uu.seUppsala University Publications
Change search
Link to record
Permanent link

Direct link
BETA
Alternative names
Publications (10 of 126) Show all publications
Laan, L., Klar, J., Sobol, M., Hoeber, J., Shahsavan, M., Kele, M., . . . Dahl, N. (2020). DNA methylation changes in Down syndrome derived neural iPSCs uncover co-dysregulation of ZNF and HOX3 families of transcription factors. Clinical Epigenetics, 12, Article ID 9.
Open this publication in new window or tab >>DNA methylation changes in Down syndrome derived neural iPSCs uncover co-dysregulation of ZNF and HOX3 families of transcription factors
Show others...
2020 (English)In: Clinical Epigenetics, E-ISSN 1868-7083, Vol. 12, article id 9Article in journal (Refereed) Published
Abstract [en]

Background: Down syndrome (DS) is characterized by neurodevelopmental abnormalities caused by partial or complete trisomy of human chromosome 21 (T21). Analysis of Down syndrome brain specimens has shown global epigenetic and transcriptional changes but their interplay during early neurogenesis remains largely unknown. We differentiated induced pluripotent stem cells (iPSCs) established from two DS patients with complete T21 and matched euploid donors into two distinct neural stages corresponding to early- and mid-gestational ages.

Results: Using the Illumina Infinium 450K array, we assessed the DNA methylation pattern of known CpG regions and promoters across the genome in trisomic neural iPSC derivatives, and we identified a total of 500 stably and differentially methylated CpGs that were annotated to CpG islands of 151 genes. The genes were enriched within the DNA binding category, uncovering 37 factors of importance for transcriptional regulation and chromatin structure. In particular, we observed regional epigenetic changes of the transcription factor genes ZNF69, ZNF700 and ZNF763 as well as the HOXA3, HOXB3 and HOXD3 genes. A similar clustering of differential methylation was found in the CpG islands of the HIST1 genes suggesting effects on chromatin remodeling.

Conclusions: The study shows that early established differential methylation in neural iPSC derivatives with T21 are associated with a set of genes relevant for DS brain development, providing a novel framework for further studies on epigenetic changes and transcriptional dysregulation during T21 neurogenesis.

Keywords
Down syndrome, induced pluripotent stem cells, DNA-methylation, neurogenesis, transcription factors, gene expression
National Category
Medical Genetics
Identifiers
urn:nbn:se:uu:diva-398619 (URN)10.1186/s13148-019-0803-1 (DOI)000512048300002 ()31915063 (PubMedID)
Funder
Swedish Research Council, 2015-02424The Swedish Brain Foundation, FO2018-0100The Swedish Brain Foundation, FO2019-0210Knut and Alice Wallenberg Foundation, Bioinformatic supportAstraZeneca
Available from: 2019-12-08 Created: 2019-12-08 Last updated: 2020-03-20Bibliographically approved
Kvarnung, M., Shahsavani, M., Taylan, F., Moslem, M., Breeuwsma, N., Laan, L., . . . Falk, A. (2019). Ataxia in Patients With Bi-Allelic NFASC Mutations and Absence of Full-Length NF186. Frontiers in Genetics, 10, Article ID 896.
Open this publication in new window or tab >>Ataxia in Patients With Bi-Allelic NFASC Mutations and Absence of Full-Length NF186
Show others...
2019 (English)In: Frontiers in Genetics, ISSN 1664-8021, E-ISSN 1664-8021, Vol. 10, article id 896Article in journal (Refereed) Published
Abstract [en]

