A Mechanism Leading to Changes in Copy Number Variations Affected by Transcriptional Level Might Be Involved in Evolution, Embryonic Development, Senescence, and Oncogenesis Mediated by Retrotransposons

In recent years, more and more evidence has emerged showing that changes in copy number variations (CNVs) correlated with the transcriptional level can be found during evolution, embryonic development, and oncogenesis. However, the underlying mechanisms remain largely unknown. The success of the induced pluripotent stem cell suggests that genome changes could bring about transformations in protein expression and cell status; conversely, genome alterations generated during embryonic development and senescence might also be the result of genome changes. With rapid developments in science and technology, evidence of changes in the genome affected by transcriptional level has gradually been revealed, and a rational and concrete explanation is needed. Given the preference of the HIV-1 genome to insert into transposons of genes with high transcriptional levels, we propose a mechanism based on retrotransposons facilitated by specific pre-mRNA splicing style and homologous recombination (HR) to explain changes in CNVs in the genome. This mechanism is similar to that of the group II intron that originated much earlier. Under this proposed mechanism, CNVs on genome are dynamically and spontaneously extended in a manner that is positively correlated with transcriptional level or contract as the cell divides during evolution, embryonic development, senescence, and oncogenesis, propelling alterations in them. Besides, this mechanism explains several critical puzzles in these processes. From evidence collected to date, it can be deduced that the message contained in genome is not just three-dimensional but will become four-dimensional, carrying more genetic information.

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Hereditary Optic Neuropathies: Induced Pluripotent Stem Cell-Based 2D/3D Approaches

Genes ◽

10.3390/genes12010112 ◽

2021 ◽

Vol 12 (1) ◽

pp. 112

Author(s):

Marta García-López ◽

Joaquín Arenas ◽

M. Esther Gallardo

Keyword(s):

Stem Cell ◽

Retinal Ganglion Cells ◽

Pluripotent Stem Cell ◽

Ganglion Cells ◽

Genetic Disorders ◽

Three Dimensional ◽

Induced Pluripotent Stem Cell ◽

Underlying Mechanism ◽

Retinal Ganglion ◽

Induced Pluripotent

Inherited optic neuropathies share visual impairment due to the degeneration of retinal ganglion cells (RGCs) as the hallmark of the disease. This group of genetic disorders are caused by mutations in nuclear genes or in the mitochondrial DNA (mtDNA). An impaired mitochondrial function is the underlying mechanism of these diseases. Currently, optic neuropathies lack an effective treatment, and the implementation of induced pluripotent stem cell (iPSC) technology would entail a huge step forward. The generation of iPSC-derived RGCs would allow faithfully modeling these disorders, and these RGCs would represent an appealing platform for drug screening as well, paving the way for a proper therapy. Here, we review the ongoing two-dimensional (2D) and three-dimensional (3D) approaches based on iPSCs and their applications, taking into account the more innovative technologies, which include tissue engineering or microfluidics.

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Three-dimensional induced pluripotent stem-cell models of human brain angiogenesis

Microvascular Research ◽

10.1016/j.mvr.2020.104042 ◽

2020 ◽

Vol 132 ◽

pp. 104042 ◽

Cited By ~ 1

Author(s):

Raleigh M. Linville ◽

Diego Arevalo ◽

Joanna C. Maressa ◽

Nan Zhao ◽

Peter C. Searson

Keyword(s):

Stem Cell ◽

Human Brain ◽

Pluripotent Stem Cell ◽

Three Dimensional ◽

Induced Pluripotent Stem Cell ◽

Cell Models ◽

Induced Pluripotent ◽

Stem Cell Models ◽

Brain Angiogenesis

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Combined Analysis with Copy Number Variation Identifies Risk Loci in Lung Cancer

BioMed Research International ◽

10.1155/2014/469103 ◽

2014 ◽

Vol 2014 ◽

pp. 1-9 ◽

Cited By ~ 2

Author(s):

Xinlei Li ◽

Xianfeng Chen ◽

Guohong Hu ◽

Yang Liu ◽

Zhenguo Zhang ◽

...

