Alexander Marson, MD, PhD

Director
Medicine
+1 415 734-4861

Our lab's goal is to understand the genetic circuits that control human immune cell function in health and disease. We have begun to identify how genetic risk variants for autoimmune diseases disrupt immune cell circuits (Farh and Marson et al., Nature 2015; Simeonov et al., Nature, 2017), and how pathogenic circuits may be targeted with novel therapeutics (Xiao et al., Immunity 2014). My lab has developed new tools for efficient CRISPR genome engineering in primary human T cells (Schumann et al., PNAS 2015; Roth et al., Nature 2018; Nguyen et al. Nature Biotech 2020). Now we are pursuing a comprehensive strategy to test how coding and non-coding genetic variation control essential programs in the human immune system (Simeonov et al. Nature, 2017; Shifrut et al., Cell 2018; Roth et al., Cell 2020; Cortez et al., Nature 2020; Schumann et al., Nature Immunology 2020). Genome engineered human T cells hold great potential for the next generation of cell-based therapies for cancer, autoimmunity and infectious diseases.

Publications: 

Antigen-Specific T Cell Receptor Discovery for Treating Progressive Multifocal Leukoencephalopathy.

bioRxiv : the preprint server for biology

Gupta S, Martinov T, Thelen A, Sunahara M, Mureli S, Vazquez A, Gerdts J, Dandekar R, Cortese I, Fouassier C, Schanzer E, Urnov FD, Marson A, Shy BR, Greenberg PD, Wilson MR

Method of moments framework for differential expression analysis of single-cell RNA sequencing data.

Cell

Kim MC, Gate R, Lee DS, Tolopko A, Lu A, Gordon E, Shifrut E, Garcia-Nieto PE, Marson A, Ntranos V, Ye CJ

Gene regulatory network inference from CRISPR perturbations in primary CD4+ T cells elucidates the genomic basis of immune disease.

Cell genomics

Weinstock JS, Arce MM, Freimer JW, Ota M, Marson A, Battle A, Pritchard JK

Phenotypic profiling of human induced regulatory T cells at early differentiation: insights into distinct immunosuppressive potential.

Cellular and molecular life sciences : CMLS

Kattelus R, Starskaia I, Lindén M, Batkulwar K, Pietilä S, Moulder R, Marson A, Rasool O, Suomi T, Elo LL, Lahesmaa R, Buchacher T

Deciphering regulation of FOXP3 expression in human conventional T cells.

bioRxiv : the preprint server for biology

Umhoefer JM, Arce MM, Dajani R, Belk JA, Mowery CT, Nguyen V, Gowen BG, Simeonov DR, Curie GL, Corn JE, Chang HY, Marson A

NKp30 and NKG2D contribute to natural killer recognition of HIV-infected cells.

bioRxiv : the preprint server for biology

Zhao NQ, Pi R, Nguyen DN, Ranganath T, Seiler C, Holmes S, Marson A, Blish CA

A model for accurate quantification of CRISPR effects in pooled FACS screens.

bioRxiv : the preprint server for biology

Pimentel H, Freimer JW, Arce MM, Garrido CM, Marson A, Pritchard JK

Systematic decoding of cis gene regulation defines context-dependent control of the multi-gene costimulatory receptor locus in human T cells.

Nature genetics

Mowery CT, Freimer JW, Chen Z, Casaní-Galdón S, Umhoefer JM, Arce MM, Gjoni K, Daniel B, Sandor K, Gowen BG, Nguyen V, Simeonov DR, Garrido CM, Curie GL, Schmidt R, Steinhart Z, Satpathy AT, Pollard KS, Corn JE, Bernstein BE, Ye CJ, Marson A

Long noncoding RNA LIRIL2R modulates FOXP3 levels and suppressive function of human CD4+ regulatory T cells by regulating IL2RA.

Proceedings of the National Academy of Sciences of the United States of America

Andrabi SBA, Kalim UU, Palani S, Khan MM, Khan MH, Fagersund J, Orpana J, Paulin N, Batkulwar K, Junttila S, Buchacher T, Grönroos T, Toikka L, Ammunet T, Sen P, Orešic M, Kumpulainen V, Tuomisto JEE, Sinha R, Marson A, Rasool O, Elo LL, Lahesmaa R

A proximal enhancer regulates RORA expression during early human Th17 cell differentiation.

Clinical immunology (Orlando, Fla.)

Kalim UU, Biradar R, Junttila S, Khan MM, Tripathi S, Khan MH, Smolander J, Kanduri K, Envall T, Laiho A, Marson A, Rasool O, Elo LL, Lahesmaa R

Bidirectional epigenetic editing reveals hierarchies in gene regulation.

Nature biotechnology

Pacalin NM, Steinhart Z, Shi Q, Belk JA, Dorovskyi D, Kraft K, Parker KR, Shy BR, Marson A, Chang HY

Publisher Correction: Advancing T cell-based cancer therapy with single-cell technologies.

Nature medicine

Bucktrout SL, Banovich NE, Butterfield LH, Cimen-Bozkus C, Giles JR, Good Z, Goodman D, Jonsson VD, Lareau C, Marson A, Maurer DM, Munson PV, Stubbington M, Taylor S, Cutchin A

Improving prime editing with an endogenous small RNA-binding protein.

