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A7433 - Gene Co-Expression Networks Analysis Reveals Novel Molecular Endotypes in Alpha-1 Antitrypsin Deficiency
Author Block: J. Chu1, W. Zang2, M. Vukmirovic1, X. Yan1, T. Adams1, B. Hu1, A. Mihaljinec1, S. M. O'Neal3, M. J. Becich3, H. Hochheiser3, K. F. Gibson3, E. S. Chen4, A. M. Morris3, J. K. Leader3, S. R. Wisniewski3, Y. Zhang3, F. C. Sciurba3, R. G. Collman5, R. Sandhaus6, C. B. Strange7, N. Kaminski1, On behalf of the GRADS Investigators; 1Yale University School of Medicine, New Haven, CT, United States, 2Biostatistics, Yale University School of Public Health, New Haven, CT, United States, 3University of Pittsburgh, Pittsburgh, PA, United States, 4Johns Hopkins University, Baltimore, MD, United States, 5University of Pennsylvania, Philadelphia, PA, United States, 6National Jewish Health, Denver, CO, United States, 7Medical University of S Carolina, Charleston, SC, United States.
Introduction: Alpha-1 antitrypsin deficiency (AATD) is a genetic condition that predisposes to early onset pulmonary emphysema and airways obstruction. While the causal genetic variant for AATD is known, the underlying mechanisms and pathobiology of AATD lung disease development are not well understood. In the Genomic Research in Alpha-1 Antitrypsin Deficiency and Sarcoidosis (GRADS) study we examined the effects of the causal PiZ genotype and augmentation therapy on bronchoalveolar lavage (BAL) and peripheral blood mononuclear cell (PBMC) gene expression profiles in AATD patients. Materials and Methods: 89 AATD patients enrolled in the GRADS study with matched BAL and PBMC samples (Strange et. al. Ann Am Thorac Soc. 2015. PMID: 26193069) were included in this study. The patients included three groups: individuals with PiZZ not receiving augmentation therapy (n=29), individuals with PiZZ receiving augmentation therapy (n=22), and heterozygous PiMZ individuals not receiving augmentation therapy (n=38). RNA extracted from PBMC and BAL samples was used for cDNA libraries preparation, and sequenced by Ion-Torrent RNA-Seq. Cufflinks was used to calculate Fragments per Kilobase of exon per Million (FPKM) values. Differential Expression Analysis and Weighted gene co-expression network analysis (WGCNA) were performed to identify potential genes and gene networks associated with AATD and other clinical variables. Results: Significant differentially expressed genes were found in BAL samples and PBMC samples when testing the effect of PIZ genotype (431 genes) and augmentation therapy (1,069 genes), with 123 genes differentially expressed in both tissue types. WGCNA clustered the genes into 13 highly co-expressed modules in BAL samples. We identified one module of 89 genes significantly correlated with multiple clinical variables, including FEV1, DLco, Emphysema and Bronchiectasis Severity. Pathway analysis of this module revealed genes enriched in immune system pathways, including T-cell activation, immune response-regulating cell surface receptor signaling pathway, and antigen receptor-mediated signaling pathway. Clustering the patients based on the transcriptomic profiles of this 89 gene module, we identified three clusters of patients with distinct phenotypic characteristics. Notably, cluster 2 (n=26) and cluster 3 (n=10) had lower predicted DLco (p=0.026) and worse emphysema (measured by fraction of the lung more negative than 950HU, p=0.001) than cluster 1 (n=43). Conclusion: We identified BAL and PBMC gene expression changes associated with genotype and augmentation therapy in AATD, as well as a collection of highly coexpressed genes that implicate multiple immune response pathways. These changes of gene expression patterns may contribute to the development of AATD lung diseases.