T32 Publications

Recent publications from the Integrated Program in Cancer and Data Science T32 include:

Alhaddad H, Wong W, Abou-Gharbia M, Childers W, Melenski E, Bell RL, Sari Y. Effects of a Novel Beta Lactam Compound, MC-100093, on the Expression of Glutamate Transporters/Receptors and Ethanol Drinking Behavior of Alcohol-Preferring Rats. J Pharmacol Exp Ther. 2022;383(3):208-16. Epub 20220924. doi: 10.1124/jpet.122.001147. PubMed PMID: 36153003; PMCID: PMC9667983.

Anderson CB, Ospina O, Beerli P, Lemmon AR, Banker SE, Hassinger AB, Dye M, Kortyna ML, Lemmon EM. The population genetics of speciation by cascade reinforcement. Ecol Evol. 2023;13(2):e9773. Epub 20230207. doi: 10.1002/ece3.9773. PubMed PMID: 36789346; PMCID: PMC9905665.

Creed JH, Wilson CM, Soupir AC, Colin-Leitzinger CM, Kimmel GJ, Ospina OE, Chakiryan NH, Markowitz J, Peres LC, Coghill A, Fridley BL. spatialTIME and iTIME: R package and Shiny application for visualization and analysis of immunofluorescence data. Bioinformatics. 2021;37(23):4584-6. doi: 10.1093/bioinformatics/btab757. PubMed PMID: 34734969; PMCID: PMC8652029.

Davis JT, Obermayer AN, Soupir AC, Hesterberg RS, Duong T, Yang CY, Dao KP, Manley BJ, Grass GD, Avram D, Rodriguez PC, Fridley BL, Yu X, Teng M, Wang X, Shaw TI. BatchFLEX: feature-level equalization of X-batch. Bioinformatics. 2024;40(10). doi: 10.1093/bioinformatics/btae587. PubMed PMID: 39360977; PMCID: PMC11486499.

Hesterberg RS, Beatty MS, Han Y, Fernandez MR, Akuffo AA, Goodheart WE, Yang C, Chang S, Colin CM, Alontaga AY, McDaniel JM, Mailloux AW, Billington JMR, Yue L, Russell S, Gillies RJ, Yun SY, Ayaz M, Lawrence NJ, Lawrence HR, Yu XZ, Fu J, Darville LN, Koomen JM, Ren X, Messina J, Jiang K, Garrett TJ, Rajadhyaksha AM, Cleveland JL, Epling-Burnette PK. Cereblon harnesses Myc-dependent bioenergetics and activity of CD8+ T lymphocytes. Blood. 2020;136(7):857-70. doi: 10.1182/blood.2019003257. PubMed PMID: 32403132; PMCID: PMC7426646.

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;10(10):1263-79. doi: 10.1158/2326-6066.CIR-21-0813. PubMed PMID: 35969234; PMCID: PMC9662872.

Lee K, Lockhart JH, Xie M, Chaudhary R, Slebos RJC, Flores ER, Chung CH, Tan AC. Deep Learning of Histopathology Images at the Single Cell Level. Front Artif Intell. 2021;4:754641. Epub 20210910. doi: 10.3389/frai.2021.754641. PubMed PMID: 34568816; PMCID: PMC8461055.

Lockhart JH, Ackerman HD, Lee K, Abdalah M, Davis AJ, Hackel N, Boyle TA, Saller J, Keske A, Hanggi 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;7(1):68. Epub 20230718. doi: 10.1038/s41698-023-00419-3. PubMed PMID: 37464050; PMCID: PMC10354042.

Moshensky A, Brand CS, Alhaddad H, Shin J, Masso-Silva JA, Advani I, Gunge D, Sharma A, Mehta S, Jahan A, Nilaad S, Olay J, Gu W, Simonson T, Almarghalani D, Pham J, Perera S, Park K, Al-Kolla R, Moon H, Das S, Byun MK, Shah Z, Sari Y, Heller Brown J, Crotty Alexander LE. Effects of mango and mint pod-based e-cigarette aerosol inhalation on inflammatory states of the brain, lung, heart, and colon in mice. Elife. 2022;11. Epub 20220412. doi: 10.7554/eLife.67621. PubMed PMID: 35411847; PMCID: PMC9005188.

Nagy MZ, Plaza-Rojas LB, Boucher JC, Kostenko E, Austin AL, Tarhini AA, Chen Z, Du D, Ojwang AME, Davis J, Obermayer A, Rejniak KA, Shaw TI, Guevara-Patino JA. Effector T cells under hypoxia have an altered transcriptome similar to tumor-stressed T cells found in non-responsive melanoma patients. J Immunother Cancer. 2025;13(2). Epub 20250225. doi: 10.1136/jitc-2024-010153. PubMed PMID: 40010774; PMCID: PMC12086921.

Napoli M, Wu SJ, Gore BL, Abbas HA, Lee K, Checker R, Dhar S, Rajapakshe K, Tan AC, Lee MG, Coarfa C, Flores ER. DeltaNp63 regulates a common landscape of enhancer associated genes in non-small cell lung cancer. Nat Commun. 2022;13(1):614. Epub 20220201. doi: 10.1038/s41467-022-28202-1. PubMed PMID: 35105868; PMCID: PMC8807845.

