Biology subjects

Liu, L.

Publications and source records attributed to Liu, L..

At least 595 records · Page 33Linked to original sources

bioRxiv2022

Can neurogenesis act as a neural regularizer?

New neurons are continuously generated in the subgranular zone of the dentate gyrus throughout adulthood. These new neurons gradually integrate into hippocampal circuits, forming new naive synapses. Viewed from this perspective, these new neurons may represent a significant source of wiring noise in hippocampal networks. In machine learning, such noise injection is commonly used as a regularization technique. Regularization techniques help prevent overfitting training data, and allow models to generalize learning to new, unseen data. Using a computational modeling approach, here we ask whether a neurogenesis-like process similarly acts as a regularizer, facilitating generalization in a category learning task. In a convolutional neural network (CNN) trained on the CIFAR-10 object recognition dataset, we modeled neurogenesis as a replacement/turnover mechanism, where weights for a randomly chosen small subset of neurons in a chosen hidden layer were re-initialized to new values as the model learned to categorize 10 different classes of objects. We found that neurogenesis enhanced generalization on unseen test data compared to networks with no neurogenesis. Moreover, neurogenic networks either outperformed or performed similarly to networks with conventional noise injection (i.e., dropout, weight decay, and neural noise). These results suggest that neurogenesis can enhance generalization in hippocampal learning through noise-injection, expanding on the roles that neurogenesis may have in cognition. Author SummaryIn deep neural networks, various forms of noise injection are used as regularization techniques to prevent overfitting and promote generalization on unseen test data. Here, we were interested in whether adult neurogenesis- the lifelong production of new neurons in the hippocampus- might similarly function as a regularizer in the brain. We explored this question computationally, assessing whether implementing a neurogenesis-like process in a hidden layer within a convolutional neural network trained in a category learning task would prevent overfitting and promote generalization. We found that neurogenesis regularization was as least as effective as, or more effective than, conventional regularizers (i.e., dropout, weight decay and neural noise) in improving model performance. These results suggest that optimal levels of hippocampal neurogenesis may improve memory-guided decision making by preventing overfitting, thereby promoting the formation of more generalized memories that can be applied in a broader range of circumstances. We outline how these predictions may be evaluated behaviorally in rodents with altered hippocampal neurogenesis.

neuroscience↗

bioRxiv2022

Plant N-glycan breakdown by human gut Bacteroides

The major nutrients available to the human colonic microbiota are complex glycans derived from the diet. To degrade this highly variable mix of sugar structures, gut microbes have acquired a huge array of different carbohydrate-active enzymes (CAZymes), predominantly glycoside hydrolases, many of which have specificities that can be exploited for a range of different applications. Plant N-glycans are prevalent on proteins produced by plants and thus components of the diet, but the breakdown of these complex molecules by the gut microbiota has not been explored. Plant N-glycans are also well characterised allergens in pollen and some plant-based foods, and when plants are used in heterologous protein production for medical applications, the N-glycans present can pose a risk to therapeutic function and stability. Here we use a novel genome association approach for enzyme discovery to identify a breakdown pathway for plant complex N-glycans encoded by a gut Bacteroides species and biochemically characterise five CAZymes involved, including structures of the PNGase and GH92 -mannosidase. These enzymes provide a toolbox for the modification of plant N-glycans for a range of potential applications. Furthermore, the keystone PNGase also has activity against insect-type N-glycans, which we discuss from the perspective of insects as a nutrient source.

biochemistry↗

bioRxiv2022

Transient Water Wires Mediate Selective Proton Conduction in Designed Channel Proteins

Summary paragraphSelective proton transport through proteins is essential for forming and utilizing proton gradients in cells. Protons are conducted along hydrogen-bonded "wires" of water molecules and polar sidechains, which, somewhat surprisingly, are often interrupted by dry apolar stretches in the conduction pathways inferred from static protein structures. We hypothesize that protons are conducted through such dry spots by forming transient water wires, often highly correlated with the presence of the excess proton itself in the water wire. To test this hypothesis, we used molecular dynamics simulations to design transmembrane channels with stable water pockets interspersed by apolar segments capable of forming flickering water wires. The minimalist designed channels conduct protons at rates similar to viral proton channels, and they are at least 106-fold more selective for H+ over Na+. These studies inform mechanisms of biological proton conduction and principles for engineering proton-conductive materials.

