---
OA_place: repository
OA_type: green
_id: '21962'
abstract:
- lang: eng
  text: The generation of faithful cell-type diversity and correct projection neuron
    numbers is essential for cerebral cortex development. Corticogenesis is however
    susceptible to genetic interference of critical signaling pathways, including
    mutations in Mtor/Rptor that lead to microcephaly. How the loss of Rptor/mTORC1
    function affects cortical developmental programs, at single cell level, is still
    unknown. Here, we utilized Mosaic Analysis with Double Markers (MADM) technology
    to probe Rptor gene function upon sparse single cell- or global tissue-wide ablation.
    We found that tissue-wide effects drive the etiology of cortical microcephaly
    upon loss of Rptor, rather than deficits in projection neuron genesis. Conversely,
    Rptor function is cell-autonomously required for postnatal projection neuron survival
    in a highly cell-type-specific manner. Collectively, our results suggest that
    the fine balance of precise cell-type-specific cell-autonomous Rptor/mTORC1 function
    in concert with non-cell-autonomous tissue-wide effects is essential for the development
    of a properly-sized cerebral cortex with accurate projection neuron diversity.
acknowledged_ssus:
- _id: PreCl
- _id: LifeSc
- _id: MassSpec
- _id: Bio
acknowledgement: "We thank A. Heger (IST Austria Preclinical Facility), A. Sommer
  (VBCF GmbH, NGS Unit), and A.\r\nNicolas (IST Austria Lab Support Facility / Mass
  Spectrometry Facility) for technical support; K. Ferencak,\r\nI. Aykara, P. Hirschfeld,
  E. Fisher, S. Laukoter, L. Andersen for initial experiments and/or assistance; and\r\nall
  members of the Hippenmeyer lab for discussion. This research was supported by the
  Scientific Service\r\nUnits (SSU) of IST Austria through resources provided by the
  Imaging and Optics- (IOF), Lab Support-\r\n(LSF) and Preclinical Facilities (PCF).
  R.B. received support from FWF Meitner-Programm (M 2416). This\r\nwork was also
  supported by IST Austria institutional funds; the People Programme (Marie Curie
  Actions)\r\nof the European Union’s Seventh Framework Programme (FP7/2007-2013)
  under REA grant agreement\r\nNo 618444 to S.H., and the European Research Council
  (ERC) under the European Union’s Horizon 2020\r\nresearch and innovation programme
  (grant agreement No 725780 LinPro) to S.H."
article_processing_charge: No
author:
- first_name: Ana
  full_name: Villalba Requena, Ana
  id: 68cb85a0-39f7-11eb-9559-9aaab4f6a247
  last_name: Villalba Requena
  orcid: 0000-0002-5615-5277
- first_name: Robert J
  full_name: Beattie, Robert J
  id: 2E26DF60-F248-11E8-B48F-1D18A9856A87
  last_name: Beattie
  orcid: 0000-0002-8483-8753
- first_name: Florian
  full_name: Pauler, Florian
  id: 48EA0138-F248-11E8-B48F-1D18A9856A87
  last_name: Pauler
  orcid: 0000-0002-7462-0048
- first_name: Carmen
  full_name: Streicher, Carmen
  id: 36BCB99C-F248-11E8-B48F-1D18A9856A87
  last_name: Streicher
- first_name: Osvaldo
  full_name: Miranda, Osvaldo
  id: 862A3C56-A8BF-11E9-B4FA-D9E3E5697425
  last_name: Miranda
  orcid: 0000-0001-6618-6889
- first_name: Thomas
  full_name: Krausgruber, Thomas
  last_name: Krausgruber
- first_name: Martin
  full_name: Senekowitsch, Martin
  last_name: Senekowitsch
- first_name: Matthias
  full_name: Farlik, Matthias
  last_name: Farlik
- first_name: Christoph
  full_name: Bock, Christoph
  last_name: Bock
- first_name: Thomas
  full_name: Rülicke, Thomas
  last_name: Rülicke
- first_name: Simon
  full_name: Hippenmeyer, Simon
  id: 37B36620-F248-11E8-B48F-1D18A9856A87
  last_name: Hippenmeyer
  orcid: 0000-0003-2279-1061
citation:
  ama: Villalba Requena A, Beattie RJ, Pauler F, et al. Mtor/Rptor function globally
    prevents cortical microcephaly and cell-autonomously promotes postnatal neuron
    survival in cell type specific manner. <i>bioRxiv</i>. doi:<a href="https://doi.org/10.64898/2026.05.01.722172">10.64898/2026.05.01.722172</a>
  apa: Villalba Requena, A., Beattie, R. J., Pauler, F., Streicher, C., Miranda, O.,
    Krausgruber, T., … Hippenmeyer, S. (n.d.). Mtor/Rptor function globally prevents
    cortical microcephaly and cell-autonomously promotes postnatal neuron survival
    in cell type specific manner. <i>bioRxiv</i>. <a href="https://doi.org/10.64898/2026.05.01.722172">https://doi.org/10.64898/2026.05.01.722172</a>
  chicago: Villalba Requena, Ana, Robert J Beattie, Florian Pauler, Carmen Streicher,
    Osvaldo Miranda, Thomas Krausgruber, Martin Senekowitsch, et al. “Mtor/Rptor Function
    Globally Prevents Cortical Microcephaly and Cell-Autonomously Promotes Postnatal
    Neuron Survival in Cell Type Specific Manner.” <i>BioRxiv</i>, n.d. <a href="https://doi.org/10.64898/2026.05.01.722172">https://doi.org/10.64898/2026.05.01.722172</a>.
