Cell Type-Specific In Vitro Gene Expression Profiling of Stem Cell-Derived Neural Models

James A. Gregory; Emily Hoelzli; Rawan Abdelaal; Catherine Braine; Miguel Cuevas; Madeline Halpern; Natalie Barretto; Nadine Schrode; Güney Akbalik; Kristy Kang; Esther Cheng; Kathryn Bowles; Steven Lotz; Susan Goderie; Celeste M. Karch; Sally Temple; Alison Goate; Kristen J. Brennand; Hemali Phatnani

doi:10.3390/cells9061406

Cell Type-Specific In Vitro Gene Expression Profiling of Stem Cell-Derived Neural Models

James A. Gregory, Emily Hoelzli, Rawan Abdelaal, Catherine Braine, Miguel Cuevas, Madeline Halpern, Natalie Barretto, Nadine Schrode, Güney Akbalik, Kristy Kang, Esther Cheng, Kathryn Bowles, Steven Lotz, Susan Goderie, Celeste M. Karch, Sally Temple, Alison Goate, Kristen J. Brennand, Hemali Phatnani

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

Abstract

Genetic and genomic studies of brain disease increasingly demonstrate disease-associated interactions between the cell types of the brain. Increasingly complex and more physiologically relevant human-induced pluripotent stem cell (hiPSC)-based models better explore the molecular mechanisms underlying disease but also challenge our ability to resolve cell type-specific perturbations. Here, we report an extension of the RiboTag system, first developed to achieve cell type-restricted expression of epitope-tagged ribosomal protein (RPL22) in mouse tissue, to a variety of in vitro applications, including immortalized cell lines, primary mouse astrocytes, and hiPSC-derived neurons. RiboTag expression enables depletion of up to 87 percent of off-target RNA in mixed species co-cultures. Nonetheless, depletion efficiency varies across independent experimental replicates, particularly for hiPSC-derived motor neurons. The challenges and potential of implementing RiboTags in complex in vitro cultures are discussed.

Original language	English
Journal	Cells
Volume	9
Issue number	6
DOIs	https://doi.org/10.3390/cells9061406
State	Published - Jun 5 2020

Keywords

RNA-seq
RiboTag
bacTRAP
genomics
glia
hiPSC
neuron

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Gregory, J. A., Hoelzli, E., Abdelaal, R., Braine, C., Cuevas, M., Halpern, M., Barretto, N., Schrode, N., Akbalik, G., Kang, K., Cheng, E., Bowles, K., Lotz, S., Goderie, S., Karch, C. M., Temple, S., Goate, A., Brennand, K. J., & Phatnani, H. (2020). Cell Type-Specific In Vitro Gene Expression Profiling of Stem Cell-Derived Neural Models. Cells, 9(6). https://doi.org/10.3390/cells9061406

Gregory, James A. ; Hoelzli, Emily ; Abdelaal, Rawan ; Braine, Catherine ; Cuevas, Miguel ; Halpern, Madeline ; Barretto, Natalie ; Schrode, Nadine ; Akbalik, Güney ; Kang, Kristy ; Cheng, Esther ; Bowles, Kathryn ; Lotz, Steven ; Goderie, Susan ; Karch, Celeste M. ; Temple, Sally ; Goate, Alison ; Brennand, Kristen J. ; Phatnani, Hemali. / Cell Type-Specific In Vitro Gene Expression Profiling of Stem Cell-Derived Neural Models. In: Cells. 2020 ; Vol. 9, No. 6.

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title = "Cell Type-Specific In Vitro Gene Expression Profiling of Stem Cell-Derived Neural Models",

abstract = "Genetic and genomic studies of brain disease increasingly demonstrate disease-associated interactions between the cell types of the brain. Increasingly complex and more physiologically relevant human-induced pluripotent stem cell (hiPSC)-based models better explore the molecular mechanisms underlying disease but also challenge our ability to resolve cell type-specific perturbations. Here, we report an extension of the RiboTag system, first developed to achieve cell type-restricted expression of epitope-tagged ribosomal protein (RPL22) in mouse tissue, to a variety of in vitro applications, including immortalized cell lines, primary mouse astrocytes, and hiPSC-derived neurons. RiboTag expression enables depletion of up to 87 percent of off-target RNA in mixed species co-cultures. Nonetheless, depletion efficiency varies across independent experimental replicates, particularly for hiPSC-derived motor neurons. The challenges and potential of implementing RiboTags in complex in vitro cultures are discussed.",

