ABSTRACT
One week after fertilization, human embryos implant into the uterus. This event requires the embryo to form a blastocyst consisting of a sphere encircling a cavity lodging the embryo proper. Stem cells can form a blastocyst model that we called a blastoid1. Here we show that naive human pluripotent stem cells cultured in PXGL medium2 and triply inhibited for the Hippo, TGF-ß and ERK pathways efficiently (with more than 70% efficiency) form blastoids generating blastocyst-stage analogues of the three founding lineages (more than 97% trophectoderm, epiblast and primitive endoderm) according to the sequence and timing of blastocyst development. Blastoids spontaneously form the first axis, and we observe that the epiblast induces the local maturation of the polar trophectoderm, thereby endowing blastoids with the capacity to directionally attach to hormonally stimulated endometrial cells, as during implantation. Thus, we propose that such a human blastoid is a faithful, scalable and ethical model for investigating human implantation and development3,4.
Subject(s)
Blastocyst , Pluripotent Stem Cells , Blastocyst/metabolism , Cell Differentiation , Cell Lineage , Embryo Implantation , Embryonic Development , Female , HumansABSTRACT
Our current understanding of early human development is limited. A study in PLOS Biology found a previously undefined group of cells that diverges from the main lineages and undergo apoptosis through the activity of young transposable elements.
Subject(s)
Blastocyst , DNA Transposable Elements , Humans , DNA Transposable Elements/genetics , Embryo, MammalianABSTRACT
Current understandings of cell specification in early mammalian pre-implantation development are based mainly on mouse studies. The first lineage differentiation event occurs at the morula stage, with outer cells initiating a trophectoderm (TE) placental progenitor program. The inner cell mass arises from inner cells during subsequent developmental stages and comprises precursor cells of the embryo proper and yolk sac1. Recent gene-expression analyses suggest that the mechanisms that regulate early lineage specification in the mouse may differ in other mammals, including human2-5 and cow6. Here we show the evolutionary conservation of a molecular cascade that initiates TE segregation in human, cow and mouse embryos. At the morula stage, outer cells acquire an apical-basal cell polarity, with expression of atypical protein kinase C (aPKC) at the contact-free domain, nuclear expression of Hippo signalling pathway effectors and restricted expression of TE-associated factors such as GATA3, which suggests initiation of a TE program. Furthermore, we demonstrate that inhibition of aPKC by small-molecule pharmacological modulation or Trim-Away protein depletion impairs TE initiation at the morula stage. Our comparative embryology analysis provides insights into early lineage specification and suggests that a similar mechanism initiates a TE program in human, cow and mouse embryos.
Subject(s)
Biological Evolution , Ectoderm/metabolism , Embryo, Mammalian/cytology , Embryo, Mammalian/metabolism , Gene Expression Regulation, Developmental , Transcription, Genetic , Trophoblasts/metabolism , Adaptor Proteins, Signal Transducing/metabolism , Animals , Blastocyst Inner Cell Mass/cytology , Blastocyst Inner Cell Mass/metabolism , Cattle , Cell Lineage , Cell Polarity , Ectoderm/cytology , Embryo, Mammalian/enzymology , Female , GATA3 Transcription Factor/metabolism , Hippo Signaling Pathway , Humans , Mice , Morula/cytology , Morula/enzymology , Morula/metabolism , Placenta/cytology , Placenta/metabolism , Pregnancy , Protein Kinase C/metabolism , Protein Serine-Threonine Kinases/metabolism , SOXB1 Transcription Factors/metabolism , Signal Transduction , Transcription Factors/metabolism , Trophoblasts/cytology , YAP-Signaling Proteins , Yolk Sac/cytology , Yolk Sac/metabolismABSTRACT
The reprogramming of human somatic cells to primed or naive induced pluripotent stem cells recapitulates the stages of early embryonic development1-6. The molecular mechanism that underpins these reprogramming processes remains largely unexplored, which impedes our understanding and limits rational improvements to reprogramming protocols. Here, to address these issues, we reconstruct molecular reprogramming trajectories of human dermal fibroblasts using single-cell transcriptomics. This revealed that reprogramming into primed and naive pluripotency follows diverging and distinct trajectories. Moreover, genome-wide analyses of accessible chromatin showed key changes in the regulatory elements of core pluripotency genes, and orchestrated global changes in chromatin accessibility over time. Integrated analysis of these datasets revealed a role for transcription factors associated with the trophectoderm lineage, and the existence of a subpopulation of cells that enter a trophectoderm-like state during reprogramming. Furthermore, this trophectoderm-like state could be captured, which enabled the derivation of induced trophoblast stem cells. Induced trophoblast stem cells are molecularly and functionally similar to trophoblast stem cells derived from human blastocysts or first-trimester placentas7. Our results provide a high-resolution roadmap for the transcription-factor-mediated reprogramming of human somatic cells, indicate a role for the trophectoderm-lineage-specific regulatory program during this process, and facilitate the direct reprogramming of somatic cells into induced trophoblast stem cells.