The etiology of hereditary ataxia syndromes is heterogeneous, and the mechanisms underlying these disorders are often unknown. Here, we utilized exome sequencing in two siblings with progressive ataxia and muscular weakness and identified a novel homozygous splice mutation (c.3020-1G > A) in neurofascin (NFASC). In RNA extracted from fibroblasts, we showed that the mutation resulted in inframe skipping of exon 26, with a deprived expression of the full-length transcript that corresponds to NFASC isoform NF186. To further investigate the disease mechanisms, we reprogrammed fibroblasts from one affected sibling to induced pluripotent stem cells, directed them to neuroepithelial stem cells and finally differentiated to neurons. In early neurogenesis, differentiating cells with selective depletion of the NF186 isoform showed significantly reduced neurite outgrowth as well as fewer emerging neurites. Furthermore, whole-cell patch-clamp recordings of patient-derived neuronal cells revealed a lower threshold for openings, indicating altered Na+ channel kinetics, suggesting a lower threshold for openings as compared to neuronal cells without the NFASC mutation. Taken together, our results suggest that loss of the full-length NFASC isoform NF186 causes perturbed neurogenesis and impaired neuronal biophysical properties resulting in a novel early-onset autosomal recessive ataxia syndrome.

Keywords
neurofascin, neuronal isoform NF186, ataxia, patient-specific induced pluripotent stem cells, neuroepithelial stem cells, neurites
National Category
Neurosciences
Identifiers
urn:nbn:se:uu:diva-395798 (URN)10.3389/fgene.2019.00896 (DOI)000487628800001 ()
Funder
Swedish Research Council, 2015-02424Swedish Research Council, 2017-03407Swedish Research Council, 2017-02936Swedish Foundation for Strategic Research , IB13-0074The Swedish Brain FoundationSwedish Society for Medical Research (SSMF)
Available from: 2019-10-25 Created: 2019-10-25 Last updated: 2019-12-09Bibliographically approved
Schuster, J., Fatima, A., Schwarz, F., Klar, J., Laan, L. & Dahl, N. (2019). Generation of human induced pluripotent stem cell (iPSC) lines from three patients with von Hippel-Lindau syndrome carrying distinct VHL gene mutations. Stem Cell Research, 38, Article ID UNSP 101474.
Open this publication in new window or tab >>Generation of human induced pluripotent stem cell (iPSC) lines from three patients with von Hippel-Lindau syndrome carrying distinct VHL gene mutations
Show others...
2019 (English)In: Stem Cell Research, ISSN 1873-5061, E-ISSN 1876-7753, Vol. 38, article id UNSP 101474Article in journal, Editorial material (Other academic) Published
Abstract [en]

Von Hippel-Lindau (VHL) syndrome is a familial cancer syndrome caused by mutations in the tumor suppressor gene VHL. We generated human iPSC lines from primary dermal fibroblasts of three VHL syndrome patients carrying distinct VHL germ line mutations (c.194C > G, c.194C > T and nt440delTCT, respectively). Characterization of the iPSC lines confirmed expression of pluripotency markers, trilineage differentiation potential and absence of exogenous vector expression. The three hiPSC lines were genetically stable and retained the VHL mutation of each donor. These iPSC lines, the first derived from VHL syndrome patients, offer a useful resource to study disease pathophysiology and for anti-cancer drug development.

National Category
Cancer and Oncology
Identifiers
urn:nbn:se:uu:diva-392899 (URN)10.1016/j.scr.2019.101474 (DOI)000477866100021 ()31176917 (PubMedID)
Funder
Swedish Research Council, 2015-02424The Swedish Brain Foundation
Available from: 2019-09-10 Created: 2019-09-10 Last updated: 2019-09-10Bibliographically approved
Schuster, J., Fatima, A., Sobol, M., Noraddin, F. H., Laan, L. & Dahl, N. (2019). Generation of three human induced pluripotent stem cell (iPSC) lines from three patients with Dravet syndrome carrying distinct SCN1A gene mutations. Stem Cell Research, 39, Article ID 101523.
Open this publication in new window or tab >>Generation of three human induced pluripotent stem cell (iPSC) lines from three patients with Dravet syndrome carrying distinct SCN1A gene mutations
Show others...
2019 (English)In: Stem Cell Research, ISSN 1873-5061, E-ISSN 1876-7753, Vol. 39, article id 101523Article in journal (Refereed) Published
Abstract [en]

