Research Summary

I am an academic neuro-oncologist involved in clinical care, clinical research and teaching. I have formal training and extensive experience in clinical trial design, implementation and analysis, including investigator-initiated, sponsored and multi-institutional consortium and cooperative group studies testing new treatments and treatment combinations in gliomas. I am Vice-Chair of the Cancer Center’s Protocol Review and Monitoring Committee (PRMC). My current research foci include (1) precision medicine approaches to glioma treatment, (2) immunotherapy, in particular development of novel CAR-T therapies in glioma in collaboration with Drs. Hideho Okada and Wendell Lim, and (3) evaluation of serial blood immune profiles as a marker of clinical outcome in glioblastoma patients, using methylation arrays. I am a Co-Associate Director of the Clinical Core for the UCSF (P01) Program Project Grant  focused on integrating advances in physiologic and metabolic imaging with tissue biomarkers in order to optimize the management of patients with molecular subtypes of glioma. In addition, I am co-PI of projects both in the UCSF Brain Tumor Center’s U19 grant in collaboration with Northwestern University and in the UCSF Brain Tumor Center’s SPORE grant.

Education

California Institute of Technology (Caltech), Pasadena, CA, B.S., 1995, Chemistry, With Honor
University of California, San Francisco, M.D., 2002, Medicine
University of California, Berkeley, M.P.H., 2001, Health Policy and Mgmt
St. Mary’s Medical Center, San Francisco, 06/03, Intern, Internal Medicine
University of California, San Francisco, 06/06, Resident, Neurology
Memorial Sloan-Kettering Cancer Center, 06/08, Fellow, Neuro-oncology

Honors & Awards

  • 1999
    Nomination for “An Outstanding Lecture” UCSF Class of 2001
  • 2000
    University Fellowship, UC-Berkeley
  • 2000
    Award for “An Outstanding Lecture” UCSF Class of 2002
  • 2001
    UCSF Class of 1966 Scholarship
  • 2003
    Intern of the Year, St. Mary’s Medical Center
  • 2008
    ASCO Foundation Merit Award
  • 2009
    Awarded a fellowship to the 2nd Annual Clinical Trials Methods Course in Neurology, in Vail, Colorado, August 17-23, 2009; the course is sponsored by NINDS

