Identifying SETBP1 haploinsufficiency molecular pathways to improve patient diagnosis using induced pluripotent stem cells and neural disease modelling.
Induced Pluripotent Stem Cells
/ metabolism
Humans
Haploinsufficiency
Cell Differentiation
Carrier Proteins
/ genetics
Nuclear Proteins
/ genetics
Mutation
GATA2 Transcription Factor
/ genetics
Neurons
/ metabolism
Neural Stem Cells
/ metabolism
Wnt Signaling Pathway
/ genetics
Intellectual Disability
/ genetics
Phenotype
CRISPR
Neural cell modelling
Neurodevelopmental disorders
SETBP1 haploinsufficiency disorder
Variants of unknown significance
iPSC
Journal
Molecular autism
ISSN: 2040-2392
Titre abrégé: Mol Autism
Pays: England
ID NLM: 101534222
Informations de publication
Date de publication:
30 Sep 2024
30 Sep 2024
Historique:
received:
03
04
2024
accepted:
23
09
2024
medline:
1
10
2024
pubmed:
1
10
2024
entrez:
1
10
2024
Statut:
epublish
Résumé
SETBP1 Haploinsufficiency Disorder (SETBP1-HD) is characterised by mild to moderate intellectual disability, speech and language impairment, mild motor developmental delay, behavioural issues, hypotonia, mild facial dysmorphisms, and vision impairment. Despite a clear link between SETBP1 mutations and neurodevelopmental disorders the precise role of SETBP1 in neural development remains elusive. We investigate the functional effects of three SETBP1 genetic variants including two pathogenic mutations p.Glu545Ter and SETBP1 p.Tyr1066Ter, resulting in removal of SKI and/or SET domains, and a point mutation p.Thr1387Met in the SET domain. Genetic variants were introduced into induced pluripotent stem cells (iPSCs) and subsequently differentiated into neurons to model the disease. We measured changes in cellular differentiation, SETBP1 protein localisation, and gene expression changes. The data indicated a change in the WNT pathway, RNA polymerase II pathway and identified GATA2 as a central transcription factor in disease perturbation. In addition, the genetic variants altered the expression of gene sets related to neural forebrain development matching characteristics typical of the SETBP1-HD phenotype. The study investigates changes in cellular function in differentiation of iPSC to neural progenitor cells as a human model of SETBP1 HD disorder. Future studies may provide additional information relevant to disease on further neural cell specification, to derive mature neurons, neural forebrain cells, or brain organoids. We developed a human SETBP1-HD model and identified perturbations to the WNT and POL2RA pathway, genes regulated by GATA2. Strikingly neural cells for both the SETBP1 truncation mutations and the single nucleotide variant displayed a SETBP1-HD-like phenotype.
Sections du résumé
BACKGROUND
BACKGROUND
SETBP1 Haploinsufficiency Disorder (SETBP1-HD) is characterised by mild to moderate intellectual disability, speech and language impairment, mild motor developmental delay, behavioural issues, hypotonia, mild facial dysmorphisms, and vision impairment. Despite a clear link between SETBP1 mutations and neurodevelopmental disorders the precise role of SETBP1 in neural development remains elusive. We investigate the functional effects of three SETBP1 genetic variants including two pathogenic mutations p.Glu545Ter and SETBP1 p.Tyr1066Ter, resulting in removal of SKI and/or SET domains, and a point mutation p.Thr1387Met in the SET domain.
METHODS
METHODS
Genetic variants were introduced into induced pluripotent stem cells (iPSCs) and subsequently differentiated into neurons to model the disease. We measured changes in cellular differentiation, SETBP1 protein localisation, and gene expression changes.
RESULTS
RESULTS
The data indicated a change in the WNT pathway, RNA polymerase II pathway and identified GATA2 as a central transcription factor in disease perturbation. In addition, the genetic variants altered the expression of gene sets related to neural forebrain development matching characteristics typical of the SETBP1-HD phenotype.
LIMITATIONS
CONCLUSIONS
The study investigates changes in cellular function in differentiation of iPSC to neural progenitor cells as a human model of SETBP1 HD disorder. Future studies may provide additional information relevant to disease on further neural cell specification, to derive mature neurons, neural forebrain cells, or brain organoids.
CONCLUSIONS
CONCLUSIONS
We developed a human SETBP1-HD model and identified perturbations to the WNT and POL2RA pathway, genes regulated by GATA2. Strikingly neural cells for both the SETBP1 truncation mutations and the single nucleotide variant displayed a SETBP1-HD-like phenotype.
