Select Publications

2023

Somatic Mutations: The Next Frontier in Demystifying Chronic Obstructive Pulmonary Disease and Idiopathic Pulmonary Fibrosis?Yan X, Kaminski N. Am J Respir Crit Care Med. 2023 Dec 1. PMID: 37856835.
Circulating Mitochondrial DNA is associated with High Levels of Fatigue in Two Independent Sarcoidosis Cohorts.Fiorini V, Hu B, Sun Y, Yu S, McGovern J, Gandhi S, Woo S, Turcotte-Foster SJ, Pivarnik T, Khan Z, Adams T, Herzog E, Kaminski N, Gulati M, Ryu C. Chest. 2023 Nov 15; 2023 Nov 15. PMID: 37977267.
Increased Expression of CXCL6 in Secretory Cells Drives Fibroblast Collagen Synthesis and is Associated With Increased Mortality in Idiopathic Pulmonary Fibrosis.Bahudhanapati H, Tan J, Apel RM, Seeliger B, Schupp J, Li X, Sullivan DI, Sembrat J, Rojas M, Tabib T, Valenzi E, Lafyatis R, Mitash N, Pineda RH, Jawale C, Peroumal D, Biswas P, Tedrow J, Adams T, Kaminski N, Wuyts WA, McDyer JF, Gibson KF, Alder JK, Königshoff M, Zhang Y, Nouraie M, Prasse A, Kass DJ. Eur Respir J. 2023 Nov 2; 2023 Nov 2. PMID: 37918852.
Distinguishing features of long COVID identified through immune profiling.Klein J, Wood J, Jaycox JR, Dhodapkar RM, Lu P, Gehlhausen JR, Tabachnikova A, Greene K, Tabacof L, Malik AA, Silva Monteiro V, Silva J, Kamath K, Zhang M, Dhal A, Ott IM, Valle G, Peña-Hernández M, Mao T, Bhattacharjee B, Takahashi T, Lucas C, Song E, McCarthy D, Breyman E, Tosto-Mancuso J, Dai Y, Perotti E, Akduman K, Tzeng TJ, Xu L, Geraghty AC, Monje M, Yildirim I, Shon J, Medzhitov R, Lutchmansingh D, Possick JD, Kaminski N, Omer SB, Krumholz HM, Guan L, Dela Cruz CS, van Dijk D, Ring AM, Putrino D, Iwasaki A. Nature. 2023 Nov; 2023 Sep 25. PMID: 37748514.
Challenges and Opportunities for Commercializing Technologies in the Pulmonary Arena: An Official American Thoracic Society Report.Vukmirovic M, Benam KH, Rose JJ, Turner S, Magin CM, Lagares D, Cohen AH, Kaminski N, Hirota JA, Maher TM, Königshoff M, Mallampalli RK, Sheppard D, Tarran R, Gomer RH, Kenyon NJ, Morris D, Hobbie S, Raju SV, Petrache I, Watkins T, Kumar R, Lam WA, Sherer T, Hecker L. Ann Am Thorac Soc. 2023 Oct 30; 2023 Oct 30. PMID: 37903340.
Correction: iDESC: identifying differential expression in single-cell RNA sequencing data with multiple subjects.Liu Y, Zhao J, Adams TS, Wang N, Schupp JC, Wu W, McDonough JE, Chupp GL, Kaminski N, Wang Z, Yan X. BMC Bioinformatics. 2023 Oct 19; 2023 Oct 19. PMID: 37858060.
Mucosal immune alterations at the early onset of tissue destruction in chronic obstructive pulmonary disease.de Fays C, Geudens V, Gyselinck I, Kerckhof P, Vermaut A, Goos T, Vermant M, Beeckmans H, Kaes J, Van Slambrouck J, Mohamady Y, Willems L, Aversa L, Cortesi EE, Hooft C, Aerts G, Aelbrecht C, Everaerts S, McDonough JE, De Sadeleer LJ, Gohy S, Ambroise J, Janssens W, Ceulemans LJ, Van Raemdonck D, Vos R, Hackett TL, Hogg JC, Kaminski N, Gayan-Ramirez G, Pilette C, Vanaudenaerde BM. Front Immunol. 2023; 2023 Oct 17. PMID: 37915582.
Mast-Cell Expressed Membrane Protein-1 (MCEMP1) is expressed in classical monocytes and alveolar macrophages in Idiopathic Pulmonary Fibrosis and regulates cell chemotaxis, adhesion, and migration in a TGFβ dependent manner.Perrot CY, Karampitsakos T, Unterman A, Adams T, Marlin K, Arsenault A, Zhao A, Kaminski N, Katlaps G, Patel K, Bandyopadhyay D, Herazo-Maya JD. bioRxiv. 2023 Oct 10; 2023 Oct 10. PMID: 37873485.
Fossil Industry and Respiratory Societies - Time for a Clear Stand.Piccari L, Kaminski N, Mann ME. Am J Respir Crit Care Med. 2023 Oct 5; 2023 Oct 5. PMID: 37796608.
Alveolar Vascular Remodeling in Nonspecific Interstitial Pneumonia: Replacement of Normal Lung Capillaries with COL15A1-Positive Endothelial Cells.Schupp JC, Manning EP, Chioccioli M, Kamp JC, Christian L, Ryu C, Herzog E, Kühnel MP, Prasse A, Kaminski N, Jonigk DD, Homer RJ. Am J Respir Crit Care Med. 2023 Oct 1. PMID: 37552025.
Genetic analyses of chr11p15.5 region identify MUC5AC-MUC5B associated with asthma-related phenotypes.Li X, Li H, Christenson SA, Castro M, Denlinger LC, Erzurum SC, Fahy JV, Gaston BM, Israel E, Jarjour NN, Levy BD, Mauger DT, Moore WC, Zein J, Kaminski N, Wenzel SE, Woodruff PG, Bleecker ER, Meyers DA. J Asthma. 2023 Oct; 2023 Apr 21. PMID: 36946148.