  ieee: A. Villalba Requena <i>et al.</i>, “Mtor/Rptor function globally prevents
    cortical microcephaly and cell-autonomously promotes postnatal neuron survival
    in cell type specific manner,” <i>bioRxiv</i>. .
  ista: Villalba Requena A, Beattie RJ, Pauler F, Streicher C, Miranda O, Krausgruber
    T, Senekowitsch M, Farlik M, Bock C, Rülicke T, Hippenmeyer S. Mtor/Rptor function
    globally prevents cortical microcephaly and cell-autonomously promotes postnatal
    neuron survival in cell type specific manner. bioRxiv, <a href="https://doi.org/10.64898/2026.05.01.722172">10.64898/2026.05.01.722172</a>.
  mla: Villalba Requena, Ana, et al. “Mtor/Rptor Function Globally Prevents Cortical
    Microcephaly and Cell-Autonomously Promotes Postnatal Neuron Survival in Cell
    Type Specific Manner.” <i>BioRxiv</i>, doi:<a href="https://doi.org/10.64898/2026.05.01.722172">10.64898/2026.05.01.722172</a>.
  short: A. Villalba Requena, R.J. Beattie, F. Pauler, C. Streicher, O. Miranda, T.
    Krausgruber, M. Senekowitsch, M. Farlik, C. Bock, T. Rülicke, S. Hippenmeyer,
    BioRxiv (n.d.).
date_created: 2026-06-09T08:08:18Z
date_published: 2026-05-05T00:00:00Z
date_updated: 2026-06-16T08:45:25Z
day: '05'
ddc:
- '570'
department:
- _id: SiHi
doi: 10.64898/2026.05.01.722172
ec_funded: 1
has_accepted_license: '1'
language:
- iso: eng
license: https://creativecommons.org/licenses/by-nc/4.0/
main_file_link:
- open_access: '1'
  url: https://doi.org/10.64898/2026.05.01.722172
month: '05'
oa: 1
oa_version: Preprint
project:
- _id: 264E56E2-B435-11E9-9278-68D0E5697425
  call_identifier: FWF
  grant_number: M02416
  name: Molecular Mechanisms Regulating Gliogenesis in the Neocortex
- _id: 25D61E48-B435-11E9-9278-68D0E5697425
  call_identifier: FP7
  grant_number: '618444'
  name: Molecular Mechanisms of Cerebral Cortex Development
- _id: 260018B0-B435-11E9-9278-68D0E5697425
  call_identifier: H2020
  grant_number: '725780'
  name: Principles of Neural Stem Cell Lineage Progression in Cerebral Cortex Development
publication: bioRxiv
publication_status: submitted
status: public
title: Mtor/Rptor function globally prevents cortical microcephaly and cell-autonomously
  promotes postnatal neuron survival in cell type specific manner
tmp:
  image: /images/cc_by_nc.png
  legal_code_url: https://creativecommons.org/licenses/by-nc/4.0/legalcode
  name: Creative Commons Attribution-NonCommercial 4.0 International (CC BY-NC 4.0)
  short: CC BY-NC (4.0)
type: preprint
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
year: '2026'
...
---
OA_place: repository
OA_type: green
_id: '21963'
abstract:
- lang: eng
  text: The cerebral cortex consists of immense numbers of neuronal and glial cell-types
    derived from radial glial progenitor (RGP) cells. How RGPs generate appropriate
    quantities of distinct cortical cell-types to safeguard a brain of correct size,
    is not well understood. However, genetic aberration in human, including mutations
    in PTEN, lead to cortical malformation such as macrocephaly, albeit with unknown
    etiology. Here we utilized Mosaic Analysis with Double Markers (MADM)-based clonal
    analysis and single cell phenotyping to decipher the role of Pten in neurogenic
    and gliogenic RGP lineage progression during cortical ontogeny. While neurogenic
    RGP lineage progression and projection neuron production was moderately altered
    in the absence of Pten, cortical astrocyte production was drastically increased.
    Through genetic epistasis experiments we show that the loss of Pten uncouples
    astrocyte generation from essential growth factor signaling hubs, funneling into
    MAPK. Collectively, our results suggest that Pten regulates RGP lineage progression
    with distinct sequential functions in cortical projection neurogenesis and astrocyte
    production to ensure the emergence of a correctly-sized cerebral cortex.
acknowledged_ssus:
- _id: Bio
- _id: LifeSc
- _id: PreCl
acknowledgement: "We thank Kay-Uwe Wagner (Wayne State University) for generously
  sharing Jak1/2–flox mouse lines; A.\r\nSommer (VBCF GmbH, NGS Unit) for technical
  support; N. Kim, V. Mick, S. Schnabl, S. Gobeil, and L.\r\nAndersen for technical
  assistance; all members of the Hippenmeyer lab for discussion and B. Novitch for\r\ncomments
  on earlier versions of the manuscript. This research was supported by the Scientific
  Service Units\r\n(SSU) of IST Austria through resources provided by the Imaging
  and Optics Facility (IOF), Lab Support-\r\n(LSF) and Preclinical Facilities (PCF).
