Molecular Oncology in the News

June 2022

Sudhir Putty Reddy, PhD accepted and started a senior principal scientist position at Bristol Myers Squibb.

Dr. Koomen's lab and the Proteomics & Metabolomics Core staff presented four posters at the American Society for Mass Spectrometry Conference in June 2022. ThP 048 Non-Small Cell Lung Cancer Tumor Phenotyping with Targeted Proteomics, The Analysis of Androgens and Cholesterols in Mouse and Human Tissue using LC-HRMS: ESI versus APCI (Min Liu, PhD), Characterization of Bile Acid Interactions in Immune Cells and Biofluids to Assess their Role in the Tumor Immune Microenvironment (Vanessa Rubio, PhD), and Mass Spectrometry-Based Proteomics of Laser Microdissected FFPE Tumors for Spatial Analysis (Lancia Darville, PhD).

May 2022

At this year's Moffitt Faculty Appreciation Event, Florian Karreth, PhD was recognized with two awards: 2021 Junior Faculty Research Award in Basic Science and 2021 Research Educator of the Year.

Dr. Koomen worked with a research team, led by Brandon Manley MD/PhD in GU Oncology, to study splice variants in renal cell carcinoma; the proteomics effort focused on the analysis of an EGFR splice variant that produced only the C-terminal intracellular portion of the protein. Proteogenomic, Epigenetic, and Clinical Implications of Recurrent Aberrant Splice Variants in Clear Cell Renal Cell Carcinoma. 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.  Eur Urol. 2022 Jun 16:S0302-2838(22)02395-8. doi: 10.1016/j.eururo.2022.05.021. Online ahead of print. PMID:35718636. (Free article)

April 2022

  • Congratulations to Tracess Smalley, PhD in the Binning lab for being awarded an ACS Fellowship.
  • Dr. John Koomen will serve as a co-mentor for Sura-Attha (Wynn) Umasangtongkul, a Cancer Biology PhD student in Ken Shain's lab. His PhD project will be on the use of proteomics and metabolomics to improve treatment for multiple myeloma.
  • Dr. John Koomen attended the Mass Spectrometry and Advances in the Clinical Lab conference in Monterey, CA and presented two posters about lung cancer biomarkers.
  • Working with Lancia Darville in the Proteomics & Metabolomics Core in collaboration with the Tabas Lab at Columbia, Dr. Koomen contributed to a publication utilizing metabolomics to understand macrophage function: Macrophages use apoptotic cell-derived methionine and DNMT3A during efferocytosis to promote tissue resolution. Ampomah PB, Cai B, Sukka SR, Gerlach BD, Yurdagul A Jr, Wang X, Kuriakose G, Darville LNF, Sun Y, Sidoli S, Koomen JM, Tall AR, Tabas I.  Nat Metab. 2022 Apr;4(4):444-457. doi: 10.1038/s42255-022-00551-7. Epub 2022 Mar 31.PMID: 35361955 Free PMC article.
  • Continuing a long-term collaboration with Eric Haura (Molecular Medicine) and Bin Fang in the Proteomics & Metabolomics Core, Dr. Koomen contributed to 2 publications using proteomics to understand lung cancer biology and targeted therapy. Deubiquitinase Vulnerabilities Identified through Activity-Based Protein Profiling in Non-Small Cell Lung Cancer. Mahajan S, Majumder A, Stewart PA, Chen YA, Adhikari E, Fang B, Yang Y, Lawrence H, Kinose F, Koomen JM, Haura EB.  ACS Chem Biol. 2022 Apr 15;17(4):776-784. doi: 10.1021/acschembio.2c00018. Epub 2022 Mar 21.PMID: 35311290
  • Integrated Proteomics-Based Physical and Functional Mapping of AXL Kinase Signaling Pathways and Inhibitors Define Its Role in Cell Migration.
  • 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.  Mol Cancer Res. 2022 Apr 1;20(4):542-555. doi: 10.1158/1541-7786.MCR-21-0275.PMID: 35022314
March 2022
  • Dr. John Koomen co-chaired the American Lung Association Review session for Lung Cancer Discovery Award grants with Sameek Roychowdhury, MD/PhD, from Ohio State University/James Cancer Center.
  • A research team led by Dr. Smalley (Molecular Medicine), including Dr. Koomen and Dr. Karreth in Molecular Oncology collaborated to examine rare acral melanoma tumors. Single cell characterization of the cellular landscape of acral melanoma identifies novel targets for immunotherapy. 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.  Clin Cancer Res. 2022 Mar 4:clincanres.3145.2021. doi: 10.1158/1078-0432.CCR-21-3145. Online ahead of print.PMID: 35247927
  • Dr. John Koomen and Min Liu helped provide metabolomics analyses to support a collaboration with Dr. Cleveland (Cancer Biology & Evolution). Disrupting the MYC-TFEB Circuit Impairs Amino Acid Homeostasis and Provokes Metabolic Anergy. 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.  Cancer Res. 2022 Apr 1;82(7):1234-1250. doi: 10.1158/0008-5472.CAN-21-1168.PMID: 35149590 Free PMC article.
  • New trainee: Virginia Minniti from the University of Pisa, Italy, joins that Karreth lab for her Master’s thesis.

