Acquisition of chromosome 1q duplication in parental and genome‐edited human‐induced pluripotent stem cell‐derived neural stem cells results in their higher proliferation rate in vitro and in vivo

Mehrjardi, Narges Zare; Molcanyi, Marek; Hatay, Firuze Fulya; Timmer, Marco; Shahbazi, Ebrahim; Ackermann, Justus P.; Herms, Stefan; Heilmann‐Heimbach, Stefanie; Wunderlich, Thomas; Prochnow, Nora; Haghikia, Aiden; Lampert, Angelika; Hescheler, Jürgen; Neugebauer, Edmund; Baharvand, Hossein; Šarić, Tomo

doi:10.1111/cpr.12892

Cited by 6 publications

(5 citation statements)

References 70 publications

(154 reference statements)

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“…Although excitatory neurons and inhibitory neurons are traditionally thought to arise from distinct pools of precursor cells originating from different regions of the developing brain [ 15 ], the presence of chr1q gain in both excitatory and inhibitory neurons (as well as astrocytes) in our patient is in line with the recent finding that a subset of cortical progenitor cells can potentially give rise to both excitatory and inhibitory neurons during human brain development [ 16 ]. The hypothesis that chr1q gain occurred in a cortical progenitor cell during neurodevelopment would also be consistent with in vitro data showing that chr1q gain confers a proliferative advantage in neural stem cells [ 17 ]. Lastly, the existence of a subpopulation markedly enriched in chr1q-gained cells in excitatory neurons (Exc.s6) but not inhibitory neurons suggests that migration defects may be more pronounced in excitatory neurons compared to inhibitory neurons.…”

Section: Discussionsupporting

confidence: 91%

Cell type specificity of mosaic chromosome 1q gain resolved by snRNA-seq in a case of epilepsy with hyaline protoplasmic astrocytopathy

Leng,

Cadwell,

Devine

et al. 2023

Preprint

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Introduction: Mosaic gain of chromosome 1q (chr1q) is a recently described driver of malformation of cortical development (MCD) and epilepsy. Hyaline protoplasmic astrocytopathy (HPA) is a rare neuropathological finding seen in cases of epilepsy with MCD. The cell-type specificity of mosaic chr1q gain in the brain and the molecular signatures of HPA are unknown. Methods: We present a child with pharmacoresistant epilepsy who underwent epileptic focus resections at age 3 and 5 years and was found to have mosaic chr1q gain and HPA. We performed single-nucleus RNA-sequencing (snRNA-seq) of brain tissue from the second resection. Results: Remarkably, snRNA-seq showed increased expression of chr1q genes only in subsets of neurons and astrocytes. Differentially expressed genes associated with inferred chr1q gain included AKT3 and genes associated with cell adhesion or migration. A subpopulation of astrocytes demonstrated marked enrichment for synapse-associated transcripts, possibly linked to the astrocytic inclusions observed in HPA. Discussion: snRNA-seq may be used to infer the cell type-specificity of mosaic chromosomal copy number changes and identify associated gene expression alterations, which in the case of chr1q gain may involve aberrations in cell migration. Future studies using spatial profiling could yield further insights on the molecular signatures of HPA.

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Section: Discussionsupporting

confidence: 91%

Cell type specificity of mosaic chromosome 1q gain resolved by snRNA-seq in a case of epilepsy with hyaline protoplasmic astrocytopathy

Leng,

Cadwell,

Devine

et al. 2023

Preprint

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“…Interestingly, no alterations on these chromosomes were found within this work using OGM. However, a duplication on chromosome 1q, which was previously reported in gene-edited hiPSCs [ 33 , 44 , 74 ], ESCs [ 20 , 33 , 65 , 66 , 74 ], and derivatives [ 75 , 76 ], was detected in the PS1-LMNB1_GFP cell line. This genetic modification has been associated with an increase in proliferation rate [ 75 ], potentially due to AKT3 overexpression [ 77 ].…”

Section: Discussionmentioning

confidence: 87%

“…However, a duplication on chromosome 1q, which was previously reported in gene-edited hiPSCs [ 33 , 44 , 74 ], ESCs [ 20 , 33 , 65 , 66 , 74 ], and derivatives [ 75 , 76 ], was detected in the PS1-LMNB1_GFP cell line. This genetic modification has been associated with an increase in proliferation rate [ 75 ], potentially due to AKT3 overexpression [ 77 ]. Strikingly, within this study, no increase in the proliferation rate was detectable in PS1-LMNB1_GFP hiPSCs harboring the 1q duplication ( Figure 1 b).…”

Section: Discussionmentioning

confidence: 87%

Optical Genome Mapping Reveals Genomic Alterations upon Gene Editing in hiPSCs: Implications for Neural Tissue Differentiation and Brain Organoid Research