Subject(s)
Cellular Reprogramming/genetics , Gene Expression Regulation , Induced Pluripotent Stem Cells/cytology , Induced Pluripotent Stem Cells/metabolism , Trophoblasts/cytology , Trophoblasts/metabolism , Adult , Chromatin/genetics , Chromatin/metabolism , Ectoderm/cytology , Ectoderm/metabolism , Female , Fibroblasts/cytology , Fibroblasts/metabolism , Humans , Transcription, GeneticABSTRACT
We designed and characterized chitosan-caseinate fibers processed through wet spinning for biomedical applications such as drug delivery from knitted medical devices. Sodium caseinate was either incorporated directly into the chitosan dope or allowed to diffuse into the chitosan hydrogel from a coagulation bath containing sodium caseinate and sodium hydroxide (NaOH). The latter route, where caseinate was incorporated in the neutralization bath, produced fibers with better mechanical properties for textile applications than those formed by the chitosan-caseinate mixed collodion route. The latter processing method consists of enriching a pre-formed chitosan hydrogel with caseinate, preserving the structure of the semicrystalline hydrogel without drastically affecting interactions involved in the chitosan self-assembly. Thus, dried fibers, after coagulation in a NaOH/sodium caseinate aqueous bath, exhibited preserved ultimate mechanical properties. The crystallinity ratio of chitosan was not significantly impacted by the presence of caseinate. However, when caseinate was incorporated into the chitosan dope, chitosan-caseinate fibers exhibited lower ultimate mechanical properties, possibly due to a lower entanglement density in the amorphous phase of the chitosan matrix. A standpoint is to optimize the chitosan-caseinate composition ratio and processing route to find a good compromise between the preservation of fiber mechanical properties and appropriate fiber composition for potential application in drug release.
Subject(s)
Chitosan , Chitosan/chemistry , Caseins , Sodium Hydroxide , Water/chemistry , HydrogelsABSTRACT
The Chromosome-centric Human Proteome Project (C-HPP) aims at identifying the proteins as gene products encoded by the human genome, characterizing their isoforms and functions. The existence of products has now been confirmed for 93.2% of the genes at the protein level. The remaining mostly correspond to proteins of low abundance or difficult to access. Over the past years, we have significantly contributed to the identification of missing proteins in the human spermatozoa. We pursue our search in the reproductive sphere with a focus on early human embryonic development. Pluripotent cells, developing into the fetus, and trophoblast cells, giving rise to the placenta, emerge during the first weeks. This emergence is a focus of scientists working in the field of reproduction, placentation and regenerative medicine. Most knowledge has been harnessed by transcriptomic analysis. Interestingly, some genes are uniquely expressed in those cells, giving the opportunity to uncover new proteins that might play a crucial role in setting up the molecular events underlying early embryonic development. Here, we analyzed naive pluripotent and trophoblastic stem cells and discovered 4 new missing proteins, thus contributing to the C-HPP. The mass spectrometry proteomics data was deposited on ProteomeXchange under the data set identifier PXD035768.
