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View the grants, clinical trials and publications from the Molecular Oncology Department.

  • Grants

    • CPTAC Phase III
      Sponsor: Nat Institutes of Health
      PI:Koomen, J.
    • Anti-tumor Potential of Temperature-Sensitive p53 Mutants
      Sponsor: Nat Institutes of Health
      PI (Contact):Chen, J.,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.
    • CARM1-mediated regulation of YAP1 as a therapeutic target in lung cancer
      Sponsor: Nat Institutes of Health
      PI:Kissil, J.
    • 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: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.
    • 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.
    • Vitamin B12 supplementation as novel therapeutic strategy to improve cancer-associated outcomes
      Sponsor: Nat Institutes of Health
      PI:Gomes, A.
    • Chromosome 1q ceRNAs in melanoma progression and metastasis
      Sponsor: Nat Institutes of Health
      PI:Karreth, F.
    • Aging as a selective pressure that drives tumor progression
      Sponsor: Nat Institutes of Health
      PI:Gomes, A.
    • Biophysical basis for enzyme mediated deglycation in protein repair
      Sponsor: Nat Institutes of Health
      PI:Binning, J.
    • 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.
    • Targeting centrosome‐mitotic kinases as a novel therapeutic approach against breast cancers in Hispanic/Latinas
      Sponsor: Nat Institutes of Health
      PI (MPI):Cress, D.
    • 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.
    • Employing functionalized fragment libraries to identify therapeutic agents for neurofibromatosis type 2
      Sponsor: Nat Institutes of Health
      PI:Kissil, J.
    • 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.
    • 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 (Contact):Gomes, A.
    • RBFOX2 deregulation promotes pancreatic cancer progression through alternative splicing
      Sponsor: Nat Institutes of Health
      PI:Mann, K.
    • The role of HPV E1 in regulating the NRF2-KEAP1 pathway
      Sponsor: Nat Institutes of Health
      PI:Binning, J.
    • Targeting Wnt Signaling Pathway
      Sponsor: Nat Institutes of Health
      PI:Chen, J.
    • Metabolic vulnerabilities of dormant disseminated breast cancer cells
      Sponsor: METAvivor Research and Support, Inc.
      PI:Gomes, A.
    • Restoring FZR1 Tumor Suppressor Function in Human Cancers
      Sponsor: Florida Biomedical Research Program (FBRP)
      PI:Wan, L.
    • Understanding the mechanisms by which STK11 loss in lung cancer leads to immune invasion
      Sponsor: Florida Biomedical Research Program (FBRP)
      PI:Cress, D.
    • Defining the glyco-RNAome in melanoma progression
      Sponsor: US Army
      PI:Karreth, F.
    • Adaptations of breast cancer metastasis to the aging lung
      Sponsor: Nat Institutes of Health
      PI:Gomes, A.
    • Community Project Funding/Congressionally Directed Spending ‐ Construction
      Sponsor: Dept of Health & Human Services (DHHS)
      PI:Flores, E.
    • Targeting a PHGDH Metabolic Vulnerability in Melanoma
      Sponsor: Nat Institutes of Health
      PI:Karreth, F.
    • Epigenetic and Metabolic Bottlenecks of Tumorigenesis
      Sponsor: Nat Institutes of Health
      PI (Contact):Gomes, A.
    • Targeting novel mediators of chemotherapy resistance in dormant breast cancer
      Sponsor: Breast Cancer Alliance
      PI:Oskarsson, T.
    • Targeting antioxidant vulnerabilities in KEAP1/NRF2 mutant NSCLC
      Sponsor: Nat Institutes of Health
      PI (Contact):Jiang, C.
    • Defining the non-canonical functions of MYBL2 in melanoma progression
      Sponsor: Florida Biomedical Research Program (FBRP)
      PI:Karreth, F.
    • How the aging tumor microenvironment affects outgrowth of leptomeningeal metastases
      Sponsor: Amer Cancer Society
      PI (Contact):Gomes, A.
    • Metabolic factors that condition breast cancer metastasis
      Sponsor: Florida Biomedical Research Program (FBRP)
      PI (Contact):Gomes, A.
    • NAD+: A Missing Link Between Aging and Pancreatic Tumorigenesis
      Sponsor: Phi Beta Psi
      PI (Contact):Gomes, A.
    • Novel genetic mouse models of uveal melanoma progression and metastasis
      Sponsor: US Army
      PI:Karreth, F.
