Photo of Winston Patrick Kuo,  DDS, DMSc

Winston Patrick Kuo, DDS, DMSc

Harvard School Of Dental Medicine

Harvard School Of Dental Medicine


wkuo@genetics.med.harvard.edu

Winston Patrick Kuo, DDS, DMSc

Harvard School Of Dental Medicine

EDUCATIONAL TITLES

  • Assistant Professor, Developmental Biology, Harvard School Of Dental Medicine
  • Director, Harvard Catalyst - LITT, Harvard Medical School

Research Abstract

Our study of oral cancer involves the mining and analysis of data for a panel of biomarkers that will allow for the identification of molecularly premalignant lesions as well histologic dysplastic lesions that are more likely to progress to cancer. Such identification would be of great value as early detection has the greatest impact on survival for oral cancer. Accordingly, gene expression profiling of microdissected keratinocytes from biopsies containing normal mucosal tissue and invasive HNSCC will be performed to define a set of genes with marked alteration in expression in the course of carcinogenic transformation. These potential markers will then be subjected to a two-step validation process to determine their potential utility as biomarkers for two distinct phases of cancer progression.

Publications

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  • Worley MJ, Liu S, Hua Y, Kwok JS, Samuel A, Hou L, Shoni M, Lu S, Sandberg EM, Keryan A, Wu D, Ng SK, Kuo WP, Parra-Herran CE, Tsui SK, Welch W, Crum C, Berkowitz RS, Ng SW. Molecular changes in endometriosis-associated ovarian clear cell carcinoma. Eur J Cancer 2015. PubMed
  • Momen-Heravi F, Trachtenberg AJ, Kuo WP, Cheng YS. Genomewide Study of Salivary MicroRNAs for Detection of Oral Cancer. J. Dent. Res. 2014; 93:86S-93S. PubMed
  • Jia S, Zocco D, Samuels ML, Chou MF, Chammas R, Skog J, Zarovni N, Momen-Heravi F, Kuo WP. Emerging technologies in extracellular vesicle-based molecular diagnostics. Expert Rev Mol Diagn 2014; 14:307-21. PubMed
  • Zhao JJ, Lin J, Zhu D, Wang X, Brooks D, Chen M, Chu ZB, Takada K, Ciccarelli B, Admin S, Tao J, Tai YT, Treon S, Pinkus G, Kuo WP, Hideshima T, Bouxsein M, Munshi N, Anderson K, Carrasco R. miR-30-5p functions as a tumor suppressor and novel therapeutic tool by targeting the oncogenic Wnt/硫-catenin/BCL9 pathway. Cancer Res 2014; 74:1801-13. PubMed
  • Gurkan UA, El Assal R, Yildiz SE, Sung Y, Trachtenberg AJ, Kuo WP, Demirci U. Engineering Anisotropic Biomimetic Fibrocartilage Microenvironment by Bioprinting Mesenchymal Stem Cells in Nanoliter Gel Droplets. Mol Pharm 2014. PubMed
  • Tullius SG, Biefer HR, Li S, Trachtenberg AJ, Edtinger K, Quante M, Krenzien F, Uehara H, Yang X, Kissick HT, Kuo WP, Ghiran I, de la Fuente MA, Arredouani MS, Camacho V, Tigges JC, Toxavidis V, El Fatimy R, Smith BD, Vasudevan A, ElKhal A. NAD(+) protects against EAE by regulating CD4(+) T-cell differentiation. Nat Commun 2014; 5:5101. PubMed
  • Sipert CR, Morandini AC, Dionísio TJ, Machado MA, Oliveira SH, Campanelli AP, Kuo WP, Santos CF. In vitro regulation of CCL3 and CXCL12 by bacterial by-products is dependent on site of origin of human oral fibroblasts. J Endod 2013; 40:95-100. PubMed
