Luke Judge, MD, PhD

Assistant Professor, Pediatrics

M_PEDS-NEONATOLOGY

Dr. Judge is a physician-scientist with extensive experience with mouse and human models of genetic disease and developing gene therapy approaches. His current research utilizes induced pluripotent stem cells (iPSC) and gene editing to develop models and therapies for neuromuscular and cardiac diseases. He is particularly focused on allele-specific gene editing for dominant disorders caused by single-nucleotide missense mutations. Dr. Judge is also an Affiliate Investigator at the Gladstone Institute of Data Science and Biotechnology and a practicing neonatologist at UCSF Benioff Children’s Hospital. He is an active mentor in both the clinical and laboratory realms and directs the Neonatal-Perinatal Medicine Fellowship Program.

Publications

Leveraging human genetic variation to therapeutically target hundreds of genes with dominant & dispensable disease alleles.

medRxiv : the preprint server for health sciences

Ramey GD, Cowan QT, Saxena AG, Macklin BL, Watry HL, Mei X, Dierks P, Judge LM, Conklin BR, Capra JA

Monitoring biological effects of somatic cell genome editing.

Nature reviews. Genetics

Freedman BS, Bulte JWM, Conklin BR, Judge LM, Dwinell MR, Geurts AM, Sitton MJ, Mahajan V, Kiani S, Gersbach CA, Ebrahimkhani MR, Kelly JJ, Ronald JA, Morizane R, Gupta N, Shakeri-Zadeh A, Vo N, Saha K, Saxena S, Gamm DM, Sinha D, Tarantal AF, Vandsburger M, Matsubara A, Fu H, Tsai SQ, SCGE Dissemination and Coordinating Center Toolkit Team, SCGE Biological Effects Initiative

Generation of WTD, a control human iPSC line for genetic research.

Stem cell research

Macklin BL, Runyon WV, Feliciano CM, Dierks PH, Kelly KR, Watry HL, Judge LM, Conklin BR

Haplotype editing with CRISPR-Cas9 as a therapeutic approach for dominant-negative missense mutations in NEFL.

Molecular therapy : the journal of the American Society of Gene Therapy

Dua PH, Simon BMJ, Marley CBE, Feliciano CM, Watry HL, Cowan QT, Steury D, Abraham A, Gilbertson EN, Ramey GD, Capra JA, Conklin BR, Judge LM

Characterizing and controlling CRISPR repair outcomes in nondividing human cells.

Nature communications

Ramadoss GN, Namaganda SJ, Kumar MM, Hamilton JR, Sharma R, Chow KG, Workley LA, Macklin BL, Sun M, Ha AS, Liu JC, Fellmann C, Watry HL, Dierks PH, Bose RS, Jin J, Perez BS, Sandoval Espinoza CR, Matia MP, Lu SH, Judge LM, Shy BR, Nussenzweig A, Adamson B, Murthy N, Doudna JA, Kampmann M, Conklin BR

A microphysiological system for screening lipid nanoparticle-mRNA complexes predicts in vivo heart transfection efficacy.

Nature biomedical engineering

Neiman G, Costa MW, Han H, Zhao S, K Ng T, Siemons B, Nishino T, Huang Y, Lal S, Wu K, M Judge L, R Conklin B, Srivastava D, Murthy N, Healy KE

Generation and characterization of a human induced pluripotent stem cell (iPSC) line from a patient with BAG3 P209L myofibrillar myopathy-6.

Stem cell research

Filippi K, Riße I, Judge LM, Conklin BR, Fleischmann BK, Hesse M

Generation and characterization of an isogenic control line by correcting the BAG3 P209L mutation of a human induced pluripotent stem cell (hiPSC) line from a patient with myofibrillar myopathy-6.

Stem cell research

Filippi K, Riße I, Judge LM, Conklin BR, Fleischmann BK, Hesse M

Advances and challenges in modeling inherited peripheral neuropathies using iPSCs.

Experimental & molecular medicine

Van Lent J, Prior R, Pérez Siles G, Cutrupi AN, Kennerson ML, Vangansewinkel T, Wolfs E, Mukherjee-Clavin B, Nevin Z, Judge L, Conklin B, Tyynismaa H, Clark AJ, Bennett DL, Van Den Bosch L, Saporta M, Timmerman V

Functional analysis of a common BAG3 allele associated with protection from heart failure.

Nature Cardiovascular Research

Perez-Bermejo JA, Judge LM, Jensen CL, Wu K, Watry HL, Truong A, Ho JJ, Carter M, Runyon WV, Kaake RM, Pulido EH, Mandegar MA, Swaney DL, So PL, Krogan NJ, Conklin BR

Allele-Specific Gene Editing Rescues Pathology in a Human Model of Charcot-Marie-Tooth Disease Type 2E.

