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Nature Apr 2023Newly made mRNAs are processed and packaged into mature ribonucleoprotein complexes (mRNPs) and are recognized by the essential transcription-export complex (TREX) for...
Newly made mRNAs are processed and packaged into mature ribonucleoprotein complexes (mRNPs) and are recognized by the essential transcription-export complex (TREX) for nuclear export. However, the mechanisms of mRNP recognition and three-dimensional mRNP organization are poorly understood. Here we report cryo-electron microscopy and tomography structures of reconstituted and endogenous human mRNPs bound to the 2-MDa TREX complex. We show that mRNPs are recognized through multivalent interactions between the TREX subunit ALYREF and mRNP-bound exon junction complexes. Exon junction complexes can multimerize through ALYREF, which suggests a mechanism for mRNP organization. Endogenous mRNPs form compact globules that are coated by multiple TREX complexes. These results reveal how TREX may simultaneously recognize, compact and protect mRNAs to promote their packaging for nuclear export. The organization of mRNP globules provides a framework to understand how mRNP architecture facilitates mRNA biogenesis and export.
Topics: Humans; Active Transport, Cell Nucleus; Cell Nucleus; Cryoelectron Microscopy; RNA, Messenger; Transcription, Genetic; Exons
PubMed: 37020021
DOI: 10.1038/s41586-023-05904-0 -
The New England Journal of Medicine Mar 2017Sickle cell disease results from a homozygous missense mutation in the β-globin gene that causes polymerization of hemoglobin S. Gene therapy for patients with this...
Sickle cell disease results from a homozygous missense mutation in the β-globin gene that causes polymerization of hemoglobin S. Gene therapy for patients with this disorder is complicated by the complex cellular abnormalities and challenges in achieving effective, persistent inhibition of polymerization of hemoglobin S. We describe our first patient treated with lentiviral vector-mediated addition of an antisickling β-globin gene into autologous hematopoietic stem cells. Adverse events were consistent with busulfan conditioning. Fifteen months after treatment, the level of therapeutic antisickling β-globin remained high (approximately 50% of β-like-globin chains) without recurrence of sickle crises and with correction of the biologic hallmarks of the disease. (Funded by Bluebird Bio and others; HGB-205 ClinicalTrials.gov number, NCT02151526 .).
Topics: Adolescent; Anemia, Sickle Cell; Clinical Trials as Topic; Gene Expression; Genetic Therapy; Genetic Vectors; Hemoglobin A; Humans; Lentivirus; Male; beta-Globins
PubMed: 28249145
DOI: 10.1056/NEJMoa1609677 -
Cell Death & Disease Jan 2023Milk fat globule epidermal growth factor 8 (MFG-E8) participates in a range of cellular processes, including reducing apoptosis and oxidative stress. However, its...
Milk fat globule epidermal growth factor 8 (MFG-E8) participates in a range of cellular processes, including reducing apoptosis and oxidative stress. However, its protective activity against cigarette smoke-induced ferroptosis in the pathogenesis of the chronic obstructive pulmonary disease (COPD) and the modulation of MFG-E8 remain unclear. Here, we showed that cigarette smoke diminished MFG-E8 protein levels but had no significant effect on its mRNA levels in lung tissues of humans and mice and in two human bronchial epithelial cell lines. MFG-E8 could attenuate ferroptosis induced by cigarette smoke extract (CSE) in vivo and in vitro. We identified ubiquitin-specific protease 14 (USP14) as a deubiquitinase of MFG-E8 in human bronchial epithelial cells. USP14 interacted with, deubiquitinated and stabilized MFG-E8. Furthermore, USP14 inhibited CSE-induced MFG-E8 proteasomal degradation. USP14 expression downregulated by CSE decreased MFG-E8 abundance and further reduced the antiferroptotic effect of MFG-E8. These findings suggest that USP14 is an essential regulator of MFG-E8 through the proteasomal pathway and that the USP14/MFG-E8 axis plays a critical role in regulating CSE-induced ferroptosis of bronchial epithelial cells.
