Student Publications

CCB Students produce substantial bodies of work that lead to high quality, peer-reviewed publications.  The menus below highlight papers our students have published in recent years.  To access each publication, click on the PMID, to be redirected to PubMed, allowing you access to the abstract, as well as providing options to read the publication.


Rosenberg, J, Cao, G, Borja-Prieto, F, Huang, J.  (2020). Lattice Light-Sheet Microscopy Multi-Dimensional Analyses (LaMDA) of T-Cell Receptor Dynamics Predict T-Cell Signaling States. Cell Systems, 433-444. PMID: 32437685

Applebaum MA, Barr EK, Karpus J, West-Szymanski DC, Olivia M, Sokol EA, Zhang S, Zhang Z, Zhang W, Chlenski A, Salwen HR, Wilkinson E. (2020). 5-Hydroxymethylcytosine Profiles in Circulating Cell-Free DNA Associate with Disease Burden in Children with Neuroblastoma. Clin Cancer Res. 2020 Mar 15; 26(6): 1309-1317. PMID: 31852832

Rosenberg, J.Huang J. Visualizing Surface T-Cell Receptor Dynamics Four-Dimensionally Using Lattice Light-Sheet Microscopy. JoVE. 2020 Jan 30;(155). PMID: 32065118

Cao JZ, Liu H, Wickrema A, Godley LA. HIF-1 Directly induces TET3 Expression To Enhance 5-hmC Density And Induce Erythroid Gene Expression In Hypoxia. Blood Advances. 2020 Jul 14;4(13):3053-3062. PMID: 32634239

Qiu Z, Lin AP, Jiang S, Elkashef SM, Myers J, Srikantan S, Sasi B, Cao JZ, Godley LA, Rakheja D, Lyu Y, Zheng S, Madesh M, Shiio Y, Dahia PLM, Aguiar RCT. MYC Regulation of D2HGDH and L2HGDH Influences the Epigenome and Epitranscriptome. Cell Chem Biol. 2020 May 21;27(5):538-550.e7. PMID: 32101699.

Betori RC, Liu Y, Mishra RK, Cohen SB, Kron SJ, Scheidt KA. Targeted Covalent Inhibition of Telomerase. ACS Chem Biol. 2020 Mar 20; 15(3): 706-707. PMID: 32017522

Brinkman JA, Liu Y, Kron SJ. Small-Molecule Drug Repurposing To Target DNA Damage Repair and Response Pathways. Semin Cancer Biol. 2020 Feb 27; 30046-8. PMID: 32113999





Tiwari P, radlank A, Cui C, hochoenfelt KQ, Zhou G, Xu Y, Khramtsova G, Olopade F, Shah AM, Khan SA, Rosner MRBecker L. Metabolically activated mammary adipose tissue macrophages link obesity to triple-negative breast cancer. J. Exp. Med. 2019 Jun 3; 216(6): 1345-1358. PMID: 31053611

Di Z, Tang Z, Huang H, Zhou G, Cui C, Weng Y, Liu W, Kim S, Lee S, Perez-Neut M, Czyz D, Hu R, Ye Z, He M, Zheng GY, Shuman H, Ding J, Dai L, Ren B, Roeder RG, Becker L, Zhao, Y. Metabolic regulation of gene expression by histone lactylation. Nature. 2019 Oct; 574(7779): 575-580. PMID: 31645732

Trendowski MR,  El Charif O,  Ratain MJ, Monahan P, Mu Z, Wheeler HE, Dinh Jr PC, Feldman DR,  Ardeshir-Rouhani-Fard S, Hamilton RJ, Vaughn DJ, Fung C, Kollmannsberger C, Mushiroda T, Kubo M, Hannigan R, Strathmann F, Einhorn LH, Fossa SD, Travis LB, Dolan ME. Clinical and Genome-Wide Analysis of Serum Platinum Levels after Cisplatin-Based Chemotherapy. Clin Cancer Res. 2019 Oct 1; 25(19): 5913-5924. PMID: 31296530  

