Peter Stoilov, PhD

Research Interests

Regulation of alternative pre-mRNA splicing; Alternative splicing in cancer progression; Drugs targeting alternative splicing as cancer therapeutics and research tools; High-throughput research methods.

Pre-mRNA splicing and disease:

The majority of eukaryotic genes are split into alternating exon and intron sequences. During the pre-mRNA maturation the introns are excised from the transcripts and the exons are spliced together. Frequently, in a process known as alternative pre-mRNA splicing, multiple mRNAs variants are generated from a single gene by skipping or including certain exons. Alternative splicing plays a significant role in generating enormous protein diversity from the limited number of genes in the eukaryotic genomes. It is also an important control point for gene expression and protein function, that is regulated during development and by various physiological processes.

Disruption and misregulation of pre-mRNA splicing are a major cause of disease in humans. Estimated 50% of disease causing mutations affect pre-mRNA splicing. Alternative splicing has been identified as therapeutic target in various pathological conditions including neurodegenerative diseases, autoimmune disorders, retroviral infections and cancer. Several recent studies show that on a global scale tumors share similar alternative splicing patterns that are distinct from those of the tissues of origin. This shift in alternative splicing adjusts the properties of multiple proteins resulting in a broad effect on the tumor physiology. Notable examples are protein isoforms with anti-apoptotic properties (Bin1, Bcl-XL), growth factor receptors with increased sensitivity and/or altered specificity (FGFR1 and 2), and enzymes that redirect metabolites from energy production to anabolic processes (PKM2). As a result drugs modulating alternative splicing can provide a new therapeutic approach that will simultaneously impact multiple molecular targets and be effective on cancers of various types and origins.

Research projects:

1. Identify alternative splicing events that are critical for cancer progression. We have successfully used genetic approaches, such as microarrays and RNA knockdown, to characterize the role alternative splicing plays in neuronal development. Now I plan to use these techniques as well as deep sequencing and genetic screens to investigate the role alternative splicing plays in cancer. In particular I am interested in identify alternative splicing events that are critical for cancer progression and dissecting the molecular mechanism that control them.
2. Develop novel cancer therapeutics that target alternative splicing. In my most recent work I developed a fluorescent reporter that can be used to monitor the splicing of alternative exons in living cells. This reporter was used in high-throughput screening of compound libraries to identify over a hundred small molecules capable of modulating alternative splicing. Interestingly some of these compounds can correct the splicing of the PKM2 transcript that is critical for cancer cell growth. The compounds targeting PKM2 splicing are now being used as leads for developing anticancer drugs. The splicing reporter is also being employed to screen for more compounds that target alternative exons with known roles in cancer, such as PKM2 M1/M2, FGFR2 IIIb/IIIc, FGFR1-alpha.

Publications

1. Koedoot E, Fokkelman M, Rogkoti VM, Smid M, van de Sandt I, de Bont H, Pont C,Klip JE, Wink S, Timmermans MA, Wiemer EAC, Stoilov P, Foekens JA, Le Dévédec SE, Martens JWM, van de Water B. Uncovering the signaling landscape controlling breast cancer cell migration identifies novel metastasis driver genes. Nat Commun. 2019 Jul 5;10(1):2983. doi: 10.1038/s41467-019-11020-3. PubMed PMID:31278301; PubMed Central PMCID: PMC6611796.

2. Wright ZC, Loskutov Y, Murphy D, Stoilov P, Pugacheva E, Goldberg AFX, Ramamurthy V. ADP-Ribosylation Factor-Like 2 (ARL2) regulates cilia stability and development of outer segments in rod photoreceptor neurons. Sci Rep. 2018 Nov16;8(1):16967. doi: 10.1038/s41598-018-35395-3. PubMed PMID: 30446707; PubMed Central PMCID: PMC6240099.

3. Bapat A, Keita N, Martelly W, Kang P, Seet C, Jacobsen JR, Stoilov P, Hu C, Crooks GM, Sharma S. Myeloid Disease Mutations of Splicing Factor SRSF2 Cause G2-M Arrest and Skewed Differentiation of Human Hematopoietic Stem and Progenitor Cells. Stem Cells. 2018 Nov;36(11):1663-1675. doi: 10.1002/stem.2885. Epub 2018Jul 27. PubMed PMID: 30004607; PubMed Central PMCID: PMC6283046.

4. Qin Z, Stoilov P, Zhang X, Xing Y. SEASTAR: systematic evaluation of alternative transcription start sites in RNA. Nucleic Acids Res. 2018 May4;46(8):e45. doi: 10.1093/nar/gky053. PubMed PMID: 29546410; PubMed Central PMCID: PMC5934623.

5. Dilan TL, Singh RK, Saravanan T, Moye A, Goldberg AFX, Stoilov P, Ramamurthy V. Bardet-Biedl syndrome-8 (BBS8) protein is crucial for the development of outer segments in photoreceptor neurons. Hum Mol Genet. 2018 Jan 15;27(2):283-294. doi:10.1093/hmg/ddx399. PubMed PMID: 29126234; PubMed Central PMCID: PMC5886228.