  O.A.M received support from the Austrian Academy of Sciences\r\nÖAW (DOC 186584),
  and N.A. from FWF Elise Richter Program (Grant V1041T). This work was also\r\nsupported
  by IST Austria institutional funds; FWF SFB F78 (Neuro Stem Modulation) to S.H.,
  and the\r\nEuropean Research Council (ERC) under the European Union’s Horizon 2020
  research and innovation\r\nprogramme (grant agreement No 725780 LinPro) to S.H."
article_processing_charge: No
author:
- first_name: Osvaldo
  full_name: Miranda, Osvaldo
  id: 862A3C56-A8BF-11E9-B4FA-D9E3E5697425
  last_name: Miranda
  orcid: 0000-0001-6618-6889
- first_name: Ximena
  full_name: Contreras, Ximena
  id: 475990FE-F248-11E8-B48F-1D18A9856A87
  last_name: Contreras
- first_name: Florian
  full_name: Pauler, Florian
  id: 48EA0138-F248-11E8-B48F-1D18A9856A87
  last_name: Pauler
  orcid: 0000-0002-7462-0048
- first_name: Amarbayasgalan
  full_name: Davaatseren, Amarbayasgalan
  id: 70ADC922-B424-11E9-99E3-BA18E6697425
  last_name: Davaatseren
- first_name: Nicole
  full_name: Amberg, Nicole
  id: 4CD6AAC6-F248-11E8-B48F-1D18A9856A87
  last_name: Amberg
  orcid: 0000-0002-3183-8207
- first_name: Carmen
  full_name: Streicher, Carmen
  id: 36BCB99C-F248-11E8-B48F-1D18A9856A87
  last_name: Streicher
- first_name: Ana
  full_name: Villalba Requena, Ana
  id: 68cb85a0-39f7-11eb-9559-9aaab4f6a247
  last_name: Villalba Requena
  orcid: 0000-0002-5615-5277
- first_name: Anna-Magdalena
  full_name: Heger, Anna-Magdalena
  id: 4B76FFD2-F248-11E8-B48F-1D18A9856A87
  last_name: Heger
- first_name: Corentine
  full_name: Marie, Corentine
  last_name: Marie
- first_name: Bassem A.
  full_name: Hassan, Bassem A.
  last_name: Hassan
- first_name: Thomas
  full_name: Rülicke, Thomas
  last_name: Rülicke
- first_name: Simon
  full_name: Hippenmeyer, Simon
  id: 37B36620-F248-11E8-B48F-1D18A9856A87
  last_name: Hippenmeyer
  orcid: 0000-0003-2279-1061
citation:
  ama: Miranda O, Contreras X, Pauler F, et al. Pten orchestrates neurogenic radial
    glia lineage progression and tunes neocortical astrocyte production. <i>bioRxiv</i>.
    doi:<a href="https://doi.org/10.64898/2026.05.01.722191">10.64898/2026.05.01.722191</a>
  apa: Miranda, O., Contreras, X., Pauler, F., Davaatseren, A., Amberg, N., Streicher,
    C., … Hippenmeyer, S. (n.d.). Pten orchestrates neurogenic radial glia lineage
    progression and tunes neocortical astrocyte production. <i>bioRxiv</i>. <a href="https://doi.org/10.64898/2026.05.01.722191">https://doi.org/10.64898/2026.05.01.722191</a>
  chicago: Miranda, Osvaldo, Ximena Contreras, Florian Pauler, Amarbayasgalan Davaatseren,
    Nicole Amberg, Carmen Streicher, Ana Villalba Requena, et al. “Pten Orchestrates
    Neurogenic Radial Glia Lineage Progression and Tunes Neocortical Astrocyte Production.”
    <i>BioRxiv</i>, n.d. <a href="https://doi.org/10.64898/2026.05.01.722191">https://doi.org/10.64898/2026.05.01.722191</a>.
  ieee: O. Miranda <i>et al.</i>, “Pten orchestrates neurogenic radial glia lineage
    progression and tunes neocortical astrocyte production,” <i>bioRxiv</i>. .
  ista: Miranda O, Contreras X, Pauler F, Davaatseren A, Amberg N, Streicher C, Villalba
    Requena A, Heger A-M, Marie C, Hassan BA, Rülicke T, Hippenmeyer S. Pten orchestrates
    neurogenic radial glia lineage progression and tunes neocortical astrocyte production.
    bioRxiv, <a href="https://doi.org/10.64898/2026.05.01.722191">10.64898/2026.05.01.722191</a>.
  mla: Miranda, Osvaldo, et al. “Pten Orchestrates Neurogenic Radial Glia Lineage
    Progression and Tunes Neocortical Astrocyte Production.” <i>BioRxiv</i>, doi:<a
    href="https://doi.org/10.64898/2026.05.01.722191">10.64898/2026.05.01.722191</a>.
  short: O. Miranda, X. Contreras, F. Pauler, A. Davaatseren, N. Amberg, C. Streicher,
    A. Villalba Requena, A.-M. Heger, C. Marie, B.A. Hassan, T. Rülicke, S. Hippenmeyer,
    BioRxiv (n.d.).