Keyword(s):

Lung Cancer ◽

Copy Number ◽

Association Studies ◽

Copy Number Variations ◽

Genome Wide Association Studies ◽

Potential Candidate ◽

Cancer Etiology ◽

Combined Analysis ◽

Recombination Hotspots ◽

Underlying Mechanisms

Background. Lung cancer is the most important cause of cancer mortality worldwide, but the underlying mechanisms of this disease are not fully understood. Copy number variations (CNVs) are promising genetic variations to study because of their potential effects on cancer.Methodology/Principal Findings. Here we conducted a pilot study in which we systematically analyzed the association of CNVs in two lung cancer datasets: the Environment And Genetics in Lung cancer Etiology (EAGLE) and the Prostate, Lung, Colorectal and Ovarian (PLCO) Cancer Screening Trial datasets. We used a preestablished association method to test the datasets separately and conducted a combined analysis to test the association accordance between the two datasets. Finally, we identified 167 risk SNP loci and 22 CNVs associated with lung cancer and linked them with recombination hotspots. Functional annotation and biological relevance analyses implied that some of our predicted risk loci were supported by other studies and might be potential candidate loci for lung cancer studies.Conclusions/Significance. Our results further emphasized the importance of copy number variations in cancer and might be a valuable complement to current genome-wide association studies on cancer.

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Tau interactome mapping reveals dynamic processes in synapses and mitochondria associated with neurodegenerative disease

10.1101/2021.06.17.448349 ◽

2021 ◽

Author(s):

Tara E Tracy ◽

Jesus Madero-Perez ◽

Danielle Swaney ◽

Timothy S Chang ◽

Michelle Moritz ◽

...

Keyword(s):

Affinity Purification ◽

Induced Pluripotent Stem Cell ◽

Proximity Ligation Assay ◽

Spatiotemporal Resolution ◽

Proximity Ligation ◽

Cytosolic Domains ◽

Presynaptic Vesicle ◽

Underlying Mechanisms ◽

Induced Pluripotent ◽

Affinity Purification Mass Spectrometry

Tau (MAPT) drives neuronal dysfunction in Alzheimer's disease (AD) and other tauopathies. To dissect the underlying mechanisms, we combined an engineered ascorbic acid peroxidase (APEX) approach with quantitative affinity purification mass spectrometry (AP-MS) followed by proximity ligation assay (PLA) to characterize Tau interactomes modified by neuronal activity and mutations that cause frontotemporal dementia (FTD) in human induced pluripotent stem cell (iPSC)-derived neurons. We established activity-dependent interactions of Tau with presynaptic vesicle proteins during Tau secretion and mapped the exact APEX-tau-induced biotinylated tyrosines to the cytosolic domains of the interacting vesicular proteins. We showed that FTD mutations impair bioenergetics and markedly diminished Tau's interaction with mitochondria proteins, which were downregulated in AD brains of multiple cohorts and correlated with disease severity. These multi-modal and dynamic Tau interactomes with unprecedented spatiotemporal resolution shed novel insights into Tau's role in neuronal function and disease-related processes with potential therapeutic targets to block Tau-mediated pathogenesis.

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Dynamic loading of human engineered heart tissue enhances contractile function and drives a desmosome-linked disease phenotype

Science Translational Medicine ◽

10.1126/scitranslmed.abd1817 ◽

2021 ◽

Vol 13 (603) ◽

pp. eabd1817

Author(s):

Jacqueline M. Bliley ◽

Mathilde C. S. C. Vermeer ◽

Rebecca M. Duffy ◽

Ivan Batalov ◽

Duco Kramer ◽

...

