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

  • Grants

    • Anti-tumor Potential of Temperature-Sensitive p53 Mutants
      Award Number:
      Sponsor: Nat Institutes of Health
      PI (Contact):Chen, J.,PI:Mann, M.
    • Characterizing oncogenic function of ITCH in melanoma
      Award Number:
      Sponsor: Nat Institutes of Health
      PI:Wan, L.
    • Targeting centrosome‐mitotic kinases as a novel therapeutic approach against breast cancers in Hispanic/Latinas
      Award Number:
      Sponsor: Nat Institutes of Health
      PI (MPI):Cress, D.
    • Allosteric Regulation of MDMX by Protein Disorder
      Award Number:
      Sponsor: Nat Institutes of Health
      PI (Contact):Chen, J.
    • RBFOX2 deregulation promotes pancreatic cancer progression through alternative splicing
      Award Number:
      Sponsor: Nat Institutes of Health
      PI:Mann, K.
    • Targeting Wnt Signaling Pathway
      Award Number:
      Sponsor: Nat Institutes of Health
      PI:Chen, J.
    • Community Project Funding/Congressionally Directed Spending ‐ Construction
      Award Number:
      Sponsor: Dept of Health & Human Services (DHHS)
      PI:Flores, E.
    • Novel genetic mouse models of uveal melanoma progression and metastasis
      Award Number:
      Sponsor: US Army
      PI:Karreth, F.
    • Interrogating the relationship between translational dynamics and non-canonical antigen presentation in lung cancer
      Award Number:
      Sponsor: Nat Institutes of Health
      PI:Jaeger, A.

  • Publications

    • Noble JD, Peixoto BC, Menges MA, Abraham-Miranda J, Savid-Frontera C, Sawyer W, Sorathia VD, Cuadrado Delgado LA, Corallo SA, Llanos JC, Merritt EC, De Avila G, Castaneda-Puglianini OA, Liu HD, Alsina M, Nishihori T, Shain KH, Siqueira Silva AS, Baz RC, Blue BJ, Grajales-Cruz AF, Hansen DK, Cleveland JL, Perna F, Lynch CC, Binning JM, Atkins RM, Song X, Locke FL, Freeman CL. Product-intrinsic NF-κB-driven transcriptional programs connote durability of CAR-T response in multiple myeloma. Blood. 2026 Sep.148(11):1409-1422. Pubmedid: 42275255.
    • Deng O, Nepomuceno TDC, Fang B, Welsh EA, Izumi V, Martin RH, George EM, Koomen JM, Monteiro AN, Rix U. Integrative proteomics reveals MSH6 to modulate PARP inhibitor sensitivity in BRCA1/2-proficient ovarian cancer. PLoS One. 2026 Sep.21(9):e0357365. Pubmedid: 42685115. Pmcid: PMC13537606.
    • Martinez-Planes E, Ramello MC, Fontela MG, Shokri MR, Tran T, Darville L, Koomen J, Kim Y, Abate-Daga D. C-terminal CD28 phosphorylation, pY218, modulates IL-2 secretion and therapeutic effect of CAR-T cells. Mol Ther. 2026 Aug. Pubmedid: 42642932.
    • Kumar NB, Schabath M, Alexandrow M, Gray J, Tanvetyanon T, Khalil F, Laborde J, Schell MJ, Klippenstein D. Multidimensional LDCT Imaging Endpoints for a Randomized Pilot Phase II Trial of Curcumin and Omega-3 Fatty Acids for Lung Cancer Chemoprevention: Results of a Randomized Pilot Trial. Cancers (Basel). 2026 Aug.18(16). Pubmedid: 42649879. Pmcid: PMC13510763.
    • Shields MD, Minton KG, Ozakinci H, Zhou T, Terry OC, Kumar P, Akel R, Girard L, Minna JD, Boyle TA, Koomen JM, Shafique M. ISL1: A Novel Neuroendocrine Subtype in Small Cell Lung Cancer Predicts Durable Response to Lurbinectedin. Mol Cancer Ther. 2026 Aug.25(8):1393-1407. Pubmedid: 41582485.
