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John Liu, MD, PhD

Assistant Professor
Departments of Radiation Oncology and Neurological Surgery
University of California, San Francisco

Meet Dr. Liu

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Research Center

Liu Lab

Dr. Liu is a radiation oncologist specialized in the treatment of malignancies of the nervous system. He is a physician scientist who leads a basic and translational research group dedicated to advancing new treatments for malignant brain tumors and understanding mechanisms of treatment resistance, including how to make radiation more effective and have fewer side effects for patients.

Education

2020-2024	University of California, San Francisco	Residency	Radiation Oncology
2019-2020	Kaiser Permanente San Francisco Medical Center	Internship	Internal Medicine
2011-2019	University of California, San Francisco	MD	Medicine
2011-2017	University of California, San Francisco	PhD	Biomedical Sciences
2007-2011	Harvard University	Undergraduate	Chemical and Physical Biology

Professional Experience

2024 – present	University of California, San Francisco	Assistant Professor	Radiation Oncology
2024 – present	University of California, San Francisco	Principal Investigator	Radiation Oncology

Awards & Honors

2024	RSNA Roentgen Resident/Fellow Research Award
2023-2024	CRISPR Cures for Cancer Initiative Pilot Award
2020-2024	ABR Holman Pathway
2022-2023	The Sontag Foundation Conquer Cancer Young Investigator Award
2022-2023	Catalyst Award
2021-2022	BTC SPORE Career Enhancement Award