biophysics↗

bioRxiv2022

T cells induce interferon-responsive oligodendrocytes during white matter aging

A hallmark of nervous system aging is a decline of white matter volume and function, but the underlying mechanisms leading to white matter pathology are unknown. Here, we found age-related alterations of oligodendrocytes with a reduction of total oligodendrocyte density in the aging murine white matter. Using single-cell RNA sequencing, we identify interferon-responsive oligodendrocytes, which localize in proximity of CD8+ T cells in the aging white matter. Absence of functional lymphocytes decreased oligodendrocyte reactivity and rescued oligodendrocyte loss, while T-cell checkpoint inhibition worsened the aging affect. In summary, we provide evidence that T cells induced interferon-responsive oligodendrocytes are important modifiers of white matter aging.

neuroscience↗

bioRxiv2022

Serum profiles of metabolomic and GDF-15 differentiate idiopathic pulmonary fibrosis from other interstital lung diseases: a preliminary study

Objective1.Explore the differential metabolites and metabolic pathways between different interstitial lung disease (ILD) and healthy controls, so as to find out new biomarkers and metabolic pathways of ILD and provide new biological targets for IPF diagnosis and treatment.2.Detect the levels of serum related fibrosis and metabolic indexes of ILD, explore the relationship between these indexes and the types and general parameters of ILD diseases, and focus on GDF-15 on the basis of metabonomics, explore new metabolic pathways related to ILD, and further expound the pathogenesis of idiopathic pulmonary fibrosis. Method1.According to the inclusion criteria and exclusion criteria, the ILD patients admitted to our hospital from January 1, 2021 to January 1, 2022 were signed with informed consent, and all of them had clear multidisciplinary diagnosis. At the same time, the physical examination in the health management center of our hospital was selected as the healthy control group. General clinical data of ILD patients and healthy controls were collected, including gender, age, onset, clinical manifestations, clinical biochemistry, lung function and other related data. Collect patients peripheral venous blood, keep serum samples, and analyze the serum of ILD patients and healthy controls by liquid chromatography-mass spectrometry (LC-MS) to obtain differential metabolites, metabolic maps and related data. According to the diagnosis, the patients were divided into Idiopathic pulmonary fibrosis (IPF), connective tissue disease-associated interstitial lung disease (CTD-ILD), other interstitial lung disease (ILD) patients and healthy control group. R statistical software was used to observe whether there are differential metabolites in IPF group and healthy control group, CTD-ILD group and healthy control group, other ILD groups and healthy control group, IPF group and CTD-ILD group, IPF group and other ILD groups, CTD-ILD group and other ILD groups by using positive and negative ion flow charts and score charts of orthogonal partial least squares-discriminant analysis. And the potential biomarkers were found through the S-plot diagram of OPLS-DA and the variable weight value VIP>1. ROC curve analysis of differential metabolites was carried out by SPSS21.0 software to analyze the value of differential diagnosis and find out new biomarkers with differential diagnosis significance. Based on KEGG database, the metabolic pathway enrichment analysis of differential metabolites was carried out to find out the main metabolic pathways. 2.Serum levels of type I collagen, KL-6, IL-1{beta}, TNF-, IGF-1 and GDF-15 were detected by Enzyme linked immunosorbent assay (ELISA) in all patients and healthy controls. Using SPSS21.0 statistical software and R statistical software, using T-test, variance analysis or nonparametric test method, according to different diagnoses (IPF/CTD-ILD/ other ILD/ healthy control group, ILD/ healthy control group, IPF/ other), the data were analyzed and compared in subgroups. Pearson correlation analysis was used to analyze the correlation between serum biomarkers and other factors such as lung function, metabolomics and so on. ROC curve was used to analyze the diagnostic efficiency of each index, and the best critical value, sensitivity and specificity were found out. Results1.Analysis of general clinical data and clinical indicators: 26 cases of IPF, 21cases of CTD-ILD, 23 cases of others ILD and 20 cases of healthy control group were included, respectively. There were significant differences in age, sex and smoking history among the four groups (P < 0.05), and the differences were statistically significant. There were statistically significant differences among IPF group, CTD-ILD group and other ILD groups in cough and expectoration symptoms, eosinophil count percentage, creatine kinase, creatine kinase isoenzyme, C-reactive protein and carbon monoxide diffusion capacity (DLco) (P < 0.05). 