Subject(s)
Proteome , Trophoblasts , Male , Humans , Proteome/genetics , Proteome/analysis , Mass Spectrometry , Chromosomes/chemistry , Cell LineABSTRACT
STUDY QUESTION: Which processes and transcription factors specify the first and second lineage segregation events during human preimplantation development? SUMMARY ANSWER: Differentiation into trophectoderm (TE) cells can be initiated independently of polarity; moreover, TEAD1 and YAP1 co-localize in (precursor) TE and primitive endoderm (PrE) cells, suggesting a role in both the first and the second lineage segregation events. WHAT IS KNOWN ALREADY: We know that polarity, YAP1/GATA3 signalling and phospholipase C signalling play a key role in TE initiation in compacted human embryos, however, little is known about the TEAD family of transcription factors that become activated by YAP1 and, especially, whether they play a role during epiblast (EPI) and PrE formation. In mouse embryos, polarized outer cells show nuclear TEAD4/YAP1 activity that upregulates Cdx2 and Gata3 expression while inner cells exclude YAP1 which upregulates Sox2 expression. The second lineage segregation event in mouse embryos is orchestrated by FGF4/FGFR2 signalling which could not be confirmed in human embryos; TEAD1/YAP1 signalling also plays a role during the establishment of mouse EPI cells. STUDY DESIGN, SIZE, DURATION: Based on morphology, we set up a development timeline of 188 human preimplantation embryos between Day 4 and 6 post-fertilization (dpf). The compaction process was divided into three subgroups: embryos at the start (C0), during (C1), and at the end (C2) of, compaction. Inner cells were identified as cells that were entirely separated from the perivitelline space and enclosed by cellular contacts on all sides. The blastulation process was divided into six subgroups, starting with early blastocysts with sickle-cell shaped outer cells (B0) and further on, blastocysts with a cavity (B1). Full blastocysts (B2) showed a visible ICM and outer cells referred to as TE. Further expanded blastocysts (B3) had accumulated fluid and started to expand due to TE cell proliferation and zona pellucida (ZP) thinning. The blastocysts then significantly expanded further (B4) and started to hatch out of the ZP (B5) until they were fully hatched (B6). PARTICIPANTS/MATERIALS, SETTING, METHODS: After informed consent and the expiration of the 5-year cryopreservation duration, 188 vitrified high quality eight-cell stage human embryos (3 dpf) were warmed and cultured until the required stages were reached. We also cultured 14 embryos that were created for research until the four- and eight-cell stage. The embryos were scored according to their developmental stage (C0-B6) displaying morphological key differences, rather than defining them according to their chronological age. They were fixed and immunostained for different combinations of cytoskeleton (F-actin), polarization (p-ERM), TE (GATA3), EPI (NANOG), PrE (GATA4 and SOX17), and members of the Hippo signalling pathway (YAP1, TEAD1 and TEAD4). We choose these markers based on previous observations in mouse embryos and single cell RNA-sequencing data of human embryos. After confocal imaging (LSM800, Zeiss), we analysed cell numbers within each lineage, different co-localization patterns and nuclear enrichment. MAIN RESULTS AND THE ROLE OF CHANCE: We found that in human preimplantation embryos compaction is a heterogeneous process that takes place between the eight-cell to the 16-cell stages. Inner and outer cells are established at the end of the compaction process (C2) when the embryos contain up to six inner cells. Full apical p-ERM polarity is present in all outer cells of compacted C2 embryos. Co-localization of p-ERM and F-actin increases steadily from 42.2% to 100% of the outer cells, between C2 and B1 stages, while p-ERM polarizes before F-actin (P < 0.00001). Next, we sought to determine which factors specify the first lineage segregation event. We found that 19.5% of the nuclei stain positive for YAP1 at the start of compaction (C0) which increases to 56.1% during compaction (C1). At the C2 stage, 84.6% of polarized outer cells display high levels of nuclear YAP1 while it is absent in 75% of non-polarized inner cells. In general, throughout the B0-B3 blastocyst stages, polarized outer/TE cells are mainly positive for YAP1 and non-polarized inner/ICM cells are negative for YAP1. From the C1 stage onwards, before polarity is established, the TE marker GATA3 is detectable in YAP1 positive cells (11.6%), indicating that differentiation into TE cells can be initiated independently of polarity. Co-localization of YAP1 and GATA3 increases steadily in outer/TE cells (21.8% in C2 up to 97.3% in B3). Transcription factor TEAD4 is ubiquitously present throughout preimplantation development from the compacted stage onwards (C2-B6). TEAD1 displays a distinct pattern that coincides with YAP1/GATA3 co-localization in the outer cells. Most outer/TE cells throughout the B0-B3 blastocyst stages are positive for TEAD1 and YAP1. However, TEAD1 proteins are also detected in most nuclei of the inner/ICM cells of the blastocysts from cavitation onwards, but at visibly lower levels as compared to that in TE cells. In the ICM of B3 blastocysts, we found one main population of cells with