Peripheral Blood Single-Cell Sequencing Uncovers Common and Specific Immune Aberrations in Fibrotic Lung Diseases.Zhao AY, Unterman A, Abu Hussein N, Sharma P, Flint J, Yan X, Adams TS, Justet A, Sumida TS, Zhao J, Schupp JC, Raredon MSB, Ahangari F, Zhang Y, Buendia-Roldan I, Adegunsoye A, Sperling AI, Prasse A, Ryu C, Herzog E, Selman M, Pardo A, Kaminski N. bioRxiv. 2023 Sep 22; 2023 Sep 22. PMID: 37786685.
SRC and TKS5 mediated podosome formation in fibroblasts promotes extracellular matrix invasion and pulmonary fibrosis.Barbayianni I, Kanellopoulou P, Fanidis D, Nastos D, Ntouskou ED, Galaris A, Harokopos V, Hatzis P, Tsitoura E, Homer R, Kaminski N, Antoniou KM, Crestani B, Tzouvelekis A, Aidinis V. Nat Commun. 2023 Sep 21; 2023 Sep 21. PMID: 37735172.
When Development of the Alveolar Gas Exchange Unit Fails: Universal Single-Cell Lessons from Rare Monogenic Disorders.Schupp JC, Kaminski N. Am J Respir Crit Care Med. 2023 Sep 15. PMID: 37555730.
An AI-powered patient triage platform for future viral outbreaks using COVID-19 as a disease model.Charkoftaki G, Aalizadeh R, Santos-Neto A, Tan WY, Davidson EA, Nikolopoulou V, Wang Y, Thompson B, Furnary T, Chen Y, Wunder EA, Coppi A, Schulz W, Iwasaki A, Pierce RW, Cruz CSD, Desir GV, Kaminski N, Farhadian S, Veselkov K, Datta R, Campbell M, Thomaidis NS, Ko AI, Thompson DC, Vasiliou V. Hum Genomics. 2023 Aug 29; 2023 Aug 29. PMID: 37641126.
A hybrid machine learning and regression method for cell type deconvolution of spatial barcoding-based transcriptomic data.Liu Y, Li N, Qi J, Xu G, Zhao J, Wang N, Huang X, Jiang W, Justet A, Adams TS, Homer R, Amei A, Rosas IO, Kaminski N, Wang Z, Yan X. bioRxiv. 2023 Aug 26; 2023 Aug 26. PMID: 37662370.
iDESC: identifying differential expression in single-cell RNA sequencing data with multiple subjects.Liu Y, Zhao J, Adams TS, Wang N, Schupp JC, Wu W, McDonough JE, Chupp GL, Kaminski N, Wang Z, Yan X. BMC Bioinformatics. 2023 Aug 22; 2023 Aug 22. PMID: 37608264.
Integrative genetic and genomic networks identify microRNA associated with COPD and ILD.Pavel AB, Garrison C, Luo L, Liu G, Taub D, Xiao J, Juan-Guardela B, Tedrow J, Alekseyev YO, Yang IV, Geraci MW, Sciurba F, Schwartz DA, Kaminski N, Beane J, Spira A, Lenburg ME, Campbell JD. Sci Rep. 2023 Aug 11; 2023 Aug 11. PMID: 37567908.
Integrative analyses for the identification of idiopathic pulmonary fibrosis-associated genes and shared loci with other diseases.Chen M, Zhang Y, Adams T, Ji D, Jiang W, Wain LV, Cho M, Kaminski N, Zhao H. Thorax. 2023 Aug; 2022 Oct 10. PMID: 36216496.
A statistical framework to identify cell types whose genetically regulated proportions are associated with complex diseases.Liu W, Deng W, Chen M, Dong Z, Zhu B, Yu Z, Tang D, Sauler M, Lin C, Wain LV, Cho MH, Kaminski N, Zhao H. PLoS Genet. 2023 Jul; 2023 Jul 31. PMID: 37523391.
Association study of human leukocyte antigen (HLA) variants and idiopathic pulmonary fibrosis.Guillen-Guio B, Paynton ML, Allen RJ, Chin DPW, Donoghue LJ, Stockwell A, Leavy OC, Hernandez-Beeftink T, Reynolds C, Cullinan P, Martinez F, Booth HL, Fahy WA, Hall IP, Hart SP, Hill MR, Hirani N, Hubbard RB, McAnulty RJ, Millar AB, Navaratnam V, Oballa E, Parfrey H, Saini G, Sayers I, Tobin MD, Whyte MKB, Adegunsoye A, Kaminski N, Shwu-Fan M, Strek ME, Zhang Y, Fingerlin TE, Molina-Molina M, Neighbors M, Sheng XR, Oldham JM, Maher TM, Molyneaux PL, Flores C, Noth I, Schwartz DA, Yaspan BL, Jenkins RG, Wain LV, Hollox EJ. medRxiv. 2023 Jul 24; 2023 Jul 24. PMID: 37546732.
COVID-19 annual update: a narrative review.Biancolella M, Colona VL, Luzzatto L, Watt JL, Mattiuz G, Conticello SG, Kaminski N, Mehrian-Shai R, Ko AI, Gonsalves GS, Vasiliou V, Novelli G, Reichardt JKV. Hum Genomics. 2023 Jul 24; 2023 Jul 24. PMID: 37488607.
VISTA (PD-1H) Is a Crucial Immune Regulator to Limit Pulmonary Fibrosis.Kim SH, Adams TS, Hu Q, Shin HJ, Chae G, Lee SE, Sharma L, Kwon HK, Lee FY, Park HJ, Huh WJ, Manning E, Kaminski N, Sauler M, Chen L, Song JW, Kim TK, Kang MJ. Am J Respir Cell Mol Biol. 2023 Jul. PMID: 36450109.
A Picture Worth a Thousand Words, Created with One Sentence: Using Artificial Intelligence-created Art to Enhance Medical Education.Huston JC, Kaminski N. ATS Sch. 2023 Jun; 2023 May 10. PMID: 37533539.