2. Metabonomics analysis: LC-MC total ion flow chart of serum samples and orthogonal partial least squares discriminant analysis (OPLS-DA) of serum samples showed the difference of ion peak intensity, and there were different metabolites among each group. The OPLS-DA model has good quality evaluation and reliable data analysis. There are 193, 115, 101, 188, 148 and 169 differential metabolites in IPF group and healthy control group, IPF group and CTD-ILD group, CTD-ILD group and other ILD groups, others ILD groups and healthy control group respectively. There is a correlation between the differential metabolites of each ILD subgroup and the healthy control group. The most relevant metabolic pathways in IPF mainly include choline metabolic pathway, metabolic pathway and linoleic acid metabolic pathway in cancer. The metabolic pathways most related to CTD-ILD and other ILD include choline metabolic pathway and retrograde neural signal metabolic pathway in cancer. Metabolic pathway and linoleic acid metabolic pathway may distinguish IPF from other ILD. Metabolites involved in metabolic pathway are L-Glutamate, PE(18:3(6Z,9Z,12Z)/P-18:0) and PC (18: 2 (9z, 12z)/20: 2 (11z, 14z)), respectively. There are three differential metabolites of linoleic acid pathway, namely 12,13-EpOME, 13S-HODE and PC(18:2(9Z,12Z)/20:2(11Z,14Z)). There are 35 kinds of differential metabolites in IPF group and healthy control group, and the top three places of AUC are 3- sulfodeoxycholic acid, 20,22-dihydrodigitalis glycoside, ({+/-}14) (15)-EET-SI, with AUC values of 0.985, sensitivity of 100% and specificity of 92.3%. L- acetylcarnitine, 5-hydroxydodecanoate and L-Glutamate are involved in significant enrichment pathways, among which the ROC curve area of L-Glutamate is the largest, with AUC value of 0.921, cutoff value of 40145.490, sensitivity of 80%, specificity of 96%, and participation in metabolic pathways. 3. Serum metabolism-related detection indexes: The six serum detection indexes of IPF group and CTD-ILD group are higher than those of healthy control group, and the difference is statistically significant (P < 0.05), but the difference between IPF group and CTD-ILD group is not statistically significant (P>0.05). The expression of GDF-15 in IPF group and non-IPF ILD group was higher than that in healthy control group, with significant difference, but there was no significant difference between IPF group and non-IPF ILD group. Type I collagen and IL-1{beta} were negatively correlated with DLco. KL-6 is negatively correlated with the measured values of VC and DLco; IGF-1 was negatively correlated with FVC, VC and DLco (all P<0.05). GDF-15 was positively correlated with type I collagen, KL-6, IL-1{beta}, TNF- and IGF-1, and the difference was statistically significant (P < 0.05). ROC curve shows that the area under ROC curve (AUC) of six serum indexes in IPF group is greater than 0.9; In CTD-ILD group, the AUC of IGF-1 was greater than 0.9, the cutoff value was 35.081ng/ml, the sensitivity was 90%, the specificity was 76%, and the area under ROC curve was greater than 0.8, and the difference was statistically significant. In other ILD groups, the ROC curve area of these six indicators ranged from 0.6 to 0.8, among which IGF-1, GDF-15 and TNF- had diagnostic value. In IPF, L-Glutamate was positively correlated with type I collagen, KL-6, IGF-1, IL-1{beta}, TNF- and GDF-15, and the difference was statistically significant (P < 0.05), with the highest correlation with IGF-1. ConclusionIn this study, the serum samples of IPF patients, CTD-ILD patients, other interstitial lung diseases and healthy controls were analyzed by LM-MS and ELISA, and the following conclusions were drawn. 1.There are differences in serum metabolites in different groups. IPF has three main metabolic pathways, namely choline metabolic pathway, metabolic pathway and linoleic acid metabolic pathway in cancer, among which metabolic pathway and linoleic acid metabolic pathway are different from other groups. There are 35 differential metabolites in IPF and healthy control group with the area under ROC curve larger than 0.80, among which the metabolites with the highest diagnostic value are 3- sulfodeoxycholic acid, 20,22-dihydrodigitalis glycoside and ({+/-}) 14 (15)-EET-SI. The AUC value of L- glutamic acid is the highest among the metabolites that participate in the enrichment pathway significantly. 2. The expressions of type I collagen, KL-6, IL-1{beta}, TNF-, IGF-1 and GDF-15 are different in different ILDs, which have potential diagnostic and differential diagnostic value, and are correlated with lung function indexes. In IPF, GDF-15 is positively correlated with L-Glutamate, which may be involved in metabolic pathway to further promote pulmonary fibrosis.

