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Article ; Online: Reproducible Differentiation of Human Pluripotent Stem Cells into Two-Dimensional Cortical Neuron Cultures with Checkpoints for Success.

Waxman, Elisa A / Dungan, Lea V / DeFlitch, Leah M / Merchant, Julie P / Gagne, Alyssa L / Goldberg, Ethan M / French, Deborah L

Current protocols

2023 Volume 3, Issue 12, Page(s) e948

Abstract: The patterning of excitatory cortical neurons from human pluripotent stem cells (hPSCs) is a desired technique for the study of neurodevelopmental disorders, as neurons can be created and compared from control hPSC lines, hPSC lines generated from ... ...

Abstract	The patterning of excitatory cortical neurons from human pluripotent stem cells (hPSCs) is a desired technique for the study of neurodevelopmental disorders, as neurons can be created and compared from control hPSC lines, hPSC lines generated from patients, and CRISPR-modified hPSC lines. Therefore, this technique allows for the examination of disease phenotypes and assists in the development of potential new therapeutics for neurodevelopmental disorders. Many protocols, however, are optimized for use with specific hPSC lines or within a single laboratory, and they often provide insufficient guidance on how to identify positive stages in the differentiation or how to troubleshoot. Here, we present an efficient and reproducible directed differentiation protocol to generate two-dimensional cultures of hPSC-derived excitatory cortical neurons without intermediary embryoid body formation. This novel protocol is supported by our data generated with five independent hPSC lines and in two independent laboratories. Importantly, as neuronal differentiations follow a long time course to reach maturity, we provide extensive guidance regarding morphological and flow cytometry checkpoints allowing for early indications of successful differentiation. We also include extensive troubleshooting tips and support protocols to assist the operator. The goal of this protocol is to assist others in the successful differentiation of excitatory cortical neurons from hPSCs. © 2023 Wiley Periodicals LLC. Basic Protocol: Directed differentiation of hPSCs into excitatory cortical neurons Support Protocol 1: Harvesting and fixing cells for flow cytometry analyses Support Protocol 2: Performing flow cytometry analyses Support Protocol 3: Thawing NPCs from a cryopreserved stock Alternate Protocol 1: Continuing Expansion of NPCs Alternate Protocol 2: Treatment of neurons with Ara-C to ablate radial glia Support Protocol 4: Experimental methods for validation of excitatory cortical neurons.
MeSH term(s)	Humans ; Cell Culture Techniques/methods ; Pluripotent Stem Cells/physiology ; Neurons/physiology ; Cell Differentiation/physiology ; Embryoid Bodies
Language	English
Publishing date	2023-11-29
Publishing country	United States
Document type	Journal Article
ISSN	2691-1299
ISSN (online)	2691-1299
DOI	10.1002/cpz1.948
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Article: Generation of a human

Wilken, Madison B / Maguire, Jean Ann / Dungan, Lea V / Gagne, Alyssa / Osorio-Quintero, Catherine / Waxman, Elisa A / Chou, Stella T / Gadue, Paul / French, Deborah L / Thom, Christopher S

bioRxiv : the preprint server for biology

2023

Abstract: The CHOPWT17_TPM1KOc28 iPSC line was generated to interrogate the functions ... ...

Abstract	The CHOPWT17_TPM1KOc28 iPSC line was generated to interrogate the functions of
Language	English
Publishing date	2023-05-04
Publishing country	United States
Document type	Preprint
DOI	10.1101/2023.05.03.539242
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Article ; Online: Generation of a human Tropomyosin 1 knockout iPSC line.

Wilken, Madison B / Maguire, Jean Ann / Dungan, Lea V / Gagne, Alyssa / Osorio-Quintero, Catherine / Waxman, Elisa A / Chou, Stella T / Gadue, Paul / French, Deborah L / Thom, Christopher S

Stem cell research

2023 Volume 71, Page(s) 103161

Abstract: The CHOPWT17_TPM1KOc28 iPSC line was generated to interrogate the functions of Tropomyosin 1 (TPM1) in primary human cell development. This line was reprogrammed from a previously published wild type control iPSC line. ...