Nature

Yan J, Oyler-Castrillo P, Ravisankar P, Ward CC, Levesque S, Jing Y, Simpson D, Zhao A, Li H, Yan W, Goudy L, Schmidt R, Solley SC, Gilbert LA, Chan MM, Bauer DE, Marson A, Parsons LR, Adamson B

CRISPR-Cas9 screen of E3 ubiquitin ligases identifies TRAF2 and UHRF1 as regulators of HIV latency in primary human T cells.

mBio

Rathore U, Haas P, Easwar Kumar V, Hiatt J, Haas KM, Bouhaddou M, Swaney DL, Stevenson E, Zuliani-Alvarez L, McGregor MJ, Turner-Groth A, Ochieng' Olwal C, Bediako Y, Braberg H, Soucheray M, Ott M, Eckhardt M, Hultquist JF, Marson A, Kaake RM, Krogan NJ

Ultra-high efficiency T cell reprogramming at multiple loci with SEED-Selection.

bioRxiv : the preprint server for biology

Chang CR, Vykunta VS, Goodman DB, Muldoon JJ, Nyberg WA, Liu C, Allain V, Rothrock A, Wang CH, Marson A, Shy BR, Eyquem J

The lncRNA Malat1 inhibits miR-15/16 to enhance cytotoxic T cell activation and memory cell formation.

eLife

Wheeler BD, Gagnon JD, Zhu WS, Muñoz-Sandoval P, Wong SK, Simeonov DS, Li Z, DeBarge R, Spitzer MH, Marson A, Ansel KM

Base-editing mutagenesis maps alleles to tune human T cell functions.

Nature

Schmidt R, Ward CC, Dajani R, Armour-Garb Z, Ota M, Allain V, Hernandez R, Layeghi M, Xing G, Goudy L, Dorovskyi D, Wang C, Chen YY, Ye CJ, Shy BR, Gilbert LA, Eyquem J, Pritchard JK, Dodgson SE, Marson A

Multiplexed CRISPR gene editing in primary human islet cells with Cas9 ribonucleoprotein.

iScience

Bevacqua RJ, Zhao W, Merheb E, Kim SH, Marson A, Gloyn AL, Kim SK

PIM kinases regulate early human Th17 cell differentiation.

Cell reports

Buchacher T, Shetty A, Koskela SA, Smolander J, Kaukonen R, Sousa AGG, Junttila S, Laiho A, Rundquist O, Lönnberg T, Marson A, Rasool O, Elo LL, Lahesmaa R

Gene regulatory network inference from CRISPR perturbations in primary CD4+ T cells elucidates the genomic basis of immune disease.

bioRxiv : the preprint server for biology

Weinstock JS, Arce MM, Freimer JW, Ota M, Marson A, Battle A, Pritchard JK

HIC1 interacts with FOXP3 multi protein complex: Novel pleiotropic mechanisms to regulate human regulatory T cell differentiation and function.

Immunology letters

Andrabi SBA, Batkulwar K, Bhosale SD, Moulder R, Khan MH, Buchacher T, Khan MM, Arnkil I, Rasool O, Marson A, Kalim UU, Lahesmaa R

Multiplexed CRISPR gene editing in primary human islet cells with Cas9 ribonucleoprotein.

bioRxiv : the preprint server for biology

Bevacqua RJ, Zhao W, Merheb E, Kim SH, Marson A, Gloyn AL, Kim SK

Modular pooled discovery of synthetic knockin sequences to program durable cell therapies.

Cell

Blaeschke F, Chen YY, Apathy R, Daniel B, Chen AY, Chen PA, Sandor K, Zhang W, Li Z, Mowery CT, Yamamoto TN, Nyberg WA, To A, Yu R, Bueno R, Kim MC, Schmidt R, Goodman DB, Feuchtinger T, Eyquem J, Jimmie Ye C, Carnevale J, Satpathy AT, Shifrut E, Roth TL, Marson A

CRISPR screens decode cancer cell pathways that trigger γδ T cell detection.

Nature

Mamedov MR, Vedova S, Freimer JW, Sahu AD, Ramesh A, Arce MM, Meringa AD, Ota M, Chen PA, Hanspers K, Nguyen VQ, Takeshima KA, Rios AC, Pritchard JK, Kuball J, Sebestyen Z, Adams EJ, Marson A

The lncRNA Malat1 Inhibits miR-15/16 to Enhance Cytotoxic T Cell Activation and Memory Cell Formation.

bioRxiv : the preprint server for biology

Wheeler BD, Gagnon JD, Zhu WS, Muñoz-Sandoval P, Wong SK, Simeonov DS, Li Z, Debarge R, Spitzer M, Marson A, Ansel KM

Non-coding sequence variation reveals fragility within interleukin 2 feedback circuitry and shapes autoimmune disease risk.

bioRxiv : the preprint server for biology

Simeonov DR, Park K, Cortez JT, Young A, Li Z, Nguyen V, Umhoefer J, Indart AC, Woo JM, Anderson MS, Tsang JS, Germain RN, Wong HS, Marson A

Peptide-mediated delivery of CRISPR enzymes for the efficient editing of primary human lymphocytes.

Nature biomedical engineering

Foss DV, Muldoon JJ, Nguyen DN, Carr D, Sahu SU, Hunsinger JM, Wyman SK, Krishnappa N, Mendonsa R, Schanzer EV, Shy BR, Vykunta VS, Allain V, Li Z, Marson A, Eyquem J, Wilson RC

Dynamic phosphatase-recruitment controls B-cell selection and oncogenic signaling.

bioRxiv : the preprint server for biology

Lee J, Robinson ME, Sun R, Kume K, Ma N, Cosgun KN, Chan LN, Leveille E, Geng H, Vykunta VS, Shy BR, Marson A, Katz S, Chen J, Paietta E, Meffre E, Vaidehi N, Müschen M

A single-amino acid substitution in the adaptor LAT accelerates TCR proofreading kinetics and alters T-cell selection, maintenance and function.

