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

Franziska Blaeschke; Yan Yi Chen; Ryan Apathy; Bence Daniel; Andy Y. Chen; Peixin Amy Chen; Katalin Sandor; Wenxi Zhang; Zhongmei Li; Cody T. Mowery; Tori N. Yamamoto; William A. Nyberg; Angela To; Ruby Yu; Raymund Bueno; Min Cheol Kim; Ralf Schmidt; Daniel B. Goodman; Tobias Feuchtinger; Justin Eyquem; Chun Jimmie Ye; Julia Carnevale; Ansuman T. Satpathy; Eric Shifrut; Theodore L. Roth; Alexander Marson

doi:https://doi.org/10.1016/j.cell.2023.08.013

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

Franziska Blaeschke, Yan Yi Chen, Ryan Apathy, Bence Daniel, Andy Y. Chen, Peixin Amy Chen, Katalin Sandor, Wenxi Zhang, Zhongmei Li, Cody T. Mowery, Tori N. Yamamoto, William A. Nyberg, Angela To, Ruby Yu, Raymund Bueno, Min Cheol Kim, Ralf Schmidt, Daniel B. Goodman, Tobias Feuchtinger, Justin EyquemChun Jimmie Ye, Julia Carnevale, Ansuman T. Satpathy, Eric Shifrut, Theodore L. Roth, Alexander Marson

Research output: Contribution to journal › Article › peer-review

Abstract

Chronic stimulation can cause T cell dysfunction and limit the efficacy of cellular immunotherapies. Improved methods are required to compare large numbers of synthetic knockin (KI) sequences to reprogram cell functions. Here, we developed modular pooled KI screening (ModPoKI), an adaptable platform for modular construction of DNA KI libraries using barcoded multicistronic adaptors. We built two ModPoKI libraries of 100 transcription factors (TFs) and 129 natural and synthetic surface receptors (SRs). Over 30 ModPoKI screens across human TCR- and CAR-T cells in diverse conditions identified a transcription factor AP4 (TFAP4) construct that enhanced fitness of chronically stimulated CAR-T cells and anti-cancer function in vitro and in vivo. ModPoKI's modularity allowed us to generate an ∼10,000-member library of TF combinations. Non-viral KI of a combined BATF-TFAP4 polycistronic construct enhanced fitness. Overexpressed BATF and TFAP4 co-occupy and regulate key gene targets to reprogram T cell function. ModPoKI facilitates the discovery of complex gene constructs to program cellular functions.

Original language	English
Pages (from-to)	4216-4234.e33
Journal	Cell
Volume	186
Issue number	19
DOIs	https://doi.org/10.1016/j.cell.2023.08.013
State	Published - 14 Sep 2023
Externally published	Yes

Keywords

CRISPR
chimeric antigen receptor
chronic stimulation
human T cells
immunotherapy
knockins
pooled screens
synthetic surface receptor
transcription factor

All Science Journal Classification (ASJC) codes

General Biochemistry,Genetics and Molecular Biology

UN SDGs

This output contributes to the following UN Sustainable Development Goals (SDGs)

Access to Document

https://doi.org/10.1016/j.cell.2023.08.013

Cite this

Blaeschke, F., Chen, Y. Y., Apathy, R., Daniel, B., Chen, A. Y., Chen, P. A., Sandor, K., Zhang, W., Li, Z., Mowery, C. T., Yamamoto, T. N., Nyberg, W. A., To, A., Yu, R., Bueno, R., Kim, M. C., Schmidt, R., Goodman, D. B., Feuchtinger, T., ... Marson, A. (2023). Modular pooled discovery of synthetic knockin sequences to program durable cell therapies. Cell, 186(19), 4216-4234.e33. https://doi.org/10.1016/j.cell.2023.08.013

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title = "Modular pooled discovery of synthetic knockin sequences to program durable cell therapies",

abstract = "Chronic stimulation can cause T cell dysfunction and limit the efficacy of cellular immunotherapies. Improved methods are required to compare large numbers of synthetic knockin (KI) sequences to reprogram cell functions. Here, we developed modular pooled KI screening (ModPoKI), an adaptable platform for modular construction of DNA KI libraries using barcoded multicistronic adaptors. We built two ModPoKI libraries of 100 transcription factors (TFs) and 129 natural and synthetic surface receptors (SRs). Over 30 ModPoKI screens across human TCR- and CAR-T cells in diverse conditions identified a transcription factor AP4 (TFAP4) construct that enhanced fitness of chronically stimulated CAR-T cells and anti-cancer function in vitro and in vivo. ModPoKI's modularity allowed us to generate an ∼10,000-member library of TF combinations. Non-viral KI of a combined BATF-TFAP4 polycistronic construct enhanced fitness. Overexpressed BATF and TFAP4 co-occupy and regulate key gene targets to reprogram T cell function. ModPoKI facilitates the discovery of complex gene constructs to program cellular functions.",

keywords = "CRISPR, chimeric antigen receptor, chronic stimulation, human T cells, immunotherapy, knockins, pooled screens, synthetic surface receptor, transcription factor",

