David T Wong

Professor, Dentistry Dept., University of California Los Angeles

Professor, Head and Neck Surgery, University of California Los Angeles

1. My laboratory spearheads the use of genome-wide and proteome-wide high-throughput technologies to harness the diagnostic and biological determinants pertaining to the pathogenesis of oral/head and neck cancer. In particular we are focusing on the genomic and proteomic determinants of oral cancer progression. Using a patient-based genome/proteome-wide approach; we are harnessing the genomic and proteomic determinants that distinguish progressing from non-progression oral precancers. For genomic defects, a concurrent approach to identify gene copy number abnormalities (CNA) by cDNA microarray comparative genomic hybridization (CGH) as well as SNP-based loss of heterozygosity (LOH) using the Affymetrix 100K SNP-based Mapping Arrays. For expression analysis, the Affymetrix 133+ 2 and all exon high-density oligonucleotide arrays are used. For proteomic analysis, LC-MS/MS as well as single cell proteomics are creatively being integrated. A key component to a systems approach (Weighted-Gene Co-Expression Network Analysis, WGCNA) is to seek out molecular concordance of detectable molecular defects. a. Das S, Ansel KM, Bitzer M, Breakefield XO, Charest A, Galas DJ, Gerstein MB, Gupta M, Milosavljevic A, McManus MT, Patel T, Raffai RL, Rozowsky J, Roth ME, Saugstad JA, Van Keuren-Jensen K, Weaver AM, Laurent LC. The Extracellular RNA Communication Consortium: Establishing Foundational Knowledge and Technologies for Extracellular RNA Research. Cell. 2019 Apr 4;177(2):231-242. PubMed Central PMCID: PMC6601620. b. Yu T, Ye H, Sun W, Li KC, Chen Z, Jacobs S, Bailey DK, Wong DT, Zhou X. A forward-backward fragment assembling algorithm for the identification of genomic amplification and deletion breakpoints using high-density single nucleotide polymorphism (SNP) array. BMC Bioinformatics. 2007 May 3;8:145. PubMed Central PMCID: PMC1868765. c. Zhou X, Temam S, Chen Z, Ye H, Mao L, Wong DT. Allelic imbalance analysis of oral tongue squamous cell carcinoma by high-density single nucleotide polymorphism arrays using whole-genome amplified DNA. Hum Genet. 2005 Dec;118(3-4):504-7. PubMed PMID: 16193324. d. Zhou X, Mok SC, Chen Z, Li Y, Wong DT. Concurrent analysis of loss of heterozygosity (LOH) and copy number abnormality (CNA) for oral premalignancy progression using the Affymetrix 10K SNP mapping array. Hum Genet. 2004 Sep;115(4):327-30. PubMed PMID: 15290239. 2. We subscribe to the belief that a central defect in human cancer lies in the dysregulation of cell cycle control. Establishing a molecular database of cell cycle regulatory genes dysregulated in head and neck cancer and understanding the molecular and biochemical pathways of these genes are areas of prime interest. Using differential expression screening assays we have identified a number of cellular genes that are differentially expressed in squamous cell carcinoma. CDK2-AP1 is a differentially expressed cellular gene that is currently being studied. CDK2-AP1 is a novel gene exhibiting growth suppressor properties. CDK2-AP1 exerts its growth suppressor function by negatively regulating the activities of DNA polymerase- /primase and cyclin-dependent kinase 2 (CDK2). CDK2-AP1 associates with DNA polymerase-/primase suppressing DNA replication, affecting predominantly the initiation step. CDK2-AP1 has been found to associates with the monomeric non-phosphorylated form of CDK2, suppressing CDK2-associated kinase activities and cell cycle progression. CDK2-AP1 also targets CDK2 for proteolysis. We are investigating the detailed biochemical and genetic mechanisms of CDK2-AP1 in cell cycle regulation, normal development and carcinogenesis. The recent excitement of this research includes finding that CDK2-AP1 -nulled mice are embryonically lethal and that CDK2-AP1 is an epigenetic regulator for differentiation competency for mouse embryonic stem cells, placing this gene at a pivotal juncture of stem cell differentiation and development. a. Kim JJ, Khalid O, Vo S, Sun HH, Wong DT, Kim Y. A novel regulatory factor recruits the nucleosome remodeling complex to wingless