Eric Shifrut, PhD
Collaborator
Business Service Ctr
Chancellor/EVC/FAS

Publications (31)

Top publication keywords:
CD4-Positive T-LymphocytesGenome, Humanras GTPase-Activating ProteinsT-LymphocytesAntigensGene EditingChromatin Assembly and DisassemblyT-Lymphocytes, RegulatoryClustered Regularly Interspaced Short Palindromic RepeatsCRISPR-Cas SystemsComplementarity Determining RegionsReceptors, Antigen, T-CellReceptors, Antigen, T-Cell, alpha-betaDNA, Single-StrandedCD8-Positive T-Lymphocytes

• TIM-3, LAG-3, or 2B4 gene disruptions increase the anti-tumor response of engineered T cells.
  Frontiers in immunology 2024 Cianciotti BC, Magnani ZI, Ugolini A, Camisa B, Merelli I, Vavassori V, Potenza A, Imparato A, Manfredi F, Abbati D, Perani L, Spinelli A, Shifrut E, Ciceri F, Vago L, Di Micco R, Naldini L, Genovese …
• Modular pooled discovery of synthetic knockin sequences to program durable cell therapies.
  Cell 2023 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, …
• High-yield genome engineering in primary cells using a hybrid ssDNA repair template and small-molecule cocktails.
  Nature biotechnology 2022 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, …
• RASA2 ablation in T cells boosts antigen sensitivity and long-term function.
  Nature 2022 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, …
• Genome-wide CRISPR screens of T cell exhaustion identify chromatin remodeling factors that limit T cell persistence.
  Cancer cell 2022 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

