Naftali Kaminski, MD
Professor of Medicine, Pathology, Human Genetics and Computational Biology


Dr. Kaminski is the Director of the Dorothy P. and Richard P. Simmons Center for Interstitial Lung Disease, the Endowed Chair for Pulmonary Research, and a member of the Cellular and Molecular Pathology Graduate Training Program.

Office Location:
NW 628 Montefiore
3459 Fifth Avenue
Pittsburgh, PA 15213 		Contact Information:
Office Telephone: 412-624-7450
Lab Telephone: 412-624-9046
Manager: 412-624-9082
Email: kaminskin@upmc.edu

Education

  • BS - 1985, Hebrew University-Hadassah
  • MD - 1989, Hebrew University-Hadassah

Clinical Expertise

Dr Kaminski’s main clinical interests are interstitial lung diseases and especially idiopathic pulmonary fibrosis.

Research Interests

Dr. Kaminski has a long time commitment to studying the basic molecular networks that underlie the lung phenotype in pulmonary fibrosis. He has pioneered the application of microarray technology to lung fibrosis and has applied this technology in a variety of models and disease states. He has also been actively involved in developing bioinformatic and computational approaches to data analysis and implementing "Systems Biology Approaches" in pulmonary medicine.

Dr Kaminski's research is currently focused on identifying new markers to improve diagnosis and outcome of IPF and on developing new therapeutic targets in the disease. Idiopathic Pulmonary Fibrosis (IPF) is a chronic progressive interstitial lung disease that is currently incurable. The main research interests of the Kaminski lab are the basic mechanisms underlying pulmonary fibrosis and other chronic lung disease and the way that molecular networks determine tissue and cellular phenotype. To study these mechanisms Dr. Kaminski applies a systems biology approach that incorporates a combination of traditional molecular biology methods, high-throughput genomic technologies such as expression and location microarrays, advanced bioinformatic approaches and targeted proteomic approaches. As a result of these studies he has identified key regulatory molecules as well as potential biomarkers that he is currently studying.

Specific research projects include:

Basic Mechanisms of Pulmonary Fibrosis and other Chronic Lung Diseases

  • High throughput analysis of promoter binding by lung disease relevant transcription factors (ChIP on chip)
  • Understanding and identifying the genetic and molecular networks that determine the lung phenotype using high throughput genomic and proteomic technologies
  • Role of miRNA in advanced lung disease (IPF, Emphysema)
  • Epigenomics of chronic lung disease
  • Using computational approaches to Integrate clinical, biological, genomic and proteomic data to identify new molecular phenotypes of disease

New Molecular Targets in Pulmonary Fibrosis

  • The role of developmental pathways in lung injury and repair
  • The role and regulation of matrix metaloproteases (MMP7, MMP19) in human pulmonary fibrosis
  • The role and regulation of microRNAs (let-7, mir-30, mir-154 families) in human pulmonary fibrosis

Biomarker Discovery and Validation in Chronic and Progressive Lung Disease

  • The use of gene expression patterns in peripheral blood mononuclear cells to diagnose and predict outcome in pulmonary fibrosis, lung cancer and acute and chronic lung transplant rejection
  • The use of targeted mini proteomic approaches to identify peripheral markers for chronic advanced lung diseases