Nature immunology

Lo WL, Kuhlmann M, Rizzuto G, Ekiz HA, Kolawole EM, Revelo MP, Andargachew R, Li Z, Tsai YL, Marson A, Evavold BD, Zehn D, Weiss A

Pooled screening of CAR T cells identifies diverse immune signaling domains for next-generation immunotherapies.

Science translational medicine

Goodman DB, Azimi CS, Kearns K, Talbot A, Garakani K, Garcia J, Patel N, Hwang B, Lee D, Park E, Vykunta VS, Shy BR, Ye CJ, Eyquem J, Marson A, Bluestone JA, Roybal KT

Advancing T cell-based cancer therapy with single-cell technologies.

Nature medicine

Bucktrout SL, Banovich NE, Butterfield LH, Cimen-Bozkus C, Giles JR, Good Z, Goodman D, Jonsson VD, Lareau C, Marson A, Maurer DM, Munson PV, Stubbington M, Taylor S, Cutchin A

High-yield genome engineering in primary cells using a hybrid ssDNA repair template and small-molecule cocktails.

Nature biotechnology

Shy BR, Vykunta VS, Ha A, Talbot A, Roth TL, Nguyen DN, Pfeifer WG, Chen YY, Blaeschke F, Shifrut E, Vedova S, Mamedov MR, Chung JJ, Li H, Yu R, Wu D, Wolf J, Martin TG, Castro CE, Ye L, Esensten JH, Eyquem J, Marson A

RASA2 ablation in T cells boosts antigen sensitivity and long-term function.

Nature

Carnevale J, Shifrut E, Kale N, Nyberg WA, Blaeschke F, Chen YY, Li Z, Bapat SP, Diolaiti ME, O'Leary P, Vedova S, Belk J, Daniel B, Roth TL, Bachl S, Anido AA, Prinzing B, Ibañez-Vega J, Lange S, Haydar D, Luetke-Eversloh M, Born-Bony M, Hegde B, Kogan S, Feuchtinger T, Okada H, Satpathy AT, Shannon K, Gottschalk S, Eyquem J, Krenciute G, Ashworth A, Marson A

A single-cell transcriptional gradient in human cutaneous memory T cells restricts Th17/Tc17 identity.

Cell reports. Medicine

Cook CP, Taylor M, Liu Y, Schmidt R, Sedgewick A, Kim E, Hailer A, North JP, Harirchian P, Wang H, Kashem SW, Shou Y, McCalmont TC, Benz SC, Choi J, Purdom E, Marson A, Ramos SBV, Cheng JB, Cho RJ

Systematic discovery and perturbation of regulatory genes in human T cells reveals the architecture of immune networks.

Nature genetics

Freimer JW, Shaked O, Naqvi S, Sinnott-Armstrong N, Kathiria A, Garrido CM, Chen AF, Cortez JT, Greenleaf WJ, Pritchard JK, Marson A

Genome-wide CRISPR screens of T cell exhaustion identify chromatin remodeling factors that limit T cell persistence.

Cancer cell

Belk JA, Yao W, Ly N, Freitas KA, Chen YT, Shi Q, Valencia AM, Shifrut E, Kale N, Yost KE, Duffy CV, Daniel B, Hwee MA, Miao Z, Ashworth A, Mackall CL, Marson A, Carnevale J, Vardhana SA, Satpathy AT

Global post-translational modification profiling of HIV-1-infected cells reveals mechanisms of host cellular pathway remodeling.

Cell reports

Johnson JR, Crosby DC, Hultquist JF, Kurland AP, Adhikary P, Li D, Marlett J, Swann J, Hüttenhain R, Verschueren E, Johnson TL, Newton BW, Shales M, Simon VA, Beltrao P, Frankel AD, Marson A, Cox JS, Fregoso OI, Young JAT, Krogan NJ

A functional map of HIV-host interactions in primary human T cells.

Nature communications

Hiatt J, Hultquist JF, McGregor MJ, Bouhaddou M, Leenay RT, Simons LM, Young JM, Haas P, Roth TL, Tobin V, Wojcechowskyj JA, Woo JM, Rathore U, Cavero DA, Shifrut E, Nguyen TT, Haas KM, Malik HS, Doudna JA, May AP, Marson A, Krogan NJ

Obesity alters pathology and treatment response in inflammatory disease.

Nature

Bapat SP, Whitty C, Mowery CT, Liang Y, Yoo A, Jiang Z, Peters MC, Zhang LJ, Vogel I, Zhou C, Nguyen VQ, Li Z, Chang C, Zhu WS, Hastie AT, He H, Ren X, Qiu W, Gayer SG, Liu C, Choi EJ, Fassett M, Cohen JN, Sturgill JL, Crotty Alexander LE, Suh JM, Liddle C, Atkins AR, Yu RT, Downes M, Liu S, Nikolajczyk BS, Lee IK, Guttman-Yassky E, Ansel KM, Woodruff PG, Fahy JV, Sheppard D, Gallo RL, Ye CJ, Evans RM, Zheng Y, Marson A

Microbial signals, MyD88, and lymphotoxin drive TNF-independent intestinal epithelial tissue damage.