Topics: Humans; Animals; Mice; Ferroptosis; Factor VIII; Cigarette Smoking; Epithelial Cells; Deubiquitinating Enzymes; Ubiquitin Thiolesterase
PubMed: 36596780
DOI: 10.1038/s41419-022-05455-8 -
Frontiers in Nutrition 2020Cow's milk and dairy products derived from this complex food source have long been proposed as beneficial to human health, yet underlying clinical evidence of direct... (Review)
Review
Cow's milk and dairy products derived from this complex food source have long been proposed as beneficial to human health, yet underlying clinical evidence of direct benefit continues to raise controversy. Limited evidence supports positive cardiometabolic effects of a number of dairy macro- and micronutrient components including whey protein and casein, unsaturated fats, milk fat globule membrane (MFGM) and polar phospholipids, vitamin D and calcium, in addition to non-bovine components including bacterial and yeast probiotics. More controversial remain lipid components fats, including vaccenic acid, palmitoleic acid, and conjugated linoleic acid (CLA), plus medium-chain and odd-chain dairy fats. New evidence is rapidly identifying multiple pathways by which these dairy nutrients may effect health. Processing, including fermentation and homogenization, may also have positive effects. Conversely, the high saturated fat content of dairy has long raised concern, aligned with international guidelines to minimize dietary intake of animal-origin saturated fatty acids (SFA) to achieve better cardiometabolic health. However, led in part by observational studies and meta-analyses showing dairy to have no or even an inverse association with cardiometabolic health, evidence from randomized controlled trials (RCTs) has been scrutinized over the last 5 years, and focus on low-fat dairy has been challenged. Recent evidence supports the hypothesis that adverse effects of SFAs on metabolic health may be ameliorated when these fats are consumed within a complex matrix such as milk, cheese or yogurt, and that dairy food categories may influence outcomes as much as total fat content. For example, yogurt and high-fat, high-SFA cheese have a negative association with risk of type 2 diabetes (T2D) in many, not all, published trials. However, large sample dairy RCTs of long duration with CVD or T2D incidence as primary endpoints are lacking. This is a clear research gap, with these clinical studies required if a causative link between dairy and improved cardiometabolic health is to be confirmed and in turn promoted through dietary guidelines. Current advisories from national guidance groups such as American Heart Association (AHA) and European Society of Cardiology (ESC) continue to promote consumption of low-fat dairy products, whilst liquid milk and yogurt remain part of nutrition guidelines from joint American Diabetes Association (ADA)/European Association for Study of Diabetes (EASD) reports, and as part of a "no-one-size-fits-all" answer to diet and T2D by the ADA in their most recent 2019 Consensus Report.
PubMed: 33364249
DOI: 10.3389/fnut.2020.574725 -
Microbiology Spectrum Dec 2022The folding and dynamics of three-dimensional (3D) genome organization are fundamental for eukaryotes executing genome functions but have been largely unexplored in...
The folding and dynamics of three-dimensional (3D) genome organization are fundamental for eukaryotes executing genome functions but have been largely unexplored in nonmodel fungi. Using high-throughput sequencing coupled with chromosome conformation capture (Hi-C) data, we generated two chromosome-level assemblies for Puccinia striiformis f. sp. , a fungus causing stripe rust disease on wheat, for studying 3D genome architectures of plant pathogenic fungi. The chromatin organization of the fungus followed a combination of the fractal globule model and the equilibrium globule model. Surprisingly, chromosome compartmentalization was not detected. Dynamics of 3D genome organization during two developmental stages of P. striiformis f. sp. indicated that regulation of gene activities might be independent of the changes of genome organization. In addition, chromatin conformation conservation was found to be independent of genome sequence synteny conservation among different fungi. These results highlighted the distinct folding principles of fungal 3D genomes. Our findings should be an important step toward a holistic understanding of the principles and functions of genome architecture across different eukaryotic kingdoms. Previously, our understanding of 3D genome architecture has mainly come from model mammals, insects, and plants. However, the organization and regulatory functions of 3D genomes in fungi are largely unknown. In this study, we comprehensively investigated P. striiformis f. sp. , a plant fungal pathogen, and revealed distinct features of the 3D genome, comparing it with the universal folding feature of 3D genomes in higher eukaryotic organisms. We further suggested that there might be distinct regulatory mechanisms of gene expression that are independent of chromatin organization changes during the developmental stages of this rust fungus. Moreover, we showed that the evolutionary pattern of 3D genomes in this fungus is also different from the cases in mammalian genomes. In addition, the genome assembly pipeline and the generated two chromosome-level genomes will be valuable resources. These results highlighted the unexplored distinct features of 3D genome organization in fungi. Therefore, our study provided complementary knowledge to holistically understand the organization and functions of 3D genomes across different eukaryotes.
Topics: Basidiomycota; Genome, Fungal; Synteny; Plant Diseases
PubMed: 36250889
DOI: 10.1128/spectrum.02608-22 -
Journal of Dairy Science Sep 2020Human colostrum is the first milk secreted by the mother after birth and constitutes the ideal food for the newborn, because its chemical composition, rich in...