Identifiants
pubmed: 39350244
doi: 10.1186/s13229-024-00625-1
pii: 10.1186/s13229-024-00625-1
doi:
Substances chimiques
SETBP1 protein, human
0
Carrier Proteins
0
Nuclear Proteins
0
GATA2 Transcription Factor
0
Types de publication
Journal Article
Langues
eng
Sous-ensembles de citation
IM
Pagination
42Subventions
Organisme : Western Australia Department of Health, Research Translation Project
ID : FEAR
Organisme : Trialect Orhpan Disease Center, Million Dollar Bike Ride, SETBP1
ID : SETBP1_HD, FEAR
Organisme : Stan Perron Charitable Foundation
ID : Lassmann
Organisme : Feilman Foundation
ID : Lassmann
Informations de copyright
© 2024. Crown.
Références
Jansen NA, Braden RO, Srivastava S, Otness EF, Lesca G, Rossi M, et al. Clinical delineation of SETBP1 haploinsufficiency disorder. Eur J Hum Genet. 2021;29(8):1198–205.
doi: 10.1038/s41431-021-00888-9
pubmed: 33867525
pmcid: 8385049
Morgan A, Braden R, Wong MM, Colin E, Amor D, Liégeois F, et al. Speech and language deficits are central to SETBP1 haploinsufficiency disorder. Eur J Hum Genet. 2021;29(8):1216–25.
doi: 10.1038/s41431-021-00894-x
pubmed: 33907317
pmcid: 8384874
Filges I, Shimojima K, Okamoto N, Röthlisberger B, Weber P, Huber AR, et al. Reduced expression by SETBP1 haploinsufficiency causes developmental and expressive language delay indicating a phenotype distinct from Schinzel-Giedion syndrome. J Med Genet. 2011;48(2):117–22.
doi: 10.1136/jmg.2010.084582
pubmed: 21037274
Antonyan L, Ernst C. Putative roles of SETBP1 dosage on the SET oncogene to affect brain development. Front Neurosci. 2022;16:813430.
doi: 10.3389/fnins.2022.813430
pubmed: 35685777
pmcid: 9173722
Hamdan FF, Srour M, Capo-Chichi J-M, Daoud H, Nassif C, Patry L, et al. De novo mutations in moderate or severe intellectual disability. PLoS Genet. 2014;10(10):e1004772.
doi: 10.1371/journal.pgen.1004772
pubmed: 25356899
pmcid: 4214635
Richardson R, Splitt M, Newbury-Ecob R, Hulbert A, Kennedy J, Weber A, et al. SET de novo frameshift variants associated with developmental delay and intellectual disabilities. Eur J Hum Genet. 2018;26(9):1306–11.
doi: 10.1038/s41431-018-0199-y
pubmed: 29907757
pmcid: 6117329
Fear VS, Forbes CA, Shaw NC, Farley KO, Mantegna JL, Htun JP, et al. Gene editing and cardiac disease modelling for the interpretation of genetic variants of uncertain significance in congenital heart disease. Stem Cell Res Ther. 2023;14(1):345.
doi: 10.1186/s13287-023-03592-1
pubmed: 38049901
pmcid: 10696868
Farley KO, Forbes CA, Shaw NC, Kuzminski E, Ward M, Baynam G, et al. CRISPR-Cas9-generated PTCHD1 2489T> G stem cells recapitulate patient phenotype when undergoing neural induction. Hum Genet Genomics Adv. 2024;5(1):100257.
doi: 10.1016/j.xhgg.2023.100257
Fear VS, Forbes CA, Anderson D, Rauschert S, Syn G, Shaw N, et al. Functional validation of variants of unknown significance using CRISPR gene editing and transcriptomics: a Kleefstra syndrome case study. Gene. 2022;821:146287.
doi: 10.1016/j.gene.2022.146287
pubmed: 35176430
Fear VS, Forbes CA, Anderson D, Rauschert S, Syn G, Shaw N, et al. CRISPR single base editing, neuronal disease modelling and functional genomics for genetic variant analysis: pipeline validation using Kleefstra syndrome EHMT1 haploinsufficiency. Stem Cell Res Ther. 2022;13(1):1–15.
doi: 10.1186/s13287-022-02740-3
Clement K, Rees H, Canver MC, Gehrke JM, Farouni R, Hsu JY, et al. CRISPResso2 provides accurate and rapid genome editing sequence analysis. Nat Biotechnol. 2019;37(3):224–6.
doi: 10.1038/s41587-019-0032-3
pubmed: 30809026
pmcid: 6533916
Wu T, Hu E, Xu S, Chen M, Guo P, Dai Z, et al. clusterProfiler 4.0: A universal enrichment tool for interpreting omics data. The innovation. 2021;2(3).
