Selected Publications

Yang F, Zhang D, Jian H, Ye J, Zhang L, Bagley SJ, Winkler J, Gong Y, Fan Y. : Small-molecule toosendanin reverses macrophage-mediated immunosuppression to overcome glioblastoma resistance to immunotherapy. Science Translational Medicine 15(683), 2023.

Stephen Bagley, Shawn Kothari, Rifaquat Rahman, Eudocia Lee, Gavin Dunn, Evanthia Galanis, Susan Chang, Louis Nabors, Manmeet Ahluwalia, Roger Stupp, Minesh Mehta, David Reardon, Stuart Grossman, Erik Sulman, John Sampson, Simon Khagi, Michael Weller, Timothy Cloughesy, Patrick Wen, and Mustafa Khasraw: Glioblastoma Clinical Trials: A Summary of the Current Landscape and Opportunities for Improvement. Clinical Cancer Research 28(4): 594-602, Feb 2022 Notes: Accepted (In Press as of Sept 15, 2021).

Rifaquat Rahman; Steffen Ventz; Jon McDunn; Bill Louv; Irmarie Reyes-Rivera; Mei-Yin Polley; Stephen Bagley; Mustafa Khasraw; Timothy Cloughesy; Patrick Y. Wen; Brian Alexander; Lorenzo Trippa: Leveraging External Data in the Design and Analysis of Clinical Trials in Neuro-Oncology. Lancet Oncology 22(10): e456-e465, Oct 2021 Notes: Accepted (In Press as of August, 2021).

Kirit Singh, Kristen Batich, Patrick Wen, Aaron Tan, Stephen Bagley, Michael Lim, Michael Platten, Howard Colman, David Ashley, Susan Chang, Rifaquat Rahman, Evanthia Galanis, Alireza Mansouri, Vinay Puduvalli, David Reardon, Solmaz Sahebjam, John Sampson, John Simes, Donald Berry, Gelareh Zadeh, Timothy Cloughesy, Minesh Mehta, Steven Piantadosi, Michael Weller, Amy Heimberger, and Mustafa Khasraw: Designing Clinical Trials for Combination Immunotherapy; A framework for Glioblastoma. Clinical Cancer Research 28(4): 585-593. Feb 2022 Notes: Accepted (In Press as of Sept 15, 2021).

Fan Yang, Zhenqiang He, Hao Duan, Duo Zhang, Juehui Li, Huijuan Yang, Jay F Dorsey, Wei Zou, S Ali Nabavizadeh, Stephen J Bagley, Kalil Abdullah, Steven Brem, Lin Zhang, Xiaowei Xu, Katelyn T Byrne, Robert H Vonderheide, Yanqing Gong, Yi Fan: Synergistic immunotherapy of glioblastoma by dual targeting of IL-6 and CD40. Nature Communications 12(1): 3424, Jun 2021.

Reed-Guy L, Desai AS, Phillips RE, Croteau D, Albright K, O’Neill M, Brem S, O’Rourke DM, Amankulor NM, Bagley SJ: Risk of intracranial hemorrhage with direct oral anticoagulants versus low molecular weight heparin in glioblastoma: a retrospective cohort study. Neuro Oncol May 2022.

Nabavizadeh SA, Ware JB, Guiry S, Nasrallah MP, Mays JJ, Till JE, Hussain J, Abdalla A, Yee SS, Binder ZA, O'Rourke DM, Brem S, Desai AS, Wolf R, Carpenter EL, Bagley SJ: Imaging and Histopathologic Correlates of Plasma Cell-Free DNA Concentration and Circulating Tumor DNA in Adult Patients With Newly Diagnosed Glioblastoma. Neurooncol Adv 2(1): vdaa016, Jan 2020.

Bagley SJ, Nabavizadeh SA, Mays JJ, Till JE, Ware JB, Levy S, Sarchiapone W, Hussain J, Prior T, Guiry S, Christensen T, Yee SS, Nasrallah MP, Morrissette JJD, Binder ZA, O'Rourke DM, Cucchiara AJ, Brem S, Desai AS, Carpenter EL: Clinical Utility of Plasma Cell-Free DNA in Adult Patients With Newly Diagnosed Glioblastoma: A Pilot Prospective Study. Clin Cancer Res 26(2): 397-407, Jan 2020.

