Molecular Oncology Department Metrics

View the grants and publications from the Department of Molecular Oncology.

Grants
  • Intrinsic Disorder Controls the Function of p53 and Other Cancer-assocoiated IDPs
    Sponsor: Univ of South Florida
    PI (MPI):Chen, J.
  • CPTAC Phase III
    Sponsor: Nat Institutes of Health
    PI:Koomen, J.
  • Identification of Non-Coding RNAs to Therapeutically Target Undruggable Pathways in Metastatic Lung Adenocarcinma and Squamous Cell Carcinoma
    Sponsor: Nat Institutes of Health
    PI:Flores, E.
  • Ubiquitination-dependent Regulation of BRAF Function in Melanoma
    Sponsor: Amer Cancer Society
    PI:Wan, L.
  • Targeting the JNK-ITCH Signaling Pathway in Melanoma
    Sponsor: Melanoma Research Alliance (MRA)
    PI:Wan, L.
  • Using the ESC-GEMM Approach to Study Mucosal Melanoma In-Vivo
    Sponsor: Melanoma Research Foundation
    PI:Karreth, F.
  • Anti-tumor Potential of Temperature-Sensitive p53 Mutants
    Sponsor: Nat Institutes of Health
    PI:Chen, J.,CO-PI:Mann, M.
  • Integrated Program in Cancer and Data Science
    Sponsor: Nat Institutes of Health
    PI (Contact):Cress, D.,PI (MPI):Flores, E.,PI (MPI):Fridley, B.,Co-Leader:Anderson, A.,Co-Leader:Cleveland, J.,Co-Leader:Kanetsky, P.
  • Cancer Research Workforce Development in FAIR Artificial Intelligence and Machine Learning
    Sponsor: Nat Institutes of Health
    PI (Contact):Cress, D.,PI (MPI):Flores, E.,PI (MPI):Fridley, B.
  • Targeting Heme Dependency in Leukemia
    Sponsor: Florida Biomedical Research Program (FBRP)
    PI:Reuther, G.
  • Incyte/Moffitt Master Research Agreement
    Sponsor: Incyte, Inc.
    PI:Reuther, G.
  • Discovery of p53 inhibitors for reducing toxicity of chemotherapy
    Sponsor: Florida Biomedical Research Program (FBRP)
    PI:Chen, J.
  • Proteogenomics of Metastatic Heterogeneity and Therapeutic Resistance inLung Cancer
    Sponsor: Florida Biomedical Research Program (FBRP)
    PI (Contact):Koomen, J.,CO-PI:Boyle, T.
  • Identifying Metabolic Vulnerabilities in Lung Cancer
    Sponsor: Nat Institutes of Health
    PI (Contact):Flores, E.,PI (MPI):Haura, E.,Core PI/Director:Fridley, B.,Core PI/Director:Cress, D.,Core PI/Director:Koomen, J.,Project PI:DeNicola, G.,Project PI:Rodriguez, P.,Project PI:Cleveland, J.
  • Elucidating Cdc20-mediated transcriptional reprogramming in ovarian cancer
    Sponsor: Moffitt Cancer Center
    PI:Wan, L.
  • Direct Control of the human CMG Helicase by Myc and Rb
    Sponsor: Nat Institutes of Health
    PI:Alexandrow, M.
  • Targeting altered phosphatase-dependent signaling to overcome the inefficacy of targeted therapy in myeloproliferative neoplasms
    Sponsor: Nat Institutes of Health
    PI:Reuther, G.
  • Propionate metabolism as an essential metabolic adaptation for tumor progression
    Sponsor: Nat Institutes of Health
    PI:Gomes, A.
  • Chromosome 1q ceRNAs in melanoma progression and metastasis
    Sponsor: Nat Institutes of Health
    PI:Karreth, F.
  • Assessing the role of TROLLs as markers of response to chemotherapy in TNBCs
    Sponsor: APIS Assay Technologies - UK
    PI:Flores, E.
  • Elucidating PTEN tumor suppression in melanoma
    Sponsor: Florida Biomedical Research Program (FBRP)
    PI:Karreth, F.
  • Biophysical basis for enzyme mediated deglycation in protein repair
    Sponsor: Nat Institutes of Health
    PI:Binning, J.