integrated (Wnt) signaling gene promoters in mouse embryonic stem cells. J Biol Chem. 2012 Nov 30;287(49):41103-17. PubMed Central PMCID: PMC3510811. b. Kim Y, Deshpande A, Dai Y, Kim JJ, Lindgren A, Conway A, Clark AT, Wong DT. Cyclin-dependent kinase 2-associating protein 1 commits murine embryonic stem cell differentiation through retinoblastoma protein regulation. J Biol Chem. 2009 Aug 28;284(35):23405-14. PubMed Central PMCID: PMC2749114. c. Deshpande AM, Dai YS, Kim Y, Kim J, Kimlin L, Gao K, Wong DT. Cdk2ap1 is required for epigenetic silencing of Oct4 during murine embryonic stem cell differentiation. J Biol Chem. 2009 Mar 6;284(10):6043-7. PubMed Central PMCID: PMC2649091. d. Shintani S, Ohyama H, Zhang X, McBride J, Matsuo K, Tsuji T, Hu MG, Hu G, Kohno Y, Lerman M, Todd R, Wong DT. p12(DOC-1) is a novel cyclin-dependent kinase 2-associated protein. Mol Cell Biol. 2000 Sep;20(17):6300-7. PubMed Central PMCID: PMC86104. 3. The early detection of cancer by non-invasive means has been the holy grail for cancer researchers. My research group has been spearheading a series of concerted efforts to spearhead the scientific and translational frontiers of salivary diagnostics. The use of saliva, a non-invasive biofluid, for oral and systemic disease detection, for disease progression, and for therapeutic monitoring are highly desirable goals. We have harnessed and defined five diagnostic alphabets from human saliva: salivary proteome, transcriptome, micro-RNA, metabolome and microbiome. The availability of these diagnostic alphabets greatly enhanced the translational utilities of saliva. In parallel to the biomarker efforts, point-of-care technologies are being developed for clinical applications. The “Oral Fluid NanoSensor Test (OFNASET)” is a prototype nanotechnology-based point-of-care sensor that will have the ability to detect multiplex analytes in saliva for disease detection. Two additional highly impactful outcomes emerged from these initiatives. One is the discovery of salivary extracellular RNA in saliva, including a previously unnoticed landscape of non-coding RNA. This project by the NIH Common Fund on “Extracellular RNA Communication Consortium” opened a new horizon of saliva biology. A second facet of excitement is the finding that saliva is an optimal biofluid for liquid biopsy (saliva liquid biopsy, sLB) for detection of actionable mutations in human cancers. Using an electrochemical technology called electric field-induced release and measurement (EFIRM), circulating tumor DNA (ctDNA) was detectable in lung cancer patients with near perfect concordance with tissue based biopsy genotyping. a. Murillo OD, Thistlethwaite W, Rozowsky J, Subramanian SL, Lucero R, Shah N, Jackson AR, Srinivasan S, Chung A, Laurent CD, Kitchen RR, Galeev T, Warrell J, Diao JA, Welsh JA, Hanspers K, Riutta A, Burgstaller-Muehlbacher S, Shah RV, Yeri A, Jenkins LM, Ahsen ME, Cordon-Cardo C, Dogra N, Gifford SM, Smith JT, Stolovitzky G, Tewari AK, Wunsch BH, Yadav KK, Danielson KM, Filant J, Moeller C, Nejad P, Paul A, Simonson B, Wong DK, Zhang X, Balaj L, Gandhi R, Sood AK, Alexander RP, Wang L, Wu C, Wong DTW, Galas DJ, Van Keuren-Jensen K, Patel T, Jones JC, Das S, Cheung KH, Pico AR, Su AI, Raffai RL, Laurent LC, Roth ME, Gerstein MB, Milosavljevic A. exRNA Atlas Analysis Reveals Distinct Extracellular RNA Cargo Types and Their Carriers Present across Human Biofluids. Cell. 2019 Apr 4;177(2):463-477.e15. PubMed Central PMCID: PMC6616370. b. Wei F, Lin CC, Joon A, Feng Z, Troche G, Lira ME, Chia D, Mao M, Ho CL, Su WC, Wong DT. Noninvasive saliva-based EGFR gene mutation detection in patients with lung cancer. Am J Respir Crit Care Med. 2014 Nov 15;190(10):1117-26. PubMed Central PMCID: PMC5447327. c. Li Y, Elashoff D, Oh M, Sinha U, St John MA, Zhou X, Abemayor E, Wong DT. Serum circulating human mRNA profiling and its utility for oral cancer detection. J Clin Oncol. 2006 Apr 10;24(11):1754-60. PubMed PMID: 16505414. d. Li Y, St John MA, Zhou X, Kim Y, Sinha U, Jordan RC, Eisele D, Abemayor E, Elashoff D, Park NH, Wong DT. Salivary transcriptome diagnostics for oral cancer detection. Clin Cancer Res. 2004 Dec 15;10(24):8442-50. PubMed PMID: 15623624.