molecular biology↗

bioRxiv2022

CMLD-2 Attenuates Myofibroblast Activation and Bleomycin-Induced Pulmonary Fibrosis in Mice through Antagonizing ELAVL1-Mediated Osteopontin mRNA Stabilization

BackgroundFibroblast-myofibroblasts transition (FMT) is one of the hallmark cellular processes in pulmonary fibrosis. This study is to investigate the effects of CMLD-2 in FMT and pulmonary fibrosis, which antagonizes HuR, a supposedly key regulatory RNA binding protein (RBP). MethodsHuR or other deferentially expressed RBPs during TGF-{beta}1-induced FMT were analyzed by transcriptomic methods, and further validated in vitro or in fibrotic lung specimens. The effects of HuR overexpression, down-regulation or inhibition by an antagonist CMLD-2 were analyzed in FMT or bleomycin-induced experimental lung fibrosis. HuR-targeting RNA and their interactions were analyzed by CLIP-seq. ResultsHuR, hnRNPA1, hnRNPE1, TIA1 and TFRC were significantly up-regulated, while ESRP1, ESRP2 and TTP were significantly down-regulated. Cytoplasmic expression of HuR was activated in IPF lung tissue and rat lungs of bleomycin-induced fibrosis. HuR overexpression induced -SMA and collagen I expression, increased the proliferation and migration capacities of fibroblasts with or without the stimulation of TGF-{beta}1. HuR knockdown by shRNA inhibited the proliferation, transition, collagen production and migration properties in fibroblasts or in TGF-{beta}1-stimulated myofibroblasts. Combinative analysis of RNA-seq and CLIP-seq data revealed major HuR binding motifs and several HuR-bound, differentially expressed mRNAs in FMT, specifically SPP1 mRNA encoding osteopontin. HuR-mediated SPP1 mRNA stabilization was further validated by RIP-PCR and half-life analysis using SPP1 mutant transcripts. Inhibiting HuR using CMLD-2 attenuated SPP1/osteopontin expression, TGF-{beta}1-induced FMT in vitro and bleomycin-induced pulmonary fibrosis in mice. Nuclear-cytoplasmic shuttle of HuR was activated in TGF-{beta}1-induced FMT, which was inhibited by p38MAPK (SB203580) or PKC (Go-6976) inhibition, but not associated with phosphorylation of HuR. ConclusionsFibroblast-myofibroblast transition is activated by HuR-SPP1 mRNA interactions, and CMLD-2 is potentiated to be a therapeutic agent targeting HuR for fibroblast-myofibroblast transition and pulmonary fibrosis.

molecular biology↗

bioRxiv2022

Lipid Accumulation Induced by APOE4 Impairs Microglial Surveillance of Neuronal-Network Activity

Apolipoprotein E4 (APOE4) is the greatest known genetic risk factor for developing late- onset Alzheimers disease and its expression in microglia is associated with pro- inflammatory states. How the interaction of APOE4 microglia with neurons differs from microglia expressing the disease-neutral allele APOE3 is currently unknown. Here, we employ CRISPR-edited induced pluripotent stem cells (iPSCs) to dissect the impact of APOE4 in neuron-microglia communication. Our results reveal that APOE4 induces a distinct metabolic program in microglia that is marked by the accumulation of intracellular neutral lipid stores through impaired lipid catabolism. Importantly, this altered lipid-accumulated state shifts microglia away from homeostatic surveillance and renders APOE4 microglia weakly responsive to neuronal activity. By examining the transcriptional signatures of APOE3 versus APOE4 microglia before and after exposure to neuronal conditioned media, we further established that neuronal soluble cues differentially induce a lipogenic program in APOE4 microglia that exacerbates pro- inflammatory signals. Pharmacological blockade of lipogenesis in APOE4 microglia is sufficient to diminish intracellular lipid accumulation and restore microglial homeostasis. Remarkably, unlike APOE3 microglia that support neuronal network activity, co-culture of APOE4 microglia with neurons disrupts the coordinated activity of neuronal ensembles. We identified that through decreased uptake of extracellular fatty acids and lipoproteins, APOE4 microglia disrupts the net flux of lipids which results in decreased neuronal activity via the potentiation of the lipid-gated K+ channel, GIRK3. These findings suggest that neurological diseases that exhibit abnormal neuronal network-level disturbances may in part be triggered by impairment in lipid homeostasis in non-neuronal cells, underscoring a novel therapeutic route to restore circuit function in the diseased brain. O_FIG O_LINKSMALLFIG WIDTH=166 HEIGHT=200 SRC="FIGDIR/small/484146v1_ufig1.gif" ALT="Figure 1"> View larger version (60K): org.highwire.dtl.DTLVardef@4d4a9corg.highwire.dtl.DTLVardef@5d888corg.highwire.dtl.DTLVardef@afa191org.highwire.dtl.DTLVardef@984340_HPS_FORMAT_FIGEXP M_FIG C_FIG