Binder Zev A, Thorne Amy Haseley, Bakas Spyridon, Wileyto E Paul, Bilello Michel, Akbari Hamed, Rathore Saima, Ha Sung Min, Zhang Logan, Ferguson Cole J, Dahiya Sonika, Bi Wenya Linda, Reardon David A, Idbaih Ahmed, Felsberg Joerg, Hentschel Bettina, Weller Michael, Bagley Stephen J, Morrissette Jennifer J D, Nasrallah MacLean P, Ma Jianhui, Zanca Ciro, Scott Andrew M, Orellana Laura, Davatzikos Christos, Furnari Frank B, O'Rourke Donald M: Epidermal Growth Factor Receptor Extracellular Domain Mutations in Glioblastoma Present Opportunities for Clinical Imaging and Therapeutic Development. Cancer cell 34(1): 163-177.e7, Jul 2018.

Bagley Stephen J, Desai Arati S, Linette Gerald P, June Carl H, O'Rourke Donald M: CAR T Cell Therapy for Glioblastoma: Recent Clinical Advances and Future Challenges. Neuro Oncology 20(11): 1429-1438, Oct 2018.

Rathore S, Bakas S, Nasrallah MP, Bagley SJ, Akbari H, Ha SM, Mamourian EC, Watt C, and Davatzikos C. : Non-invasive determination of the O6-methylguanine-DNA-methyltransferase promoter methylation status in glioblastoma using magnetic resonance imaging. Journal of Clinical Oncology 36(15_suppl), May 2018.

Bagley SJ, Hwang WT, Brem S, Linette GP, O'Rourke DM, and Desai AS: RNA-seq for identification of therapeutically targetable determinants of immune activation in human glioblastoma. Journal of Neuro-Oncology 141(1): 95-102, January 2019.

Bagley SJ, Talento S, Mitra N, Meropol NJ, Cohen RB, Langer CJ, and Vachani A: Comparative effectiveness of carboplatin-pemetrexed with vs without bevacizumab for advanced non-squamous non-small cell lung cancer. J Natl Compr Canc Netw 17(5): 469-477, May 2019.

Bagley SJ, Schwab RD, Nelson E, Viaene AN, Binder AZ, Lustig RA, O’Rourke DM, Brem S, Desai AS, and Nasrallah MP: Histopathologic quantification of viable tumor versus treatment effect in surgically resected recurrent glioblastoma. Journal of Neurooncology 141(2): 421-429, January 2019.

Nabavizadeh SA, Akbari H, Ware JB, Nasrallah M, Guiry S, Bagley SJ, Desai A, Levy S, Sarchiapone W, Prior T, Detre J, Wolf RL, O'Rourke DM, Brem S, Davatzikos C. : Arterial Spin Labeling and Dynamic Susceptibility Contrast-enhanced MRI Imaging for evaluation of arteriovenous shunting and tumor hypoxia in glioblastoma. Scientific Reports 9(1): 8747, Jun 2019.

Bagley SJ, Dhopeshwarkare, Narayan V, Meropol NJ, Mamtani R, and Boursi B. : Impact of antibiotics on overall survival in patients with advanced non-small cell lung cancer and melanoma treated with first-line immune checkpoint inhibition. J Clin Oncol 37(suppl; abstr e20643): e20643, Jun 2019 Notes: "Poster Presentation"

Stephen J. Bagley: Complications Associated with CAR T Cell Therapy Neuro-Oncology for the Clinical Neurologist Roy E. Strowd, MD (eds.). Elsevier, Jun 2019 Notes: Book Chapter, Accepted.

Hoffman DI, Abdullah KG, McCoskey M, Binder ZA, O'Rourke DM, Desai AS, Nasrallah MP, Bigdeli 5, Morrissette JJD, Brem S, Bagley SJ.: Negative prognostic impact of epidermal growth factor receptor copy number gain in young adults with isocitrate dehydrogenase wild-type glioblastoma. J Neurooncol. 145(2): 321-328, Nov 2019.

