Molecular Oncology Department Metrics

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

Grants
  • Intrinsic Disorder Controls the Function 0f p53 and Other Cancer Associated 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.
  • Anti-tumor Potential of Temperature-Sensitive p53 Mutants
    Sponsor: Nat Institutes of Health
    PI (Contact):Chen, J.,PI (MPI):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.
  • 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 in Lung 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.,Project PI:DeNicola, G.,Project PI:Rodriguez, P.,Project PI:Cleveland, J.,Core PI/Director:Fridley, B.,Core PI/Director:Cress, D.,Core PI/Director:Koomen, J.
  • Direct Control of the human CMG Helicase by Myc and Rb
    Sponsor: Nat Institutes of Health
    PI:Alexandrow, M.
  • Exploring miR-29 in Melanoma Progression and Prevention
    Sponsor: Nat Institutes of Health
    PI:Karreth, F.
  • 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.
  • Molecular Drivers of Lung Cancer in Hispanics
    Sponsor: Nat Institutes of Health
    PI (Contact):Cress, D.,PI (MPI):Teer, J.
  • Aging as a selective pressure that drives tumor progression
    Sponsor: Nat Institutes of Health
    PI:Gomes, A.
  • 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.
  • Characterizing oncogenic function of ITCH in melanoma
    Sponsor: Nat Institutes of Health
    PI:Wan, L.
  • Mechanisms of age-induced chemotherapeutic resistance in lung cancer
    Sponsor: Amer Lung Assoc
    PI:Gomes, A.
  • Characterization of the Oncogenic Potential of circRNAs in Melanoma
    Sponsor: Nat Institutes of Health
    PI:Karreth, F.
  • Elucidating the Oncogenic Role of sMAF Proteins in Melanoma
    Sponsor: Amer Cancer Society
    PI:Karreth, F.
  • Allosteric Regulation of MDMX by Protein Disorder
    Sponsor: Nat Institutes of Health
    PI (Contact):Chen, J.
  • Dual Source Ion Mobility-Mass Spectrometer
    Sponsor: Nat Institutes of Health
    PI:Koomen, J.
  • NAD+: A Missing Link Between Aging and Pancreatic Tumorigenesis
    Sponsor: Phi Beta Psi
    PI:Gomes, A.
  • Elucidating the epigenetic landscape of neurofibromatosis and development of therapeutic targets
    Sponsor: Nat Institutes of Health
    PI:Kissil, J.
  • Establishing the functional differences between variant oncogenic KRAS alleles and identification of allele-selective inhibitors
    Sponsor: Florida Biomedical Research Program (FBRP)
    PI:Kissil, J.
  • Pilot Study of Bladder Cancer Chemo Sensitization by Hypothermia
    Sponsor: Moffitt Cancer Center
    PI (Contact):Chen, J.,PI:Huang, J.,PI:Li, R.,PI:Spiess, P.
  • Novel Mouse Models of Uveal Melanoma
    Sponsor: Melanoma Research Alliance (MRA)
    PI:Karreth, F.
  • Exploring the Impact of HSP90 Inhibition on Antigen Presentation and Anti-Tumor Immune Responses
    Sponsor: Nat Institutes of Health
    PI:Jaeger, A.
  • Epigenetic mechanisms that underlie breast cancer dormancy
    Sponsor: Amer Cancer Society
    PI:Gomes, A.
  • Assessing novel therapeutics against RAS activation in models of myeloproliferative neoplasm and JAK2 inhibitor resistance
    Sponsor: Revolution Medicines Inc
    PI:Reuther, G.
  • Defining and Modeling Pediatric Melanoma Development
    Sponsor: Moffitt Cancer Center
    PI:Karreth, F.
  • Immunosuppressive mechanism of ITCH in the melanoma tumor microenvironment
    Sponsor: Moffitt Cancer Center
    PI:Wan, L.
  • Mapping the antigenic landscape of intraductal papillary mucinous neoplasm (IPMN)
    Sponsor: Moffitt Cancer Center
    PI:Jaeger, A.,CO-PI:Fleming, J.
Publications
  • Welsch JT, Smalley TB, Matlack JK, Avalon NE, Binning JM, Johnson MP, Allcock AL, Baker BJ. Tuaimenals B-H, Merosesquiterpenes from the Irish Deep-Sea Soft Coral Duva florida with Bioactivity against Cervical Cancer Cell Lines. J Nat Prod. 2022 Dec. Pubmedid: 36580354.
