Publications

2024

Mast-cell expressed membrane protein-1 is expressed in classical monocytes and alveolar macrophages in idiopathic pulmonary fibrosis and regulates cell chemotaxis, adhesion, and migration in a TGFβ-dependent mannerPerrot C, Karampitsakos T, Unterman A, Adams T, Marlin K, Arsenault A, Zhao A, Kaminski N, Katlaps G, Patel K, Bandyopadhyay D, Herazo-Maya J. Mast-cell expressed membrane protein-1 is expressed in classical monocytes and alveolar macrophages in idiopathic pulmonary fibrosis and regulates cell chemotaxis, adhesion, and migration in a TGFβ-dependent manner. American Journal Of Physiology - Cell Physiology 2024, 326: c964-c977. PMID: 38189137, PMCID: PMC11193480, DOI: 10.1152/ajpcell.00563.2023.

2023

Somatic Mutations: The Next Frontier in Demystifying Chronic Obstructive Pulmonary Disease and Idiopathic Pulmonary Fibrosis?Yan X, Kaminski N. Somatic Mutations: The Next Frontier in Demystifying Chronic Obstructive Pulmonary Disease and Idiopathic Pulmonary Fibrosis? American Journal Of Respiratory And Critical Care Medicine 2023, 208: 1150-1151. PMID: 37856835, PMCID: PMC10868359, DOI: 10.1164/rccm.202310-1774ed.
Circulating Mitochondrial DNA Is Associated With High Levels of Fatigue in Two Independent Sarcoidosis CohortsFiorini V, Hu B, Sun Y, Yu S, McGovern J, Gandhi S, Woo S, Turcotte-Foster S, Pivarnik T, Khan Z, Adams T, Herzog E, Kaminski N, Gulati M, Ryu C. Circulating Mitochondrial DNA Is Associated With High Levels of Fatigue in Two Independent Sarcoidosis Cohorts. CHEST Journal 2023, 165: 1174-1185. PMID: 37977267, PMCID: PMC11110677, DOI: 10.1016/j.chest.2023.11.020.
Correction: iDESC: identifying differential expression in single-cell RNA sequencing data with multiple subjectsLiu Y, Zhao J, Adams T, Wang N, Schupp J, Wu W, McDonough J, Chupp G, Kaminski N, Wang Z, Yan X. Correction: iDESC: identifying differential expression in single-cell RNA sequencing data with multiple subjects. BMC Bioinformatics 2023, 24: 394. PMID: 37858060, PMCID: PMC10588114, DOI: 10.1186/s12859-023-05523-6.
Alveolar Vascular Remodeling in Nonspecific Interstitial Pneumonia: Replacement of Normal Lung Capillaries with COL15A1-Positive Endothelial Cells.Schupp J, Manning E, Chioccioli M, Kamp J, Christian L, Ryu C, Herzog E, Kühnel M, Prasse A, Kaminski N, Jonigk D, Homer R, Neubert L, Ius F, stringJustet A, Hariri L, Seeliger B, Welte T, Knipe R, Gottlieb J. Alveolar Vascular Remodeling in Nonspecific Interstitial Pneumonia: Replacement of Normal Lung Capillaries with COL15A1-Positive Endothelial Cells. American Journal Of Respiratory And Critical Care Medicine 2023, 208: 819-822. PMID: 37552025, PMCID: PMC10563189, DOI: 10.1164/rccm.202303-0544le.
S1581 Assessing the Effectiveness of Incorporating Weight Management Treatments Into a Fatty Liver Disease ProgramDo A, Ilagan-Ying Y, Deng Y, Banini B, Lim J, Mehal W. S1581 Assessing the Effectiveness of Incorporating Weight Management Treatments Into a Fatty Liver Disease Program. The American Journal Of Gastroenterology 2023, 118: s1193-s1194. DOI: 10.14309/01.ajg.0000955964.73046.7b.