  • Graduation: Ilah Bok, PhD student in the Karreth lab, successfully defended her thesis. She will move to Washington University in St. Louis for a postdoc.

February 2022
  • Dr. John Koomen and Lancia Darville developed estrogen assays with liquid chromatography-high resolution mass spectrometry to help Dr. Egan (Cancer Epidemiology) assess their relevance to breast cancer risk. Associations of established breast cancer risk factors with urinary estrogens in postmenopausal women. Yaghjyan L, Darville LNF, Cline J, Martinez YC, Rich S, Austin-Datta RJ, Koomen JM, Tworoger SS, Egan KM.  Cancer Causes Control. 2022 Feb;33(2):279-291. doi: 10.1007/s10552-021-01528-9. Epub 2022 Jan 6.PMID: 34988766
  • Dr. John Koomen and Bin Fang provided support for proteomics to help Dr. Rix’s lab (Molecular Medicine) understand the target profiles of Talazoparib, which is used for breast cancer treatment. The non-canonical target PARP16 contributes to polypharmacology of the PARP inhibitor talazoparib and its synergy with WEE1 inhibitors. 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.  Cell Chem Biol. 2022 Feb 17;29(2):202-214.e7. doi: 10.1016/j.chembiol.2021.07.008. Epub 2021 Jul 29.PMID: 34329582
  • New trainee: After finishing her rotations, Nicol Mecozzi joins the Karreht lab as a PhD student

  • New publication: Nicol Mecozzi publishes the results of her Master’s thesis in the Karreth lab in RNA Biology in a paper titled Genetic tools for the stable overexpression of circular RNAs.

January 2022

New trainee: Manon Chadourne, PhD joins the Karreth lab as a postdoctoral fellow.

December 2021

  • Congratulations to the Winners of the Molecular Oncology Research in Progress series for Outstanding Presentations (July-December 2021):

Junior Trainee Awards:

  • 1st Place, Daniel Lester (Lau lab)
  • 2nd Place, Nicol Mecozzi (Karreth lab)
  • 3rd Place Tie, Tie Tracess Smalley, PhD (Binning lab) & Kaizhen Wang (Karreth lab)
Daniel Lester Nicol Mecozzi Tracess Smalley Kaizhe Wang
Daniel Lester, 1st Place Junior Trainee Nicol Mecozzi, 2nd Place Junior Trainee From left, Tracess Smalley, PhD, and Kaizhen Wang, 3rd Place Junior Trainee

Senior Trainee Awards:

  • 1st Place, Marco Napoli, PhD (Flores lab)
  • 2nd Place, Laura Torrente, PhD (DeNicola lab)
  • 3rd Place, John Lockhart, PhD (Flores lab)
Marco Napoli Laura Torrente John Lockhart
Marco Napoli, PhD, 1st Place Senior Trainee Laura Torrente, PhD, 2nd Place Senior Trainee John Lockhart, PhD, 3rd Place Senior Trainee
  • New Grant Award: Doug Cress, PhD received notification of an R21 award from NCI to support the project “Molecular Drivers of Lung Cancer in Hispanics” as contact MPI.
  • New Grant Award: Florian Karreth, PhD received a notice of award from the NIH for an R21 grant on assessing the role of oncogenic circRNAs in melanoma development.
  • New Trainee:  Nicol Mecozzi, PhD student in the Cancer Biology program, starts her rotation in the Karreth lab.
  • New Patent: Mark G. Alexandrow, PhD is named inventor for a Provisional Patent submission covering new chemical composition of CMG helicase inhibitor-degrader compounds (CMGidTM).

November 2021

  • New Publication: Postdoctoral fellow Xiaonan Xu, PhD, from the Karreth lab posted a preprint on bioRxiv titledChromosome 1q amplification perturbs a ceRNA network to promote melanoma metastasis.

October 2021

  • New Grant Award: Doug Cress, PhD received notification of award from M2GEN to support the project “Analysis of genetic ancestry across the ORIEN Network” as co-Investigator.
  • New Grant Award: Florian Karreth, PhD was awarded a Research Scholar Grant from the American Cancer Society to explore the role of MAFG in melanoma.
  • New Trainee: Nicole Wang and Sabrina Chowdhury, USF Master students in Medical Sciences, join the Karreth lab as volunteers.
  • New Patent: Mark G. Alexandrow, PhD is named inventor for a final PCT Patent submission #10110-266WO1. Patent covers new CMG helicase and HPV helicase inhibitors.
  • Jennifer Binning, PhD was appointed as Co-Director of the Moffitt Chemical Biology Core.