El Charif O, Mapes B, Trendowski MR, Wheeler HE, Wing C, Dinh Jr PC, Frisina RD, Feldman DR, Hamilton RJ, Vaughn DJ, Fung C, Kollmannsberger C, Mushiroda T, Michiaki Kubo M, Gamazon ER, Cox NJ, Huddart R, Ardeshir-Rouhani-Fard S, Monahan P, Fossa SD, Einhorn LH, Travis LB, Dolan ME. Clinical and genome-wide analysis of cisplatin-induced tinnitus implicates novel ototoxic mechanisms. Clin Cancer Res. 2019 Jul 1; 25(13): 4104-4116. PMID: 30952644

Trendowski MR, El Charif O, Dinh Jr. PC, Travis LB, and Dolan ME. Genetic and modifiable risk factors contributing to cisplatin-induced toxicities. Clin Cancer Res. 2019 Feb 15; 25(4): 1147-1155. PMID: 30305294

Chlenski A, Park C, Dobratic M, Salwen HR, Budke B, Hyun-Park J, Miller R, Applebaum MA, Wilkinson E, Nakamura Y,  Connell PP, Cohn SL. Maternal Embryonic Leucine Zipper Kinase (MELK), a Potential Therapeutic Target for Neuroblastoma. Mol Cancer Ther. 2019 Mar; 18(3): 507-516. PMID: 30674566

Yuan TL, Amzallag A, Bagni R, Yi M, Afghani S, Burgan W, Fer N, Garvey L, Powell K, Smith B, Waters A, Drubin D, Thomson T, Liao R, Lee CS, Fellmann C, Stephens R, Luo J, Lowe S, Benes CH, McCormick F. Differential Effector Engagement by Oncogenic KRAS. Cell Reports. 2019 Feb 13; 22(7): 1889-1902. PMID: 29444439

Sulahian R, Kwon JJ, Walsh KH, Pailler E, Bosse TL, Thaker M, Almanza D, Dempster JM, Pan J, Piccioni F, Dumont N, Gonzalez A, Rennhack J, Nabet B, Bchman JA, Goodale A, Lee Y, Bagul M, Liao R, Navarro A, Yuan TL, Ng R, Raghavan S, Gray NS, Tsherniak A, Vazquez F, Root D, Firestone AJ, Settleman J, Hahn W, Aguirre AJ. Synthetic Lethal Interaction of SHOC2 Depletion with MEK Inhibition in RAS-Driven Cancers. Cell Reports 29.1. 2019 Oct 1;29(1): 118-134. PMID: 31577942

Jeong JJ, Gu X, Nie J, Sundaravel S, Liu H, Kuo WL, Bhagat TD, Pradhan K, Cao J, Nischal S, McGraw KL, Bhattacharyya S, Bishop MR, Artz A, Thirman MJ, Moliterno A, Ji P, Levine RL, Godley LA, Steidl U, Bieker J, List AF, Sauntharajah Y, He C, Verma A, and Wickrema A. Cytokine regulated phosphorylation and activation of TET2 by JAK2 in hematopoiesis. Cancer Discov. 2019 Jun; 9(6): 778-795. PMID: 30944118

Moshfegh CM, Collins CW, Gunda V, Vasanthakumar A, Cao JZ, Singh PK, Godley LA, and Case AJ. Mitochondrial superoxide disrupts the metabolic and epigenetic landscape of CD4+ and CD8+ T-lymphocytes. Redox Biol. 2019 Oct; 27:101141. PMID: 30819616

Ludwig L. M, Maxcy K, LaBelle J. Flow Cytometry-Based Detection and Analysis of BCL-2 Family Proteins and Mitochondrial Outer Membrane Permeabilization (MOMP). Methods Mol Biol. 2019; 1877:77-91. PMID: 30535999

Fessler J, Matson V, Gajewski TF. Exploring The Emerging Role of the Microbiome in Cancer Immunotherapy.  J Immunother Cancer. 2019 Apr 17; 7(1):108. PMID: 30995949

Edimova EV, Appelbe OK, Ricco N, Lee SSY, Liu Y, Wolfgeher DJ, Collins TN, Flor AC, Ramamurthy A, Warrington S, Bindokas VP, Kron SJ. O-GlcNAcylation Enhances Double-Strand Break Repair, Promotes Cancer Cell Proliferation, and Prevents Therapy-Induced Senescence in Irradiated Tumors. Mol Cancer Res. 2019 Jun; 17(6):1338-50. PMID: 30885991.