    • Interrogating the relationship between translational dynamics and non-canonical antigen presentation in lung cancer
      Sponsor: Nat Institutes of Health
      PI:Jaeger, A.
    • Targeting "Undruggable" Pathways
      Sponsor: Florida Biomedical Research Program (FBRP)
      PI:Flores, E.
    • Elucidating the oncogenic role of sMAF proteins in melanoma (supplement)
      Sponsor: Amer Cancer Society
      PI:Karreth, F.
    • Defining the age-induced metabolic liabilities of lung adenocarcinoma
      Sponsor: Moffitt Cancer Center
      PI (Contact):Gomes, A.,CO-PI:Jiang, C.
    • Engineering approaches to exploit MHC-II antigen presentation in cancer
      Sponsor: Damon Runyon Cancer Research Inst
      PI:Jaeger, A.
    • CD320-mediated vitamin B12 uptake in triple negative breast cancer
      Sponsor: Florida Breast Cancer Foundation
      PI:Gomes, A.

  • Publications

    • Adapa SR, Hunter GA, Amin NE, Marinescu C, Borsky A, Sagatys EM, Sebti SM, Reuther GW, Ferreira GC, Jiang RH. Porphyrin overdrive rewires cancer cell metabolism. Life Sci Alliance. 2024 Jul.7(7). Pubmedid: 38649187. Pmcid: PMC11035860.
    • Flores ER, Sawyer WG. Engineering cancer's end: An interdisciplinary approach to confront the complexities of cancer. Cancer Cell. 2024 Jul.42(7):1133-1137. Pubmedid: 38848721.
    • Xiang S, Craig KC, Luo X, Welch DL, Ferreira RB, Lawrence HR, Lawrence NJ, Reed DR, Alexandrow MG. Identification of ATP-Competitive Human CMG Helicase Inhibitors for Cancer Intervention that Disrupt CMG-Replisome Function. Mol Cancer Ther. 2024 Jul. Pubmedid: 38982858.
    • Pandey G, Mazzacurati L, Rowsell TM, Horvat NP, Amin NE, Zhang G, Akuffo AA, Colin-Leitzinger CM, Haura EB, Kuykendall AT, Zhang L, Epling-Burnette PK, Reuther GW. SHP2 inhibition displays efficacy as a monotherapy and in combination with JAK2 inhibition in preclinical models of myeloproliferative neoplasms. Am J Hematol. 2024 Jun.99(6):1040-1055. Pubmedid: 38440831. Pmcid: PMC11096011.
    • Wu Q, Hatse S, Kenis C, Fernández-García J, Altea-Manzano P, Billen J, Planque M, Vandekeere A, Lambrechts Y, Richard F, Punie K, Neven P, Smeets A, Nevelsteen I, Floris G, Desmedt C, Gomes AP, Fendt SM, Wildiers H. Aging-accumulated methylmalonic acid serum levels at breast cancer diagnosis are not associated with distant metastases. Breast Cancer Res Treat. 2024 Jun.205(3):555-565. Pubmedid: 38472594.
    • Alontaga AY, Cano P, Ozakinci H, Puskas JA, Stewart PA, Welsh EA, Yoder SJ, Hicks JK, Saltos AN, Bossler AD, Haura EB, Koomen JM, Boyle TA. Implementation of a High-Accuracy Targeted Gene Expression Panel for Clinical Care. J Mol Diagn. 2024 May. Pubmedid: 38777037.
    • Peak T, Tian Y, Patel A, Shaw T, Obermayer A, Laborde J, Kim Y, Johnson J, Stewart P, Fang B, Teer JK, Koomen J, Berglund A, Marchion D, Francis N, Echevarria PR, Dhillon J, Clark N, Chang A, Sexton W, Zemp L, Chahoud J, Wang L, Manley B. Pathogenic Roles for RNASET2 in Clear Cell Renal Cell Carcinoma. Lab Invest. 2024 May.104(5):102041. Pubmedid: 38431116.
    • Gomes AP. Methylmalonic acid's potential as a prognostic indicator for cancer-related mortality. Am J Clin Nutr. 2024 May.119(5):1099-1100. Pubmedid: 38702108.
    • Jasani N, Xu X, Posorske B, Kim Y, Vera O, Tsai KY, DeNicola GM, Karreth FA. MAPK-mediated PHGDH induction is essential for melanoma formation and represents an actionable vulnerability. bioRxiv. 2024 Apr. Pubmedid: 38659816. Pmcid: PMC11042198.
