Identification of phagocytosis regulators using magnetic genome-wide CRISPR screens

Michael S. Haney; Christopher J. Bohlen; David W. Morgens; James A. Ousey; Amira A. Barkal; C. Kimberly Tsui; Braeden K. Ego; Roni Levin; Roarke A. Kamber; Hannah Collins; Andrew Tucker; Amy Li; Daan Vorselen; Lorenzo Labitigan; Emily Crane; Evan Boyle; Lihua Jiang; Joanne Chan; Esther Rincón; William J. Greenleaf; Billy Li; Michael P. Snyder; Irving L. Weissman; Julie A. Theriot; Sean Collins; Ben A. Barres; Michael C. Bassik

doi:10.1038/s41588-018-0254-1

Identification of phagocytosis regulators using magnetic genome-wide CRISPR screens

Michael S. Haney, Christopher J. Bohlen, David W. Morgens, James A. Ousey, Amira A. Barkal, C. Kimberly Tsui, Braeden K. Ego, Roni Levin, Roarke A. Kamber, Hannah Collins, Andrew Tucker, Amy Li, Daan Vorselen, Lorenzo Labitigan, Emily Crane, Evan Boyle, Lihua Jiang, Joanne Chan, Esther Rincón, William J. GreenleafBilly Li, Michael P. Snyder, Irving L. Weissman, Julie A. Theriot, Sean Collins, Ben A. Barres, Michael C. Bassik

Microbiology and Molecular Genetics

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

55 Scopus citations

Abstract

Phagocytosis is required for a broad range of physiological functions, from pathogen defense to tissue homeostasis, but the mechanisms required for phagocytosis of diverse substrates remain incompletely understood. Here, we developed a rapid magnet-based phenotypic screening strategy, and performed eight genome-wide CRISPR screens in human cells to identify genes regulating phagocytosis of distinct substrates. After validating select hits in focused miniscreens, orthogonal assays and primary human macrophages, we show that (1) the previously uncharacterized gene NHLRC2 is a central player in phagocytosis, regulating RhoA-Rac1 signaling cascades that control actin polymerization and filopodia formation, (2) very-long-chain fatty acids are essential for efficient phagocytosis of certain substrates and (3) the previously uncharacterized Alzheimer’s disease–associated gene TM2D3 can preferentially influence uptake of amyloid-β aggregates. These findings illuminate new regulators and core principles of phagocytosis, and more generally establish an efficient method for unbiased identification of cellular uptake mechanisms across diverse physiological and pathological contexts.

Original language	English (US)
Journal	Nature Genetics
DOIs	https://doi.org/10.1038/s41588-018-0254-1
State	Accepted/In press - Jan 1 2018

ASJC Scopus subject areas

Genetics

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Haney, M. S., Bohlen, C. J., Morgens, D. W., Ousey, J. A., Barkal, A. A., Tsui, C. K., Ego, B. K., Levin, R., Kamber, R. A., Collins, H., Tucker, A., Li, A., Vorselen, D., Labitigan, L., Crane, E., Boyle, E., Jiang, L., Chan, J., Rincón, E., ... Bassik, M. C. (Accepted/In press). Identification of phagocytosis regulators using magnetic genome-wide CRISPR screens. Nature Genetics. https://doi.org/10.1038/s41588-018-0254-1

Identification of phagocytosis regulators using magnetic genome-wide CRISPR screens. / Haney, Michael S.; Bohlen, Christopher J.; Morgens, David W.; Ousey, James A.; Barkal, Amira A.; Tsui, C. Kimberly; Ego, Braeden K.; Levin, Roni; Kamber, Roarke A.; Collins, Hannah; Tucker, Andrew; Li, Amy; Vorselen, Daan; Labitigan, Lorenzo; Crane, Emily; Boyle, Evan; Jiang, Lihua; Chan, Joanne; Rincón, Esther; Greenleaf, William J.; Li, Billy; Snyder, Michael P.; Weissman, Irving L.; Theriot, Julie A.; Collins, Sean; Barres, Ben A.; Bassik, Michael C.

In: Nature Genetics, 01.01.2018.

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

Haney, MS, Bohlen, CJ, Morgens, DW, Ousey, JA, Barkal, AA, Tsui, CK, Ego, BK, Levin, R, Kamber, RA, Collins, H, Tucker, A, Li, A, Vorselen, D, Labitigan, L, Crane, E, Boyle, E, Jiang, L, Chan, J, Rincón, E, Greenleaf, WJ, Li, B, Snyder, MP, Weissman, IL, Theriot, JA, Collins, S, Barres, BA & Bassik, MC 2018, 'Identification of phagocytosis regulators using magnetic genome-wide CRISPR screens', Nature Genetics. https://doi.org/10.1038/s41588-018-0254-1

Haney, Michael S. ; Bohlen, Christopher J. ; Morgens, David W. ; Ousey, James A. ; Barkal, Amira A. ; Tsui, C. Kimberly ; Ego, Braeden K. ; Levin, Roni ; Kamber, Roarke A. ; Collins, Hannah ; Tucker, Andrew ; Li, Amy ; Vorselen, Daan ; Labitigan, Lorenzo ; Crane, Emily ; Boyle, Evan ; Jiang, Lihua ; Chan, Joanne ; Rincón, Esther ; Greenleaf, William J. ; Li, Billy ; Snyder, Michael P. ; Weissman, Irving L. ; Theriot, Julie A. ; Collins, Sean ; Barres, Ben A. ; Bassik, Michael C. / Identification of phagocytosis regulators using magnetic genome-wide CRISPR screens. In: Nature Genetics. 2018.