author = "Franziska Blaeschke and Chen, {Yan Yi} and Ryan Apathy and Bence Daniel and Chen, {Andy Y.} and Chen, {Peixin Amy} and Katalin Sandor and Wenxi Zhang and Zhongmei Li and Mowery, {Cody T.} and Yamamoto, {Tori N.} and Nyberg, {William A.} and Angela To and Ruby Yu and Raymund Bueno and Kim, {Min Cheol} and Ralf Schmidt and Goodman, {Daniel B.} and Tobias Feuchtinger and Justin Eyquem and {Jimmie Ye}, Chun and Julia Carnevale and Satpathy, {Ansuman T.} and Eric Shifrut and Roth, {Theodore L.} and Alexander Marson",

note = "Publisher Copyright: {\textcopyright} 2023 The Authors",

year = "2023",

month = sep,

day = "14",

doi = "https://doi.org/10.1016/j.cell.2023.08.013",

language = "الإنجليزيّة",

volume = "186",

pages = "4216--4234.e33",

journal = "Cell",

issn = "0092-8674",

publisher = "Elsevier B.V.",

number = "19",

}

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 2023, 'Modular pooled discovery of synthetic knockin sequences to program durable cell therapies', Cell, vol. 186, no. 19, pp. 4216-4234.e33. https://doi.org/10.1016/j.cell.2023.08.013

TY - JOUR

T1 - Modular pooled discovery of synthetic knockin sequences to program durable cell therapies

AU - Blaeschke, Franziska

AU - Chen, Yan Yi

AU - Apathy, Ryan

AU - Daniel, Bence

AU - Chen, Andy Y.

AU - Chen, Peixin Amy

AU - Sandor, Katalin

AU - Zhang, Wenxi

AU - Li, Zhongmei

AU - Mowery, Cody T.

AU - Yamamoto, Tori N.

AU - Nyberg, William A.

AU - To, Angela

AU - Yu, Ruby

AU - Bueno, Raymund

AU - Kim, Min Cheol

AU - Schmidt, Ralf

AU - Goodman, Daniel B.

AU - Feuchtinger, Tobias

AU - Eyquem, Justin

AU - Jimmie Ye, Chun

AU - Carnevale, Julia

AU - Satpathy, Ansuman T.

AU - Shifrut, Eric

AU - Roth, Theodore L.

AU - Marson, Alexander

PY - 2023/9/14

Y1 - 2023/9/14

N2 - Chronic stimulation can cause T cell dysfunction and limit the efficacy of cellular immunotherapies. Improved methods are required to compare large numbers of synthetic knockin (KI) sequences to reprogram cell functions. Here, we developed modular pooled KI screening (ModPoKI), an adaptable platform for modular construction of DNA KI libraries using barcoded multicistronic adaptors. We built two ModPoKI libraries of 100 transcription factors (TFs) and 129 natural and synthetic surface receptors (SRs). Over 30 ModPoKI screens across human TCR- and CAR-T cells in diverse conditions identified a transcription factor AP4 (TFAP4) construct that enhanced fitness of chronically stimulated CAR-T cells and anti-cancer function in vitro and in vivo. ModPoKI's modularity allowed us to generate an ∼10,000-member library of TF combinations. Non-viral KI of a combined BATF-TFAP4 polycistronic construct enhanced fitness. Overexpressed BATF and TFAP4 co-occupy and regulate key gene targets to reprogram T cell function. ModPoKI facilitates the discovery of complex gene constructs to program cellular functions.

AB - Chronic stimulation can cause T cell dysfunction and limit the efficacy of cellular immunotherapies. Improved methods are required to compare large numbers of synthetic knockin (KI) sequences to reprogram cell functions. Here, we developed modular pooled KI screening (ModPoKI), an adaptable platform for modular construction of DNA KI libraries using barcoded multicistronic adaptors. We built two ModPoKI libraries of 100 transcription factors (TFs) and 129 natural and synthetic surface receptors (SRs). Over 30 ModPoKI screens across human TCR- and CAR-T cells in diverse conditions identified a transcription factor AP4 (TFAP4) construct that enhanced fitness of chronically stimulated CAR-T cells and anti-cancer function in vitro and in vivo. ModPoKI's modularity allowed us to generate an ∼10,000-member library of TF combinations. Non-viral KI of a combined BATF-TFAP4 polycistronic construct enhanced fitness. Overexpressed BATF and TFAP4 co-occupy and regulate key gene targets to reprogram T cell function. ModPoKI facilitates the discovery of complex gene constructs to program cellular functions.

KW - CRISPR

KW - chimeric antigen receptor

KW - chronic stimulation

KW - human T cells

KW - immunotherapy

KW - knockins

KW - pooled screens

KW - synthetic surface receptor

KW - transcription factor

UR - http://www.scopus.com/inward/record.url?scp=85170716982&partnerID=8YFLogxK

U2 - https://doi.org/10.1016/j.cell.2023.08.013

DO - https://doi.org/10.1016/j.cell.2023.08.013

M3 - مقالة

C2 - 37714135

SN - 0092-8674

VL - 186

SP - 4216-4234.e33

JO - Cell

JF - Cell

IS - 19

ER -

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

Abstract

Keywords

All Science Journal Classification (ASJC) codes

UN SDGs

Access to Document

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