neuroscience↗

bioRxiv2022

Pore-forming protein βγ-CAT promptly responses to fasting with capacity to deliver macromolecular nutrients

During animal fasting, the nutrient supply and metabolism switch from carbohydrates to a new reliance on the catabolism of energy-dense lipid stores. Assembled under tight regulation, {beta}{gamma}-CAT is a pore-forming protein and trefoil factor complex identified in toad Bombina maxima. Here, we determined that this protein complex is a constitutive component in toad blood, that actively responds to the animal fasting. The protein complex was able to promote cellular albumin and albumin-bound fatty acid uptake in a variety of epithelial and endothelial cells, and the effects were attenuated by a macropinocytosis inhibitor. Endothelial cell-derived exosomes containing largely enriched albumin and fatty acids, called nutrisomes, were released in the presence of {beta}{gamma}-CAT. These specific nutrient vesicles were readily taken by starved muscle cells to support their survival. The results uncovered that pore-forming protein {beta}{gamma}-CAT is a fasting responsive element able to drive cell vesicular import and export of macromolecular nutrients.

cell biology↗

bioRxiv2022

STOmicsDB: a database of Spatial Transcriptomic data

Recent technological development in spatial transcriptomics allows researchers to measure gene expression of cells and their spatial locations at the almost single-cell level, which generates detailed biological insight into biological processes. However, specialized spatial transcriptomics databases are rare. Here, we present the Spatial TranscriptOmics DataBase (STOmicsDB), a user-friendly database with multifunctions including search of relevant publications and tools, public dataset visualization, customized specialized databases, new data archive, and online analysis. The current version of STOmicsDB consists of 141 curated spatial transcript datasets covering 12 species, and includes 5,618 spatial multi-omics publications and 674 tools. STOmicsDB is freely accessible at https://db.cngb.org/stomics/.

genomics↗

bioRxiv2022

A WAX INDUCER1/SHINE transcription factor controls cuticular wax in barley

All land plants seal their above ground body parts with a lipid-rich hydrophobic barrier called the cuticle that protects tissues from dehydration and other terrestrial threats. Mutational studies in several model species, including barley, have resolved multiple loci regulating cuticular metabolism and development. Of particular importance are the eceriferum (cer) mutants characterized by visual alterations in cuticular wax. In barley, some cer mutants, such as cer-x lines, show defects in the distinctive {beta}-diketone-enriched wax bloom on reproductive stage leaf sheaths, stems and spikes. In our study we exploited extensive allelic populations, near-isogenic lines and powerful genotyping platforms to identify variation in the HvWAX INDUCER1 (HvWIN1) gene as causal for cer-x mutants. We show that HvWIN1 function reduces cuticular permeability, promotes the accumulation of {beta}-diketones, and regulates cuticular metabolic gene expression. Analyses across the barley pangenome and hundreds of exome-capture datasets revealed high sequence conservation of HvWIN1 but also two non-synonymous variants exclusive to cultivated germplasm. Taken together, we suggest that variation in HvWIN1 controls multiple cuticular features in barley by controlling the expression of genes involved in cuticle development.

plant biology↗

bioRxiv2022

Balancing activation and costimulation of CAR tunes signaling dynamics and enhances therapeutic potency