The Journal of clinical investigation

Rusu I, Mennillo E, Bain JL, Li Z, Sun X, Ly KM, Rosli YY, Naser M, Wang Z, Advincula R, Achacoso P, Shao L, Razani B, Klein OD, Marson A, Turnbaugh JA, Turnbaugh PJ, Malynn BA, Ma A, Kattah MG

Hypoxia Is a Dominant Remodeler of the Effector T Cell Surface Proteome Relative to Activation and Regulatory T Cell Suppression.

Molecular & cellular proteomics : MCP

Byrnes JR, Weeks AM, Shifrut E, Carnevale J, Kirkemo L, Ashworth A, Marson A, Wells JA

CRISPR-Cas9-mediated nuclear transport and genomic integration of nanostructured genes in human primary cells.

Nucleic acids research

Lin-Shiao E, Pfeifer WG, Shy BR, Saffari Doost M, Chen E, Vykunta VS, Hamilton JR, Stahl EC, Lopez DM, Sandoval Espinoza CR, Deyanov AE, Lew RJ, Poirer MG, Marson A, Castro CE, Doudna JA

CD97 promotes spleen dendritic cell homeostasis through the mechanosensing of red blood cells.

Science (New York, N.Y.)

Liu D, Duan L, Rodda LB, Lu E, Xu Y, An J, Qiu L, Liu F, Looney MR, Yang Z, Allen CDC, Li Z, Marson A, Cyster JG

CRISPR activation and interference screens decode stimulation responses in primary human T cells.

Science (New York, N.Y.)

Schmidt R, Steinhart Z, Layeghi M, Freimer JW, Bueno R, Nguyen VQ, Blaeschke F, Ye CJ, Marson A

ATF7ip Targets Transposable Elements for H3K9me3 Deposition to Modify CD8+ T Cell Effector and Memory Responses.

Journal of immunology (Baltimore, Md. : 1950)

Sin JH, Kashyap S, Acenas D, Cortez JT, Lee J, Marson A, Matloubian M, Waterfield MR

Robust T cell activation requires an eIF3-driven burst in T cell receptor translation.

eLife

De Silva D, Ferguson L, Chin GH, Smith BE, Apathy RA, Roth TL, Blaeschke F, Kudla M, Marson A, Ingolia NT, Cate JH

PICS2: next-generation fine mapping via probabilistic identification of causal SNPs.

Bioinformatics (Oxford, England)

Taylor KE, Ansel KM, Marson A, Criswell LA, Farh KK

Genome editing to define the function of risk loci and variants in rheumatic disease.

Nature reviews. Rheumatology

Baglaenko Y, Macfarlane D, Marson A, Nigrovic PA, Raychaudhuri S

Abcc1 and Ggt5 support lymphocyte guidance through export and catabolism of S-geranylgeranyl-l-glutathione.

Science immunology

Gallman AE, Wolfreys FD, Nguyen DN, Sandy M, Xu Y, An J, Li Z, Marson A, Lu E, Cyster JG

Targeted delivery of CRISPR-Cas9 and transgenes enables complex immune cell engineering.

Cell reports

Hamilton JR, Tsuchida CA, Nguyen DN, Shy BR, McGarrigle ER, Sandoval Espinoza CR, Carr D, Blaeschke F, Marson A, Doudna JA

Efficient generation of isogenic primary human myeloid cells using CRISPR-Cas9 ribonucleoproteins.

Cell reports

Hiatt J, Cavero DA, McGregor MJ, Zheng W, Budzik JM, Roth TL, Haas KM, Wu D, Rathore U, Meyer-Franke A, Bouzidi MS, Shifrut E, Lee Y, Kumar VE, Dang EV, Gordon DE, Wojcechowskyj JA, Hultquist JF, Fontaine KA, Pillai SK, Cox JS, Ernst JD, Krogan NJ, Marson A

XYZeq: Spatially resolved single-cell RNA sequencing reveals expression heterogeneity in the tumor microenvironment.

Science advances

Lee Y, Bogdanoff D, Wang Y, Hartoularos GC, Woo JM, Mowery CT, Nisonoff HM, Lee DS, Sun Y, Lee J, Mehdizadeh S, Cantlon J, Shifrut E, Ngyuen DN, Roth TL, Song YS, Marson A, Chow ED, Ye CJ

The CD28-Transmembrane Domain Mediates Chimeric Antigen Receptor Heterodimerization With CD28.

Frontiers in immunology

Muller YD, Nguyen DP, Ferreira LMR, Ho P, Raffin C, Valencia RVB, Congrave-Wilson Z, Roth TL, Eyquem J, Van Gool F, Marson A, Perez L, Wells JA, Bluestone JA, Tang Q

Epithelial miR-141 regulates IL-13-induced airway mucus production.

JCI insight

Siddiqui S, Johansson K, Joo A, Bonser LR, Koh KD, Le Tonqueze O, Bolourchi S, Bautista RA, Zlock L, Roth TL, Marson A, Bhakta NR, Ansel KM, Finkbeiner WE, Erle DJ, Woodruff PG

Inhibitory CD161 receptor identified in glioma-infiltrating T cells by single-cell analysis.

Cell

Mathewson ND, Ashenberg O, Tirosh I, Gritsch S, Perez EM, Marx S, Jerby-Arnon L, Chanoch-Myers R, Hara T, Richman AR, Ito Y, Pyrdol J, Friedrich M, Schumann K, Poitras MJ, Gokhale PC, Gonzalez Castro LN, Shore ME, Hebert CM, Shaw B, Cahill HL, Drummond M, Zhang W, Olawoyin O, Wakimoto H, Rozenblatt-Rosen O, Brastianos PK, Liu XS, Jones PS, Cahill DP, Frosch MP, Louis DN, Freeman GJ, Ligon KL, Marson A, Chiocca EA, Reardon DA, Regev A, Suvà ML, Wucherpfennig KW

TCF-1 regulates HIV-specific CD8+ T cell expansion capacity.

