scholarly journals CRISPR-Mediated Knockout of Long 3′ UTR mRNA Isoforms in mESC-Derived Neurons

2021 ◽  
Vol 12 ◽  
Author(s):  
Bongmin Bae ◽  
Pedro Miura
Keyword(s):  
Genetic Manipulation ◽  
Embryonic Stem ◽  
Mouse Embryonic Stem Cell ◽  
Cellular Functions ◽  
Mrna Isoforms ◽  
Mouse Cortex ◽  
Long Read ◽  
Sequencing Strategy ◽  
Cost Efficient ◽  
A Site

Alternative cleavage and polyadenylation (APA) is pervasive, occurring for more than 70% of human and mouse genes. Distal poly(A) site selection to generate longer 3′ UTR mRNA isoforms is prevalent in the nervous system, affecting thousands of genes. Here, we establish mouse embryonic stem cell (mESC)-derived neurons (mES-neurons) as a suitable system to study long 3′ UTR isoforms. RNA-seq analysis revealed that mES-neurons show widespread 3′ UTR lengthening that closely resembles APA patterns found in mouse cortex. mESCs are highly amenable to genetic manipulation. We present a method to eliminate long 3′ UTR isoform expression using CRISPR/Cas9 editing. This approach can lead to clones with the desired deletion within several weeks. We demonstrate this strategy on the Mprip gene as a proof-of-principle. To confirm loss of long 3′ UTR expression and the absence of cryptic poly(A) site usage stemming from the CRISPR deletion, we present a simple and cost-efficient targeted long-read RNA-sequencing strategy using the Oxford Nanopore Technologies platform. Using this method, we confirmed specific loss of the Mprip long 3′ UTR isoform. CRISPR gene editing of mESCs thus serves as a highly relevant platform for studying the molecular and cellular functions of long 3′ UTR mRNA isoforms.

scholarly journals Spontaneous induction of an homologous Robertsonian translocation, Rb(11.11) in a murine embryonic stem cell line

1990 ◽  
Vol 55 (2) ◽  
pp. 107-110 ◽  
Author(s):  
John Anthony Crolla ◽  
David Brown ◽  
David G. Whittingham
Keyword(s):  
Stem Cell ◽  
Embryonic Stem Cell ◽  
Recombinant Dna ◽  
Genetic Manipulation ◽  
Embryonic Stem Cell Line ◽  
Embryonic Stem ◽  
Mouse Embryonic Stem Cell ◽  
Transgenic Animals ◽  
Translocation Chromosome

SummaryKaryotype analysis of a series of established mouse embryonic stem cell (MESC) lines showed that the majority were aneuploid by the 7th and 9th passage and that all lines contained a single Robertsonian (Rb) translocation chromosome with a symmetrical, homologous, arm composition Rb(11.11). Although the chromosomal imbalance makes these MESC lines unsuitable for genetic manipulation in vitro and hence for subsequent production of transgenic animals, the spontaneous occurrence and stable retention of the homologous Rb(11.11) as the only metacentric chromosome in an otherwise all acrocentric karyotype, provides potentially useful cell lines for gene assignment and recombinant DNA studies.

scholarly journals Internalization of Foldamer-Based DNA Mimics through a Site-Specific Antibody Conjugate to Target HER2-Positive Cancer Cells

2021 ◽  
Vol 14 (7) ◽  
pp. 624
Author(s):  
Valentina Corvaglia ◽  
Imène Ait Mohamed Amar ◽  
Véronique Garambois ◽  
Stéphanie Letast ◽  
Aurélie Garcin ◽  
...  
Keyword(s):  
Cancer Cells ◽  
Topoisomerase I ◽  
Ovarian Cancer Cells ◽  
Cellular Functions ◽  
Antibody Drug Conjugate ◽  
Her2 Positive ◽  
Dna Topoisomerase ◽  
Antibody Conjugate ◽  
A Site

Inhibition of protein–DNA interactions represents an attractive strategy to modulate essential cellular functions. We reported the synthesis of unique oligoamide-based foldamers that adopt single helical conformations and mimic the negatively charged phosphate moieties of B-DNA. These mimics alter the activity of DNA interacting enzymes used as targets for cancer treatment, such as DNA topoisomerase I, and they are cytotoxic only in the presence of a transfection agent. The aim of our study was to improve internalization and selective delivery of these highly charged molecules to cancer cells. For this purpose, we synthesized an antibody-drug conjugate (ADC) using a DNA mimic as a payload to specifically target cancer cells overexpressing HER2. We report the bioconjugation of a 16-mer DNA mimic with trastuzumab and its functional validation in breast and ovarian cancer cells expressing various levels of HER2. Binding of the ADC to HER2 increased with the expression of the receptor. The ADC was internalized into cells and was more efficient than trastuzumab at inhibiting their growth in vitro. These results provide proof of concept that it is possible to site-specifically graft high molecular weight payloads such as DNA mimics onto monoclonal antibodies to improve their selective internalization and delivery in cancer cells.