Selected Publications

  1. Chen J, Oberheim Bush NA, Grabowsky JA, Kline C, Kroetz DL, Taylor JW, Villanueva-Meyer J, Molinaro AM, de Groot JF, Butowski NA, Tedesco M, Rabbitt J, Phillips JJ, Hervey-Jumper S, Aghi MK, Berger MS, Chang EF, Chang SM, Solomon DA, Clarke JL. A Genomically Tailored Multiagent Precision Medicine Clinical Trial for Adults with Recurrent Glioblastoma. Clin Cancer Res. 2026 May 01; 32(9):1652-1665. View on PubMed
  2. Vaziri S, Lupo JM, Autry AW, LaFontaine M, Villanueva-Meyer J, Vigneron DB, Oberheim-Bush NA, Chang SM, Clarke JL, Li Y. Evaluation of treatment response in patients with recurrent grade 4 glioma using hyperpolarized [1-13C]pyruvate MRI. Res Sq. 2026 Apr 07. View on PubMed
  3. Kuwahara A, Fenton EM, Lovejoy C, Lee T, Wang L, Fogarty M, Jung J, Guo SM, Maynard LH, May AP, Rossenberg-Hasson Y, Clarke JL, Diaz AA, Phillips JJ, Kelly L, Clément N, Paulk NK. AAV immuno-gene therapy platform delivering vectorized cytokines defines a new modality for high-grade glioma treatment. Mol Ther Oncol. 2026 Jun 18; 34(2):201183. View on PubMed
  4. Zhang Y, Ntsiful DA, Israel R, Vandenburg B, Barnett S, Riethoven JJ, Clarke JL, Lagisetty KH, Lin J, Reddy RM, Chang AC, Odell DD, DiFeo A, Sartor MA, Kresty LA. Identification of isoform switching events linked with esophageal adenocarcinoma patient survival informs novel prognostic and therapeutic targets. Cell Death Dis. 2026 Mar 11; 17(1). View on PubMed
  5. Suhr Van Haute MJ, Yang Q, Korth N, Happ MM, Kok CR, Miao C, Clarke JL, Karnik K, Eskridge KM, Urrea CA, Hyten DL, Schnable JC, Rose DJ, Benson AK. Genetic variation and historical breeding patterns in common bean (Phaseolus vulgaris L.) affect fermentation patterns by the human gut microbiome. Commun Biol. 2025 Nov 26; 8(1):1690. View on PubMed
  6. Cloughesy TF, van den Bent MJ, Touat M, Blumenthal DT, Peters KB, Ellingson BM, Clarke JL, Mendez J, Yust-Katz S, Welsh L, Mason WP, Ducray F, Umemura Y, Nabors B, Holdhoff M, Hottinger AF, Arakawa Y, Sepulveda JM, Wick W, Soffietti R, Perry J, Giglio P, de la Fuente M, Maher E, Bottomley A, Tron AE, Yi D, Zhao D, Pandya SS, Steelman L, Hassan I, Wen PY, Mellinghoff IK, INDIGO trial investigators. Vorasidenib in IDH1-mutant or IDH2-mutant low-grade glioma (INDIGO): secondary and exploratory endpoints from a randomised, double-blind, placebo-controlled, phase 3 trial. Lancet Oncol. 2025 Dec; 26(12):1665-1675. View on PubMed
  7. Tran N, Luks TL, Li Y, Jakary A, Ellison J, Liu B, Adegbite O, Nair D, Kakhandiki P, Molinaro AM, Villanueva-Meyer JE, Butowski N, Clarke JL, Chang SM, Braunstein SE, Morin O, Lin H, Lupo JM. Novel radiotherapy target definition using AI-driven predictions of glioblastoma recurrence from metabolic and diffusion MRI. NPJ Digit Med. 2025 Aug 07; 8(1):508. View on PubMed
  8. Weyer-Jamora C, Brie MS, Bracci PM, Smith EM, Luks TL, Phan S, Braunstein SE, Oberheim-Bush NA, Butowski NA, Clarke JL, Gehring K, Aguilera A, de Groot J, Chang SM, Hervey-Jumper SL, Taylor JW. Tele-cognitive rehabilitation for adult lower-grade glioma: An interim prospective pilot feasibility study. Neurooncol Pract. 2026 Feb; 13(1):126-138. View on PubMed
  9. Guerra G, Wendt G, McCoy L, Hansen HM, Kachuri L, Molinaro AM, Rice T, Guan V, Capistrano L, Hsieh A, Kalsi V, Sallee J, Taylor JW, Clarke JL, Almaraz ER, Wiencke JK, Eckel-Passow JE, Jenkins RB, Wrensch M, Francis SS. Functional germline variants in DNA damage repair pathways are associated with altered survival in adults with glioma treated with temozolomide. Neuro Oncol. 2025 Jun 21; 27(5):1385-1398. View on PubMed
  10. Salmi L, Lewis DM, Clarke JL, Dong Z, Fischmann R, McIntosh EI, Sarabu CR, DesRoches CM. A proof-of-concept study for patient use of open notes with large language models. JAMIA Open. 2025 Apr; 8(2):ooaf021. View on PubMed