September 2021

  • New Grant Award: Tracess Smalley, PhD, a Postdoctoral Fellow in the Binning Lab, received an AIDS Malignancy Consortium Scholar Award.
  • New Publication:
  • New Trainee: Nick Spinosa, PhD student in the Cancer Biology program, starts his rotation in the Karreth lab.
  • New Trainee: Ben Posorske joins the Karreth lab as a Research Associate II.
Qian Liu, First Place Junior Trainee
Qian Liu, first place Junior Trainee
Olga Vera Puente, PhD (left) 2nd Place; Ilah Bok (right) 3rd Place Junior Trainees
From left, Olga Vera Puente, PhD, second place, and Ilah Bok, third place Junior Trainees
Hayley Ackerman, PhD 2nd Place Senior Trainee
Hayley Ackerman, PhD, second place Senior Trainee

August 2021

  • Winners of the Molecular Oncology Research in Progress series for Outstanding Presentations (January-June 2021) were announced:

    Junior Trainees:

    • 1st Place, Qian Liu (Lau lab)
    • 2nd Place, Olga Vera Puente, PhD (Karreth lab)
    • 3rd Place, Ilah Bok (Karreth lab)

    Senior Trainees:

    • 1st Place, Junhao Lu, PhD (Chen lab)
    • 2nd Place, Hayley Ackerman, PhD (Flores lab)
    • 3rd Place, Yun Pyo Kang, PhD (DeNicola lab)
  • New Grant Award: Florian Karreth, PhD received a notice of award from the NIH for an R21 grant on exploring miR-29 in melanoma progression and prevention.
  • Ana P. Gomes, PhD was named a Forbeck Scholar by the William Guy Forbeck Research Foundation.
  • New Publication: Tumor-infiltrating lymphocyte treatment for anti-PD-1-resistant metastatic lung cancer: a phase 1 trial. 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. Nat Med. 2021 Aug;27(8):1410-1418. doi: 10.1038/s41591-021-01462-y. Epub 2021 Aug 12. PMID: 34385708
  • New Publication: PLoS Genetics Research Article featuring Mol Onc trainees Aziz Aiderus, Justin Y. Newberg, Ana Contreras-Sandoval, and Amanda Meshey and Mol Onc faculty Karen M. Mann and Michael B. Mann: Transposon mutagenesis identifies cooperating genetic drivers during keratinocyte transformation and cutaneous squamous cell carcinoma progression. Aiderus, Newberg JY, Guzman-Rojas L, Contreras-Sandoval AM, Meshey AL, et al., 2021, PLOS Genetics 17(8): e1009094. https://doi.org/10.1371/journal.pgen.1009094
  • New Trainee: Jheng-Yu Wu, PhD (Johnny) joins the Alexandrow Lab as a Postdoctoral Fellow
  • New Trainee: Yifeng Gao, PhD joins the Flores Lab as a Postdoctoral Fellow.

July 2021

  • New Grant Award: Florian Karreth, PhD received a notice of award from the Florida Department of Health for a Bankhead Coley grant to study non-canonical tumor suppressor functions of PTEN in melanoma.
  • New Publication: Xiaonan Xu, PhD, Postdoctoral Fellow in the Karreth lab published a methods chapter titled "Pseudogenes as Competitive Endogenous RNAs: Testing miRNA Dependency" in Methods in Molecular Biology. PMID: 34165713
  • New Publication: Ilah Bok, Graduate Student in the Karreth lab published a methods chapter titled "Strategies to Study the Function of Pseudogenes in Mouse Models of Cancer" in Methods in Molecular Biology. PMID: 34165722
  • New Publication: Florian Karreth, PhD, published a methods chapter titled "Pseudogenes as Competitive Endogenous RNAs: Target Prediction and Validation" in Methods in Molecular Biology. PMID: 34165712
  • New Publication: Nicol Mecozzi, Research Associate in the Karreth lab published a review article titled "Squaring the circle: circRNAs in melanoma" in Oncogene. PMID: 34331015New Publication: The non-canonical target PARP16 contributes to polypharmacology of the PARP inhibitor talazoparib and its synergy with WEE1 inhibitors. 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.  Cell Chem Biol. 2021 Jul 22:S2451-9456(21)00348-2. doi: 10.1016/j.chembiol.2021.07.008. Online ahead of print. PMID: 34329582
  • New Publication: Macrophage-derived cholesterol contributes to therapeutic resistance in prostate cancer.  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. Cancer Res. 2021 Jul 23:canres.4028.2020. doi: 10.1158/0008-5472.CAN-20-4028. Online ahead of print. PMID: 34301759
  • New Publication: A Mutational Survey of Acral Nevi.  Smalley KSM, Teer JK, Chen YA, Wu JY, Yao J, Koomen JM, Chen WS, Rodriguez-Waitkus P, Karreth FA, Messina JL.  JAMA Dermatol. 2021 Jul 1;157(7):831-835. doi: 10.1001/jamadermatol.2021.0793.  PMID: 33978681
  • New Publication:  Global Phosphoproteomics Reveal CDK Suppression as a Vulnerability to KRas Addiction in Pancreatic Cancer. Kazi A, Chen L, Xiang S, Vangipurapu R, Yang H, Beato F, Fang B, Williams TM, Husain K, Underwood P, Fleming JB, Malafa M, Welsh EA, Koomen J, Trevino J, Sebti SM.  Clin Cancer Res. 2021 Jul 15;27(14):4012-4024. doi: 10.1158/1078-0432.CCR-20-4781. Epub 2021 Apr 20. PMID: 33879459
  • New Trainee: S. Hossein Kashfi, PhD joins the Gomes Lab as a postdoctoral fellow.