  • Xiang S, Reed DR, Alexandrow MG. The CMG helicase and cancer: a tumor "engine" and weakness with missing mutations. Oncogene. 2022 Dec. Pubmedid: 36522488.
  • Sarcar B, Fang B, Izumi V, Nunez-Lopez Y, Tassielli A, Pratley R, Jeong D, Permuth JB, Koomen JM, Fleming JB, Stewart PA. A comparative Proteomics Analysis Identified Differentially Expressed Proteins in Pancreatic Cancer-Associated Stellate Cell Small Extracellular Vesicles. Mol Cell Proteomics. 2022 Dec.21(12):100438. Pubmedid: 36332889. Pmcid: PMC9792568.
  • Rodriguez CP, Kang H, Geiger JL, Burtness B, Chung CH, Pickering CR, Fakhry C, Le QT, Yom SS, Galloway TJ, Golemis E, Li A, Shoop J, Wong S, Mehra R, Skinner H, Saba NF, Flores ER, Myers JN, Ford JM, Karchin R, Ferris RL, Kunos C, Lynn JM, Malik S. Clinical Trial Development in TP53-Mutated Locally Advanced and Recurrent and/or Metastatic Head and Neck Squamous Cell Carcinoma. J Natl Cancer Inst. 2022 Dec.114(12):1619-1627. Pubmedid: 36053203. Pmcid: PMC9745425.
  • Yousefi H, Khosla M, Lauterboeck L, Okpechi SC, Worthylake D, Garai J, Zabaleta J, Guidry J, Zarandi MA, Wyczechowska D, Jayawickramarajah J, Yang Q, Kissil J, Alahari SK. A combination of novel NSC small molecule inhibitor along with doxorubicin inhibits proliferation of triple-negative breast cancer through metabolic reprogramming. Oncogene. 2022 Nov.41(47):5076-5091. Pubmedid: 36243802.
  • Deng O, Dash S, Nepomuceno TC, Fang B, Yun SY, Welsh EA, Lawrence HR, Marchion D, Koomen JM, Monteiro AN, Rix U. Integrated proteomics identifies PARP inhibitor-induced prosurvival signaling changes as potential vulnerabilities in ovarian cancer. J Biol Chem. 2022 Nov.298(11):102550. Pubmedid: 36183837. Pmcid: PMC9636579.
  • Fenton M, Borcherds W, Chen L, Anbanandam A, Levy R, Chen J, Daughdrill G. The MDMX Acidic Domain Uses Allovalency to Bind Both p53 and MDMX. J Mol Biol. 2022 Nov.434(22):167844. Pubmedid: 36181774. Pmcid: PMC9644833.
  • Vaishnavi A, Juan J, Jacob M, Stehn C, Gardner EE, Scherzer MT, Schuman S, van Veen JE, Murphy B, Hackett CS, Dupuy AJ, Chmura SA, van der Weyden L, Newberg JY, Liu A, Mann K, Rust AG, Weiss WA, Kinsey CG, Adams DJ, Grossmann A, Mann MB, McMahon M. Transposon Mutagenesis Reveals RBMS3 Silencing as a Promoter of Malignant Progression of BRAFV600E-Driven Lung Tumorigenesis. Cancer Res. 2022 Nov.82(22):4261-4273. Pubmedid: 36112789. Pmcid: PMC9664136.
  • Amini AP, Kirkpatrick JD, Wang CS, Jaeger AM, Su S, Naranjo S, Zhong Q, Cabana CM, Jacks T, Bhatia SN. Multiscale profiling of protease activity in cancer. Nat Commun. 2022 Oct.13(1):5745. Pubmedid: 36192379. Pmcid: PMC9530178.
  • Hesterberg RS, Liu M, Elmarsafawi AG, Koomen JM, Welsh EA, Hesterberg SG, Ranatunga S, Yang C, Li W, Lawrence HR, Rodriguez PC, Berglund AE, Cleveland JL. TCR-Independent Metabolic Reprogramming Precedes Lymphoma-Driven Changes in T-cell Fate. Cancer Immunol Res. 2022 Oct.10(10):1263-1279. Pubmedid: 35969234. Pmcid: PMC9662872.