An integrated cell atlas of the lung in health and disease.Sikkema L, Ramírez-Suástegui C, Strobl DC, Gillett TE, Zappia L, Madissoon E, Markov NS, Zaragosi LE, Ji Y, Ansari M, Arguel MJ, Apperloo L, Banchero M, Bécavin C, Berg M, Chichelnitskiy E, Chung MI, Collin A, Gay ACA, Gote-Schniering J, Hooshiar Kashani B, Inecik K, Jain M, Kapellos TS, Kole TM, Leroy S, Mayr CH, Oliver AJ, von Papen M, Peter L, Taylor CJ, Walzthoeni T, Xu C, Bui LT, De Donno C, Dony L, Faiz A, Guo M, Gutierrez AJ, Heumos L, Huang N, Ibarra IL, Jackson ND, Kadur Lakshminarasimha Murthy P, Lotfollahi M, Tabib T, Talavera-López C, Travaglini KJ, Wilbrey-Clark A, Worlock KB, Yoshida M, van den Berge M, Bossé Y, Desai TJ, Eickelberg O, Kaminski N, Krasnow MA, Lafyatis R, Nikolic MZ, Powell JE, Rajagopal J, Rojas M, Rozenblatt-Rosen O, Seibold MA, Sheppard D, Shepherd DP, Sin DD, Timens W, Tsankov AM, Whitsett J, Xu Y, Banovich NE, Barbry P, Duong TE, Falk CS, Meyer KB, Kropski JA, Pe'er D, Schiller HB, Tata PR, Schultze JL, Teichmann SA, Misharin AV, Nawijn MC, Luecken MD, Theis FJ. Nat Med. 2023 Jun; 2023 Jun 8. PMID: 37291214.
Vascular-Parenchymal Cross-Talk Promotes Lung Fibrosis through BMPR2 Signaling.Yanagihara T, Tsubouchi K, Zhou Q, Chong M, Otsubo K, Isshiki T, Schupp JC, Sato S, Scallan C, Upagupta C, Revill S, Ayoub A, Chong SG, Dvorkin-Gheva A, Kaminski N, Tikkanen J, Keshavjee S, Paré G, Guignabert C, Ask K, Kolb MRJ. Am J Respir Crit Care Med. 2023 Jun 1. PMID: 36917778.
Medical Societies Must Choose Professional Meeting Locations Responsibly in a Post-Roe World.Lee AG, Maley J, Hibbert K, Akgün KM, Hauschildt KE, Law A, Kaminski N, Hayes M, Gesthalter Y, Bosslet GT, Santhosh L, Witkin A, Hills-Dunlap K, Çoruh B, Gershengorn HB, Hardin CC. Ann Am Thorac Soc. 2023 Jun. PMID: 36812378.
PCSK6 and Survival in Idiopathic Pulmonary Fibrosis.Oldham JM, Allen RJ, Lorenzo-Salazar JM, Molyneaux PL, Ma SF, Joseph C, Kim JS, Guillen-Guio B, Hernández-Beeftink T, Kropski JA, Huang Y, Lee CT, Adegunsoye A, Pugashetti JV, Linderholm AL, Vo V, Strek ME, Jou J, Muñoz-Barrera A, Rubio-Rodriguez LA, Hubbard R, Hirani N, Whyte MKB, Hart S, Nicholson AG, Lancaster L, Parfrey H, Rassl D, Wallace W, Valenzi E, Zhang Y, Mychaleckyj J, Stockwell A, Kaminski N, Wolters PJ, Molina-Molina M, Banovich NE, Fahy WA, Martinez FJ, Hall IP, Tobin MD, Maher TM, Blackwell TS, Yaspan BL, Jenkins RG, Flores C, Wain LV, Noth I. Am J Respir Crit Care Med. 2023 Jun 1. PMID: 36780644.
Emergence of division of labor in tissues through cell interactions and spatial cues.Adler M, Moriel N, Goeva A, Avraham-Davidi I, Mages S, Adams TS, Kaminski N, Macosko EZ, Regev A, Medzhitov R, Nitzan M. Cell Rep. 2023 May 30; 2023 Apr 21. PMID: 37086403.
Single-cell profiling reveals immune aberrations in progressive idiopathic pulmonary fibrosis.Unterman A, Zhao AY, Neumark N, Schupp JC, Ahangari F, Cosme C Jr, Sharma P, Flint J, Stein Y, Ryu C, Ishikawa G, Sumida TS, Gomez JL, Herazo-Maya J, Dela Cruz CS, Herzog EL, Kaminski N. medRxiv. 2023 Apr 29; 2023 Apr 29. PMID: 37163015.
Rational engineering of lung alveolar epithelium.Leiby KL, Yuan Y, Ng R, Raredon MSB, Adams TS, Baevova P, Greaney AM, Hirschi KK, Campbell SG, Kaminski N, Herzog EL, Niklason LE. NPJ Regen Med. 2023 Apr 28; 2023 Apr 28. PMID: 37117221.
Thyroid hormone modulates hyperoxic neonatal lung injury and mitochondrial function.Vamesu BM, Nicola T, Li R, Hazra S, Matalon S, Kaminski N, Ambalavanan N, Kandasamy J. JCI Insight. 2023 Apr 24; 2023 Apr 24. PMID: 36917181.
A Multi-omic Analysis of the Human Lung Reveals Distinct Cell Specific Aging and Senescence Molecular Programs.De Man R, McDonough JE, Adams TS, Manning EP, Myers G, Vos R, Ceulemans L, Dupont L, Vanaudenaerde BM, Wuyts WA, Rosas IO, Hagood JS, Ambalavanan N, Niklason L, Hansen KC, Yan X, Kaminski N. bioRxiv. 2023 Apr 19; 2023 Apr 19. PMID: 37131739.
Transbronchial Lung Cryobiopsy for the Diagnosis of Interstitial Lung Disease: A Right Answer to a Wrong Question Is Still a Wrong Answer.Low SW, Kaminski N, Maldonado F. J Bronchology Interv Pulmonol. 2023 Apr 1; 2023 Apr 1. PMID: 37005378.