NANOG+/SOX17-/GATA4- nuclei (89.1%), but exceptionally we found NANOG+/SOX17+/GATA4+ cells (0.8%). In seven out of nine B3 blastocysts, nuclear NANOG was found in all the ICM cells, supporting the previously reported hypothesis that PrE cells arise from EPI cells. Finally, to determine which factors specify the second lineage segregation event, we co-stained for TEAD1, YAP1, and GATA4. We identified two main ICM cell populations in B4-6 blastocysts: the EPI (negative for the three markers, 46.5%) and the PrE (positive for the three markers, 28.1%) cells. We conclude that TEAD1 and YAP1 co-localise in (precursor) TE and PrE cells, indicating that TEAD1/YAP1 signalling plays a role in the first and the second lineage segregation events. LIMITATIONS, REASONS FOR CAUTION: In this descriptive study, we did not perform functional studies to investigate the role of TEAD1/YAP1 signalling during the first and second lineage segregation events. WIDER IMPLICATIONS OF THE FINDINGS: Our detailed roadmap on polarization, compaction, position and lineage segregation events during human preimplantation development paves the way for further functional studies. Understanding the gene regulatory networks and signalling pathways involved in early embryogenesis could ultimately provide insights into why embryonic development is sometimes impaired and facilitate the establishment of guidelines for good practice in the IVF lab. STUDY FUNDING/COMPETING INTERESTS: This work was financially supported by Wetenschappelijk Fonds Willy Gepts (WFWG) of the University Hospital UZ Brussel (WFWG142) and the Fonds Wetenschappelijk Onderzoek-Vlaanderen (FWO, G034514N). M.R. is doctoral fellow at the FWO. The authors have no conflicts of interest to declare. TRIAL REGISTRATION NUMBER: N/A.
Subject(s)
Actins , Blastocyst , Pregnancy , Female , Humans , Mice , Animals , Actins/metabolism , Blastocyst/metabolism , Embryonic Development/physiology , Transcription Factors/genetics , Embryo, Mammalian/metabolism , TEA Domain Transcription FactorsABSTRACT
Proteins ensure their biological functions by interacting with each other. Hence, characterising protein interactions is fundamental for our understanding of the cellular machinery, and for improving medicine and bioengineering. Over the past years, a large body of experimental data has been accumulated on who interacts with whom and in what manner. However, these data are highly heterogeneous and sometimes contradictory, noisy, and biased. Ab initio methods provide a means to a "blind" protein-protein interaction network reconstruction. Here, we report on a molecular cross-docking-based approach for the identification of protein partners. The docking algorithm uses a coarse-grained representation of the protein structures and treats them as rigid bodies. We applied the approach to a few hundred of proteins, in the unbound conformations, and we systematically investigated the influence of several key ingredients, such as the size and quality of the interfaces, and the scoring function. We achieved some significant improvement compared to previous works, and a very high discriminative power on some specific functional classes. We provide a readout of the contributions of shape and physico-chemical complementarity, interface matching, and specificity, in the predictions. In addition, we assessed the ability of the approach to account for protein surface multiple usages, and we compared it with a sequence-based deep learning method. This work may contribute to guiding the exploitation of the large amounts of protein structural models now available toward the discovery of unexpected partners and their complex structure characterisation.
Subject(s)
Binding Sites/physiology , Molecular Docking Simulation , Protein Conformation , Protein Interaction Maps/physiology , Proteins , Algorithms , Computational Biology , Databases, Protein , Protein Interaction Mapping , Proteins/chemistry , Proteins/metabolismABSTRACT
The multiple roles of iron in the body have been known for decades, particularly its involvement in iron overload diseases such as hemochromatosis. More recently, compelling evidence has emerged regarding the critical role of non-transferrin bound iron (NTBI), also known as catalytic iron, in the care of critically ill patients in intensive care units (ICUs). These trace amounts of iron constitute a small percentage of the serum iron, yet they are heavily implicated in the exacerbation of diseases, primarily by catalyzing the formation of reactive oxygen species, which promote oxidative stress. Additionally, catalytic iron activates macrophages and facilitates the growth of pathogens. This review aims to shed light on this underappreciated phenomenon and explore the various common sources of NTBI in ICU patients, which lead to transient iron dysregulation during acute phases of disease. Iron serves as the linchpin of a vicious cycle in many ICU pathologies that are often multifactorial. The clinical evidence showing its detrimental impact on patient outcomes will be outlined in the major ICU pathologies. Finally, different therapeutic strategies will be reviewed, including the targeting of proteins involved in iron metabolism, conventional chelation therapy, and the combination of renal replacement therapy with chelation therapy.