Keyword(s):

Dynamic Loading ◽

Disease Modeling ◽

Contractile Function ◽

Three Dimensional ◽

Induced Pluripotent Stem Cell ◽

Heart Tissue ◽

Disease Phenotype ◽

Heart Formation ◽

Induced Pluripotent ◽

And Function

The role that mechanical forces play in shaping the structure and function of the heart is critical to understanding heart formation and the etiology of disease but is challenging to study in patients. Engineered heart tissues (EHTs) incorporating human induced pluripotent stem cell (hiPSC)–derived cardiomyocytes have the potential to provide insight into these adaptive and maladaptive changes. However, most EHT systems cannot model both preload (stretch during chamber filling) and afterload (pressure the heart must work against to eject blood). Here, we have developed a new dynamic EHT (dyn-EHT) model that enables us to tune preload and have unconstrained contractile shortening of >10%. To do this, three-dimensional (3D) EHTs were integrated with an elastic polydimethylsiloxane strip providing mechanical preload and afterload in addition to enabling contractile force measurements based on strip bending. Our results demonstrated that dynamic loading improves the function of wild-type EHTs on the basis of the magnitude of the applied force, leading to improved alignment, conduction velocity, and contractility. For disease modeling, we used hiPSC-derived cardiomyocytes from a patient with arrhythmogenic cardiomyopathy due to mutations in the desmoplakin gene. We demonstrated that manifestation of this desmosome-linked disease state required dyn-EHT conditioning and that it could not be induced using 2D or standard 3D EHT approaches. Thus, a dynamic loading strategy is necessary to provoke the disease phenotype of diastolic lengthening, reduction of desmosome counts, and reduced contractility, which are related to primary end points of clinical disease, such as chamber thinning and reduced cardiac output.

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Direct SARS-CoV-2 infection of the human inner ear may underlie COVID-19-associated audiovestibular dysfunction

Communications Medicine ◽

10.1038/s43856-021-00044-w ◽

2021 ◽

Vol 1 (1) ◽

Author(s):

Minjin Jeong ◽

Karen E. Ocwieja ◽

Dongjun Han ◽

P. Ashley Wackym ◽

Yichen Zhang ◽

...

Keyword(s):

Inner Ear ◽

Hair Cells ◽

Molecular Mechanisms ◽

Three Dimensional ◽

Induced Pluripotent Stem Cell ◽

In Vitro Models ◽

Cellular Models ◽

Induced Pluripotent ◽

Human Inner Ear

Abstract Background COVID-19 is a pandemic respiratory and vascular disease caused by SARS-CoV-2 virus. There is a growing number of sensory deficits associated with COVID-19 and molecular mechanisms underlying these deficits are incompletely understood. Methods We report a series of ten COVID-19 patients with audiovestibular symptoms such as hearing loss, vestibular dysfunction and tinnitus. To investigate the causal relationship between SARS-CoV-2 and audiovestibular dysfunction, we examine human inner ear tissue, human inner ear in vitro cellular models, and mouse inner ear tissue. Results We demonstrate that adult human inner ear tissue co-expresses the angiotensin-converting enzyme 2 (ACE2) receptor for SARS-CoV-2 virus, and the transmembrane protease serine 2 (TMPRSS2) and FURIN cofactors required for virus entry. Furthermore, hair cells and Schwann cells in explanted human vestibular tissue can be infected by SARS-CoV-2, as demonstrated by confocal microscopy. We establish three human induced pluripotent stem cell (hiPSC)-derived in vitro models of the inner ear for infection: two-dimensional otic prosensory cells (OPCs) and Schwann cell precursors (SCPs), and three-dimensional inner ear organoids. Both OPCs and SCPs express ACE2, TMPRSS2, and FURIN, with lower ACE2 and FURIN expression in SCPs. OPCs are permissive to SARS-CoV-2 infection; lower infection rates exist in isogenic SCPs. The inner ear organoids show that hair cells express ACE2 and are targets for SARS-CoV-2. Conclusions Our results provide mechanistic explanations of audiovestibular dysfunction in COVID-19 patients and introduce hiPSC-derived systems for studying infectious human otologic disease.

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A multimodal 3D neuro-microphysiological system with neurite-trapping microelectrodes

10.1101/2021.04.16.436793 ◽

2021 ◽

Author(s):

Beatriz Molina-Martinez ◽

Laura V Jentsch ◽

Fulya Ersoy ◽

Matthijs van der Moolen ◽

Stella Donato ◽

...