scholarly journals GAMIBHEAR: whole-genome haplotype reconstruction from Genome Architecture Mapping data

2021 ◽  
Author(s):  
Julia Markowski ◽  
Rieke Kempfer ◽  
Alexander Kukalev ◽  
Ibai Irastorza-Azcarate ◽  
Gesa Loof ◽  
...  
Keyword(s):  
Genetic Variants ◽  
Embryonic Stem Cell Line ◽  
Embryonic Stem ◽  
Mouse Embryonic Stem Cell ◽  
Supplementary Information ◽  
Model Organisms ◽  
Genome Architecture ◽  
Chromatin Conformation ◽  
Haplotype Reconstruction ◽  
Allele Specific

Abstract Motivation Genome Architecture Mapping (GAM) was recently introduced as a digestion- and ligation-free method to detect chromatin conformation. Orthogonal to existing approaches based on chromatin conformation capture (3C), GAM’s ability to capture both inter- and intra-chromosomal contacts from low amounts of input data makes it particularly well suited for allele-specific analyses in a clinical setting. Allele-specific analyses are powerful tools to investigate the effects of genetic variants on many cellular phenotypes including chromatin conformation, but require the haplotypes of the individuals under study to be known a-priori. So far however, no algorithm exists for haplotype reconstruction and phasing of genetic variants from GAM data, hindering the allele-specific analysis of chromatin contact points in non-model organisms or individuals with unknown haplotypes. Results We present GAMIBHEAR, a tool for accurate haplotype reconstruction from GAM data. GAMIBHEAR aggregates allelic co-observation frequencies from GAM data and employs a GAM-specific probabilistic model of haplotype capture to optimise phasing accuracy. Using a hybrid mouse embryonic stem cell line with known haplotype structure as a benchmark dataset, we assess correctness and completeness of the reconstructed haplotypes, and demonstrate the power of GAMIBHEAR to infer accurate genome-wide haplotypes from GAM data. Availability GAMIBHEAR is available as an R package under the open source GPL-2 license at https://bitbucket.org/schwarzlab/gamibhear Maintainer [email protected] Supplementary information Supplementary information is available at Bioinformatics online.

Feeder-Dependent/Independent Mouse Embryonic Stem Cell Culture Protocol

2021 ◽  
Author(s):  
Hatice Burcu Şişli ◽  
Selinay Şenkal ◽  
Derya Sağraç ◽  
Taha Bartu Hayal ◽  
Ayşegül Doğan
Keyword(s):  
Cell Culture ◽  
Stem Cell ◽  
Embryonic Stem Cell ◽  
Embryonic Stem ◽  
Mouse Embryonic Stem Cell ◽  
Stem Cell Culture ◽  
Cell Culture Protocol ◽  
Culture Protocol

scholarly journals Advanced maternal age perturbs mouse embryo development and alters the phenotype of derived embryonic stem cells

2021 ◽  
pp. 1-11
Author(s):  
Pooja Khurana ◽  
Neil R. Smyth ◽  
Bhavwanti Sheth ◽  
Miguel A. Velazquez ◽  
Judith J. Eckert ◽  
...  
Keyword(s):  
Maternal Age ◽  
Embryonic Stem ◽  
Mouse Embryonic Stem Cell ◽  
Advanced Maternal Age ◽  
Preimplantation Embryos ◽  
Dependent Manner ◽  
Ki 67 ◽  
Altered Expression ◽  
Developmental Potential ◽  
Developmental Mechanisms

Abstract Advanced maternal age (AMA) is known to reduce fertility, increases aneuploidy in oocytes and early embryos and leads to adverse developmental consequences which may associate with offspring lifetime health risks. However, investigating underlying effects of AMA on embryo developmental potential is confounded by the inherent senescence present in maternal body systems further affecting reproductive success. Here, we describe a new model for the analysis of early developmental mechanisms underlying AMA by the derivation and characterisation of mouse embryonic stem cell (mESC-like) lines from naturally conceived embryos. Young (7–8 weeks) and Old (7–8 months) C57BL/6 female mice were mated with young males. Preimplantation embryos from Old dams displayed developmental retardation in blastocyst morphogenesis. mESC lines established from these blastocysts using conventional techniques revealed differences in genetic, cellular and molecular criteria conserved over several passages in the standardised medium. mESCs from embryos from AMA dams displayed increased incidence of aneuploidy following Giemsa karyotyping compared with those from Young dams. Moreover, AMA caused an altered pattern of expression of pluripotency markers (Sox2, OCT4) in mESCs. AMA further diminished mESC survival and proliferation and reduced the expression of cell proliferation marker, Ki-67. These changes coincided with altered expression of the epigenetic marker, Dnmt3a and other developmental regulators in a sex-dependent manner. Collectively, our data demonstrate the feasibility to utilise mESCs to reveal developmental mechanisms underlying AMA in the absence of maternal senescence and with reduced animal use.

scholarly journals Characterisation of protein-truncating and missense variants in PALB2 in 15 768 women from Malaysia and Singapore