June 2021

  • New Grant Award: Mark G. Alexandrow, PhD received a notice of award from the NIH for an R01 grant to study the roles of Rb and Myc in directly controlling enzymatic activity of the replicative CMG helicase. Damon Reed, MD, is a collaborator on the project.
  • Jennifer Binning, PhD, received a notice of award from the NIH for an R35 MIRA grant to study the molecular details governing deglycation and protein repair.
  • New Grant Award: Ana P. Gomes, PhD, received an Innovation Award from the American Lung Association to study age-related mechanisms of drug resistance in non-small cell lung cancer.
  • New Grant Award: Ana P. Gomes, PhD, received a Scientific Research Grant from the Florida Breast Cancer Foundation to evaluate NAD+ Kinase’s role in metastatic triple negative breast cancer.
  • New Grant Award: Ana P. Gomes, PhD, in collaboration with Gina DeNicola, PhD and Stephen Gardell, PhD (Advent Health) received a Bankhead-Coley Cancer Research Award from the State of Florida to study the role of aging and pyridine nucleotides in non-small cell lung cancers.
  • New Publication: 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;16(6):e0252927. Epub 2021/06/18. doi: 10.1371/journal.pone.0252927. PubMed PMID: 34138895.
  • New Publication: Ana P. Gomes, PhD, co-lead a study describing how NAD+ kinase is regulated by oncogenic KRAS to sustain de novo NADP+ production in pancreatic ductal adenocarcinoma. “NADK is activated by oncogenic signaling to sustain pancreatic ductal adenocarcinoma”. Cell Rep. 2021 Jun 15;35(11):109238. PMID: 34133937
  • New Trainee: Stanislav Drapela, PhD joins the Gomes Lab as a postdoctoral fellow.

May 2021

  • New Grant Award: Florian Karreth, PhD received a notice of award from the NIH for an R01 grant focused on chromosome 1q ceRNAs in melanoma progression and metastasis.
  • New Publication: Florian Karreth, PhD, co-authored a study lead by Keiran Smalley, PhD and Jane Messina, MD describing mutations found in acral nevi. "A Mutational Survey of Acral Nevi”. JAMA Dermatol. 2021 May 12. PMID: 33978681
  • Nicol Mecozzi, Research Associate in the Karreth lab submitted a preprint to bioRxiv titled "Genetic Tools for the Stable Overexpression of Circular RNAs." doi: https://doi.org/10.1101/2021.05.27.446018
  • Ana P. Gomes, PhD, presented at the 2020 AACR Annual Meeting at the Educational Session: Understanding Mechanisms of Aging in Cancer Development in Human Populations.
  • New Trainee: Devesh Raizada, a graduate student in the Moffitt-USF Cancer Biology Ph.D. Program, selects Ana P. Gomes, PhD, as his major professor and joins the Gomes Lab.

April 2021

  • New Publication: Olga Vera, PhD, Postdoctoral Fellow in the Karreth lab published an article titled "A MAPK/miR-29 Axis Suppresses Melanoma by Targeting MAFG and MYBL2." Cancers. 2021 Mar 19. PMID: 33808771
  • Ana P. Gomes, PhD, was selected as a Rising Star of Cancer Metabolism and Signaling by the New York Academy of Sciences.
  • New Trainee: Joanne Tejero, a graduate student in the USF Molecular Medicine Ph.D. Program, selects Ana P. Gomes, PhD, as her major professor and joins the Gomes Lab.

Joseph Kissil, Vice-Chair