  • Momen-Heravi F, Balaj L, Alian S, Mantel PY, Halleck AE, Trachtenberg AJ, Soria CE, Oquin S, Bonebreak CM, Saracoglu E, Skog J, Kuo WP. Current methods for the isolation of extracellular vesicles. Biol Chem 2013; 394:1253-62. PubMed
  • Wang G, Lunardi A, Zhang J, Chen Z, Ala U, Webster KA, Tay Y, Gonzalez-Billalabeitia E, Egia A, Shaffer DR, Carver B, Liu XS, Taulli R, Kuo WP, Nardella C, Signoretti S, Cordon-Cardo C, Gerald WL, Pandolfi PP. Zbtb7a suppresses prostate cancer through repression of a Sox9-dependent pathway for cellular senescence bypass and tumor invasion. Nat Genet 2013; 45:739-46. PubMed
  • Wei P, Kuo WP, Chen F, Hua H. Diagnostic model of saliva peptide finger print analysis of primary Sj旦gren's syndrome patients by using weak cation exchange magnetic beads. 2013. PubMed
  • Yamano S, Kuo WP, Sukotjo C. Downregulated gene expression of TGF-硫s in diabetic oral wound healing. 2012. PubMed
  • Jafari M, Primo V, Smejkal GB, Moskovets EV, Kuo WP, Ivanov AR. Comparison of in-gel protein separation techniques commonly used for fractionation in mass spectrometry-based proteomic profiling. Electrophoresis 2012; 33:2516-26. PubMed
  • Momen-Heravi F, Balaj L, Alian S, Trachtenberg AJ, Hochberg FH, Skog J, Kuo WP. Impact of biofluid viscosity on size and sedimentation efficiency of the isolated microvesicles. Front Physiol 2012; 3:162. PubMed
  • Liu F, Kuo WP, Jenssen TK, Hovig E. Performance comparison of multiple microarray platforms for gene expression profiling. Methods Mol Biol 2011; 802:141-55. PubMed
  • Momen-Heravi F, Balaj L, Alian S, Tigges J, Toxavidis V, Ericsson M, Distel RJ, Ivanov AR, Skog J, Kuo WP. Alternative methods for characterization of extracellular vesicles. Front Physiol 2012; 3:354. PubMed
  • Smejkal GB, Rivas-Morello C, Chang JH, Freeman E, Trachtenberg AJ, Lazarev A, Ivanov AR, Kuo WP. Thermal stabilization of tissues and the preservation of protein phosphorylation states for two-dimensional gel electrophoresis. Electrophoresis 2011. PubMed
  • Kim J, Patel K, Jung H, Kuo WP, Ohno-Machado L. AnyExpress: Integrated toolkit for analysis of cross-platform gene expression data using a fast interval matching algorithm. BMC Bioinformatics 2011; 12:75. PubMed
  • Kamberov YG, Kim J, Mazitschek R, Kuo WP, Whitman M. Microarray profiling reveals the integrated stress response is activated by halofuginone in mammary epithelial cells. BMC Res Notes 2011; 4:381. PubMed
  • Buchtová M, Kuo WP, Nimmagadda S, Benson SL, Geetha-Loganathan P, Logan C, Au-Yeung T, Chiang E, Fu K, Richman JM. Whole genome microarray analysis of chicken embryo facial prominences. Dev Dyn 2010; 239:574-91. PubMed
  • Hinske LC, Galante PA, Kuo WP, Ohno-Machado L. A potential role for intragenic miRNAs on their hosts' interactome. BMC Genomics 2010; 11:533. PubMed
  • Chow CK, Zhu HL, Lacy J, Kuo WP. Error margin analysis for feature gene extraction. BMC Bioinformatics 2010; 11:241. PubMed
  • da Cunha JP, Galante PA, de Souza JE, de Souza RF, Carvalho PM, Ohara DT, Moura RP, Oba-Shinja SM, Marie SK, Silva WA, Perez RO, Stransky B, Pieprzyk M, Moore J, Caballero O, Gama-Rodrigues J, Habr-Gama A, Kuo WP, Simpson AJ, Camargo AA, Old LJ, de Souza SJ. Bioinformatics construction of the human cell surfaceome. Proc Natl Acad Sci U S A 2009; 106:16752-7. PubMed