SH2 Domain-Containing Phosphatase-SHP2 Attenuates Fibrotic Responses through Negative Regulation of Mitochondrial Metabolism in Lung Fibroblasts.Karampitsakos T, Galaris A, Barbayianni I, DeIuliis G, Ahangari F, Sampsonas F, Sotiropoulou V, Aidinis V, Bennett AM, Herazo-Maya JD, Xylourgidis N, Bakakos P, Bouros D, Kaminski N, Tzouvelekis A. Diagnostics (Basel). 2023 Mar 18; 2023 Mar 18. PMID: 36980473.
microRNA-33 deficiency in macrophages enhances autophagy, improves mitochondrial homeostasis, and protects against lung fibrosis.Ahangari F, Price NL, Malik S, Chioccioli M, Bärnthaler T, Adams TS, Kim J, Pradeep SP, Ding S, Cosmos C Jr, Rose KS, McDonough JE, Aurelien NR, Ibarra G, Omote N, Schupp JC, DeIuliis G, Villalba Nunez JA, Sharma L, Ryu C, Dela Cruz CS, Liu X, Prasse A, Rosas I, Bahal R, Fernández-Hernando C, Kaminski N. JCI Insight. 2023 Feb 22; 2023 Feb 22. PMID: 36626225.
Low CC16 mRNA Expression Levels in Bronchial Epithelial Cells Are Associated with Asthma Severity.Li X, Guerra S, Ledford JG, Kraft M, Li H, Hastie AT, Castro M, Denlinger LC, Erzurum SC, Fahy JV, Gaston B, Israel E, Jarjour NN, Levy BD, Mauger DT, Moore WC, Zein J, Kaminski N, Wenzel SE, Woodruff PG, Meyers DA, Bleecker ER. Am J Respir Crit Care Med. 2023 Feb 15. PMID: 36066606.
Lung Cell Atlases in Health and Disease.Adams TS, Marlier A, Kaminski N. Annu Rev Physiol. 2023 Feb 10; 2022 Nov 9. PMID: 36351366.
Single-cell RNA-seq uncovers cellular heterogeneity and provides a signature for paediatric sleep apnoea.Cortese R, Adams TS, Cataldo KH, Hummel J, Kaminski N, Kheirandish-Gozal L, Gozal D. Eur Respir J. 2023 Feb; 2023 Feb 9. PMID: 36356973.
PD-1(high)CXCR5(-)CD4(+) peripheral helper T cells promote CXCR3(+) plasmablasts in human acute viral infection.Asashima H, Mohanty S, Comi M, Ruff WE, Hoehn KB, Wong P, Klein J, Lucas C, Cohen I, Coffey S, Lele N, Greta L, Raddassi K, Chaudhary O, Unterman A, Emu B, Kleinstein SH, Montgomery RR, Iwasaki A, Dela Cruz CS, Kaminski N, Shaw AC, Hafler DA, Sumida TS. Cell Rep. 2023 Jan 31; 2023 Jan 2. PMID: 36596303.
A novel Bayesian framework for harmonizing information across tissues and studies to increase cell type deconvolution accuracy.Deng W, Li B, Wang J, Jiang W, Yan X, Li N, Vukmirovic M, Kaminski N, Wang J, Zhao H. Brief Bioinform. 2023 Jan 19. PMID: 36631398.
Comprehensive visualization of cell-cell interactions in single-cell and spatial transcriptomics with NICHES.Raredon MSB, Yang J, Kothapalli N, Lewis W, Kaminski N, Niklason LE, Kluger Y. Bioinformatics. 2023 Jan 1. PMID: 36458905.
Longitudinal lung function and gas transfer in individuals with idiopathic pulmonary fibrosis: a genome-wide association study.Allen RJ, Oldham JM, Jenkins DA, Leavy OC, Guillen-Guio B, Melbourne CA, Ma SF, Jou J, Kim JS, Fahy WA, Oballa E, Hubbard RB, Navaratnam V, Braybrooke R, Saini G, Roach KM, Tobin MD, Hirani N, Whyte MKB, Kaminski N, Zhang Y, Martinez FJ, Linderholm AL, Adegunsoye A, Strek ME, Maher TM, Molyneaux PL, Flores C, Noth I, Gisli Jenkins R, Wain LV. Lancet Respir Med. 2023 Jan; 2022 Aug 16. PMID: 35985358.

2022

Metagenomic sequencing of the bronchoalveolar lavage extracellular virome and cellular transcriptome of sarcoidosis patients does not detect rubella virus.Keeler EL, Vukmirovic M, Yan X, Gulino K, Ghedin E, Kaminski N, Sullivan KE, Bushman FD, Collman RG, Rosenbach M. Sarcoidosis Vasc Diffuse Lung Dis. 2022 Dec 19; 2022 Dec 19. PMID: 36533601.
Saracatinib, a Selective Src Kinase Inhibitor, Blocks Fibrotic Responses in Preclinical Models of Pulmonary Fibrosis.Ahangari F, Becker C, Foster DG, Chioccioli M, Nelson M, Beke K, Wang X, Justet A, Adams T, Readhead B, Meador C, Correll K, Lili LN, Roybal HM, Rose KA, Ding S, Barnthaler T, Briones N, DeIuliis G, Schupp JC, Li Q, Omote N, Aschner Y, Sharma L, Kopf KW, Magnusson B, Hicks R, Backmark A, Dela Cruz CS, Rosas I, Cousens LP, Dudley JT, Kaminski N, Downey GP. Am J Respir Crit Care Med. 2022 Dec 15. PMID: 35998281.
A lung targeted miR-29 mimic as a therapy for pulmonary fibrosis.Chioccioli M, Roy S, Newell R, Pestano L, Dickinson B, Rigby K, Herazo-Maya J, Jenkins G, Ian S, Saini G, Johnson SR, Braybrooke R, Yu G, Sauler M, Ahangari F, Ding S, DeIuliis J, Aurelien N, Montgomery RL, Kaminski N. EBioMedicine. 2022 Nov; 2022 Oct 17. PMID: 36265417.
Airway basal cells show a dedifferentiated KRT17(high)Phenotype and promote fibrosis in idiopathic pulmonary fibrosis.Jaeger B, Schupp JC, Plappert L, Terwolbeck O, Artysh N, Kayser G, Engelhard P, Adams TS, Zweigerdt R, Kempf H, Lienenklaus S, Garrels W, Nazarenko I, Jonigk D, Wygrecka M, Klatt D, Schambach A, Kaminski N, Prasse A. Nat Commun. 2022 Sep 26; 2022 Sep 26. PMID: 36163190.
