Biology subjects

Song, R.

Publications and source records attributed to Song, R..

52 records · Page 3Linked to original sources

bioRxiv2021

A distinct CD115- erythro-myeloid precursor present at the maternal-embryonic interface and in the bone marrow of adult mice

During ontogeny, macrophages develop from CD115+ precursors, including erythro-myeloid progenitors (EMP). EMP arise in the embryonic yolk sac, the primary site of early haematopoiesis. In adults, CD115+ bone marrow-derived monocytes represent essential macrophage precursors. Herein, we identify a CD115- macrophage precursor within the adult bone marrow that is unrelated to the classical monocyte lineage but rather shares transcriptomic and functional characteristics of embryonic EMP. These EMPROR (for Erythro Myeloid Precursor) cells are capable of efficiently generating macrophages in disease settings. During early development, EMPROR cells were largely absent from the yolk sac but were instead found at the embryonic-maternal interface in the uterine wall. Unexpectedly, the latter site contains robust haematopoietic activity and harbours defined embryonic haematopoietic progenitor cells, including classical CD115+ EMP. Our data suggest the existence of an alternative pathway of macrophage generation in the adult. Further, we uncover a hitherto unknown site of earliest blood cell development.

immunology↗

bioRxiv2021

circMRPS35 promotes malignant progression and cisplatin resistance in hepatocellular cancer

Hepatocellular carcinoma (HCC), a common malignant tumor, is one of the main causes of cancer-related deaths worldwide. Circular RNAs (circRNAs), a novel class of non-coding RNA, have been reported to be involved in the etiology of various malignancy. However, the functions of circRNAs in HCC remain unclear. In this study, through mining the RNA sequencing databases from GEO datasets and subsequent experimental verification, we identified that hsa_circ_0000384 (circMRPS35) was highly expressed in HCC. Knockdown of circMRPS35 suppressed the proliferation, migration, invasion, clone formation and cell cycle of HCC cell lines both in vitro and in a xenograft mouse model. Mechanically, circMRPS35 sponged microRNA-148a-3p (miR-148a), which in turn regulated STX3-PTEN axis. Surprisingly, we detected a peptide encoded by circMRPS35 (circMRPS35-168aa), which was significantly induced by chemotherapeutic drugs and promoted cisplatin resistance in HCC cells. These results demonstrated that circMRPS35 might be a novel factor in HCC progress, and has a great potential as a new diagnosis and therapeutic target for treatment of HCC.

cell biology↗

bioRxiv2021

Chromatin accessibility regulates intron retention in a cell type-specific manner

Dynamic intron retention (IR) in vertebrate cells is of widespread biological importance. Aberrant IR is associated with numerous human diseases including cancer. Despite consistent reports demonstrating intrinsic sequence features that predispose introns to become retained, conflicting findings about cell type-specific IR regulation demand a systematic analysis in a controlled experimental setting. We integrated matched transcriptomics and epigenetics data (including DNA methylation, nucleosome occupancy, histone modifications) from primary human myeloid and lymphoid cells. Using machine learning we trained two complementary models to determine the role of epigenetic factors in the regulation of IR. We show that increased chromatin accessibility contributes substantially to the retention of introns in a cell-specific manner. We also confirm that intrinsic characteristics of introns are key for them to evade splicing. With mounting reports linking pathogenic alterations to RNA processing, our findings may have profound implications for the design of therapeutic approaches targeting aberrant splicing.

bioinformatics↗

bioRxiv2020

Deletion of Letmd1 leads to the disruption of mitochondrial function in brown adipose tissue