Frontiers in Cell and Developmental Biology

Feliciano CM, Wu K, Watry HL, Marley CBE, Ramadoss GN, Ghanim HY, Liu AZ, Zholudeva LV, McDevitt TC, Saporta MA, Conklin BR, Judge LM

Bioengineered optogenetic model of human neuromuscular junction.

Biomaterials

Vila OF, Chavez M, Ma SP, Yeager K, Zholudeva LV, Colón-Mercado JM, Qu Y, Nash TR, Lai C, Feliciano CM, Carter M, Kamm RD, Judge LM, Conklin BR, Ward ME, McDevitt TC, Vunjak-Novakovic G

Rapid, precise quantification of large DNA excisions and inversions by ddPCR.

Scientific reports

Watry HL, Feliciano CM, Gjoni K, Takahashi G, Miyaoka Y, Conklin BR, Judge LM

Mapping cis-regulatory chromatin contacts in neural cells links neuropsychiatric disorder risk variants to target genes.

Nature genetics

Song M, Yang X, Ren X, Maliskova L, Li B, Jones IR, Wang C, Jacob F, Wu K, Traglia M, Tam TW, Jamieson K, Lu SY, Ming GL, Li Y, Yao J, Weiss LA, Dixon JR, Judge LM, Conklin BR, Song H, Gan L, Shen Y

Unbiased detection of CRISPR off-targets in vivo using DISCOVER-Seq.

Science (New York, N.Y.)

Wienert B, Wyman SK, Richardson CD, Yeh CD, Akcakaya P, Porritt MJ, Morlock M, Vu JT, Kazane KR, Watry HL, Judge LM, Conklin BR, Maresca M, Corn JE

Two patients with FOXF1 mutations with alveolar capillary dysplasia with misalignment of pulmonary veins and other malformations: Two different presentations and outcomes.

American journal of medical genetics. Part A

Abu-El-Haija A, Fineman J, Connolly AJ, Murali P, Judge LM, Slavotinek AM

Variable rescue of microtubule and physiological phenotypes in mdx muscle expressing different miniaturized dystrophins.

Human molecular genetics

Nelson DM, Lindsay A, Judge LM, Duan D, Chamberlain JS, Lowe DA, Ervasti JM

A BAG3 chaperone complex maintains cardiomyocyte function during proteotoxic stress.

JCI insight

Judge LM, Perez-Bermejo JA, Truong A, Ribeiro AJ, Yoo JC, Jensen CL, Mandegar MA, Huebsch N, Kaake RM, So PL, Srivastava D, Pruitt BL, Krogan NJ, Conklin BR

Miniaturized iPS-Cell-Derived Cardiac Muscles for Physiologically Relevant Drug Response Analyses.

Scientific reports

Huebsch N, Loskill P, Deveshwar N, Spencer CI, Judge LM, Mandegar MA, Fox CB, Mohamed TM, Ma Z, Mathur A, Sheehan AM, Truong A, Saxton M, Yoo J, Srivastava D, Desai TA, So PL, Healy KE, Conklin BR

CRISPR Interference Efficiently Induces Specific and Reversible Gene Silencing in Human iPSCs.

Cell stem cell

Mandegar MA, Huebsch N, Frolov EB, Shin E, Truong A, Olvera MP, Chan AH, Miyaoka Y, Holmes K, Spencer CI, Judge LM, Gordon DE, Eskildsen TV, Villalta JE, Horlbeck MA, Gilbert LA, Krogan NJ, Sheikh SP, Weissman JS, Qi LS, So PL, Conklin BR

Automated Video-Based Analysis of Contractility and Calcium Flux in Human-Induced Pluripotent Stem Cell-Derived Cardiomyocytes Cultured over Different Spatial Scales.

Tissue engineering. Part C, Methods

Huebsch N, Loskill P, Mandegar MA, Marks NC, Sheehan AS, Ma Z, Mathur A, Nguyen TN, Yoo JC, Judge LM, Spencer CI, Chukka AC, Russell CR, So PL, Conklin BR, Healy KE

Isolation of single-base genome-edited human iPS cells without antibiotic selection.

Nature methods

Miyaoka Y, Chan AH, Judge LM, Yoo J, Huang M, Nguyen TD, Lizarraga PP, So PL, Conklin BR

Expression of the dystrophin isoform Dp116 preserves functional muscle mass and extends lifespan without preventing dystrophy in severely dystrophic mice.

Human molecular genetics

Judge LM, Arnett AL, Banks GB, Chamberlain JS

The polyproline site in hinge 2 influences the functional capacity of truncated dystrophins.

PLoS genetics

Banks GB, Judge LM, Allen JM, Chamberlain JS

Sarcolemmal nNOS anchoring reveals a qualitative difference between dystrophin and utrophin.

