Yuzuru Shiio, MD, PhD

  • Rank: Associate Professor
  • Department: Biochemistry & Structural Biology
  • Office: 3.100.08
  • Location: Greehey CCCRI
  • Tel: 1.210.562.9089


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
  1. 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. Ewing sarcoma is a bone and soft tissue cancer in children and is characterized by the chromosomal translocation generating a fusion oncogene between EWS and an Ets family transcription factor, most commonly FLI-1. While studying the interactome and the biochemical properties of EWS-FLI-1, we found that EWS-FLI-1 turns over by the lysosome-dependent mechanism, unlike most cellular proteins that turn over by the proteasome-dependent mechanism. We went on to demonstrate that torin 1, which stimulates the TFEB – lysosomes biogenesis pathway, can accelerate the turn-over of EWS-FLI-1. This suggested a new strategy to deplete EWS-FLI-1 in Ewing sarcoma. We are identifying additional compounds that target EWS-FLI-1 for degradation. It is widely believed that cancer is caused by multiple genetic alterations (mutational activation and inactivation of multiple oncogenes and anti-oncogenes, respectively). Ewing sarcoma was considered an exception because there appeared to be only one cancer-causing gene in this cancer, the gene encoding for EWS-FLI-1. We found that there is the second cancer-causing gene in this cancer, FLI-1-EWS, a fusion gene reciprocal to EWS-FLI-1. We demonstrated that FLI-1-EWS makes a positive contribution to in vitro and in vivo growth of Ewing sarcoma and cooperates with EWS-FLI-1 in human mesenchymal stem cells, putative cells of origin of Ewing sarcoma. We are studying how FLI-1-EWS cooperates with EWS-FLI-1 in the initiation and progression of Ewing sarcoma. (CPRIT RP160487; NIH R21CA202485)


  3. 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)


    We found that fibroblasts induced to senesce by DNA damage over-secrete SFRP1 (Secreted Frizzled-related Protein 1), a secreted antagonist of Wnt signaling and tumor suppressor. SFRP1 mediated senescence phenotypes through inhibition of Wnt signaling and activation of the Rb pathway. The role of Wnt inhibition in cellular senescence was also supported by senescence induction by different Wnt antagonists (SFRP1-5 and DKK1), by pharmacological inhibition of Wnt signaling, and by knock-down of β-catenin. Interestingly, cancer-associated SFRP1 mutants were defective for senescence induction. These results suggest that SFRP1 is an extracellular component of stress-induced senescence signaling that responds to potentially carcinogenic stresses such as DNA damage and induces cellular senescence in an autocrine and paracrine fashion, which may lead to non-cell autonomous tumor suppression. : (Mol. Cell. Biol. 32: 4388-99, 2012.)


    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.)


    Interestingly, IGFBP3 is specifically silenced in Ewing sarcoma, a childhood cancer of bone and soft tissues, and its re-expression potently inhibits Ewing sarcoma growth. We have identified the downstream targets of IGFBP3 in Ewing sarcoma cells and are characterizing their roles in mediating anti-Ewing sarcoma effect.

  5. 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)

  7. 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.