Dravet syndrome (DS) is a childhood epilepsy syndrome caused by heterozygous mutations in the SCN1A gene encoding voltage-gated sodium channel Nav1.1. We generated iPSCs from fibroblasts of three DS patients carrying distinct SCN1A mutations (c.5502-5509dupGCTTGAAC, c.2965G>C and c.651C>G). The iPSC lines were genetically stable and each line retained the SCN1A gene mutation of the donor fibroblasts. Characterization of the iPSC lines confirmed expression of pluripotency markers, absence of exogenous vector expression and trilineage differentiation potential. These iPSC lines offer a useful resource to investigate the molecular mechanisms underlying Nav1.1 haploinsufficiency and for drug development to improve treatment of DS patients.

National Category
Cell and Molecular Biology
Identifiers
urn:nbn:se:uu:diva-398822 (URN)10.1016/j.scr.2019.101523 (DOI)000487828400037 ()31400703 (PubMedID)
Funder
Swedish Research Council, 2015-02424AstraZenecaThe Swedish Brain Foundation, FO2018-0100
Available from: 2019-12-13 Created: 2019-12-13 Last updated: 2019-12-13Bibliographically approved
Schuster, J., Sobol, M., Fatima, A., Khalfallah, A., Laan, L., Anderlid, B.-M., . . . Dahl, N. (2019). Mowat-Wilson syndrome: Generation of two human iPS cell lines (UUIGPi004A and UUIGPi005A) from siblings with a truncating ZEB2 gene variant. Stem Cell Research, 39, Article ID 101518.
Open this publication in new window or tab >>Mowat-Wilson syndrome: Generation of two human iPS cell lines (UUIGPi004A and UUIGPi005A) from siblings with a truncating ZEB2 gene variant
Show others...
2019 (English)In: Stem Cell Research, ISSN 1873-5061, E-ISSN 1876-7753, Vol. 39, article id 101518Article in journal (Refereed) Published
Abstract [en]

Mowat-Wilson syndrome (MWS) is a complex developmental syndrome caused by heterozygous mutations in the Zinc finger E-box-binding homeobox 2 gene (ZEB2). We generated the first human iPSC lines from primary fibroblasts of two siblings with MWS carrying a heterozygous ZEB2 stop mutation (c.1027C > T; p.Arg343*) using the Sendai virus reprogramming system. Both iPSC lines were free from reprogramming vector genes, expressed pluripotency markers and showed potential to differentiate into the three germ layers. Genetic analysis confirmed normal karyotypes and a preserved stop mutation. These iPSC lines will provide a useful resource to study altered neural lineage fate and neuropathophysiology in MWS.

National Category
Cell and Molecular Biology
Identifiers
urn:nbn:se:uu:diva-398823 (URN)10.1016/j.scr.2019.101518 (DOI)000487828400033 ()31376723 (PubMedID)
Funder
Swedish Research Council, 2015-02424The Swedish Brain Foundation, FO2018-0100
Available from: 2019-12-13 Created: 2019-12-13 Last updated: 2019-12-13Bibliographically approved
Zakaria, M., Fatima, A., Klar, J., Wikström, J., Abdullah, U., Ali, Z., . . . Dahl, N. (2019). Primary microcephaly, primordial dwarfism, and brachydactyly in adult cases with biallelic skipping of RTTN exon 42. Human Mutation, 40(7), 899-903
Open this publication in new window or tab >>Primary microcephaly, primordial dwarfism, and brachydactyly in adult cases with biallelic skipping of RTTN exon 42
Show others...
2019 (English)In: Human Mutation, ISSN 1059-7794, E-ISSN 1098-1004, Vol. 40, no 7, p. 899-903Article in journal (Refereed) Published
Abstract [en]

