Employing a combination of proteomics and traditional molecular cell biology approaches, our laboratory mainly studies:
- Cytokine signaling and function of fusion oncoproteins in children’s cancers
- Secreted mediators of cellular senescence
- Using secretome proteomics, we determined that hepatoblastoma (children’s liver cancer) is dependent on the autocrine secretion of FGF19, a growth factor for liver cells. FGF19 signals through FGFR4 and we found that the growth of hepatoblastoma can be blocked by an inhibitor of FGFR4 tyrosine kinase.
- Cellular senescence plays key roles in tumor suppression and organismal aging. Accumulating evidence suggests profoundly altered protein secretion from senescent cells, which may recruit immune cells for clearance of senescent cells, affect the architecture or function of surrounding tissues, modulate tumor progression, and contribute to aging and age-related diseases. Using quantitative proteomic analysis of protein secretion from senescent cells, we identified two secreted mediators of senescence, SFRP1 and IGFBP3. (NIH R21AG029587)
In addition to normal cells, cancer cells also undergo senescence upon chemotherapeutic drug treatment. We found that MCF-7 breast cancer cells induced to senesce by doxorubicin treatment display elevated extracellular IGFBP3 (Insulin-like Growth Factor Binding Protein 3), a secreted inhibitor of IGF signaling. We determined that IGFBP3 induces senescence through suppression of Akt kinase signaling and requiring the Rb and p53 pathways. To dissect the biochemical pathways regulating IGFBP3, we undertook a proteomic screen for IGFBP3-interacting proteins and identified t-PA (tissue-type plasminogen activator) as interactor. t-PA is a protease that cleaves plasminogen. We found that t-PA can also cleave IGFBP3 and counteract the senescence induction by IGFBP3. The protease activity of t-PA is specifically inhibited by PAI-1 (plasminogen activator inhibitor 1). We found that PAI-1 also inhibits IGFBP3 cleavage by t-PA and induces senescence. PAI-1 was previously identified as a mediator of cellular senescence and by using shRNA-mediated knockdown of IGFBP3, we demonstrated that IGFBP3 is a critical downstream target of PAI-1-induced senescence. These results suggest a role for extracellular PAI-1 – t-PA – IGFBP3 cascade in the regulation of stress-induced senescence. (Proc. Natl. Acad. Sci. U S A. 24;109: 12052-7, 2012.)
- Mutation of the VHL tumor suppressor plays a central role in the generation of both hereditary and non-hereditary kidney cancers. VHL is a ubiquitin ligase, an enzyme that attaches a small protein called ubiquitin to its substrate proteins. A major bottleneck in understanding the functions of ubiquitin ligases has been the difficulty in identifying their ubiquitination substrates. We are using quantitative proteomics approaches to identify the ubiquitination substrates and interaction partners for VHL. (NIH R01CA125020)
- The serum cancer biomarkers that can be measured by a simple blood test have great potential for early diagnosis, disease monitoring, and assessment of therapeutic response. However, direct proteomic analysis of cancer patient serum is technically difficult. As an alternative, we are identifying candidate cancer biomarkers by analyzing proteins secreted from cancer cells in culture, which will be validated using serum samples from cancer patients and healthy controls. (NIH R21CA139170)
Dr. Shiio received his M.D. and Ph.D. from the University of Tokyo where he studied the function of the p53 and Rb tumor suppressors. As a post-doctoral fellow with Dr. Robert N. Eisenman at the Fred Hutchinson Cancer Research Center, he started research on Myc, a gene frequently altered in human cancers. The Myc protein induces proliferation, apoptosis, genomic instability, and tumorigenesis, but how Myc induces these diverse biological activities is not well understood.
To gain insight into the mechanism of Myc action, Dr. Shiio initiated a collaboration with Dr. Ruedi Aebersold's group at the Institute for Systems Biology to use ICAT (isotope-coded affinity tags) quantitative proteomic analysis. The ICAT technology involves stable isotope labeling of proteins in a complex mixture, affinity isolation of labeled peptides, and amino acid sequence determination and quantification by mass spectrometry. Using ICAT-based protein expression profiling, they performed a whole proteome comparison of Myc-null and Myc-plus cells and revealed a novel cytoskeletal function for Myc (EMBO J. 21: 5088-5096, 2002) as well as a critical mediator of myc-induced apoptosis (J. Biol. Chem. 281(5):2750-6, 2006.). In addition to global protein expression profiling, the ICAT technology can also be used for the quantitative analysis of a sub-proteome such as sub-cellular fractions, protein complexes, and modified proteins. For example, he also developed an ICAT-based method to identify and quantify chromatin-associated regulatory factors (J. Am. Soc. Mass Spectrom. 14: 696-703, 2003) and analyzed the components of a new mSin3 interacting co-repressor complex (Mol. Cell. Biol. 26:1386-97, 2006.). Dr. Shiio has also discovered a novel histone modification, sumoylation, and demonstrated that it is associated with transcriptional repression (P.N.A.S. 100: 13225-30, 2003).