JCI insight

Rutishauser RL, Deguit CDT, Hiatt J, Blaeschke F, Roth TL, Wang L, Raymond KA, Starke CE, Mudd JC, Chen W, Smullin C, Matus-Nicodemos R, Hoh R, Krone M, Hecht FM, Pilcher CD, Martin JN, Koup RA, Douek DC, Brenchley JM, Sékaly RP, Pillai SK, Marson A, Deeks SG, McCune JM, Hunt PW

Genetic Disease and Therapy.

Annual review of pathology

Roth TL, Marson A

Dysregulated RASGRP1 expression through RUNX1 mediated transcription promotes autoimmunity.

European journal of immunology

Baars MJD, Douma T, Simeonov DR, Myers DR, Kulhanek K, Banerjee S, Zwakenberg S, Baltissen MP, Amini M, de Roock S, van Wijk F, Vermeulen M, Marson A, Roose JP, Vercoulen Y

Author Correction: Multiplexed droplet single-cell RNA-sequencing using natural genetic variation.

Nature biotechnology

Kang HM, Subramaniam M, Targ S, Nguyen M, Maliskova L, McCarthy E, Wan E, Wong S, Byrnes L, Lanata CM, Gate RE, Mostafavi S, Marson A, Zaitlen N, Criswell LA, Ye CJ

Functional CRISPR dissection of gene networks controlling human regulatory T cell identity.

Nature immunology

Schumann K, Raju SS, Lauber M, Kolb S, Shifrut E, Cortez JT, Skartsis N, Nguyen VQ, Woo JM, Roth TL, Yu R, Nguyen MLT, Simeonov DR, Nguyen DN, Targ S, Gate RE, Tang Q, Bluestone JA, Spitzer MH, Ye CJ, Marson A

Layilin augments integrin activation to promote antitumor immunity.

The Journal of experimental medicine

Mahuron KM, Moreau JM, Glasgow JE, Boda DP, Pauli ML, Gouirand V, Panjabi L, Grewal R, Luber JM, Mathur AN, Feldman RM, Shifrut E, Mehta P, Lowe MM, Alvarado MD, Marson A, Singer M, Wells J, Jupp R, Daud AI, Rosenblum MD

NR4A nuclear receptors restrain B cell responses to antigen when second signals are absent or limiting.

Nature immunology

Tan C, Hiwa R, Mueller JL, Vykunta V, Hibiya K, Noviski M, Huizar J, Brooks JF, Garcia J, Heyn C, Li Z, Marson A, Zikherman J

Evaluation of SARS-CoV-2 serology assays reveals a range of test performance.

Nature biotechnology

Whitman JD, Hiatt J, Mowery CT, Shy BR, Yu R, Yamamoto TN, Rathore U, Goldgof GM, Whitty C, Woo JM, Gallman AE, Miller TE, Levine AG, Nguyen DN, Bapat SP, Balcerek J, Bylsma SA, Lyons AM, Li S, Wong AW, Gillis-Buck EM, Steinhart ZB, Lee Y, Apathy R, Lipke MJ, Smith JA, Zheng T, Boothby IC, Isaza E, Chan J, Acenas DD, Lee J, Macrae TA, Kyaw TS, Wu D, Ng DL, Gu W, York VA, Eskandarian HA, Callaway PC, Warrier L, Moreno ME, Levan J, Torres L, Farrington LA, Loudermilk RP, Koshal K, Zorn KC, Garcia-Beltran WF, Yang D, Astudillo MG, Bernstein BE, Gelfand JA, Ryan ET, Charles RC, Iafrate AJ, Lennerz JK, Miller S, Chiu CY, Stramer SL, Wilson MR, Manglik A, Ye CJ, Krogan NJ, Anderson MS, Cyster JG, Ernst JD, Wu AHB, Lynch KL, Bern C, Hsu PD, Marson A

Rewired signaling network in T cells expressing the chimeric antigen receptor (CAR).

The EMBO journal

Dong R, Libby KA, Blaeschke F, Fuchs W, Marson A, Vale RD, Su X

Test performance evaluation of SARS-CoV-2 serological assays.

medRxiv : the preprint server for health sciences

Whitman JD, Hiatt J, Mowery CT, Shy BR, Yu R, Yamamoto TN, Rathore U, Goldgof GM, Whitty C, Woo JM, Gallman AE, Miller TE, Levine AG, Nguyen DN, Bapat SP, Balcerek J, Bylsma SA, Lyons AM, Li S, Wong AW, Gillis-Buck EM, Steinhart ZB, Lee Y, Apathy R, Lipke MJ, Smith JA, Zheng T, Boothby IC, Isaza E, Chan J, Acenas DD, Lee J, Macrae TA, Kyaw TS, Wu D, Ng DL, Gu W, York VA, Eskandarian HA, Callaway PC, Warrier L, Moreno ME, Levan J, Torres L, Farrington LA, Loudermilk R, Koshal K, Zorn KC, Garcia-Beltran WF, Yang D, Astudillo MG, Bernstein BE, Gelfand JA, Ryan ET, Charles RC, Iafrate AJ, Lennerz JK, Miller S, Chiu CY, Stramer SL, Wilson MR, Manglik A, Ye CJ, Krogan NJ, Anderson MS, Cyster JG, Ernst JD, Wu AHB, Lynch KL, Bern C, Hsu PD, Marson A

CRISPR screen in regulatory T cells reveals modulators of Foxp3.