Biallelic and pathogenic variants in the RTTN gene, encoding the centrosomal protein Rotatin, are associated with variable degrees of neurodevelopmental abnormalities, microcephaly, and extracranial malformations. To date, no reported case has reached their third decade. Herein, we report on a consanguineous family with three adult members, age 43, 57, and 60 years respectively, with primary microcephaly, developmental delay, primordial dwarfism, and brachydactyly segregating a homozygous splice site variant NM_173630.3:c.5648–5T>A in RTTN. The variant RTTN allele results in a nonhypomorphic skipping of exon 42 and a frameshift [(NP_775901.3:p.Ala1883Glyfs*6)]. Brain MRI of one affected individual showed markedly reduced volume of cerebral lobes and enlarged sulci but without signs of neural migration defects. Our assessment of three adult cases with a biallelic RTTN variant shows that a predicted shortened Rotatin, lacking the C‐terminal end, are associated with stationary clinical features into the seventh decade. Furthermore, our report adds brachydactyly to the phenotypic spectrum in this pleiotropic entity.

Keywords
RTTN gene variant, Microcephaly, Rotatin, brachydatyly, exon skipping
National Category
Medical Genetics
Research subject
Clinical Genetics
Identifiers
urn:nbn:se:uu:diva-382043 (URN)10.1002/humu.23755 (DOI)000477673000007 ()30927481 (PubMedID)
Funder
The Swedish Brain Foundation, FO2018-0100Swedish Research Council, 2015-02424
Note

De 3 första författarna delar förstaförfattarskapet

Available from: 2019-04-17 Created: 2019-04-17 Last updated: 2019-09-26Bibliographically approved
Lam, M., Moslem, M., Bryois, J., Pronk, R. J., Uhlin, E., Ellström, I. D., . . . Falk, A. (2019). Single cell analysis of autism patient with bi-allelic NRXN1-alpha deletion reveals skewed fate choice in neural progenitors and impaired neuronal functionality. Experimental Cell Research, 383(1), Article ID UNSP 111469.
Open this publication in new window or tab >>Single cell analysis of autism patient with bi-allelic NRXN1-alpha deletion reveals skewed fate choice in neural progenitors and impaired neuronal functionality
Show others...
2019 (English)In: Experimental Cell Research, ISSN 0014-4827, E-ISSN 1090-2422, Vol. 383, no 1, article id UNSP 111469Article in journal (Refereed) Published
Abstract [en]

We generated human iPS derived neural stem cells and differentiated cells from healthy control individuals and an individual with autism spectrum disorder carrying bi-allelic NRXN1-alpha deletion. We investigated the expression of NRXN1-alpha during neural induction and neural differentiation and observed a pivotal role for NRXN1-alpha during early neural induction and neuronal differentiation. Single cell RNA-seq pinpointed neural stem cells carrying NRXN1-alpha deletion shifting towards radial glia-like cell identity and revealed higher proportion of differentiated astroglia. Furthermore, neuronal cells carrying NRXN1-alpha deletion were identified as immature by single cell RNA-seq analysis, displayed significant depression in calcium signaling activity and presented impaired maturation action potential profile in neurons investigated with electrophysiology. Our observations propose NRXN1-alpha plays an important role for the efficient establishment of neural stem cells, in neuronal differentiation and in maturation of functional excitatory neuronal cells.

Keywords
Autism spectrum disorder, Neurexin, Neurexin-1 alpha, Induced pluripotent stem cell, Neural stem cell, Single cell RNA sequencing, Neural development, Disease modeling
National Category
Neurosciences
Identifiers
urn:nbn:se:uu:diva-395420 (URN)10.1016/j.yexcr.2019.06.014 (DOI)000486736600011 ()31302032 (PubMedID)
Funder
Swedish Foundation for Strategic Research , IB13-0074Swedish Research Council, 2015-02424Swedish Research Council, D0886501Swedish Research Council, 2017-03407
Available from: 2019-10-22 Created: 2019-10-22 Last updated: 2019-10-22Bibliographically approved
Sobol, M., Klar, J., Laan, L., Shahsavani, M., Schuster, J., Annerén, G., . . . Dahl, N. (2019). Transcriptome and Proteome Profiling of Neural Induced Pluripotent Stem Cells from Individuals with Down Syndrome Disclose Dynamic Dysregulations of Key Pathways and Cellular Functions. Molecular Neurobiology, 56(10), 7113-7127
Open this publication in new window or tab >>Transcriptome and Proteome Profiling of Neural Induced Pluripotent Stem Cells from Individuals with Down Syndrome Disclose Dynamic Dysregulations of Key Pathways and Cellular Functions
Show others...
2019 (English)In: Molecular Neurobiology, ISSN 0893-7648, E-ISSN 1559-1182, Vol. 56, no 10, p. 7113-7127Article in journal (Refereed) Published
Abstract [en]