Liu Y, Efimova EV, Ramamurthy A, Kron SJ. Redependent Functions of DNA-PKcs Protect Irradiated Cells From Mitotic Slippage and Accelerated Senescence. J Cell Sci. 2019 Jun 1; 132(13). PMID: 31189537.

Smith AG, Macleod KF. Autophagy, Cancer Stem Cells and Drug Resistance. J Pathol. 2019 Apr; 247(5); 708-18. PMID: 30570140.

Godfrey J, Tumuluru S, Bao R, Leukam M, Venkataraman G, Phillip J, Fitzpatrick C, McElherne J, MacNabb BW, Orlowski R, Smith SM, Kline J. PD-L1 Gene Alterations Identify A Subset of Diffuse Large B-Cell Lymphoma Harboring a T-Cell Inflamed Phenotype. Blood. 2019 May 23. 133(21); 2279- 90. PMID: 30910787.

Thekkan S, Jani M, Cui C, Dan K, Zhou G, Becker L, Krishnan Y. A DNA-based fluorescent reporter maps HOCl production in the maturing phagosome. Nat. Chem. Bio. 2019 Dec; 15(12):1165-72. PMID: 30531966


Reardon, CA, Lingaraju A, Schoenfelt KQ, Zhou G, Cui C, Babenko I, Becker L. Obesity and Insulin Resistance Promote Atherosclerosis Through An IFNgamma-regulated Macrophage Protein Network. Cell Report. 2018 Jun 5; 23(10): 3021-3030. PMID: 29874587

Rosenberg JHuang J. CD8+ T Cells and NK Cells: Parallel and Complementary Soldiers of Immunotherapy. Current Opinion in Chemical Engineering. 2018 Mar; 19: 9-20. PMID: 29623254

Gamazon ER, Trendowski MR, Wen Y, Wing C, Delaney SM, Huh W, Wong S, Cox NJ, Dolan ME. Gene and MicroRNA Perturbations of Cellular Response to Pemetrexed Implicate Biological Networks and Enable Imputation of Response in Lung Adenocarcinoma. Sci Rep. 2018 Jan 15; 8(1):733. PMID: 29335598

Kathayat, RS, Cao Y, Elvira PD, Sandoz PA, Zaballa ME, Springer MZ, Drake LE, Macleod KF, van der Goot FG, Dickinson BC. Active and dynamic mitochondrial S-depalmitoylation revealed by targeted fluorescent probes. Nat Commun 9. 2018 Jan 23; 9(1): 334. PMID: 29362370

Ling A, Gruener RF,  Fessler J, Huang R S. More than Fishing for a Cure: The Promises and Pitfalls of High Throughput Cancer Cell Line Screens. Pharmacol Ther. 2018 Nov; 191: 178-189. PMID: 29953899.

Emmanuel AO, Arnovitz S, Haghi L, Mathur PS, Mondal S, Quandt J, Okoreeh MK, Maienschein-Cline M, Khazaie K, Dose M, Gounari F. TCF-1 and HEB Cooperate To Establish The Epigenetic And Transcription Profiles of CD4+ CD8+ Thymocytes. Nat Immunol. 2018 Dec. 19(12);1366-78. PMID: 30420627.

West DC, Kocherginsky M, Tonsing-Carter EY, Dolcen DN, Hosfield DJ, Lastra RR, Sinnwell JP, Thompson KJ, Bowie KR, Varkless RV, Skor MN, Pierce CF, Style SC, Kim CR, de Wet L, Greene GL, Boughey JC, Goetz MP, Kalari KR, Wang K, Fleming GF, Györffy B, Conzen SD. Discovery of a Glucocorticoid Receptor (GR) Activity Signature Using Selective GR Antagonism in ER-Negative Breast Cancer. Clin Cancer Res. 2018 Jul 15. 24(14); 3433-46. PMID: 29636357.