Human cervical cancer oncogene (HCCR-1), also named as LETMD1, is a LETM-domain containing outer mitochondrial membrane protein which plays an important role in the carcinogenesis of cancers. Surprisingly, we found that loss of Letmd1 in mice leads to multiply severe abnormities, such as the brown adipose tissue (BAT) whitening, disruption of thermogenesis, cold-induced death, diet-induced obesity, hyperglycinemia and insulin resistance. Mechanistically, deletion of Letmd1 in BAT causes the reduction of mitochondrial calcium ion, which in turn results in the suppressed fission of mitochondria, and ultimately leads to the depletion of Ucp1-mediated BAT heat production. This study indicates that LETMD1 plays a crucial role in controlling BAT thermogenesis and energy homeostasis by regulating mitochondrial structures and functions, and also provides a novel insight for the clinical biomarker and therapeutical target of oncogene for the metabolic disorders. HighlightsO_LILetmd1 is an oncogene and also highly expressed in brown adipose tissue (BAT) of human and mice. C_LIO_LILoss of Letmd1 leads to BAT whitening, diet-induced obesity, hyperglycemia and insulin resistant. C_LIO_LILetmd1 knockout causes the disruption of thermogenesis and death at 4{degrees}C exposure. C_LIO_LIDeletion of Letmd1 results in mitochondrial calcium homeostasis disorders. C_LI Graphic abstract O_FIG O_LINKSMALLFIG WIDTH=159 HEIGHT=200 SRC="FIGDIR/small/388199v2_ufig1.gif" ALT="Figure 1"> View larger version (65K): org.highwire.dtl.DTLVardef@bee6adorg.highwire.dtl.DTLVardef@11a7cc1org.highwire.dtl.DTLVardef@1f4699forg.highwire.dtl.DTLVardef@142699a_HPS_FORMAT_FIGEXP M_FIG C_FIG

physiology↗

bioRxiv2020

One-step multiple site-specific base editing by direct embryo injection for precision and pyramid pig breeding

Precise and simultaneous acquisition of multiple beneficial alleles in the genome to improve pig performance are pivotal for making elite breeders. Cytidine base editors (CBEs) have emerged as powerful tools for site-specific single nucleotide replacement. Here, we compare the editing efficiency of four CBEs in porcine embryonic cells and embryos to show that hA3A-BE3-Y130F and hA3A-eBE3-Y130F consistently results in higher base-editing efficiency and lower toxic effects to in vitro embryo development. We also show that zygote microinjection of hA3A-BE3-Y130F results in one-step generation of pigs (3BE pigs) harboring C-to-T point mutations, including a stop codon in CD163 and in MSTN and induce beneficial allele in IGF2. The 3BE pigs showed improved growth performance, hip circumference, food conversion rate. Our results demonstrate that CBEs can mediate high throughput genome editing by direct embryo microinjection. Our approach allows immediate introduction of novel alleles for beneficial traits in transgene-free animals for pyramid breeding.

genetics↗

bioRxiv2020

Inflammation Drives Alternative First Exon usage to Regulate Immune Genes including a Novel Iron Regulated Isoform of Aim2

Determining the layers of gene regulation within the innate immune response is critical to our understanding of the cellular responses to infection and dysregulation in disease. We identified a conserved mechanism of gene regulation in human and mouse via changes in alternative first exon (AFE) usage following inflammation, resulting in changes to isoform usage. Of these AFE events, we identified 50 unannotated transcription start sites (TSS) in mice using Oxford Nanopore native RNA sequencing, one of which is the cytosolic receptor for dsDNA and known inflammatory inducible gene, Aim2. We show that this unannotated AFE isoform of Aim2 is the predominant isoform transcribed during inflammation and contains an iron-responsive element in its 5′UTR enabling mRNA translation to be regulated by iron levels. This work highlights the importance of examining alternative isoform changes and translational regulation in the innate immune response and uncovers novel regulatory mechanisms of Aim2.Summary Sentence Alternative first exon usage was the major splicing event observed in macrophages during inflammation, which resulted in the elucidation of a novel isoform and iron mediated regulatory mechanism of the protein coding gene, Aim2.Competing Interest StatementThe authors have declared no competing interest.View Full Text

immunology↗

bioRxiv2020

Moderating Effect of Social Support on Role Conflict and Job Satisfaction Among Nurses with Multiple Roles

Registered nurses perform multiple roles in their lives at work, at home, and at school when they decide to pursue various types of advanced degrees. Work-family conflict was found to be negatively correlated with job satisfaction among nurses. This study aimed to determine the moderating effect of social support on the relationship between role conflicts and job satisfaction among registered nurses in mainland China. The study had a cross-sectional correlational design. Convenience sampling was applied to recruit 320 nurses with multiple roles from 8 nursing universities and 3 hospitals in China between January and August 2017. SPSS (version 20.0) software and PROCESS program was used to examine to moderating effect of social support between the relationship of role conflicts and job satisfaction. It was found that role conflicts were negatively correlated with job satisfaction. Support from work and support from family negatively moderated the relationship between role conflicts and job satisfaction. These findings suggest that support from family, coworkers and nursing administrators, and the implementation of school- and family-friendly policies would help nurses who are pursuing further nursing degrees to handle their multiple roles and improve their job satisfaction.

