Emily Ling-Lin Pai, MD, PhD
UCSF Clinical Cancer Genomic Laboratory
During my graduate training at the University of California, San Francisco (UCSF), my doctoral research focused on the transcriptional regulation of cortical interneuron development, with particular emphasis on the roles of large MAF transcription factors. Using genetic knockout mouse models, I investigated the molecular mechanisms underlying interneuron specification through a combination of immunohistochemistry, fluorescent in situ hybridization, in situ hybridization, microscopy, and molecular profiling to characterize the phenotypic and transcriptional consequences of these genetic alterations.
During residency and fellowship training, I developed a strong interest in the diverse clinical, histopathologic, and molecular features of central nervous system tumors, particularly as advances in molecular diagnostics have led to the recognition of new tumor entities and refined disease classification. I have collaborated with multidisciplinary teams—including neurosurgeons, neuro-oncologists, neuroradiologists, radiation oncologists, and molecular pathologists—to characterize and publish instructive brain tumor cases integrating histopathologic, radiologic, and molecular findings. In addition, I have participated in a collaborative research program evaluating chimeric antigen receptor (CAR) T-cell therapies for glioblastoma, contributing to translational efforts aimed at advancing molecularly targeted and immunotherapeutic approaches for patients with aggressive brain tumors.
As a faculty member, I aim to integrate my subspecialty training in neuropathology and molecular genetic pathology to advance both clinical practice and research. My clinical and research interests include brain tumors, molecular pathology of solid tumors, and neuromuscular diseases. I am particularly interested in investigating the molecular alterations and oncogenic mechanisms underlying rare and emerging tumor entities and in pursuing collaborative research that bridges diagnostic pathology with translational and precision medicine.
-
Pai ELL*, Vogt D*, Clemente-Perez A*, McKinsey GL*, Cho FS, Hu JS, Wimer M, Paul A, Fazel Darbandi S, Pla R, Nowakowski T, Goodrich LV, Paz JT, Rubenstein JL. Mafb and c-Maf have prenatal compensatory and postnatal antagonistic roles in cortical interneuron fate and function. Cell Rep. 2019;26(5):1157-1173.e5. doi:10.1016/j.celrep.2019.01.031. PMID: 30699346
-
Malik R, Pai ELL, Rubin AN, Stafford AM, Angara K, Minasi P, Rubenstein JL, Sohal VS, Vogt D. Tsc1 represses parvalbumin expression and fast-spiking properties in somatostatin lineage cortical interneurons. Nat Commun. 2019;10(1):4994. doi:10.1038/s41467-019-12962-4. PMID: 31676823
-
Angara K, Pai ELL, Bilinovich SM, Stafford AM, Nguyen JT, Li KX, Paul A, Rubenstein JL, Vogt D. Nf1 deletion results in depletion of the Lhx6 transcription factor and a specific loss of parvalbumin+ cortical interneurons. Proc Natl Acad Sci U S A. 2020;117(11):6189-6195. doi:10.1073/pnas.1915458117. PMID: 32123116
-
Pai ELL*, Chen J*, Fazel Darbandi S, Cho FS, Chen J, Lindtner S, Chu JS, Paz JT, Vogt D, Paredes MF, Rubenstein JL. Maf and Mafb control mouse pallial interneuron fate and maturation through neuropsychiatric disease gene regulation. Elife. 2020;9:e54903. doi:10.7554/eLife.54903. PMID: 32452758
-
Jones FJS*, Pai ELL*, Magee R, Boylan K, Chioma V, Little J, Yoshor D, Pascual JL, Banihashemi A, Prasad S, Lee EB, Orthmann-Murphy J. Consecutive brain biopsies illustrate the histological evolution of acute hemorrhagic leukoencephalitis. J Neuropathol Exp Neurol. 2025 Apr 4:nlaf019. doi:10.1093/jnen/nlaf019. PMID: 40183946
-
Pai ELL*, Matsumoto Y*, Dan D*, Nelluri S*, Devi P, Priori S, Amankulor N, Alonso-Basanta M, Singh O, Abdullaev Z, Aldape K, Desai A, Mohan S, Nasrallah M. Molecularly-defined oligodendroglioma evolving to osseous metastases. J Neuropathol Exp Neurol. 2025 Apr 18:nlaf038. doi: 10.1093/jnen/nlaf038. PMID: 40249402
-
Sun Y, Wang X, Zhang DY, Zhang Z, Bhattarai JP, Wang Y, Dong W, Zhang F, Park KH, Galanaugh J, Sambangi A, Yang Q, Kim SH, Wheeler G, Goncalves T, Wang Q, Geschwind D, Kawaguchi R, Wang H, Xu F, Binder ZA, Chen IH, Pai ELL, Stone S, Nasrallah M, Christian KM, Fuccillo M, O'Rourke DM, Ma M, Ming GL, Song HJ. Brain-wide neuronal circuit connectome of human glioblastoma. Nature. 2025;641(8061):222-231. doi:10.1038/s41586-025-08634-7. PMID: 38496540
-
Pai ELL, Nazarian MN, Kenyon AL, Abdullaev Z, Arisi M, Johnson ES, Surrey LF, Quezado M, Schwartz LE, Dumoff KL, Cooper K, Aldape K, Kenyon L, Nasrallah MP, Desai AS. Longitudinal neuropathologic and molecular characterization of a retroperitoneal ependymoma. J Neuropathol Exp Neurol. 2025 Dec 23:nlaf143. doi: 10.1093/jnen/nlaf143. Epub ahead of print. PMID: 41435511.
-
Pai ELL, Herzog C, Halper-Stromberg E, Odintsov I, Baranov E Ultramutated Colonic Adenocarcinoma With Mismatch Repair Deficiency and Distinctive Mutational Signature Following Solid Organ Transplantation. Mod Pathol. 2026 Apr;39(4):100974. doi: 10.1016/j.modpat.2026.100974. Epub 2026 Mar 9. PMID: 41806570.
2010 Fellowship for Summer Research, National Yang-Ming University
2013 Fellowship for Summer Research, National Yang-Ming University
2013 Best Intern Physician Award, Taipei Veterans General Hospital
2014 Scholarship for Overseas Studies, Taiwan Ministry of Education
2014 Best Intern Physician Award, Taipei Veterans General Hospital
2014 Honors in Clinical Performance, National Yang-Ming University
2016 Bay Area Autism Consortium Conference Travel Award
2018 American Epilepsy Society Predoctoral Fellowship, Honorable Mention
2021 UMPDA Professional Development Award, University of Michigan
2021 Cajal Club Kudos Cortical Scholar Award
2022 Society for Pediatric Pathology Resident Recruitment Award
2023 Award for Distinguished Contributions by a Resident, Hospital of the University of Pennsylvania
2024 American Association of Neuropathologists Women and Diversity Award
2026 American Association of Neuropathologists Travel Award