Screening, Diagnosis, and Staging of Non-Alcoholic Fatty Liver Disease (NAFLD): Application of Society Guidelines to Clinical PracticeIlagan-Ying Y, Banini B, Do A, Lam R, Lim J. Screening, Diagnosis, and Staging of Non-Alcoholic Fatty Liver Disease (NAFLD): Application of Society Guidelines to Clinical Practice. Current Gastroenterology Reports 2023, 25: 213-224. PMID: 37768417, DOI: 10.1007/s11894-023-00883-8.
Bioactive signalling lipids as drivers of chronic liver diseasesKaffe E, Tisi A, Magkrioti C, Aidinis V, Mehal W, Flavell R, Maccarrone M. Bioactive signalling lipids as drivers of chronic liver diseases. Journal Of Hepatology 2023, 80: 140-154. PMID: 37741346, DOI: 10.1016/j.jhep.2023.08.029.
Exercise Does Not Independently Improve Histological Outcomes in Biopsy-Proven Non-Alcoholic Fatty Liver Disease: A Systematic Review and Meta-AnalysisChen G, Banini B, Do A, Gunderson C, Zaman S, Lim J. Exercise Does Not Independently Improve Histological Outcomes in Biopsy-Proven Non-Alcoholic Fatty Liver Disease: A Systematic Review and Meta-Analysis. Genes 2023, 14: 1811. PMID: 37761951, PMCID: PMC10531443, DOI: 10.3390/genes14091811.
Mechanisms of liver fibrosis in metabolic syndromeMehal W. Mechanisms of liver fibrosis in metabolic syndrome. EGastroenterology 2023, 1: e100015. PMID: 37946713, PMCID: PMC10634657, DOI: 10.1136/egastro-2023-100015.
iDESC: identifying differential expression in single-cell RNA sequencing data with multiple subjectsLiu Y, Zhao J, Adams T, Wang N, Schupp J, Wu W, McDonough J, Chupp G, Kaminski N, Wang Z, Yan X. iDESC: identifying differential expression in single-cell RNA sequencing data with multiple subjects. BMC Bioinformatics 2023, 24: 318. PMID: 37608264, PMCID: PMC10463720, DOI: 10.1186/s12859-023-05432-8.
Humanized mouse liver reveals endothelial control of essential hepatic metabolic functionsKaffe E, Roulis M, Zhao J, Qu R, Sefik E, Mirza H, Zhou J, Zheng Y, Charkoftaki G, Vasiliou V, Vatner D, Mehal W, AlcHepNet, Kluger Y, Flavell R. Humanized mouse liver reveals endothelial control of essential hepatic metabolic functions. Cell 2023, 186: 3793-3809.e26. PMID: 37562401, PMCID: PMC10544749, DOI: 10.1016/j.cell.2023.07.017.
Mitochondrial DNA-Sensing Pathogen Recognition Receptors in Systemic Sclerosis-Associated Interstitial Lung Disease: a ReviewGhincea A, Woo S, Yu S, Pivarnik T, Fiorini V, Herzog E, Ryu C. Mitochondrial DNA-Sensing Pathogen Recognition Receptors in Systemic Sclerosis-Associated Interstitial Lung Disease: a Review. Current Treatment Options In Rheumatology 2023, 9: 204-220. PMID: 38230363, PMCID: PMC10791121, DOI: 10.1007/s40674-023-00211-1.
Multiomics identifies metabolic subtypes based on fatty acid degradation allocating personalized treatment in hepatocellular carcinomaLi B, Li Y, Zhou H, Xu Y, Cao Y, Cheng C, Peng J, Li H, Zhang L, Su K, Xu Z, Hu Y, Lu J, Lu Y, Qian L, Wang Y, Zhang Y, Liu Q, Xie Y, Guo S, Mehal W, Yu D. Multiomics identifies metabolic subtypes based on fatty acid degradation allocating personalized treatment in hepatocellular carcinoma. Hepatology 2023, 79: 289-306. PMID: 37540187, PMCID: PMC10789383, DOI: 10.1097/hep.0000000000000553.
