Cortical overgrowth in a preclinical forebrain organoid model of CNTNAP2-associated autism spectrum disorder

Job O. de Jong; Ceyda Llapashtica; Matthieu Genestine; Kevin Strauss; Frank Provenzano; Yan Sun; Huixiang Zhu; Giuseppe P. Cortese; Francesco Brundu; Karlla W. Brigatti; Barbara Corneo; Bianca Migliori; Raju Tomer; Steven A. Kushner; Christoph Kellendonk; Jonathan A. Javitch; Bin Xu; Sander Markx; Sander Markx

doi:10.1038/s41467-021-24358-4

Cortical overgrowth in a preclinical forebrain organoid model of CNTNAP2-associated autism spectrum disorder

Job O. de Jong, Ceyda Llapashtica, Matthieu Genestine, Kevin Strauss, Frank Provenzano, Yan Sun, Huixiang Zhu, Giuseppe P. Cortese, Francesco Brundu, Karlla W. Brigatti, Barbara Corneo, Bianca Migliori, Raju Tomer, Steven A. Kushner, Christoph Kellendonk, Jonathan A. Javitch, Bin Xu^*, Sander Markx, Sander Markx

^*Corresponding author for this work

Psychiatry

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Abstract

We utilized forebrain organoids generated from induced pluripotent stem cells of patients with a syndromic form of Autism Spectrum Disorder (ASD) with a homozygous protein-truncating mutation in CNTNAP2, to study its effects on embryonic cortical development. Patients with this mutation present with clinical characteristics of brain overgrowth. Patient-derived forebrain organoids displayed an increase in volume and total cell number that is driven by increased neural progenitor proliferation. Single-cell RNA sequencing revealed PFC-excitatory neurons to be the key cell types expressing CNTNAP2. Gene ontology analysis of differentially expressed genes (DEgenes) corroborates aberrant cellular proliferation. Moreover, the DEgenes are enriched for ASD-associated genes. The cell-type-specific signature genes of the CNTNAP2-expressing neurons are associated with clinical phenotypes previously described in patients. The organoid overgrowth phenotypes were largely rescued after correction of the mutation using CRISPR-Cas9. This CNTNAP2-organoid model provides opportunity for further mechanistic inquiry and development of new therapeutic strategies for ASD.

Original language	English
Article number	4087
Journal	Nature Communications
Volume	12
Issue number	1
DOIs	https://doi.org/10.1038/s41467-021-24358-4
Publication status	Published - 1 Sept 2021

Bibliographical note

Funding Information:
The authors would like to thank Dr. Yuanjia Wang and Chen Chen for their advice on the statistical analyses using the linear mixed model. We thank Dr. Maura Boldrini for her advice on the BrdU labeling experiments. We thank Drs. Alexander Sosunov, Andrew Dwork and Gorazd Rosoklija for their advice on histology experiments. We thank Joseph Sall from NYU Langone’s Microscopy Laboratory (supported by the Cancer Center Support Grant P30CA016087 at the Laura and Isaac Perlmutter Cancer Center) for technical assistance with the light-sheet microscopy image acquisition. We thank Luis Aparicio de Santiago for his contribution to the scRNAseq analysis. We thank Julie Shabto, Qanetha Ahmed, Yelizaveta Gribkova, and Huber Rodriguez-Tejada for their contribution to western Blotting and imaging experiments. We thank Dr. Theresa Swayne and Dr. Laura Munteanu for their advice on image processing and analysis at the Confocal and Specialized Microscopy Shared Resource of the Herbert Irving Comprehensive Cancer Center at Columbia University, supported by NIH grant #P30 CA013696 (National Cancer Institute). This research was partially supported by Irving Institute/ CTO Pilot Award (UR007953) to B.X.; B.X. and S.M. are supported by NCAT UG3 NS115598.

