Naftali Kaminski, MD
Professor of Medicine, with Secondary Appointments in Human Genetics, Pathology and Computational Biology
Dorothy P. and Richard P. Simmons Endowed Chair for Pulmonary Research
Director, Dorothy P. & Richard P. Simmons Center for Interstitial Lung Disease
Director, Lung , Blood, and Vascular Center for Genomics Medicine
MD, Hebrew University -
Hadassah Medical School - 1989
Email: kaminskin@upmc.edu
Research Interests:
Idiopathic Pulmonary Fibrosis (IPF) is a chronic progressive interstitial lung disease that is currently incurable. The main research interests of my team are the basic mechanisms underlying pulmonary fibrosis and the way that molecular networks determine tissue and cellular phenotype. To study these mechanisms we apply 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 we have identified key regulatory molecules as well as potential biomarkers that we are currently studying. The specific research projects and interests are detailed below:
Basic mechanisms of pulmonary fibrosis
- Understanding and identifying the genetic and molecular networks that lead to the fibrotic lung phenotype using high throughput genomic and proteomic technologies.
- Understanding specific transcriptional signatures of normal and abnormal cell populations in the fibrotic lung and dissecting the temporal changes that occur in these cell populations during this abnormal process (laser capture microdissection).
- The role of WNT pathway in lung injury and repair.
- The role and regulation of MMP7 in human pulmonary fibrosis
- The role and regulation of osteopontin in human pulmonary fibrosis
Understanding regulatory networks in complex organs
- High throughput analysis of promoter binding by lung disease relevant transcription factors (Chip on CHIP)
- Role of miRNA in advanced lung disease (IPF, Emphysema)
Diagnostic markers in chronic and progressive lung disease
- The impact of organ confined disease on peripheral blood gene expression patterns
- 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.
Cellular and molecular networks in the living organism
- TIdentifying stimulus specific transcriptional signatures in primary cells
- Identifying disease specific transcriptional signature in surrogate tissues and circulating peripheral blood cells
- Modeling the response of epithelial and circulating peripheral blood cells to a complex injury
Tools and analytical approaches for gene expression analysis
- Statistical analysis of microarray results
- Identifying regulatory modules using gene expression data
- Integrating multiple levels of biological and clinical information with gene expression and proteomic data
Recent Publications (selected out of >100)
Selman M, Pardo A, Kaminski N. Idiopathic Pulmonary Fibrosis - Aberrant Recapitulation of Developmental Pathways. PLoS Med. 2008 Mar 4;5(3):e62.
Rosas IO, Richards TJ, Konishi K, Zhang Y, Gibson, K, Lokshin AE, Lindell, KO, Cisneros J, MacDonald S, Pardo A, Sciurba F, Dauber, J, Selman, M, Gochuico BR, Kaminski N. MMP1 and MMP7 as Potential Peripheral Blood Biomarkers in Idiopathic Pulmonary Fibrosis. 2008 PLoS Med 5(4):e93.
Lin TH, Kaminski N, Bar-Joseph Z. Alignment and classification of time series gene expression in clinical studies. Bioinformatics. 2008 Jul 1;24(13):i147-55.
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.
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.
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.
Corcoran DL, Pandit KV, GordonB, Bhattacharjee A, Kaminski N+*, Benos PV*. Features of mammalian microRNA promoters emerge from polymerase II chromatin
immunoprecipitation data. PLoS One 2009; 4(4):e5279
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
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.
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 April 15.
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