VISTA (PD-1H) Is a Crucial Immune Regulator to Limit Pulmonary Fibrosis.Kim S, Adams T, Hu Q, Shin H, Chae G, Lee S, Sharma L, Kwon H, Lee F, Park H, Huh W, Manning E, Kaminski N, Sauler M, Chen L, Song J, Kim T, Kang M. VISTA (PD-1H) Is a Crucial Immune Regulator to Limit Pulmonary Fibrosis. American Journal Of Respiratory Cell And Molecular Biology 2023, 69: 22-33. PMID: 36450109, PMCID: PMC10324045, DOI: 10.1165/rcmb.2022-0219oc.
Pharmacologic Management of Obesity after Liver Transplantation: A Critical Review.Zahrawi F, Fathma S, Mehal W, Banini B. Pharmacologic Management of Obesity after Liver Transplantation: A Critical Review. Annals Of Gastroenterology And Digestive Disorders 2023, 6: 17-25. PMID: 38098758, PMCID: PMC10719957.
Vascular-Parenchymal Cross-Talk Promotes Lung Fibrosis through BMPR2 Signaling.Yanagihara T, Tsubouchi K, Zhou Q, Chong M, Otsubo K, Isshiki T, Schupp J, Sato S, Scallan C, Upagupta C, Revill S, Ayoub A, Chong S, Dvorkin-Gheva A, Kaminski N, Tikkanen J, Keshavjee S, Paré G, Guignabert C, Ask K, Kolb M. Vascular-Parenchymal Cross-Talk Promotes Lung Fibrosis through BMPR2 Signaling. American Journal Of Respiratory And Critical Care Medicine 2023, 207: 1498-1514. PMID: 36917778, DOI: 10.1164/rccm.202109-2174oc.
PCSK6 and Survival in Idiopathic Pulmonary FibrosisOldham J, Allen R, Lorenzo-Salazar J, Molyneaux P, Ma S, Joseph C, Kim J, Guillen-Guio B, Hernández-Beeftink T, Kropski J, Huang Y, Lee C, Adegunsoye A, Pugashetti J, Linderholm A, Vo V, Strek M, Jou J, Muñoz-Barrera A, Rubio-Rodriguez L, Hubbard R, Hirani N, Whyte M, Hart S, Nicholson A, Lancaster L, Parfrey H, Rassl D, Wallace W, Valenzi E, Zhang Y, Mychaleckyj J, Stockwell A, Kaminski N, Wolters P, Molina-Molina M, Banovich N, Fahy W, Martinez F, Hall I, Tobin M, Maher T, Blackwell T, Yaspan B, Jenkins R, Flores C, Wain L, Noth I. PCSK6 and Survival in Idiopathic Pulmonary Fibrosis. American Journal Of Respiratory And Critical Care Medicine 2023, 207: 1515-1524. PMID: 36780644, PMCID: PMC10263132, DOI: 10.1164/rccm.202205-0845oc.
Call for Papers: Special Issue on Modulation of the Immune System to Improve Tissue Regeneration StrategiesBracaglia L, Kyriakides T. Call for Papers: Special Issue on Modulation of the Immune System to Improve Tissue Regeneration Strategies. Tissue Engineering Part B Reviews 2023, 29: 189-189. DOI: 10.1089/ten.teb.2023.29018.cfp.
Call for Papers: Special Issue on Modulation of the Immune System to Improve Tissue Regeneration StrategiesBracaglia L, Kyriakides T. Call for Papers: Special Issue on Modulation of the Immune System to Improve Tissue Regeneration Strategies. Tissue Engineering Part C Methods 2023 PMID: 37222726, DOI: 10.1089/tec.2023.29038.cfp.
