Exploring targeted therapy of osteosarcoma using proteomics data

Figures & data

Table 1 Proteomics studies of osteosarcoma in PubMed database

Proteomic study	Number of articles
OS vs OB cells^Citation15^–^Citation22	8
OS vs benign bone tumor tissues^Citation49^–^Citation53	5
Metastasis vs non-metastasis^Citation21,Citation54^–^Citation56	4
Chemoresistance^Citation57,Citation58	2
Responsiveness to various medicines^Citation59^–^Citation64	6
Responsiveness under specific stimulus conditions^Citation37,Citation38	2
OS cell lines^Citation65^–^Citation69	5
Serum or plasma of OS patients^Citation70^–^Citation74	5
Total	37

Abbreviations: OS, osteosarcoma; OB, osteoblastic.

Table 2 Proteomics studies of OS/OB experimental groups

Model		Techniques	Year	Citation
OB cells	OS cells
Primary cells: bone samples	OS cell line: SaOS-2	2DE, MALDI-TOF	2006	Spreafico et al^Citation15
OB cell line: hFOB1.19	OS cell lines: U2OS, SaOS-2, and IOR/OS9	2DE, MALDI-TOF	2007	Guo et al^Citation16
Primary cells: corresponding normal tissues from patients	Primary OS cells: paired biopsy from chemonaive high-grade patients	2D-DIGE, LC-ESI-MS/MS	2009	Folio et al^Citation17
Primary cells: bone samples	OS cell line: SaOS-2	2DE, MALDI-TOF	2009	Liu et al^Citation18
OB cell line: hFOB1.19	OS cell line: MG-63	iTRAQ labeling, LC-MS/MS	2010	Zhang et al^Citation19
OB cell line: hFOB1.19	OS cell line: MG-63	2DE, ESI-MS/MS	2011	Hua et al^Citation22
Primary OB cells: ORT-1, Hum31, and Hum54	OS cell lines: MG-63, U2OS, Cal-72, SaOS-2, and LM7	1DE, LC-MS/MS, label-free quantitative protein analysis	2013	PosthumaDeboer et al^Citation20
OB cell line: hFOB1.19	OS cell lines: Hs 39.T, Hs 184.T, and Hs 188.T	2DE, TOF/TOF	2015	Gemoll et al^Citation21

Abbreviations: OS, osteosarcoma; OB, osteoblastic; 2DE, two-dimensional gel electrophoresis; MALDI-TOF, matrix-assisted laser desorption/ionization time-of-flight mass spectrometry; 2D-DIGE, two-dimensional difference gel electrophoresis; iTRAQ, isobaric tags for relative and absolute quantitation; LC-MS/MS, liquid chromatography–tandem mass spectrometry; ESI-MS/MS, electrospray ionization mass spectrometry; TOF/TOF, tandem time-of-flight.

Table 3 Proteomics studies of metastasis in OS

Model		Techniques	Year	Citation
Non-metastasis	Metastasis
OS cell lines: HOS, SaOS-2	OS metastatic sublines: 143B, LM7	A lectin column followed by MudPIT	2012	Flores et al^Citation54
Low-metastatic subline: F4	Highly metastatic subline: F5M2	2D-DIGE, MALDI-TOF	2014	Chen et al^Citation55
OS tissue without metastasis	OS tissue with metastasized to lung	2DE, MALDI-TOF	2014	Tang et al^Citation56
OB cell line: hFOB1.19	OS cell lines: Hs 39.T, Hs 184.T, and Hs 188.T	2DE, TOF/TOF	2015	Gemoll et al^Citation21

Abbreviations: OS, osteosarcoma; MudPIT, multidimensional protein identification technology; 2D-DIGE, two-dimensional difference gel electrophoresis; MALDI-TOF, matrix-assisted laser desorption/ionization time-of-flight mass spectrometry; 2DE, two-dimensional gel electrophoresis; TOF/TOF, tandem time-of-flight.

