Assistant Professor of Biochemistry
Assistant Professor of Medical Biochemistry at the College of Medicine
Affiliate, Institute for Genomic Biology
Bioinformatics, Development, Genomics, Protein-Nucleic Acid Interactions, Regulation of Gene Expression, RNA Biology
B.S., 1999, Birla Institute of Technology and Science, Pilani, India
Ph.D., 2005, University of Texas, Houston
Postdoc., 2006-2010, Baylor College of Medicine, Houston
Inst. 2011-2012 Baylor College of Medicine, Houston
Video Interview with Professor Kalsotra
Tissue development, regeneration and disease, MicroRNAs, Myotonic dystrophy, RNA therapeutics
The unifying theme of Kalsotra lab's research is to identify post-transcriptional mechanisms that are key for normal tissue development, and if misregulated result in disease. Our major goal is to capitalize on these insights and apply them as therapeutic approaches for tissue regeneration and repair.
We employ tissue-specific knockout/transgenic mouse models, biochemistry, and genome-wide molecular approaches (RNA-seq and iCLIP) to define the post-transcriptional regulatory networks that coordinate developmental and regenerative programs.
1. Alternative splicing regulation in heart and liver development.
Alternative splicing is a process by which a single gene produces multiple polypeptides with potentially different functions. Over 90% of human genes are alternatively spliced giving rise to greater than 100,000 proteins from less than 20,000 genes. Due to tight spatiotemporal control, alternative splicing not only generates an extremely diverse proteome but also directs its regulated expression in response to a wide range of cues. Importantly, splicing defects are now recognized as central to many human diseases including neurological disorders, muscular dystrophies and cancer.
In this project we are systematically investigating the role of alternative splicing in mammalian heart and liver tissue development. We are also utilizing modified antisense oligonucleotides to investigate the phenotypic consequences of individual mRNA processing events on liver physiology and function.
2. Functional role of alternative splicing in liver regeneration.
The liver carries out a large number of physiological processes, and is therefore, indispensable for organismal survival. Although the human liver possesses an exceptional ability to regenerate, it often fails to repair itself during many liver disorders.
We have recently identified a developmentally regulated splicing network in mice that is redeployed during adult liver regeneration. The major goal of this project is to delineate the mechanisms that are instrumental in re-initiating the developmental splicing program in response to liver injury. These studies will provide important insights into how quiescent stem cells and hepatic progenitors may be instructed to proliferate or differentiate to combat different liver disorders.
3. MicroRNAs and small molecule therapeutics for myotonic dystrophy.
Myotonic dystrophy type 1 (DM1) is an autosomal dominant, multi-systemic neuromuscular disorder that is a common cause of congenital and adult onset muscular dystrophy. The causative mutation is a CTG expansion in the 3’-UTR of DMPK gene resulting in aberrant expression of CUG repeat containing RNA that accumulates in nuclear foci, depletes a splicing regulatory protein, MBNL1, and causes misregulation of developmentally regulated alternative splicing.
From a global screen in a heart-specific and inducible DM1 mouse model, we have recently discovered a specific defect in Mef2 transcriptional program in DM1 that results in loss of expression of its target genes including scores of cardiac microRNAs. We are currently optimizing different therapeutic approaches to correct microRNA misregulation in DM1 cell culture and mouse models.
In collaboration with Steve Zimmerman and Paul Hergenrother labs, (UIUC), we are also testing the in vivo efficacy of their small molecule inhibitors that can release Mbnl1 from the CUG RNA in a DM1 mouse model.
4. mRNA polyadenylation in heart development and disease.
As transcription terminates, the 3’-end of most eukaryotic mRNAs is cleaved and polyadenylated. Polyadenylation adds a 3’-poly(A) tail that is bound by the poly(A)-binding proteins to regulate mRNA stability, localization and translation.
More than 50% of mammalian genes use alternative poly(A) sites, which affect the mRNA’s accessibility to regulatory factors including microRNAs and RNA binding proteins. While the choice of poly(A) site(s) selection is tightly regulated during development, the key determinative factors affecting this process are largely unknown.
We are currently studying the regulatory programs that control alternative polyadenylation during mouse heart development. We are also characterizing the roles of poly(A) binding proteins in cardiac development and disease.
2016- Beckman Fellow, Center for Advanced Study, UIUC
2016, 15, 14- Listed in "Teachers Ranked as Excellent", UIUC
2014- Member, Faculty of 1000
2014- Basil O' Connor Starter Scholar Research Award, March of Dimes
2013- Young Investigator Award, Roy J. Carver Charitable Trust
2011- Scientist Development Grant, American Heart Association
2009- Post-doctoral Fellow, Myotonic Dystrophy Foundation
2005- President Research Scholar, University of Texas-M.D. Anderson Cancer Center
2004- Dean’s Excellence in Research Award, University of Texas
2003- Pre-doctoral Fellow, Harry S. and Isabel Cameron Foundation
1. Lewis CJ, Pan T and Kalsotra A (2017). RNA modifications and structures cooperate to guide RNA-protein interactions. Nature Reviews Mol. Cell Biol. Mar;18(3):202-210. doi: 10.1038/nrm.2016.163.