Down syndrome (DS) or trisomy 21 (T21) is a leading genetic cause of intellectual disability. To gain insights into dynamics of molecular perturbations during neurogenesis in DS, we established a model using induced pluripotent stem cells (iPSC) with transcriptome profiles comparable to that of normal fetal brain development. When applied on iPSCs with T21, transcriptome and proteome signatures at two stages of differentiation revealed strong temporal dynamics of dysregulated genes, proteins and pathways belonging to 11 major functional clusters. DNA replication, synaptic maturation and neuroactive clusters were disturbed at the early differentiation time point accompanied by a skewed transition from the neural progenitor cell stage and reduced cellular growth. With differentiation, growth factor and extracellular matrix, oxidative phosphorylation and glycolysis emerged as major perturbed clusters. Furthermore, we identified a marked dysregulation of a set of genes encoded by chromosome 21 including an early upregulation of the hub gene APP, supporting its role for disturbed neurogenesis, and the transcription factors OLIG1, OLIG2 and RUNX1, consistent with deficient myelination and neuronal differentiation. Taken together, our findings highlight novel sequential and differentiation-dependent dynamics of disturbed functions, pathways and elements in T21 neurogenesis, providing further insights into developmental abnormalities of the DS brain.

Keywords
Down syndrome, Induced pluripotent stem cells (iPSC), Neural differentiation, RNA sequencing, Proteome profiling
National Category
Neurosciences
Identifiers
urn:nbn:se:uu:diva-395428 (URN)10.1007/s12035-019-1585-3 (DOI)000486010800032 ()30989628 (PubMedID)
Funder
Swedish Research Council, 2015-02424Swedish Research Council, 2015-4870Knut and Alice Wallenberg FoundationAstraZenecaScience for Life Laboratory - a national resource center for high-throughput molecular bioscienceThe Swedish Brain Foundation, FO2018-0100
Available from: 2019-10-23 Created: 2019-10-23 Last updated: 2019-12-09Bibliographically approved
Schuster, J., Laan, L., Klar, J., Jin, Z., Huss, M., Korol, S., . . . Dahl, N. (2019). Transcriptomes of Dravet syndrome iPSC derived GABAergic cells reveal dysregulated pathways for chromatin remodeling and neurodevelopment. Neurobiology of Disease, 132, Article ID 104583.
Open this publication in new window or tab >>Transcriptomes of Dravet syndrome iPSC derived GABAergic cells reveal dysregulated pathways for chromatin remodeling and neurodevelopment
Show others...
2019 (English)In: Neurobiology of Disease, ISSN 0969-9961, E-ISSN 1095-953X, Vol. 132, article id 104583Article in journal (Refereed) Published
Abstract [en]