Subject(s)
Hemochromatosis , Iron Overload , Humans , Iron , Critical Illness/therapy , Transferrin/metabolismABSTRACT
Trophoblasts are specialized epithelial cells that perform critical functions during blastocyst implantation and mediate maternal-fetal communication during pregnancy. However, our understanding of human trophoblast biology remains limited since access to first-trimester placental tissue is scarce, especially between the first and fourth weeks of development. Moreover, animal models inadequately recapitulate unique aspects of human placental physiology. In the mouse system, the isolation of self-renewing trophoblast stem cells has provided a valuable in vitro model system of placental development, but the derivation of analogous human trophoblast stem cells (hTSCs) has remained elusive until recently. Building on a landmark study reporting the isolation of bona fide hTSCs from blastocysts and first-trimester placental tissues in 2018, several groups have developed methods to derive hTSCs from pluripotent and somatic cell sources. Here we review the biological and molecular properties that define authentic hTSCs, the trophoblast potential of distinct pluripotent states, and methods for inducing hTSCs in somatic cells by direct reprogramming. The generation of hTSCs from pluripotent and somatic cells presents exciting opportunities to elucidate the molecular mechanisms of human placental development and the etiology of pregnancy-related diseases.
Subject(s)
Placenta , Trophoblasts , Humans , Female , Mice , Pregnancy , Animals , Cell Differentiation , Stem Cells , PlacentationABSTRACT
Rationale: Brain injury induces systemic immunosuppression, increasing the risk of viral reactivations and altering neurological recovery. Objectives: To determine if systemic immune alterations and lung replication of herpesviridae are associated and can help predict outcomes after brain injury. Methods: We collected peripheral blood mononuclear cells in patients with severe brain injury requiring invasive mechanical ventilation. We systematically searched for respiratory herpes simplex virus (HSV) replications in tracheal aspirates. We also performed chromatin immunoprecipitation sequencing, RNA-sequencing, and in vitro functional assays of monocytes and CD4 T cells collected on Day 1 to characterize the immune response to severe acute brain injury. The primary outcome was the Glasgow Outcome Scale Extended at 6 months. Measurements and Main Results: In 344 patients with severe brain injury, lung HSV reactivations were observed in 39% of the 232 patients seropositive for HSV and independently associated with poor neurological recovery at 6 months (hazard ratio, 1.90; 95% confidence interval, 1.08-3.57). Weighted gene coexpression network analyses of the transcriptomic response of monocytes to brain injury defined a module of 721 genes, including PD-L1 and CD80, enriched for the binding DNA motif of the transcriptional factor Zeb2 and whose ontogenic analyses revealed decreased IFN-γ-mediated and antiviral response signaling pathways. This monocyte signature was preserved in a validation cohort and predicted the neurological outcome at 6 months with good accuracy (area under the curve, 0.786; 95% confidence interval, 0.593-0.978). Conclusions: A specific monocyte signature is associated with HSV reactivation and predicts poor recovery after brain injury. The alterations of the immune control of herpesviridae replication are understudied and represent a novel therapeutic target.
Subject(s)
Brain Injuries , Herpes Simplex , Herpesvirus 1, Human , Herpesvirus 1, Human/genetics , Humans , Leukocytes, Mononuclear , MonocytesABSTRACT
Recombinant Adeno-Associated Virus (rAAV) is considered as one of the most successful and widely used viral vectors for in vivo gene therapy. However, host immune responses to the vector and/or the transgene product remain a major hurdle to successful AAV gene transfer. In contrast to antivector adaptive immunity, the initiation of the innate immunity towards rAAV is still poorly understood but is directly dependent on the interaction between the viral vector and innate immune cells. Here, we used a quantitative transcriptomic-based approach to determine the activation of inflammatory and anti-viral pathways after rAAV8-based infection of monocyte-derived dendritic cells (moDCs) obtained from 12 healthy human donors. We have shown that rAAV8 particles are efficiently internalized, but that this uptake does not induce any detectable transcriptomic change in moDCs in contrast to an adenoviral infection, which upregulates anti-viral pathways. These findings suggest an immunologically favorable profile for rAAV8 serotype with regard to in vitro activation of moDC model. Transcriptomic analysis of rAAV-infected innate immune cells is a powerful method to determine the ability of the viral vector to be seen by these sensor cells, which remains of great importance to better understand the immunogenicity of rAAV vectors and to design immune-stealth products.