  • Targeting USP9X-mediated RIT1 stabilization for cancer therapy
    Sponsor: Amer Cancer Society
    PI:Wan, L.
  • Characterizing oncogenic function of ITCH in melanoma
    Sponsor: Nat Institutes of Health
    PI:Wan, L.
  • Mitochondrial DNA diversity: Missing link between African Americans and Lung Cancer disparity
    Sponsor: Moffitt Cancer Center
    PI:Gomes, A.,CO-PI:DeNicola, G.
  • Mechanisms of age-induced chemotherapeutic resistance in lung cancer
    Sponsor: Amer Lung Assoc
    PI:Gomes, A.
  • NADK as an essential metabolic adaptation of metastatic triple negative breast cancer
    Sponsor: Florida Breast Cancer Foundation
    PI:Gomes, A.
  • Employing functionalized fragment libraries to identify therapeutic agents for neurofibromatosis type 2
    Sponsor: Nat Institutes of Health
    PI:Kissil, J.
  • A Chemical Proteomic Strategy for Mapping Codependency Pathways in KRAS Driven Lung Cancer
    Sponsor: US Army
    PI:Kissil, J.
  • Elucidating the epigenetic landscape of neurofibromatosis and development of therapeutic targets
    Sponsor: Nat Institutes of Health
    PI:Kissil, J.
Publications
  • Napoli M, Deshpande AA, Flores ER. The Landmark Discovery That Paved the Way to a Mechanistic Understanding of P53 Gain of Function and Personalized Medicine. Cancer Res. 2021 Sep.81(17):4394-4396. Pubmedid: 34470782.
  • Mecozzi N, Vera O, Karreth FA. Squaring the circle: circRNAs in melanoma. Oncogene. 2021 Sep.40(37):5559-5566. Pubmedid: 34331015.
  • Aiderus A, Newberg JY, Guzman-Rojas L, Contreras-Sandoval AM, Meshey AL, Jones DJ, Amaya-Manzanares F, Rangel R, Ward JM, Lee SC, Ban KH, Rogers K, Rogers SM, Selvanesan L, McNoe LA, Copeland NG, Jenkins NA, Tsai KY, Black MA, Mann KM, Mann MB. Transposon mutagenesis identifies cooperating genetic drivers during keratinocyte transformation and cutaneous squamous cell carcinoma progression. PLoS Genet. 2021 Aug.17(8):e1009094. Pubmedid: 34398873. Pmcid: PMC8389471.
  • Creelan BC, Wang C, Teer JK, Toloza EM, Yao J, Kim S, Landin AM, Mullinax JE, Saller JJ, Saltos AN, Noyes DR, Montoya LB, Curry W, Pilon-Thomas SA, Chiappori AA, Tanvetyanon T, Kaye FJ, Thompson ZJ, Yoder SJ, Fang B, Koomen JM, Sarnaik AA, Chen DT, Conejo-Garcia JR, Haura EB, Antonia SJ. Tumor-infiltrating lymphocyte treatment for anti-PD-1-resistant metastatic lung cancer: a phase 1 trial. Nat Med. 2021 Aug.27(8):1410-1418. Pubmedid: 34385708.
  • Amit M, Liu C, Mansour J, Gleber-Netto FO, Tam S, Baruch EN, Aashiq M, El-Naggar AK, Moreno AC, Rosenthal DI, Glisson BS, Ferrarotto R, Wong MK, Tsai K, Flores ER, Migden MR, Silverman DA, Li G, Khanna A, Goepfert RP, Nagarajan P, Weber RS, Myers JN, Gross ND. Elective neck dissection versus observation in patients with head and neck cutaneous squamous cell carcinoma. Cancer. 2021 Aug. Pubmedid: 34358340.
  • Shepard A, Hoxha S, Troutman S, Harbaugh D, Kareta MS, Kissil JL. Transcriptional regulation of miR-30a by YAP impacts PTPN13 and KLF9 levels and Schwann cell proliferation. J Biol Chem. 2021 Aug.297(2):100962. Pubmedid: 34265306. Pmcid: PMC8348554.
