaenman J, Steen H, Levy O, Diray-Arce J, Langelier C, Erle D, Hendrickson C, Kangelaris K, Nguyen V, Lee D, Chak S, Ghale R, Gonzalez A, Jauregui A, Leroux C, Altamirano L, Rashid A, Willmore A, Woodruff P, Krummel M, Carrillo S, Ward A, Patel R, Wilson M, Dandekar R, Alvarenga B, Rajan J, Schroeder A, Fragiadakis G, Mick E, Guerrero Y, Love C, Maliskova L, Adkisson M, Ehrlich L, Melamed E, Rousseau J, Hurley K, Geltman J, Siles N, Rogers J, Kutzler M, Bernui M, Cusimano G, Connors J, Woloszczuk K, Joyner D, Edwards C, Lin E, Melnyk N, Powell D, Kim J, Goonewardene I, Simmons B, Smith C, Martens M, Croen B, Semenza N, Bell M, Furukawa S, McLin R, Tegos G, Rogowski B, Mege N, Ulring K, Holland S, Rosen L, Lee S, Vaysman T, Fernandez-Sesma A, Simon V, Van Bakel H, Gonzalez-Reiche A, Qi J, Carreño J, Singh G, Raskin A, Tcheou J, Khalil Z, van de Guchte A, Farrugia K, Khan Z, Kelly G, Srivastava K, Eaker L, Bermúdez González M, Mulder L, Beach K, Fatou B, Smolen K, Viode A, van Haren S, Jha M, Kho A, Milliren C, Chang A, McEnaney K, Barton B, Lentucci C, Murphy M, Saluvan M, Shaheen T, Liu S, Syphurs C, Albert M, Hayati A, Bryant R, Abraham J, Salehi-Rad R, Rivera A, Sen S, Elashoff D, Ward D, Presnell S, Kohr B, Arnett A, Boddapati A, Tharp G, Pellegrini K, Johnson B, Panganiban B, Huerta C, Anderson E, Samaha H, Sevransky J, Bristow L, Beagle E, Cowan D, Hamilton S, Hodder T, Esserman D, Brito A, Rothman J, Grubaugh N, Ko A, Hafler D, Shaw A, Gygi J, Pawar S, Konstorum A, Chen E, Cotsapas C, Wang X, Xu L, Dela Cruz C, Iwasaki A, Mohanty S, Nelson A, Zhao Y, Farhadian S, Asashima H, Pulendran B, Nadeau R, Rosenberg-Hasson Y, Leipold M, Sigal N, Rogers A, Fernandez A, Manohar M, Do E, Chang I, Vita R, Westendorf K, Corry D, Kheradmand F, Song L, Nelson E, Baden L, Mendez K, Lasky-Su J, Tong A, Rooks R, Sekaly R, Fourati S, McComsey G, Harris P, Sieg S, Ribeiro S, Overton J, Rahman A, Hutton S, Michelotti G, Wong K, Seyfert-Margolis V, Metcalf J, Agudelo Higuita N, Sinko L, Booth J, Messer W, Hough C, Siegel S, Sullivan P, Lu Z, Kraft M, Bime C, Mosier J, Erickson H, Schunk R, Kimura H, Conway M, Atkinson M, Brakenridge S, Ungaro R, Manning B, Oberhaus J, Guirgis F, Borresen B, Anderson M. Host-microbe multiomic profiling reveals age-dependent immune dysregulation associated with COVID-19 immunopathology. Science Translational Medicine 2024, 16: eadj5154. PMID: 38630846, DOI: 10.1126/scitranslmed.adj5154.Peer-Reviewed Original ResearchConceptsPro-inflammatory genesViral clearanceUpper airwayImmune signaling pathwaysInduction of pro-inflammatory genesBiomarkers of disease severityDelayed viral clearanceImpaired viral clearanceSevere coronavirus disease 2019B cell populationsAge-dependent up-regulationExpression of pro-inflammatory genesHost immune responseSignaling pathwayType I interferon gene expressionCOVID-19 immunopathologyInnate immune signaling pathwaysSerum chemokinesAge-dependent impairmentNaive TMulticenter cohortNasal transcriptomeAcute respiratory syndrome coronavirus 2Monocyte populationsSerum protein profilesAnti-inflammatory roles of type I interferon signaling in the lung
Feng J, Liu Y, Kim J, Ahangari F, Kaminski N, Bain W, Jie Z, Dela Cruz C, Sharma L. Anti-inflammatory roles of type I interferon signaling in the lung. American Journal Of Physiology - Lung Cellular And Molecular Physiology 2024, 326: l551-l561. PMID: 38375579, PMCID: PMC11380987, DOI: 10.1152/ajplung.00353.2023.Peer-Reviewed Original ResearchType I interferon signalingIfnar1-/- miceI interferon signalingInflammatory cell responseInflammatory responseIfnar1-/-Bleomycin injuryCell responsesWild-type miceBroncho-alveolar lavageElevated inflammatory responsePersistent inflammatory responseChemotherapeutic agent bleomycinAnti-inflammatory roleClinically relevant stimuliAnti-inflammatory mechanismsMyeloid cellsPersistent inflammationLung injuryFibrotic remodelingBacterial clearanceRIG-I signalingNOD-like receptor signalingLung tissueReceptor signalingDevelopmental changes in lung function of mice are independent of sex as a biological variable
Bärnthaler T, Ramachandra A, Ebanks S, Guerrera N, Sharma L, Dela Cruz C, Humphrey J, Manning E. Developmental changes in lung function of mice are independent of sex as a biological variable. American Journal Of Physiology - Lung Cellular And Molecular Physiology 2024, 326: l627-l637. PMID: 38375577, PMCID: PMC11380952, DOI: 10.1152/ajplung.00120.2023.Peer-Reviewed Original ResearchPulmonary function testsWeeks of ageStatic complianceMale miceInspiratory capacityLung functionBody weight-basedHuman lung pathologiesLung function of miceFemale C57BL/6J miceLung function parametersSex-dependent changesFunction of miceMeasures of lung functionIndependent of sexPreclinical modelsFemale miceC57BL/6J miceLung pathologyFunction testsMiceWeight-basedLungLung disease researchWeeks