Yu G, Wang L-G, Yan G-R, He Q-Y. DOSE: an R/Bioconductor package for disease ontology semantic and enrichment analysis. Bioinformatics. 2014;31(4):608–9.
doi: 10.1093/bioinformatics/btu684
pubmed: 25677125
Lachmann A, Torre D, Keenan AB, Jagodnik KM, Lee HJ, Wang L, et al. Massive mining of publicly available RNA-seq data from human and mouse. Nat Commun. 2018;9(1):1366.
doi: 10.1038/s41467-018-03751-6
pubmed: 29636450
pmcid: 5893633
Fischer B, Smith M, Pau G, Morgan M, van Twisk D. rhdf5: R Interface to HDF5. R package version. 2019;2(0).
DePristo MA, Banks E, Poplin R, Garimella KV, Maguire JR, Hartl C, et al. A framework for variation discovery and genotyping using next-generation DNA sequencing data. Nat Genet. 2011;43(5):491–8.
doi: 10.1038/ng.806
pubmed: 21478889
pmcid: 3083463
Shu J, Zhang K, Zhang M, Yao A, Shao S, Du F, et al. GATA family members as inducers for cellular reprogramming to pluripotency. Cell Res. 2015;25(2):169–80.
doi: 10.1038/cr.2015.6
pubmed: 25591928
pmcid: 4650575
Lentjes MH, Niessen HE, Akiyama Y, De Bruine AP, Melotte V, Van Engeland M. The emerging role of GATA transcription factors in development and disease. Expert Rev Mol Med. 2016;18:e3.
doi: 10.1017/erm.2016.2
pubmed: 26953528
pmcid: 4836206
Manville RW, Abbott GW. Teamwork: Ion channels and transporters join forces in the brain. Neuropharmacology. 2019;161:107601.
doi: 10.1016/j.neuropharm.2019.04.007
pubmed: 30959022
pmcid: 7737636
Munji RN, Choe Y, Li G, Siegenthaler JA, Pleasure SJ. Wnt signaling regulates neuronal differentiation of cortical intermediate progenitors. J Neurosci. 2011;31(5):1676–87.
doi: 10.1523/JNEUROSCI.5404-10.2011
pubmed: 21289176
pmcid: 3040956
Elizalde C, Campa VM, Caro M, Schlangen K, Maria Aransay A, dM Vivanco M, et al. Distinct roles for Wnt-4 and Wnt-11 during retinoic acid-induced neuronal differentiation. Stem Cells. 2011;29(1):141–53.
doi: 10.1002/stem.562
pubmed: 21280163
Ciani L, Boyle KA, Dickins E, Sahores M, Anane D, Lopes DM, et al. Wnt7a signaling promotes dendritic spine growth and synaptic strength through Ca
doi: 10.1073/pnas.1018132108
pubmed: 21670302
pmcid: 3127879
Piazza R, Magistroni V, Redaelli S, Mauri M, Massimino L, Sessa A, et al. SETBP1 induces transcription of a network of development genes by acting as an epigenetic hub. Nat Commun. 2018;9(1):2192.
doi: 10.1038/s41467-018-04462-8
pubmed: 29875417
pmcid: 5989213
Cardo LF, de la Fuente DC, Li M. Impaired neurogenesis and neural progenitor fate choice in a human stem cell model of SETBP1 disorder. Mol Autism. 2023;14(1):8.
doi: 10.1186/s13229-023-00540-x
pubmed: 36805818
pmcid: 9940404
Haijes HA, Koster MJ, Rehmann H, Li D, Hakonarson H, Cappuccio G, et al. De novo heterozygous POLR2A variants cause a neurodevelopmental syndrome with profound infantile-onset hypotonia. Am J Hum Genet. 2019;105(2):283–301.
doi: 10.1016/j.ajhg.2019.06.016
pubmed: 31353023
pmcid: 6699192
Tang C, Wang J, Yao M, Ji X, Shi W, Xu C, et al. Hippo signaling activates hedgehog signaling by Taz-driven Gli3 processing. Cell Regen. 2023;12(1):3.
doi: 10.1186/s13619-022-00151-6
pubmed: 36720733
pmcid: 9889595
Nefzger CM, Haynes JM, Pouton CW. Directed expression of Gata2, Mash1, and Foxa2 synergize to induce the serotonergic neuron phenotype during in vitro differentiation of embryonic stem cells. Stem Cells. 2011;29(6):928–39.
doi: 10.1002/stem.640
pubmed: 21472823
Largeaud L, Collin M, Monselet N, Vergez F, Fregona V, Larcher L, et al. Somatic genetic alterations predict hematological progression in GATA2 deficiency. Haematologica. 2023;108(6):1515.
doi: 10.3324/haematol.2022.282250
pubmed: 36727400
pmcid: 10230419
Leonardi E, Bettella E, Pelizza MF, Aspromonte MC, Polli R, Boniver C, et al. Identification of Setbp1 mutations by gene panel sequencing in individuals with intellectual disability or with “developmental and epileptic encephalopathy.” Front Neurol. 2020;11:593446.
doi: 10.3389/fneur.2020.593446
pubmed: 33391157
pmcid: 7772201