Abstract	The CHOPWT17_TPM1KOc28 iPSC line was generated to interrogate the functions of Tropomyosin 1 (TPM1) in primary human cell development. This line was reprogrammed from a previously published wild type control iPSC line.
MeSH term(s)	Humans ; Tropomyosin/genetics ; Tropomyosin/metabolism ; Induced Pluripotent Stem Cells/metabolism ; Cell Line, Tumor
Chemical Substances	Tropomyosin
Language	English
Publishing date	2023-06-28
Publishing country	England
Document type	Journal Article ; Research Support, N.I.H., Extramural
ZDB-ID	2393143-7
ISSN	1876-7753 ; 1873-5061
ISSN (online)	1876-7753
ISSN	1873-5061
DOI	10.1016/j.scr.2023.103161
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Article ; Online: Generation of a human Tropomyosin 1 knockout iPSC line

Madison B. Wilken / Jean Ann Maguire / Lea V. Dungan / Alyssa Gagne / Catherine Osorio-Quintero / Elisa A Waxman / Stella T. Chou / Paul Gadue / Deborah L. French / Christopher S. Thom

Stem Cell Research, Vol 71, Iss , Pp 103161- (2023)

2023

Abstract	The CHOPWT17_TPM1KOc28 iPSC line was generated to interrogate the functions of Tropomyosin 1 (TPM1) in primary human cell development. This line was reprogrammed from a previously published wild type control iPSC line.
Keywords	Biology (General) ; QH301-705.5
Language	English
Publishing date	2023-09-01T00:00:00Z
Publisher	Elsevier
Document type	Article ; Online
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Article ; Online: Mapping PTBP2 binding in human brain identifies SYNGAP1 as a target for therapeutic splice switching.

Dawicki-McKenna, Jennine M / Felix, Alex J / Waxman, Elisa A / Cheng, Congsheng / Amado, Defne A / Ranum, Paul T / Bogush, Alexey / Dungan, Lea V / Maguire, Jean Ann / Gagne, Alyssa L / Heller, Elizabeth A / French, Deborah L / Davidson, Beverly L / Prosser, Benjamin L

Nature communications

2023 Volume 14, Issue 1, Page(s) 2628

Abstract: Alternative splicing of neuronal genes is controlled partly by the coordinated action of polypyrimidine tract binding proteins (PTBPs). While PTBP1 is ubiquitously expressed, PTBP2 is predominantly neuronal. Here, we define the PTBP2 footprint in the ... ...

Abstract	Alternative splicing of neuronal genes is controlled partly by the coordinated action of polypyrimidine tract binding proteins (PTBPs). While PTBP1 is ubiquitously expressed, PTBP2 is predominantly neuronal. Here, we define the PTBP2 footprint in the human transcriptome using brain tissue and human induced pluripotent stem cell-derived neurons (iPSC-neurons). We map PTBP2 binding sites, characterize PTBP2-dependent alternative splicing events, and identify novel PTBP2 targets including SYNGAP1, a synaptic gene whose loss-of-function leads to a complex neurodevelopmental disorder. We find that PTBP2 binding to SYNGAP1 mRNA promotes alternative splicing and nonsense-mediated decay, and that antisense oligonucleotides (ASOs) that disrupt PTBP binding redirect splicing and increase SYNGAP1 mRNA and protein expression. In SYNGAP1 haploinsufficient iPSC-neurons generated from two patients, we show that PTBP2-targeting ASOs partially restore SYNGAP1 expression. Our data comprehensively map PTBP2-dependent alternative splicing in human neurons and cerebral cortex, guiding development of novel therapeutic tools to benefit neurodevelopmental disorders.
MeSH term(s)	Humans ; Nerve Tissue Proteins/genetics ; Nerve Tissue Proteins/metabolism ; Induced Pluripotent Stem Cells/metabolism ; RNA Splicing ; Alternative Splicing/genetics ; Brain/metabolism ; RNA, Messenger/genetics ; RNA, Messenger/metabolism ; ras GTPase-Activating Proteins/genetics ; Heterogeneous-Nuclear Ribonucleoproteins/genetics ; Heterogeneous-Nuclear Ribonucleoproteins/metabolism ; Polypyrimidine Tract-Binding Protein/genetics ; Polypyrimidine Tract-Binding Protein/metabolism
Chemical Substances	Nerve Tissue Proteins ; RNA, Messenger ; SYNGAP1 protein, human ; ras GTPase-Activating Proteins ; PTBP1 protein, human ; Heterogeneous-Nuclear Ribonucleoproteins ; Polypyrimidine Tract-Binding Protein (139076-35-0) ; PTBP2 protein, human
Language	English
Publishing date	2023-05-06
Publishing country	England
Document type	Journal Article ; Research Support, N.I.H., Extramural
ZDB-ID	2553671-0
ISSN	2041-1723 ; 2041-1723
ISSN (online)	2041-1723
ISSN	2041-1723
DOI	10.1038/s41467-023-38273-3
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Article: Cross-site reproducibility of human cortical organoids reveals consistent cell type composition and architecture.