Kluger BM, Ney DE, Bagley SJ, Mohile N, Taylor LP, Walbert T, Jones CA.: Top Ten Tips Palliative Care Clinicians Should Know When Caring for Patients with Brain Cancer. J Palliat Med. 23(3): 415-421, Mar 2020.

Bagley SJ, Carpenter EL: Plasma cfDNA in Glioblastoma - Response. Clinical Cancer Research 26(9): 2276, May 2020.

Bagley SJ, Desai AS, Nasrallah MP, and O'Rourke DM : Immunotherapy and Response Assessment in Malignant Glioma: Neuro-oncology Perspective. Top Magn Reson Imaging 29(2): 95-102, April 2020.

Henderson F Jr, Brem S, O'Rourke DM, Nasrallah M, Buch VP, Young AJ, Doot RK, Pantel A, Desai A, Bagley SJ, Nabavizadeh SA: 18 F-Fluciclovine PET to Distinguish Treatment-Related Effects From Disease Progression in Recurrent Glioblastoma: PET Fusion With MRI Guides Neurosurgical Sampling. Neurooncol Pract 7(2): 152-157, Mar 2020.

Fathi Kazerooni A, Akbari H, Shukla G, Badve C, Rudie JD, Sako C, Rathore S, Bakas S, Pati S, Singh A, Bergman M, Ha SM, Kontos D, Nasrallah M, Bagley SJ, Lustig RA, O'Rourke DM, Sloan AE, Barnholtz-Sloan JS, Mohan S, Bilello M, Davatzikos C: Cancer Imaging Phenomics via CaPTk: Multi-Institutional Prediction of Progression-Free Survival and Pattern of Recurrence in Glioblastoma. JCO Clin Cancer Inform 4: 234-244, Mar 2020.

Davatzikos C, Barnholtz-Sloan JS, Bakas S, Colen R, Mahajan A, Quintero CB, Font JC, Puig J, Jain R, Sloan AE, Badve C, Marcus DS, Choi YS, Lee SK, Chang JH, Poisson LM, Griffith B, Dicker AP, Flanders AE, Booth TC, Rathore S, Akbari H, Sako C, Bilello M, Shukla G, Kazerooni AF, Brem S, Lustig R, Mohan S, Bagley S, Nasrallah M, O'Rourke DM: AI-based Prognostic Imaging Biomarkers for Precision Neurooncology: The ReSPOND Consortium. Neuro Oncol 22(6): 886-888, Jun 2020.

Akbari H, Rathore S, Bakas S, Nasrallah MP, Shukla G, Mamourian E, Rozycki M, Bagley SJ, Rudie JD, Flanders AE, Dicker AP, Desai AS, O'Rourke DM, Brem S, Lustig R, Mohan S, Wolf RL, Bilello M, Martinez-Lage M, Davatzikos C: Histopathology-validated Machine Learning Radiographic Biomarker for Noninvasive Discrimination Between True Progression and Pseudo-Progression in Glioblastoma. Cancer 126(11): 2625-2636, Jun 2020.

Struve N, Binder ZA, Stead LF, Brend T, Bagley SJ, Faulkner C, Ott L, Müller-Goebel J, Weik AS, Hoffer K, Krug L, Rieckmann T, Bußmann L, Henze M, Morrissette JJD, Kurian KM, Schüller U, Petersen C, Rothkamm K, O Rourke DM, Short SC, Kriegs M: EGFRvIII Upregulates DNA Mismatch Repair Resulting in Increased Temozolomide Sensitivity of MGMT Promoter Methylated Glioblastoma. Oncogene 39(15): 3041-3055, Apr 2020.

Lee EQ, Weller M, Sul J, Bagley SJ, Sahebjam S, van den Bent M, Ahluwalia M, Campian JL, Galanis E, Gilbert MR, Holdhoff M, Lesser GJ, Lieberman FS, Mehta MP, Penas-Prado M, Schreck KC, Strowd RE, Vogelbaum MA, Walbert T, Chang SM, Nabors LB, Grossman S, Reardon DA, Wen PY: Optimizing Eligibility Criteria and Clinical Trial Conduct to Enhance Clinical Trial Participation for Primary Brain Tumor Patients. Neuro Oncol 22(5): 601-612, May 2020.

