Somatic Cell Genome Research Articles

A somatic view of the genomic impact of mitochondrial endosymbiosis.

The endosymbiosis of mitochondrial ancestors resulted in the transfer of genetic material on an evolutionary scale for eukaryotic species. A new study in PLOS Biology expands this to the genome of somatic cells within individuals and highlights its correlation with aging and disease.

Somatic Genome Editing: Technical Challenges and Ethical Appraisal

The ability to modify the DNA sequences with molecular tools that employ nucleases has made it possible to edit genomes. Somatic genome editing is the procedure to alter the genome of somatic cells, making the changes introduced into the nucleotide sequence not inheritable. Powerful tools have been developed for therapeutic purposes to correct monogenic inherited disorders that often cause premature death and for which effective treatment options are not available. To ensure positive impact and minimise potential harms of these techniques, require to understand their limits in addition to apply values and principles that guide their use. This study reviews technical challenges of genome editing and appraises the Ethics of its application.

Somatic mutations in aging and disease.

Time always leaves its mark, and our genome is no exception. Mutations in the genome of somatic cells were first hypothesized to be the cause of aging in the 1950s, shortly after the molecular structure of DNA had been described. Somatic mutation theories of aging are based on the fact that mutations in DNA as the ultimate template for all cellular functions are irreversible. However, it took until the 1990s to develop the methods to test if DNA mutations accumulate with age in different organs and tissues and estimate the severity of the problem. By now, numerous studies have documented the accumulation of somatic mutations with age in normal cells and tissues of mice, humans, and other animals, showing clock-like mutational signatures that provide information on the underlying causes of the mutations. In this review, we will first briefly discuss the recent advances in next-generation sequencing that now allow quantitative analysis of somatic mutations. Second, we will provide evidence that the mutation rate differs between cell types, with a focus on differences between germline and somatic mutation rate. Third, we will discuss somatic mutational signatures as measures of aging, environmental exposure, and activities of DNA repair processes. Fourth, we will explain the concept of clonally amplified somatic mutations, with a focus on clonal hematopoiesis. Fifth, we will briefly discuss somatic mutations in the transcriptome and in our other genome, i.e., the genome of mitochondria. We will end with a brief discussion of a possible causal contribution of somatic mutations to the aging process.

Recent Advances in In Vivo Somatic Cell Gene Modification in Newborn Pups.

Germline manipulation at the zygote stage using the CRISPR/Cas9 system has been extensively employed for creating genetically modified animals and maintaining established lines. However, this approach requires a long and laborious task. Recently, many researchers have attempted to overcome these limitations by generating somatic mutations in the adult stage through tail vein injection or local administration of CRISPR reagents, as a new strategy called "in vivo somatic cell genome editing". This approach does not require manipulation of early embryos or strain maintenance, and it can test the results of genome editing in a short period. The newborn is an ideal stage to perform in vivo somatic cell genome editing because it is immune-privileged, easily accessible, and only a small amount of CRISPR reagents is required to achieve somatic cell genome editing throughout the entire body, owing to its small size. In this review, we summarize in vivo genome engineering strategies that have been successfully demonstrated in newborns. We also report successful in vivo genome editing through the neonatal introduction of genome editing reagents into various sites in newborns (as exemplified by intravenous injection via the facial vein), which will be helpful for creating models for genetic diseases or treating many genetic diseases.

Downregulation of transposable elements extends lifespan in Caenorhabditis elegans

Mobility of transposable elements (TEs) frequently leads to insertional mutations in functional DNA regions. In the potentially immortal germline, TEs are effectively suppressed by the Piwi-piRNA pathway. However, in the genomes of ageing somatic cells lacking the effects of the pathway, TEs become increasingly mobile during the adult lifespan, and their activity is associated with genomic instability. Whether the progressively increasing mobilization of TEs is a cause or a consequence of ageing remains a fundamental problem in biology. Here we show that in the nematode Caenorhabditis elegans, the downregulation of active TE families extends lifespan. Ectopic activation of Piwi proteins in the soma also promotes longevity. Furthermore, DNA N6-adenine methylation at TE stretches gradually rises with age, and this epigenetic modification elevates their transcription as the animal ages. These results indicate that TEs represent a novel genetic determinant of ageing, and that N6-adenine methylation plays a pivotal role in ageing control.