corr_author: '1'
date_created: 2026-06-09T08:08:53Z
date_published: 2026-05-05T00:00:00Z
date_updated: 2026-06-16T08:57:20Z
day: '05'
ddc:
- '570'
department:
- _id: SiHi
- _id: PreCl
- _id: GradSch
doi: 10.64898/2026.05.01.722191
ec_funded: 1
has_accepted_license: '1'
language:
- iso: eng
main_file_link:
- open_access: '1'
  url: https://doi.org/10.64898/2026.05.01.722191
month: '05'
oa: 1
oa_version: Preprint
project:
- _id: 059F6AB4-7A3F-11EA-A408-12923DDC885E
  grant_number: F7805
  name: Stem Cell Modulation in Neural Development and Regeneration/ P05-Molecular
    Mechanisms of Neural Stem Cell Lineage Progression
- _id: 260018B0-B435-11E9-9278-68D0E5697425
  call_identifier: H2020
  grant_number: '725780'
  name: Principles of Neural Stem Cell Lineage Progression in Cerebral Cortex Development
publication: bioRxiv
publication_status: submitted
status: public
title: Pten orchestrates neurogenic radial glia lineage progression and tunes neocortical
  astrocyte production
tmp:
  image: /images/cc_by_nc.png
  legal_code_url: https://creativecommons.org/licenses/by-nc/4.0/legalcode
  name: Creative Commons Attribution-NonCommercial 4.0 International (CC BY-NC 4.0)
  short: CC BY-NC (4.0)
type: preprint
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
year: '2026'
...
---
OA_place: publisher
_id: '20212'
acknowledged_ssus:
- _id: Bio
- _id: PreCl
acknowledgement: "I would also like to\r\nthank the Austrian Academy of Sciences for
  awarding me a 2-year DOC fellowship\r\n(DOC26253)."
alternative_title:
- ISTA Thesis
article_processing_charge: No
author:
- first_name: Osvaldo
  full_name: Miranda, Osvaldo
  id: 862A3C56-A8BF-11E9-B4FA-D9E3E5697425
  last_name: Miranda
  orcid: 0000-0001-6618-6889
citation:
  ama: Miranda O. Unraveling the role of Pten in cortical stem cell lineage progression
    using MADM. 2025. doi:<a href="https://doi.org/10.15479/AT-ISTA-20212">10.15479/AT-ISTA-20212</a>
  apa: Miranda, O. (2025). <i>Unraveling the role of Pten in cortical stem cell lineage
    progression using MADM</i>. Institute of Science and Technology Austria. <a href="https://doi.org/10.15479/AT-ISTA-20212">https://doi.org/10.15479/AT-ISTA-20212</a>
  chicago: Miranda, Osvaldo. “Unraveling the Role of Pten in Cortical Stem Cell Lineage
    Progression Using MADM.” Institute of Science and Technology Austria, 2025. <a
    href="https://doi.org/10.15479/AT-ISTA-20212">https://doi.org/10.15479/AT-ISTA-20212</a>.
  ieee: O. Miranda, “Unraveling the role of Pten in cortical stem cell lineage progression
    using MADM,” Institute of Science and Technology Austria, 2025.
  ista: Miranda O. 2025. Unraveling the role of Pten in cortical stem cell lineage
    progression using MADM. Institute of Science and Technology Austria.
  mla: Miranda, Osvaldo. <i>Unraveling the Role of Pten in Cortical Stem Cell Lineage
    Progression Using MADM</i>. Institute of Science and Technology Austria, 2025,
    doi:<a href="https://doi.org/10.15479/AT-ISTA-20212">10.15479/AT-ISTA-20212</a>.
  short: O. Miranda, Unraveling the Role of Pten in Cortical Stem Cell Lineage Progression
    Using MADM, Institute of Science and Technology Austria, 2025.
corr_author: '1'
date_created: 2025-08-22T14:07:00Z
date_published: 2025-08-22T00:00:00Z
date_updated: 2026-08-26T22:30:03Z
day: '22'
ddc:
- '570'
degree_awarded: PhD
department:
- _id: GradSch
- _id: SiHi
doi: 10.15479/AT-ISTA-20212
file:
- access_level: closed
  checksum: 3331f76bbef74ff4908e2d2c9262045c
  content_type: application/vnd.openxmlformats-officedocument.wordprocessingml.document
  creator: omiranda
  date_created: 2025-08-26T09:03:50Z
  date_updated: 2026-08-26T22:30:02Z
  embargo_to: open_access
  file_id: '20230'
  file_name: 2025_MirandaRomero_OsvaldoAntonio_Thesis.docx
  file_size: 32887334
  relation: source_file
- access_level: open_access
  checksum: 02509d50cff8e35c5bcbf71e8d658176
  content_type: application/pdf
  creator: omiranda
  date_created: 2025-08-26T09:05:55Z
  date_updated: 2026-08-26T22:30:02Z
  embargo: 2026-08-26
  file_id: '20231'
  file_name: 2025_MirandaRomero_OsvaldoAntonio_Thesis.pdf
  file_size: 28636240
  relation: main_file
file_date_updated: 2026-08-26T22:30:02Z
has_accepted_license: '1'
keyword:
- Pten
- mtor
- cortical development
- MADM
- Mapk
language:
- iso: eng
month: '08'
oa: 1
oa_version: Published Version
page: '119'
project:
- _id: 34c9fbcb-11ca-11ed-8bc3-98fa5658610d
  grant_number: '26253'
  name: Molecular Mechanisms Regulating Cortical Neural Stem Cell Lineage Progression
    and Astrocyte Development
publication_identifier:
  isbn:
  - 978-3-99078-063-3
  issn:
  - 2663-337X
publication_status: published
publisher: Institute of Science and Technology Austria
related_material:
  record:
  - id: '17425'
    relation: part_of_dissertation
    status: public
status: public
supervisor:
- first_name: Simon
  full_name: Hippenmeyer, Simon
  id: 37B36620-F248-11E8-B48F-1D18A9856A87
  last_name: Hippenmeyer
  orcid: 0000-0003-2279-1061
title: Unraveling the role of Pten in cortical stem cell lineage progression using
  MADM
type: dissertation
user_id: ba8df636-2132-11f1-aed0-ed93e2281fdd
year: '2025'
...