Table 4 Proteomics studies of chemoresistance in OS

Model	Treatment	Techniques	Year	Citation
OS cell lines: HS-Os-1, NOS-1, SaOS-2, SJSA-1, 143B, HOS, HuO9, KHOS/NP, MG-63, MNNG-HOS, and NOS-10	Doxorubicin	2D-DIGE, annotated mass spectra in Genome Medicine Database of Japan Proteomics	2013	Arai et al^Citation57
Frozen tissue: poor responders (<90% necrosis), good responders (>90% necrosis)	Methotrexate, doxorubicin, and cisplatin	2D-DIGE, Orbitrap mass spectrometer	2013	Kubota et al^Citation58

Abbreviations: OS, osteosarcoma; 2D-DIGE, two-dimensional difference gel electrophoresis.

Figure 1 Enriched biological processes (GO annotation) of DEPs in OS/OB, metastasis, and chemoresistance.

Abbreviations: GO, gene ontology; DEPs, differentially expressed proteins; OS, osteosarcoma; OB, osteoblastic.

Figure 2 Pathway analysis of DEPs in OS/OB (from KEGG and BIOCARTA databases).

Abbreviations: DEPs, differentially expressed proteins; OS, osteosarcoma; OB, osteoblastic; ECM, extracellular matrix; tRNA, transfer RNA; TCA, the tricarboxylic acid; CBL, E3 ubiquitin-protein ligase CBL; EGF, epidermal growth factor.

Figure 3 Pathway analysis of DEPs in metastasis and chemoresistance (from KEGG and BIOCARTA databases).^75,76

Abbreviations: DEPs, differentially expressed proteins; OS, osteosarcoma; ER, estrogen receptor.

Figure 4 Generating the list of druggable targets for the treatment of OS: (A) overview of all steps used in generating the list and (B) diagrams of targets of FDA-approved non-antineoplastic drugs and non-FDA-approved chemical agents from studies of proteomics in three experimental groups.

Abbreviations: OS, osteosarcoma; FDA, Food and Drug Administration; DEPs, differentially expressed proteins; OB, osteoblastic; PPAT, amidophosphoribosyltransferase; CTSD, cathepsin D; LDHB, l-lactate dehydrogenase B chain; PKM2, pyruvate kinase M2; GAPDH, Glyceraldehyde-3-phosphate dehydrogenase.