  • Madanayake TW, Welsh EA, Darville LNF, Koomen JM, Chalfant CE, Haura EB, Robinson TJ. Inhibition of Epidermal Growth Factor Receptor Signaling by Antisense Oligonucleotides as a Novel Approach to Epidermal Growth Factor Receptor Inhibition. Nucleic Acid Ther. 2022 Oct.32(5):391-400. Pubmedid: 35861718. Pmcid: PMC9595651.
  • Chang A, Chakiryan NH, Du D, Stewart PA, Zhang Y, Tian Y, Soupir AC, Bowers K, Fang B, Morganti A, Teer JK, Kim Y, Spiess PE, Chahoud J, Noble JD, Putney RM, Berglund AE, Robinson TJ, Koomen JM, Wang L, Manley BJ. Proteogenomic, Epigenetic, and Clinical Implications of Recurrent Aberrant Splice Variants in Clear Cell Renal Cell Carcinoma. Eur Urol. 2022 Oct.82(4):354-362. Pubmedid: 35718636.
  • Ullah R, Yin Q, Snell AH, Wan L. RAF-MEK-ERK pathway in cancer evolution and treatment. Semin Cancer Biol. 2022 Oct.85:123-154. Pubmedid: 33992782.
  • Yang Y, Peng Z, Flores ER, Kleinerman ES. Pramlintide: A Novel Therapeutic Approach for Osteosarcoma through Metabolic Reprogramming. Cancers (Basel). 2022 Sep.14(17). Pubmedid: 36077845. Pmcid: PMC9454976.
  • Xu X, Wang K, Vera O, Verma A, Jasani N, Bok I, Elemento O, Du D, Yu X, Karreth FA. Gain of Chromosome 1q Perturbs a Competitive Endogenous RNA Network to Promote Melanoma Metastasis. Cancer Res. 2022 Sep.82(17):3016-3031. Pubmedid: 36052492.
  • Ragland NH, Compo NR, Wiltshire N, Shepard A, Troutman S, Kissil JL, Engelman RW. Housing and Husbandry Alternatives for Naked Mole Rat Colonies Used in Research Settings. J Am Assoc Lab Anim Sci. 2022 Sep.61(5):412-418. Pubmedid: 35944976. Pmcid: PMC9536831.
  • Drapela S, Ilter D, Gomes AP. Metabolic reprogramming: a bridge between aging and tumorigenesis. Mol Oncol. 2022 Sep.16(18):3295-3318. Pubmedid: 35666002. Pmcid: PMC9490145.
  • Remsing Rix LL, Sumi NJ, Hu Q, Desai B, Bryant AT, Li X, Welsh EA, Fang B, Kinose F, Kuenzi BM, Chen YA, Antonia SJ, Lovly CM, Koomen JM, Haura EB, Marusyk A, Rix U. IGF-binding proteins secreted by cancer-associated fibroblasts induce context-dependent drug sensitization of lung cancer cells. Sci Signal. 2022 Aug.15(747):eabj5879. Pubmedid: 35973030. Pmcid: PMC9528501.
  • Xu X, Wang K, Vera O, Verma A, Jasani N, Bok I, Elemento O, Du D, Yu X, Karreth FA. Gain of chromosome 1q perturbs a competitive endogenous RNA network to promote melanoma metastasis. Cancer Res. 2022 Aug. Pubmedid: 35820070.
  • Bekker RA, Zahid MU, Binning JM, Spring BQ, Hwu P, Pilon-Thomas S, Enderling H. Rethinking the immunotherapy numbers game. J Immunother Cancer. 2022 Jul.10(7). Pubmedid: 35793871. Pmcid: PMC9260835.
  • Jaeger AM, Stopfer LE, Ahn R, Sanders EA, Sandel DA, Freed-Pastor WA, Rideout WM, Naranjo S, Fessenden T, Nguyen KB, Winter PS, Kohn RE, Westcott PMK, Schenkel JM, Shanahan SL, Shalek AK, Spranger S, White FM, Jacks T. Deciphering the immunopeptidome in vivo reveals new tumour antigens. Nature. 2022 Jul.607(7917):149-155. Pubmedid: 35705813.
  • Chitsazzadeh V, Nguyen TN, de Mingo Pulido A, Bittencourt BB, Du L, Adelmann CH, Rivera IO, Nguyen KA, Guerra LD, Davis A, Napoli M, Ma W, Davis RE, Rajapakshe K, Coarfa C, Flores ER, Tsai KY. miR-181a Promotes Multiple Protumorigenic Functions by Targeting TGFβR3. J Invest Dermatol. 2022 Jul.142(7):1956-1965.e2. Pubmedid: 34890627. Pmcid: PMC9174350.