---
_id: '17425'
abstract:
- lang: eng
  text: Mosaic Analysis with Double Markers (MADM) is a powerful genetic method typically
    used for lineage tracing and to disentangle cell autonomous and tissue-wide roles
    of candidate genes with single cell resolution. Given the relatively sparse labeling,
    depending on which of the 19 MADM chromosomes one chooses, the MADM approach represents
    the perfect opportunity for cell morphology analysis. Various MADM studies include
    reports of morphological anomalies and phenotypes in the central nervous system
    (CNS). MADM for any candidate gene can easily incorporate morphological analysis
    within the experimental workflow. Here, we describe the methods of morphological
    cell analysis which we developed in the course of diverse recent MADM studies.
    This chapter will specifically focus on methods to quantify aspects of the morphology
    of neurons and astrocytes within the CNS, but these methods can broadly be applied
    to any MADM-labeled cells throughout the entire organism. We will cover two analyses—soma
    volume and dendrite characterization—of physical characteristics of pyramidal
    neurons in the somatosensory cortex, and two analyses—volume and Sholl analysis—of
    astrocyte morphology.
acknowledged_ssus:
- _id: Bio
acknowledgement: We thank all Hippenmeyer lab members for support and discussions.
  This work was supported by the Scientific Service Units (SSU) at ISTA through resources
  provided by the Imaging & Optics Facility (IOF). O.A.M was a recipient of a DOC
  Fellowship (26253) of the Austrian Academy of Sciences. This work was supported
  by ISTA institutional funds, and The Austrian Science Fund Special Research Programmes
  (FWF SFB F78 Neuro Stem Modulation) to S.H.
alternative_title:
- Methods in Molecular Biology
article_processing_charge: No
author:
- first_name: Osvaldo
  full_name: Miranda, Osvaldo
  id: 862A3C56-A8BF-11E9-B4FA-D9E3E5697425
  last_name: Miranda
  orcid: 0000-0001-6618-6889
- first_name: Giselle T
  full_name: Cheung, Giselle T
  id: 471195F6-F248-11E8-B48F-1D18A9856A87
  last_name: Cheung
  orcid: 0000-0001-8457-2572
- first_name: Simon
  full_name: Hippenmeyer, Simon
  id: 37B36620-F248-11E8-B48F-1D18A9856A87
  last_name: Hippenmeyer
  orcid: 0000-0003-2279-1061
citation:
  ama: 'Miranda O, Cheung GT, Hippenmeyer S. Morphological Analysis of Neurons and
    Glia Using Mosaic Analysis with Double Markers. In: Toyooka K, ed. <i>Neuronal
    Morphogenesis</i>. Vol 2831. 1st ed. MIMB. New York, NY: Springer Nature; 2024:283-299.
    doi:<a href="https://doi.org/10.1007/978-1-0716-3969-6_19">10.1007/978-1-0716-3969-6_19</a>'
  apa: 'Miranda, O., Cheung, G. T., &#38; Hippenmeyer, S. (2024). Morphological Analysis
    of Neurons and Glia Using Mosaic Analysis with Double Markers. In K. Toyooka (Ed.),
    <i>Neuronal Morphogenesis</i> (1st ed., Vol. 2831, pp. 283–299). New York, NY:
    Springer Nature. <a href="https://doi.org/10.1007/978-1-0716-3969-6_19">https://doi.org/10.1007/978-1-0716-3969-6_19</a>'
  chicago: 'Miranda, Osvaldo, Giselle T Cheung, and Simon Hippenmeyer. “Morphological
    Analysis of Neurons and Glia Using Mosaic Analysis with Double Markers.” In <i>Neuronal
    Morphogenesis</i>, edited by Kazuhito Toyooka, 1st ed., 2831:283–99. MIMB. New
    York, NY: Springer Nature, 2024. <a href="https://doi.org/10.1007/978-1-0716-3969-6_19">https://doi.org/10.1007/978-1-0716-3969-6_19</a>.'
  ieee: 'O. Miranda, G. T. Cheung, and S. Hippenmeyer, “Morphological Analysis of
    Neurons and Glia Using Mosaic Analysis with Double Markers,” in <i>Neuronal Morphogenesis</i>,
    1st ed., vol. 2831, K. Toyooka, Ed. New York, NY: Springer Nature, 2024, pp. 283–299.'
  ista: 'Miranda O, Cheung GT, Hippenmeyer S. 2024.Morphological Analysis of Neurons
    and Glia Using Mosaic Analysis with Double Markers. In: Neuronal Morphogenesis.
    Methods in Molecular Biology, vol. 2831, 283–299.'
  mla: Miranda, Osvaldo, et al. “Morphological Analysis of Neurons and Glia Using
    Mosaic Analysis with Double Markers.” <i>Neuronal Morphogenesis</i>, edited by
    Kazuhito Toyooka, 1st ed., vol. 2831, Springer Nature, 2024, pp. 283–99, doi:<a
    href="https://doi.org/10.1007/978-1-0716-3969-6_19">10.1007/978-1-0716-3969-6_19</a>.
  short: O. Miranda, G.T. Cheung, S. Hippenmeyer, in:, K. Toyooka (Ed.), Neuronal
    Morphogenesis, 1st ed., Springer Nature, New York, NY, 2024, pp. 283–299.
