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. 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.  View on PubMed
  2. 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.  View on PubMed
  3. 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
  4. 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
  5. 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 Jan 02.  View on PubMed
  6. 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 Dec 30; 15(1):10757.  View on PubMed
  7. 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
  8. 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
  9. 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
  10. 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
  11. 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.  View on PubMed
  12. 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
  13. Autry AW, Vaziri S, Gordon JW, Chen HY, Kim Y, Dang D, LaFontaine M, Noeske R, Bok R, Villanueva-Meyer JE, Clarke JL, Oberheim Bush NA, Chang SM, Xu D, Lupo JM, Larson PEZ, Vigneron DB, Li Y. Advanced Hyperpolarized 13C Metabolic Imaging Protocol for Patients with Gliomas: A Comprehensive Multimodal MRI Approach. Cancers (Basel). 2024 Jan 13; 16(2).  View on PubMed
  14. Tuggle CK, Clarke JL, Murdoch BM, Lyons E, Scott NM, Beneš B, Campbell JD, Chung H, Daigle CL, Das Choudhury S, Dekkers JCM, Dórea JRR, Ertl DS, Feldman M, Fragomeni BO, Fulton JE, Guadagno CR, Hagen DE, Hess AS, Kramer LM, Lawrence-Dill CJ, Lipka AE, Lübberstedt T, McCarthy FM, McKay SD, Murray SC, Riggs PK, Rowan TN, Sheehan MJ, Steibel JP, Thompson AM, Thornton KJ, Van Tassell CP, Schnable PS Current challenges and future of agricultural genomes to phenomes in the USA.  View on PubMed
  15. Mellinghoff IK, Lu M, Wen PY, Taylor JW, Maher EA, Arrillaga-Romany I, Peters KB, Ellingson BM, Rosenblum MK, Chun S, Le K, Tassinari A, Choe S, Toubouti Y, Schoenfeld S, Pandya SS, Hassan I, Steelman L, Clarke JL, Cloughesy TF. Author Correction: Vorasidenib and ivosidenib in IDH1-mutant low-grade glioma: a randomized, perioperative phase 1 trial. Nat Med. 2024 Jan; 30(1):302.  View on PubMed
  16. Hadad S, Gupta R, Oberheim Bush NA, Taylor JW, Villanueva-Meyer JE, Young JS, Wu J, Ravindranathan A, Zhang Y, Warrier G, McCoy L, Shai A, Pekmezci M, Perry A, Bollen AW, Phillips JJ, Braunstein SE, Raleigh DR, Theodosopoulos P, Aghi MK, Chang EF, Hervey-Jumper SL, Costello JF, de Groot J, Butowski NA, Clarke JL, Chang SM, Berger MS, Molinaro AM, Solomon DA. "De novo replication repair deficient glioblastoma, IDH-wildtype" is a distinct glioblastoma subtype in adults that may benefit from immune checkpoint blockade. Acta Neuropathol. 2023 12 11; 147(1):3.  View on PubMed
  17. Zhang Y, Weh KM, Tripp BA, Clarke JL, Howard CL, Sunilkumar S, Howell AB, Kresty LA Cranberry Proanthocyanidins Mitigate Reflux-Induced Transporter Dysregulation in an Esophageal Adenocarcinoma Model.  View on PubMed
  18. Clarke JL, Cooper LD, Poelchau MF, Berardini TZ, Elser J, Farmer AD, Ficklin S, Kumari S, Laporte MA, Nelson RT, Sadohara R, Selby P, Thessen AE, Whitehead B, Sen TZ Data sharing and ontology use among agricultural genetics, genomics, and breeding databases and resources of the Agbiodata Consortium.  View on PubMed
  19. Strowd R, Ellingson B, Raymond C, Yao J, Wen PY, Ahluwalia M, Piotrowski A, Desai A, Clarke JL, Lieberman FS, Desideri S, Nabors LB, Ye X, Grossman S. Activity of a first-in-class oral HIF2-alpha inhibitor, PT2385, in patients with first recurrence of glioblastoma. J Neurooncol. 2023 Oct; 165(1):101-112.  View on PubMed
  20. Autry AW, Vaziri S, LaFontaine M, Gordon JW, Chen HY, Kim Y, Villanueva-Meyer JE, Molinaro A, Clarke JL, Oberheim Bush NA, Xu D, Lupo JM, Larson PEZ, Vigneron DB, Chang SM, Li Y. Multi-parametric hyperpolarized 13C/1H imaging reveals Warburg-related metabolic dysfunction and associated regional heterogeneity in high-grade human gliomas. Neuroimage Clin. 2023; 39:103501.  View on PubMed

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