    • Xu X, Liu X, Jarajapu V, Neelature Sriramareddy S, Konecny F, Posorske B, Dollar JJ, Liu X, Jasani N, Wang K, Mecozzi N, Soto-Vargas Z, Ochoa-Rios SL, Murikipudi H, Phan N, Chadourne M, Kuznetsoff JN, Sinard J, Bennett RL, Licht JD, Smalley KSM, Harbour JW, Yu X, Karreth FA. A Multistep Immune-Competent Genetically Engineered Mouse Model Reveals Phenotypic Plasticity in Uveal Melanoma. Cancer Res. 2026 Aug.86(15):3666-3686. Pubmedid: 41661679. Pmcid: PMC12974268.
    • Qasrawi F, Bergmann F, Straube P, Thiesler H, Hildebrandt H, Sinha S, Flores ER, Trowe MO, Rudat C, Kispert A. ΔNP63 regulates epithelial stratification and differentiation in the murine ureter. Am J Physiol Renal Physiol. 2026 Aug.331(2):F286-F303. Pubmedid: 42412652.
    • Shultz ZP, Lee-Sam A, Chang YP, Sun L, Grassie D, Gabellini A, Pedretty K, Scattolin T, Izumi V, Fang B, Sansil S, Kakumanu R, Wojtas L, Koomen J, Schönbrunn E, Monastyrskyi A, Duckett D, Lopchuk JM. Late-stage functionalization with strain-release warheads enables tunable covalent inhibition. Science. 2026 Jul.393(6809):408-416. Pubmedid: 42490492.
    • Davis EW, Park MA, Sinnamon AJ, Koomen J, Permuth JB. Reframing pancreatic cancer diagnosis: metabolic signatures and the challenge of rule-out testing. Transl Gastroenterol Hepatol. 2026 Jul.11:81. Pubmedid: 42592552. Pmcid: PMC13466748.
    • Aplin AE, Alsina K, Betof AS, Birkett J, Butler MO, Cole G, Haq R, Karreth FA, Mahajan VB, Marpadga R, Mruthyunjaya P, Nathan P, Nilsson JA, Palmer G, Sacco JJ, Sato T, Stanhope S, Teng PN, LiPira K. Meeting Report From the 2025 Cure Ocular Melanoma (CURE OM) Global Science Meeting, Amsterdam, the Netherlands, October 2025. Pigment Cell Melanoma Res. 2026 Jul.39(4):e70102. Pubmedid: 42338188.
    • Chen J, Fatima Z, Chen L, Yin M, Cui Y, Cai J. MDM2 Amplification Enables Selective PROTAC Targeting of Tumor Cells. Mol Cancer Ther. 2026 Jun.25(6):948-956. Pubmedid: 41517892.
    • Bontekoe E, Zhang M, Jiang P, Montoya A, Shulga Y, Slone JK, Paul E, Polera C, Forward S, Nassif Rausseo B, Assita ER, Xing C, Molkentine DP, Morris BB, Polic I, Roszik J, Salgado R, Vaishnavi A, Deniger D, Tran HT, Gibbons DL, Vaporciyan A, Gillison ML, Wistuba II, Kavraki LE, Zhang J, Lizee G, Yee C, Hwu P, Kwok S, Jaeger AM, Heymach JV, Reuben A. FOXM1-Specific TCR-Engineered T Cells Target Non-Small Cell Lung Cancer. Cancer Immunol Res. 2026 Jun.14(6):958-973. Pubmedid: 41854516. Pmcid: PMC13119620.
    • Deshpande AA, Lockhart JH, Napoli M, Flores ER. Lnc-ing the Hallmarks of Cancer: The Interplay between lncRNAs and the p53 Family Members across the Hallmarks of Cancer. Mol Cell Biol. 2026 May.1-20. Pubmedid: 42117182.