  • Palve V, Knezevic CE, Bejan DS, Luo Y, Li X, Novakova S, Welsh EA, Fang B, Kinose F, Haura EB, Monteiro AN, Koomen JM, Cohen MS, Lawrence HR, Rix U. The non-canonical target PARP16 contributes to polypharmacology of the PARP inhibitor talazoparib and its synergy with WEE1 inhibitors. Cell Chem Biol. 2021 Jul. Pubmedid: 34329582.
  • El-Kenawi A, Dominguez-Viqueira W, Liu M, Awasthi S, Abraham-Miranda J, Keske A, Steiner KK, Noel L, Serna AN, Dhillon J, Gillies RJ, Yu X, Koomen JM, Yamoah K, Gatenby RA, Ruffell B. Macrophage-derived cholesterol contributes to therapeutic resistance in prostate cancer. Cancer Res. 2021 Jul. Pubmedid: 34301759.
  • Smalley KSM, Teer JK, Chen YA, Wu JY, Yao J, Koomen JM, Chen WS, Rodriguez-Waitkus P, Karreth FA, Messina JL. A Mutational Survey of Acral Nevi. JAMA Dermatol. 2021 Jul.157(7):831-835. Pubmedid: 33978681. Pmcid: PMC8117064.
  • Kazi A, Chen L, Xiang S, Vangipurapu R, Yang H, Beato F, Fang B, Williams TM, Husain K, Underwood PW, Fleming JB, Malafa MP, Welsh EA, Koomen JM, Trevino JG, Sebti SM. Global Phosphoproteomics Reveal CDK Suppression as a Vulnerability to KRas Addiction in Pancreatic Cancer. Clin Cancer Res. 2021 Jul.27(14):4012-4024. Pubmedid: 33879459.
  • Gordian E, Welsh EA, Gimbrone N, Siegel EM, Shibata D, Creelan BC, Cress WD, Eschrich SA, Haura EB, Muñoz-Antonia T. Correction: Transforming growth factor β-induced epithelial-to-mesenchymal signature predicts metastasis-free survival in non-small cell lung cancer. Oncotarget. 2021 Jun.12(13):1325. Pubmedid: 34194632. Pmcid: PMC8238243.
  • Karreth FA, Ala U, Provero P, Pandolfi PP. Pseudogenes as Competitive Endogenous RNAs: Target Prediction and Validation. Methods Mol Biol. 2021 Jun.2324:115-129. Pubmedid: 34165712.
  • Xu X, Karreth FA. Pseudogenes as Competitive Endogenous RNAs: Testing miRNA Dependency. Methods Mol Biol. 2021 Jun.2324:131-147. Pubmedid: 34165713.
  • Bok I, Karreth FA. Strategies to Study the Functions of Pseudogenes in Mouse Models of Cancer. Methods Mol Biol. 2021 Jun.2324:287-304. Pubmedid: 34165722.
  • Schild T, McReynolds MR, Shea C, Low V, Schaffer BE, Asara JM, Piskounova E, Dephoure N, Rabinowitz JD, Gomes AP, Blenis J. NADK is activated by oncogenic signaling to sustain pancreatic ductal adenocarcinoma. Cell Rep. 2021 Jun.35(11):109238. Pubmedid: 34133937.
  • Jinesh GG, Napoli M, Smallin MT, Davis A, Ackerman HD, Raulji P, Montey N, Flores ER, Brohl AS. Mutant p53s and chromosome 19 microRNA cluster overexpression regulate cancer testis antigen expression and cellular transformation in hepatocellular carcinoma. Sci Rep. 2021 Jun.11(1):12673. Pubmedid: 34135394. Pmcid: PMC8209049.
  • Wright GM, Gimbrone NT, Sarcar B, Percy TR, Gordián ER, Kinose F, Sumi NJ, Rix U, Cress WD. CDK4/6 inhibition synergizes with inhibition of P21-Activated Kinases (PAKs) in lung cancer cell lines. PLoS One. 2021 Jun.16(6):e0252927. Pubmedid: 34138895. Pmcid: PMC8211232.