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title = "Identification of phagocytosis regulators using magnetic genome-wide CRISPR screens",

abstract = "Phagocytosis is required for a broad range of physiological functions, from pathogen defense to tissue homeostasis, but the mechanisms required for phagocytosis of diverse substrates remain incompletely understood. Here, we developed a rapid magnet-based phenotypic screening strategy, and performed eight genome-wide CRISPR screens in human cells to identify genes regulating phagocytosis of distinct substrates. After validating select hits in focused miniscreens, orthogonal assays and primary human macrophages, we show that (1) the previously uncharacterized gene NHLRC2 is a central player in phagocytosis, regulating RhoA-Rac1 signaling cascades that control actin polymerization and filopodia formation, (2) very-long-chain fatty acids are essential for efficient phagocytosis of certain substrates and (3) the previously uncharacterized Alzheimer{\textquoteright}s disease–associated gene TM2D3 can preferentially influence uptake of amyloid-β aggregates. These findings illuminate new regulators and core principles of phagocytosis, and more generally establish an efficient method for unbiased identification of cellular uptake mechanisms across diverse physiological and pathological contexts.",

author = "Haney, {Michael S.} and Bohlen, {Christopher J.} and Morgens, {David W.} and Ousey, {James A.} and Barkal, {Amira A.} and Tsui, {C. Kimberly} and Ego, {Braeden K.} and Roni Levin and Kamber, {Roarke A.} and Hannah Collins and Andrew Tucker and Amy Li and Daan Vorselen and Lorenzo Labitigan and Emily Crane and Evan Boyle and Lihua Jiang and Joanne Chan and Esther Rinc{\'o}n and Greenleaf, {William J.} and Billy Li and Snyder, {Michael P.} and Weissman, {Irving L.} and Theriot, {Julie A.} and Sean Collins and Barres, {Ben A.} and Bassik, {Michael C.}",

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AU - Bohlen, Christopher J.

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AU - Tsui, C. Kimberly

AU - Ego, Braeden K.

AU - Levin, Roni

AU - Kamber, Roarke A.

AU - Collins, Hannah

AU - Tucker, Andrew

AU - Li, Amy

AU - Vorselen, Daan

AU - Labitigan, Lorenzo

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AU - Boyle, Evan

AU - Jiang, Lihua

AU - Chan, Joanne

AU - Rincón, Esther

AU - Greenleaf, William J.

AU - Li, Billy

AU - Snyder, Michael P.

AU - Weissman, Irving L.

AU - Theriot, Julie A.

AU - Collins, Sean

AU - Barres, Ben A.

AU - Bassik, Michael C.

PY - 2018/1/1

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N2 - Phagocytosis is required for a broad range of physiological functions, from pathogen defense to tissue homeostasis, but the mechanisms required for phagocytosis of diverse substrates remain incompletely understood. Here, we developed a rapid magnet-based phenotypic screening strategy, and performed eight genome-wide CRISPR screens in human cells to identify genes regulating phagocytosis of distinct substrates. After validating select hits in focused miniscreens, orthogonal assays and primary human macrophages, we show that (1) the previously uncharacterized gene NHLRC2 is a central player in phagocytosis, regulating RhoA-Rac1 signaling cascades that control actin polymerization and filopodia formation, (2) very-long-chain fatty acids are essential for efficient phagocytosis of certain substrates and (3) the previously uncharacterized Alzheimer’s disease–associated gene TM2D3 can preferentially influence uptake of amyloid-β aggregates. These findings illuminate new regulators and core principles of phagocytosis, and more generally establish an efficient method for unbiased identification of cellular uptake mechanisms across diverse physiological and pathological contexts.

AB - Phagocytosis is required for a broad range of physiological functions, from pathogen defense to tissue homeostasis, but the mechanisms required for phagocytosis of diverse substrates remain incompletely understood. Here, we developed a rapid magnet-based phenotypic screening strategy, and performed eight genome-wide CRISPR screens in human cells to identify genes regulating phagocytosis of distinct substrates. After validating select hits in focused miniscreens, orthogonal assays and primary human macrophages, we show that (1) the previously uncharacterized gene NHLRC2 is a central player in phagocytosis, regulating RhoA-Rac1 signaling cascades that control actin polymerization and filopodia formation, (2) very-long-chain fatty acids are essential for efficient phagocytosis of certain substrates and (3) the previously uncharacterized Alzheimer’s disease–associated gene TM2D3 can preferentially influence uptake of amyloid-β aggregates. These findings illuminate new regulators and core principles of phagocytosis, and more generally establish an efficient method for unbiased identification of cellular uptake mechanisms across diverse physiological and pathological contexts.

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Identification of phagocytosis regulators using magnetic genome-wide CRISPR screens

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