Specialties

Internal Medicine, Pulmonary Medicine

Selected Publications

View Dr. Kaminski's publications on PubMed

Peer-Reviewed Articles

  1. Zemke AC, Snyder JC, Brockway BL, Drake JA, Reynolds SD, Kaminski N, Stripp BR. Molecular Staging of Epithlieial Maturation Using Secretory Cell-Specific Genes as Markers. Am J Respir Cell Mol Biol 2009 Mar;40(3):340-8.
  2. Ben-Dov I, Kaminski N, Reichert N, Rosenman J, Shulimzon T. Diaphragmatic paralysis: a clinical imitator of cardiorespiratory diseases. Isr Med Assoc J. 2008 Aug-Sep;10(8-9):579-83.
  3. Wu W*, Dave NB*, Yu G, Strollo PJ, Kovkarova-Naumovski E, Ryter SW. Reeves SR, Dayyat E, Wang Y, Choi AMK, Gozal D, Kaminski N.+ Network Analysis of Temporal Effects of Intermittent- and Sustained Hypoxia on Rat Lungs. Physiological Genomics 2008 36:2-34.
  4. Zheng L, Zhou Z, Lin L, Alber S, Watkins S, Kaminski N, Choi AM, Morse D. Carbon Monoxide Modulates {alpha}-smooth Muscle Actin and Small Proline Rich-1a Expression in Fibrosis. Am J Respir Cell Mol Biol 2009 Jul;41(1):85-92.
  5. Kliment CR, Englert JM, Gochuico BR, Yu G, Kaminski N, Rosas IO, Oury TD. Oxidative stress alters syndecan-1 distribution in lungs with pulmonary fibrosis. J Biol Chem. 2009 Feb 6;284(6):3537-45.
  6. Vuga L, Ben-Yehudah A, Kovkarova-Naumovski E, Oriss T, Gibson K, Feghali-Bostwick C, Kaminski N.+ WNT5A is Increased in Usual Interstitial Pneumonia Fibroblasts and is an Inducer of Fibroblast Proliferation and Survival. Am J Respir Cell Mol Biol 2009 Feb 27.
  7. Richards TJ , Eggebeen A, Gibson K, Yousem S, Fuhrman S, Gochuico BR, Fertig N, Oddis CV, Kaminski N, Rosas IO, Ascherman DP. Characterization and Peripheral Blood Biomarker Assessment of Jo-1 Antibody-Positive Interstitial Lung Disease. Arthritis and Rheumatism 2009 Jun 29;60(7):2183-2192.
  8. Konishi K, Gibson K, Lindell K, Richards T, Zhang Y, Dhir R, Biceglia M, Yousem S, Gilbert S, Song JW, Kim DS, Kaminski, N+. Gene Expression Profiles of Acute Exacerbations of Idiopathic Pulmonary Fibrosis. Am J Respir Crit Care Med 2009 Jul 15;180(2):167-75.
  9. Corcoran DL, Pandit KV, Gordon B, Bhattacharjee A, Kaminski N+*, Benos PV*. Features of mammalian microRNA promoters emerge from polymerase II chromatin immunoprecipitation data. PLoS One 2009; 4(4):e5279
  10. Di Giuseppe M, Gambelli F, Hoyle G Lungarella G, Studer SM, Richards T, Yousem, S McCurry K, Dauber J, Kaminski N, Leikauf G, and Ortiz LA. Systemic Inhibition of NF-κB Activation Protects from Silicosis. PLoS One. 2009 May 25;4(5):e5689.
  11. Snyder JC, Reynolds SD, Hollingsworth JW, Li Z, Kaminski N, Stripp BR. Clara Cells Attenuate the Inflammatory Response through Regulation of Macrophage Behavior. Am J Respir Cell Mol Biol. 2010 Feb;42(2):161-71. PMID: 19423773. PMCID: PMC2822978.
  12. Scotton CJ, Krupiczojc MA, Konigshoff M, Mercer PF, Gary YC, Kaminski N, Morser J, Post JM, Maher TM, Nicholson AG, Moffatt JD, Laurent GJ, Derian CK, Eickelberg O and Chambers. Increased local expression of coagulation factor X contributes to the fibrotic response in human and murine lung injury. J Clin Invest. 2009 Aug 3. pii: 33288. doi: 10.1172/JCI33288.
  13. Stuckenholz C, Lu L, Thakur P, Kaminski N and Bahary N. FACS-Assisted Microarray Profiling Implicates Novel Genes and Pathways in Zebrafish Gastrointestinal Tract Development. Gastroenterology 2009 Jun 26.
  14. Bon JM, Leader JK, Weissfeld JL, Coxson HO, Zheng B, Branch RA, Kondragunta V, Lee JS, Zhang Y, Choi AM, Lokshin AE, Kaminski N, Gur D, Sciurba FC. The influence of radiographic phenotype and smoking status on peripheral blood biomarker patterns in chronic obstructive pulmonary disease. PLoS One. 2009 Aug 31;4(8):e6865.
  15. Ben-Yehudah A, Navara CS, Redinger CJ, Mich-Basso JD, Oliver S, Chensny LJ, Richards TJ, Kaminski N, Shatten G. Pluripotency Genes Overexpressed in Primate Embryonic Stem Cells Are Localized on Homologues of Human Chromosomes 16, 17, 19 and X. Stem Cell Res. 2009 Sep 17. PMID: 19854689.