    • Vera O, Martinez M, Soto-Vargas Z, Wang K, Xu X, Mecozzi N, Murikipudi H, Ruiz-Buceta S, Chadourne M, Posorske B, Angarita A, Bok I, Ulloa Arrieta JD, Liu Q, Kim Y, Messina JL, Tsai KY, Major MB, Lau EK, Yu X, Ibanez de Caceres I, Karreth FA. A MAFG~MITF complex drives melanoma phenotype switching and progression. Nat Commun. 2026 May. Pubmedid: 42168173.
    • Welles JE, Garifallou JP, Gonzalez MV, Santoleri D, Choudhury FK, DeNicola GM, Martin RW, Jiang C, Kim J, Li G, Aki Y, Chang CJ, Li D, Wells RG, Xiao Y, Zhang J, Lazar MA, Brady DC, Titchenell PM. Reduction in Hepatic Phosphatidylcholine Biosynthesis Promotes MASH Through Copper Deficiency. bioRxiv. 2026 May. Pubmedid: 42182421. Pmcid: PMC13192769.
    • Fini MS, Alley JR, Vensko SP, Karthikeyan D, Lee JS, Garness JA, Paul E, Jaeger AM, Goonetilleke N, Kim WY, Vincent BG. Immunodominance Hierarchy of Endogenous BBN963 Bladder Cancer Antigens Remains Stable Under Anti-PD1 and Anti-CTLA4 Immunotherapy. bioRxiv. 2026 May. Pubmedid: 42239304. Pmcid: PMC13228343.
    • Son J, Remsing Rix LL, Fang B, Welsh EA, Bremer NV, Foglizzo V, Roa P, Sigcha-Coello N, Liao Y, Haura EB, Drilon A, Koomen JM, Cocco E, Rix U. Dual targeting of RET and SRC synergizes in RET fusion-positive cancer cells. Mol Oncol. 2026 Apr.20(4):1041-1060. Pubmedid: 41194587. Pmcid: PMC13060644.
    • Matlack JK, Miner RE, Lokhandwala J, Binning JM. Ancestral protein reconstruction reveals the mechanism of substrate specificity in FN3K-mediated deglycation. Commun Biol. 2026 Apr.9(1). Pubmedid: 41933252.
    • Nowak JA, Cho E, Davis MA, Zheng S, Bell L, Sha F, Magdalenski JS, Lui A, Napoli M, Falahat R, Mulé JJ, Flores ER, Farha OK, Teplensky MH. Strengthening Antisense Oligonucleotide-Mediated Anti-Tumor Immunity via Metal-Organic Framework Nanoparticles. Nano Lett. 2026 Mar.26(8):2861-2868. Pubmedid: 41712689.
    • Ramesh PS, Nicolaci AA, Graham LE, Nouel J, Xu K, Binning JM, Munger K, White EA. Inactivation of the RB1 and PTPN14 tumor suppressors cooperatively enables the carcinogenic activity of the human papillomavirus E7 oncoprotein. bioRxiv. 2026 Mar. Pubmedid: 41890011. Pmcid: PMC13015474.
    • Kim Y, Sun LJ, Long M, Caldwell S, Maurer HC, Olive KP, Karreth F, DeNicola GM. PHGDH is a targetable driver of PDAC progression. bioRxiv. 2026 Mar. Pubmedid: 41959234. Pmcid: PMC13060845.
    • Martinez-Planes E, Ramello MC, Fontela MG, Shokri MR, Darville L, Koomen J, Kim Y, Abate-Daga D. C-terminus CD28 phosphorylation (Y218) modulates IL-2 secretion and antitumor effect of CAR-T cells. bioRxiv. 2026 Feb. Pubmedid: 41659581. Pmcid: PMC12874040.
    • Polera CA, Jaeger AM. TCRAFT: A Rosetta Stone for T cell receptors. Immunity. 2026 Feb.59(2):238-240. Pubmedid: 41672041.
    • Perez XB, Tordesillas L, Martinez-Planes E, Fontela MG, Rossetti RM, Izumi V, Fang B, Koomen J, Welsh E, Hwu P, Abate-Daga D. CAR Signaling Informs Mechanisms to EnhanceMetabolism and Function in γδ T Cells. Res Sq. 2026 Feb. Pubmedid: 41674831. Pmcid: PMC12889835.