Human colostrum is the first milk secreted by the mother after birth and constitutes the ideal food for the newborn, because its chemical composition, rich in immunoglobulins, antimicrobial peptides, growth factors, bioactive lipids, and other important molecules, is perfectly adapted to the metabolic, digestive, and immunological immaturity of the newborn. An incomplete gestational period can affect the maturity of the mammary gland and its ability to secrete milk with the proper composition for the newborn's condition. Previous studies indicate that the mammary gland modulates the profiles of bioactive lipids present in the different phases of lactation from colostrum to mature milk. Given the key role played by the polar lipids (PL) (phospho- and sphingolipids) of the milk fat globule membrane (MFGM) in the immune system and cognitive development of the newborn, it is crucial to analyze whether the content and distribution of the PL are affected by gestation period. Therefore, this study aimed to determine the milk fat globule (MFG) and MFGM lipid compositions of human colostrum samples from 20 healthy preterm and full-term mothers. Lipid characterization using chromatographic techniques (gas chromatograph mass spectrometry and HPLC-evaporative light-scattering detection) revealed differences related to length of gestation in the profiles of lipid classes and fatty acid and triacylglyceride contents of colostrum. This comparative analysis leads to noteworthy outcomes about the changing roles of the PL, considering the preterm or full-term condition. We found a lack of correlation of some PL (such as phosphatidylcholine, phosphatidylinositol, and phosphatidylserine) with the delivery term; these could be denoted as structural category lipids. However, sphingomyelin and phosphatidyl-ethanolamine exhibited trends to decrease in full-term colostrum, indicating that in the final stage of pregnancy specific accretion of some PL occurs, which should be denoted as a nutritional redistribution.
Topics: Chromatography, High Pressure Liquid; Colostrum; Fatty Acids; Female; Gestational Age; Glycolipids; Glycoproteins; Humans; Infant, Newborn; Lactation; Lipid Droplets; Milk, Human; Phosphatidylcholines; Phosphatidylethanolamines; Pregnancy; Sphingomyelins
PubMed: 32622597
DOI: 10.3168/jds.2020-18428 -
The Journal of Cell Biology Jan 2024Eukaryotic chromosomes compact during mitosis into elongated cylinders-and not the spherical globules expected of self-attracting long flexible polymers. This process is...
Eukaryotic chromosomes compact during mitosis into elongated cylinders-and not the spherical globules expected of self-attracting long flexible polymers. This process is mainly driven by condensin-like proteins. Here, we present Brownian-dynamic simulations involving two types of such proteins with different activities. One, which we refer to as looping condensins, anchors long-lived chromatin loops to create bottlebrush structures. The second, referred to as bridging condensins, forms multivalent bridges between distant parts of these loops. We show that binding of bridging condensins leads to the formation of shorter and stiffer mitotic-like cylinders without requiring any additional energy input. These cylinders have several features matching experimental observations. For instance, the axial condensin backbone breaks up into clusters as found by microscopy, and cylinder elasticity qualitatively matches that seen in chromosome pulling experiments. Additionally, simulating global condensin depletion or local faulty condensin loading gives phenotypes seen experimentally and points to a mechanistic basis for the structure of common fragile sites in mitotic chromosomes.
Topics: Adenosine Triphosphatases; Chromatin; Chromosomes; DNA-Binding Proteins; Mitosis; Multiprotein Complexes
PubMed: 37976091
DOI: 10.1083/jcb.202209113 -
Frontiers in Immunology 2017Inefficient and abnormal clearance of apoptotic cells (efferocytosis) contributes to systemic autoimmune disease in humans and mice, and inefficient chromosomal DNA... (Review)
Review
Inefficient and abnormal clearance of apoptotic cells (efferocytosis) contributes to systemic autoimmune disease in humans and mice, and inefficient chromosomal DNA degradation by DNAse II leads to systemic polyarthritis and a cytokine storm. By contrast, efficient clearance allows immune homeostasis, generally leads to a non-inflammatory state for both macrophages and dendritic cells (DCs), and contributes to maintenance of peripheral tolerance. As many as 3 × 10 cells undergo apoptosis every hour in our bodies, and one of the primary "eat me" signals expressed by apoptotic cells is phosphatidylserine (PtdSer). Apoptotic cells themselves are major contributors to the "anti-inflammatory" nature of the engulfment process, some by secreting thrombospondin-1 (TSP-1) or adenosine monophosphate and possibly other immune modulating "calm-down" signals that interact with macrophages and DCs. Apoptotic cells also produce "find me" and "tolerate me" signals to attract and immune modulate macrophages and DCs that express specific receptors for some of these signals. Neither macrophages nor DCs are uniform, and each cell type may variably express membrane proteins that function as receptors for PtdSer or for opsonins like complement or opsonins that bind to PtdSer, such as protein S and growth arrest-specific 6. Macrophages and DCs also express scavenger receptors, CD36, and integrins that function bridging molecules such as TSP-1 or milk fat globule-EGF factor 8 protein and that differentially engage in various multi-ligand interactions between apoptotic cells and phagocytes. In this review, we describe the anti-inflammatory and pro-homeostatic nature of apoptotic cell interaction with the immune system. We do not review some forms of immunogenic cell death. We summarize the known apoptotic cell signaling events in macrophages and DCs that are related to toll-like receptors, nuclear factor kappa B, inflammasome, the lipid-activated nuclear receptors, Tyro3, Axl, and Mertk receptors, as well as induction of signal transducer and activator of transcription 1 and suppressor of cytokine signaling that lead to immune system silencing and DC tolerance. These properties of apoptotic cells are the mechanisms that enable their successful use as therapeutic modalities in mice and humans in various autoimmune diseases, organ transplantation, graft-versus-host disease, and sepsis.
