Garima Pandey (Reuther lab) was awarded an American Society of Hematology (ASH) Abstract Achievement Award for her presentation of her work at the ASH Annual Meeting in New Orleans.
Dr. Koomen has a Poster Presentation at the Association for Molecular Pathology Conference (amp22.amp.org): Converting Targeted Proteomics into Molecular Classification for Non Small Cell Lung Cancers (TT053) Authors: John Koomen, PhD, Sudhir Putty Reddy, PhD, Aileen Alontaga, PhD, Paul Stewart, PhD, Gina Nazario, MS, Eric Welsh, PhD, Lamees Saeed, MD, Lancia Darville-Bowleg, PhD, Bin Fang, PhD, Steven Eschrich, PhD, Eric Haura, MD, Theresa Boyle, MD/PhD.
Drs. Uwe Rix and Elsa Flores (MPIs) were among recipients of the 2022 Miles for Moffitt Award for their project "Targeting the POU2F3 transcription factor in small cell lung cancer." (Lung Cancer Center of Excellence and DeBartolo Family Personalized Medicine Institute 2022).
TCR-Independent Metabolic Reprogramming Precedes Lymphoma-Driven Changes in T-cell Fate. 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. Cancer Immunol Res. 2022 Oct 4; 10(10):1263-1279. doi: 10.1158/2326-6066.CIR-21-0813. PMID: 35969234
Inhibition of Epidermal Growth Factor Receptor Signaling by Antisense Oligonucleotides as a Novel Approach to Epidermal Growth Factor Receptor Inhibition. Madanayake TW, Welsh EA, Darville LNF, Koomen JM, Chalfant CE, Haura EB, Robinson TJ. Nucleic Acid Ther. 2022 Oct; 32(5):391-400. doi: 10.1089/nat.2021.0101. Epub 2022 Jul 20. PMID: 358617181.
Integrated proteomics identifies PARP inhibitor-induced pro-survival signaling changes as potential vulnerabilities in ovarian cancer. Deng O, Dash S, Nepomuceno TC, Fang B, Yun SY, Welsh EA, Lawrence HR, Marchion D, Koomen JM, Monteiro AN, Rix U. J Biol Chem. 2022 Sep 29: 102550. doi: 10.1016/j.jbc.2022.102550. Online ahead of print. PMID: 36183837
Dr. Koomen co-chaired the NCI IMAT Biospecimen Science grant review meeting.
IGF-binding proteins secreted by cancer-associated fibroblasts induce context-dependent drug sensitization of lung cancer cells. 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. Sci Signal. 2022 Aug 16; 15(747):eabj5879. doi:10.1126/scisignal.abj5879. Epub 2022 Aug 16. PMID: 35973030
Alex Klug, an undergraduate at the University of Florida working in the Koomen lab as a summer intern, presented his research using mass spectrometry and solvent accessibility probes to examine NTRK protein structure as part of the Summer Program to Advance Research Knowledge (SPARK) Program. This project is in collaboration with Emiliano Cocco, PhD (University of Miami).
Dr. Lixin Wan recruited the following new members to his lab: Michael Grant, Research Associate I, Md Wahiduzzaman, Postdoc Fellow, and Yifeng Gao, Postdoc Fellow.
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).
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. 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)
- 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
- 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.
- 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.
New trainee: Manon Chadourne, PhD joins the Karreth lab as a postdoctoral fellow.