    • Jinesh G, Godwin I, Napoli M, Flores E, Brohl A. Pericentromeric Transcription of Novel Pathogen-Related Human GPS Genes in Cancers is Regulated by C19MC miRNAs, CEBPB, IFN-γ, and IFN-β. Res Sq. 2026 Feb. Pubmedid: 41674814. Pmcid: PMC12889837.
    • Narváez-Bandera I, Lui A, Mekonnen YA, Rubio V, Takyi A, Sulman N, Wilson C, Ackerman HD, Ospina OE, Gonzalez-Calderon G, Flores E, Li Q, Chen A, Fridley B, Stewart P. iModMix: integrative module analysis for multi-omics data. Bioinformatics. 2026 Feb.42(2). Pubmedid: 41555479. Pmcid: PMC12925246.
    • Lantz AE, Gebert R, Li J, Oliveras JA, Gordián ER, Perez-Morales J, Eschrich S, Chen DT, Rosa M, Dutil J, Saavedra HI, Muñoz-Antonia T, Flores I, Cress WD. Worse Clinical and Survival Outcomes in Breast Cancer Patients Living in Puerto Rico Compared to Hispanics, Non-Hispanic Blacks, and Non-Hispanic Whites from Florida. J Racial Ethn Health Disparities. 2026 Feb.13(1):130-140. Pubmedid: 39543072. Pmcid: PMC12281488.
    • García-Irizarry KD, Rojas-Brenes ME, Oliveras-Torres JA, Ortiz-Ortiz CN, Cress WD, Gordián E, Martínez RG, Quintana-González FJ, Escobar-Rodríguez PF, Muñoz-Antonia T, Flores I. Profiling Sociodemographic Risk Factors and Clinical Outcomes of Women with Endometrial Cancer in Puerto Rico: The Central Role of Obesity and Obstetric Features. J Racial Ethn Health Disparities. 2026 Feb.13(1):552-561. Pubmedid: 39833653. Pmcid: PMC12795853.
    • Wang M, Bieging-Rolett KT, Kaiser AM, Brady CA, Lockhart JH, Ferreira S, Nguyen KT, Rajeevan A, Evans SA, Zhao T, Raj N, Elkrief A, Tischfield SE, Ladanyi M, Ozawa MG, Bui NQ, Chen CT, Flores ER, Attardi LD. p53 Drives Lung Cancer Regression through a TSC2/TFEB-dependent Senescence Program. Cancer Discov. 2026 Feb.16(2):391-411. Pubmedid: 41115251. Pmcid: PMC12877752.
    • Shepard A, Lester DK, Troutman S, Hoxha S, Khaled WT, Smith ESJ, Park TJ, Buffenstein R, Du D, Teng M, Dengler-Crish CM, Tsai KY, Flores ER, Ventura A, Kissil JL. An Autochthonous Model of Lung Cancer Identifies Requirements for Cellular Transformation in the Naked Mole Rat. Cancer Discov. 2026 Jan.16(1):35-45. Pubmedid: 40920097. Pmcid: PMC12486303.
    • Solanki HS, Shah H, Imbody D, Desai B, Kato R, Miroshnychenko D, Stern YE, Majumder A, Sarcar B, Xieraili A, Stewart PA, Fang B, Zhang Y, Yao J, Darville LN, Koomen JM, Rix U, Evans JW, Yang YC, Ahler E, Marusyk A, Singh M, Aronchik I, Haura EB. RAS-GTP Inhibition Overcomes Acquired Resistance to KRASG12C Inhibitors Mediated by Oncogenic and Wild-Type RAS Activation in Non-Small Cell Lung Cancer. Cancer Res. 2026 Jan.86(2):467-484. Pubmedid: 41165456. Pmcid: PMC12962340.
    • Avasthi KK, Manley BJ, Pellini B, Zhang J, Bloomer AM, Jean-Baptiste E, Marchion DC, Fang B, Koomen JM, Siegel EM, Wang L. Different plasma exosome isolation methods generated distinct microRNA and protein profiles in healthy controls and patients with advanced prostate and lung cancer. BMC Cancer. 2025 Dec.26(1):160. Pubmedid: 41469584. Pmcid: PMC12859987.