Narvaez-Bandera I, Lui A, Mekonnen YA, Rubio V, 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. bioRxiv. 2025. Epub 20250514. doi: 10.1101/2024.11.12.623208. PubMed PMID: 39605665; PMCID: PMC11601443.

Obermayer A, Davis J, Talada DP, Teng M, Eschrich S, Yin V, Spakowicz D, Dhrubo D, Rounbehler RJ, Churchman ML, Tarhini AA, Wang X, Gupta S, Markowitz J, Goecks J, Li R, Rodriguez-Pessoa R, Manley BJ, Tan AC, Grass GD, Chen DT, Shaw TI. ShinyEvents: harmonizing longitudinal data for real world survival estimation. Res Sq. 2025. Epub 20250806. doi: 10.21203/rs.3.rs-7231850/v1. PubMed PMID: 40799741; PMCID: PMC12340904.

Ospina OE, Wilson CM, Soupir AC, Berglund A, Smalley I, Tsai KY, Fridley BL. spatialGE: quantification and visualization of the tumor microenvironment heterogeneity using spatial transcriptomics. Bioinformatics. 2022;38(9):2645-7. doi: 10.1093/bioinformatics/btac145. PubMed PMID: 35258565; PMCID: PMC9890305.

Patel RS, Lui A, Hudson C, Moss L, Sparks RP, Hill SE, Shi Y, Cai J, Blair LJ, Bickford PC, Patel NA. Small molecule targeting long noncoding RNA GAS5 administered intranasally improves neuronal insulin signaling and decreases neuroinflammation in an aged mouse model. Sci Rep. 2023;13(1):317. Epub 20230106. doi: 10.1038/s41598-022-27126-6. PubMed PMID: 36609440; PMCID: PMC9822944.

Reinstein ZZ, Zhang Y, Ospina OE, Nichols MD, Chu VA, Pulido AM, Prieto K, Nguyen JV, Yin R, Moran Segura C, Usman A, Sell B, Ng S, de la Iglesia JV, Chandra S, Sosman JA, Cho RJ, Cheng JB, Ivanova E, Koralov SB, Slebos RJC, Chung CH, Khushalani NI, Messina JL, Sarnaik AA, Zager JS, Sondak VK, Vaske C, Kim S, Brohl AS, Mi X, Pierce BG, Wang X, Fridley BL, Tsai KY, Choi J. Preexisting Skin-Resident CD8 and gammadelta T-cell Circuits Mediate Immune Response in Merkel Cell Carcinoma and Predict Immunotherapy Efficacy. Cancer Discov. 2024;14(9):1631-52. doi: 10.1158/2159-8290.CD-23-0798. PubMed PMID: 39058036; PMCID: PMC11954000.

Rollison DE, Messina JL, Cherpelis BS, Fenske NA, Schell MJ, Adeegbe DO, Zhao Y, Amorrortu RP, Akuffo AA, Hesterberg RS, Epling-Burnette PK. Circulating Immunosuppressive Regulatory T Cells Predict Risk of Incident Cutaneous Squamous Cell Carcinoma. Front Med (Lausanne). 2021;8:735585. Epub 20211102. doi: 10.3389/fmed.2021.735585. PubMed PMID: 34796183; PMCID: PMC8593034.

Tejero JD, Hesterberg RS, Drapela S, Ilter D, Raizada D, Lazure F, Kashfi H, Liu M, Silvane L, Avram D, Fernandez-Garcia J, Asara JM, Fendt SM, Cleveland JL, Gomes AP. Methylmalonic acid induces metabolic abnormalities and exhaustion in CD8(+) T cells to suppress anti-tumor immunity. Oncogene. 2025;44(2):105-14. Epub 20241029. doi: 10.1038/s41388-024-03191-1. PubMed PMID: 39472497.

Wilson CM, Ospina OE, Townsend MK, Nguyen J, Moran Segura C, Schildkraut JM, Tworoger SS, Peres LC, Fridley BL. Challenges and Opportunities in the Statistical Analysis of Multiplex Immunofluorescence Data. Cancers (Basel). 2021;13(12). Epub 20210617. doi: 10.3390/cancers13123031. PubMed PMID: 34204319; PMCID: PMC8233801.

Xie M, Chaudhary R, Slebos RJC, Lee K, Song F, Poole MI, Hoening DS, Noel LC, Hernandez-Prera JC, Conejo-Garcia JR, Chung CH, Tan AC. Immune landscape in molecular subtypes of human papillomavirus-negative head and neck cancer. Mol Carcinog. 2024;63(1):120-35. Epub 20230926. doi: 10.1002/mc.23640. PubMed PMID: 37750589; PMCID: PMC10841270.

Xie M, Lee K, Lockhart JH, Cukras SD, Carvajal R, Beg AA, Flores ER, Teng M, Chung CH, Tan AC. TIMEx: tumor-immune microenvironment deconvolution web-portal for bulk transcriptomics using pan-cancer scRNA-seq signatures. Bioinformatics. 2021;37(20):3681-3. doi: 10.1093/bioinformatics/btab244. PubMed PMID: 33901274; PMCID: PMC11025676.