Subject(s)
Monocytes , Transcriptome , Humans , Genetic Vectors/genetics , Adaptive Immunity , Dendritic Cells , Dependovirus/geneticsABSTRACT
Natural polymers, as extracted from biomass, may exhibit large macromolecular polydispersity. We investigated the impact of low molar mass chitosan (LMW, DPw~115) on the properties of chitosan fibers obtained by wet spinning of chitosan solutions with bimodal distributions of molar masses. The fiber crystallinity index (CrI) was assessed by synchrotron X-ray diffraction and the mechanical properties were obtained by uniaxial tensile tests. The LMW chitosan showed to slightly increase the crystallinity index in films which were initially processed from the bimodal molar mass chitosan solutions, as a result of increased molecular mobility and possible crystal nucleating effects. Nevertheless, the CrI remained almost constant or slightly decreased in stretched fibers at increasing content of LMW chitosan in the bidisperse chitosan collodion. The ultimate mechanical properties of fibers were altered by the addition of LMW chitosan as a result of a decrease of entanglement density and chain orientation in the solid state. An increase of crystallinity might not be expected from LMW chitosan with a still relatively high degree of polymerization (DPw ≥ 115). Instead, different nucleation agents-either smaller molecules or nanoparticles-should be used to improve the mechanical properties of chitosan fibers for textile applications.
Subject(s)
Chitosan , Nanoparticles , Chitosan/chemistry , Molecular Weight , Polymers , TextilesABSTRACT
Background and Objectives: To test the long-term ability of human ovarian cortex cells to develop in unconventional culture conditions. Materials and Methods. Ovarian cortex cells from fetuses aged 23 to 39 weeks gestation were cultured for 90 days in hollow chitosan hydrogel micro-bioreactors and concurrently in traditional wells. Various cell-type counts were considered. Results: With intact follicles as a denominator, the percentage of growing intact follicles at Day 0 varied widely between ovaries (0 to 31.7%). This percentage tended to increase or stay relatively constant in bioreactor as in control cultures; it tended more toward an increase over time in bioreactor vs. control cultures. Modeled percentages showed differences (though not significant) in favor of bioreactor cultures (16.12% difference at D50 but only 0.12% difference at D90). With all follicles present as a denominator, the percentage of growing primary and secondary follicles at D0 varied widely between ovaries (0 to 29.3%). This percentage tended to increase over time in bioreactor cultures but to decrease in control cultures. Modeled percentages showed significant differences in favor of bioreactor cultures (8.9% difference at D50 and 11.1% difference at D90). At D50 and D90, there were only few and sparse apoptotic cells in bioreactor cultures vs. no apoptotic cells in control cultures. Conclusions: Over three months, bioreactor folliculogenesis outperformed slightly traditional culture. This is an interesting perspective for follicle preservation and long-term toxicological studies.
Subject(s)
Chitosan , Ovary , Female , Humans , Hydrogels , Tissue Culture Techniques/methods , BioreactorsABSTRACT
MOTIVATION: The understanding of the ever-increasing number of metagenomic sequences accumulating in our databases demands for approaches that rapidly 'explore' the content of multiple and/or large metagenomic datasets with respect to specific domain targets, avoiding full domain annotation and full assembly. RESULTS: S3A is a fast and accurate domain-targeted assembler designed for a rapid functional profiling. It is based on a novel construction and a fast traversal of the Overlap-Layout-Consensus graph, designed to reconstruct coding regions from domain annotated metagenomic sequence reads. S3A relies on high-quality domain annotation to efficiently assemble metagenomic sequences and on the design of a new confidence measure for a fast evaluation of overlapping reads. Its implementation is highly generic and can be applied to any arbitrary type of annotation. On simulated data, S3A achieves a level of accuracy similar to that of classical metagenomics assembly tools while permitting to conduct a faster and sensitive profiling on domains of interest. When studying a few dozens of functional domains-a typical scenario-S3A is up to an order of magnitude faster than general purpose metagenomic assemblers, thus enabling the analysis of a larger number of datasets in the same amount of time. S3A opens new avenues to the fast exploration of the rapidly increasing number of metagenomic datasets displaying an ever-increasing size. AVAILABILITY AND IMPLEMENTATION: S3A is available at http://www.lcqb.upmc.fr/S3A_ASSEMBLER/. SUPPLEMENTARY INFORMATION: Supplementary data are available at Bioinformatics online.