    • Wu Q, Hatse S, Kenis C, Fernández-García J, Altea-Manzano P, Billen J, Planque M, Vandekeere A, Lambrechts Y, Richard F, Punie K, Neven P, Smeets A, Nevelsteen I, Floris G, Desmedt C, Gomes AP, Fendt SM, Wildiers H. Serum methylmalonic acid concentrations at breast cancer diagnosis significantly correlate with clinical frailty. Geroscience. 2024 Apr.46(2):1489-1498. Pubmedid: 37632634. Pmcid: PMC10828366.
    • Zheng XQ, Guo JP, Yang H, Kanai M, He LL, Li YY, Koomen JM, Minton S, Gao M, Ren XB, Coppola D, Cheng JQ. Retraction Note: Aurora-A is a determinant of tamoxifen sensitivity through phosphorylation of ERα in breast cancer. Oncogene. 2024 Apr.43(15):1160. Pubmedid: 38396296. Pmcid: PMC11036404.
    • Palma FR, Coelho DR, Pulakanti K, Sakiyama MJ, Huang Y, Ogata FT, Danes JM, Meyer A, Furdui CM, Spitz DR, Gomes AP, Gantner BN, Rao S, Backman V, Bonini MG. Histone H3.1 is a chromatin-embedded redox sensor triggered by tumor cells developing adaptive phenotypic plasticity and multidrug resistance. Cell Rep. 2024 Mar.43(3):113897. Pubmedid: 38493478.
    • Tejero J, Lazure F, Gomes AP. Methylmalonic acid in aging and disease. Trends Endocrinol Metab. 2024 Mar.35(3):188-200. Pubmedid: 38030482. Pmcid: PMC10939937.
    • Liao Y, Remsing Rix LL, Li X, Fang B, Izumi V, Welsh EA, Monastyrskyi A, Haura EB, Koomen JM, Doebele RC, Rix U. Differential network analysis of ROS1 inhibitors reveals lorlatinib polypharmacology through co-targeting PYK2. Cell Chem Biol. 2024 Feb.31(2):284-297.e10. Pubmedid: 37848034. Pmcid: PMC10922442.
    • Napoli M, Deshpande AA, Chakravarti D, Rajapakshe K, Gunaratne PH, Coarfa C, Flores ER. Genome-wide p63-Target Gene Analyses Reveal TAp63/NRF2-Dependent Oxidative Stress Responses. Cancer Res Commun. 2024 Feb.4(2):264-278. Pubmedid: 38165157. Pmcid: PMC10832605.
    • Yin T, Wang G, Wang L, Mudgal P, Wang E, Pan CC, Alexander PB, Wu H, Cao C, Liang Y, Tan L, Huang D, Chong M, Chen R, Lim BJW, Xiang K, Xue W, Wan L, Hu H, Loh YH, Wang XF, Li QJ. Breaking NGF-TrkA immunosuppression in melanoma sensitizes immunotherapy for durable memory T cell protection. Nat Immunol. 2024 Feb.25(2):268-281. Pubmedid: 38195702.
    • Xu X, Bok I, Jasani N, Wang K, Chadourne M, Mecozzi N, Deng O, Welsh EA, Kinose F, Rix U, Karreth FA. PTEN Lipid Phosphatase Activity Suppresses Melanoma Formation by Opposing an AKT/mTOR/FRA1 Signaling Axis. Cancer Res. 2024 Feb.84(3):388-404. Pubmedid: 38193852. Pmcid: PMC10842853.
    • Liu Q, Adhikari E, Lester DK, Fang B, Johnson JO, Tian Y, Mockabee-Macias AT, Izumi V, Guzman KM, White MG, Koomen JM, Wargo JA, Messina JL, Qi J, Lau EK. Androgen drives melanoma invasiveness and metastatic spread by inducing tumorigenic fucosylation. Nat Commun. 2024 Feb.15(1):1148. Pubmedid: 38326303. Pmcid: PMC10850104.
    • Liu X, Gillis N, Jiang C, McCofie A, Shaw TI, Tan AC, Zhao B, Wan L, Duckett DR, Teng M. An Epigenomic fingerprint of human cancers by landscape interrogation of super enhancers at the constituent level. PLoS Comput Biol. 2024 Feb.20(2):e1011873. Pubmedid: 38335222. Pmcid: PMC10883583.