Hematological changes in descendants of animals irradiated in different doses

An urgent problem today is not only the study of changes in the stability of the genome of somatic cells, the clarification of the mechanisms of its destabilization under the influence of a complex of environmental factors, including radiation, but also the study of the possibility of hereditary transmission of these changes. In the modern experimental and clinical medicine, the most important problem is the harmful effect of ionizing radiation on the descendants of irradiated parents and the specifics of the effect of radiation on the developing organism. An important aspect of the problem of long-term post-radiation effects is the state of reproductive function and health of the descendants of the irradiated population, due to the physiological characteristics inherent to the mother and child - high sensitivity to the action of ionizing radiation, the consequences of which may manifest after a long period of imaginary well-being. The purpose of the work is to investigate the dynamics of body weight and hematological indiexes in the descendants of intact sexually mature animals and descendants born to animals irradiated at different doses, which were exposed to radiation at a dose of 1.0 Gy. The authors revealed that in descendants born to animals irradiated at different doses, which were exposed to radiation at a dose of 1.0 Gy, it was established that by the 30th day after irradiation at a dose of 1.0 Gy, the general condition of pup rats born from animals irradiated at a dose of 0.5 Gy and exposed to irradiation at a dose of 1.0 Gy is satisfactory against the background of an insignificant decrease in the body weight. This also applies to pup rats born to animals irradiated at a dose of 1.0 Gy, whose general condition slightly improves compared to the previous period of the study. The data obtained showed in the peripheral blood after 1 day in the descendants born to animals irradiated at a dose of 0.5 Gy, after irradiation at a dose of 1.0 Gy, a reduced content of hemoglobin and erythrocytes against the background of an increase in the content of platelets, leukocytes, lymphocytes and reticulocytes in comparison with non-irradiated animals, which was maintained throughout the experiment. Pronounced changes in hematological parameters were observed in the descendants born to animals irradiated at a dose of 1.0 Gy, which were exposed to total γ-irradiation at a dose of 1.0 Gy. The authors suppose their data are in favour of the pronounced adaptationof organisms’ regulatiory systems to ionizing irradiation effect that, firstly, outline the adaptative physiologcal mechanisms and, secondly, show the main launches of pathophysiologcial mechamisns in case of irradiation-induced hematological changes.

Epidemiology, Genetics and Pathogenesis of Pituitary Neuroendocrine Tumors

As the molecular pathology of pituitary cell development and the process of tumorigenesis in this organ continues to advance, it is recommended that pituitary neuroendocrine tumors(PitNETs)be classified based on three lineage-specific transcription factors(PIT1, Tpit, and SF1). In the hyperaging society of Japan, the number of cases traditionally classified as nonfunctioning PitNETs is increasing, and it is possible that some of these tumors may be associated with tumors that are known to exhibit aggressive behavior. The molecular pathological background of PitNET development is highly variable, and its pathogenesis in many cases remains unclear. As genomic analysis of PitNETs progresses, it is becoming increasingly clear that abnormalities in germline and somatic cell genomes contribute to our understanding of their etiology but do not explain most of them. Epigenetic modifications, such as deoxyribonucleic acid methylation and histone modifications(methylation and acetylation), are thought to be intricately related to tumorigenesis.

Safety and Ethical Considerations of CRISPR/Cas9-based Human Germline Genome Editing

Clustered regularly interspaced short palindromic repeats (CRISPR)/Cas9 adapted from natural immune defense systems of bacteria and archaea can edit genes in numerous organisms including humans. This has revolutionized genetic engineering and can help better understand genetic diseases as well as potentially correct causative mutations. Current CRISPR/Cas9-based genome editing is focused on either somatic cells or germline cells. In contrast to somatic cell genome editing, germline genome editing raises significant ethical issues as the genomic modifications in those reproductive cells by CRISPR/Cas9 can potentially be passed on to future generations. In this article, we focus on discussion of safety and ethical issues of CRISPR/Cas9-based germline genome editing in humans from several aspects including off-targets, Immunogenicity, autonomy, religion and eugenics.

Massive Somatic and Germline Chromosomal Integrations of Polydnaviruses in Lepidopterans