Publications

Liu SJ, Pak J, Zou C, Casey-Clyde T, Borah AA, Wu D, Seo K, O’Loughlin T, Lim DA, Ozawa T, Berger MS, Weiss WA, Raleigh DR, Gilbert LA. In vivo perturb-seq of cancer and immune cells dissects oncologic drivers and therapy response. In Review. bioRxiv: 2023.09.01.555831
CRISPRi screens identify the lncRNA, LOUP, as a multifunctional locus regulating macrophage differentiation and inflammatory signaling. Proc Natl Acad Sci U S A. 2024 May 28; 121(22):e2322524121.Halasz H, Malekos E, Covarrubias S, Yitiz S, Montano C, Sudek L, Katzman S, Liu SJ, Horlbeck MA, Namvar L, Weissman JS, Carpenter S. PMID: 38781216; PMCID: PMC11145268.
Spatial genomic, biochemical and cellular mechanisms underlying meningioma heterogeneity and evolution. Nat Genet. 2024 May 17.Lucas CG, Mirchia K, Seo K, Najem H, Chen WC, Zakimi N, Foster K, Eaton CD, Cady MA, Choudhury A, Liu SJ, Phillips JJ, Magill ST, Horbinski CM, Solomon DA, Perry A, Vasudevan HN, Heimberger AB, Raleigh DR. PMID: 38760638.
Eed controls craniofacial osteoblast differentiation and mesenchymal proliferation from the neural crest. bioRxiv. 2024 Mar 14.Casey-Clyde T, Liu SJ, Serrano JAC, Teng C, Jang YG, Vasudevan HN, Bush JO, Raleigh DR. PMID: 38558995; PMCID: PMC10979956.
Hypoxia-informed RBE-weighted beam orientation optimization for intensity modulated proton therapy. Med Phys. 2024 Mar; 51(3):2320-2333.Ramesh P, Ruan D, Liu SJ, Seo Y, Braunstein S, Sheng K. PMID: 38345134; PMCID: PMC10940223.
Epigenetic reprogramming shapes the cellular landscape of schwannoma. Nat Commun. 2024 Jan 12; 15(1):476.Liu SJ, Casey-Clyde T, Cho NW, Swinderman J, Pekmezci M, Dougherty MC, Foster K, Chen WC, Villanueva-Meyer JE, Swaney DL, Vasudevan HN, Choudhury A, Pak J, Breshears JD, Lang UE, Eaton CD, Hiam-Galvez KJ, Stevenson E, Chen KH, Lien BV, Wu D, Braunstein SE, Sneed PK, Magill ST, Lim D, McDermott MW, Berger MS, Perry A, Krogan NJ, Hansen MR, Spitzer MH, Gilbert L, Theodosopoulos PV, Raleigh DR. PMID: 38216587; PMCID: PMC10786948.
Spatial genomic, biochemical, and cellular mechanisms drive meningioma heterogeneity and evolution. Res Sq. 2023 May 15.Lucas CH, Mirchia K, Seo K, Najem H, Chen W, Zakimi N, Choudhury A, Liu SJ, Phillips J, Magill S, Horbinski C, Solomon D, Perry A, Vasudevan H, Heimberger A, Raleigh D. PMID: 37292686; PMCID: PMC10246120.
MerlinS13 phosphorylation controls meningioma Wnt signaling and magnetic resonance imaging features. Res Sq. 2023 Mar 14.Eaton C, Avalos L, Liu SJ, Casey-Clyde T, Bisignano P, Lucas CH, Stevenson E, Choudhury A, Vasudevan H, Magill S, Krogan N, Villanueva-Meyer J, Swaney D, Raleigh D. PMID: 36993679; PMCID: PMC10055685.
Dual genome-wide coding and lncRNA screens in neural induction of induced pluripotent stem cells. Cell Genom. 2022 Nov 09; 2(11).Wu D, Poddar A, Ninou E, Hwang E, Cole MA, Liu SJ, Horlbeck MA, Chen J, Replogle JM, Carosso GA, Eng NWL, Chang J, Shen Y, Weissman JS, Lim DA. PMID: 36381608; PMCID: PMC9648144.
Meningioma DNA methylation groups identify biological drivers and therapeutic vulnerabilities. Nat Genet. 2022 05; 54(5):649-659.Choudhury A, Magill ST, Eaton CD, Prager BC, Chen WC, Cady MA, Seo K, Lucas CG, Casey-Clyde TJ, Vasudevan HN, Liu SJ, Villanueva-Meyer JE, Lam TC, Pu JK, Li LF, Leung GK, Swaney DL, Zhang MY, Chan JW, Qiu Z, Martin MV, Susko MS, Braunstein SE, Bush NAO, Schulte JD, Butowski N, Sneed PK, Berger MS, Krogan NJ, Perry A, Phillips JJ, Solomon DA, Costello JF, McDermott MW, Rich JN, Raleigh DR. PMID: 35534562; PMCID: PMC9374001.
