scholarly journals Non-coding RNAs Associated with Prader-Willi Syndrome Regulate Transcription of Neurodevelopmental Genes in Human Induced Pluripotent Stem Cells

2021 ◽  
Author(s):  
Monika Sledziowska ◽  
Matt Jones ◽  
Ruba Al Maghrabi ◽  
Daniel Hebenstreit ◽  
Paloma Garcia ◽  
...  
Keyword(s):  
Gene Expression ◽  
Specific Gene ◽  
Chromosome 15 ◽  
Prader Willi Syndrome ◽  
Transcriptional Signature ◽  
Induced Pluripotent Cells ◽  
Non Coding Rnas ◽  
Induced Pluripotent ◽  
Human Induced Pluripotent Cells ◽  
Aberrant Gene

Mutations and aberrant gene expression during cellular differentiation lead to neurodevelopmental disorders such as Prader-Willi syndrome (PWS) which results from the deletion of an imprinted locus on chromosome 15. We analysed chromatin-associated RNA in human induced pluripotent cells (iPSCs) upon depletion of hybrid small nucleolar long non-coding RNAs (sno-lncRNAs) and 5 snoRNA capped and polyadenylated long non-coding RNAs (SPA-lncRNAs) transcribed from the locus deleted in PWS. We found that rapid ablation of these lncRNAs affects transcription of specific gene classes. Downregulated genes contribute to neurodevelopment and neuronal maintenance while genes that are upregulated are predominantly involved in the negative regulation of cellular metabolism and apoptotic processes. Our data revealed the importance of SPA-lncRNAs and sno-lncRNAs in controlling gene expression in iPSCs and provided a platform for synthetic experimental approaches in PWS studies. We conclude that ncRNAs transcribed from the PWS locus are critical regulators of a transcriptional signature important for neuronal differentiation and development.

scholarly journals Questioned validity of Gene Expression Dysregulated Domains in Down's Syndrome

F1000Research ◽  
2015 ◽  
Vol 4 ◽  
pp. 269 ◽  
Author(s):  
Long H. Do ◽  
William C. Mobley ◽  
Nishant Singhal
Keyword(s):  
Gene Expression ◽  
Monozygotic Twins ◽  
Recent Analysis ◽  
Ts65dn Mouse ◽  
Pluripotent Cells ◽  
Induced Pluripotent Cells ◽  
Independent Analysis ◽  
Human Ipscs ◽  
Rnaseq Data ◽  
Induced Pluripotent

Recently, in studies examining fibroblasts obtained from the tissues of one set of monozygotic twins (i.e. fetuses derived from the same egg) discordant for trisomy 21 (Down syndrome; DS), Letourneau et al., reported the presence of a defined pattern of dysregulation within specific genomic domains they referred to as Gene Expression Dysregulated Domains (GEDDs). GEDDs were described as alternating segments of increased or decreased gene expression affecting all chromosomes. Strikingly, GEDDs in fibroblasts were largely conserved in induced pluripotent cells (iPSCs) generated from the twin’s fibroblasts as well as in fibroblasts from the Ts65Dn mouse model of DS. Our recent analysis failed to find GEDDs. We reexamined the human iPSCs RNAseq data from Letourneau et al., and data from this same research group published earlier examining iPSCs from the same monozygotic twins. An independent analysis of RNAseq data from Ts65Dn fibroblasts also failed to confirm presence of GEDDs. Our analysis questions the validity of GEDDs in DS.

scholarly journals Comparative Analysis of Tenogenic Gene Expression in Tenocyte-Derived Induced Pluripotent Stem Cells and Bone Marrow-Derived Mesenchymal Stem Cells in Response to Biochemical and Biomechanical Stimuli

2021 ◽  
Vol 2021 ◽  
pp. 1-18
Author(s):  
Feikun Yang ◽  
Dean W. Richardson
Keyword(s):  
Gene Expression ◽  
Stem Cells ◽  
Bone Marrow ◽  
Mesenchymal Stem Cells ◽  
Induced Pluripotent Stem Cells ◽  
Pluripotent Stem Cells ◽  
Ectopic Expression ◽  
Mechanical Stretch ◽  
Specific Gene ◽  
Induced Pluripotent