Table 5 Up-regulated proteins and targets of FDA-approved antineoplastic drugs

Gene	Protein name	FDA-approved drug	Disease indicationa
DNMT1	DNA (cytosine-5)-methyltransferase 1	Azacitidine (Vidaza) Decitabine (Dacogen)	Myelodysplastic syndrome, chronic myelomonocytic leukemia Myelodysplastic syndrome
ERBB2	Receptor tyrosine-protein kinase erbB-2	Trastuzumab (HERCEPTIN) Lapatinib (Tycerb)	HER2-positive breast cancer Advanced or metastatic breast cancer whose tumors overexpress HER2 and who have received prior therapy including an anthracycline, a taxane, and trastuzumab
		Ado-trastuzumab emtansine (KADCYLA)	HER2-positive, metastatic breast cancer patients who have already used taxane and/or trastuzumab for metastatic disease or had their cancer recur within 6 months of adjuvant treatment
		Afatinib (GILOTRIF)	The first-line treatment of patients with metastatic NSCLC whose tumors have EGFR exon 19 deletions or exon 21 (L858R) substitution mutations as detected by an FDA-approved test
		Pertuzumab (PERJETA)	In combination with trastuzumab and docetaxel for the treatment of patients with HER2-positive metastatic breast cancer who have not received prior anti-HER2 therapy or chemotherapy for metastatic disease
GSR	Glutathione reductase, mitochondrial	Carmustine (GLIADEL^® WAFER)	Brain tumors, multiple myeloma, Hodgkin’s disease, and non-Hodgkin’s lymphomas
HDAC1	Histone deacetylase 1	Vorinostat (Zolinza)	Cutaneous T-cell lymphoma
HDAC2	Histone deacetylase 2	Romidepsin (Istodax)	Cutaneous T-cell lymphoma with at least one prior systemic therapy
KIT	Mast/stem cell growth factor receptor kit	Imatinib mesylate (Gleevec)	ALL, GIST, dermatofibrosarcoma protuberans, CML, myelodysplastic syndrome
		Sorafenib (Nexavar)	Advance renal cell carcinoma, some hepatocellular carcinoma
		Sunitinib (Sutent)	Metastatic renal cell carcinoma, GIST (no response to imatinib), pancreatic neuroendocrine tumor
		Pazopanib (Votrient)	Advanced renal cell carcinoma, advanced soft tissue sarcoma
		Dasatinib (Sprycel)	ALL, CML
		Axitinib (Inlyta)	Advanced renal cell carcinoma
		Nilotinib (Tasigna)	CML
FGFR1	Fibroblast growth factor receptor 1	Lenvatinib (Lenvima)	Locally recurrent or metastatic, progressive, radioactive iodine-refractory differentiated thyroid cancer
MET	Hepatocyte growth factor receptor	Cabozantinib (COMETRIQ)	Medullary thyroid cancer and patients with advanced RCC who have received prior antiangiogenic therapy
		Crizotinib (XALKORI)	Locally advanced or metastatic NSCLC that is ALK positive as detected by an FDA-approved test
MTOR	Serine/threonine protein kinase mTOR	Temsirolimus (Torisel) Everolimus (Afinitor)	Advance renal cell carcinoma Advanced renal cancer, subependymal giant cell astrocytoma, breast cancer, pancreatic cancer
PARP1	Poly (ADP-ribose) polymerase 1	Olaparib (AZD2281)	Monotherapy in patients with deleterious or suspected deleterious germline BRCA mutated (as detected by an FDA-approved test) advanced ovarian cancer who have been treated with three or more prior lines of chemotherapy
PDGFRα	Platelet-derived growth factor receptor alpha	Imatinib mesylate (Gleevac)	ALL, GIST, dermatofibrosarcoma protuberans, CML, myelodysplastic syndrome, systemic mastocytosis
		Sorafenib (Nexavar)	Advance renal cell carcinoma, some hepatocellular carcinoma
		Sunitinib (Sutent)	Metastatic renal cell carcinoma, GIST (no response to imatinib), pancreatic neuroendocrine tumor
		Pazopanib (Votrient)	Advanced renal cell carcinoma, advanced soft tissue sarcoma
		Nilotinib (Tasigna)	CML
		Axitinib (Inlyta)	Advanced renal cell carcinoma
		Dasatinib (Sprycel)	ALL, CML
PSMC2	26S protease regulatory subunit 7	Bortezomib (Velcade)	Multiple myeloma, mantle cell lymphoma
PSMC5	26S protease regulatory subunit 8	Carfilzomib (Kyprolis)	Multiple myeloma
PSMC6	26S protease regulatory subunit 10B

Note:

a Information from Termglinchan et al and DrugBank Version 4.5. Republished with permission of Dovepress, from Onco Targets Ther, Candidate cancer-targeting agents identified by expression-profiling arrays, Termglinchan V, Wanichnopparat W, Suwanwongse K, et al, 6, copyright 2013; permission conveyed through Copyright Clearance Center, Inc.⁷⁷ Wishart DS, Knox C, Guo AC, et al. DrugBank: a comprehensive resource for in silico drug discovery and exploration. Nucleic Acids Res. 2006;34(Database issue):D668–D672, by permission of Oxford University Press.⁷⁸

Abbreviations: FDA, Food and Drug Administration; HER2, human epidermal growth factor receptor 2; NSCLC, non-small-cell lung cancer; EGFR, epidermal growth factor receptor; ALL, acute lymphoid leukemia; GIST, gastrointestinal stromal tumor; CML, chronic myeloid leukemia; RCC, renal cell carcinoma; ALK, anaplastic lymphoma kinase.