Resection with intraoperative cesium-131 brachytherapy as salvage therapy for recurrent brain tumors. J Neurosurg. 2022 Jan 21; 1-7.Chen WC, Lafreniere M, Phuong C, Liu SJ, Baal JD, Lometti M, Morin O, Ziemer B, Vasudevan HN, Lucas CG, Hervey-Jumper SL, Theodosopoulos PV, Magill ST, Fogh S, Nakamura JL, Boreta L, Sneed PK, McDermott MW, Raleigh DR, Braunstein SE. PMID: 35061986.
Long noncoding RNAs in cancer metastasis. Nat Rev Cancer. 2021 07; 21(7):446-460.Liu SJ, Dang HX, Lim DA, Feng FY, Maher CA. PMID: 33953369; PMCID: PMC8288800.
miRNA-independent function of long noncoding pri-miRNA loci. Proc Natl Acad Sci U S A. 2021 03 30; 118(13).He D, Wu D, Muller S, Wang L, Saha P, Ahanger SH, Liu SJ, Cui M, Hong SJ, Jain M, Olson HE, Akeson M, Costello JF, Diaz A, Lim DA. PMID: 33758101; PMCID: PMC8020771.
Genome-Scale Perturbation of Long Noncoding RNA Expression Using CRISPR Interference. Methods Mol Biol. 2021; 2254:323-338.Liu SJ, Horlbeck MA, Weissman JS, Lim DA. PMID: 33326085; PMCID: PMC7917014.
CRISPRi-based radiation modifier screen identifies long non-coding RNA therapeutic targets in glioma. Genome Biol. 2020 03 31; 21(1):83.Liu SJ, Malatesta M, Lien BV, Saha P, Thombare SS, Hong SJ, Pedraza L, Koontz M, Seo K, Horlbeck MA, He D, Birk HS, Jain M, Olsen HE, Akeson M, Weissman JS, Monje M, Gupta N, Raleigh DR, Ullian EM, Lim DA. PMID: 32234056; PMCID: PMC7110660.
Fitness effects of CRISPR/Cas9-targeting of long noncoding RNA genes. Nat Biotechnol. 2020 May; 38(5):573-576.Horlbeck MA, Liu SJ, Chang HY, Lim DA, Weissman JS. PMID: 32094656; PMCID: PMC8128075.
Multiplatform Molecular Profiling Reveals Epigenomic Intratumor Heterogeneity in Ependymoma. Cell Rep. 2020 02 04; 30(5):1300-1309.e5.Liu SJ, Magill ST, Vasudevan HN, Hilz S, Villanueva-Meyer JE, Lastella S, Daggubati V, Spatz J, Choudhury A, Orr BA, Demaree B, Seo K, Ferris SP, Abate AR, Oberheim Bush NA, Bollen AW, McDermott MW, Costello JF, Raleigh DR. PMID: 32023450; PMCID: PMC7313374.
Outer Radial Glia-like Cancer Stem Cells Contribute to Heterogeneity of Glioblastoma. Cell Stem Cell. 2020 01 02; 26(1):48-63.e6.Bhaduri A, Di Lullo E, Jung D, Müller S, Crouch EE, Espinosa CS, Ozawa T, Alvarado B, Spatazza J, Cadwell CR, Wilkins G, Velmeshev D, Liu SJ, Malatesta M, Andrews MG, Mostajo-Radji MA, Huang EJ, Nowakowski TJ, Lim DA, Diaz A, Raleigh DR, Kriegstein AR. PMID: 31901251; PMCID: PMC7029801.
The Long Noncoding RNA Pnky Is a Trans-acting Regulator of Cortical Development In Vivo. Dev Cell. 2019 05 20; 49(4):632-642.e7.Andersen RE, Hong SJ, Lim JJ, Cui M, Harpur BA, Hwang E, Delgado RN, Ramos AD, Liu SJ, Blencowe BJ, Lim DA. PMID: 31112699; PMCID: PMC6556063.
Modulating the expression of long non-coding RNAs for functional studies. EMBO Rep. 2018 12; 19(12).Liu SJ, Lim DA. PMID: 30467236; PMCID: PMC6280642.
Reirradiation and PD-1 inhibition with nivolumab for the treatment of recurrent diffuse intrinsic pontine glioma: a single-institution experience. J Neurooncol. 2018 Dec; 140(3):629-638.Kline C, Liu SJ, Duriseti S, Banerjee A, Nicolaides T, Raber S, Gupta N, Haas-Kogan D, Braunstein S, Mueller S. PMID: 30206764.