  11. Rodriguez Almaraz E, Guerra GA, Al-Adli NN, Young JS, Dada A, Quintana D, Taylor JW, Oberheim Bush NA, Clarke JL, Butowski NA, de Groot J, Pekmezci M, Perry A, Bollen AW, Scheffler AW, Glidden DV, Phillips JJ, Costello JF, Chang EF, Hervey-Jumper S, Berger MS, Francis SS, Chang SM, Solomon DA. Longitudinal profiling of IDH-mutant astrocytomas reveals acquired RAS-MAPK pathway mutations associated with inferior survival. Neurooncol Adv. 2025 Jan-Dec; 7(1):vdaf024. View on PubMed
  12. Lucas CG, Al-Adli NN, Young JS, Gupta R, Morshed RA, Wu J, Ravindranathan A, Shai A, Oberheim Bush NA, Taylor JW, de Groot J, Villanueva-Meyer JE, Pekmezci M, Perry A, Bollen AW, Theodosopoulos PV, Aghi MK, Chang EF, Hervey-Jumper SL, Raleigh DR, Molinaro AM, Costello JF, Diaz AA, Clarke JL, Butowski NA, Phillips JJ, Chang SM, Berger MS, Solomon DA. Longitudinal multimodal profiling of IDH-wildtype glioblastoma reveals the molecular evolution and cellular phenotypes underlying prognostically different treatment responses. Neuro Oncol. 2025 Jan 12; 27(1):89-105. View on PubMed
  13. Narsinh KH, Kumar K, Bankiewicz K, Martin AJ, Berger M, Clarke J, Taylor J, Bush NAO, Molinaro AM, Aghi M, Butowski N. A phase I study of convection-enhanced delivery (CED) of liposomal-irinotecan using real-time magnetic resonance imaging in patients with recurrent high-grade glioma. J Neurooncol. 2025 Mar; 172(1):219-227. View on PubMed
  14. McFaline-Figueroa JR, Sun L, Youssef GC, Huang R, Li G, Kim J, Lee EQ, Nayak L, Chukwueke U, Beroukhim R, Batchelor TT, Chiocca EA, Everson RG, Doherty L, Stefanik J, Partridge K, Spearman A, Myers A, Westergaard C, Russ A, Lavallee M, Smokovich A, LaForest-Roys C, Garcia Fox R, McCluskey C, Bi WL, Arnaout O, Peruzzi P, Cosgrove GR, Ligon KL, Arrillaga-Romany I, Clarke JL, Reardon DA, Cloughesy TF, Prins RM, Wen PY. Neoadjuvant anti-PD1 immunotherapy for surgically accessible recurrent glioblastoma: clinical and molecular outcomes of a stage 2 single-arm expansion cohort. Nat Commun. 2024 12 30; 15(1):10757. View on PubMed
  15. Guerra G, Wendt G, McCoy L, Hansen HM, Kachuri L, Molinaro AM, Rice T, Guan V, Capistrano L, Hsieh A, Kalsi V, Sallee J, Taylor JW, Clarke JL, Rodriguez Almaraz E, Wiencke JK, Eckel-Passow JE, Jenkins RB, Wrensch M, Francis SS. Functional germline variants in DNA damage repair pathways are associated with altered survival in adults with glioma treated with temozolomide. medRxiv. 2024 Oct 10. View on PubMed
  16. Taylor JW, Warrier G, Hansen HM, McCoy L, Rice T, Guerra G, Francis SS, Clarke JL, Bracci PM, Hadad S, Kelsey KT, Wrensch M, Molinaro AM, Wiencke JK. Oligodendroglioma patient survival is associated with circulating B-cells and age. Neurooncol Adv. 2024 Jan-Dec; 6(1):vdae143. View on PubMed
  17. Bazer DA, Kolchinski A, Bush NAO, Clarke JL, Bagley SJ, Schreck KC. No drug holidays in BRAFV600E glioma patients: An argument for dose reduction of targeted therapies. Neurooncol Pract. 2024 Oct; 11(5):660-664. View on PubMed
  18. Liu J, Jakary A, Villanueva-Meyer JE, Butowski NA, Saloner D, Clarke JL, Taylor JW, Oberheim Bush NA, Chang SM, Xu D, Lupo JM. Automatic Brain Tissue and Lesion Segmentation and Multi-Parametric Mapping of Contrast-Enhancing Gliomas without the Injection of Contrast Agents: A Preliminary Study. Cancers (Basel). 2024 Apr 17; 16(8). View on PubMed
  19. Weh KM, Howard CL, Zhang Y, Tripp BA, Clarke JL, Howell AB, Rubenstein JH, Abrams JA, Westerhoff M, Kresty LA. Prebiotic proanthocyanidins inhibit bile reflux-induced esophageal adenocarcinoma through reshaping the gut microbiome and esophageal metabolome. JCI Insight. 2024 02 08; 9(6). View on PubMed
  20. Saijo A, Ogino H, Butowski NA, Tedesco MR, Gibson D, Watchmaker PB, Okada K, Wang AS, Shai A, Salazar AM, Molinaro AM, Rabbitt JE, Shahin M, Perry A, Clarke JL, Taylor JW, Daras M, Oberheim Bush NA, Hervey-Jumper SL, Phillips JJ, Chang SM, Hilf N, Mayer-Mokler A, Keler T, Berger MS, Okada H. A combinatory vaccine with IMA950 plus varlilumab promotes effector memory T-cell differentiation in the peripheral blood of patients with low-grade gliomas. Neuro Oncol. 2024 02 02; 26(2):335-347. View on PubMed

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