Increasing numbers of horizontal transfer (HT) of genes and transposable elements are reported in insects. Yet the mechanisms underlying these transfers remain unknown. Here we first quantify and characterize the patterns of chromosomal integration of the polydnavirus (PDV) encoded by the Campopleginae Hyposoter didymator parasitoid wasp (HdIV) in somatic cells of parasitized fall armyworm (Spodoptera frugiperda). PDVs are domesticated viruses injected by wasps together with their eggs into their hosts in order to facilitate the development of wasp larvae. We found that six HdIV DNA circles integrate into the genome of host somatic cells. Each host haploid genome suffers between 23 and 40 integration events (IEs) on average 72 h post-parasitism. Almost all IEs are mediated by DNA double-strand breaks occurring in the host integration motif (HIM) of HdIV circles. We show that despite their independent evolutionary origins, PDV from both Campopleginae and Braconidae wasps use remarkably similar mechanisms for chromosomal integration. Next, our similarity search performed on 775 genomes reveals that PDVs of both Campopleginae and Braconidae wasps have recurrently colonized the germline of dozens of lepidopteran species through the same mechanisms they use to integrate into somatic host chromosomes during parasitism. We found evidence of HIM-mediated HT of PDV DNA circles in no less than 124 species belonging to 15 lepidopteran families. Thus, this mechanism underlies a major route of HT of genetic material from wasps to lepidopterans with likely important consequences on lepidopterans.

Isolation, purification and PEG-mediated transient expression of mesophyll protoplasts in Camellia oleifera

BackgroundCamellia oleifera (C. oleifera) is a woody edible oil crop of great economic importance. Because of the lack of modern biotechnology research, C. oleifera faces huge challenges in both breeding and basic research. The protoplast and transient transformation system plays an important role in biological breeding, plant regeneration and somatic cell fusion. The objective of this present study was to develop a highly efficient protocol for isolating and purifying mesophyll protoplasts and transient transformation of C. oleifera. Several critical factors for mesophyll protoplast isolation from C. oleifera, including starting material (leaf age), pretreatment, enzymatic treatment (type of enzyme, concentration and digestion time), osmotic pressure and purification were optimized. Then the factors affecting the transient transformation rate of mesophyll protoplasts such as PEG molecular weights, PEG4000 concentration, plasmid concentration and incubation time were explored.ResultsThe in vitro grown seedlings of C. oleifera ‘Huashuo’ were treated in the dark for 24 h, then the 1st to 2nd true leaves were picked and vacuumed at − 0.07 MPa for 20 min. The maximum yield (3.5 × 107/g·FW) and viability (90.9%) of protoplast were reached when the 1st to 2nd true leaves were digested in the enzymatic solution containing1.5% (w/v) Cellulase R-10, 0.5% (w/v) Macerozyme R-10 and 0.25% (w/v) Snailase and 0.4 M mannitol for 10 h. Moreover, the protoplast isolation method was also applicable to the other two cultivars, the protoplast yield for ‘TXP14’ and ‘DP47’ was 1.1 × 107/g·FW and 2.6 × 107/g·FW, the protoplast viability for ‘TXP14’ and ‘DP47’ was 90.0% and 88.2%. The purification effect was the best when using W buffer as a cleaning agent by centrifugal precipitation. The maximum transfection efficiency (70.6%) was obtained with the incubation of the protoplasts with 15 µg plasmid and 40% PEG4000 for 20 min.ConclusionIn summary, a simple and efficient system for isolation and transient transformation of C. oleifera mesophyll protoplast is proposed, which is of great significance in various aspects of C. oleifera research, including the study of somatic cell fusion, genome editing, protein function, signal transduction, transcriptional regulation and multi-omics analyses.

Did circular DNA shape the evolution of mammalian genomes?

Extrachromosomal circular DNA (eccDNA) can shape the genomes of somatic cells, but how it impacts genomes across generations is largely unexplored. We propose that genomes can rearrange via circular intermediates across generations and show that up to 6% of a mammalian genome can have changed gene order through eccDNA.

Insights into the editing of the human genome: where can novel non-viral polymeric delivery agents take us