corr_author: '1'
date_created: 2024-08-13T12:16:41Z
date_published: 2024-08-13T00:00:00Z
date_updated: 2026-08-26T22:30:02Z
day: '13'
department:
- _id: GradSch
- _id: SiHi
doi: 10.1007/978-1-0716-3969-6_19
edition: '1'
editor:
- first_name: Kazuhito
  full_name: Toyooka, Kazuhito
  last_name: Toyooka
external_id:
  pmid:
  - '39134857'
intvolume: '      2831'
language:
- iso: eng
month: '08'
oa_version: None
page: 283-299
place: New York, NY
pmid: 1
project:
- _id: 34c9fbcb-11ca-11ed-8bc3-98fa5658610d
  grant_number: '26253'
  name: Molecular Mechanisms Regulating Cortical Neural Stem Cell Lineage Progression
    and Astrocyte Development
- _id: 059F6AB4-7A3F-11EA-A408-12923DDC885E
  grant_number: F7805
  name: Stem Cell Modulation in Neural Development and Regeneration/ P05-Molecular
    Mechanisms of Neural Stem Cell Lineage Progression
publication: Neuronal Morphogenesis
publication_identifier:
  eisbn:
  - '9781071639696'
  eissn:
  - 1940-6029
  isbn:
  - '9781071639689'
  issn:
  - 1064-3745
publication_status: published
publisher: Springer Nature
quality_controlled: '1'
related_material:
  record:
  - id: '20212'
    relation: dissertation_contains
    status: public
scopus_import: '1'
series_title: MIMB
status: public
title: Morphological Analysis of Neurons and Glia Using Mosaic Analysis with Double
  Markers
type: book_chapter
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 2831
year: '2024'
...
---
OA_place: publisher
OA_type: green
_id: '6995'
abstract:
- lang: eng
  text: Human brain organoids represent a powerful tool for the study of human neurological
    diseases particularly those that impact brain growth and structure. However, many
    neurological diseases lack obvious anatomical abnormalities, yet significantly
    impact neural network functions, raising the question of whether organoids possess
    sufficient neural network architecture and complexity to model these conditions.
    Here, we explore the network level functions of brain organoids using calcium
    sensor imaging and extracellular recording approaches that together reveal the
    existence of complex oscillatory network behaviors reminiscent of intact brain
    preparations. We further demonstrate strikingly abnormal epileptiform network
    activity in organoids derived from a Rett Syndrome patient despite only modest
    anatomical differences from isogenically matched controls, and rescue with an
    unconventional neuromodulatory drug Pifithrin-α. Together, these findings provide
    an essential foundation for the utilization of human brain organoids to study
    intact and disordered human brain network formation and illustrate their utility
    in therapeutic discovery.
acknowledgement: We thank S. Butler, T. Carmichael and members of the laboratory of
  B.G.N. for helpful discussions and comments on the manuscript; N. Vishlaghi and
  F. Turcios-Hernandez for technical assistance, and J. Lee, S.-K. Lee, H. Shinagawa
  and K. Yoshikawa for valuable reagents. We also thank the UCLA Eli and Edythe Broad
  Stem Cell Research Center (BSCRC) and Intellectual and Developmental Disabilities
  Research Center microscopy cores for access to imaging facilities. This work was
  supported by grants from the California Institute for Regenerative Medicine (CIRM)
  (DISC1-08819 to B.G.N.), the National Institute of Health (R01NS089817, R01DA051897
  and P50HD103557 to B.G.N.; K08NS119747 to R.A.S.; K99HD096105 to M.W.; R01MH123922,
  R01MH121521 and P50HD103557 to M.J.G.; R01GM099134 to K.P.; R01NS103788 to W.E.L.;
  R01NS088571 to J.M.P.; R01NS030549 and R01AG050474 to I.M.), and research awards
  from the UCLA Jonsson Comprehensive Cancer Center and BSCRC Ablon Scholars Program
  (to B.G.N.), the BSCRC Innovation Program (to B.G.N., K.P. and W.E.L.), the UCLA
  BSCRC Steffy Brain Aging Research Fund (to B.G.N. and W.E.L.) and the UCLA Clinical
  and Translational Science Institute (to B.G.N.), Paul Allen Family Foundation Frontiers
  Group (to K.P. and W.E.L.), the March of Dimes Foundation (to W.E.L.) and the Simons
  Foundation Autism Research Initiative Bridge to Independence Program (to R.A.S.
  and M.J.G.). R.A.S. was also supported by the UCLA/NINDS Translational Neuroscience
  Training Grant (R25NS065723), a Research and Training Fellowship from the American
  Epilepsy Society, a Taking Flight Award from CURE Epilepsy and a Clinician Scientist
  training award from the UCLA BSCRC. J.E.B. was supported by the UCLA BSCRC Rose
  Hills Foundation Graduate Scholarship Training Program. M.W. was supported by postdoctoral
  training awards provided by the UCLA BSCRC and the Uehara Memorial Foundation. O.A.M.
  and A.K. were supported in part by the UCLA-California State University Northridge
  CIRM-Bridges training program (EDUC2-08411). We also acknowledge the support of
  the IDDRC Cells, Circuits and Systems Analysis, Microscopy and Genetics and Genomics
  Cores of the Semel Institute of Neuroscience at UCLA, which are supported by the
  NICHD (U54HD087101 and P50HD10355701). We lastly acknowledge support from a Quantitative
  and Computational Biosciences Collaboratory Postdoctoral Fellowship to S.M. and
  the Quantitative and Computational Biosciences Collaboratory community, directed
  by M. Pellegrini.
article_processing_charge: No
article_type: review
author:
- first_name: Ranmal A.