Keyword(s):

Neurological Diseases ◽

Three Dimensional ◽

Induced Pluripotent Stem Cell ◽

Electrophysiological Recording ◽

Neuronal Cultures ◽

Novel Approach ◽

Clinical Models ◽

Induced Pluripotent ◽

Therapeutic Compounds ◽

Automated Handling

Three-dimensional cell technologies as pre-clinical models are emerging tools mimicking the structural and functional complexity of the nervous system. The accurate exploration of phenotypes in engineered 3D neuronal cultures, however, demands morphological, molecular and especially functional measurements. Particularly crucial is measurement of electrical activity of individual neurons with millisecond resolution. Current techniques rely on customized electrophysiological recording set-ups, characterized by limited throughput and poor integration with other readout modalities. Here we describe a novel approach, using multiwell glass microfluidic microelectrode arrays, allowing non-invasive electrical recording from engineered 3D neural tissues. We demonstrate parallelized studies with reference compounds, calcium imaging and optogenetic stimulation. Additionally, we show how microplate compatibility allows automated handling and high-content analysis of human-induced pluripotent stem cell-derived neurons. This microphysiological platform opens up new avenues for high-throughput studies on the functional, morphological and molecular details of neurological diseases and their potential treatment by therapeutic compounds.

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Copy Number Variation at 16p11.2 Imparts Transcriptional Alterations in Neural Development in an hiPSC-derived Model of Corticogenesis

10.1101/2020.04.22.055731 ◽

2020 ◽

Author(s):

Julien G. Roth ◽

Kristin L. Muench ◽

Aditya Asokan ◽

Victoria M. Mallett ◽

Hui Gai ◽

...

Keyword(s):

Neural Development ◽

Copy Number ◽

Developmental Disorders ◽

Neural Progenitor Cells ◽

Copy Number Variations ◽

Chromosomal Locus ◽

Research Initiative ◽

Transcriptional Alterations ◽

Number Variation ◽

Induced Pluripotent

ABSTRACTMicrodeletions and microduplications of the 16p11.2 chromosomal locus are associated with syndromic neurodevelopmental disorders and reciprocal physiological conditions such as macro/microcephaly and high/low body mass index. To facilitate cellular and molecular investigations of these phenotypes, 65 clones of human induced pluripotent stem cells (hiPSCs) were generated from 13 individuals with 16p11.2 copy number variations (CNVs). Cortical neural progenitor cells derived from these hiPSCs were profiled using RNA-Seq, which identified alterations in radial glial gene expression that precede morphological abnormalities reported at later neurodevelopmental stages. Moreover, a customizable bioinformatic strategy for the detection of random integration and expression of reprogramming vectors was developed and leveraged towards identifying a subset of “footprint”-free hiPSC clones that are available by request from the Simons Foundation Autism Research Initiative. This publicly available resource of 65 human hiPSC clones can serve as a powerful medium for probing the etiology of developmental disorders associated with 16p11.2 CNVs.

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Probabilistic method corrects previously uncharacterized Hi-C artifact

10.1101/2020.10.07.325332 ◽

2020 ◽

Author(s):

Yihang Shen ◽

Carl Kingsford

Keyword(s):

Copy Number ◽

Computational Models ◽

High Throughput Sequencing ◽

Probabilistic Method ◽

Three Dimensional ◽

Copy Number Variations ◽

Chromosome Conformation ◽

Chromosomal Structure ◽

Processing Pipeline ◽

Capture Techniques

AbstractThree-dimensional chromosomal structure plays an important role in gene regulation. Chromosome conformation capture techniques, especially the high-throughput, sequencing-based technique Hi-C, provide new insights on spatial architectures of chromosomes. However, Hi-C data contains artifacts and systemic biases that substantially influence subsequent analysis. Computational models have been developed to address these biases explicitly, however, it is difficult to enumerate and eliminate all the biases in models. Other models are designed to correct biases implicitly, but they will also be invalid in some situations such as copy number variations. We characterize a new kind of artifact in Hi-C data. We find that this artifact is caused by incorrect alignment of Hi-C reads against approximate repeat regions and can lead to erroneous chromatin contact signals. The artifact cannot be corrected by current Hi-C correction methods. We design a probabilistic method and develop a new Hi-C processing pipeline by integrating our probabilistic method with the HiC-Pro pipeline. We find that the new pipeline can remove this new artifact effectively, while preserving important features of the original Hi-C matrices.

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