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de Jong, J. O., Llapashtica, C., Genestine, M., Strauss, K., Provenzano, F., Sun, Y., Zhu, H., Cortese, G. P., Brundu, F., Brigatti, K. W., Corneo, B., Migliori, B., Tomer, R., Kushner, S. A., Kellendonk, C., Javitch, J. A., Xu, B., Markx, S., & Markx, S. (2021). Cortical overgrowth in a preclinical forebrain organoid model of CNTNAP2-associated autism spectrum disorder. Nature Communications, 12(1), Article 4087. https://doi.org/10.1038/s41467-021-24358-4

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title = "Cortical overgrowth in a preclinical forebrain organoid model of CNTNAP2-associated autism spectrum disorder",

abstract = "We utilized forebrain organoids generated from induced pluripotent stem cells of patients with a syndromic form of Autism Spectrum Disorder (ASD) with a homozygous protein-truncating mutation in CNTNAP2, to study its effects on embryonic cortical development. Patients with this mutation present with clinical characteristics of brain overgrowth. Patient-derived forebrain organoids displayed an increase in volume and total cell number that is driven by increased neural progenitor proliferation. Single-cell RNA sequencing revealed PFC-excitatory neurons to be the key cell types expressing CNTNAP2. Gene ontology analysis of differentially expressed genes (DEgenes) corroborates aberrant cellular proliferation. Moreover, the DEgenes are enriched for ASD-associated genes. The cell-type-specific signature genes of the CNTNAP2-expressing neurons are associated with clinical phenotypes previously described in patients. The organoid overgrowth phenotypes were largely rescued after correction of the mutation using CRISPR-Cas9. This CNTNAP2-organoid model provides opportunity for further mechanistic inquiry and development of new therapeutic strategies for ASD.",

author = "{de Jong}, {Job O.} and Ceyda Llapashtica and Matthieu Genestine and Kevin Strauss and Frank Provenzano and Yan Sun and Huixiang Zhu and Cortese, {Giuseppe P.} and Francesco Brundu and Brigatti, {Karlla W.} and Barbara Corneo and Bianca Migliori and Raju Tomer and Kushner, {Steven A.} and Christoph Kellendonk and Javitch, {Jonathan A.} and Bin Xu and Sander Markx and Sander Markx",

note = "Funding Information: The authors would like to thank Dr. Yuanjia Wang and Chen Chen for their advice on the statistical analyses using the linear mixed model. We thank Dr. Maura Boldrini for her advice on the BrdU labeling experiments. We thank Drs. Alexander Sosunov, Andrew Dwork and Gorazd Rosoklija for their advice on histology experiments. We thank Joseph Sall from NYU Langone{\textquoteright}s Microscopy Laboratory (supported by the Cancer Center Support Grant P30CA016087 at the Laura and Isaac Perlmutter Cancer Center) for technical assistance with the light-sheet microscopy image acquisition. We thank Luis Aparicio de Santiago for his contribution to the scRNAseq analysis. We thank Julie Shabto, Qanetha Ahmed, Yelizaveta Gribkova, and Huber Rodriguez-Tejada for their contribution to western Blotting and imaging experiments. We thank Dr. Theresa Swayne and Dr. Laura Munteanu for their advice on image processing and analysis at the Confocal and Specialized Microscopy Shared Resource of the Herbert Irving Comprehensive Cancer Center at Columbia University, supported by NIH grant #P30 CA013696 (National Cancer Institute). This research was partially supported by Irving Institute/ CTO Pilot Award (UR007953) to B.X.; B.X. and S.M. are supported by NCAT UG3 NS115598. Publisher Copyright: {\textcopyright} 2021, The Author(s).",

year = "2021",

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de Jong, JO, Llapashtica, C, Genestine, M, Strauss, K, Provenzano, F, Sun, Y, Zhu, H, Cortese, GP, Brundu, F, Brigatti, KW, Corneo, B, Migliori, B, Tomer, R, Kushner, SA, Kellendonk, C, Javitch, JA, Xu, B, Markx, S & Markx, S 2021, 'Cortical overgrowth in a preclinical forebrain organoid model of CNTNAP2-associated autism spectrum disorder', Nature Communications, vol. 12, no. 1, 4087. https://doi.org/10.1038/s41467-021-24358-4

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AU - de Jong, Job O.