Subject(s)
Algorithms , Metagenomics , Metagenome , Sequence Analysis, DNA , SoftwareABSTRACT
The leukemia inhibitory factor (LIF)/glycoprotein (GP) 130/Janus kinase (JAK)/signal transducer and activator of transcription (STAT) 3 signaling pathway is a hallmark of naïve pluripotency in mice. In this review, we discuss the role of the LIF/GP130/JAK/STAT3 pathway in supporting the naïve-state pluripotency in human, monkey, and pig pluripotent stem cells (PSCs). We highlight the role of LIF/GP130/JAK/STAT3 signaling in reprogramming conventional human and monkey PSCs to naïve-like pluripotency. We analyze published single-cell RNA sequencing datasets of human and monkey embryos and note that the main components of the GP130/JAK/STAT3 pathway are expressed in pluripotent cells at preimplantation stages. We conclude that there is a growing body of evidence supporting the involvement of GP130/JAK/STAT3 in the regulation of naïve pluripotency in non-rodent species including humans, monkeys, and pigs.
Subject(s)
Cell Differentiation , Cytokine Receptor gp130/metabolism , Pluripotent Stem Cells/metabolism , Signal Transduction , Animals , Haplorhini , Humans , Janus Kinases/metabolism , Pluripotent Stem Cells/cytology , STAT Transcription Factors/metabolism , SwineABSTRACT
Fe3O4 nanoparticles coated with chito-oligosaccharides (COS) were prepared in situ by a simple co-precipitation method through a mixing of iron ions (Fe3+ and Fe2+) and COS aqueous solutions followed by precipitation with ammonia. The impact of COS with different degree of polymerization (DP 10, 24 and 45) and degree of N-acetylation (DA) â¼ 24% and 50% (exhibiting high solubility) on the synthesis and physical properties of the coated magnetic nanoparticles was evaluated. Several advantages were found when the magnetic nanoparticles were prepared in the presence of the studied COS, such as: preparation of functionalized magnetic nanoparticles with narrower size distributions and, consequently, higher saturation magnetization (an increase of up to 22%); and an expressive increasing in the concentration of COS-coated magnetic nanoparticles (up to twice) in the cell viability test in comparison with pure Fe3O4 nanoparticles. Furthermore, among the analyzed samples, the magnetic nanoparticles coated by COS with DA â¼ 50% present a higher cytocompatibility. Our results allow envisioning various biomedical applications, valorizing the use of coated-magnetic nanoparticles for magnetic-field assisted drug delivery, enzyme or cell immobilization, or as a marker for specific cell tracking, among others.
Subject(s)
Chitosan/chemistry , Magnetite Nanoparticles/chemistry , Oligosaccharides/pharmacology , Acetylation , Animals , Cell Line , Cell Survival/drug effects , Dogs , Drug Delivery Systems , Oligosaccharides/chemistry , Particle Size , SolubilityABSTRACT
AIMS: The Brugada syndrome (BrS) is an inherited cardiac disorder predisposing to ventricular arrhythmias. Despite considerable efforts, its genetic basis and cellular mechanisms remain largely unknown. The objective of this study was to identify a new susceptibility gene for BrS through familial investigation. METHODS AND RESULTS: Whole-exome sequencing performed in a three-generation pedigree with five affected members allowed the identification of one rare non-synonymous substitution (p.R211H) in RRAD, the gene encoding the RAD GTPase, carried by all affected members of the family. Three additional rare missense variants were found in 3/186 unrelated index cases. We detected higher levels of RRAD transcripts in subepicardium than in subendocardium in human heart, and in the right ventricle outflow tract compared to the other cardiac compartments in mice. The p.R211H variant was then subjected to electrophysiological and structural investigations in human cardiomyocytes derived from induced pluripotent stem cells (iPSC-CMs). Cardiomyocytes derived from induced pluripotent stem cells from two affected family members exhibited reduced action potential upstroke velocity, prolonged action potentials and increased incidence of early afterdepolarizations, with decreased Na+ peak current amplitude and increased Na+ persistent current amplitude, as well as abnormal distribution of actin and less focal adhesions, compared with intra-familial control iPSC-CMs Insertion of p.R211H-RRAD variant in control iPSCs by genome editing confirmed these results. In addition, iPSC-CMs from affected patients exhibited a decreased L-type Ca2+ current amplitude. CONCLUSION: This study identified a potential new BrS-susceptibility gene, RRAD. Cardiomyocytes derived from induced pluripotent stem cells expressing RRAD variant recapitulated single-cell electrophysiological features of BrS, including altered Na+ current, as well as cytoskeleton disturbances.