  • Hasina R, Whipple ME, Martin LE, Kuo WP, Ohno-Machado L, Lingen MW. Angiogenic heterogeneity in head and neck squamous cell carcinoma: biological and therapeutic implications. Lab Invest 2008; 88:342-53. PubMed
  • Fu S, Zhao H, Shi J, Abzhanov A, Crawford K, Ohno-Machado L, Zhou J, Du Y, Kuo WP, Zhang J, Jiang M, Jin JG. Peripheral arterial occlusive disease: global gene expression analyses suggest a major role for immune and inflammatory responses. BMC Genomics 2008; 9:369. PubMed
  • Nygaard V, Liu F, Holden M, Kuo WP, Trimarchi J, Ohno-Machado L, Cepko CL, Frigessi A, Glad IK, Wiel MA, Hovig E, Lyng H. Validation of oligoarrays for quantitative exploration of the transcriptome. BMC Genomics 2008; 9:258. PubMed
  • Liu F, Jenssen TK, Trimarchi J, Punzo C, Cepko CL, Ohno-Machado L, Hovig E, Kuo WP. Comparison of hybridization-based and sequencing-based gene expression technologies on biological replicates. BMC Genomics 2007; 8:153. PubMed
  • , Shi L, Reid LH, Jones WD, Shippy R, Warrington JA, Baker SC, Collins PJ, de Longueville F, Kawasaki ES, Lee KY, Luo Y, Sun YA, Willey JC, Setterquist RA, Fischer GM, Tong W, Dragan YP, Dix DJ, Frueh FW, Goodsaid FM, Herman D, Jensen RV, Johnson CD, Lobenhofer EK, Puri RK, Schrf U, Thierry-Mieg J, Wang C, Wilson M, Wolber PK, Zhang L, Amur S, Bao W, Barbacioru CC, Lucas AB, Bertholet V, Boysen C, Bromley B, Brown D, Brunner A, Canales R, Cao XM, Cebula TA, Chen JJ, Cheng J, Chu TM, Chudin E, Corson J, Corton JC, Croner LJ, Davies C, Davison TS, Delenstarr G, Deng X, Dorris D, Eklund AC, Fan XH, Fang H, Fulmer-Smentek S, Fuscoe JC, Gallagher K, Ge W, Guo L, Guo X, Hager J, Haje PK, Han J, Han T, Harbottle HC, Harris SC, Hatchwell E, Hauser CA, Hester S, Hong H, Hurban P, Jackson SA, Ji H, Knight CR, Kuo WP, LeClerc JE, Levy S, Li QZ, Liu C, Liu Y, Lombardi MJ, Ma Y, Magnuson SR, Maqsodi B, McDaniel T, Mei N, Myklebost O, Ning B, Novoradovskaya N, Orr MS, Osborn TW, Papallo A, Patterson TA, Perkins RG, Peters EH, Peterson R, Philips KL, Pine PS, Pusztai L, Qian F, Ren H, Rosen M, Rosenzweig BA, Samaha RR, Schena M, Schroth GP, Shchegrova S, Smith DD, Staedtler F, Su Z, Sun H, Szallasi Z, Tezak Z, Thierry-Mieg D, Thompson KL, Tikhonova I, Turpaz Y, Vallanat B, Van C, Walker SJ, Wang SJ, Wang Y, Wolfinger R, Wong A, Wu J, Xiao C, Xie Q, Xu J, Yang W, Zhang L, Zhong S, Zong Y, Slikker W. The MicroArray Quality Control (MAQC) project shows inter- and intraplatform reproducibility of gene expression measurements. Nat Biotechnol 2006; 24:1151-61. PubMed
  • Abzhanov A, Kuo WP, Hartmann C, Grant BR, Grant PR, Tabin CJ. The calmodulin pathway and evolution of elongated beak morphology in Darwin's finches. Nature 2006; 442:563-7. PubMed
  • Kuo WP, Liu F, Trimarchi J, Punzo C, Lombardi M, Sarang J, Whipple ME, Maysuria M, Serikawa K, Lee SY, McCrann D, Kang J, Shearstone JR, Burke J, Park DJ, Wang X, Rector TL, Ricciardi-Castagnoli P, Perrin S, Choi S, Bumgarner R, Kim JH, Short GF 3rd, Freeman MW, Seed B, Jensen R, Church GM, Hovig E, Cepko CL, Park P, Ohno-Machado L, Jenssen TK. A sequence-oriented comparison of gene expression measurements across different hybridization-based technologies. Nat Biotechnol 2006; 24:832-840. PubMed