  full_name: Samarasinghe, Ranmal A.
  last_name: Samarasinghe
- first_name: Osvaldo
  full_name: Miranda, Osvaldo
  id: 862A3C56-A8BF-11E9-B4FA-D9E3E5697425
  last_name: Miranda
  orcid: 0000-0001-6618-6889
- first_name: Jessie E.
  full_name: Buth, Jessie E.
  last_name: Buth
- first_name: Simon
  full_name: Mitchell, Simon
  last_name: Mitchell
- first_name: Isabella
  full_name: Ferando, Isabella
  last_name: Ferando
- first_name: Momoko
  full_name: Watanabe, Momoko
  last_name: Watanabe
- first_name: Arinnae
  full_name: Kurdian, Arinnae
  last_name: Kurdian
- first_name: Peyman
  full_name: Golshani, Peyman
  last_name: Golshani
- first_name: Kathrin
  full_name: Plath, Kathrin
  last_name: Plath
- first_name: William E.
  full_name: Lowry, William E.
  last_name: Lowry
- first_name: Jack M.
  full_name: Parent, Jack M.
  last_name: Parent
- first_name: Istvan
  full_name: Mody, Istvan
  last_name: Mody
- first_name: Bennett G.
  full_name: Novitch, Bennett G.
  last_name: Novitch
citation:
  ama: Samarasinghe RA, Miranda O, Buth JE, et al. Identification of neural oscillations
    and epileptiform changes in human brain organoids. <i>Nature Neuroscience</i>.
    2021;24:32. doi:<a href="https://doi.org/10.1038/s41593-021-00906-5">10.1038/s41593-021-00906-5</a>
  apa: Samarasinghe, R. A., Miranda, O., Buth, J. E., Mitchell, S., Ferando, I., Watanabe,
    M., … Novitch, B. G. (2021). Identification of neural oscillations and epileptiform
    changes in human brain organoids. <i>Nature Neuroscience</i>. Springer Nature.
    <a href="https://doi.org/10.1038/s41593-021-00906-5">https://doi.org/10.1038/s41593-021-00906-5</a>
  chicago: Samarasinghe, Ranmal A., Osvaldo Miranda, Jessie E. Buth, Simon Mitchell,
    Isabella Ferando, Momoko Watanabe, Arinnae Kurdian, et al. “Identification of
    Neural Oscillations and Epileptiform Changes in Human Brain Organoids.” <i>Nature
    Neuroscience</i>. Springer Nature, 2021. <a href="https://doi.org/10.1038/s41593-021-00906-5">https://doi.org/10.1038/s41593-021-00906-5</a>.
  ieee: R. A. Samarasinghe <i>et al.</i>, “Identification of neural oscillations and
    epileptiform changes in human brain organoids,” <i>Nature Neuroscience</i>, vol.
    24. Springer Nature, p. 32, 2021.
  ista: Samarasinghe RA, Miranda O, Buth JE, Mitchell S, Ferando I, Watanabe M, Kurdian
    A, Golshani P, Plath K, Lowry WE, Parent JM, Mody I, Novitch BG. 2021. Identification
    of neural oscillations and epileptiform changes in human brain organoids. Nature
    Neuroscience. 24, 32.
  mla: Samarasinghe, Ranmal A., et al. “Identification of Neural Oscillations and
    Epileptiform Changes in Human Brain Organoids.” <i>Nature Neuroscience</i>, vol.
    24, Springer Nature, 2021, p. 32, doi:<a href="https://doi.org/10.1038/s41593-021-00906-5">10.1038/s41593-021-00906-5</a>.
  short: R.A. Samarasinghe, O. Miranda, J.E. Buth, S. Mitchell, I. Ferando, M. Watanabe,
    A. Kurdian, P. Golshani, K. Plath, W.E. Lowry, J.M. Parent, I. Mody, B.G. Novitch,
    Nature Neuroscience 24 (2021) 32.
date_created: 2019-11-10T11:23:58Z
date_published: 2021-08-23T00:00:00Z
date_updated: 2025-07-09T09:00:12Z
day: '23'
department:
- _id: GradSch
- _id: SiHi
doi: 10.1038/s41593-021-00906-5
external_id:
  isi:
  - '000687516300001'
  pmid:
  - '34426698 '
intvolume: '        24'
isi: 1
language:
- iso: eng
main_file_link:
- open_access: '1'
  url: https://doi.org/10.1101/820183
month: '08'
oa: 1
oa_version: Preprint
page: '32'
pmid: 1
publication: Nature Neuroscience
publication_identifier:
  eissn:
  - 1546-1726
  issn:
  - 1097-6256
publication_status: published
publisher: Springer Nature
quality_controlled: '1'
scopus_import: '1'
status: public
title: Identification of neural oscillations and epileptiform changes in human brain
  organoids
type: journal_article
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 24
year: '2021'
...
---
_id: '7358'
abstract:
- lang: eng
  text: Telencephalic organoids generated from human pluripotent stem cells (hPSCs)
    are emerging as an effective system to study the distinct features of the developing
    human brain and the underlying causes of many neurological disorders. While progress
    in organoid technology has been steadily advancing, many challenges remain including
    rampant batch-to-batch and cell line-to-cell line variability and irreproducibility.
    Here, we demonstrate that a major contributor to successful cortical organoid
    production is the manner in which hPSCs are maintained prior to differentiation.
    Optimal results were achieved using fibroblast-feeder-supported hPSCs compared
    to feeder-independent cells, related to differences in their transcriptomic states.