    • Xu X, Jarajapu V, Chadourne M, Soto-Vargas Z, Ochoa-Rios SL, Jasani N, Wang K, Mecozzi N, Yao J, Yu X, Karreth FA. FRA1 drives melanoma metastasis through an actionable transcriptional network. Oncogene. 2025 Dec.44(50):4895-4909. Pubmedid: 41286309. Pmcid: PMC12669035.
    • Elzaafarany O, Lester D, Mokhtari S, Kissil JL. NF2-associated schwannomatosis (NF2): genetics, manifestations, and emerging therapeutic approaches. Trends Mol Med. 2025 Dec.31(12):1154-1155. Pubmedid: 40885618. Pmcid: PMC12404673.
    • Yadav VK, Fang B, Koomen JM, Srivastava J, Premi S. Quantitative Proteomics of Nitrosylated Proteins in Melanoma Using the Biotin-Switch Technique Combined With Tandem Mass Tag Labeling. Bio Protoc. 2025 Dec.15(23):e5535. Pubmedid: 41377102. Pmcid: PMC12689159.
    • Park MA, Davis EW, Alhassan S, Arnoletti JP, Basinski TL, McKee AB, Bloomston M, Carson TL, Biachi de Castria T, Chen DT, Cortizas EM, Crowder SL, Delgado MG, Douglas WG, Fleming JB, Hodul P, Huguet KL, Jiang K, Kim DW, Koomen J, Luthra AK, Malafa M, Menon AA, Morales R, Merchant NB, Meredith K, Mo Q, Molina-Vega MA, Moreno-Urazan L, Olumoyin KD, Parker N, Pimiento JM, Rasool G, Rejniak KA, Sansil S, Sparks LM, Stewart P, Tassielli AF, Teer JK, Tran DV, Trevino JG, Velanovich V, Whelan CJ, Jeong D, Judge SM, Judge AR, Permuth JB. Race-based differences in serum biomarkers for cancer-associated cachexia in a diverse cohort of patients with pancreatic ductal adenocarcinoma. Commun Med (Lond). 2025 Dec.6(1):19. Pubmedid: 41413302. Pmcid: PMC12789063.
    • Hu Q, Remsing Rix LL, Desai B, Miroshnychenko D, Li X, Welsh EA, Fang B, Wright GM, Chaudhary N, Kroeger JL, Doebele RC, Koomen JM, Haura EB, Marusyk A, Rix U. Cancer-associated fibroblasts confer ALK inhibitor resistance in EML4-ALK-driven lung cancer by concurrent integrin and MET signaling. Sci Signal. 2025 Dec.18(918):eads7662. Pubmedid: 41433419.
    • Smalley TB, Nicolaci AA, Tran KC, Lokhandwala J, Obertopp N, Matlack JK, Miner RE, Teng MN, Pilon-Thomas S, Binning JM. Targeted degradation of the HPV oncoprotein E6 reduces tumor burden in cervical cancer. Mol Ther. 2025 Nov.33(11):5415-5426. Pubmedid: 40873032. Pmcid: PMC12582245.
    • Chen L, Shultz ZP, Sansone M, Fang B, Liu X, Teng M, Schonbrunn E, Lopchuk JM, Chen J. PROTAC-Mediated Degradation of TAF1 Induces Apoptosis in AML Cells and Inhibits Tumor Growth In Vivo. Mol Cancer Ther. 2025 Nov.24(11):1712-1721. Pubmedid: 40376796. Pmcid: PMC12353786.
    • Hortin GL, Koomen JM. Evaluation of Proteinuria in Plasma Cell Disorders: Shortcomings of Measurements Based on 24-Hour Collections and Alternative Approaches. J Appl Lab Med. 2025 Nov.10(6):1664-1674. Pubmedid: 40928885.