2021 ◽  
pp. jmedgenet-2020-107471
Author(s):  
Pei Sze Ng ◽  
Rick ACM Boonen ◽  
Eldarina Wijaya ◽  
Chan Eng Chong ◽  
Milan Sharma ◽  
...  
Keyword(s):  
Breast Cancer ◽  
Rare Variants ◽  
Embryonic Stem ◽  
Mouse Embryonic Stem Cell ◽  
Population Based ◽  
Breast Cancer Patients ◽  
Dna Double Strand Breaks ◽  
Functional Impact ◽  
Missense Variants ◽  
Increased Risk

BackgroundRare protein-truncating variants (PTVs) in partner and localiser of BRCA2 (PALB2) confer increased risk to breast cancer, but relatively few studies have reported the prevalence in South-East Asian populations. Here, we describe the prevalence of rare variants in PALB2 in a population-based study of 7840 breast cancer cases and 7928 healthy Chinese, Malay and Indian women from Malaysia and Singapore, and describe the functional impact of germline missense variants identified in this population.MethodsMutation testing was performed on germline DNA (n=15 768) using targeted sequencing panels. The functional impact of missense variants was tested in mouse embryonic stem cell based functional assays.ResultsPTVs in PALB2 were found in 0.73% of breast cancer patients and 0.14% of healthy individuals (OR=5.44; 95% CI 2.85 to 10.39, p<0.0001). In contrast, rare missense variants in PALB2 were not associated with increased risk of breast cancer. Whereas PTVs were associated with later stage of presentation and higher-grade tumours, no significant association was observed with missense variants in PALB2. However, two novel rare missense variants (p.L1027R and p.G1043V) produced unstable proteins and resulted in a decrease in homologous recombination-mediated repair of DNA double-strand breaks.ConclusionDespite genetic and lifestyle differences between Asian and other populations, the population prevalence of PALB2 PTVs and associated relative risk of breast cancer, are similar to those reported in European populations.

scholarly journals Mouse embryonic stem cell-derived cardiomyocytes cease to beat following exposure to monochromatic light: association with increased ROS and loss of calcium transients

2019 ◽  
Vol 317 (4) ◽  
pp. C725-C736
Author(s):  
Gurbind Singh ◽  
Divya Sridharan ◽  
Mahmood Khan ◽  
Polani B. Seshagiri
Keyword(s):  
Cell Biology ◽  
Fluorescent Protein ◽  
Es Cells ◽  
Monochromatic Light ◽  
Embryonic Stem ◽  
Mouse Embryonic Stem Cell ◽  
Medical Diagnostics ◽  
Calcium Transients ◽  
Egfp Expression ◽  
Mitochondrial Activity

We earlier established the mouse embryonic stem (ES) cell “GS-2” line expressing enhanced green fluorescent protein (EGFP) and have been routinely using it to understand the molecular regulation of differentiation into cardiomyocytes. During such studies, we made a serendipitous discovery that functional cardiomyocytes derived from ES cells stopped beating when exposed to blue light. We observed a gradual cessation of contractility within a few minutes, regardless of wavelength (nm) ranges tested: blue (~420–495), green (~510–575), and red (~600–700), with green light manifesting the strongest impact. Following shifting of cultures back into the incubator (darkness), cardiac clusters regained beatings within a few hours. The observed light-induced contractility-inhibition effect was intrinsic to cardiomyocytes and not due to interference from other cell types. Also, this was not influenced by any physicochemical parameters or intracellular EGFP expression. Interestingly, the light-induced cardiomyocyte contractility inhibition was accompanied by increased intracellular reactive oxygen species (ROS), which could be abolished in the presence of N-acetylcysteine (ROS quencher). Besides, the increased intracardiomyocyte ROS levels were incidental to the inhibition of calcium transients and suppression of mitochondrial activity, both being essential for sarcomere function. To the best of our knowledge, ours is the first report to demonstrate the monochromatic light-mediated inhibition of contractions of cardiomyocytes with no apparent loss of cell viability and contractility. Our findings have implications in cardiac cell biology context in terms of 1) mechanistic insights into light impact on cardiomyocyte contraction, 2) potential use in laser beam-guided (cardiac) microsurgery, photo-optics-dependent medical diagnostics, 3) transient cessation of hearts during coronary artery bypass grafting, and 4) functional preservation of hearts for transplantation.

scholarly journals Pituitary adenylyl cyclase-activating peptide counteracts hedgehog-dependent motor neuron production in mouse embryonic stem cell cultures

2011 ◽  
Vol 89 (9) ◽  
pp. 1363-1374 ◽  
Author(s):  
Megumi Hirose ◽  
Pawel Niewiadomski ◽  
Gary Tse ◽  
Gloria C. Chi ◽  
Hongmei Dong ◽  
...  
Keyword(s):  
Stem Cell ◽  
Embryonic Stem Cell ◽  
Motor Neuron ◽  
Adenylyl Cyclase ◽  
Cell Cultures ◽  
Embryonic Stem ◽  
Mouse Embryonic Stem Cell
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