The tendon is highly prone to injury, overuse, or age-related degeneration in both humans and horses. Natural healing of injured tendon is poor, and cell-based therapeutic treatment is still a significant clinical challenge. In this study, we extensively investigated the expression of tenogenic genes in equine bone marrow mesenchymal stem cells (BMSCs) and tenocyte-derived induced pluripotent stem cells (teno-iPSCs) stimulated by growth factors (TGF-β3 and BMP12) combined with ectopic expression of tenogenic transcription factor MKX or cyclic uniaxial mechanical stretch. Western blotting revealed that TGF-β3 and BMP12 increased the expression of transcription factors SCX and MKX in both cells, but the tenocyte marker tenomodulin (TNMD) was detected only in BMSCs and upregulated by either inducer. On the other hand, quantitative real-time PCR showed that TGF-β3 increased the expression of EGR1, COL1A2, FMOD, and TNC in BMSCs and SCX, COL1A2, DCN, FMOD, and TNC in teno-iPSCs. BMP12 treatment elevated SCX, MKX, DCN, FMOD, and TNC in teno-iPSCs. Overexpression of MKX increased SCX, DCN, FMOD, and TNC in BMSCs and EGR1, COL1A2, DCN, FMOD, and TNC in teno-iPSCs; TGF-β3 further enhanced TNC in BMSCs. Moreover, mechanical stretch increased SCX, EGR1, DCN, ELN, and TNC in BMSCs and SCX, MKX, EGR1, COL1A2, DCN, FMOD, and TNC in teno-iPSCs; TGF-β3 tended to further elevate SCX, ELN, and TNC in BMSCs and SCX, MKX, COL1A2, DCN, and TNC in teno-iPSCs, while BMP12 further uptrended the expression of SCX and DCN in BMSCs and DCN in teno-iPSCs. Additionally, the aforementioned tenogenic inducers also affected the expression of signaling regulators SMAD7, ETV4, and SIRT1 in BMSCs and teno-iPSCs. Taken together, our data demonstrate that, in respect to the tenocyte-lineage-specific gene expression, BMSCs and teno-iPSCs respond differently to the tenogenic stimuli, which may affect the outcome of their application in tendon repair or regeneration.

scholarly journals Patient iPSC-astrocytes show transcriptional and functional dysregulation in schizophrenia

2020 ◽  
Author(s):  
Marja Koskuvi ◽  
Šárka Lehtonen ◽  
Kalevi Trontti ◽  
Meike Keuters ◽  
Ying Chieh Wu ◽  
...  
Keyword(s):  
Gene Expression ◽  
Familial Risk ◽  
Monozygotic Twins ◽  
Behavioral Changes ◽  
Brain Cells ◽  
Specific Gene ◽  
Neuronal Responses ◽  
Clozapine Treatment ◽  
Synaptic Functions ◽  
Induced Pluripotent

AbstractHuman astrocytes are multifunctional brain cells and may contribute to the pathophysiology of schizophrenia (SCZ). We differentiated astrocytes from induced pluripotent stem cells of monozygotic twins discordant for SCZ, and found sex-specific gene expression and signaling pathway alterations related particularly to inflammation and synaptic functions. While Ingenuity Pathway Analysis identified SCZ disease and synaptic transmission pathway changes in SCZ astrocytes, the most consistent findings were related to collagen and cell adhesion associated pathways. Neuronal responses to glutamate and GABA differed between astrocytes from control persons, affected twins, and their unaffected co-twins, and were normalized by clozapine treatment. SCZ astrocyte cell transplantation to the mouse forebrain caused gene expression changes in demyelination, synaptic dysfunction and inflammation pathways of mouse brain cells and resulted in behavioral changes in cognitive and olfactory functions. Altogether, our results show that astrocytes contribute to both familial risk and clinical manifestation of SCZ in a sex-specific manner.

scholarly journals Engineered human induced pluripotent cells enable genetic code expansion in brain organoids

2021 ◽  
Author(s):  
Lea van Husen ◽  
Anna Maria Katsori ◽  
Birthe Meineke ◽  
Lars O Tjernberg ◽  
Sophia Schedin-Weiss ◽  
...  
Keyword(s):  
Genetic Code ◽  
Fluorescent Dyes ◽  
Induced Pluripotent Stem Cell ◽  
Cell Types ◽  
Trna Synthetase ◽  
Induced Pluripotent Cells ◽  
Wide Range ◽  
Induced Pluripotent ◽  
Human Induced Pluripotent Cells ◽  
Tissue Models

Human induced pluripotent stem cell (hiPSC) technology has revolutionized human biology. A wide range of cell types and tissue models can be derived from hiPSCs to study complex human diseases. Here, we use PiggyBac mediated transgenesis to engineer hiPSCs with an expanded genetic code. We demonstrate that genomic integration of expression cassettes for a pyrrolysyl-tRNA synthetase (PylRS), pyrrolysyl-tRNA (PylT) and the target protein of interest enables site-specific incorporation of a non-canonical amino acid (ncAA) in response to amber stop codons. Neural stem cells, neurons and brain organoids derived from the engineered hiPSCs continue to express the amber suppression machinery and produce ncAA-bearing reporter. The incorporated ncAA can serve as a minimal bioorthogonal handle for further modifications by labeling with fluorescent dyes. Site-directed ncAA mutagenesis will open a wide range of applications to probe and manipulate proteins in brain organoids and other hiPSC-derived cell types and complex tissue models.

scholarly journals Reintroduction of the archaic variant of NOVA1 in cortical organoids alters neurodevelopment