2. Yum K, Wang ET and Kalsotra A (2017). Myotonic dystrophy: disease repeat range, penetrance, age of onset, and relationship between repeat size and phenotypes.
Curr. Opin. Genet. Dev. Feb 14;44:30-37. doi: 10.1016/j.gde.2017.01.007.
3. Arif W, Datar G and Kalsotra A (2017). Intersections of post-transcriptional gene regulatory mechanisms with intermediary metabolism. Biochim. Biophys. Acta. Jan 11;1860(3):349-362. doi: 10.1016/j.bbagrm.2017.01.004.
4. Bangru S, Kalsotra A (2016). Advances in analyzing RNA diversity in eukaryotic transcriptomes: peering through the Omics lens. F1000Research 5:2668 doi: 10.12688/f1000research.9511.1
5. Bhate A*, Parker DJ*, Bebee TW, Ahn J, Arif W, Rashan EH, Chorghade S, Chau A, Lee JH, Anakk S, Carstens RP, Xiao X and Kalsotra A (2015). ESRP2 controls an adult splicing program in hepatocytes to support postnatal liver maturation.
Nature Commun. 2015 Nov 4;6:8768. doi: 10.1038/ncomms9768.
* denotes equal authors
6. Jaiswal M, Haelterman NA, Sandoval H, Xiong B, Donti T, Kalsotra A, Yamamoto S, Cooper TA, Graham BH and Bellen HJ (2015) Impaired Mitochondrial Energy Production Causes Light-Induced Photoreceptor Degeneration Independent of Oxidative Stress. PLoS Biol. 13(7): e1002197. doi:10.1371/journal.pbio.1002197
Highlighted on the cover of PLos Biol.
7. Li W, You B, Hoque M, Luo W, Park JY, Ji Z, Zheng D, Gunderson SI, Kalsotra A, Manley JL and Tian B (2015). Systematic profiling of poly(A)+ transcripts modulated by core 3' end processing and splicing factors reveals regulatory rules of alternative cleavage and polyadenylation. PLoS Genet. doi:10.1371/journal.pgen.1005166
8. Chaturvedi P, Neelamraju Y, Arif W, Kalsotra A, and Janga SC (2015). Uncovering RNA binding proteins associated with age and gender during liver maturation. Sci Rep. 5: 9512 doi:10.1038/srep09512
9. Chau A, Kalsotra A (2015). Developmental insights Into the pathology of and therapeutic strategies for DM1: Back to the Basics. Dev Dyn. 244:377–390.doi: 10.1002/DVDY.24240
10. Singh RK, Xia Z, Bland CS, Kalsotra A, Ruddy M, Curk T, Ule J, Li W and Cooper, TA (2014). Rbfox2-coordinated alternative splicing of Mef2d and Rock2 controls myoblast fusion during myogenesis. Mol Cell. 55, 1–12. Jul 30.doi: 10.1016/j.molcel.2014.06.035.
11. Giudice J, Zheng X, Wang ET, Scavuzzo MA, Ward AJ, Kalsotra A, Wei W, Wehrens XHT, Burge CB, Li W and Cooper TA (2014). Alternative splicing regulates vesicular trafficking genes in cardiomyocytes during postnatal heart development. Nature Commun. 22 (5):3603. doi:10.1038/ncomms4603.
12. Kalsotra A, Singh RK, Gurha P, Ward AJ, Creighton C and Cooper TA (2014). The Mef2 transcription network is disrupted in myotonic dystrophy heart tissue dramatically altering miRNA and mRNA expression. Cell Rep. 6(1):336–345.
13. Kalsotra A and Cooper TA (2011). “Functional consequences of developmentally regulated alternative splicing”. Nature Rev. Genet. 12, 715-29.
Chosen as featured article.
Highlighted on the cover of Nature Rev. Genet.
14. Kalsotra A, Wang K, Li PF, and Cooper TA (2010). “MicroRNAs coordinate an alternative splicing network during mouse postnatal heart development”. Genes Dev. 24, 653-58.
Highlighted on the cover of Genes Dev.
Recommended by Faculty of 1000.
15. Kalsotra A, Xiao X, Ward A, Castle JC, Johnson JM, Burge CB, and Cooper TA (2008). “A postnatal switch of CELF and MBNL proteins reprograms alternative splicing in the developing heart”. Proc. Natl. Acad. Sci. U.S.A. 105, 20333-8.
16. Castle JC, Zhang C, Shah JK, Kulkarni AV, Kalsotra A, Cooper TA and Johnson JM (2008) Differential expression of 24,426 human alternative splicing events and predicted cis-regulation in 48 tissues and cell lines. Nature Genet. 40, 1416-25.
Editorial in Nature Genet.