Rebecca Kusko
Education
2009 B.S. Biological Engineering, MIT
Research Interests
The incidences of COPD and pulmonary fibrosis have been increasing annually, with COPD being thefourth leading cause of death in the USA. Studies of these diseases using microarrays have establisheda role for severe α1-antitrypsin deficiency in promoting inflammation and the importance of oxidativestress genes. While next generation RNA sequencing (mRNA-seq) has the potential to provide moreinsight into the complex pathogenesis of COPD and pulmonary fibrosis, no such studies have beenreported to date. As part of the Lung Genomics Research Consortium (LGRC) we are performingpoly-A non-directional mRNA-seq using an Illumina GA IIX and HI-Seq sequencer on a large set oflung tissue samples (n=400) from the Lung Tissue Research Consortium (LTRC) which can be broadlyclassified into 4 groups: normal, small airway COPD, emphysema, or interstitial lung disease (ILD).The goal is to combine clinical characteristics with insights from mRNA-seq to begin to understand thegreat heterogeneity that underlies these lung diseases. In this study, mRNA-seq is used to identifydisease associated gene expression patterns. In addition, we are exploring alternative splicing events,alternative promoter usage, and alternative start site usage. We are also in the process of characterizingexpressed yet un-annotated regions of the transcriptome to find novel transcripts, UTR and exonextensions, and novel alternative splicing events. In order to understand drivers of changes in geneexpression, methylation and miRNA expression data on these same samples from other LGRC labs isbeing integrated with our gene expression data. This project will also utilize non-poly-A directionalmRNA-seq in order to more deeply explore the transcriptome.
Oral Presentations
R. Kusko, J. Brothers, G. Liu, L. Luo, Y. Aleksyev, M. Lenburg, A. Spira, J. Beane. “Redefining theLung Disease Transcriptome with Next Generation RNA-sequencing”. Genone Science Institue (GSI)Symposium. Boston, MA October 2010
R. Kusko, J. Brothers, G. Liu, L. Luo, Y. Aleksyev, M. Lenburg, A. Spira, J. Beane. “Redefining theLung Disease Transcriptome with Next Generation RNA-sequencing”. Illumina User Group Meeting. Cambridge, MA September 2011
R. Kusko, J. Brothers, G. Liu, L. Luo, Y. Aleksyev, M. Lenburg, A. Spira, J. Beane. “Comprehensive Profiling of the Emphysema and IPF Lung Transcriptome using RNA sequencing”. Advances in Genome Biology and Technology (AGBT) Conference. Marco Island, FL Feb 2012
R. Kusko, J. Brothers, G. Liu, L. Luo, Y. Aleksyev, M. Lenburg, A. Spira, J. Beane. “Comprehensive Profiling of the Emphysema and IPF Lung Transcriptome using RNA sequencing”. Henry I Russek Student Achievement Day. Boston, MA June 2012
R. Kusko, J. Brothers, G. Liu, L. Luo, Y. Aleksyev, M. Lenburg, A. Spira, J. Beane. “Comprehensive Profiling of the Emphysema and IPF Lung Transcriptome using RNA sequencing”. The Lung Epithelium in Health and Disease, FASEB. Saxtons River, VT July 2012
Poster Presentations
R. Kusko, J. Brothers II, J. Beane, G. Liu, L. Luo, B. Juan-Guardela, J. Tedrow, Y. Aleksyev, I. V. Yang,M. Correll, M. Geraci, J. Quackenbush, F. Sciurba, M. Lenburg , D. A. Schwartz, N. Kaminski, A.Spira. “Characterizing the COPD and IPF Transcriptome Using RNA sequencing”. Russek StudentAchivement Day Poster Session. BUMC, Boston. May 2011 R. Kusko, J. Brothers II, J. Beane, G. Liu, L. Luo, B. Juan-Guardela, J. Tedrow, Y. Aleksyev, I. V. Yang,M. Correll, M. Geraci, J. Quackenbush, F. Sciurba, M. Lenburg , D. A. Schwartz, N. Kaminski, A.Spira. “Characterizing the COPD and IPF Transcriptome Using RNA sequencing”. Second Annual CTSISymposium. BU, Boston. May 2011R. Kusko, J. Brothers II, J. Beane, G. Liu, L. Luo, B. Juan-Guardela, J. Tedrow, Y. Aleksyev, I. V. Yang, M. Correll, M. Geraci, J. Quackenbush, F. Sciurba, M. Lenburg , D. A. Schwartz, N. Kaminski, A.Spira. “Characterizing the COPD and IPF Transcriptome Using RNA sequencing”. American ThoracicSoceity(ATS). Denver, CO May 2011R. Kusko, J. Brothers, G. Liu, L. Luo, Y. Aleksyev, M. Lenburg A. Spira, J. Beane. “Characterizing the COPDand IPF Transcriptome Using RNA sequencing”.Next Generation Sequencing Congress. Boston, MA April2011 R. Kusko, J. Brothers, G. Liu, L. Luo, Y. Aleksyev, M. Lenburg, A. Spira, J. Beane. “Redefining theCOPD and IPF Transcriptome with Next Generation RNA-sequencing”. Evans Day. BUSM, Boston, MADecember 2010R. Kusko, J. Brothers, G. Liu, L. Luo, Y. Aleksyev, M. Lenburg, A. Spira, J. Beane. “Redefining the LungDisease Transcriptome with Next Generation RNA-sequencing”. Beyond the Genome 2010. Boston, MAOctober 2010R. Kusko, P. Sebastiani, M. Montano. “Characterizing Expression Profiles in Aging Muscle and HIV”Longevity Consortium. Washington D.C. June 2010R. Kusko, P. Sebastiani, M. Montano. “Gene Expression Profiles in Aging Muscle and HIV” Russek StudentAchivement Day Poster Session. BUSM, Boston. June 2010
Publications
Kusko, R.L., Banerjee, C., Long, K.K., Darcy, A., Otis, J., Sebastiani, P., Melov, S., Tarnapolsky, M., Bhasin, S., Montano, M., (2012) Premature expression of muscle fibrosis axis in chronic HIV infection. Skeletal Muscle 2012, 2:10. Article URL: http://www.skeletalmusclejournal.com/content/pdf/2044-5040-2-10.pdf