  16. Gilani SE, Vuga LJ, Lindell KO, Gibson KF, Xue J, Lindsay EK, Kaminski N, Valentine VG, George MP, Steele C, Duncan SR. CD28 Down-regulation on Circulating CD4-T-cells is Associated with Poor Prognoses of Patients with Idiopathic Pulmonary Fibrosis. PLoS One 2010 Jan 29;5(1):e8959. PMID: 20126467.
  17. Rajkumar R, Konishi K, Richards T, Ishizawar D, Wiechert A, Kaminski N, Ahmad F Genome-Wide RNA Expression Profiling in Lung Identifies Distinct Signatures in Idiopathic Pulmonary Arterial Hypertension and Secondary Pulmonary Hypertension Am J Physiol Heart Circ Physiol. 2010 Jan 15. PMID: 20081107.
  18. Yousem SA, Gibson K, Kaminski N, Oddis CV, Ascherman DP. The Pulmonary Histopathologic Manifestations of the anti-Jo-1 tRNA Synthetase Syndrome. Modern Pathology 2010 Mar 10.
  19. Pandit KV, Corcoran D, Yousef H, Yarlagadda M, Tzouvelekis A, Gibson KF, Kazuhisa K, Yousem S, Singh M, Handley D, Richards T, Selman M, Watkins SC, Pardo A, Ben-Yehudah A, Bouros D, Eickelberg O, Ray P, Benos PV, Kaminski N. Inhibition and role of let-7d in Idiopathic Pulmonary Fibrosis. Am J Respir Crit Care Med 2010 (182) 220-229.
  20. Lindell KO, Olshansky E, Song MK, Zullo T, Gibson K, Kaminski N, Hoffman L. Impact of a disease-management program on symptom burden and health-related quality of life in patients with idiopathic pulmonary fibrosis and their care partners. Heart & Lung 2010 July 16
  21. Liu G, Friggeri A, Yang Y, Milosevic J, Ding Q, Thannickal VJ, Kaminski N, Abraham E. miR-21 mediates fibrogenic activation of pulmonary fibroblasts and lung fibrosis. J Exp Med. 2010 Aug 2;207(8):1589-97. Epub 2010 Jul 19.PMID: 20643828
  22. Leikauf GD, Pope-Varsalona H, Concel VJ, Liu P, Bein K, Brant KA, Dopico RA, Di YP, Jang AS, Dietsch M, Medvedovic M, Li Q, Vuga LJ, Kaminski N, You M, Prows DR Functional genomics of chlorine-induced acute lung injury in mice. Proc Am Thorac Soc. 2010 Jul;7(4):294-6. PMID: 20601635.
  23. Mi Z, Shen K, Song N, Cheng C, Song C, Kaminski N, Tseng GC. Module-based prediction approach for robust inter-study predictions in microarray data. Bioinformatics. 2010 Aug 17. [Epub ahead of print] PMID: 20719761.
  24. Xue J, Gochuico BR, Alawad AS, Feghali-Bostwick CA, Noth I, Nathan S, Rosen GD, Rosas IO, Dacic S, Ocak I, Furhrman CR, Cuenco, KT, Smith MA, Jacobs SS, Zeevi A, Morel P, Pilewski JM, Valentine VG, Gibson KF, Kaminski N, Sciurba FC, Zhang Y, Duncan SR. The HLA Class II Allele DRB1*1501 Is Over-Represented in Patients with Idiopathic Pulmonary Fibrosis. PLoS ONE 2011 Feb 23;6(2):e14715. PMID: 21373184. PMCID: PMC3044131.
  25. Leikauf GD, Concel VJ, Liu P, Bein K, Berndt A, Ganguly K, Jang AS, Brant KA, Dietsch M, Pope-Varsalona H, Dopico Jr RA, Di YP, Li Q, Vuga LJ, Medvedovic M, Kaminski N, You M, Prows DR. Haplotype Association Mapping of Acute Lung Injury in Mice Implicates Activin A Receptor, Type 1. Am J Respir Crit Care Med. 2011 Feb 25. PMID: 21297076.
  26. Pandit KV, Milosevic J, Kaminski N+. MicroRNAs in Idiopathic Pulmonary Fibrosis. Translational Research ,Volume 157, Issue 4, April 2011, Pages 191-199. PMID: 21420029.
  27. Gupta D, Harvey S, Kaminski N, Swamynathan S. Mouse conjunctival forniceal gene expression during postnatal development and its regulation by Kruppel-like factor 4. Investigative Ophthalmology & Visual Science (IOVS) 2011. PMID: 21398290.
  28. Zhang Y, Noth I, Garcia JG, Kaminski N+. A variant in the promoter of MUC5B and idiopathic pulmonary fibrosis. NEJM 2011 Apr 21;364(16):1576-7.
  29. Bais AF, Kaminski N, Benos PV. Finding subtypes of transcription factor motif pairs with distinct regulatory roles. Nucleic Acids Research, April 12, 2011 1-13.