  • Ho JS, Di Tullio F, Schwarz M, Low D, Incarnato D, Gay F, Tabaglio T, Zhang J, Wollmann H, Chen L, An O, Chan THM, Hall Hickman A, Zheng S, Roudko V, Chen S, Karz A, Ahmed M, He HH, Greenbaum BD, Oliviero S, Serresi M, Gargiulo G, Mann KM, Hernando E, Mulholland D, Marazzi I, Wee DKB, Guccione E. HNRNPM controls circRNA biogenesis and splicing fidelity to sustain cancer cell fitness. Elife. 2021 Jun.10. Pubmedid: 34075878. Pmcid: PMC8346284.
  • Koomen DC, Meads MB, Magaletti DM, Guingab-Cagmat JD, Oliveira PS, Fang B, Liu M, Welsh EA, Meke LE, Jiang Z, Hampton OA, Tungesvik A, De Avila G, Alugubelli RR, Nishihori T, Silva AS, Eschrich SA, Garrett TJ, Koomen JM, Shain KH. Metabolic Changes Are Associated with Melphalan Resistance in Multiple Myeloma. J Proteome Res. 2021 Jun.20(6):3134-3149. Pubmedid: 34014671.
  • Dai X, Bu X, Gao Y, Guo J, Hu J, Jiang C, Zhang Z, Xu K, Duan J, He S, Zhang J, Wan L, Liu T, Zhou X, Hung MC, Freeman GJ, Wei W. Energy status dictates PD-L1 protein abundance and anti-tumor immunity to enable checkpoint blockade. Mol Cell. 2021 Jun.81(11):2317-2331.e6. Pubmedid: 33909988. Pmcid: PMC8178223.
  • Watson G, Lester D, Ren H, Forsyth CM, Medina E, Gonzalez Perez D, Darville L, Yao J, Luca V, Koomen J, Cen L, Lau E. Fucosylated Proteome Profiling Identifies a Fucosylated, Non-Ribosomal, Stress-Responsive Species of Ribosomal Protein S3. Cells. 2021 May.10(6). Pubmedid: 34070332. Pmcid: PMC8228307.
  • Ullah R, Yin Q, Snell AH, Wan L. RAF-MEK-ERK pathway in cancer evolution and treatment. Semin Cancer Biol. 2021 May. Pubmedid: 33992782.
  • Solanki HS, Welsh EA, Fang B, Izumi V, Darville LNF, Stone B, Franzese R, Chavan S, Kinose F, Imbody D, Koomen JM, Rix U, Haura EB. Cell Type-specific Adaptive Signaling Responses to KRASG12C Inhibition. Clin Cancer Res. 2021 May.27(9):2533-2548. Pubmedid: 33619172.
  • Patton EE, Mueller KL, Adams DJ, Anandasabapathy N, Aplin AE, Bertolotto C, Bosenberg M, Ceol CJ, Chi P, Burd CE, Herlyn M, Holmen SL, Karreth FA, Kaufman CK, Khan S, Kobold S, Leucci E, Levy C, Lombard DB, Lund AW, Marie KL, Marine JC, Marais R, McMahon M, Robles-Espinoza CD, Ronai ZA, Samuels Y, Soengas MS, Villanueva J, Weeraratna AT, White RM, Yeh I, Zhu J, Zon LI, Hurlbert MS, Merlino G. Melanoma models for the next generation of therapies. Cancer Cell. 2021 May.39(5):610-631. Pubmedid: 33545064. Pmcid: PMC8378471.
  • Xie M, Lee K, Lockhart JH, Cukras SD, Carvajal R, Beg AA, Flores ER, Teng M, Chung CH, Tan AC. TIMEx: tumor-immune microenvironment deconvolution web-portal for bulk transcriptomics using pan-cancer scRNA-seq signatures. Bioinformatics. 2021 Apr. Pubmedid: 33901274.
  • Hajiran A, Chakiryan N, Aydin AM, Zemp L, Nguyen J, Laborde JM, Chahoud J, Spiess PE, Zaman S, Falasiri S, Fournier M, Teer JK, Dhillon J, McCarthy S, Moran-Segura C, Katende EN, Sexton WJ, Koomen JM, Mulé J, Kim Y, Manley B. Reconnaissance of tumor immune microenvironment spatial heterogeneity in metastatic renal cell carcinoma and correlation with immunotherapy response. Clin Exp Immunol. 2021 Apr.204(1):96-106. Pubmedid: 33346915. Pmcid: PMC7944355.