BackgroundPrimary human T cells engineered with chimeric antigen receptors (CARs) ex vivo can be adoptively transferred to treat cancer. CD19-targeting CAR with CD28 costimulatory domain and CD3{zeta} activation domain have been approved by the US FDA for treating B cell malignancies. MethodsHere we generated mutation of immunorecpetor tyrosine-based activation motifs (ITAMs) in CD3{zeta}, namely 1XX CAR, which altered the balance of activation and costimulation. Next we investigated whether 1XX design could enhance therapeutic potency against solid tumors. We constructed both CD19- and AXL-specific 1XX CARs and compared their in vitro and in vivo functions with their WT counterparts. ResultsEven though 1XX CARs decreased cytotoxicity against tumor cells in vitro, they showed better anti-tumor efficacy in both pancreatic and melanoma mouse models. Detailed analysis revealed that 1XX CAR-T cells proliferated more in response to antigen stimulation in vitro, persisted longer in vivo and had higher percentage of central memory cells. As 1XX modification directly calibrates CAR activation potential, we utilized fluorescence resonance energy transfer (FRET)-based biosensor to monitor signaling dynamics downstream of CARs. Decreased ITAM numbers in 1XX resulted in similar ZAP70 activation, while 1XX induced higher Ca2+ elevation and faster Erk activation than WT CAR, which may contribute to the better therapeutic potency of 1XX. ConclusionsOur results established the surpiosity of 1XX against two targets in different solid tumor models and shed light on the underlying molecular mechanism of CAR signaling, paving the way for the clinical application of 1XX CARs against solid tumors.

immunology↗

bioRxiv2022

Structure of IgG-Fc hexamer reveals a mutual lock-and-key mode of Fc-Fc interaction

IgG exists mainly as monomer, but recent studies suggest that IgG forms hexamer to mediate antibody functions. Although many structures of IgG monomer and its fragments are determined, there is no IgG hexamer structure at atomic level due to the weak Fc-Fc interactions. Here we engineered a hexameric IgG with IgM tailpiece fusion and determined the structure by cryo-EM. IgG-Fc hexamer forms hexagon symmetry with the six Fcs lie in a plane with Fc-Fc interaction in a mutual lock-and-key mode. This structure provides structural insights into Fc-Fc interaction of IgG and reveals molecular basis for its function.

biophysics↗

bioRxiv2022

Estrogen suppresses DMRT1 expression during ovarian development in the chicken

Primary sex determination is the choice between two different developmental fates, a testis or an ovary. This selection is thought to require the action of a master regulator gene that triggers expression of a gene cascade in the bipotential gonad precursor in one sex. The selection of a particular developmental pathway is also thought to suppress the alternative developmental pathway. In birds, where the male is the homogametic sex (ZZ) and females the heterogametic sex (ZW), the Z-linked transcription factor DMRT1 is considered the master regulator and has been shown to be essential for testis development, and to also inhibit the ovarian pathway. Here, we characterise in detail, DMRT1 transcription and protein levels during gonadal development in the chick. Our analysis suggests that DMRT1 protein levels are equivalent in male and female gonads during the bipotential phase of development, and that DMRT1 protein levels are reduced in the developing ovary during the differentiation phase. The reduction in DMRT1 protein levels in the somatic cells of the female medulla, coincides with the induction of aromatase expression and the initiation of estrogen synthesis. Analysis of sex-reversed gonads and mixed-sex chimeric gonads, suggests that the reduction in DMRT1 protein is due to inhibition of DMRT1 expression by estrogen. Our data suggests that estrogen signalling is involved in primary sex determination by regulation of DMRT1 protein expression.

developmental biology↗

bioRxiv2022

Increased Relative Biological Effectiveness of Orthovoltage X-rays Compared to γ-rays in Preclinical Irradiation