Makhlin I, Salinas RD, Zhang D, Jacob F, Ming GL, Song H, Saxena D, Dorsey JF, Nasrallah MP, Morrissette JJ, Binder ZA, O'Rourke DM, Desai AS, Brem S, Bagley SJ: Clinical Activity of the EGFR Tyrosine Kinase Inhibitor Osimertinib in EGFR-mutant Glioblastoma. CNS Oncol 8(3), Nov 2019.

Bagley SJ and O'Rourke DM: Clinical Investigation of CAR T Cells for Solid Tumors: Lessons Learned and Future Directions. Pharmacol Ther Page: 205:107419. Jan 2020 Notes: doi: 10.1016/j.pharmthera.2019.107419.

Stephen J Bagley, Jacob Till, Aseel Abdalla, Hareena K Sangha, Stephanie S Yee, Jake Freedman, Taylor A Black, Jasmin Hussain, Zev A Binder, Steven Brem, Arati S Desai, Donald M O'Rourke, Qi Long, Seyed Ali Nabavizadeh, Erica L Carpenter: Association of plasma cell-free DNA with survival in patients with IDH wild-type glioblastoma. Neurooncology Advances 3(1): vdab011, Jan 2021.

Hamed Akbari, Anahita Fathi Kazerooni, Jeffrey B Ware, Elizabeth Mamourian, Hannah Anderson, Samantha Guiry, Chiharu Sako, Catalina Raymond, Jingwen Yao, Steven Brem, Donald M O'Rourke, Arati S Desai, Stephen J Bagley, Benjamin M Ellingson, Christos Davatzikos, Ali Nabavizadeh: Quantification of tumor microenvironment acidity in glioblastoma using principal component analysis of dynamic susceptibility contrast enhanced MR imaging. Scientific Reports 11(1): 15011, Jul 2021.

Alfredo Lucas, James H Eberwine, Stephen J Bagley, Yi Fan, MacLean P Nasrallah, Steven Brem: "Zooming in" on Glioblastoma: Understanding Tumor Heterogeneity and Its Clinical Implications in the Era of Single-Cell Ribonucleic Acid Sequencing. Neurosurgery 89(5): E262-E263, Oct 2021.

Xiaoming Zhang, Levon Katsakhyan, Virginia A LiVolsi, Jacquelyn J Roth, Christopher H Rassekh, Stephen J Bagley, MacLean P Nasrallah: TP53 Mutation and Extraneural Metastasis of Glioblastoma: Insights From an Institutional Experience and Comprehensive Literature Review. Am J Surg Pathol 45(11): 1516-1526, Nov 2021.

Lauren Reed-Guy, Stephen P Miranda, Tyler D Alexander, Gregory Biggiani, M Sean Grady, Joshua A Jones, Stephen J Bagley, Pallavi Kumar, Nina R O'Connor: Serious Illness Communication Practices in Glioblastoma: An Institutional Perspective. Journal of Palliative Medicine 25(2): 234-242, Feb 2022.

Aaron C Tan, Stephen J Bagley, Patrick Y Wen, Michael Lim, Michael Platten, Howard Colman, David M Ashley, Wolfgang Wick, Susan M Chang, Evanthia Galanis, Alireza Mansouri, Simon Khagi, Minesh P Mehta, Amy B Heimberger, Vinay K Puduvalli, David A Reardon, Solmaz Sahebjam, John Simes, Scott J Antonia, Don Berry, Mustafa Khasraw: Systematic review of combinations of targeted or immunotherapy in advanced solid tumors. J Immunother Cancer 9(7): e002459, Jul 2021.

Stephen J Bagley and Cassie N Kline: Understanding the global impact of primary brain tumors: the untapped potential of population-based cancer registries. Neuro Oncology 23(10): 1625-1626, Oct 2021.

Stephen J Bagley: Treatment and resistance of glioblastoma to CAR-T cell immunotherapies. Glioblastoma Resistance to Chemotherapy: Molecular Mechanisms and Innovative Reversal Strategies, 1st Edition. Elsevier Press, 2021.