Gallego Villarejo,

Gerding,

Bachmann

et al. 2024

Cells

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Genome editing, notably CRISPR (cluster regularly interspaced short palindromic repeats)/Cas9 (CRISPR-associated protein 9), has revolutionized genetic engineering allowing for precise targeted modifications. This technique’s combination with human induced pluripotent stem cells (hiPSCs) is a particularly valuable tool in cerebral organoid (CO) research. In this study, CRISPR/Cas9-generated fluorescently labeled hiPSCs exhibited no significant morphological or growth rate differences compared with unedited controls. However, genomic aberrations during gene editing necessitate efficient genome integrity assessment methods. Optical genome mapping, a high-resolution genome-wide technique, revealed genomic alterations, including chromosomal copy number gain and losses affecting numerous genes. Despite these genomic alterations, hiPSCs retain their pluripotency and capacity to generate COs without major phenotypic changes but one edited cell line showed potential neuroectodermal differentiation impairment. Thus, this study highlights optical genome mapping in assessing genome integrity in CRISPR/Cas9-edited hiPSCs emphasizing the need for comprehensive integration of genomic and morphological analysis to ensure the robustness of hiPSC-based models in cerebral organoid research.

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“…We support the second possibility for the following reasons: 1) it has been shown in many literatures that the presence of extra chromosome has a negative impact of cell fitness in vivo and in vitro [ 9 , 10 , 14 , 15 ]; 2) we confirmed that disomic cells become majority over the passages in mixed cell culture ( S3 Fig ); and 3) non-disjunction leading to chromosomal trisomy is the most reported karyotypic change in cultured human iPSCs [ 16 ] . In this study, we identified iPSC clones with chromosome numerical abnormalities, such as trisomies 1, 6, 11, 20, and XXY and monosomies 4, 10, and 13, and the most prevalent chromosome numerical abnormality was trisomy 1, where genes involved in cell survival, proliferation, and differentiation are present [ 17 , 18 ] . Moreover, trisomy 20 was reported to show a selective growth advantage by inhibiting apoptosis with the BCL2L1 gene as a driver [ 19 ] .…”

Section: Discussionmentioning

confidence: 99%

iPSC reprogramming-mediated aneuploidy correction in autosomal trisomy syndromes

et al. 2022

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Trisomy 21, 18, and 13 are the major autosomal aneuploidy disorders in humans. They are mostly derived from chromosome non-disjunction in maternal meiosis, and the extra trisomic chromosome can cause several congenital malformations. Various genes on the trisomic chromosomes are intricately involved in the development of disease, and fundamental treatments have not yet been established. However, chromosome therapy has been developed to correct the extra chromosome in cultured patient cells, and it was recently reported that during reprogramming into iPSCs, fibroblasts from a Down syndrome patient lost the extra chromosome 21 due to a phenomenon called trisomy-biased chromosome loss. To gain preliminary insights into the underlying mechanism of trisomy rescue during the early stages of reprogramming, we reprogrammed skin fibroblasts from patients with trisomy syndromes 21, 18, 13, and 9 to iPSC, and evaluated the genomes of the individual iPSC colonies by molecular cytogenetic techniques. We report the spontaneous correction from trisomy to disomy upon cell reprogramming in at least one cell line examined from each of the trisomy syndromes, and three possible combinations of chromosomes were selected in the isogenic trisomy-rescued iPSC clones. Single nucleotide polymorphism analysis showed that the trisomy-rescued clones exhibited either heterodisomy or segmental uniparental isodisomy, ruling out the possibility that two trisomic chromosomes were lost simultaneously and the remaining one was duplicated, suggesting instead that one trisomic chromosome was lost to generate disomic cells. These results demonstrated that trisomy rescue may be a phenomenon with random loss of the extra chromosome and subsequent selection for disomic iPSCs, which is analogous to the karyotype correction in early preimplantation embryos. Our finding is relevant for elucidating the mechanisms of autonomous karyotype correction and future application in basic and clinical research on aneuploidy disorders.

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Acquisition of chromosome 1q duplication in parental and genome‐edited human‐induced pluripotent stem cell‐derived neural stem cells results in their higher proliferation rate in vitro and in vivo

Abstract: This is an open access article under the terms of the Creative Commons Attribution License, which permits use, distribution and reproduction in any medium, provided the original work is properly cited.

Cited by 6 publications

References 70 publications

Cell type specificity of mosaic chromosome 1q gain resolved by snRNA-seq in a case of epilepsy with hyaline protoplasmic astrocytopathy

Cell type specificity of mosaic chromosome 1q gain resolved by snRNA-seq in a case of epilepsy with hyaline protoplasmic astrocytopathy

Optical Genome Mapping Reveals Genomic Alterations upon Gene Editing in hiPSCs: Implications for Neural Tissue Differentiation and Brain Organoid Research

iPSC reprogramming-mediated aneuploidy correction in autosomal trisomy syndromes

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