  • Blackshaw S, Harpavat S, Trimarchi J, Cai L, Huang H, Kuo WP, Weber G, Lee K, Fraioli RE, Cho SH, Yung R, Asch E, Ohno-Machado L, Wong WH, Cepko CL. Genomic analysis of mouse retinal development. PLoS Biol 2004; 2:E247. PubMed
  • Kuo WP, Kim EY, Trimarchi J, Jenssen TK, Vinterbo SA, Ohno-Machado L. A primer on gene expression and microarrays for machine learning researchers. J Biomed Inform 2004; 37:293-303. PubMed
  • Jaroszewicz S, Simovici DA, Kuo WP, Ohno-Machado L. The Goodman-Kruskal coefficient and its applications in genetic diagnosis of cancer. 2004; 51:1095-102. PubMed
  • Kuo WP, Whipple ME, Epstein JB, Jenssen TK, Santos GS, Ohno-Machado L, Sonis ST. Deciphering gene expression profiles generated from DNA microarrays and their applications in oral medicine. Oral Surg Oral Med Oral Pathol Oral Radiol Endod 2004; 97:584-91. PubMed
  • Kuo WP. Overview of bioinformatics and its application to oral genomics. Adv. Dent. Res. 2004; 17:89-94. PubMed
  • Kuo WP, Whipple ME, Jenssen TK, Todd R, Epstein JB, Ohno-Machado L, Sonis ST, Park PJ. Microarrays and clinical dentistry. J Am Dent Assoc 2003; 134:456-62. PubMed
  • Kuo WP, Hasina R, Ohno-Machado L, Lingen MW. Classification and identification of genes associated with oral cancer based on gene expression profiles. A preliminary study. 2003; 69:23-6. PubMed
  • Kuo WP, Mendez E, Chen C, Whipple ME, Farell G, Agoff N, Park PJ. Functional relationships between gene pairs in oral squamous cell carcinoma. AMIA Annu Symp Proc 2004. PubMed
  • Blackshaw S, Kuo WP, Park PJ, Tsujikawa M, Gunnersen JM, Scott HS, Boon WM, Tan SS, Cepko CL. MicroSAGE is highly representative and reproducible but reveals major differences in gene expression among samples obtained from similar tissues. Genome Biol 2003; 4:R17. PubMed
  • Kuo WP, Whipple ME, Sonis ST, Ohno-Machado L, Jenssen TK. Gene expression profiling by DNA microarrays and its application to dental research. Oral Oncol 2002; 38:650-6. PubMed
  • Jenssen TK, Kuo WP, Stokke T, Hovig E. Associations between gene expressions in breast cancer and patient survival. Hum Genet 2002; 111:411-20. PubMed
  • Todd R, Lingen MW, Kuo WP. Gene expression profiling using laser capture microdissection. Expert Rev Mol Diagn 2002; 2:497-507. PubMed
  • Whipple ME, Kuo WP. DNA microarrays in otolaryngology-head and neck surgery. 2002; 127:196-204. PubMed
  • Jenssen TK, Langaas M, Kuo WP, Smith-Sørensen B, Myklebost O, Hovig E. Analysis of repeatability in spotted cDNA microarrays. Nucleic Acids Res 2002; 30:3235-44. PubMed
  • Kuo WP, Jenssen TK, Butte AJ, Ohno-Machado L, Kohane IS. Analysis of matched mRNA measurements from two different microarray technologies. Bioinformatics 2002; 18:405-12. PubMed
  • Kuo WP, Jenssen TK, Park PJ, Lingen MW, Hasina R, Ohno-Machado L. Gene expression levels in different stages of progression in oral squamous cell carcinoma. Proc AMIA Symp 2002. PubMed
  • Kuo WP. Placing enabling technologies at the forefront of translational research. 2009. PubMed
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