6. Xu M, Xie YA, Abouzeid H, et al.  Mutations in the Spliceosome Component CWC27 Cause Retinal Degeneration with or without Additional Developmental Anomalies. Am J Hum Genet. 2017 Apr 6;100(4):592-604. doi:10.1016/j.ajhg.2017.02.008. Epub 2017 Mar 9. PubMed PMID: 28285769; PubMed Central PMCID: PMC5384039.

7. Corbin DR, Rehg JE, Shepherd DL, Stoilov P, Percifield RJ, Horner L, Frase S, Zhang YM, Rock CO, Hollander JM, Jackowski S, Leonardi R. Excess coenzyme A reduces skeletal muscle performance and strength in mice overexpressing humanPANK2. Mol Genet Metab. 2017 Apr;120(4):350-362. doi:10.1016/j.ymgme.2017.02.001. Epub 2017 Feb 3. PubMed PMID: 28189602; PubMed Central PMCID: PMC5382100.

8. Balachandran A, Wong R, Stoilov P, Pan S, Blencowe B, Cheung P, Harrigan PR, Cochrane A. Identification of small molecule modulators of HIV-1 Tat and Rev protein accumulation. Retrovirology. 2017 Jan 26;14(1):7. doi:10.1186/s12977-017-0330-0. PubMed PMID: 28122580; PubMed Central PMCID: PMC5267425.

9. Fang J, Bolanos LC, Choi K, Liu X, Christie S, Akunuru S, Kumar R, Wang D,Chen X, Greis KD, Stoilov P, Filippi MD, Maciejewski JP, Garcia-Manero G, Weirauch MT, Salomonis N, Geiger H, Zheng Y, Starczynowski DT. Ubiquitination of hnRNPA1 by TRAF6 links chronic innate immune signaling with myelodysplasia. Nat Immunol. 2017 Feb;18(2):236-245. doi: 10.1038/ni.3654. Epub 2016 Dec 26. Erratum in: Nat Immunol. 2017 Mar 22;18(4):474. PubMed PMID: 28024152; PubMed Central PMCID: PMC5423405.

10. Grosso F, Stoilov P, Lingwood C, Brown M, Cochrane A. Suppression of Adenovirus Replication by Cardiotonic Steroids. J Virol. 2017 Jan 18;91(3). pii: e01623-16. doi: 10.1128/JVI.01623-16. Print 2017 Feb 1. PubMed PMID: 27881644; PubMed Central PMCID: PMC5244322.

11. Murphy D, Cieply B, Carstens R, Ramamurthy V, Stoilov P. The Musashi 1 Controls the Splicing of Photoreceptor-Specific Exons in the Vertebrate Retina. PLoS Genet. 2016 Aug 19;12(8):e1006256. doi: 10.1371/journal.pgen.1006256.eCollection 2016 Aug. Erratum in: PLoS Genet. 2016 Nov 3;12 (11):e1006432. PubMed PMID: 27541351; PubMed Central PMCID: PMC4991804.

12. Pifer PM, Farris JC, Thomas AL, Stoilov P, Denvir J, Smith DM, Frisch SM. Grainyhead-like 2 inhibits the coactivator p300, suppressing tubulogenesis and the epithelial-mesenchymal transition. Mol Biol Cell. 2016 Aug 1;27(15):2479-92. doi: 10.1091/mbc.E16-04-0249. Epub 2016 Jun 1. PubMed PMID: 27251061; PubMed Central PMCID: PMC4966987.

13. Murphy D, Kolandaivelu S, Ramamurthy V, Stoilov P. Analysis of Alternative Pre-RNA Splicing in the Mouse Retina Using a Fluorescent Reporter. Methods Mol Biol. 2016; 1421:269-86. doi: 10.1007/978-1-4939-3591-8_20. PubMed PMID: 26965271.

14. Gall BJ, Wilson A, Schroer AB, Gross JD, Stoilov P, Setola V, Watkins CM, Siderovski DP. Genetic variations in GPSM3 associated with protection from rheumatoid arthritis affect its transcript abundance. Genes Immun. 2016Mar;17(2):139-47. doi: 10.1038/gene.2016.3. Epub 2016 Jan 28. PubMed PMID:26821282; PubMed Central PMCID: PMC4777669.

15. Farrugia MK, Sharma SB, Lin CC, McLaughlin SL, Vanderbilt DB, Ammer AG, Salkeni MA, Stoilov P, Agazie YM, Creighton CJ, Ruppert JM. Regulation of anti-apoptotic signaling by Kruppel-like factors 4 and 5 mediates lapatinib resistance in breast cancer. Cell Death Dis. 2015 Mar 19;6:e1699. doi:10.1038/cddis.2015.65. PubMed PMID: 25789974; PubMed Central PMCID: PMC4385942.

16. Murphy D, Singh R, Kolandaivelu S, Ramamurthy V, Stoilov P. Alternative Splicing Shapes the Phenotype of a Mutation in BBS8 To Cause Nonsyndromic Retinitis Pigmentosa. Mol Cell Biol. 2015 May;35(10):1860-70. doi:10.1128/MCB.00040-15. Epub 2015 Mar 16. PubMed PMID: 25776555; PubMed Central PMCID: PMC4405636.

17. Percifield R, Murphy D, Stoilov P. Medium throughput analysis of alternative splicing by fluorescently labeled RT-PCR. Methods Mol Biol. 2014; 1126:299-313.doi: 10.1007/978-1-62703-980-2_22. PubMed PMID: 24549673.