  • Zhang C, Smalley I, Emmons MF, Sharma R, Izumi V, Messina J, Koomen JM, Pasquale EB, Forsyth PA, Smalley KSM. Noncanonical EphA2 Signaling Is a Driver of Tumor-Endothelial Cell Interactions and Metastatic Dissemination in BRAF Inhibitor‒Resistant Melanoma. J Invest Dermatol. 2021 Apr.141(4):840-851.e4. Pubmedid: 32890629. Pmcid: PMC7921215.
  • Vera O, Bok I, Jasani N, Nakamura K, Xu X, Mecozzi N, Angarita A, Wang K, Tsai KY, Karreth FA. A MAPK/miR-29 Axis Suppresses Melanoma by Targeting MAFG and MYBL2. Cancers (Basel). 2021 Mar.13(6). Pubmedid: 33808771. Pmcid: PMC8003541.
  • Wu HH, Wang B, Armstrong SR, Abuetabh Y, Leng S, Roa WHY, Atfi A, Marchese A, Wilson B, Sergi C, Flores ER, Eisenstat DD, Leng RP. Hsp70 acts as a fine-switch that controls E3 ligase CHIP-mediated TAp63 and ΔNp63 ubiquitination and degradation. Nucleic Acids Res. 2021 Mar.49(5):2740-2758. Pubmedid: 33619536. Pmcid: PMC7969027.
  • Ilter D, Gomes AP. Age-induced metabolic reprogramming underlies cancer progression. Mol Cell Oncol. 2021 Feb.8(2):1876506. Pubmedid: 33860078. Pmcid: PMC8018342.
  • Davis RR, Li B, Yun SY, Chan A, Nareddy P, Gunawan S, Ayaz M, Lawrence HR, Reuther GW, Lawrence NJ, Schönbrunn E. Structural Insights into JAK2 Inhibition by Ruxolitinib, Fedratinib, and Derivatives Thereof. J Med Chem. 2021 Feb.64(4):2228-2241. Pubmedid: 33570945. Pmcid: PMC8327781.
  • Aiderus A, Contreras-Sandoval AM, Meshey AL, Newberg JY, Ward JM, Swing DA, Copeland NG, Jenkins NA, Mann KM, Mann MB. Promoterless Transposon Mutagenesis Drives Solid Cancers via Tumor Suppressor Inactivation. Cancers (Basel). 2021 Jan.13(2). Pubmedid: 33435458. Pmcid: PMC7827284.
  • Liu J, Peng Y, Shi L, Wan L, Inuzuka H, Long J, Guo J, Zhang J, Yuan M, Zhang S, Wang X, Gao J, Dai X, Furumoto S, Jia L, Pandolfi PP, Asara JM, Kaelin WG, Liu J, Wei W. Author Correction: Skp2 dictates cell cycle-dependent metabolic oscillation between glycolysis and TCA cycle. Cell Res. 2021 Jan.31(1):104. Pubmedid: 32859994. Pmcid: PMC7852582.
  • Liu J, Peng Y, Shi L, Wan L, Inuzuka H, Long J, Guo J, Zhang J, Yuan M, Zhang S, Wang X, Gao J, Dai X, Furumoto S, Jia L, Pandolfi PP, Asara JM, Kaelin WG, Liu J, Wei W. Skp2 dictates cell cycle-dependent metabolic oscillation between glycolysis and TCA cycle. Cell Res. 2021 Jan.31(1):80-93. Pubmedid: 32669607. Pmcid: PMC7852548.
  • Muradova E, Patel N, Sell B, Bittencourt BB, Ojeda SS, Adelmann CH, Cen L, Cheng CH, Shen J, Davis CM, Ehli EA, Newberg JY, Cherpelis B, Black MA, Mann MB, Mitragotri S, Tsai KY. Noninvasive Assessment of Epidermal Genomic Markers of UV Exposure in Skin. J Invest Dermatol. 2021 Jan.141(1):124-131.e2. Pubmedid: 32553564. Pmcid: PMC7736225.
