Yuzuru Shiio, MD, PhD
Employing a combination of proteomics and molecular cell biology, our laboratory studies:
- Novel cytokine–receptor pairs and their downstream signaling in children’s cancers
- Fusion oncoproteins in children’s cancers
Dr. Shiio received his MD and PhD 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 (Nature Protoc. 1:139-45, 2006). 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., 281:2750-6, 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).
1. NELL2 – cdc42 – BAF complex signaling in Ewing sarcoma
Ewing sarcoma is a cancer of the bone and soft tissue in children that is characterized by a chromosomal translocation generating a fusion between EWS and an Ets family transcription factor, most commonly FLI1. We used proteomics to analyze the proteins secreted from Ewing sarcoma cells and found that these cancer cells abundantly secrete a cytokine called NELL2 (Neural Epidermal Growth Factor-like 2) and depend on the autocrine signaling mediated by NELL2 and its receptor, Robo3. NELL2 signaling inhibits cdc42 and upregulates the BAF chromatin remodeling complexes and EWS-FLI1 transcriptional output. We determined that cdc42 is a negative regulator of the BAF complexes, inducing actin polymerization and complex disassembly. Furthermore, we identified two cell populations, NELL2highCD133highEWS-FLI1high and NELL2lowCD133lowEWS-FLI1low, in Ewing sarcoma which display phenotypes consistent with high and low NELL2 signaling, respectively. We found that NELL2, CD133, and EWS-FLI1 positively regulate each other and upregulate the BAF complexes and cell proliferation in Ewing sarcoma. These results uncovered a signaling pathway regulating critical chromatin remodeling complexes and cancer cell proliferation. (Cell Reports 36(1): 109254, 2021; CPRIT RP190385)
2. GDF6 – CD99 – Src signaling in Ewing sarcoma
Using secretome proteomics and molecular cell biology, we found that Ewing sarcoma depends on the autocrine signaling mediated by growth and differentiation factor 6 (GDF6), a member of the BMP family of cytokines. Surprisingly, Ewing sarcoma depends on the prodomain, not the BMP domain, of GDF6. We demonstrated that the GDF6 prodomain is a ligand for CD99, a transmembrane protein that has been widely used as a marker of Ewing sarcoma. The binding of the GDF6 prodomain to the CD99 extracellular domain results in the recruitment of CSK to the YQKKK motif in the intracellular domain of CD99, inhibiting Src activity. GDF6 silencing causes hyperactivation of Src and p21-dependent growth arrest. We demonstrated that two GDF6 prodomain mutants linked to Klippel-Feil syndrome are hyperactive in CD99 – Src signaling. These results revealed a cytokine signaling pathway that regulates the CSK – Src axis and cancer cell proliferation and suggest the gain-of-function activity for disease-causing GDF6 mutants.
(Cell Reports 33(5):108332, 2020; CPRIT RP160487)