    Feeder-supported hPSCs display elevated activation of diverse TGFβ superfamily
    signaling pathways and increased expression of genes associated with naïve pluripotency.
    We further identify combinations of TGFβ-related growth factors that are necessary
    and together sufficient to impart broad telencephalic organoid competency to feeder-free
    hPSCs and enable reproducible formation of brain structures suitable for disease
    modeling.
article_processing_charge: No
author:
- first_name: Momoko
  full_name: Watanabe, Momoko
  last_name: Watanabe
- first_name: Jillian R.
  full_name: Haney, Jillian R.
  last_name: Haney
- first_name: Neda
  full_name: Vishlaghi, Neda
  last_name: Vishlaghi
- first_name: Felix
  full_name: Turcios, Felix
  last_name: Turcios
- first_name: Jessie E.
  full_name: Buth, Jessie E.
  last_name: Buth
- first_name: Wen
  full_name: Gu, Wen
  last_name: Gu
- first_name: Amanda J.
  full_name: Collier, Amanda J.
  last_name: Collier
- first_name: Osvaldo
  full_name: Miranda, Osvaldo
  id: 862A3C56-A8BF-11E9-B4FA-D9E3E5697425
  last_name: Miranda
  orcid: 0000-0001-6618-6889
- first_name: Di
  full_name: Chen, Di
  last_name: Chen
- first_name: Shan
  full_name: Sabri, Shan
  last_name: Sabri
- first_name: Amander T.
  full_name: Clark, Amander T.
  last_name: Clark
- first_name: Kathrin
  full_name: Plath, Kathrin
  last_name: Plath
- first_name: Heather R.
  full_name: Christofk, Heather R.
  last_name: Christofk
- first_name: Michael J.
  full_name: Gandal, Michael J.
  last_name: Gandal
- first_name: Bennett G.
  full_name: Novitch, Bennett G.
  last_name: Novitch
citation:
  ama: Watanabe M, Haney JR, Vishlaghi N, et al. TGFβ superfamily signaling regulates
    the state of human stem cell pluripotency and competency to create telencephalic
    organoids. <i>bioRxiv</i>. 2019. doi:<a href="https://doi.org/10.1101/2019.12.13.875773">10.1101/2019.12.13.875773</a>
  apa: Watanabe, M., Haney, J. R., Vishlaghi, N., Turcios, F., Buth, J. E., Gu, W.,
    … Novitch, B. G. (2019). TGFβ superfamily signaling regulates the state of human
    stem cell pluripotency and competency to create telencephalic organoids. <i>bioRxiv</i>.
    Cold Spring Harbor Laboratory. <a href="https://doi.org/10.1101/2019.12.13.875773">https://doi.org/10.1101/2019.12.13.875773</a>
  chicago: Watanabe, Momoko, Jillian R. Haney, Neda Vishlaghi, Felix Turcios, Jessie
    E. Buth, Wen Gu, Amanda J. Collier, et al. “TGFβ Superfamily Signaling Regulates
    the State of Human Stem Cell Pluripotency and Competency to Create Telencephalic
    Organoids.” <i>BioRxiv</i>. Cold Spring Harbor Laboratory, 2019. <a href="https://doi.org/10.1101/2019.12.13.875773">https://doi.org/10.1101/2019.12.13.875773</a>.
  ieee: M. Watanabe <i>et al.</i>, “TGFβ superfamily signaling regulates the state
    of human stem cell pluripotency and competency to create telencephalic organoids,”
    <i>bioRxiv</i>. Cold Spring Harbor Laboratory, 2019.
  ista: Watanabe M, Haney JR, Vishlaghi N, Turcios F, Buth JE, Gu W, Collier AJ, Miranda
    O, Chen D, Sabri S, Clark AT, Plath K, Christofk HR, Gandal MJ, Novitch BG. 2019.
    TGFβ superfamily signaling regulates the state of human stem cell pluripotency
    and competency to create telencephalic organoids. bioRxiv, <a href="https://doi.org/10.1101/2019.12.13.875773">10.1101/2019.12.13.875773</a>.
  mla: Watanabe, Momoko, et al. “TGFβ Superfamily Signaling Regulates the State of
    Human Stem Cell Pluripotency and Competency to Create Telencephalic Organoids.”
    <i>BioRxiv</i>, Cold Spring Harbor Laboratory, 2019, doi:<a href="https://doi.org/10.1101/2019.12.13.875773">10.1101/2019.12.13.875773</a>.
  short: M. Watanabe, J.R. Haney, N. Vishlaghi, F. Turcios, J.E. Buth, W. Gu, A.J.
    Collier, O. Miranda, D. Chen, S. Sabri, A.T. Clark, K. Plath, H.R. Christofk,
    M.J. Gandal, B.G. Novitch, BioRxiv (2019).
date_created: 2020-01-23T09:53:40Z
date_published: 2019-12-13T00:00:00Z
date_updated: 2022-06-17T08:03:32Z
day: '13'
doi: 10.1101/2019.12.13.875773
extern: '1'
language:
- iso: eng
main_file_link:
- open_access: '1'
  url: https://doi.org/10.1101/2019.12.13.875773
month: '12'
oa: 1
oa_version: Preprint
page: '75'
publication: bioRxiv
publication_status: published
publisher: Cold Spring Harbor Laboratory
status: public
title: TGFβ superfamily signaling regulates the state of human stem cell pluripotency
  and competency to create telencephalic organoids
type: preprint
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
year: '2019'
...