Glass, Madison R / Waxman, Elisa A / Yamashita, Satoshi / Lafferty, Michael / Beltran, Alvaro / Farah, Tala / Patel, Niyanta K / Matoba, Nana / Ahmed, Sara / Srivastava, Mary / Drake, Emma / Davis, Liam T / Yeturi, Meghana / Sun, Kexin / Love, Michael I / Hashimoto-Torii, Kazue / French, Deborah L / Stein, Jason L

bioRxiv : the preprint server for biology

2023

Abstract: Background: Reproducibility of human cortical organoid (hCO) phenotypes remains a concern for modeling neurodevelopmental disorders. While guided hCO protocols reproducibly generate cortical cell types in multiple cell lines at one site, variability ... ...

Abstract	Background: Reproducibility of human cortical organoid (hCO) phenotypes remains a concern for modeling neurodevelopmental disorders. While guided hCO protocols reproducibly generate cortical cell types in multiple cell lines at one site, variability across sites using a harmonized protocol has not yet been evaluated. We present an hCO cross-site reproducibility study examining multiple phenotypes. Methods: Three independent research groups generated hCOs from one induced pluripotent stem cell (iPSC) line using a harmonized miniaturized spinning bioreactor protocol. scRNA-seq, 3D fluorescent imaging, phase contrast imaging, qPCR, and flow cytometry were used to characterize the 3 month differentiations across sites. Results: In all sites, hCOs were mostly cortical progenitor and neuronal cell types in reproducible proportions with moderate to high fidelity to the Conclusions: We identified hCO phenotypes that are reproducible across sites using a harmonized differentiation protocol. Previously described limitations of hCO models were also reproduced including off-target differentiations, necrotic cores, and cellular stress. Improving our understanding of how stem cell states influence early hCO cell types may increase reliability of hCO differentiations. Cross-site reproducibility of hCO cell type proportions and organization lays the foundation for future collaborative prospective meta-analytic studies modeling neurodevelopmental disorders in hCOs.
Language	English
Publishing date	2023-07-29
Publishing country	United States
Document type	Preprint
DOI	10.1101/2023.07.28.550873
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Article ; Online: A novel iPSC model reveals selective vulnerability of neurons in multiple sulfatase deficiency.

Pham, Vi / Sertori Finoti, Livia / Cassidy, Margaret M / Maguire, Jean Ann / Gagne, Alyssa L / Waxman, Elisa A / French, Deborah L / King, Kaitlyn / Zhou, Zitao / Gelb, Michael H / Wongkittichote, Parith / Hong, Xinying / Schlotawa, Lars / Davidson, Beverly L / Ahrens-Nicklas, Rebecca C

Molecular genetics and metabolism

2023 Volume 141, Issue 2, Page(s) 108116

Abstract: Multiple sulfatase deficiency (MSD) is an ultra-rare, inherited lysosomal storage disease caused by mutations in the gene sulfatase modifying factor 1 (SUMF1). MSD is characterized by the functional deficiency of all sulfatase enzymes, leading to the ... ...