Nature

Cortez JT, Montauti E, Shifrut E, Gatchalian J, Zhang Y, Shaked O, Xu Y, Roth TL, Simeonov DR, Zhang Y, Chen S, Li Z, Woo JM, Ho J, Vogel IA, Prator GY, Zhang B, Lee Y, Sun Z, Ifergan I, Van Gool F, Hargreaves DC, Bluestone JA, Marson A, Fang D

Pooled Knockin Targeting for Genome Engineering of Cellular Immunotherapies.

Cell

Roth TL, Li PJ, Blaeschke F, Nies JF, Apathy R, Mowery C, Yu R, Nguyen MLT, Lee Y, Truong A, Hiatt J, Wu D, Nguyen DN, Goodman D, Bluestone JA, Ye CJ, Roybal K, Shifrut E, Marson A

Cyclophilin A Prevents HIV-1 Restriction in Lymphocytes by Blocking Human TRIM5α Binding to the Viral Core.

Cell reports

Selyutina A, Persaud M, Simons LM, Bulnes-Ramos A, Buffone C, Martinez-Lopez A, Scoca V, Di Nunzio F, Hiatt J, Marson A, Krogan NJ, Hultquist JF, Diaz-Griffero F

A Quantitative Genetic Interaction Map of HIV Infection.

Molecular cell

Gordon DE, Watson A, Roguev A, Zheng S, Jang GM, Kane J, Xu J, Guo JZ, Stevenson E, Swaney DL, Franks-Skiba K, Verschueren E, Shales M, Crosby DC, Frankel AD, Marson A, Marazzi I, Cagney G, Krogan NJ

Regulatory T cells use arginase 2 to enhance their metabolic fitness in tissues.

JCI insight

Lowe MM, Boothby I, Clancy S, Ahn RS, Liao W, Nguyen DN, Schumann K, Marson A, Mahuron KM, Kingsbury GA, Liu Z, Munoz Sandoval P, Rodriguez RS, Pauli ML, Taravati K, Arron ST, Neuhaus IM, Harris HW, Kim EA, Shin US, Krummel MF, Daud A, Scharschmidt TC, Rosenblum MD

Polymer-stabilized Cas9 nanoparticles and modified repair templates increase genome editing efficiency.

Nature biotechnology

Nguyen DN, Roth TL, Li PJ, Chen PA, Apathy R, Mamedov MR, Vo LT, Tobin VR, Goodman D, Shifrut E, Bluestone JA, Puck JM, Szoka FC, Marson A

Landscape of stimulation-responsive chromatin across diverse human immune cells.

Nature genetics

Calderon D, Nguyen MLT, Mezger A, Kathiria A, Müller F, Nguyen V, Lescano N, Wu B, Trombetta J, Ribado JV, Knowles DA, Gao Z, Blaeschke F, Parent AV, Burt TD, Anderson MS, Criswell LA, Greenleaf WJ, Marson A, Pritchard JK

miR-15/16 Restrain Memory T Cell Differentiation, Cell Cycle, and Survival.

Cell reports

Gagnon JD, Kageyama R, Shehata HM, Fassett MS, Mar DJ, Wigton EJ, Johansson K, Litterman AJ, Odorizzi P, Simeonov D, Laidlaw BJ, Panduro M, Patel S, Jeker LT, Feeney ME, McManus MT, Marson A, Matloubian M, Sanjabi S, Ansel KM

Large dataset enables prediction of repair after CRISPR-Cas9 editing in primary T cells.

Nature biotechnology

Leenay RT, Aghazadeh A, Hiatt J, Tse D, Roth TL, Apathy R, Shifrut E, Hultquist JF, Krogan N, Wu Z, Cirolia G, Canaj H, Leonetti MD, Marson A, May AP, Zou J

ARIH2 Is a Vif-Dependent Regulator of CUL5-Mediated APOBEC3G Degradation in HIV Infection.

Cell host & microbe

Hüttenhain R, Xu J, Burton LA, Gordon DE, Hultquist JF, Johnson JR, Satkamp L, Hiatt J, Rhee DY, Baek K, Crosby DC, Frankel AD, Marson A, Harper JW, Alpi AF, Schulman BA, Gross JD, Krogan NJ

The HVEM-BTLA Axis Restrains T Cell Help to Germinal Center B Cells and Functions as a Cell-Extrinsic Suppressor in Lymphomagenesis.

Immunity

Mintz MA, Felce JH, Chou MY, Mayya V, Xu Y, Shui JW, An J, Li Z, Marson A, Okada T, Ware CF, Kronenberg M, Dustin ML, Cyster JG

Orthotopic replacement of T-cell receptor α- and β-chains with preservation of near-physiological T-cell function.

Nature biomedical engineering

Schober K, Müller TR, Gökmen F, Grassmann S, Effenberger M, Poltorak M, Stemberger C, Schumann K, Roth TL, Marson A, Busch DH

A large CRISPR-induced bystander mutation causes immune dysregulation.

Communications biology

Simeonov DR, Brandt AJ, Chan AY, Cortez JT, Li Z, Woo JM, Lee Y, Carvalho CMB, Indart AC, Roth TL, Zou J, May AP, Lupski JR, Anderson MS, Buaas FW, Rokhsar DS, Marson A

CRISPR-Based Tools in Immunity.