Science ◽  
2021 ◽  
Vol 371 (6530) ◽  
pp. eaax2537 ◽  
Author(s):  
Cleber A. Trujillo ◽  
Edward S. Rice ◽  
Nathan K. Schaefer ◽  
Isaac A. Chaim ◽  
Emily C. Wheeler ◽  
...  
Keyword(s):  
Neural Development ◽  
Modern Human ◽  
Protein Coding ◽  
Electrophysiological Properties ◽  
Induced Pluripotent Cells ◽  
Synaptic Markers ◽  
Functional Consequences ◽  
Induced Pluripotent ◽  
Human Induced Pluripotent Cells ◽  
And Function

The evolutionarily conserved splicing regulator neuro-oncological ventral antigen 1 (NOVA1) plays a key role in neural development and function. NOVA1 also includes a protein-coding difference between the modern human genome and Neanderthal and Denisovan genomes. To investigate the functional importance of an amino acid change in humans, we reintroduced the archaic allele into human induced pluripotent cells using genome editing and then followed their neural development through cortical organoids. This modification promoted slower development and higher surface complexity in cortical organoids with the archaic version of NOVA1. Moreover, levels of synaptic markers and synaptic protein coassociations correlated with altered electrophysiological properties in organoids expressing the archaic variant. Our results suggest that the human-specific substitution in NOVA1, which is exclusive to modern humans since divergence from Neanderthals, may have had functional consequences for our species’ evolution.

scholarly journals Genomic Imprinting

2016 ◽  
Vol 4 (1) ◽  
pp. 181-184 ◽  
Author(s):  
Emirjeta Bajrami ◽  
Mirko Spiroski
Keyword(s):  
Gene Expression ◽  
Autism Spectrum Disorder ◽  
Dna Methylation ◽  
Genomic Imprinting ◽  
Environmental Influence ◽  
Autism Spectrum ◽  
Chromosome 15 ◽  
Prader Willi Syndrome ◽  
Epigenetic Mechanisms ◽  
Active Allele

BACKGROUND: Genomic imprinting is the inheritance out of Mendelian borders. Many of inherited diseases and human development violates Mendelian law of inheritance, this way of inheriting is studied by epigenetics.AIM: The aim of this review is to analyze current opinions and options regarding to this way of inheriting.RESULTS: Epigenetics shows that gene expression undergoes changes more complex than modifications in the DNA sequence; it includes the environmental influence on the gametes before conception. Humans inherit two alleles from mother and father, both are functional for the majority of the genes, but sometimes one is turned off or “stamped” and doesn’t show in offspring, that gene is imprinted. Imprinting means that that gene is silenced, and gene from other parent is expressed. The mechanisms for imprinting are still incompletely defined, but they involve epigenetic modifications that are erased and then reset during the creation of eggs and sperm. Genomic imprinting is a process of silencing genes through DNA methylation. The repressed allele is methylated, while the active allele is unmethylated. The most well-known conditions include Prader-Willi syndrome, and Angelman syndrome. Both of these syndromes can be caused by imprinting or other errors involving genes on the long arm of chromosome 15.CONCLUSIONS: Genomic imprinting and other epigenetic mechanisms such as environment is shown that plays role in offspring neurodevelopment and autism spectrum disorder.

scholarly journals Self-organized Kidney Rudiments: Prospects for Better in vitro Nephrotoxicity Assays

2015 ◽  
Vol 10s1 ◽  
pp. BMI.S20056 ◽  
Author(s):  
Jamie A. Davies
Keyword(s):  
Stem Cells ◽  
In Vitro Assays ◽  
Limiting Factor ◽  
Induced Pluripotent Cells ◽  
Therapeutic Drugs ◽  
Vascular Regulation ◽  
Single Cell Type ◽  
Induced Pluripotent ◽  
Human Induced Pluripotent Cells

Kidneys are essential to life but vulnerable to a range of toxicants, including therapeutic drugs and their metabolites. Indeed, nephrotoxicity is often a limiting factor in both drug use and drug development. Most toxicants damage kidneys by one of four mechanisms: damage to the membrane and its junctions, oxidative stress and free radical generation, activation of inflammatory processes, and interference with vascular regulation. Traditionally, animal models were used in preclinical screening for nephrotoxicity, but these can be poorly predictive of human reactions. Animal screens have been joined by simple single-cell–type in vitro assays using primary or immortalized human cells, particularly proximal tubule cells as these are especially vulnerable to toxicants. Recent research, aimed mainly at engineering new kidneys for transplant purposes, has resulted in a method for constructing anatomically realistic mini-kidneys from renogenic stem cells. So far, this has been done only using renogenic stem cells obtained directly from mouse embryos but, in principle, it should be possible to make them from renogenically directed human-induced pluripotent cells. If this can be done, the resulting human-based mini-kidneys would be a promising system for detecting some types of nephrotoxicity and for developing nephroprotective drugs.

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