3. A cell surface protease, pappalysin-1, enhances IGF signaling in Ewing sarcoma.
We used proteomics to analyze how the EWS-FLI1 fusion oncoprotein alters extracellular proteins in Ewing sarcoma and found that EWS-FLI1 induces the expression of pappalysin-1 (PAPPA), a cell surface protease that degrades IGF binding proteins (IGFBPs) and increases the bioavailability of IGF. EWS-FLI1 binds to the pappalysin-1 gene promoter and stimulates the expression of pappalysin-1, leading to degradation of IGFBPs and enhanced IGF signaling. Silencing of pappalysin-1 strongly inhibited anchorage-dependent and anchorage-independent growth as well as xenograft tumorigenicity of Ewing sarcoma cells. These results suggest that EWS-FLI1 creates a cell surface microenvironment conducive to IGF signaling by inducing pappalysin-1, which emerged as a novel target to inhibit IGF signaling in Ewing sarcoma. (Genes & Cancer 8(11-12):762-770, 2017)
4. FGF19 signaling in hepatoblastoma
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 an inhibitor of FGFR4 tyrosine kinase blocks the growth of hepatoblastoma. (Genes & Cancer 7(3-4):125-35, 2016)
5. The role of FLI1-EWS, a fusion gene reciprocal to EWS-FLI1, in Ewing sarcoma
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-FLI1. We found that there is the second cancer-causing gene in this cancer, FLI1-EWS, a fusion gene reciprocal to EWS-FLI1. We demonstrated that FLI1-EWS makes a positive contribution to in vitro and in vivo growth of Ewing sarcoma and cooperates with EWS-FLI1 in human mesenchymal stem cells, putative cells of origin of Ewing sarcoma. We are studying how FLI1-EWS cooperates with EWS-FLI1 in the initiation and progression of Ewing sarcoma. (Genes & Cancer 6(11-12):452-61, 2015; NIH R21CA202485)
6. Lysosomal degradation of EWS-FLI1 in Ewing sarcoma
While studying the interactome and the biochemical properties of EWS-FLI1, we found that EWS-FLI1 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-FLI1. This suggested a new strategy to deplete EWS-FLI1 in Ewing sarcoma. We are identifying additional compounds that target EWS-FLI1 for degradation. (J Proteome Res. 13(8):3783-91, 2014; CPRIT RP160841)
7. Cytokines mediating cellular senescence: SFRP1 and IGFBP3
Cellular senescence plays a critical role 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 knockdown 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 an 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 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.)
8. Characterization of the VHL tumor suppressor pathway
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 employed quantitative proteomics approaches to identify the ubiquitination substrates and interaction partners for VHL. (NIH R01CA125020)
9. Secretome proteomics for cancer biomarker discovery
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 are validated using serum samples from cancer patients and healthy controls. (NIH R21CA139170)
Selected Publications: (pdf format)
- Cell Reports 2021 36(1): 109254, “NELL2-cdc42 signaling regulates BAF complexes and Ewing sarcoma cell growth”
- Cell Reports: 2020. “GDF6-CD99 Signaling Regulates Src and Ewing Sarcoma Growth”
- Genes & Cancer: 2017, “EWS-FLI-1 creates a cell surface microenvironment conducive to IGF signaling by inducing pappalysin-1r”
- Genes & Cancer: 2016, “FGF19 functions as an autocrine growth factor for hepatoblastoma”
- Genes & Cancer: 2015: “The role of FLI-1-EWS, a fusion gene reciprocal to EWS-FLI-1, in Ewing sarcoma”
- Journal of Proteome Research: 2014, “Proteomic Analysis of the EWS-Fli.1 Interactome Reveals the Role of the Lysosome in EWS-Fli.1 Turnover”
- Molecular Cellular Biology: 2012, “Wnt Antagonist SFRP1 Functions as a Secreted Mediator of Senescence”
- PNAS: 2012, “Plasminogen activator inhibitor 1 – insulin-like growth factor binding protein 3 cascade regulates stress-induced senescence”
Panneerselvam Jayabal, PhD
Xiuye Ma, MS
Kruthi Suvarna, Ph.D.
Sung-Jen Wei, PhD
- SAVE-THE-DATE: San Antonio Pediatric Cancer Symposium (SAPCS) May 10, 2022
- Genes & Cancer: EZH2 suppresses endogenous retroviruses and an interferon response in cancers (Shiio Lab) January 10, 2022
- eLife Sciences: Loss of MGA repression mediated by an atypical polycomb complex promotes tumor progression and invasiveness (Shiio Lab) July 9, 2021
- BIOC5013 Dental Biochemistry “Transcription, Protein synthesis, targeting, and degradation, Inflammation, Blood coagulation, Wound healing, Humoral immunity, Cellular immunity, Nucleotide metabolism, Fibrous proteins and connective tissue, Cancer biology”
- BIOC6037 Integration of Metabolic Pathways “Glycogen metabolism, Nitrogen fixation and amino acid biosynthesis, Amino acid catabolism, Protein metabolism, Nucleotide metabolism”
- BIOC6010 Gene expression “Proteomics, Protein turnover, Post-translational modifications, Gene expression and cancer”
- IBMS5000 Fundamentals of Biomedical Sciences “Post-translational modifications & small group discussion”