Annual review of immunology

Simeonov DR, Marson A

A Mutation in the Transcription Factor Foxp3 Drives T Helper 2 Effector Function in Regulatory T Cells.

Immunity

Van Gool F, Nguyen MLT, Mumbach MR, Satpathy AT, Rosenthal WL, Giacometti S, Le DT, Liu W, Brusko TM, Anderson MS, Rudensky AY, Marson A, Chang HY, Bluestone JA

Thymic regulatory T cells arise via two distinct developmental programs.

Nature immunology

Owen DL, Mahmud SA, Sjaastad LE, Williams JB, Spanier JA, Simeonov DR, Ruscher R, Huang W, Proekt I, Miller CN, Hekim C, Jeschke JC, Aggarwal P, Broeckel U, LaRue RS, Henzler CM, Alegre ML, Anderson MS, August A, Marson A, Zheng Y, Williams CB, Farrar MA

CRISPR-Cas9 genome engineering of primary CD4+ T cells for the interrogation of HIV-host factor interactions.

Nature protocols

Hultquist JF, Hiatt J, Schumann K, McGregor MJ, Roth TL, Haas P, Doudna JA, Marson A, Krogan NJ

Genome-wide CRISPR Screens in Primary Human T Cells Reveal Key Regulators of Immune Function.

Cell

Shifrut E, Carnevale J, Tobin V, Roth TL, Woo JM, Bui CT, Li PJ, Diolaiti ME, Ashworth A, Marson A

CRL4AMBRA1 targets Elongin C for ubiquitination and degradation to modulate CRL5 signaling.

The EMBO journal

Chen SH, Jang GM, Hüttenhain R, Gordon DE, Du D, Newton BW, Johnson JR, Hiatt J, Hultquist JF, Johnson TL, Liu YL, Burton LA, Ye J, Reichermeier KM, Stroud RM, Marson A, Debnath J, Gross JD, Krogan NJ

Reprogramming human T cell function and specificity with non-viral genome targeting.

Nature

Roth TL, Puig-Saus C, Yu R, Shifrut E, Carnevale J, Li PJ, Hiatt J, Saco J, Krystofinski P, Li H, Tobin V, Nguyen DN, Lee MR, Putnam AL, Ferris AL, Chen JW, Schickel JN, Pellerin L, Carmody D, Alkorta-Aranburu G, Del Gaudio D, Matsumoto H, Morell M, Mao Y, Cho M, Quadros RM, Gurumurthy CB, Smith B, Haugwitz M, Hughes SH, Weissman JS, Schumann K, Esensten JH, May AP, Ashworth A, Kupfer GM, Greeley SAW, Bacchetta R, Meffre E, Roncarolo MG, Romberg N, Herold KC, Ribas A, Leonetti MD, Marson A

Revisiting IL-2: Biology and therapeutic prospects.

Science immunology

Abbas AK, Trotta E, R Simeonov D, Marson A, Bluestone JA

Author Correction: Discovery of stimulation-responsive immune enhancers with CRISPR activation.

Nature

Simeonov DR, Gowen BG, Boontanrart M, Roth TL, Gagnon JD, Mumbach MR, Satpathy AT, Lee Y, Bray NL, Chan AY, Lituiev DS, Nguyen ML, Gate RE, Subramaniam M, Li Z, Woo JM, Mitros T, Ray GJ, Curie GL, Naddaf N, Chu JS, Ma H, Boyer E, Van Gool F, Huang H, Liu R, Tobin VR, Schumann K, Daly MJ, Farh KK, Ansel KM, Ye CJ, Greenleaf WJ, Anderson MS, Bluestone JA, Chang HY, Corn JE, Marson A

Enhanced Genome Editing with Cas9 Ribonucleoprotein in Diverse Cells and Organisms.

Journal of visualized experiments : JoVE

Farboud B, Jarvis E, Roth TL, Shin J, Corn JE, Marson A, Meyer BJ, Patel NH, Hochstrasser ML

Light-activated cell identification and sorting (LACIS) for selection of edited clones on a nanofluidic device.

Communications biology

Mocciaro A, Roth TL, Bennett HM, Soumillon M, Shah A, Hiatt J, Chapman K, Marson A, Lavieu G

Genetic engineering in primary human B cells with CRISPR-Cas9 ribonucleoproteins.

Journal of immunological methods

Wu CM, Roth TL, Baglaenko Y, Ferri DM, Brauer P, Zuniga-Pflucker JC, Rosbe KW, Wither JE, Marson A, Allen CDC

Multiplexed droplet single-cell RNA-sequencing using natural genetic variation.

Nature biotechnology

Kang HM, Subramaniam M, Targ S, Nguyen M, Maliskova L, McCarthy E, Wan E, Wong S, Byrnes L, Lanata CM, Gate RE, Mostafavi S, Marson A, Zaitlen N, Criswell LA, Ye CJ

Enhancer connectome in primary human cells identifies target genes of disease-associated DNA elements.

Nature genetics

Mumbach MR, Satpathy AT, Boyle EA, Dai C, Gowen BG, Cho SW, Nguyen ML, Rubin AJ, Granja JM, Kazane KR, Wei Y, Nguyen T, Greenside PG, Corces MR, Tycko J, Simeonov DR, Suliman N, Li R, Xu J, Flynn RA, Kundaje A, Khavari PA, Marson A, Corn JE, Quertermous T, Greenleaf WJ, Chang HY

"T-bet"-ing on autoimmunity variants.