Matson V, Fessler J, Bao R, Chongsuwat T, Za Y, Alegre M, Luke JJ, Gajewski TF. The Commensal Microbiome is Associated With PD-1 Efficacy in Metastatic Melanoma Patients. Science. 2018 Jan 5. 359(6371); 104-8. PMID: 29302014

Ling A, Gruener RF, Fessler JL, Huang RS. More Than Fishing For A Cure: The Promises and Pitfalls of High Throughput Cancer Cell Line Screens. Pharmacol Ther. 2018 Nov. 191; 178-89. PMID: 29953899.

Huang H, Zhang D, Wang Y, Perez-Neut M, Han Z, Zheng YG, Hao Q, Zhao Y. Lysine Benzoylation Is A Histone Mark Regulated By SIRT2. Nat Commun 2018 Aug 28. 9(1); 3374. PMID: 30154464.

Bhanvadia R, VanOpstall C, Brechka H, Barashi N, Gillard M, McAuley E, Paner G, Chan WC, DeMarzo A, Han M, Szmulewitz RZ, and Vander Griend DJ. MEIS1 and MEIS2 Expression and Prostate Cancer Progression: A Role for HOXB13 Binding Partners in Metastatic Disease. Clin Cancer Res. 2018 Aug 1; 24(15): 3668-3680. PMID: 29716922


Coats BR, Schoenfelt KQ, Barbosa-Lorenzi VC, Peris E, Cui C, Hoffman A, Zhou G, Becker L. Metabolically activated adipose tissue macrophages perform detrimental and beneficial functions during diet-induced obesity. Cell reports. 2017 Sept 26; 20(13): 3149-3161. PMID: 28954231

Guo A, Lu P, Lee J, Zhen C, Chiosis G, Wang YL. HSP90 stabilizes B-cell receptor kinases in a multi-client interactome: PU-H71 induces CLL apoptosis in a cytoprotective microenvironment. Oncogene. 2017 Jun15; 36(24): 3441-3449. PMID: 28114285

Wang WG, Liu ZB, Jiang XN, Lee J, Zhou XY, Li XQ. MYC Protein Dysregulation is Driven by BCR-PI3K Signaling in Diffuse Large B-cell Lymphoma. Histopathology. 2017 Nov; 71(5): 778-85. PMID: 28639315

Lee J, Lee P, Wu X. Molecular and cytoskeletal regulations in epidermal development. Semin Cell Dev Biol. 2017 Sept; 69:18-25. PMID: 28577925

Li Y, Zhang J, Yue J, Gou X, Wu X. Epidermal Stem Cells in Skin Wound Healing. Adv Wound Care (New Rochelle). 2017 Sept 1; 6(9): 297-307. PMID: 28894637

Yue J, Gou X, Li Y, Wicksteed B, Wu X. Engineered Epidermal Progenitor Cells Can Correct Diet-Induced Obesity and Diabetes. Cell Stem Cell. 2017 Aug 3; 21(2): 256-263.e4. PMID: 28777946

Lee P, Jiang S, Li Y, Yue J, Gou X, Chen SY, Zhao Y, Schober M, Tan M, Wu X. Phosphorylation of Pkp1 by RIPK4 regulates epidermal differentiation and skin tumorigenesis. EMBO J. 2017 Jul 3; 36(13): 1963-1980. PMID: 28507225

Bainer RO, Trendowski MR, Cheng C, Pei D, Yang W, Paugh SW, Goss KH, Skol AD, Pavlidis P, Pui C, Gilliam TC, Evans WE , Onel K. A p53-regulated apoptotic gene signature predicts treatment response and outcome in pediatric ALL. Cancer Manag Res: In Press. 2017 Sep 13; 9: 397-410. PMID: 28979163

Zhou, D, Zhou D, Springer MZ, Xu D, Liu D, Hudmon A, Macleod KF, Meroueh SO. Small molecules inhibit STAT3 activation, autophagy, and cancer cell anchorage-independent growth. Bioorg Med Chem 25. 2017 Jun 15; 25(12): 2995-3005. PMID: 28438385