PubMed: 29118755
DOI: 10.3389/fimmu.2017.01356 -
Journal of Nippon Medical School =... 2012Sepsis is a devastating and complex syndrome and continues to be a major cause of morbidity and mortality among critically ill patients at the surgical intensive care... (Review)
Review
Sepsis is a devastating and complex syndrome and continues to be a major cause of morbidity and mortality among critically ill patients at the surgical intensive care unit setting in the United States. The occurrence of sepsis and septic shock has increased significantly over the past two decades. Despite of highly dedicated basic research and numerous clinical trials, remarkable progress has not been made in the development of novel and effective therapeutics. The sepsis-induced physiologic derangements are due largely to the host responses to the invading microorganism in contrast to the direct effects of the microorganism itself. Sepsis, the systemic inflammatory response to infection, is marked by dysregulated production of pro-inflammatory cytokines. Although pro-inflammatory cytokine production is normally indispensable to protect against pathogens and promote tissue repair, the dysregulated and prolonged production of these cytokines can trigger a systemic inflammatory cascade mediated by chemokines, vasoactive amines, the complement and coagulation system, and reactive oxygen species (ROS), amongst others. These mediators collectively lead to multiple organ failure, and ultimately to death. In this regard, the role of inflammation in the pathophysiology of sepsis, although still incompletely understood, is clearly critical. Recent findings resulting from vigorous investigations have contributed to delineate various novel directions of sepsis therapeutics. Among these, this review article is focused on new promising mechanisms and concepts that could have a key role in anti-inflammatory strategies against sepsis, including 1) "inflammasome": a multiprotein complex that activates caspase-1; 2) "the cholinergic anti-inflammatory pathway": the efferent arm of the vagus nerve-mediated, brain-to-immune reflex; 3) "stem cells": unspecialized and undifferentiated precursor cells with the capacity for self-renewal and potential to change into cells of multiple lineages; 4) "milk fat globule-EGF factor VIII (MFG-E8)": a bridging molecule between apoptotic cells and phagocytes, which promotes phagocytosis of apoptotic cells.
Topics: Animals; Caspase 1; Humans; Inflammasomes; Inflammation; Molecular Targeted Therapy; Sepsis; Stem Cells
PubMed: 22398786
DOI: 10.1272/jnms.79.4 -
Pediatric Nephrology (Berlin, Germany) Mar 2023Accurate diagnosis of primary hyperoxaluria (PH) has important therapeutic consequences. Since biochemical assessment can be unreliable, genetic testing is a crucial... (Review)
Review
Accurate diagnosis of primary hyperoxaluria (PH) has important therapeutic consequences. Since biochemical assessment can be unreliable, genetic testing is a crucial diagnostic tool for patients with PH to define the disease type. Patients with PH type 1 (PH1) have a worse prognosis than those with other PH types, despite the same extent of oxalate excretion. The relation between genotype and clinical phenotype in PH1 is extremely heterogeneous with respect to age of first symptoms and development of kidney failure. Some mutations are significantly linked to pyridoxine-sensitivity in PH1, such as homozygosity for p.G170R and p.F152I combined with a common polymorphism. Although patients with these mutations display on average better outcomes, they may also present with CKD stage 5 in infancy. In vitro studies suggest pyridoxine-sensitivity for some other mutations, but confirmatory clinical data are lacking (p.G47R, p.G161R, p.I56N/major allele) or scarce (p.I244T). These studies also suggest that other vitamin B6 derivatives than pyridoxine may be more effective and should be a focus for clinical testing. PH patients displaying the same mutation, even within one family, may have completely different clinical outcomes. This discordance may be caused by environmental or genetic factors that are unrelated to the effect of the causative mutation(s). No relation between genotype and clinical or biochemical phenotypes have been found so far in PH types 2 and 3. This manuscript reviews the current knowledge on the genetic background of the three types of primary hyperoxaluria and its impact on clinical management, including prenatal diagnosis.
Topics: Humans; Hyperoxaluria, Primary; Pyridoxine; Mutation; Genetic Testing; Genotype; Transaminases
PubMed: 35695965
DOI: 10.1007/s00467-022-05613-2