The Pulmonary Fibrosis Drug ConnectomeFlint J, Sharma P, Adams T, Lepe A, Kim H, Abu Hussein N, Schupp J, Cosme Jr. C, Mcdonough J, Sauler M, Yan X, Kaminski N. The Pulmonary Fibrosis Drug Connectome. 2023, a2234-a2234. DOI: 10.1164/ajrccm-conference.2023.207.1_meetingabstracts.a2234.
Identification of Molecular Profiles Predictive of Outcome by RNA-Sequencing of Formalin-Fixed, Paraffin-Embedded (FFPE) Lung Tissue From Patients With Idiopathic Pulmonary FibrosisKarampitsakos T, Juan-Guardela B, Vukmirovic M, Perrot C, Zhang Y, Gibson K, Vamvakaris I, Tzouvelekis A, Yan X, Kaminski N, Herazo-Maya J. Identification of Molecular Profiles Predictive of Outcome by RNA-Sequencing of Formalin-Fixed, Paraffin-Embedded (FFPE) Lung Tissue From Patients With Idiopathic Pulmonary Fibrosis. 2023, a1505-a1505. DOI: 10.1164/ajrccm-conference.2023.207.1_meetingabstracts.a1505.
The Therapeutic Gap in Idiopathic Pulmonary Fibrosis: Insights From Single Cell Transcriptional ProfilingMckenna N, Ochsner S, Moss B, Cala Garcia J, Cardenas Castillo R, Poli F, Poli De Frias S, Tsoyi K, Polverino F, Koenigshoff M, Kaminski N, Coarfa C, Rosas I. The Therapeutic Gap in Idiopathic Pulmonary Fibrosis: Insights From Single Cell Transcriptional Profiling. 2023, a2235-a2235. DOI: 10.1164/ajrccm-conference.2023.207.1_meetingabstracts.a2235.
Age-related Changes in Structure, Function, and Transcriptomics of the Human Proximal Pulmonary ArteryManning E, Ramachandra A, Cavinato C, Schupp J, Justet A, Lee P, Heerdt P, Singh I, Murphy T, Gill T, Tellides G, Kaminski N, Humphrey J. Age-related Changes in Structure, Function, and Transcriptomics of the Human Proximal Pulmonary Artery. 2023, a4656-a4656. DOI: 10.1164/ajrccm-conference.2023.207.1_meetingabstracts.a4656.
High-dimensional Analysis of Cell-cell Signaling in Pulmonary Biology and Disease Using NichesRaredon M, Yang J, Kothapalli N, Greaney A, Justet A, Adams T, Zhao A, Kim H, Manning E, Medzhitov R, Niklason L, Kaminski N, Kluger Y. High-dimensional Analysis of Cell-cell Signaling in Pulmonary Biology and Disease Using Niches. 2023, a4697-a4697. DOI: 10.1164/ajrccm-conference.2023.207.1_meetingabstracts.a4697.
Pulmonary Hypertension-related Changes in Structure and Function of the Human Proximal Pulmonary ArteryManning E, Ramachandra A, Cavinato C, Lee P, Heerdt P, Singh I, Tellides G, Kaminski N, Humphrey J. Pulmonary Hypertension-related Changes in Structure and Function of the Human Proximal Pulmonary Artery. 2023, a6133-a6133. DOI: 10.1164/ajrccm-conference.2023.207.1_meetingabstracts.a6133.
Mitochondrial DNA-toll-like Receptor 9 Interactions Drives Fibrosis in the Adult LungRyu C, Hu B, Sun Y, Yu S, Woo S, Fiorini V, Pivarnik T, Mcgovern J, Peng X, Herzog E, Trujillo G. Mitochondrial DNA-toll-like Receptor 9 Interactions Drives Fibrosis in the Adult Lung. 2023, a1376-a1376. DOI: 10.1164/ajrccm-conference.2023.207.1_meetingabstracts.a1376.