Tom Foti has more than 25 years of biotechnology experience and serves as Vice President/GM of the Protein Business Unit. He was one of the original founders of Aldevron’s protein services business, which was formed in 2009. Prior to working for Aldevron, Foti served in several roles in the Merck KGaA Bioscience Division, most recently as the Director of its Global Custom Services Business. He started his career in 1992, with Novagen, Inc. serving in manufacturing and operational roles until 1999. He played college basketball while earning a Bachelor’s of Science in Biotechnology and Microbiology from North Dakota State University. Foti also holds a Master’s in Business Administration from Edgewood College and a Management Leadership Certificate from Massachusetts Institute of Technology.Kris Saha is an Associate Professor of Biomedical Engineering and Medical History and Bioethics at the University of Wisconsin-Madison. He was recently named the McPherson Eye Research Institute’s Retina Research Foundation Kathryn and Latimer Murfee Chair for 2019-2022. His lab is at the Wisconsin Institute for Discovery (WID), and he participates on campus in the executive committees of the Stem Cell and Regenerative Medicine Center, Robert F. Holtz Center on Science and Technology Studies, and Forward Bio Institute. Prior to his arrival in Madison, Dr. Saha studied chemical engineering and biotechnology at Cornell University, University of Cambridge, and the University of California, Berkeley. In 2007 he became a Society in Science: Branco-Weiss fellow in the laboratory of Professor Rudolf Jaenisch at the Whitehead Institute for Biomedical Research at MIT and in the Science and Technology Studies program at Harvard University with Professor Sheila Jasanoff in Cambridge, Massachusetts. At UW-Madison, major thrusts of his lab involve gene editing and cell engineering of human cells found in the retina, central nervous system, liver, and blood. He has published more than 75 scientific manuscripts, filed several patents, and received awards that include the National Science Foundation CAREER Award, Biomedical Engineering Society’s Rising Star Award, and Gund Harrington Scholar Award. He is the leader of the gene therapy biomanufacturing impact area of the Grainger Institute for Engineering, a member of the National Academies’ Forum on Regenerative Medicine, a co-lead for the T cell testbed within the National Science Foundation’s Center for Cell Manufacturing Technologies (CMaT) and on the Executive Committee of the National Institutes for Health’s Somatic Cell Genome Editing (SCGE) Consortium.

Advances in haploid embryonic stem cell research†.

Haploid embryonic stem cells are embryonic stem cells of a special type. Their nuclei contain one complete set of genetic material, and they are capable of self-renewal and differentiation. The emergence of haploid embryonic stem cells has aided research in functional genomics, genetic imprinting, parthenogenesis, genetic screening, and somatic cell nuclear transfer. This article reviews current issues in haploid stem cell research based on reports published in recent years and assesses the potential applications of these cells in somatic cell nuclear transfer, genome imprinting, and parthenogenesis.

Examining clustered somatic mutations with SigProfilerClusters.

MotivationClustered mutations are found in the human germline as well as in the genomes of cancer and normal somatic cells. Clustered events can be imprinted by a multitude of mutational processes, and they have been implicated in both cancer evolution and development disorders. Existing tools for identifying clustered mutations have been optimized for a particular subtype of clustered event and, in most cases, relied on a predefined inter-mutational distance (IMD) cutoff combined with a piecewise linear regression analysis.ResultsHere, we present SigProfilerClusters, an automated tool for detecting all types of clustered mutations by calculating a sample-dependent IMD threshold using a simulated background model that takes into account extended sequence context, transcriptional strand asymmetries and regional mutation densities. SigProfilerClusters disentangles all types of clustered events from non-clustered mutations and annotates each clustered event into an established subclass, including the widely used classes of doublet-base substitutions, multi-base substitutions, omikli and kataegis. SigProfilerClusters outputs non-clustered mutations and clustered events using standard data formats as well as provides multiple visualizations for exploring the distributions and patterns of clustered mutations across the genome.Availability and implementationSigProfilerClusters is supported across most operating systems and made freely available at https://github.com/AlexandrovLab/SigProfilerClusters with an extensive documentation located at https://osf.io/qpmzw/wiki/home/.Supplementary information Supplementary data are available at Bioinformatics online.

Nematode chromosomes.

The nematode Caenorhabditis elegans has shed light on many aspects of eukaryotic biology, including genetics, development, cell biology, and genomics. A major factor in the success of C. elegans as a model organism has been the availability, since the late 1990s, of an essentially gap-free and well-annotated nuclear genome sequence, divided among 6 chromosomes. In this review, we discuss the structure, function, and biology of C. elegans chromosomes and then provide a general perspective on chromosome biology in other diverse nematode species. We highlight malleable chromosome features including centromeres, telomeres, and repetitive elements, as well as the remarkable process of programmed DNA elimination (historically described as chromatin diminution) that induces loss of portions of the genome in somatic cells of a handful of nematode species. An exciting future prospect is that nematode species may enable experimental approaches to study chromosome features and to test models of chromosome evolution. In the long term, fundamental insights regarding how speciation is integrated with chromosome biology may be revealed.

Beatrice Mintz (1921-2022): an innovator in embryo research and cancer biology

Beatrice Mintz (1921-2022): an innovator in embryo research and cancer biology

Nonhuman Primates in Translational Research.