Table 6 Up-regulated proteins and genes that are targets of FDA-approved non-antineoplastic drugs

Gene	Protein name	FDA-approved drug	Drug category	Disease indicationa
ATP1A1 ATP1B1	Na^+/K^+-ATPase	Digoxin Digitoxin	Antiarrhythmia agent	For the treatment and management of congestive cardiac insufficiency, arrhythmias, and heart failure.
DHODH	Dihydroorotate dehydrogenase (quinone), mitochondrial	Leflunomide	Immunosuppressive agent	For the management of the signs and symptoms of active RA. Has also been used for the prevention of acute and chronic rejection in recipients of solid organ trasnplants and is designated by the FDA as an orphan drug for this use.
IMPDH1	Inosine-5′-monophosphate dehydrogenase	Mycophenolate mofetil	Immunosuppressive agent	For the prophylaxis of organ rejection in patients receiving allogeneic renal, cardiac, or hepatic transplants.
IMPDH2		Ribavirin		For the treatment of chronic hepatitis C and for RSV.
PPAT	Amidophosphoribosyltransferase	Azathioprine	Immunosuppressive agent	For use in RA, preventing renal transplant rejection, Crohn’s disease, and colitis.

Note:

a Information from Termglinchan et al and DrugBank Version 4.5.^77,78

Abbreviations: FDA, Food and Drug Administration; RA, rheumatoid arthritis; RSV, respiratory syncytial virus.

Figure 5 Groups of up-regulated proteins, targets of non-FDA-approved chemical agents.

Abbreviations: FDA, Food and Drug Administration; GO, gene ontology.

SpreaficoAFredianiBCapperucciCA proteomic study on human osteoblastic cells proliferation and differentiationProteomics20066123520353216705754

 PubMedGoogle Scholar

HuaYJiaXSunMPlasma membrane proteomic analysis of human osteosarcoma and osteoblastic cells: revealing NDRG1 as a marker for osteosarcomaTumour Biol20113251013102121706236

 PubMedGoogle Scholar

SueharaYKondoTFujiiKProteomic signatures corresponding to histological classification and grading of soft-tissue sarcomasProteomics20066154402440916807943

 PubMed Web of Science ®Google Scholar

BonaAPapaiZMaaszGMass spectrometric identification of ancient proteins as potential molecular biomarkers for a 2000-year-old osteogenic sarcomaPLoS One201491e8721524475253

 PubMedGoogle Scholar

GemollTEppingFHeinrichLIncreased cathepsin D protein expression is a biomarker for osteosarcomas, pulmonary metastases and other bone malignanciesOncotarget2015618165171652626203049

 PubMedGoogle Scholar

FloresRJLiYYuAA systems biology approach reveals common metastatic pathways in osteosarcomaBMC Syst Biol201265022640921

 PubMedGoogle Scholar

TangJShenLYangQZhangCOverexpression of metadherin mediates metastasis of osteosarcoma by regulating epithelial-mesenchymal transitionCell Prolif201447542743425174891

 PubMed Web of Science ®Google Scholar

AraiKSakamotoRKubotaDKondoTProteomic approach toward molecular backgrounds of drug resistance of osteosarcoma cells in spheroid culture systemProteomics201313152351236023712969

 PubMed Web of Science ®Google Scholar

KubotaDMukaiharaKYoshidaATsudaHKawaiAKondoTProteomics study of open biopsy samples identifies peroxiredoxin 2 as a predictive biomarker of response to induction chemotherapy in osteosarcomaJ Proteomics20139139340423911960