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• A functional map of HIV-host interactions in primary human T cells.
  Nature communications 2022 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, …
• Hypoxia Is a Dominant Remodeler of the Effector T Cell Surface Proteome Relative to Activation and Regulatory T Cell Suppression.
  Molecular & cellular proteomics : MCP 2022 Byrnes JR, Weeks AM, Shifrut E, Carnevale J, Kirkemo L, Ashworth A, Marson A, Wells JA
• Efficient generation of isogenic primary human myeloid cells using CRISPR-Cas9 ribonucleoproteins.
  Cell reports 2021 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, …
• XYZeq: Spatially resolved single-cell RNA sequencing reveals expression heterogeneity in the tumor microenvironment.
  Science advances 2021 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
• Functional CRISPR dissection of gene networks controlling human regulatory T cell identity.
  Nature immunology 2020 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,…
• Layilin augments integrin activation to promote antitumor immunity.
  The Journal of experimental medicine 2020 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, …
• CRISPR screen in regulatory T cells reveals modulators of Foxp3.
  Nature 2020 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, …
• Pooled Knockin Targeting for Genome Engineering of Cellular Immunotherapies.
  Cell 2020 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
• Polymer-stabilized Cas9 nanoparticles and modified repair templates increase genome editing efficiency.
  Nature biotechnology 2019 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
• Large dataset enables prediction of repair after CRISPR-Cas9 editing in primary T cells.
  Nature biotechnology 2019 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
• Molecular constraints on CDR3 for thymic selection of MHC-restricted TCRs from a random pre-selection repertoire.
  Nature communications 2019 Lu J, Van Laethem F, Bhattacharya A, Craveiro M, Saba I, Chu J, Love NC, Tikhonova A, Radaev S, Sun X, Ko A, Arnon T, Shifrut E, Friedman N, Weng NP, Singer A, Sun PD
• Genome-wide CRISPR Screens in Primary Human T Cells Reveal Key Regulators of Immune Function.
  Cell 2018 Shifrut E, Carnevale J, Tobin V, Roth TL, Woo JM, Bui CT, Li PJ, Diolaiti ME, Ashworth A, Marson A
• Predicting CD4 T-cell epitopes based on antigen cleavage, MHCII presentation, and TCR recognition.
  PloS one 2018 Schneidman-Duhovny D, Khuri N, Dong GQ, Winter MB, Shifrut E, Friedman N, Craik CS, Pratt KP, Paz P, Aswad F, Sali A
• Reprogramming human T cell function and specificity with non-viral genome targeting.
  Nature 2018 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…
• McPAS-TCR: a manually curated catalogue of pathology-associated T cell receptor sequences.
  Bioinformatics (Oxford, England) 2017 Tickotsky N, Sagiv T, Prilusky J, Shifrut E, Friedman N
• T cell receptor repertoires of mice and humans are clustered in similarity networks around conserved public CDR3 sequences.
  eLife 2017 Madi A, Poran A, Shifrut E, Reich-Zeliger S, Greenstein E, Zaretsky I, Arnon T, Laethem FV, Singer A, Lu J, Sun PD, Cohen IR, Friedman N
• Specificity, Privacy, and Degeneracy in the CD4 T Cell Receptor Repertoire Following Immunization.
  Frontiers in immunology 2017 Sun Y, Best K, Cinelli M, Heather JM, Reich-Zeliger S, Shifrut E, Friedman N, Shawe-Taylor J, Chain B
• Feature selection using a one dimensional naïve Bayes' classifier increases the accuracy of support vector machine classification of CDR3 repertoires.
  Bioinformatics (Oxford, England) 2017 Cinelli M, Sun Y, Best K, Heather JM, Reich-Zeliger S, Shifrut E, Friedman N, Shawe-Taylor J, Chain B
• Perforin-Positive Dendritic Cells Exhibit an Immuno-regulatory Role in Metabolic Syndrome and Autoimmunity.
  Immunity 2015 Zlotnikov-Klionsky Y, Nathansohn-Levi B, Shezen E, Rosen C, Kagan S, Bar-On L, Jung S, Shifrut E, Reich-Zeliger S, Friedman N, Aharoni R, Arnon R, Yifa O, Aronovich A, Reisner Y
• Tracking global changes induced in the CD4 T-cell receptor repertoire by immunization with a complex antigen using short stretches of CDR3 protein sequence.
  Bioinformatics (Oxford, England) 2014 Thomas N, Best K, Cinelli M, Reich-Zeliger S, Gal H, Shifrut E, Madi A, Friedman N, Shawe-Taylor J, Chain B
• T-cell receptor repertoires share a restricted set of public and abundant CDR3 sequences that are associated with self-related immunity.
  Genome research 2014 Madi A, Shifrut E, Reich-Zeliger S, Gal H, Best K, Ndifon W, Chain B, Cohen IR, Friedman N
• CD4(+) T Cell-Receptor Repertoire Diversity is Compromised in the Spleen but Not in the Bone Marrow of Aged Mice Due to Private and Sporadic Clonal Expansions.
  Frontiers in immunology 2013 Shifrut E, Baruch K, Gal H, Ndifon W, Deczkowska A, Schwartz M, Friedman N
• CNS-specific immunity at the choroid plexus shifts toward destructive Th2 inflammation in brain aging.
  Proceedings of the National Academy of Sciences of the United States of America 2013 Baruch K, Ron-Harel N, Gal H, Deczkowska A, Shifrut E, Ndifon W, Mirlas-Neisberg N, Cardon M, Vaknin I, Cahalon L, Berkutzki T, Mattson MP, Gomez-Pinilla F, Friedman N, Schwartz M
• Monitoring the dynamics of primary T cell activation and differentiation using long term live cell imaging in microwell arrays.
  Lab on a chip 2012 Zaretsky I, Polonsky M, Shifrut E, Reich-Zeliger S, Antebi Y, Aidelberg G, Waysbort N, Friedman N
• Dynamic response diversity of NFAT isoforms in individual living cells.
  Molecular cell 2012 Yissachar N, Sharar Fischler T, Cohen AA, Reich-Zeliger S, Russ D, Shifrut E, Porat Z, Friedman N
• Chromatin conformation governs T-cell receptor Jβ gene segment usage.
  Proceedings of the National Academy of Sciences of the United States of America 2012 Ndifon W, Gal H, Shifrut E, Aharoni R, Yissachar N, Waysbort N, Reich-Zeliger S, Arnon R, Friedman N