Kazerooni AF, Bashyam V, Akbari H, Sako C, Mamourian E, Till J, Abdalla A, Yee S, Binder Z, Nabavizadeh SA, Carpenter E, Davatzikos C, and Bagley SJ. : Integration of a radiomic signature, clinical variables and plasma cell-free DNA in adult patients with newly diagnosed glioblastoma predicts patient survival and improves disease stratification. Neuro Oncol 22(suppl_2): ii151-ii152, Nov 2020.

Nazem A, Guiry SC, Pourfathi M, Ware JB, Anderson H, Iyer SK, Moon BF, Fan Y, Witschey WR, Rizi R, Bagley SJ, Desai A, O’Rourke DM, Brem S, Nasrallah M, Nabavizadeh A: MR susceptibility imaging for detection of tumor-associated macrophages in glioblastoma. J Neurooncology 156(3): 645-653, Jan 2022.

Chawla S, Bukhari S, Afridi OM, Wang S, Yadav SK, Akbari H, Verma G, Nath K, Haris M, Bagley SJ, Davatzikos C, Loevner LA, Mohan : Metabolic and physiologic magnetic resonance imaging in distinguishing true progression from pseudoprogression in patients with glioblastoma. NMR Biomed 35(7): e4719, Jun 2022.

Fathi KA, Saxena S, Toorens E, Tu D, Bashyam V, Akbari H, Mamourian E, Sako C, Koumenis C, Verginadis I, Verma R, Shinohara RT, Desai AS, Lustig RA, Brem S, Mohan S, Bagley SJ, Ganguly T, O’Rourke DM, Bakas S, Nasrallah MP, Davatzikos C: Clinical measures, radiomics, and genomics offer synergistic value in AI-based prediction of overall survival in patients with glioblastoma. Scientific Reports 12(1): 8784, May 2022.

Bakas S, Sako C, Akbari H, Billelo M, Sotiras A, Shukla G, Rudie JD, Santamaria NF, Kazerooni AF, Pati S, Rathore S, Mamourian H, Ha SM, Parker W, Doshi J, Baid U, Bergman M, Binder ZA, Verma R, Lustig RA, Desai AS, Bagley SJ, Mourelatos Z, Morrissette J, Watt CD, Brem S, Wolf RL, Melhem ER, Nasrallah MP, Mohan S, O’Rourke DM, Davatzikos C: The University of Pennsylvania glioblastoma (Upenn-GBM) cohort: advanced MRI, clinical, genomics, and radiomics. Scientific Data 9(1): 453, Jul 2022.

Carpenter EL, Bagley SJ: Clinical utility of plasma cell-free DNA in gliomas. Neuro-Oncology Advances 2022.

Nabavizadeh A, Bagley SJ, Doot RK, Ware JB, Young AJ, Ghodasara S, Zhao C, Anderson H, Schubert E, Carpenter EL, Till JA, Henderson F, Pantel AR, Chen HI, Lee JYK, Amankulor NM, O’Rourke DM, Desai A, Nasrallah MP, Brem S: Distinguishing progression from pseudoprogression in glioblastoma using 18F-fluciclovine PET. Journal of Nuclear Medicine 64(6), 2023.

Jo J, Diaz M, Horbinski C, Mackman N, Bagley SJ, Broekman M, Rak J, Perry J, Pabinger I, Key NS, Shiff D: Epidemiology, biology, and management of venous thromboembolism in glioma: an interdisciplinary review. Neuro-Oncology 2023.

De Godoy LL, Mohan S, Wang S, Nasrallah MP, Sakai Y, O’Rourke DM, Bagley SJ, Desai A, Loevner LA, Poptani H, Chawla S: Validation of multiparametric MRI based prediction model in identification of pseudoprogression in glioblastomas. Journal of Translational Medicine 21(1), 2023.

Stephen J Bagley: Phase II trials in the era of glioblastoma immunotherapy: new mechanisms of action, familiar challenges in trial design and tumor response assessment. Neuro-Oncology 25(6), 2023.

Bagley SJ, Till JE, Abdalla A, Nasrallah M, Lauterman T, Tavassoly I, Oklander B, Zviran A, and Carpenter EL: A pilot study of whole genome sequencing (WGS) of plasma cell-free DNA (cfDNA) for ultrasensitive detection of tumor DNA in patients with glioblastoma. Neuro-Oncology 23(Suppl_6), 2021.