CINS: Cell Interaction Network inference from Single cell expression data.Yuan Y, Cosme C Jr, Adams TS, Schupp J, Sakamoto K, Xylourgidis N, Ruffalo M, Li J, Kaminski N, Bar-Joseph Z. PLoS Comput Biol. 2022 Sep; 2022 Sep 12. PMID: 36095011.
CD38 Mediates Lung Fibrosis by Promoting Alveolar Epithelial Cell Aging.Cui H, Xie N, Banerjee S, Dey T, Liu RM, Antony VB, Sanders YY, Adams TS, Gomez JL, Thannickal VJ, Kaminski N, Liu G. Am J Respir Crit Care Med. 2022 Aug 15. PMID: 35687485.
Microenvironmental sensing by fibroblasts controls macrophage population size.Zhou X, Franklin RA, Adler M, Carter TS, Condiff E, Adams TS, Pope SD, Philip NH, Meizlish ML, Kaminski N, Medzhitov R. Proc Natl Acad Sci U S A. 2022 Aug 9; 2022 Aug 5. PMID: 35930670.
From COVID to fibrosis: lessons from single-cell analyses of the human lung.Justet A, Zhao AY, Kaminski N. Hum Genomics. 2022 Jun 13; 2022 Jun 13. PMID: 35698166.
Bronchial epithelium epithelial-mesenchymal plasticity forms aberrant basaloid-like cells in vitro.Uthaya Kumar DB, Motakis E, Yurieva M, Kohar V, Martinek J, Wu TC, Khoury J, Grassmann J, Lu M, Palucka K, Kaminski N, Koff JL, Williams A. Am J Physiol Lung Cell Mol Physiol. 2022 Jun 1; 2022 Apr 19. PMID: 35438006.
BAL Transcriptomes Characterize Idiopathic Pulmonary Fibrosis Endotypes With Prognostic Impact.De Sadeleer LJ, Verleden SE, Schupp JC, McDonough JE, Goos T, Yserbyt J, Bargagli E, Rottoli P, Kaminski N, Prasse A, Wuyts WA. Chest. 2022 Jun; 2022 Jan 19. PMID: 35063449.
FK506-Binding Protein 11 Is a Novel Plasma Cell-Specific Antibody Folding Catalyst with Increased Expression in Idiopathic Pulmonary Fibrosis.Preisendörfer S, Ishikawa Y, Hennen E, Winklmeier S, Schupp JC, Knüppel L, Fernandez IE, Binzenhöfer L, Flatley A, Juan-Guardela BM, Ruppert C, Guenther A, Frankenberger M, Hatz RA, Kneidinger N, Behr J, Feederle R, Schepers A, Hilgendorff A, Kaminski N, Meinl E, Bächinger HP, Eickelberg O, Staab-Weijnitz CA. Cells. 2022 Apr 14; 2022 Apr 14. PMID: 35456020.
Type I interferon transcriptional network regulates expression of coinhibitory receptors in human T cells.Sumida TS, Dulberg S, Schupp JC, Lincoln MR, Stillwell HA, Axisa PP, Comi M, Unterman A, Kaminski N, Madi A, Kuchroo VK, Hafler DA. Nat Immunol. 2022 Apr; 2022 Mar 17. PMID: 35301508.
Computation and visualization of cell-cell signaling topologies in single-cell systems data using Connectome.Raredon MSB, Yang J, Garritano J, Wang M, Kushnir D, Schupp JC, Adams TS, Greaney AM, Leiby KL, Kaminski N, Kluger Y, Levchenko A, Niklason LE. Sci Rep. 2022 Mar 9; 2022 Mar 9. PMID: 35264704.
Pseudohypoxic HIF pathway activation dysregulates collagen structure-function in human lung fibrosis.Brereton CJ, Yao L, Davies ER, Zhou Y, Vukmirovic M, Bell JA, Wang S, Ridley RA, Dean LSN, Andriotis OG, Conforti F, Brewitz L, Mohammed S, Wallis T, Tavassoli A, Ewing RM, Alzetani A, Marshall BG, Fletcher SV, Thurner PJ, Fabre A, Kaminski N, Richeldi L, Bhaskar A, Schofield CJ, Loxham M, Davies DE, Wang Y, Jones MG. Elife. 2022 Feb 21; 2022 Feb 21. PMID: 35188460.
Characterization of the COPD alveolar niche using single-cell RNA sequencing.Sauler M, McDonough JE, Adams TS, Kothapalli N, Barnthaler T, Werder RB, Schupp JC, Nouws J, Robertson MJ, Coarfa C, Yang T, Chioccioli M, Omote N, Cosme C Jr, Poli S, Ayaub EA, Chu SG, Jensen KH, Gomez JL, Britto CJ, Raredon MSB, Niklason LE, Wilson AA, Timshel PN, Kaminski N, Rosas IO. Nat Commun. 2022 Jan 25; 2022 Jan 25. PMID: 35078977.
Single-cell multi-omics reveals dyssynchrony of the innate and adaptive immune system in progressive COVID-19.Unterman A, Sumida TS, Nouri N, Yan X, Zhao AY, Gasque V, Schupp JC, Asashima H, Liu Y, Cosme C Jr, Deng W, Chen M, Raredon MSB, Hoehn KB, Wang G, Wang Z, DeIuliis G, Ravindra NG, Li N, Castaldi C, Wong P, Fournier J, Bermejo S, Sharma L, Casanovas-Massana A, Vogels CBF, Wyllie AL, Grubaugh ND, Melillo A, Meng H, Stein Y, Minasyan M, Mohanty S, Ruff WE, Cohen I, Raddassi K, Niklason LE, Ko AI, Montgomery RR, Farhadian SF, Iwasaki A, Shaw AC, van Dijk D, Zhao H, Kleinstein SH, Hafler DA, Kaminski N, Dela Cruz CS. Nat Commun. 2022 Jan 21; 2022 Jan 21. PMID: 35064122.