Abstract	Multiple sulfatase deficiency (MSD) is an ultra-rare, inherited lysosomal storage disease caused by mutations in the gene sulfatase modifying factor 1 (SUMF1). MSD is characterized by the functional deficiency of all sulfatase enzymes, leading to the storage of sulfated substrates including glycosaminoglycans (GAGs), sulfolipids, and steroid sulfates. Patients with MSD experience severe neurological impairment, hearing loss, organomegaly, corneal clouding, cardiac valve disease, dysostosis multiplex, contractures, and ichthyosis. Here, we generated a novel human model of MSD by reprogramming patient peripheral blood mononuclear cells to establish an MSD induced pluripotent stem cell (iPSC) line (SUMF1 p.A279V). We also generated an isogenic control iPSC line by correcting the pathogenic variant with CRISPR/Cas9 gene editing. We successfully differentiated these iPSC lines into neural progenitor cells (NPCs) and NGN2-induced neurons (NGN2-iN) to model the neuropathology of MSD. Mature neuronal cells exhibited decreased SUMF1 gene expression, increased lysosomal stress, impaired neurite outgrowth and maturation, reduced sulfatase activities, and GAG accumulation. Interestingly, MSD iPSCs and NPCs did not exhibit as severe of phenotypes, suggesting that as neurons differentiate and mature, they become more vulnerable to loss of SUMF1. In summary, we demonstrate that this human iPSC-derived neuronal model recapitulates the cellular and biochemical features of MSD. These cell models can be used as tools to further elucidate the mechanisms of MSD pathology and for the development of therapeutics.
MeSH term(s)	Humans ; Multiple Sulfatase Deficiency Disease ; Induced Pluripotent Stem Cells ; Leukocytes, Mononuclear/metabolism ; Neurons/pathology ; Sulfatases ; Oxidoreductases Acting on Sulfur Group Donors
Chemical Substances	Sulfatases (EC 3.1.6.-) ; SUMF1 protein, human (EC 3.1.6.-) ; Oxidoreductases Acting on Sulfur Group Donors (EC 1.8.-)
Language	English
Publishing date	2023-12-21
Publishing country	United States
Document type	Journal Article
ZDB-ID	1418518-0
ISSN	1096-7206 ; 1096-7192
ISSN (online)	1096-7206
ISSN	1096-7192
DOI	10.1016/j.ymgme.2023.108116
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Article ; Online: Drug screening identifies tazarotene and bexarotene as therapeutic agents in multiple sulfatase deficiency.

EMBO molecular medicine

2023 Volume 15, Issue 3, Page(s) e14837

Abstract: Multiple sulfatase deficiency (MSD, MIM #272200) results from pathogenic variants in the SUMF1 gene that impair proper function of the formylglycine-generating enzyme (FGE). FGE is essential for the posttranslational activation of cellular sulfatases. ... ...