  • Avalon NE, Nafie J, De Marco Verissimo C, Warrensford LC, Dietrick SG, Pittman AR, Young RM, Kearns FL, Smalley T, Binning JM, Dalton JP, Johnson MP, Woodcock HL, Allcock AL, Baker BJ. Tuaimenal A, a Meroterpene from the Irish Deep-Sea Soft Coral Duva florida, Displays Inhibition of the SARS-CoV-2 3CLpro Enzyme. J Nat Prod. 2022 May.85(5):1315-1323. Pubmedid: 35549259. Pmcid: PMC9127705.
  • Li J, Smalley I, Chen Z, Wu JY, Phadke MS, Teer JK, Nguyen T, Karreth FA, Koomen JM, Sarnaik AA, Zager JS, Khushalani NI, Tarhini AA, Sondak VK, Rodriguez PC, Messina JL, Chen YA, Smalley KSM. Single-cell Characterization of the Cellular Landscape of Acral Melanoma Identifies Novel Targets for Immunotherapy. Clin Cancer Res. 2022 May.28(10):2131-2146. Pubmedid: 35247927. Pmcid: PMC9106889.
  • Hongu T, Pein M, Insua-Rodríguez J, Gutjahr E, Mattavelli G, Meier J, Decker K, Descot A, Bozza M, Harbottle R, Trumpp A, Sinn HP, Riedel A, Oskarsson T. Perivascular tenascin C triggers sequential activation of macrophages and endothelial cells to generate a pro-metastatic vascular niche in the lungs. Nat Cancer. 2022 Apr.3(4):486-504. Pubmedid: 35469015. Pmcid: PMC9046090.
  • Riedel A, Helal M, Pedro L, Swietlik JJ, Shorthouse D, Schmitz W, Haas L, Young T, da Costa ASH, Davidson S, Bhandare P, Wolf E, Hall BA, Frezza C, Oskarsson T, Shields JD. Tumor-Derived Lactic Acid Modulates Activation and Metabolic Status of Draining Lymph Node Stroma. Cancer Immunol Res. 2022 Apr.10(4):482-497. Pubmedid: 35362044. Pmcid: PMC7612582.
  • Wang B, Wu HH, Abuetabh Y, Leng S, Davidge ST, Flores ER, Eisenstat DD, Leng R. p63, a key regulator of Ago2, links to the microRNA-144 cluster. Cell Death Dis. 2022 Apr.13(4):397. Pubmedid: 35459267. Pmcid: PMC9033807.
  • Gomes AP, Ilter D, Low V, Drapela S, Schild T, Mullarky E, Han J, Elia I, Broekaert D, Rosenzweig A, Nagiec M, Nunes JB, Schaffer BE, Mutvei AP, Asara JM, Cantley LC, Fendt SM, Blenis J. Altered propionate metabolism contributes to tumour progression and aggressiveness. Nat Metab. 2022 Apr.4(4):435-443. Pubmedid: 35361954. Pmcid: PMC9050834.
  • Ampomah PB, Cai B, Sukka SR, Gerlach BD, Yurdagul A, Wang X, Kuriakose G, Darville LNF, Sun Y, Sidoli S, Koomen JM, Tall AR, Tabas I. Macrophages use apoptotic cell-derived methionine and DNMT3A during efferocytosis to promote tissue resolution. Nat Metab. 2022 Apr.4(4):444-457. Pubmedid: 35361955. Pmcid: PMC9050866.
  • Mahajan S, Majumder A, Stewart PA, Chen YA, Adhikari E, Fang B, Yang Y, Lawrence H, Kinose F, Koomen JM, Haura EB. Deubiquitinase Vulnerabilities Identified through Activity-Based Protein Profiling in Non-Small Cell Lung Cancer. Acs Chem Biol. 2022 Apr.17(4):776-784. Pubmedid: 35311290.
  • Fernandez MR, Schaub FX, Yang C, Li W, Yun S, Schaub SK, Dorsey FC, Liu M, Steeves MA, Ballabio A, Tzankov A, Chen Z, Koomen JM, Berglund AE, Cleveland JL. Disrupting the MYC-TFEB Circuit Impairs Amino Acid Homeostasis and Provokes Metabolic Anergy. Cancer Res. 2022 Apr.82(7):1234-1250. Pubmedid: 35149590. Pmcid: PMC9004540.
