Temporal transcriptional control of neural induction in human induced pluripotent stem cells
IntroductionNeural induction of human induced pluripotent stem cells represents a critical switch in cell state during which pluripotency is lost and commitment to a neural lineage is initiated. Although many of the key transcription factors involved in neural induction are known, we know little of...
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| Format: | Article |
| Language: | English |
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Frontiers Media S.A.
2023-05-01
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| Series: | Frontiers in Molecular Neuroscience |
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| Online Access: | https://www.frontiersin.org/articles/10.3389/fnmol.2023.1139287/full |
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| author | Shakti Gupta Lucia Dutan Polit Michael Fitzgerald Helen A. Rowland Divya Murali Noel J. Buckley Shankar Subramaniam Shankar Subramaniam |
| author_facet | Shakti Gupta Lucia Dutan Polit Michael Fitzgerald Helen A. Rowland Divya Murali Noel J. Buckley Shankar Subramaniam Shankar Subramaniam |
| author_sort | Shakti Gupta |
| collection | DOAJ |
| description | IntroductionNeural induction of human induced pluripotent stem cells represents a critical switch in cell state during which pluripotency is lost and commitment to a neural lineage is initiated. Although many of the key transcription factors involved in neural induction are known, we know little of the temporal and causal relationships that are required for this state transition.MethodsHere, we have carried out a longitudinal analysis of the transcriptome of human iPSCs undergoing neural induction. Using the temporal relationships between the changing profile of key transcription factors and subsequent changes in their target gene expression profiles, we have identified distinct functional modules operative throughout neural induction.ResultsIn addition to modules that govern loss of pluripotency and gain of neural ectoderm identity, we discover other modules governing cell cycle and metabolism. Strikingly, some of these functional modules are retained throughout neural induction, even though the gene membership of the module changes. Systems analysis identifies other modules associated with cell fate commitment, genome integrity, stress response and lineage specification. We then focussed on OTX2, one of the most precociously activated transcription factors during neural induction. Our temporal analysis of OTX2 target gene expression identified several OTX2 regulated gene modules representing protein remodelling, RNA splicing and RNA processing. Further CRISPRi inhibition of OTX2 prior to neural induction promotes an accelerated loss of pluripotency and a precocious and aberrant neural induction disrupting some of the previously identified modules.DiscussionWe infer that OTX2 has a diverse role during neural induction and regulates many of the biological processes that are required for loss of pluripotency and gain of neural identity. This dynamical analysis of transcriptional changes provides a unique perspective of the widespread remodelling of the cell machinery that occurs during neural induction of human iPSCs. |
| first_indexed | 2024-04-09T14:18:41Z |
| format | Article |
| id | doaj.art-a30239e08ad74ede8fa328bc18a09c36 |
| institution | Directory Open Access Journal |
| issn | 1662-5099 |
| language | English |
| last_indexed | 2024-04-09T14:18:41Z |
| publishDate | 2023-05-01 |
| publisher | Frontiers Media S.A. |
| record_format | Article |
| series | Frontiers in Molecular Neuroscience |
| spelling | doaj.art-a30239e08ad74ede8fa328bc18a09c362023-05-05T04:58:35ZengFrontiers Media S.A.Frontiers in Molecular Neuroscience1662-50992023-05-011610.3389/fnmol.2023.11392871139287Temporal transcriptional control of neural induction in human induced pluripotent stem cellsShakti Gupta0Lucia Dutan Polit1Michael Fitzgerald2Helen A. Rowland3Divya Murali4Noel J. Buckley5Shankar Subramaniam6Shankar Subramaniam7Department of Bioengineering, University of California, San Diego, San Diego, CA, United StatesMaurice Wohl Clinical Neuroscience Institute, King’s College London, London, United KingdomDepartment of Bioengineering, University of California, San Diego, San Diego, CA, United StatesDepartment of Psychiatry and Kavli Institute for Nanoscience Discovery, University of Oxford, Oxford, United KingdomDepartment of Bioengineering, University of California, San Diego, San Diego, CA, United StatesDepartment of Psychiatry and Kavli Institute for Nanoscience Discovery, University of Oxford, Oxford, United KingdomDepartment of Bioengineering, University of California, San Diego, San Diego, CA, United StatesDepartments of Computer Science and Engineering, and Cellular and Molecular Medicine, University of California, San Diego, San Diego, CA, United StatesIntroductionNeural induction of human induced pluripotent stem cells represents a critical switch in cell state during which pluripotency is lost and commitment to a neural lineage is initiated. Although many of the key transcription factors involved in neural induction are known, we know little of the temporal and causal relationships that are required for this state transition.MethodsHere, we have carried out a longitudinal analysis of the transcriptome of human iPSCs undergoing neural induction. Using the temporal relationships between the changing profile of key transcription factors and subsequent changes in their target gene expression profiles, we have identified distinct functional modules operative throughout neural induction.ResultsIn addition to modules that govern loss of pluripotency and gain of neural ectoderm identity, we discover other modules governing cell cycle and metabolism. Strikingly, some of these functional modules are retained throughout neural induction, even though the gene membership of the module changes. Systems analysis identifies other modules associated with cell fate commitment, genome integrity, stress response and lineage specification. We then focussed on OTX2, one of the most precociously activated transcription factors during neural induction. Our temporal analysis of OTX2 target gene expression identified several OTX2 regulated gene modules representing protein remodelling, RNA splicing and RNA processing. Further CRISPRi inhibition of OTX2 prior to neural induction promotes an accelerated loss of pluripotency and a precocious and aberrant neural induction disrupting some of the previously identified modules.DiscussionWe infer that OTX2 has a diverse role during neural induction and regulates many of the biological processes that are required for loss of pluripotency and gain of neural identity. This dynamical analysis of transcriptional changes provides a unique perspective of the widespread remodelling of the cell machinery that occurs during neural induction of human iPSCs.https://www.frontiersin.org/articles/10.3389/fnmol.2023.1139287/fullpluripotencyinduced pluripotent stem cellneural inductiontranscriptionOTX2 |
| spellingShingle | Shakti Gupta Lucia Dutan Polit Michael Fitzgerald Helen A. Rowland Divya Murali Noel J. Buckley Shankar Subramaniam Shankar Subramaniam Temporal transcriptional control of neural induction in human induced pluripotent stem cells Frontiers in Molecular Neuroscience pluripotency induced pluripotent stem cell neural induction transcription OTX2 |
| title | Temporal transcriptional control of neural induction in human induced pluripotent stem cells |
| title_full | Temporal transcriptional control of neural induction in human induced pluripotent stem cells |
| title_fullStr | Temporal transcriptional control of neural induction in human induced pluripotent stem cells |
| title_full_unstemmed | Temporal transcriptional control of neural induction in human induced pluripotent stem cells |
| title_short | Temporal transcriptional control of neural induction in human induced pluripotent stem cells |
| title_sort | temporal transcriptional control of neural induction in human induced pluripotent stem cells |
| topic | pluripotency induced pluripotent stem cell neural induction transcription OTX2 |
| url | https://www.frontiersin.org/articles/10.3389/fnmol.2023.1139287/full |
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