Abstract	Multiple sulfatase deficiency (MSD, MIM #272200) results from pathogenic variants in the SUMF1 gene that impair proper function of the formylglycine-generating enzyme (FGE). FGE is essential for the posttranslational activation of cellular sulfatases. MSD patients display reduced or absent sulfatase activities and, as a result, clinical signs of single sulfatase disorders in a unique combination. Up to date therapeutic options for MSD are limited and mostly palliative. We performed a screen of FDA-approved drugs using immortalized MSD patient fibroblasts. Recovery of arylsulfatase A activity served as the primary readout. Subsequent analysis confirmed that treatment of primary MSD fibroblasts with tazarotene and bexarotene, two retinoids, led to a correction of MSD pathophysiology. Upon treatment, sulfatase activities increased in a dose- and time-dependent manner, reduced glycosaminoglycan content decreased and lysosomal position and size normalized. Treatment of MSD patient derived induced pluripotent stem cells (iPSC) differentiated into neuronal progenitor cells (NPC) resulted in a positive treatment response. Tazarotene and bexarotene act to ultimately increase the stability of FGE variants. The results lay the basis for future research on the development of a first therapeutic option for MSD patients.
MeSH term(s)	Humans ; Multiple Sulfatase Deficiency Disease/diagnosis ; Multiple Sulfatase Deficiency Disease/genetics ; Multiple Sulfatase Deficiency Disease/pathology ; Bexarotene ; Drug Evaluation, Preclinical ; Sulfatases/genetics ; Oxidoreductases Acting on Sulfur Group Donors
Chemical Substances	Bexarotene (A61RXM4375) ; tazarotene (81BDR9Y8PS) ; Sulfatases (EC 3.1.6.-) ; SUMF1 protein, human (EC 3.1.6.-) ; Oxidoreductases Acting on Sulfur Group Donors (EC 1.8.-)
Language	English
Publishing date	2023-02-15
Publishing country	England
Document type	Journal Article ; Research Support, Non-U.S. Gov't ; Research Support, N.I.H., Extramural
ZDB-ID	2467145-9
ISSN	1757-4684 ; 1757-4676
ISSN (online)	1757-4684
ISSN	1757-4676
DOI	10.15252/emmm.202114837
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Article ; Online: Induction of intracellular tau aggregation is promoted by α-synuclein seeds and provides novel insights into the hyperphosphorylation of tau.

Waxman, Elisa A / Giasson, Benoit I

The Journal of neuroscience : the official journal of the Society for Neuroscience

2011 Volume 31, Issue 21, Page(s) 7604–7618

Abstract: Intracytoplasmic proteinaceous inclusions, primarily composed of tau or α-synuclein (α-syn), are predominant pathological features of Alzheimer's disease (AD) and Parkinson's disease (PD), respectively. However, the coexistence of these pathological ... ...

Abstract	Intracytoplasmic proteinaceous inclusions, primarily composed of tau or α-synuclein (α-syn), are predominant pathological features of Alzheimer's disease (AD) and Parkinson's disease (PD), respectively. However, the coexistence of these pathological aggregates is identified in many neurodegenerative disorders, including spectrum disorders of AD and PD. Whereas α-syn can spontaneously polymerize into amyloidogenic fibrils, in vitro, tau polymerization requires an inducing agent. The current study presents a human-derived cellular model, in which recombinant, preformed α-syn fibrils cross-seed intracellular tau to promote the formation of neurofibrillary tangle-like aggregates. These aggregates were hyperphosphorylated, Triton insoluble, and thioflavin-S positive, either comingling with endogenously expressed α-syn aggregates or induced by only exogenously applied recombinant α-syn fibrils. Furthermore, filamentous, amyloidogenic tau took over the cellular soma, displacing the nucleus and isolating or displacing organelles, likely preventing cellular function. Although a significant proportion of wild-type tau formed these cellular inclusions, the P301L mutation in tau increased aggregation propensity resulting from α-syn seeds to over 50% of total tau protein. The role of phosphorylation on the development of these tau aggregates was investigated by coexpressing glycogen synthase kinase 3 β or microtubule-associated protein/microtubule affinity-regulating kinase 2. Expression of either kinase inhibited the formation of α-syn-induced tau aggregates. Analyses of phosphorylation sites suggest that multiple complex factors may be associated with this effect and that Triton-soluble versus Triton-insoluble tau may be independently targeted by kinases. The current work not only provides an exceptional cellular model of tau pathology, but also examines α-syn-induced tau inclusion formation and provides novel insights into hyperphosphorylation observed in disease.
MeSH term(s)	Cells, Cultured ; DNA, Complementary/genetics ; DNA, Complementary/metabolism ; DNA, Complementary/ultrastructure ; Embryonic Stem Cells/metabolism ; Embryonic Stem Cells/ultrastructure ; Humans ; Intracellular Fluid/metabolism ; Phosphorylation/physiology ; Recombinant Proteins/genetics ; Recombinant Proteins/metabolism ; Recombinant Proteins/ultrastructure ; alpha-Synuclein/genetics ; alpha-Synuclein/metabolism ; alpha-Synuclein/ultrastructure ; tau Proteins/genetics ; tau Proteins/metabolism ; tau Proteins/ultrastructure
Chemical Substances	DNA, Complementary ; Recombinant Proteins ; alpha-Synuclein ; tau Proteins
Language	English
Publishing date	2011-05-25
Publishing country	United States
Document type	Comparative Study ; Journal Article ; Research Support, N.I.H., Extramural ; Research Support, Non-U.S. Gov't
ZDB-ID	604637-x
ISSN	1529-2401 ; 0270-6474
ISSN (online)	1529-2401
ISSN	0270-6474
DOI	10.1523/JNEUROSCI.0297-11.2011
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Article ; Online: A novel, high-efficiency cellular model of fibrillar alpha-synuclein inclusions and the examination of mutations that inhibit amyloid formation.