  30. Lindell KO, Kaminski N, Gibson KF, Lareau S, Fahy B, & Swigris, JJ. (2011) ATS Patient Information Series: Idiopathic Pulmonary Fibrosis (IPF), Am J Respir Crit Care Med, (183) 67.
  31. Zhang, Y, Handley D, Kaplan T, Bais A, Richards, T, Pandit K, Qilu Z, Benos T, Friedman N, Kaminski N+. High Throughput Determination of TGFβ 1/SMAD3 Targets in A549 Lung Epithelial Cells. PLOS One 2011 6 (5) 5 e20319. PMID: 21625455. PMCID: PMC3098871.
  32. Richards T, Kaminski N+, Baribaud F, Flavin S, Brodmerkel C, Horowitz D, Li K, Choi J, Vuga L, Lindell K, Klesen M, Zhang Y, Gibson K. Peripheral blood proteins predict mortality in Idiopathic Pulmonary Fibrosis. Am J Respir Crit Care Med. Oct 20 2011 PMID: 22016448.
  33. Kang DD, Sibille E, Kaminski N and Tseng GC. MetaQC: objective quality control and inclusion/exclusion criteria for meta-analysis. Nucleic Acids Research, 2011, 1–14.
  34. Yamashita CM, Dolgonos L, Zemans RL, Young SK, Robertson J, Briones N, Suzuki T, Campbell MN, Gauldie J, Radisky DC, Riches DW, Yu G, Kaminski N, McCulloch CA, Downey GP. Matrix metalloproteinase 3 is a mediator of pulmonary fibrosis. Am J Pathol. 2011 Oct;179(4):1733-45. Epub 2011 Aug 24. PMID: 21871427. PMCID: PMC3181358
  35. Fabisiak JP, Medvedovic M, Alexander DC, McDunn JE, Concel VJ, Bein K, Jang AS, Berndt A, Vuga LJ, Brant KA, Pope-Varsalona H, Dopico RA Jr, Ganguly K, Upadhyay S, Li Q, Hu Z, Kaminski N, Leikauf GD. Integrative metabolome and transcriptome profiling reveals discordant energetic stress between mouse strains with differential sensitivity to acrolein-induced acute lung injury. Mol Nutr Food Res. 2011 Sep;55(9):1423-34. Epub 2011 Aug 8. PMID:21823223
  36. Zhou X, Wu W, Hu H, Milosevic J, Konishi K, Kaminski N, Wenzel SE. Genomic differences distinguish the myofibroblast phenotype of distal lung fibroblasts from airway fibroblasts. Am J Respir Cell Mol Biol. 2011 Dec;45(6):1256-62. Epub 2011 Jul 14. PMID: 21757679.
  37. Keohavong P, Lenzner D, Rothstein M, Stabile L, Land S, Gaither-Davis A, Kim KJ, Kaminski N, Siegfried J . Therapeutic targeting of both the c-Met and EGFR pathways results in additive inhibition of lung tumorigenesis in transgenic mice. Cancers 2012. In press
  38. Richards TJ, Park C, Chen, Y, Gibson KF, Di YP, Pardo A, Watkins S, Choi AMK, Selman M, Pilewski, J, Kaminski N, Zhang Y. Allele Specific Transactivation of Matrix Metalloproteinase 7 by FOXA2 and Correlation with Plasma Levels in Idiopathic Pulmonary Fibrosis. AJP Lung in press
  39. Kass DJ, Yu G, Loh K, A Savir A, Borczuk A, Kahloon R, Guardela B, Deiuliis G, Tedrow J, Choi J, Richards T, Kaminski N, and Greenberg S. CYTOKINE-LIKE FACTOR 1 GENE EXPRESSION IS ENRICHED IN IDIOPATHIC PULMONARY FIBROSIS AND DRIVES THE ACCUMULATION OF CD4+ T-CELLS IN MURINE LUNGS: Evidence for an anti-fibrotic role in bleomycin injury Am J Path in press.
  40. Rabinovich EI, Kapetanaki MG, Steinfeld I, Gibson KF, Pandit KV, Yu G, Yakhini Z, Kaminski N+. Global Methylation Patterns in Idiopathic Pulmonary Fibrosis, PLoS One 2012;7(4):e33770. Epub 2012 Apr 10.
  41. Leikauf GD, Pope-Varsalona H, Concel VJ, Liu P, Bein K, Berndt A, Martin TM, Ganguly K, Jang AS, Brant KA, Dopico RA Jr, Upadhyay S, Di YP, Li Q, Hu Z, Vuga LJ, Medvedovic M, Kaminski N, You M, Alexander DC, McDunn JE, Prows DR, Knoell DL, Fabisiak JP. Integrative Assessment of Chlorine-induced Acute Lung Injury in Mice. Am J Respir Cell Mol Biol. 2012 Mar 23. [Epub ahead of print]
  42. Kass DJ, Yu G, Loh KS, Savir A, Borczuk A, Kahloon R, Juan-Guardela B, Deiuliis G, Tedrow J, Choi J, Richards T, Kaminski N, Greenberg SM. Cytokine-Like Factor 1 Gene Expression Is Enriched in Idiopathic Pulmonary Fibrosis and Drives the Accumulation of CD4(+) T Cells in Murine Lungs: Evidence for an Antifibrotic Role in Bleomycin Injury. Am J Pathol. 2012 May;180(5):1963-78. Epub 2012 Mar 16.