    • Jimenez J, Dubey P, Carter B, Koomen J, Markowitz J. A metabolic perspective on nitric oxide function in melanoma. BBA. Reviews on cancer. 2024 Jan.1879(1):189038. Pubmedid: 38061664.
    • Jinesh GG, Smallin MT, Mtchedlidze N, Godwin I, Napoli M, Hackel N, Phadke MS, Deshpande AA, Li X, Lockhart JH, Baldwin JR, Acevedo-Acevedo S, Gao Y, Reiser MA, Smalley KSM, Flores ER, Brohl AS. C19MC miRNA-520G induces SP100 antiviral gene transcription and inhibits melanin production in skin cutaneous melanoma. Genes Dis. 2024 Jan.11(1):60-63. Pubmedid: 37588194. Pmcid: PMC10425800.
    • Burger KL, Fernandez MR, Meads MB, Sudalagunta PR, Oliveira PS, Renatino Canevarolo R, Alugubelli RR, Tungsevik A, De Avila G, Silva M, Graeter AI, Dai H, Vincelette ND, Prabhu A, Magaletti D, Yang C, Li W, Kulkarni A, Hampton OA, Koomen JM, Roush WR, Monastyrskyi A, Berglund AE, Silva AS, Cleveland JL, Shain KH. CK1δ and CK1ε Signaling Sustains Mitochondrial Metabolism and Cell Survival in Multiple Myeloma. Cancer Res. 2023 Dec.83(23):3901-3919. Pubmedid: 37702657. Pmcid: PMC10690099.
    • Khaled ML, Ren Y, Kundalia R, Alhaddad H, Chen Z, Wallace GC, Evernden B, Ospina OE, Hall M, Liu M, Darville LNF, Izumi V, Chen YA, Pilon-Thomas S, Stewart PA, Koomen JM, Corallo SA, Jain MD, Robinson TJ, Locke FL, Forsyth PA, Smalley I. Branched-chain keto acids promote an immune-suppressive and neurodegenerative microenvironment in leptomeningeal disease. bioRxiv. 2023 Dec. Pubmedid: 38187773. Pmcid: PMC10769272.
    • Alhaddad H, Ospina OE, Khaled ML, Ren Y, Forsyth P, Pina Y, Macaulay R, Law V, Tsai KY, Cress WD, Fridley B, Smalley I. Spatial transcriptomics analysis identifies a unique tumor-promoting function of the meningeal stroma in melanoma leptomeningeal disease. bioRxiv. 2023 Dec. Pubmedid: 38187574. Pmcid: PMC10769278.
    • Adhikari E, Liu Q, Johnson J, Stewart P, Marusyk V, Fang B, Izumi V, Bowers K, Guzman KM, Koomen JM, Marusyk A, Lau EK. Brain metastasis-associated fibroblasts secrete fucosylated PVR/CD155 that induces breast cancer invasion. Cell Rep. 2023 Dec.42(12):113463. Pubmedid: 37995180.
    • Riley AK, Grant M, Snell A, Vichas A, Moorthi S, Urisman A, Castel P, Wan L, Berger AH. The deubiquitinase USP9X regulates RIT1 protein abundance and oncogenic phenotypes. bioRxiv. 2023 Dec. Pubmedid: 38077017. Pmcid: PMC10705424.
    • Maurin M, Ranjouri M, Megino-Luque C, Newberg JY, Du D, Martin K, Miner RE, Prater MS, Wee DKB, Centeno B, Pruett-Miller SM, Stewart P, Fleming JB, Yu X, Bravo-Cordero JJ, Guccione E, Black MA, Mann KM. RBFOX2 deregulation promotes pancreatic cancer progression and metastasis through alternative splicing. Nat Commun. 2023 Dec.14(1):8444. Pubmedid: 38114498. Pmcid: PMC10730836.
    • Welch DL, Fridley BL, Cen L, Teer JK, Yoder SJ, Pettersson F, Xu L, Cheng CH, Zhang Y, Alexandrow MG, Xiang S, Robertson-Tessi M, Brown JS, Metts J, Brohl AS, Reed DR. Modeling phenotypic heterogeneity towards evolutionarily inspired osteosarcoma therapy. Sci Rep. 2023 Nov.13(1):20125. Pubmedid: 37978271. Pmcid: PMC10656496.