Lung Microenvironments and Disease Progression in Fibrotic Hypersensitivity Pneumonitis.De Sadeleer LJ, McDonough JE, Schupp JC, Yan X, Vanstapel A, Van Herck A, Everaerts S, Geudens V, Sacreas A, Goos T, Aelbrecht C, Nawrot TS, Martens DS, Schols D, Claes S, Verschakelen JA, Verbeken EK, Ackermann M, Decottignies A, Mahieu M, Hackett TL, Hogg JC, Vanaudenaerde BM, Verleden SE, Kaminski N, Wuyts WA. Am J Respir Crit Care Med. 2022 Jan 1. PMID: 34724391.

2021

Fibroblasts positive for meflin have anti-fibrotic properties in pulmonary fibrosis.Nakahara Y, Hashimoto N, Sakamoto K, Enomoto A, Adams TS, Yokoi T, Omote N, Poli S, Ando A, Wakahara K, Suzuki A, Inoue M, Hara A, Mizutani Y, Imaizumi K, Kawabe T, Rosas IO, Takahashi M, Kaminski N, Hasegawa Y. Eur Respir J. 2021 Dec; 2021 Dec 23. PMID: 34049947.
Distinct roles of KLF4 in mesenchymal cell subtypes during lung fibrogenesis.Chandran RR, Xie Y, Gallardo-Vara E, Adams T, Garcia-Milian R, Kabir I, Sheikh AQ, Kaminski N, Martin KA, Herzog EL, Greif DM. Nat Commun. 2021 Dec 10; 2021 Dec 10. PMID: 34893592.
Transcriptomics of bronchoalveolar lavage cells identifies new molecular endotypes of sarcoidosis.Vukmirovic M, Yan X, Gibson KF, Gulati M, Schupp JC, DeIuliis G, Adams TS, Hu B, Mihaljinec A, Woolard TN, Lynn H, Emeagwali N, Herzog EL, Chen ES, Morris A, Leader JK, Zhang Y, Garcia JGN, Maier LA, Collman RG, Drake WP, Becich MJ, Hochheiser H, Wisniewski SR, Benos PV, Moller DR, Prasse A, Koth LL, Kaminski N. Eur Respir J. 2021 Dec; 2021 Dec 2. PMID: 34083402.
A Pulmonary Vascular Model From Endothelialized Whole Organ Scaffolds.Yuan Y, Leiby KL, Greaney AM, Raredon MSB, Qian H, Schupp JC, Engler AJ, Baevova P, Adams TS, Kural MH, Wang J, Obata T, Yoder MC, Kaminski N, Niklason LE. Front Bioeng Biotechnol. 2021; 2021 Nov 19. PMID: 34869270.
Machine learning implicates the IL-18 signaling axis in severe asthma.Camiolo MJ, Zhou X, Wei Q, Trejo Bittar HE, Kaminski N, Ray A, Wenzel SE. JCI Insight. 2021 Nov 8; 2021 Nov 8. PMID: 34591794.
A Markov random field model for network-based differential expression analysis of single-cell RNA-seq data.Li H, Zhu B, Xu Z, Adams T, Kaminski N, Zhao H. BMC Bioinformatics. 2021 Oct 26; 2021 Oct 26. PMID: 34702190.
Mechanisms of Hypoxia-Induced Pulmonary Arterial Stiffening in Mice Revealed by a Functional Genetics Assay of Structural, Functional, and Transcriptomic Data.Manning EP, Ramachandra AB, Schupp JC, Cavinato C, Raredon MSB, Bärnthaler T, Cosme C Jr, Singh I, Tellides G, Kaminski N, Humphrey JD. Front Physiol. 2021; 2021 Sep 14. PMID: 34594238.
Integrated transcriptomic analysis of human tuberculosis granulomas and a biomimetic model identifies therapeutic targets.Reichmann MT, Tezera LB, Vallejo AF, Vukmirovic M, Xiao R, Reynolds J, Jogai S, Wilson S, Marshall B, Jones MG, Leslie A, D'Armiento JM, Kaminski N, Polak ME, Elkington P. J Clin Invest. 2021 Aug 2. PMID: 34128839.
Integrated Single-Cell Atlas of Endothelial Cells of the Human Lung.Schupp JC, Adams TS, Cosme C Jr, Raredon MSB, Yuan Y, Omote N, Poli S, Chioccioli M, Rose KA, Manning EP, Sauler M, DeIuliis G, Ahangari F, Neumark N, Habermann AC, Gutierrez AJ, Bui LT, Lafyatis R, Pierce RW, Meyer KB, Nawijn MC, Teichmann SA, Banovich NE, Kropski JA, Niklason LE, Pe'er D, Yan X, Homer RJ, Rosas IO, Kaminski N. Circulation. 2021 Jul 27; 2021 May 25. PMID: 34030460.
Blood Transcriptomics Predicts Progression of Pulmonary Fibrosis and Associated Natural Killer Cells.Huang Y, Oldham JM, Ma SF, Unterman A, Liao SY, Barros AJ, Bonham CA, Kim JS, Vij R, Adegunsoye A, Strek ME, Molyneaux PL, Maher TM, Herazo-Maya JD, Kaminski N, Moore BB, Martinez FJ, Noth I. Am J Respir Crit Care Med. 2021 Jul 15. PMID: 33689671.
Chronic lung diseases are associated with gene expression programs favoring SARS-CoV-2 entry and severity.Bui LT, Winters NI, Chung MI, Joseph C, Gutierrez AJ, Habermann AC, Adams TS, Schupp JC, Poli S, Peter LM, Taylor CJ, Blackburn JB, Richmond BW, Nicholson AG, Rassl D, Wallace WA, Rosas IO, Jenkins RG, Kaminski N, Kropski JA, Banovich NE. Nat Commun. 2021 Jul 14; 2021 Jul 14. PMID: 34262047.
Cutting Edge: Distinct B Cell Repertoires Characterize Patients with Mild and Severe COVID-19.Hoehn KB, Ramanathan P, Unterman A, Sumida TS, Asashima H, Hafler DA, Kaminski N, Dela Cruz CS, Sealfon SC, Bukreyev A, Kleinstein SH. J Immunol. 2021 Jun 15; 2021 May 28. PMID: 34049971.