Rational engineering of lung alveolar epitheliumLeiby K, Yuan Y, Ng R, Raredon M, Adams T, Baevova P, Greaney A, Hirschi K, Campbell S, Kaminski N, Herzog E, Niklason L. Rational engineering of lung alveolar epithelium. Npj Regenerative Medicine 2023, 8: 22. PMID: 37117221, PMCID: PMC10147714, DOI: 10.1038/s41536-023-00295-2.
Emergence of division of labor in tissues through cell interactions and spatial cuesAdler M, Moriel N, Goeva A, Avraham-Davidi I, Mages S, Adams T, Kaminski N, Macosko E, Regev A, Medzhitov R, Nitzan M. Emergence of division of labor in tissues through cell interactions and spatial cues. Cell Reports 2023, 42: 112412. PMID: 37086403, PMCID: PMC10242439, DOI: 10.1016/j.celrep.2023.112412.
Correction: Chitinase 1 regulates pulmonary fibrosis by modulating TGF-β/SMAD7 pathway via TGFBRAP1 and FOXO3Lee C, He C, Park J, Lee J, Kamle S, Ma B, Akosman B, Cotez R, Chen E, Zhou Y, Herzog E, Ryu C, Peng X, Rosas I, Poli S, Bostwick C, Choi A, Elias J, Lee C. Correction: Chitinase 1 regulates pulmonary fibrosis by modulating TGF-β/SMAD7 pathway via TGFBRAP1 and FOXO3. Life Science Alliance 2023, 6: e202302065. PMID: 37037591, PMCID: PMC10088146, DOI: 10.26508/lsa.202302065.
Mitochondrial DNA and the STING pathway are required for hepatic stellate cell activationArumugam S, Li B, Boodapati S, Nathanson M, Sun B, Ouyang X, Mehal W. Mitochondrial DNA and the STING pathway are required for hepatic stellate cell activation. Hepatology 2023, 78: 1448-1461. PMID: 37013923, PMCID: PMC10804318, DOI: 10.1097/hep.0000000000000388.
New uses for an old remedy: Digoxin as a potential treatment for steatohepatitis and other disordersJamshed F, Dashti F, Ouyang X, Mehal W, Banini B. New uses for an old remedy: Digoxin as a potential treatment for steatohepatitis and other disorders. World Journal Of Gastroenterology 2023, 29: 1824-1837. PMID: 37032732, PMCID: PMC10080697, DOI: 10.3748/wjg.v29.i12.1824.
microRNA-33 deficiency in macrophages enhances autophagy, improves mitochondrial homeostasis, and protects against lung fibrosisAhangari F, Price N, Malik S, Chioccioli M, Bärnthaler T, Adams T, Kim J, Pradeep S, Ding S, Cosme C, Rose K, McDonough J, Aurelien N, Ibarra G, Omote N, Schupp J, DeIuliis G, Nunez J, Sharma L, Ryu C, Dela Cruz C, Liu X, Prasse A, Rosas I, Bahal R, Fernandez-Hernando C, Kaminski N. microRNA-33 deficiency in macrophages enhances autophagy, improves mitochondrial homeostasis, and protects against lung fibrosis. JCI Insight 2023, 8: e158100. PMID: 36626225, PMCID: PMC9977502, DOI: 10.1172/jci.insight.158100.
α1 Adrenoreceptor antagonism mitigates extracellular mitochondrial DNA accumulation in lung fibrosis models and in patients with idiopathic pulmonary fibrosisIshikawa G, Peng X, McGovern J, Woo S, Perry C, Liu A, Yu S, Ghincea A, Kishchanka A, Fiorini V, Hu B, Sun Y, Sun H, Ryu C, Herzog E. α1 Adrenoreceptor antagonism mitigates extracellular mitochondrial DNA accumulation in lung fibrosis models and in patients with idiopathic pulmonary fibrosis. American Journal Of Physiology - Lung Cellular And Molecular Physiology 2023, 324: l639-l651. PMID: 36648147, PMCID: PMC10110730, DOI: 10.1152/ajplung.00119.2022.

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