PLoS genetics

Nguyen MLT, Simeonov DR, Marson A

Discovery of stimulation-responsive immune enhancers with CRISPR activation.

Nature

Simeonov DR, Gowen BG, Boontanrart M, Roth TL, Gagnon JD, Mumbach MR, Satpathy AT, Lee Y, Bray NL, Chan AY, Lituiev DS, Nguyen ML, Gate RE, Subramaniam M, Li Z, Woo JM, Mitros T, Ray GJ, Curie GL, Naddaf N, Chu JS, Ma H, Boyer E, Van Gool F, Huang H, Liu R, Tobin VR, Schumann K, Daly MJ, Farh KK, Ansel KM, Ye CJ, Greenleaf WJ, Anderson MS, Bluestone JA, Chang HY, Corn JE, Marson A

CRISPR/Cas9-mediated PD-1 disruption enhances anti-tumor efficacy of human chimeric antigen receptor T cells.

Scientific reports

Rupp LJ, Schumann K, Roybal KT, Gate RE, Ye CJ, Lim WA, Marson A

A genome-wide CRISPR screen identifies a restricted set of HIV host dependency factors.

Nature genetics

Park RJ, Wang T, Koundakjian D, Hultquist JF, Lamothe-Molina P, Monel B, Schumann K, Yu H, Krupzcak KM, Garcia-Beltran W, Piechocka-Trocha A, Krogan NJ, Marson A, Sabatini DM, Lander ES, Hacohen N, Walker BD

A Cas9 Ribonucleoprotein Platform for Functional Genetic Studies of HIV-Host Interactions in Primary Human T Cells.

Cell reports

Hultquist JF, Schumann K, Woo JM, Manganaro L, McGregor MJ, Doudna J, Simon V, Krogan NJ, Marson A

A tissue checkpoint regulates type 2 immunity.

Nature immunology

Van Dyken SJ, Nussbaum JC, Lee J, Molofsky AB, Liang HE, Pollack JL, Gate RE, Haliburton GE, Ye CJ, Marson A, Erle DJ, Locksley RM

Generation of knock-in primary human T cells using Cas9 ribonucleoproteins.

Proceedings of the National Academy of Sciences of the United States of America

Schumann K, Lin S, Boyer E, Simeonov DR, Subramaniam M, Gate RE, Haliburton GE, Ye CJ, Bluestone JA, Doudna JA, Marson A

Genetic basis of autoimmunity.

The Journal of clinical investigation

Marson A, Housley WJ, Hafler DA

The chromatin-modifying enzyme Ezh2 is critical for the maintenance of regulatory T cell identity after activation.

Immunity

DuPage M, Chopra G, Quiros J, Rosenthal WL, Morar MM, Holohan D, Zhang R, Turka L, Marson A, Bluestone JA

Genetic and epigenetic fine mapping of causal autoimmune disease variants.

Nature

Farh KK, Marson A, Zhu J, Kleinewietfeld M, Housley WJ, Beik S, Shoresh N, Whitton H, Ryan RJ, Shishkin AA, Hatan M, Carrasco-Alfonso MJ, Mayer D, Luckey CJ, Patsopoulos NA, De Jager PL, Kuchroo VK, Epstein CB, Daly MJ, Hafler DA, Bernstein BE

Decreased RORC-dependent silencing of prostaglandin receptor EP2 induces autoimmune Th17 cells.

The Journal of clinical investigation

Kofler DM, Marson A, Dominguez-Villar M, Xiao S, Kuchroo VK, Hafler DA

Small-molecule RORγt antagonists inhibit T helper 17 cell transcriptional network by divergent mechanisms.

Immunity

Xiao S, Yosef N, Yang J, Wang Y, Zhou L, Zhu C, Wu C, Baloglu E, Schmidt D, Ramesh R, Lobera M, Sundrud MS, Tsai PY, Xiang Z, Wang J, Xu Y, Lin X, Kretschmer K, Rahl PB, Young RA, Zhong Z, Hafler DA, Regev A, Ghosh S, Marson A, Kuchroo VK

Transcriptional role of cyclin D1 in development revealed by a genetic-proteomic screen.

Nature

Bienvenu F, Jirawatnotai S, Elias JE, Meyer CA, Mizeracka K, Marson A, Frampton GM, Cole MF, Odom DT, Odajima J, Geng Y, Zagozdzon A, Jecrois M, Young RA, Liu XS, Cepko CL, Gygi SP, Sicinski P

Connecting microRNA genes to the core transcriptional regulatory circuitry of embryonic stem cells.

Cell

Marson A, Levine SS, Cole MF, Frampton GM, Brambrink T, Johnstone S, Guenther MG, Johnston WK, Wernig M, Newman J, Calabrese JM, Dennis LM, Volkert TL, Gupta S, Love J, Hannett N, Sharp PA, Bartel DP, Jaenisch R, Young RA

Wnt signaling promotes reprogramming of somatic cells to pluripotency.

Cell stem cell

Marson A, Foreman R, Chevalier B, Bilodeau S, Kahn M, Young RA, Jaenisch R

Foxp3 occupancy and regulation of key target genes during T-cell stimulation.

Nature

Marson A, Kretschmer K, Frampton GM, Jacobsen ES, Polansky JK, MacIsaac KD, Levine SS, Fraenkel E, von Boehmer H, Young RA

PML bodies control the nuclear dynamics and function of the CHFR mitotic checkpoint protein.

Nature structural & molecular biology

Daniels MJ, Marson A, Venkitaraman AR

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