Waxman, Elisa A / Giasson, Benoit I

Journal of neurochemistry

2010 Volume 113, Issue 2, Page(s) 374–388

Abstract: Intracytoplasmic alpha-synuclein (alpha-syn) amyloidogenic inclusions are a major pathological feature of Parkinson's disease, dementia with Lewy body disease and multiple systems atrophy. The mechanisms involved in the formation and inhibition of these ... ...

Abstract	Intracytoplasmic alpha-synuclein (alpha-syn) amyloidogenic inclusions are a major pathological feature of Parkinson's disease, dementia with Lewy body disease and multiple systems atrophy. The mechanisms involved in the formation and inhibition of these aggregates are areas of intense investigation. The present study characterizes a novel cellular model for the study of alpha-syn aggregation, incorporating nucleation-dependent aggregation and a new function for calcium phosphate precipitation. Cultured cells were readily induced to develop large, cytoplasmic alpha-syn filamentous aggregates that were hyperphosphorylated, often ubiquitinated and thioflavin positive. These cellular aggregates formed in the majority of transfected cells and recruited approximately half of endogenously expressed alpha-syn. Using this system, we examined single-point mutations that inhibit alpha-syn amyloid formation in vitro. Three mutations (V66P, T72P and T75P) significantly hindered alpha-syn aggregation in this cell model. The T75P mutant, which could abrogate amyloid formation of wild-type alpha-syn in vitro, did not prevent wild-type alpha-syn cellular aggregates. These studies suggest that the propensity of alpha-syn to form cellular aggregates may be more pronounced than in isolated in vitro studies. This novel high-efficiency cellular model of alpha-syn aggregation is a valuable system that may be used to further understand alpha-syn aggregation and allow for the generation of future therapeutics.
MeSH term(s)	Amyloid/metabolism ; Amyloid/ultrastructure ; Benzothiazoles ; Calcium Phosphates/pharmacology ; Cell Line, Transformed ; Humans ; Hydrophobic and Hydrophilic Interactions ; Inclusion Bodies/drug effects ; Inclusion Bodies/genetics ; Inclusion Bodies/metabolism ; Inclusion Bodies/ultrastructure ; Point Mutation/genetics ; Thiazoles/metabolism ; Transfection/methods ; alpha-Synuclein/genetics ; alpha-Synuclein/metabolism
Chemical Substances	Amyloid ; Benzothiazoles ; Calcium Phosphates ; Thiazoles ; alpha-Synuclein ; thioflavin T (2390-54-7) ; calcium phosphate, monobasic, anhydrous (701EKV9RMN)
Language	English
Publishing date	2010-02-02
Publishing country	England
Document type	Journal Article ; Research Support, N.I.H., Extramural ; Research Support, Non-U.S. Gov't
ZDB-ID	80158-6
ISSN	1471-4159 ; 0022-3042 ; 1474-1644
ISSN (online)	1471-4159
ISSN	0022-3042 ; 1474-1644
DOI	10.1111/j.1471-4159.2010.06592.x
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