  • Fang B, Izumi V, Rix LLR, Welsh E, Pike I, Reuther GW, Haura EB, Rix U, Koomen JM. Lowering Sample Requirements to Study Tyrosine Kinase Signaling Using Phosphoproteomics with the TMT Calibrator Approach. Proteomics. 2020 Dec.20(24):e2000116. Pubmedid: 32865326. Pmcid: PMC7771371.
  • Yin Q, Wyatt CJ, Han T, Smalley KSM, Wan L. ITCH as a potential therapeutic target in human cancers. Semin Cancer Biol. 2020 Dec.67(Pt 2):117-130. Pubmedid: 32165318. Pmcid: PMC7724637.
  • Sharma V, Wright KL, Epling-Burnette PK, Reuther GW. Metabolic Vulnerabilities and Epigenetic Dysregulation in Myeloproliferative Neoplasms. Front Immunol. 2020 Nov.11:604142. Pubmedid: 33329600. Pmcid: PMC7734315.
  • Garg SK, Welsh EA, Fang B, Hernandez YI, Rose T, Gray J, Koomen JM, Berglund A, Mulé JJ, Markowitz J. Multi-Omics and Informatics Analysis of FFPE Tissues Derived from Melanoma Patients with Long/Short Responses to Anti-PD1 Therapy Reveals Pathways of Response. Cancers (Basel). 2020 Nov.12(12). Pubmedid: 33255891. Pmcid: PMC7768436.
  • Shi Y, Sang P, Lu J, Higbee P, Chen L, Yang L, Odom T, Daughdrill G, Chen J, Cai J. Rational Design of Right-Handed Heterogeneous Peptidomimetics as Inhibitors of Protein-Protein Interactions. J Med Chem. 2020 Nov.63(21):13187-13196. Pubmedid: 33140956. Pmcid: PMC8170677.
  • Zon L, Gomes AP, Cance WG, Ribas A, Tuveson D, Postel-Vinay S, Massard C, Barlési F. Impact of COVID-19 Pandemic on Cancer Research. Cancer Cell. 2020 Nov.38(5):591-593. Pubmedid: 33086030. Pmcid: PMC7543995.
  • Napoli M, Flores ER. The p53 family reaches the final frontier: the variegated regulation of the dark matter of the genome by the p53 family in cancer. RNA Biol. 2020 Nov.17(11):1636-1647. Pubmedid: 31910062. Pmcid: PMC7567494.
  • Darville LNF, Cline JK, Rozmeski C, Martinez YC, Rich S, Eschrich SA, Egan KM, Yaghjyan L, Koomen JM. LC-HRMS of derivatized urinary estrogens and estrogen metabolites in postmenopausal women. J Chromatogr B Analyt Technol Biomed Life Sci. 2020 Oct.1154:122288. Pubmedid: 32769047. Pmcid: PMC7882395.
  • Nguyen TN, Rajapakshe K, Nicholas C, Tordesillas L, Ehli EA, Davis CM, Coarfa C, Flores ER, Dickinson SE, Curiel-Lewandrowski C, Tsai KY. Integrative transcriptomic analysis for linking acute stress responses to squamous cell carcinoma development. Sci Rep. 2020 Oct.10(1):17209. Pubmedid: 33057049. Pmcid: PMC7560606.
  • Napoli M, Li X, Ackerman HD, Deshpande AA, Barannikov I, Pisegna MA, Bedrosian I, Mitsch J, Quinlan P, Thompson A, Rajapakshe K, Coarfa C, Gunaratne PH, Marchion DC, Magliocco AM, Tsai KY, Flores ER. Pan-cancer analysis reveals TAp63-regulated oncogenic lncRNAs that promote cancer progression through AKT activation. Nat Commun. 2020 Oct.11(1):5156. Pubmedid: 33056990. Pmcid: PMC7561725.
  • Taylor NJ, Gaynanova I, Eschrich SA, Welsh EA, Garrett TJ, Beecher C, Sharma R, Koomen JM, Smalley KSM, Messina JL, Kanetsky PA. Metabolomics of primary cutaneous melanoma and matched adjacent extratumoral microenvironment. PLoS One. 2020 Oct.15(10):e0240849. Pubmedid: 33108391. Pmcid: PMC7591037.