Book Chapters and Invited Reviews

  1. Richards TJ, Kaminski N+. Genomics of Lung Diseases in Textbook of Interstitial Lung Disease, Schwartz and King Eds, 5th edition Chapter 10 August 2009.
  2. Wu W, Kaminski, N+. “Systems biology and medicine: chronic lung diseases” John Wiley & Sons, Inc. WIREs Syst Biol Med 2009:1: 298-308.
  3. Ask K, Eickelberg O, Gauldie J, Kaminski N, Kolb M. Have advanced research technologies made real impact on respiratory medicine? Respirology. 2010 Aug;15(6):876-80. Epub 2010 Jul 20.PMID: 20646243
  4. Zhang Y, Noth, I, Garcia GN, Kaminski N. A Variant in the Promoter of MUC5B and Idiopathic Pulmonary Fibrosis. N Engl J Med 364;16 April 21, 2011.
  5. Noble, P, Richeldi L, Kaminski N. End of an ERA: Lessons from Negative Clinical trials in Idiopathic Pulmonary Fibrosis. Am J Respir Crit Care Med 2011: 184; 4-5. PMID:21737589
  6. Kass, D and Kaminski N. Evolving Genomic Approaches to Idiopathic Pulmonary Fibrosis: Moving Beyond Genes. Clinical and Translational Science 2011 Oct;4(5):372-9. PMID:22029812 PMCID: PMC3229869
  7. Ahmad, F, Champion H, Kaminski N+. Towards Systems Biology of Pulmonary Hypertension. Circulation. in press