    • Mattavelli G, Helal M, Cetkovic A, Krämer MJ, Herbert SL, Mielert K, Schlaiß T, Frank A, Riemer E, John M, Del Pilar J, Vasquez M, Kindl L, Swietlik JJ, Gansen BO, Krafft M, Stanojkovska E, Fischer H, Albert US, Bauer J, Delgobo M, Aintablian A, Alattar H, Lutz MB, Meissner F, Oskarsson T, Rasche L, Ramos G, Rosenwald A, Wöckel A, Riedel A. A TLR4-dependent fibroblast-monocyte axis in tumor-draining lymph nodes contributes to metastasis in triple-negative breast cancer. Immunity. 2025 Nov.58(11):2830-2846.e15. Pubmedid: 40957419.
    • Underwood MT, Devarapalli V, Jinesh GG, Lockhart JH, Napoli M, Mtchedlidze N, Flores ER, Brohl AS. The Chromosome 19 microRNA Cluster Facilitates Cancer Stemness in Hepatocellular Carcinoma. Noncoding RNA. 2025 Oct.11(6). Pubmedid: 41283329. Pmcid: PMC12641929.
    • Jinesh G, Mtchedlidze N, Devarapalli V, Adhikary S, Lockhart J, Napoli M, Isha I, Reiser M, Cen L, Liu X, Yoder S, Mesa T, Flores E, Brohl A. CEBPB, C19MC, and Defective Autophagy Drive Novel Podosomal Belt to Macropinocytosis Transition, Lipid Accumulation, and HBV A-to-I RNA-editing. Res Sq. 2025 Oct. Pubmedid: 41282072. Pmcid: PMC12636704.
    • Chadourne M, Griffith C, Jasani N, Xu X, Brennan E, Vera O, Mecozzi N, Wang K, Jaeger AM, Karreth FA. CDH3-AS1 antisense RNA enhances P-cadherin translation and acts as a tumor suppressor in melanoma. Cell Rep. 2025 Oct.44(10):116362. Pubmedid: 41037395. Pmcid: PMC12588357.
    • Colin-Leitzinger C, Mekonnen YA, Narvaez-Bandera I, Rubio VY, Ercan D, Welsh EA, Darville LNF, Liu M, Ackerman HD, Avila-Pacheco J, Clish CB, Hicks K, Koomen JM, Gillis N, Fridley BL, Flores ER, Zeleznik OA, Stewart PA. A machine learning framework for classifying lipids in untargeted metabolomics using mass-to-charge ratios and retention times. Metabolomics. 2025 Oct.21(6):151. Pubmedid: 41109916. Pmcid: PMC12535499.
    • Davis EW, Park MA, Basinski TL, Arnoletti JP, Bloomston M, Carson TL, Biachi De Castria T, Chen DT, Cortizas EM, Crowder SL, Genilo-Delgado M, Douglas WG, Huguet KL, Jiang K, Hodul PJ, Karolak A, Kim DW, Koomen JM, Menon AA, Mo Q, Mok SR, Molina-Vega MA, Moreno-Urazan L, Ahmed S, Parker NH, Pimiento JM, Rasool G, Sparks LM, Stewart PA, Tassielli AF, Teer JK, Trevino JG, Velanovich V, Wang X, Whelan CJ, Judge SM, Judge AR, Fleming JB, Malafa MP, Jeong D, Permuth JB. The Impact of Edema on Skeletal Muscle Changes among Patients with Pancreatic Ductal Adenocarcinoma. Cancer Epidemiol Biomarkers Prev. 2025 Sep.34(9):1609-1617. Pubmedid: 40553455.
    • Matlack JK, Miner RE, Lokhandwala J, Binning JM. Ancestral protein reconstruction reveals the mechanism of substrate specificity in FN3K-mediated deglycation. Res Sq. 2025 Sep. Pubmedid: 41041572. Pmcid: PMC12486099.
    • Parkman GL, Xu X, Holmen SL, Karreth FA. The Roles of PTEN in Melanoma Suppression. Pigment Cell Melanoma Res. 2025 Sep.38(5):e70054. Pubmedid: 40976930. Pmcid: PMC12451098.

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