Dravet syndrome (DS) is an early onset refractory epilepsy typically caused by de novo heterozygous variants in SCN1A encoding the a-subunit of the neuronal sodium channel Na(v)1.1. The syndrome is characterized by age related progression of seizures, cognitive decline and movement disorders. We hypothesized that the distinct neurodevelopmental features in DS are caused by the disruption of molecular pathways in Na(v)1.1 haploinsufficient cells resulting in perturbed neural differentiation and maturation. Here, we established DS-patient and control induced pluripotent stem cell derived neural progenitor cells (iPSC NPC) and GABAergic interneuronal (iPSC GABA) cells. The DS-patient iPSC GABA cells showed a shift in sodium current activation and a perturbed response to induced oxidative stress. Transcriptome analysis revealed specific dysregulations of genes for chromatin structure, mitotic progression, neural plasticity and excitability in DS-patient iPSC NPCs and DS-patient iPSC GABA cells versus controls. The transcription factors FOXM1 and E2F1, positive regulators of the disrupted pathways for histone modification and cell cycle regulation, were markedly up-regulated in DS-iPSC GABA lines. Our study highlights transcriptional changes and disrupted pathways of chromatin remodeling in Na(v)1.1 haploinsufficient GABAergic cells, providing a molecular framework that overlaps with that of neurodevelopmental disorders and other epilepsies.

Place, publisher, year, edition, pages
ACADEMIC PRESS INC ELSEVIER SCIENCE, 2019
Keywords
Dravet syndrome, SCN1A, Na(v)1.1, iPSC, Neural differentiation, Neurodevelopment, Chromatin architecture
National Category
Neurosciences
Identifiers
urn:nbn:se:uu:diva-398427 (URN)10.1016/j.nbd.2019.104583 (DOI)000497252500015 ()31445158 (PubMedID)
Funder
Swedish Research Council, 2015-02424Swedish Research Council, 2015-02417Knut and Alice Wallenberg FoundationAstraZenecaThe Swedish Brain Foundation, FO2018-0100The Swedish Brain Foundation, FO2019-0210Science for Life Laboratory - a national resource center for high-throughput molecular bioscience
Note

De tre första författarna delar förstaförfattarskapet.

Available from: 2019-12-06 Created: 2019-12-06 Last updated: 2019-12-09Bibliographically approved
Zulfiqar, S., Tariq, M., Ali, Z., Fatima, A., Klar, J., Abdullah, U., . . . Baig, S. M. (2019). Whole exome sequencing identifies novel variant underlying hereditary spastic paraplegia in consanguineous Pakistani families. Journal of clinical neuroscience, 67, 19-23
Open this publication in new window or tab >>Whole exome sequencing identifies novel variant underlying hereditary spastic paraplegia in consanguineous Pakistani families
Show others...
2019 (English)In: Journal of clinical neuroscience, ISSN 0967-5868, E-ISSN 1532-2653, Vol. 67, p. 19-23Article in journal (Refereed) Published
Abstract [en]

Hereditary Spastic paraplegias (HSPs) are heterogeneous group of degenerative disorders characterized by progressive weakness and spasticity of the lower limbs, combined with additional neurological features. This study aimed to identify causative gene variants in two nonrelated consanguineous Pakistani families segregating HSP. Whole exome sequencing (WES) was performed on a total of five individuals from two families including four affected and one phenotypically normal individual. The variants were validated by Sanger sequencing and segregation analysis. In family A, a novel homozygous variant c.604G > A (p.Glu202Lys) was identified in the CYP2U1 gene with clinical symptoms of SPG56 in 3 siblings. Whereas, a previously reported variant c.5769delT (p.Ser1923Argfs*28) in the SPG11 gene was identified in family B manifesting clinical features of SPG11 in 3 affected individuals. Our combined findings add to the clinical and genetic variability associated with CYP2U1 and SPG11 variants highlighting the complexity of HSPs. These findings further emphasize the usefulness of WES as a powerful diagnostic tool.

Keywords
SPG11, SPG56, Ataxia, Spastic paraplegia, Peripheral neuropathy
National Category
Neurosciences Medical Genetics
Identifiers
urn:nbn:se:uu:diva-394260 (URN)10.1016/j.jocn.2019.06.039 (DOI)000483413600005 ()31281085 (PubMedID)
Funder
Swedish Research Council
Available from: 2019-10-11 Created: 2019-10-11 Last updated: 2019-10-11Bibliographically approved
Organisations
Identifiers
ORCID iD: ORCID iD iconorcid.org/0000-0002-8122-0800

Search in DiVA

Show all publications