  • Majumder A, Hosseinian S, Stroud M, Adhikari E, Saller JJ, Smith MA, Zhang G, Agarwal S, Creixell M, Meyer BS, Kinose F, Bowers K, Fang B, Stewart PA, Welsh EA, Boyle TA, Meyer AS, Koomen JM, Haura EB. Integrated Proteomics-Based Physical and Functional Mapping of AXL Kinase Signaling Pathways and Inhibitors Define Its Role in Cell Migration. Mol Cancer Res. 2022 Apr.20(4):542-555. Pubmedid: 35022314. Pmcid: PMC8983558.
  • Bok I, Angarita A, Douglass SM, Weeraratna AT, Karreth FA. A Series of BRAF- and NRAS-Driven Murine Melanoma Cell Lines with Inducible Gene Modulation Capabilities. JID Innov. 2022 Mar.2(2):100076. Pubmedid: 35146482. Pmcid: PMC8819036.
  • Wang Y, Binning JM, Pintilie GD, Chiu W, Amarasinghe GK, Leung DW, Su Z. Cryo-EM analysis of Ebola virus nucleocapsid-like assembly. STAR Protoc. 2022 Mar.3(1):101030. Pubmedid: 34977676. Pmcid: PMC8689349.
  • Andor N, Altrock PM, Jain N, Gomes AP. Tipping Cancer Cells Over the Edge: The Context-Dependent Cost of High Ploidy. Cancer Res. 2022 Mar.82(5):741-748. Pubmedid: 34785577. Pmcid: PMC8898264.
  • Napoli M, Wu SJ, Gore BL, Abbas HA, Lee K, Checker R, Dhar S, Rajapakshe K, Tan AC, Lee MG, Coarfa C, Flores ER. Author Correction: ΔNp63 regulates a common landscape of enhancer associated genes in non-small cell lung cancer. Nat Commun. 2022 Mar.13(1):1717. Pubmedid: 35338160. Pmcid: PMC8956651.
  • Karim RM, Yang L, Chen L, Bikowitz MJ, Lu J, Grassie D, Shultz ZP, Lopchuk JM, Chen J, Schönbrunn E. Discovery of Dual TAF1-ATR Inhibitors and Ligand-Induced Structural Changes of the TAF1 Tandem Bromodomain. J Med Chem. 2022 Mar.65(5):4182-4200. Pubmedid: 35191694.
  • Napoli M, Wu SJ, Gore BL, Abbas H, Lee K, Checker R, Dhar S, Rajapakshe K, Tan AC, Lee MG, Coarfa C, Flores ER. ΔNp63 regulates a common landscape of enhancer associated genes in non-small cell lung cancer. Nat Commun. 2022 Feb.13(1):614. Pubmedid: 35105868. Pmcid: PMC8807845.
  • Yaghjyan L, Darville LNF, Cline J, Martinez YC, Rich S, Austin-Datta RJ, Koomen JM, Tworoger SS, Egan KM. Associations of established breast cancer risk factors with urinary estrogens in postmenopausal women. Cancer Causes Control. 2022 Feb.33(2):279-291. Pubmedid: 34988766.
  • 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. 2022 Feb.29(2):202-214.e7. Pubmedid: 34329582. Pmcid: PMC8782927.
  • Nakamura K, Reid BM, Chen A, Chen Z, Goode EL, Permuth JB, Teer JK, Tyrer J, Yu X, Kanetsky PA, Pharoah PD, Gayther SA, Sellers TA, Lawrenson K, Karreth FA. Functional analysis of the 1p34.3 risk locus implicates GNL2 in high-grade serous ovarian cancer. Am J Hum Genet. 2022 Jan.109(1):116-135. Pubmedid: 34965383. Pmcid: PMC8764204.
  • Pandey G, Kuykendall AT, Reuther GW. JAK2 inhibitor persistence in MPN: uncovering a central role of ERK activation. Blood Cancer J. 2022 Jan.12(1):13. Pubmedid: 35082276. Pmcid: PMC8792018.
  • Mecozzi N, Nenci A, Vera O, Bok I, Falzone A, DeNicola GM, Karreth FA. Genetic tools for the stable overexpression of circular RNAs. RNA Biol. 2022 Jan.19(1):353-363. Pubmedid: 35289721. Pmcid: PMC8928841.