Nonhuman primates are critically important animal models in which to study complex human diseases, understand biological functions, and address the safety of new diagnostics and therapies proposed for human use. They have genetic, physiologic, immunologic, and developmental similarities when compared to humans and therefore provide important preclinical models of human health and disease. This review highlights select research areas that demonstrate the importance of nonhuman primates in translational research. These include pregnancy and developmental disorders, infectious diseases, gene therapy, somatic cell genome editing, and applications of in vivo imaging. The power of the immune system and our increasing understanding of the role it plays in acute and chronic illnesses are being leveraged to produce new treatments for a range of medical conditions. Given the importance of the human immune system in health and disease, detailed study of the immune system of nonhuman primates is essential to advance preclinical translational research. The need for nonhuman primates continues to remain a high priority, which has been acutely evident during the severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) global pandemic. Nonhuman primates will continue to address key questions and provide predictive models to identify the safety and efficiency of new diagnostics and therapies for human use across the lifespan.

Chimeric chromosome landscapes of human somatic cell cultures show dependence on stress and regulation of genomic repeats by CGGBP1

Genomes of somatic cells in culture are prone to spontaneous mutations due to errors in replication and DNA repair. Some of these errors, such as chromosomal fusions, are not rectifiable and subject to selection or elimination in growing cultures. Somatic cell cultures are thus expected to generate background levels of potentially stable chromosomal chimeras. A description of the landscape of such spontaneously generated chromosomal chimeras in cultured cells will help understand the factors affecting somatic mosaicism. Here we show that short homology-associated non-homologous chromosomal chimeras occur in normal human fibroblasts and HEK293T cells at genomic repeats. The occurrence of chromosomal chimeras is enhanced by heat stress and depletion of a repeat regulatory protein CGGBP1. We also present evidence of homologous chromosomal chimeras between allelic copies in repeat-rich DNA obtained by methylcytosine immunoprecipitation. The formation of homologous chromosomal chimeras at Alu and L1 repeats increases upon depletion of CGGBP1. Our data are derived from de novo sequencing from three different cell lines under different experimental conditions and our chromosomal chimera detection pipeline is applicable to long as well as short read sequencing platforms. These findings present significant information about the generation, sensitivity and regulation of somatic mosaicism in human cell cultures.

Reading Frame Repair of TTN Truncation Variants Restores Titin Quantity and Functions.

Titin truncation variants (TTNtvs) are the most common inheritable risk factor for dilated cardiomyopathy (DCM), a disease with high morbidity and mortality. The pathogenicity of TTNtvs has been associated with structural localization as A-band variants overlapping myosin heavy chain-binding domains are more pathogenic than I-band variants by incompletely understood mechanisms. Demonstrating why A-band variants are highly pathogenic for DCM could reveal new insights into DCM pathogenesis, titin (TTN) functions, and therapeutic targets. We constructed human cardiomyocyte models harboring DCM-associated TTNtvs within A-band and I-band structural domains using induced pluripotent stem cell and CRISPR technologies. We characterized normal TTN isoforms and variant-specific truncation peptides by their expression levels and cardiomyocyte localization using TTN protein gel electrophoresis and immunofluorescence, respectively. Using CRISPR to ablate A-band variant-specific truncation peptides through introduction of a proximal I-band TTNtv, we studied genetic mechanisms in single cardiomyocyte and 3-dimensional, biomimetic cardiac microtissue functional assays. Last, we engineered a full-length TTN protein reporter assay and used next-generation sequencing assays to develop a CRISPR therapeutic for somatic cell genome editing TTNtvs. An A-band TTNtv dose-dependently impaired cardiac microtissue twitch force, reduced full-length TTN levels, and produced abundant TTN truncation peptides. TTN truncation peptides integrated into nascent myofibril-like structures and impaired myofibrillogenesis. CRISPR ablation of TTN truncation peptides using a proximal I-band TTNtv partially restored cardiac microtissue twitch force deficits. Cardiomyocyte genome editing using SpCas9 and a TTNtv-specific guide RNA restored the TTN protein reading frame, which increased full-length TTN protein levels, reduced TTN truncation peptides, and increased sarcomere function in cardiac microtissue assays. An A-band TTNtv diminished sarcomere function greater than an I-band TTNtv in proportion to estimated DCM pathogenicity. Although both TTNtvs resulted in full-length TTN haploinsufficiency, only the A-band TTNtv produced TTN truncation peptides that impaired myofibrillogenesis and sarcomere function. CRISPR-mediated reading frame repair of the A-band TTNtv restored functional deficits, and could be adapted as a one-and-done genome editing strategy to target ≈30% of DCM-associated TTNtvs.

AAV-mediated gene editing lights up the lung

AAV-mediated gene editing lights up the lung