PurposeRadionuclide irradiators (137Cs and 60Co) are commonly used in preclinical studies ranging from cancer therapy to stem cell biology. There are institutional initiatives to replace radionuclide sources with lower-energy X-ray sources amidst concerns of radiological terrorism. As researchers transition, there are questions whether the biological effects of {gamma}-rays may be recapitulated with orthovoltage X-rays, since different energy may cause different biological effects. We, therefore, sought to compare the effects of orthovoltage X-rays and 137Cs {gamma}-rays using mouse models of acute radiation syndrome. Experimental Design137Cs {gamma}-rays were compared with Orthovoltage X-rays, generated at 300 kVp, 10 mA with 1 mm Cu or Thoraeus filtration. We assessed 30-day overall survival following whole-body irradiation and calculated LD50 by logistic regression. Comparing equivalent doses delivered with different average energies ([E]), we assessed bone marrow, spleen, and intestinal histology and flow cytometry. ResultsThe LD50 doses are 6.7 Gy, 7.4 Gy and 8.1 Gy with 1 mm Cu filtered ([E]=120 keV), and Thoraeus filtered X-rays ([E]=160 keV), and 137Cs (E=662 keV), respectively. At constant dose, hematopoietic injury was most severe with 1 mm Cu filtered X-rays with the greatest reduction in bone marrow cellularity, stem and progenitor populations, and intestinal crypts and OLFM4+ intestinal stem cells. Thoraeus filtered X-rays provoked an intermediate phenotype, with 137Cs showing the least damage. ConclusionsOur study reveals a dichotomy between physical dose and biological effect relevant as researchers transition to orthovoltage X-rays. With decreasing energy, there is increasing hematopoietic and intestinal injury, necessitating dose-reduction to achieve comparable biological effects. Statement of Translational RelevanceRadiation is used in translational studies in fields ranging from hematopoiesis and stem cell biology to cancer radiotherapy, with 137Cs and 60Co radionuclide sources serving as the most common irradiators. Due to the threat of radiological terrorism using stolen radionuclides, there are institutional initiatives to replace these sources with orthovoltage X-ray irradiators. Yet, as shown in this study, the biological effects of radiation are highly dependent on radiation energy. Lower energy orthovoltage X-rays are absorbed differently than higher energy radionuclide {gamma}-rays, provoking more severe hematopoietic, immunologic, and gastrointestinal radiation injury. Thus, an identical physical dose delivered with beams of differing energy does not produce the same biologic effect. As researchers transition between these sources, it is critical that we appreciate that radiation doses are not interchangeable between them. Understanding the significance of physical dose delivered using different methods will allow us to contextualize past results with future studies.

pathology↗

bioRxiv2022

gamma aminobutyrate (GAB) functions as a bioenergetic and signaling gatekeeper to control T cell inflammation

{gamma}-Aminobutyrate (GAB) is the biochemical form of {gamma}-aminobutyric acid (GABA) at physiological pH and functions as an essential neurotransmitter in the vertebrates central nervous system (CNS). Growing evidence suggests that GAB may also mediate intercellular communications to shape various physiological processes, including immune response. Beyond acting as a paracrine signaling molecule, how GAB metabolism is controlled to exert many distinct functions remains elusive. By an integrated analysis of the extracellular metabolome, stable isotope traced metabolic pathway analysis, and metabolic transcriptome, we revealed that GAB is one of the most abundant metabolites produced through glutamine and arginine catabolism in CD4+ T help 17 (TH17) and induced T regulatory (iTreg) cells. GAB functions as a bioenergetic and signaling gatekeeper by reciprocally controlling pro-inflammatory TH17 cell and anti-inflammatory iTreg cell differentiation through distinct mechanisms. The expression of 4-aminobutyrate aminotransferase (ABAT) funnels GAB, as an anaplerotic substrate, into the TCA cycle to maximize carbon allocation in promoting TH17 cell differentiation. By contrast, the absence of ABAT activities in iTreg cells enables GAB exporting to the extracellular environment and acting as an autocrine signaling metabolite to promote iTreg cell differentiation. Accordingly, genetic or pharmacological ablation of ABAT activity in T cells confers protection against experimental autoimmune encephalomyelitis (EAE) pathogenic progression. Conversely, genetic ablation of GABA(A) receptor in T cells deteriorates EAE pathogenic progression. Collectively, our results suggest that the cell-autonomous control exerted by GAB on CD4+ T cell is bimodal and consists of the sequential action of two discrete processes, ABAT-dependent mitochondrial anaplerosis and the receptor-dependent autocrine signaling response, both of which are required for a properly controlled T cell-mediated inflammation.

immunology↗

bioRxiv2022

Building an atlas of transposable elements reveals the extensive roles of young SINE in gene regulation, genetic diversity, and complex traits in pigs