Proteomics-based biology -
proteomics-based biology of protein secretion (in relation to cellular senescence and childhood cancers) and oncoprotein function.
- FGF19 functions as autocrine growth factor for hepatoblastoma. Elzi DJ, Song M, Blackman B, Weintraub ST, Lopez-Terrada D, Chen Y, Tomlinson GE, and Shiio Y. Genes & Cancer, in press, 2016
- The role of FLI-1-EWS, a fusion gene reciprocal to EWS-FLI-1, in Ewing sarcoma Elzi DJ, Song M, Houghton PJ, Chen Y, and Shiio Y. Genes & Cancer 6: 452-461, 2015
- Role of galactose in cellular senescence. Elzi DJ, Song M, Shiio Y. Exp Gerontol. 2015 Nov 10;73:1-4. [Epub ahead of print]
- Proteomic Analysis of the EWS-Fli-1 Interactome Reveals the Role of the Lysosome in EWS-Fli-1 Turnover. Elzi DJ, Song M, Hakala K, Weintraub ST, Shiio Y. J Proteome Res. 13(8):3783-91, 2014
- Wnt antagonist SFRP1 functions as a secreted mediator of senescence. Elzi DJ, Song M, Hakala K, Weintraub ST, Shiio Y. Mol Cell Biol. 32(21):4388-99, 2012.
- Plasminogen activator inhibitor 1--insulin-like growth factor binding protein 3 cascade regulates stress-induced senescence. Elzi DJ, Lai Y, Song M, Hakala K, Weintraub ST, Shiio Y. Proc Natl Acad Sci U S A. 109(30):12052-7, 2012.
- The interaction of the von Hippel-Lindau tumor suppressor and heterochromatin protein 1. Lai Y, Song M, Hakala K, Weintraub ST, Shiio Y. Arch Biochem Biophys. 518(2):103-10, 2012.
- Quantitative proteomic identification of the BRCA1 ubiquitination substrates. Song M, Hakala K, Weintraub ST, Shiio Y. J Proteome Res. 10(11):5191-8, 2011.
- Proteomic dissection of the von Hippel-Lindau (VHL) interactome. Lai Y, Song M, Hakala K, Weintraub ST, Shiio Y. J Proteome Res. 10(11):5175-82, 2011.
- Quantitative proteomics identifies the Myb-binding protein p160 as a novel target of the von Hippel-Lindau tumor suppressor. Lai Y, Qiao M, Song M, Weintraub ST, Shiio Y. PLoS One. 6(2):e16975, 2011.
- Quantitative proteomic analysis of myc-induced apoptosis: a direct role for Myc induction of the mitochondrial chloride ion channel, mtCLIC/CLIC4. Shiio Y, Suh KS, Lee H, Yuspa SH, Eisenman RN, Aebersold R. J Biol Chem. 281(5):2750-6, 2006.
- Identification and characterization of SAP25, a novel component of the mSin3 corepressor complex. Shiio Y, Rose DW, Aur R, Donohoe S, Aebersold R, Eisenman RN. Mol Cell Biol. 26(4):1386-97, 2006.
- Quantitative proteome analysis using isotope-coded affinity tags and mass spectrometry. Shiio Y, Aebersold R. Nature Protoc. 1(1):139-45, 2006.
- Histone sumoylation is associated with transcriptional repression. Shiio Y, Eisenman RN. Proc Natl Acad Sci U S A. 100(23):13225-30, 2003.
- Quantitative proteomic analysis of chromatin-associated factors. Shiio Y, Eisenman RN, Yi EC, Donohoe S, Goodlett DR, Aebersold R. J Am Soc Mass Spectrom. 14(7):696-703, 2003.
- Quantitative proteomic analysis of Myc oncoprotein function. Shiio Y, Donohoe S, Yi EC, Goodlett DR, Aebersold R, Eisenman RN. EMBO J. 21(19):5088-96, 2002.
- Myc and Max homologs in Drosophila. Gallant P, Shiio Y, Cheng PF, Parkhurst SM, Eisenman RN. Science. 274(5292):1523-7, 1996.
- Activation of the retinoblastoma gene expression by Bcl-3: implication for muscle cell differentiation. Shiio Y, Sawada J, Handa H, Yamamoto T, Inoue J. Oncogene. 12(9):1837-45, 1996.
- Epitope tagging. Shiio Y, Itoh M, Inoue J. Methods Enzymol. 254:497-502, 1995.
- Identification of a DNA element that can enhance p53-mediated transactivation. Shiio Y, Yamamoto T, Yamaguchi N. Oncogene. 8(8):2059-65, 1993.
- Negative regulation of Rb expression by the p53 gene product. Shiio Y, Yamamoto T, Yamaguchi N. Proc Natl Acad Sci U S A. 89(12):5206-10, 1992.