Type I Interferon Transcriptional Network Regulates Expression of Coinhibitory Receptors in Human T cells.Hafler D, Sumida T, Dulberg S, Schupp J, Stillwell H, Axisa PP, Comi M, Lincoln M, Unterman A, Kaminski N, Madi A, Kuchroo V. Res Sq. 2021 Jun 8; 2021 Jun 8. PMID: 34127967.
Elevated IL-15 concentrations in the sarcoidosis lung are independent of granuloma burden and disease phenotypes.Minasyan M, Sharma L, Pivarnik T, Liu W, Adams T, Bermejo S, Peng X, Liu A, Ishikawa G, Perry C, Kaminski N, Gulati M, Herzog EL, Dela Cruz CS, Ryu C. Am J Physiol Lung Cell Mol Physiol. 2021 Jun 1; 2021 Apr 14. PMID: 33851886.
PINK1 mediates the protective effects of thyroid hormone T3 in hyperoxia-induced lung injury.Zhang Y, Yu G, Kaminski N, Lee PJ. Am J Physiol Lung Cell Mol Physiol. 2021 Jun 1; 2021 Apr 14. PMID: 33851544.
Cathepsin B promotes collagen biosynthesis, which drives bronchiolitis obliterans syndrome.Morrone C, Smirnova NF, Jeridi A, Kneidinger N, Hollauer C, Schupp JC, Kaminski N, Jenne D, Eickelberg O, Yildirim AÖ. Eur Respir J. 2021 May; 2021 May 13. PMID: 33303550.
Immune dysregulation and autoreactivity correlate with disease severity in SARS-CoV-2-associated multisystem inflammatory syndrome in children.Ramaswamy A, Brodsky NN, Sumida TS, Comi M, Asashima H, Hoehn KB, Li N, Liu Y, Shah A, Ravindra NG, Bishai J, Khan A, Lau W, Sellers B, Bansal N, Guerrerio P, Unterman A, Habet V, Rice AJ, Catanzaro J, Chandnani H, Lopez M, Kaminski N, Dela Cruz CS, Tsang JS, Wang Z, Yan X, Kleinstein SH, van Dijk D, Pierce RW, Hafler DA, Lucas CL. Immunity. 2021 May 11; 2021 Apr 13. PMID: 33891889.
Response.Price CC, Altice FL, Azar MM, McManus D, Gleeson SE, Britto CJ, Azmy V, Kaman K, Davis M, Chupp G, Bucala R, Kaminski N, Topal JE, Dela Cruz C, Malinis M. Chest. 2021 May. PMID: 33965143.
Mitochondrial antiviral signaling protein is crucial for the development of pulmonary fibrosis.Kim SH, Lee JY, Yoon CM, Shin HJ, Lee SW, Rosas I, Herzog E, Dela Cruz CS, Kaminski N, Kang MJ. Eur Respir J. 2021 Apr; 2021 Apr 15. PMID: 33093124.
Post-infectious inflammatory disease in MIS-C features elevated cytotoxicity signatures and autoreactivity that correlates with severity.Ramaswamy A, Brodsky NN, Sumida TS, Comi M, Asashima H, Hoehn KB, Li N, Liu Y, Shah A, Ravindra NG, Bishai J, Khan A, Lau W, Sellers B, Bansal N, Guerrerio P, Unterman A, Habet V, Rice AJ, Catanzaro J, Chandnani H, Lopez M, Kaminski N, Dela Cruz CS, Tsang JS, Wang Z, Yan X, Kleinstein SH, van Dijk D, Pierce RW, Hafler DA, Lucas CL. medRxiv. 2021 Apr 3; 2021 Apr 3. PMID: 33300011.
Elevated plasma level of Pentraxin 3 is associated with emphysema and mortality in smokers.Zhang Y, Tedrow J, Nouraie M, Li X, Chandra D, Bon J, Kass DJ, Fuhrman CR, Leader JK, Duncan SR, Kaminski N, Sciurba FC. Thorax. 2021 Apr; 2021 Jan 21. PMID: 33479043.
Genetic analyses identify GSDMB associated with asthma severity, exacerbations, and antiviral pathways.Li X, Christenson SA, Modena B, Li H, Busse WW, Castro M, Denlinger LC, Erzurum SC, Fahy JV, Gaston B, Hastie AT, Israel E, Jarjour NN, Levy BD, Moore WC, Woodruff PG, Kaminski N, Wenzel SE, Bleecker ER, Meyers DA. J Allergy Clin Immunol. 2021 Mar; 2020 Aug 11. PMID: 32795586.
Long noncoding RNA TINCR is a novel regulator of human bronchial epithelial cell differentiation state.Omote N, Sakamoto K, Li Q, Schupp JC, Adams T, Ahangari F, Chioccioli M, DeIuliis G, Hashimoto N, Hasegawa Y, Kaminski N. Physiol Rep. 2021 Feb. PMID: 33527707.
Gene coexpression networks reveal novel molecular endotypes in alpha-1 antitrypsin deficiency.Chu JH, Zang W, Vukmirovic M, Yan X, Adams T, DeIuliis G, Hu B, Mihaljinec A, Schupp JC, Becich MJ, Hochheiser H, Gibson KF, Chen ES, Morris A, Leader JK, Wisniewski SR, Zhang Y, Sciurba FC, Collman RG, Sandhaus R, Herzog EL, Patterson KC, Sauler M, Strange C, Kaminski N. Thorax. 2021 Feb; 2020 Dec 10. PMID: 33303696.
MicroRNA miR-24-3p reduces DNA damage responses, apoptosis, and susceptibility to chronic obstructive pulmonary disease.Nouws J, Wan F, Finnemore E, Roque W, Kim SJ, Bazan I, Li CX, Skold CM, Dai Q, Yan X, Chioccioli M, Neumeister V, Britto CJ, Sweasy J, Bindra R, Wheelock ÅM, Gomez JL, Kaminski N, Lee PJ, Sauler M. JCI Insight. 2021 Jan 25; 2021 Jan 25. PMID: 33290275.