Transposable elements (TEs) are an extensive source of genetic polymorphisms and play an indispensable role in chromatin architecture, transcriptional regulatory networks, and genomic evolution. The pig is an important source of animal protein and serves as a biomedical model for humans, yet the functional role of TEs in pigs and their contributions to complex traits are largely unknown. Here, we built a comprehensive catalog of TEs (n = 3,087,929) in pigs by a newly developed pipeline. Through integrating multi-omics data from 21 tissues, we found that SINEs with different ages were significantly associated with genomic regions with distinct functions across tissues. The majority of young SINEs were predominantly silenced by histone modifications, DNA methylation, and decreased accessibility. However, the expression of transcripts that were derived from the remaining active young SINEs exhibited strong tissue specificity through cross-examining 3,570 RNA-seq from 79 tissues and cell types. Furthermore, we detected 211,067 polymorphic SINEs (polySINEs) in 374 individuals genome-wide and found that they clearly recapitulated known patterns of population admixture in pigs. Out of them, 340 population-specific polySINEs were associated with local adaptation. Mapping these polySINEs to genome-wide associations of 97 complex traits in pigs, we found 54 candidate genes (e.g., ANK2 and VRTN) that might be mediated by TEs. Our findings highlight the important roles of young SINEs in functional genomics and provide a supplement for genotype-to-phenotype associations and modern breeding in pigs.

genomics↗

bioRxiv2022

Antibody Evasion Properties of SARS-CoV-2 Omicron Sublineages

The identification of the Omicron variant (B.1.1.529.1 or BA.1) of SARS-CoV-2 (severe acute respiratory syndrome coronavirus 2) in Botswana in November 20211 immediately raised alarms due to the sheer number of mutations in the spike glycoprotein that could lead to striking antibody evasion. We2 and others3-6 recently reported results in this Journal confirming such a concern. Continuing surveillance of Omicron evolution has since revealed the rise in prevalence of two sublineages, BA.1 with an R346K mutation (BA.1+R346K) and B.1.1.529.2 (BA.2), with the latter containing 8 unique spike mutations while lacking 13 spike mutations found in BA.1. We therefore extended our studies to include antigenic characterization of these new sublineages. Polyclonal sera from patients infected by wild-type SARS-CoV-2 or recipients of current mRNA vaccines showed a substantial loss in neutralizing activity against both BA.1+R346K and BA.2, with drops comparable to that already reported for BA.12,3,5,6. These findings indicate that these three sublineages of Omicron are antigenically equidistant from the wild-type SARS-CoV-2 and thus similarly threaten the efficacies of current vaccines. BA.2 also exhibited marked resistance to 17 of 19 neutralizing monoclonal antibodies tested, including S309 (sotrovimab)7, which had retained appreciable activity against BA.1 and BA.1+R346K2-4,6. This new finding shows that no presently approved or authorized monoclonal antibody therapy could adequately cover all sublineages of the Omicron variant.

microbiology↗

bioRxiv2022

The Goldilocks Principle conferred by LDH isoenzymes controls murine T cell glycolysis and differentiation

Isoenzyme divergence is a prevalent mechanism governing tissue-specific and developmental stage-specific metabolism in mammals. The isoenzyme pattern (spectrum) of lactate dehydrogenase (LDH) reflects the status of glucose metabolism in different organs such as muscle, liver, and heart. T cells are highly dependent on glucose metabolism for survival, proliferation, and differentiation. However, the LDH isoenzyme spectrum in T cells and its potential impact on T cell-mediated immune response remain unclear. Here, we discovered that the LDH spectrum in murine T cells is characterized by three tetrameric isoenzymes composed of LDHA and LDHB (LDH-3/4/5). Genetic deletion of LDHA or LDHB altered the isoenzyme spectrum by removing all heterotetramers and leaving T cell with LDH-1 (the homotetramer of LDHB) or LDH-5 (the homotetramer of LDHA), respectively. Accordingly, altering the isoenzyme spectrum by deleting LDHA or LDHB compromises T cell metabolic fitness and effector cell differentiation in vivo. Unexpectedly, deleting LDHA suppressed glycolysis, whereas deleting LDHB further enhanced it, indicating that an optimal zone of glycolytic activity is critical to driving effector T cell differentiation. Mechanistically, the LDH isoenzyme spectrum imposed by LDHA and LDHB is required to optimize glycolysis to maintain a balanced NAD+/NADH pool, a hallmark of metabolic fitness. Together, our results suggest that the LDH isoenzyme spectrum enables "Goldilocks levels" of glycolytic and redox activity (i.e., not too high, not too low, but just right) to control T cell differentiation function.

immunology↗