Subject(s)
Brugada Syndrome/genetics , Mutation, Missense , Myocytes, Cardiac/pathology , ras Proteins/genetics , Action Potentials/genetics , Adult , Brugada Syndrome/pathology , Brugada Syndrome/physiopathology , Cytoskeleton/genetics , Cytoskeleton/pathology , Female , Genetic Markers , Genetic Predisposition to Disease , Humans , Male , Myocytes, Cardiac/physiologyABSTRACT
Chitosan-caseinate nanoparticles were synthesized by polyelectrolyte complex (PEC) formation. Caseinate is an anionic micellar nanocolloid in aqueous solutions, which association with the polycationic chitosan yielded polyelectrolyte complexes with caseinate cores surrounded by a chitosan corona. The pre-structuration of caseinate micelles facilitates the formation of natural polyelectrolyte nanoparticles with good stability and sizes around 200 nm. Such natural nanoparticles can be loaded with molecules for applications in drug-controlled release. In the nanoparticles processing, parameters such as the chitosan degree of acetylation (DA) and molecular weight, order of addition of the polyelectrolytes chitosan (polycation) and caseinate (polyanion), and added weight ratio of polycation:polyanion were varied, which were shown to influence the structure of the polyelectrolyte association, the nanoparticle size and zeta potential. Attenuated total reflection-Fourier transform infrared (ATR-FTIR) analyses revealed the chemical structure of hydrogel colloidal systems consisting of nanoparticles that contain chitosan and caseinate. Transmission electron microscopy (TEM) allowed further characterization of the spherical morphology of the nanoparticles. Furtherly, insulin was chosen as a model drug to study the application of the nanoparticles as a safe biodegradable nanocarrier system for drug-controlled release. An insulin entrapment efficiency of 75% was achieved in the chitosan-caseinate nanoparticles.
Subject(s)
Chitosan/chemistry , Drug Liberation , Hydrogels/pharmacology , Nanoparticles/chemistry , Caseins/chemistry , Chitosan/pharmacology , Colloids/chemistry , Colloids/pharmacology , Humans , Hydrogels/chemistry , Hydrogen-Ion Concentration , Particle Size , Polyelectrolytes/chemistryABSTRACT
Chitosans, a family of ß-(1,4)-linked, partially N-acetylated polyglucosamines, are considered to be among the most versatile and most promising functional biopolymers. Chemical analysis and bioactivity studies revealed that the functionalities of chitosans strongly depend on the polymers' degree of polymerization and fraction of acetylation. More recently, the pattern of acetylation ( PA) has been proposed as another important parameter to influence functionalities of chitosans. We therefore carried out studies on the acetylation pattern of chitosan polymers produced by three recombinant fungal chitin deacetylases (CDAs) originating from different species, namely, Podospora anserina, Puccinia graminis f. sp. tritici, and Pestalotiopsis sp. We analyzed the chitosans by 1H NMR, 13C NMR, and SEC-MALS and established new methods for PA analysis based on enzymatic mass spectrometric fingerprinting and in silico simulations. Our studies strongly indicate that the different CDAs indeed produce chitosans with different PA. Finally, Zimm plot analysis revealed that enzymatically treated polymers differ with respect to their second virial coefficient and radius of gyration indicating an influence of PA on polymer-solvent interactions.