    • Emmons MF, Bennett RL, Riva A, Gupta K, Carvalho LADC, Zhang C, Macaulay R, Dupéré-Richér D, Fang B, Seto E, Koomen JM, Li J, Chen YA, Forsyth PA, Licht JD, Smalley KSM. HDAC8-mediated inhibition of EP300 drives a transcriptional state that increases melanoma brain metastasis. Nat Commun. 2023 Nov.14(1):7759. Pubmedid: 38030596. Pmcid: PMC10686983.
    • Shao A, Kissil JL, Fan CM. The L27 Domain of MPP7 enhances TAZ-YY1 Cooperation to Renew Muscle Stem Cells. Res Sq. 2023 Nov. Pubmedid: 38077061. Pmcid: PMC10705706.
    • Shao A, Kissil JL, Fan CM. The L27 Domain of MPP7 enhances TAZ-YY1 Cooperation to Renew Muscle Stem Cells. bioRxiv. 2023 Nov. Pubmedid: 37961392. Pmcid: PMC10635061.
    • Yaghjyan L, Mai V, Darville LNF, Cline J, Wang X, Ukhanova M, Tagliamonte MS, Martinez YC, Rich SN, Koomen JM, Egan KM. Associations of gut microbiome with endogenous estrogen levels in healthy postmenopausal women. Cancer Causes Control. 2023 Oct.34(10):873-881. Pubmedid: 37286847.
    • Nowicka Z, Rentzeperis F, Beck R, Tagal V, Pinto AF, Scanu E, Veith T, Cole J, Ilter D, Viqueira WD, Teer JK, Maksin K, Pasetto S, Abdalah MA, Fiandaca G, Prabhakaran S, Schultz A, Ojwang M, Barnholtz-Sloan JS, Farinhas JM, Gomes AP, Katira P, Andor N. Interactions between ploidy and resource availability shape clonal interference at initiation and recurrence of glioblastoma. bioRxiv. 2023 Oct. Pubmedid: 37905142. Pmcid: PMC10614845.
    • Nguyen T, Sridaran D, Chouhan S, Weimholt C, Wilson A, Luo J, Li T, Koomen J, Fang B, Putluri N, Sreekumar A, Feng FY, Mahajan K, Mahajan NP. Author Correction: Histone H2A Lys130 acetylation epigenetically regulates androgen production in prostate cancer. Nat Commun. 2023 Sep.14(1):6022. Pubmedid: 37758702. Pmcid: PMC10533897.
    • Elmarsafawi AG, Hesterberg RS, Fernandez MR, Yang C, Darville LN, Liu M, Koomen JM, Phanstiel Iv O, Atkins R, Mullinax JE, Pilon-Thomas SA, Locke FL, Epling-Burnette PK, Cleveland JL. Modulating the polyamine/hypusine axis controls generation of CD8+ tissue-resident memory T cells. JCI Insight. 2023 Sep.8(18). Pubmedid: 37581943. Pmcid: PMC10561731.
    • Letson CT, Balasis ME, Newman H, Binder M, Vedder A, Kinose F, Ball M, Kruer T, Quintana A, Lasho TL, Finke CM, Almada LL, Grants JM, Zhang G, Fernandez-Zapico ME, Gaspar-Maia A, Lancet J, Komrokji R, Haura E, Sallman DA, Reuther GW, Karsan A, Rix U, Patnaik MM, Padron E. Targeting BET Proteins Downregulates miR-33a To Promote Synergy with PIM Inhibitors in CMML. Clin Cancer Res. 2023 Aug.29(15):2919-2932. Pubmedid: 37223910. Pmcid: PMC10524644.
    • Tasoulas J, Srivastava S, Xu X, Tarasova V, Maniakas A, Karreth FA, Amelio AL. Genetically engineered mouse models of head and neck cancers. Oncogene. 2023 Aug.42(35):2593-2609. Pubmedid: 37474617. Pmcid: PMC10457205.
    • Lockhart JH, Ackerman HD, Lee K, Abdalah M, Davis AJ, Hackel N, Boyle TA, Saller J, Keske A, Hänggi K, Ruffell B, Stringfield O, Cress WD, Tan AC, Flores ER. Grading of lung adenocarcinomas with simultaneous segmentation by artificial intelligence (GLASS-AI). NPJ Precis Oncol. 2023 Jul.7(1):68. Pubmedid: 37464050. Pmcid: PMC10354042.