keywords = "RNA-seq, RiboTag, bacTRAP, genomics, glia, hiPSC, neuron",

author = "Gregory, {James A.} and Emily Hoelzli and Rawan Abdelaal and Catherine Braine and Miguel Cuevas and Madeline Halpern and Natalie Barretto and Nadine Schrode and G{\"u}ney Akbalik and Kristy Kang and Esther Cheng and Kathryn Bowles and Steven Lotz and Susan Goderie and Karch, {Celeste M.} and Sally Temple and Alison Goate and Brennand, {Kristen J.} and Hemali Phatnani",

year = "2020",

month = jun,

day = "5",

doi = "10.3390/cells9061406",

language = "English",

volume = "9",

journal = "Cells",

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Gregory, JA, Hoelzli, E, Abdelaal, R, Braine, C, Cuevas, M, Halpern, M, Barretto, N, Schrode, N, Akbalik, G, Kang, K, Cheng, E, Bowles, K, Lotz, S, Goderie, S, Karch, CM, Temple, S, Goate, A, Brennand, KJ & Phatnani, H 2020, 'Cell Type-Specific In Vitro Gene Expression Profiling of Stem Cell-Derived Neural Models', Cells, vol. 9, no. 6. https://doi.org/10.3390/cells9061406

Cell Type-Specific In Vitro Gene Expression Profiling of Stem Cell-Derived Neural Models. / Gregory, James A.; Hoelzli, Emily; Abdelaal, Rawan; Braine, Catherine; Cuevas, Miguel; Halpern, Madeline; Barretto, Natalie; Schrode, Nadine; Akbalik, Güney; Kang, Kristy; Cheng, Esther; Bowles, Kathryn; Lotz, Steven; Goderie, Susan; Karch, Celeste M.; Temple, Sally; Goate, Alison; Brennand, Kristen J.; Phatnani, Hemali.

In: Cells, Vol. 9, No. 6, 05.06.2020.

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

TY - JOUR

T1 - Cell Type-Specific In Vitro Gene Expression Profiling of Stem Cell-Derived Neural Models

AU - Gregory, James A.

AU - Hoelzli, Emily

AU - Abdelaal, Rawan

AU - Braine, Catherine

AU - Cuevas, Miguel

AU - Halpern, Madeline

AU - Barretto, Natalie

AU - Schrode, Nadine

AU - Akbalik, Güney

AU - Kang, Kristy

AU - Cheng, Esther

AU - Bowles, Kathryn

AU - Lotz, Steven

AU - Goderie, Susan

AU - Karch, Celeste M.

AU - Temple, Sally

AU - Goate, Alison

AU - Brennand, Kristen J.

AU - Phatnani, Hemali

PY - 2020/6/5

Y1 - 2020/6/5

N2 - Genetic and genomic studies of brain disease increasingly demonstrate disease-associated interactions between the cell types of the brain. Increasingly complex and more physiologically relevant human-induced pluripotent stem cell (hiPSC)-based models better explore the molecular mechanisms underlying disease but also challenge our ability to resolve cell type-specific perturbations. Here, we report an extension of the RiboTag system, first developed to achieve cell type-restricted expression of epitope-tagged ribosomal protein (RPL22) in mouse tissue, to a variety of in vitro applications, including immortalized cell lines, primary mouse astrocytes, and hiPSC-derived neurons. RiboTag expression enables depletion of up to 87 percent of off-target RNA in mixed species co-cultures. Nonetheless, depletion efficiency varies across independent experimental replicates, particularly for hiPSC-derived motor neurons. The challenges and potential of implementing RiboTags in complex in vitro cultures are discussed.

AB - Genetic and genomic studies of brain disease increasingly demonstrate disease-associated interactions between the cell types of the brain. Increasingly complex and more physiologically relevant human-induced pluripotent stem cell (hiPSC)-based models better explore the molecular mechanisms underlying disease but also challenge our ability to resolve cell type-specific perturbations. Here, we report an extension of the RiboTag system, first developed to achieve cell type-restricted expression of epitope-tagged ribosomal protein (RPL22) in mouse tissue, to a variety of in vitro applications, including immortalized cell lines, primary mouse astrocytes, and hiPSC-derived neurons. RiboTag expression enables depletion of up to 87 percent of off-target RNA in mixed species co-cultures. Nonetheless, depletion efficiency varies across independent experimental replicates, particularly for hiPSC-derived motor neurons. The challenges and potential of implementing RiboTags in complex in vitro cultures are discussed.

KW - RNA-seq

KW - RiboTag

KW - bacTRAP

KW - genomics

KW - glia

KW - hiPSC

KW - neuron

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U2 - 10.3390/cells9061406

DO - 10.3390/cells9061406

M3 - Article

C2 - 32516938

AN - SCOPUS:85086354608

VL - 9

JO - Cells

JF - Cells

SN - 2073-4409

IS - 6

ER -

Cell Type-Specific In Vitro Gene Expression Profiling of Stem Cell-Derived Neural Models

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Keywords

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