 PubMed Web of Science ®Google Scholar

IzbickaECamposDMartyJCarrizalesGMangoldGTolcherAMolecular determinants of differential sensitivity to docetaxel and paclitaxel in human pediatric cancer modelsAnticancer Res2006263A1983198816827133

 PubMedGoogle Scholar

SauAFilomeniGPezzolaSTargeting GSTP1-1 induces JNK activation and leads to apoptosis in cisplatin-sensitive and -resistant human osteosarcoma cell linesMol Biosyst201284994100622068640

 PubMedGoogle Scholar

AlhefdhiABurkeJFRedlichAKunnimalaiyaanMChenHLeflunomide suppresses growth in human medullary thyroid cancer cellsJ Surg Res2013185121221623816245

 PubMedGoogle Scholar

KoYJSmallEJKabbinavarFA multi-institutional phase ii study of SU101, a platelet-derived growth factor receptor inhibitor, for patients with hormone-refractory prostate cancerClin Cancer Res20017480080511309325

 PubMedGoogle Scholar

KlevebringDFagerbergLLundbergEEmanuelssonOUhlenMLundebergJAnalysis of transcript and protein overlap in a human osteosarcoma cell lineBMC Genomics20101168421126332

 PubMedGoogle Scholar

NiforouKMAnagnostopoulosAKVougasKKittasCGorgoulisVGTsangarisGTThe proteome profile of the human osteosarcoma U2OS cell lineCancer Genomics Proteomics200851637818359981

 PubMedGoogle Scholar

LiGZhangWZengHAn integrative multi-platform analysis for discovering biomarkers of osteosarcomaBMC Cancer2009915019445706

 PubMedGoogle Scholar

JinSShenJNGuoQC2-D DIGE and MALDI-TOF-MS analysis of the serum proteome in human osteosarcomaProteomics Clin Appl20071327228521136678

 PubMedGoogle Scholar

GuoQCShenJNJinSComparative proteomic analysis of human osteosarcoma and SV40-immortalized normal osteoblastic cell linesActa Pharmacol Sin200728685085817506944

 PubMed Web of Science ®Google Scholar

FolioCMoraMIZalacainMProteomic analysis of chemonaive pediatric osteosarcomas and corresponding normal bone reveals multiple altered molecular targetsJ Proteome Res2009883882388819492781

 PubMedGoogle Scholar

LiuXZengBMaJWanCComparative proteomic analysis of osteosarcoma cell and human primary cultured osteoblastic cellCancer Invest200927334535219212829

 PubMed Web of Science ®Google Scholar

ZhangZZhangLHuaYComparative proteomic analysis of plasma membrane proteins between human osteosarcoma and normal osteoblastic cell linesBMC Cancer20101020620470422

 PubMedGoogle Scholar

PosthumaDeboerJPiersmaSRPhamTVSurface proteomic analysis of osteosarcoma identifies EPHA2 as receptor for targeted drug deliveryBr J Cancer201310982142215424064975

 PubMed Web of Science ®Google Scholar

ChenXYangTTZhouYProteomic profiling of osteosarcoma cells identifies ALDOA and SULT1A3 as negative survival markers of human osteosarcomaMol Carcinog201453213814422949271

 PubMedGoogle Scholar

KanehisaMGotoSKEGG: Kyoto encyclopedia of genes and genomesNucleic Acids Res200028273010592173

 PubMed Web of Science ®Google Scholar

NishimuraDBiotech Software & Internet ReportNYMary Ann Liebert, Inc200123117120

 Google Scholar

TermglinchanVWanichnopparatWSuwanwongseKCandidate cancer-targeting agents identified by expression-profiling arraysOnco Targets Ther2013644745823637543

 PubMed Web of Science ®Google Scholar

WishartDSKnoxCGuoACDrugBank: a comprehensive resource for in silico drug discovery and explorationNucleic Acids Res200634Database issueD668D67216381955

 PubMed Web of Science ®Google Scholar