Macrophage-derived netrin-1 drives adrenergic nerve-associated lung fibrosis.Gao R, Peng X, Perry C, Sun H, Ntokou A, Ryu C, Gomez JL, Reeves BC, Walia A, Kaminski N, Neumark N, Ishikawa G, Black KE, Hariri LP, Moore MW, Gulati M, Homer RJ, Greif DM, Eltzschig HK, Herzog EL. J Clin Invest. 2021 Jan 4. PMID: 33393489.
Chronic lung diseases are associated with gene expression programs favoring SARS-CoV-2 entry and severity.Bui LT, Winters NI, Chung MI, Joseph C, Gutierrez AJ, Habermann AC, Adams TS, Schupp JC, Poli S, Peter LM, Taylor CJ, Blackburn JB, Richmond BW, Nicholson AG, Rassl D, Wallace WA, Rosas IO, Jenkins RG, Kaminski N, Kropski JA, Banovich NE. bioRxiv. 2021 Jan 4; 2021 Jan 4. PMID: 33106805.
Genetic determinants of ammonia-induced acute lung injury in mice.Bein K, Ganguly K, Martin TM, Concel VJ, Brant KA, Di YPP, Upadhyay S, Fabisiak JP, Vuga LJ, Kaminski N, Kostem E, Eskin E, Prows DR, Jang AS, Leikauf GD. Am J Physiol Lung Cell Mol Physiol. 2021 Jan 1; 2020 Oct 14. PMID: 33050709.

2020

Toward a Cell Atlas of the Human Airway.Schupp JC, Yan X, Kaminski N. Am J Respir Crit Care Med. 2020 Dec 15. PMID: 32841575.
The Idiopathic Pulmonary Fibrosis Cell Atlas.Neumark N, Cosme C Jr, Rose KA, Kaminski N. Am J Physiol Lung Cell Mol Physiol. 2020 Dec 1; 2020 Sep 30. PMID: 32996785.
Single-Cell Transcriptional Archetypes of Airway Inflammation in Cystic Fibrosis.Schupp JC, Khanal S, Gomez JL, Sauler M, Adams TS, Chupp GL, Yan X, Poli S, Zhao Y, Montgomery RR, Rosas IO, Dela Cruz CS, Bruscia EM, Egan ME, Kaminski N, Britto CJ. Am J Respir Crit Care Med. 2020 Nov 15. PMID: 32603604.
Type I Interferon Transcriptional Network Regulates Expression of Coinhibitory Receptors in Human T cells.Sumida TS, Dulberg S, Schupp J, Stillwell HA, Axisa PP, Comi M, Lincoln M, Unterman A, Kaminski N, Madi A, Kuchroo VK, Hafler DA. bioRxiv. 2020 Oct 31; 2020 Oct 31. PMID: 33140047.
Reduced development of COVID-19 in children reveals molecular checkpoints gating pathogenesis illuminating potential therapeutics.Steinman JB, Lum FM, Ho PP, Kaminski N, Steinman L. Proc Natl Acad Sci U S A. 2020 Oct 6; 2020 Sep 3. PMID: 32883878.
Tocilizumab Treatment for Cytokine Release Syndrome in Hospitalized Patients With Coronavirus Disease 2019: Survival and Clinical Outcomes.Price CC, Altice FL, Shyr Y, Koff A, Pischel L, Goshua G, Azar MM, Mcmanus D, Chen SC, Gleeson SE, Britto CJ, Azmy V, Kaman K, Gaston DC, Davis M, Burrello T, Harris Z, Villanueva MS, Aoun-Barakat L, Kang I, Seropian S, Chupp G, Bucala R, Kaminski N, Lee AI, LoRusso PM, Topal JE, Dela Cruz C, Malinis M. Chest. 2020 Oct; 2020 Jun 15. PMID: 32553536.
An allosteric site on MKP5 reveals a strategy for small-molecule inhibition.Gannam ZTK, Min K, Shillingford SR, Zhang L, Herrington J, Abriola L, Gareiss PC, Pantouris G, Tzouvelekis A, Kaminski N, Zhang X, Yu J, Jamali H, Ellman JA, Lolis E, Anderson KS, Bennett AM. Sci Signal. 2020 Aug 25; 2020 Aug 25. PMID: 32843541.
Expression of SARS-CoV-2 receptor ACE2 and coincident host response signature varies by asthma inflammatory phenotype.Camiolo M, Gauthier M, Kaminski N, Ray A, Wenzel SE. J Allergy Clin Immunol. 2020 Aug; 2020 Jun 10. PMID: 32531372.
Single-cell RNA-seq reveals ectopic and aberrant lung-resident cell populations in idiopathic pulmonary fibrosis.Adams TS, Schupp JC, Poli S, Ayaub EA, Neumark N, Ahangari F, Chu SG, Raby BA, DeIuliis G, Januszyk M, Duan Q, Arnett HA, Siddiqui A, Washko GR, Homer R, Yan X, Rosas IO, Kaminski N. Sci Adv. 2020 Jul; 2020 Jul 8. PMID: 32832599.
CMH-Small Molecule Docks into SIRT1, Elicits Human IPF-Lung Fibroblast Cell Death, Inhibits Ku70-deacetylation, FLIP and Experimental Pulmonary Fibrosis.Konikov-Rozenman J, Breuer R, Kaminski N, Wallach-Dayan SB. Biomolecules. 2020 Jul 2; 2020 Jul 2. PMID: 32630842.
Small airways pathology in idiopathic pulmonary fibrosis: a retrospective cohort study.Verleden SE, Tanabe N, McDonough JE, Vasilescu DM, Xu F, Wuyts WA, Piloni D, De Sadeleer L, Willems S, Mai C, Hostens J, Cooper JD, Verbeken EK, Verschakelen J, Galban CJ, Van Raemdonck DE, Colby TV, Decramer M, Verleden GM, Kaminski N, Hackett TL, Vanaudenaerde BM, Hogg JC. Lancet Respir Med. 2020 Jun; 2020 Feb 13. PMID: 32061334.
COVID-19 vulnerability: the potential impact of genetic susceptibility and airborne transmission.Godri Pollitt KJ, Peccia J, Ko AI, Kaminski N, Dela Cruz CS, Nebert DW, Reichardt JKV, Thompson DC, Vasiliou V. Hum Genomics. 2020 May 12; 2020 May 12. PMID: 32398162.