Drake LE, Springer MZ, Poole LP, Kim CJ, Macleod, KF. Expanding perspectives on the significance of mitophagy in cancer. Semin Cancer Biol. 2017 Dec; 47: 110-124 PMID: 28450176

Kach J, Long TM, Selman P, Tonsing-Carter EY, Bacalao MA, Lastra RR, de Wet L, Comiskey S, Gillard M, VanOpstall C, West DC, Chan WC, Griend DV, Conzen SD, Szmulewitz RZ. Selective Glucocorticoid Receptor Modulators (SGRMs) Delay Castrate-Resistant Prostate Cancer Growth. Mol Cancer Ther. 2017 Aug; 16(8):1680-1692. PMID: 28428441

Looyenga B, Lanning N, VanOpstall C, Goodall M, and MacKeigan J. LRRK2 Deficiency Impairs trans-Golgi to Lysosome Trafficking and Endocytic Degradation in Human Renal Epithelial Cells. Am J Physiol Renal Physiol. 2017 Nov 1; 315(5): F1465-F1477. PMID: 30089035

Carron EC, Homra S, Rosenberg J, Coffelt SB, Kittrell F, Zhang Y, Creighton CJ, Fuqua S. A, Medina D, Machado H. L. Macrophages promote the progression of premalignant mammary lesions to invasive cancer. Oncotarget. 2017 Jan 31; 8(31): 50731-50746. PMID: 28881599 

Geeleher P, Zhang Z, Wang F, Gruener R, Nath A, Morrison G, Bhutra S, Grossman R, Huang RS. Discovering novel pharmacogenomic biomarkers by imputing drug response in cancer patients from large genomics studies. Genome Res. 2017 Oct; 27(10): 1743-1751 PMID: 28847918

Fessler JL, Gajewski TF. The Microbiota: A New Variable Impacting Cancer Treatment Outcomes. Clin Cancer Res. 2017 Jul 1. 23(13); 3229-31. PMID: 28446507.


Singhal H, Greene ME, Tarulli G, Zarnke AL, Bourgo RJ, Laine M, Chang YF, Ma S, Dembo AG, Raj GV, Hickey TE, Tilley WD, Greene GL. Genomic agonism and phenotypic antagonism between estrogen and progesterone receptors in breast cancer. Sci Adv. 2016 Jun 24; 2(6): e150924. PMID: 27386569

Sharma S, Galanina N, Guo A, Lee J, Kadri S, Van Slambrouck C, Long B, Wang W, Ming M, Furtado LV, Segal JP, Stock W, Venkataraman G, Tang WJ, Lu P, Wang YL. Identification of a structurally novel BTK mutation that drives ibrutinib resistance in CLL. Oncotarget. 68833-68841. 2016 Oct 18; 7(42): 68833- 68841. PMID: 27626698

Springer MZ, Macleod KF. In Brief: Mitophagy: mechanisms and role in human disease. The Journal of Pathology. 2016 Nov; 240(3): 253-255. PMID: 27453450

Looyenga B, VanOpstall C, Lee Z, Bell J, Lodge E, Wrobel K, Arnoys E, and Louters L. Determination of GLUT1 Oligomerization Parameters using Bioluminescent Forster Resonance Energy Transfer. Sci Rep. 2016 Jun 30; 6: 29130. PMID: 27357903

Laukka T, Mariana CJ, Ihantola T, Cao JZ, Hokkanen J, Kaelin WG, Godley LA, Koivunen P. Fumarate and Succinate Regulate Expression of Hypoxia-Inducible Genes via TET Enzymes. J Biol Chem. 2016 Feb 19. 291(8); 4256-65. PMID: 26703470.

Wananthakumar A, Arnovitz S, Marquez R, Lepore J, Rafidi G, Asom A, Weatherly M, Davis EM, Neistadt B, Duszynski R, Vardiman JW, Le Beau MM, Godley LA, Churpek JE. BRCA1 Deficiency Causes Bone Marrow Failure And Spontaneous Hematologic Malignancies In Mice. Blood. 2016 Jan 21. 127(3); 310-3. PMID: 26644450.