Promoter of lncRNA Gene PVT1 Is a Tumor-Suppressor DNA Boundary Element. Cell. 2018 05 31; 173(6):1398-1412.e22.Cho SW, Xu J, Sun R, Mumbach MR, Carter AC, Chen YG, Yost KE, Kim J, He J, Nevins SA, Chin SF, Caldas C, Liu SJ, Horlbeck MA, Lim DA, Weissman JS, Curtis C, Chang HY. PMID: 29731168; PMCID: PMC5984165.
Single-cell profiling of human gliomas reveals macrophage ontogeny as a basis for regional differences in macrophage activation in the tumor microenvironment. Genome Biol. 2017 Dec 20; 18(1):234.Müller S, Kohanbash G, Liu SJ, Alvarado B, Carrera D, Bhaduri A, Watchmaker PB, Yagnik G, Di Lullo E, Malatesta M, Amankulor NM, Kriegstein AR, Lim DA, Aghi M, Okada H, Diaz A. PMID: 29262845; PMCID: PMC5738907.
Spatiotemporal gene expression trajectories reveal developmental hierarchies of the human cortex. Science. 2017 12 08; 358(6368):1318-1323.Nowakowski TJ, Bhaduri A, Pollen AA, Alvarado B, Mostajo-Radji MA, Di Lullo E, Haeussler M, Sandoval-Espinosa C, Liu SJ, Velmeshev D, Ounadjela JR, Shuga J, Wang X, Lim DA, West JA, Leyrat AA, Kent WJ, Kriegstein AR. PMID: 29217575; PMCID: PMC5991609.
CRISPRi-based genome-scale identification of functional long noncoding RNA loci in human cells. Science. 2017 01 06; 355(6320).Liu SJ, Horlbeck MA, Cho SW, Birk HS, Malatesta M, He D, Attenello FJ, Villalta JE, Cho MY, Chen Y, Mandegar MA, Olvera MP, Gilbert LA, Conklin BR, Chang HY, Weissman JS, Lim DA. PMID: 27980086; PMCID: PMC5394926.
Single-cell sequencing maps gene expression to mutational phylogenies in PDGF- and EGF-driven gliomas. Mol Syst Biol. 2016 Nov 25; 12(11):889.Müller S, Liu SJ, Di Lullo E, Malatesta M, Pollen AA, Nowakowski TJ, Kohanbash G, Aghi M, Kriegstein AR, Lim DA, Diaz A. PMID: 27888226; PMCID: PMC5147052.
Single-cell analysis of long non-coding RNAs in the developing human neocortex. Genome Biol. 2016 Apr 14; 17:67.Liu SJ, Nowakowski TJ, Pollen AA, Lui JH, Horlbeck MA, Attenello FJ, He D, Weissman JS, Kriegstein AR, Diaz AA, Lim DA. PMID: 27081004; PMCID: PMC4831157.
Molecular identity of human outer radial glia during cortical development. Cell. 2015 Sep 24; 163(1):55-67.Pollen AA, Nowakowski TJ, Chen J, Retallack H, Sandoval-Espinosa C, Nicholas CR, Shuga J, Liu SJ, Oldham MC, Diaz A, Lim DA, Leyrat AA, West JA, Kriegstein AR. PMID: 26406371; PMCID: PMC4583716.
The long noncoding RNA Pnky regulates neuronal differentiation of embryonic and postnatal neural stem cells. Cell Stem Cell. 2015 Apr 02; 16(4):439-447.Ramos AD, Andersen RE, Liu SJ, Nowakowski TJ, Hong SJ, Gertz C, Salinas RD, Zarabi H, Kriegstein AR, Lim DA. PMID: 25800779; PMCID: PMC4388801.
Activation of neuronal gene expression by the JMJD3 demethylase is required for postnatal and adult brain neurogenesis. Cell Rep. 2014 Sep 11; 8(5):1290-9.Park DH, Hong SJ, Salinas RD, Liu SJ, Sun SW, Sgualdino J, Testa G, Matzuk MM, Iwamori N, Lim DA. PMID: 25176653; PMCID: PMC4201382.
Pluripotency factors in embryonic stem cells regulate differentiation into germ layers. Cell. 2011 Jun 10; 145(6):875-89.Thomson M, Liu SJ, Zou LN, Smith Z, Meissner A, Ramanathan S. PMID: 21663792; PMCID: PMC5603300.
Logic integration of mRNA signals by an RNAi-based molecular computer. Nucleic Acids Res. 2010 May; 38(8):2692-701.Xie Z, Liu SJ, Bleris L, Benenson Y. PMID: 20194121; PMCID: PMC2860122.