AU - Llapashtica, Ceyda

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AU - Provenzano, Frank

AU - Sun, Yan

AU - Zhu, Huixiang

AU - Cortese, Giuseppe P.

AU - Brundu, Francesco

AU - Brigatti, Karlla W.

AU - Corneo, Barbara

AU - Migliori, Bianca

AU - Tomer, Raju

AU - Kushner, Steven A.

AU - Kellendonk, Christoph

AU - Javitch, Jonathan A.

AU - Xu, Bin

AU - Markx, Sander

N1 - Funding Information: The authors would like to thank Dr. Yuanjia Wang and Chen Chen for their advice on the statistical analyses using the linear mixed model. We thank Dr. Maura Boldrini for her advice on the BrdU labeling experiments. We thank Drs. Alexander Sosunov, Andrew Dwork and Gorazd Rosoklija for their advice on histology experiments. We thank Joseph Sall from NYU Langone’s Microscopy Laboratory (supported by the Cancer Center Support Grant P30CA016087 at the Laura and Isaac Perlmutter Cancer Center) for technical assistance with the light-sheet microscopy image acquisition. We thank Luis Aparicio de Santiago for his contribution to the scRNAseq analysis. We thank Julie Shabto, Qanetha Ahmed, Yelizaveta Gribkova, and Huber Rodriguez-Tejada for their contribution to western Blotting and imaging experiments. We thank Dr. Theresa Swayne and Dr. Laura Munteanu for their advice on image processing and analysis at the Confocal and Specialized Microscopy Shared Resource of the Herbert Irving Comprehensive Cancer Center at Columbia University, supported by NIH grant #P30 CA013696 (National Cancer Institute). This research was partially supported by Irving Institute/ CTO Pilot Award (UR007953) to B.X.; B.X. and S.M. are supported by NCAT UG3 NS115598. Publisher Copyright: © 2021, The Author(s).

PY - 2021/9/1

Y1 - 2021/9/1

N2 - We utilized forebrain organoids generated from induced pluripotent stem cells of patients with a syndromic form of Autism Spectrum Disorder (ASD) with a homozygous protein-truncating mutation in CNTNAP2, to study its effects on embryonic cortical development. Patients with this mutation present with clinical characteristics of brain overgrowth. Patient-derived forebrain organoids displayed an increase in volume and total cell number that is driven by increased neural progenitor proliferation. Single-cell RNA sequencing revealed PFC-excitatory neurons to be the key cell types expressing CNTNAP2. Gene ontology analysis of differentially expressed genes (DEgenes) corroborates aberrant cellular proliferation. Moreover, the DEgenes are enriched for ASD-associated genes. The cell-type-specific signature genes of the CNTNAP2-expressing neurons are associated with clinical phenotypes previously described in patients. The organoid overgrowth phenotypes were largely rescued after correction of the mutation using CRISPR-Cas9. This CNTNAP2-organoid model provides opportunity for further mechanistic inquiry and development of new therapeutic strategies for ASD.

AB - We utilized forebrain organoids generated from induced pluripotent stem cells of patients with a syndromic form of Autism Spectrum Disorder (ASD) with a homozygous protein-truncating mutation in CNTNAP2, to study its effects on embryonic cortical development. Patients with this mutation present with clinical characteristics of brain overgrowth. Patient-derived forebrain organoids displayed an increase in volume and total cell number that is driven by increased neural progenitor proliferation. Single-cell RNA sequencing revealed PFC-excitatory neurons to be the key cell types expressing CNTNAP2. Gene ontology analysis of differentially expressed genes (DEgenes) corroborates aberrant cellular proliferation. Moreover, the DEgenes are enriched for ASD-associated genes. The cell-type-specific signature genes of the CNTNAP2-expressing neurons are associated with clinical phenotypes previously described in patients. The organoid overgrowth phenotypes were largely rescued after correction of the mutation using CRISPR-Cas9. This CNTNAP2-organoid model provides opportunity for further mechanistic inquiry and development of new therapeutic strategies for ASD.

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Cortical overgrowth in a preclinical forebrain organoid model of CNTNAP2-associated autism spectrum disorder

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