Journal of cell science

Li D, Bareja A, Judge L, Yue Y, Lai Y, Fairclough R, Davies KE, Chamberlain JS, Duan D

Dystrophins carrying spectrin-like repeats 16 and 17 anchor nNOS to the sarcolemma and enhance exercise performance in a mouse model of muscular dystrophy.

The Journal of clinical investigation

Lai Y, Thomas GD, Yue Y, Yang HT, Li D, Long C, Judge L, Bostick B, Chamberlain JS, Terjung RL, Duan D

Dissecting the signaling and mechanical functions of the dystrophin-glycoprotein complex.

Journal of cell science

Judge LM, Haraguchiln M, Chamberlain JS

Gene therapy for Duchenne muscular dystrophy: AAV leads the way.

Acta myologica : myopathies and cardiomyopathies : official journal of the Mediterranean Society of Myology

Judge LM, Chamberlain JS

Discovery and SAR of a novel selective and orally bioavailable nonpeptide classical competitive inhibitor class of protein-tyrosine phosphatase 1B.

Journal of medicinal chemistry

Andersen HS, Olsen OH, Iversen LF, Sørensen AL, Mortensen SB, Christensen MS, Branner S, Hansen TK, Lau JF, Jeppesen L, Moran EJ, Su J, Bakir F, Judge L, Shahbaz M, Collins T, Vo T, Newman MJ, Ripka WC, Møller NP

Link

https://profiles.ucsf.edu/luke.judge

Publications

Leveraging human genetic variation to therapeutically target hundreds of genes with dominant & dispensable disease alleles.

Monitoring biological effects of somatic cell genome editing.

Generation of WTD, a control human iPSC line for genetic research.

Haplotype editing with CRISPR-Cas9 as a therapeutic approach for dominant-negative missense mutations in NEFL.

Characterizing and controlling CRISPR repair outcomes in nondividing human cells.

A microphysiological system for screening lipid nanoparticle-mRNA complexes predicts in vivo heart transfection efficacy.

Generation and characterization of a human induced pluripotent stem cell (iPSC) line from a patient with BAG3 P209L myofibrillar myopathy-6.

Generation and characterization of an isogenic control line by correcting the BAG3 P209L mutation of a human induced pluripotent stem cell (hiPSC) line from a patient with myofibrillar myopathy-6.

Advances and challenges in modeling inherited peripheral neuropathies using iPSCs.

Functional analysis of a common BAG3 allele associated with protection from heart failure.

Allele-Specific Gene Editing Rescues Pathology in a Human Model of Charcot-Marie-Tooth Disease Type 2E.

Bioengineered optogenetic model of human neuromuscular junction.

Rapid, precise quantification of large DNA excisions and inversions by ddPCR.

Mapping cis-regulatory chromatin contacts in neural cells links neuropsychiatric disorder risk variants to target genes.

Unbiased detection of CRISPR off-targets in vivo using DISCOVER-Seq.

Two patients with FOXF1 mutations with alveolar capillary dysplasia with misalignment of pulmonary veins and other malformations: Two different presentations and outcomes.

Variable rescue of microtubule and physiological phenotypes in mdx muscle expressing different miniaturized dystrophins.

A BAG3 chaperone complex maintains cardiomyocyte function during proteotoxic stress.

Miniaturized iPS-Cell-Derived Cardiac Muscles for Physiologically Relevant Drug Response Analyses.

CRISPR Interference Efficiently Induces Specific and Reversible Gene Silencing in Human iPSCs.

Automated Video-Based Analysis of Contractility and Calcium Flux in Human-Induced Pluripotent Stem Cell-Derived Cardiomyocytes Cultured over Different Spatial Scales.

Isolation of single-base genome-edited human iPS cells without antibiotic selection.

Expression of the dystrophin isoform Dp116 preserves functional muscle mass and extends lifespan without preventing dystrophy in severely dystrophic mice.

The polyproline site in hinge 2 influences the functional capacity of truncated dystrophins.

Sarcolemmal nNOS anchoring reveals a qualitative difference between dystrophin and utrophin.

Dystrophins carrying spectrin-like repeats 16 and 17 anchor nNOS to the sarcolemma and enhance exercise performance in a mouse model of muscular dystrophy.

Dissecting the signaling and mechanical functions of the dystrophin-glycoprotein complex.

Gene therapy for Duchenne muscular dystrophy: AAV leads the way.

Discovery and SAR of a novel selective and orally bioavailable nonpeptide classical competitive inhibitor class of protein-tyrosine phosphatase 1B.

A convenient large-scale chiral synthesis of protected 2-substituted 4-oxo-piperidine derivatives.

Protein engineering of protein kinase A catalytic subunits results in the acquisition of novel inhibitor sensitivity.

A hydrazino nicotinamide derivative of cholesterol for radiolabelling liposomes with 99mTc.