scientific communication and education↗

bioRxiv2019

Deep learning enables structured illumination microscopy with low light levels and enhanced speed

Using deep learning to augment structured illumination microscopy (SIM), we obtained a fivefold reduction in the number of raw images required for super-resolution SIM, and generated images under extreme low light conditions (100X fewer photons). We validated the performance of deep neural networks on different cellular structures and achieved multi-color, live-cell super-resolution imaging with greatly reduced photobleaching.

biophysics↗

bioRxiv2019

The role of swnR gene on the biosynthesis pathway of the swainsonine in Metarhizium anisopliae

Swainsonine (SW) is the principal toxic ingredient of locoweeds, and is produced by fungi including Metarhizium anisopliae, Slafractonia leguminicola, and Alternaria oxytropis. Studies of the SW biosynthesis pathway in these fungi have demonstrated the requirement for a swnK gene and the presence of a variety of other SWN cluster genes, but have not determined a precise role for the swnR gene, which encodes a NADB Rossmann-fold reductase, nor if it is necessary for the biosynthesis of SW. In this study, we used homologous recombination (HR) to knock out the swnR gene of M. anisopliae to determine its effect on the SW biosynthesis pathway. The concentration of SW was measured in the fermentation broth of M. anisopliae at 1 d, 3 d, 5 d and 7 d using a Q Exactive Mass Spectrometer. The gene for swnR was detected by RT-qPCR. To determine the role of the swnR gene in the SW biosynthesis pathway of M. anisopliae, we used PEG-mediated homologous recombination (HR) to transform a wild-type strain (WT) with a Benomyl (ben)-resistant fragment to knock out the swnR gene producing a mutant-type strain (MT). A complemented-type (CT) strain was produced by adding a complementation vector that contains the glufosinate (herbicide) resistance (bar) gene as a marker. The content of SW decreased, but was not eliminated in the fermentation broth of the MT strain, and returned to the original level in the CT strain. These results indicate that the swnR gene plays a crucial role in the SW biosynthesis pathway of M. anisopliae, but suggests that another gene in the fungus may share the function of swnR.

molecular biology↗

bioRxiv2019

Impact of Candida auris infection in a neutropenic murine model

Candida auris has become a global public health threat due to its multidrug resistance and persistence in hospital and nursing home settings. Although a skin colonizer, C. auris can cause fatal bloodstream infections and most patients succumb to multi-organ failure. Currently, there are limited animal models to study the progression of C. auris infection. Here we compare two murine models of neutrophil depletion using monoclonal antibodies 1A8, anti-Ly6G+ and RB6-8C5 anti-Ly6G+-Ly6C+. We also compare inoculums of 107 and 108 as well as the intravenous and gavage routes of infection. The results reveal that neutrophil depletion in BALB/c mice is sustained long-term with the 1A8 antibody and short-term with RB6-8C5. Target organs were kidney, heart and brain as these had the highest organ fungal burden in neutrophil depleted and to some extent in infected control mice. We found that C. auris is shed in urine and feces for neutrophil depleted mice. The gavage model is not an ideal route as dissemination was not detected. Eight days post C. auris infection all surviving mice display a unique behavioral phenotype characterized by torticollis and tail spin that progresses to head bobbing and body curling like phenotype by day 22, that continues to persist even 104 days post infection. Lastly, we found C. auris remains in tissues of infected control mice, 34 plus days post infection suggesting that C. auris stays present in the host without causing disease but becomes opportunistic upon a change in the hosts immune status such as neutrophil depletion.

microbiology↗

bioRxiv2019

Using a bar-coded AAV capsid library to select for novel clinically relevant gene therapy vectors

ABSTRACTWhile gene transfer using recombinant adeno-associated viral (rAAV) vectors have shown success in some clinical trials, there remain many tissues that are not well transduced. Because of the recent success in reprogramming islet derived cells into functional {beta}-cells in animal models, we constructed two highly complex barcoded replication competent capsid shuffled libraries and selected for high transducing variants on primary human islets. We describe a chimeric capsid (AAV-KP1) that penetrated and transduced primary human islet cells and human embryonic stem cell derived {beta}-cells with up to 10-fold higher efficiency compared to previously studied best in class AAV vectors. Remarkably, this chimeric capsid was also able to transduce both mouse and human hepatocytes at very high levels in a humanized-chimeric mouse model, thus providing a versatile vector which has the potential to be used in both preclinical testing and human clinical trials for both liver-based diseases and diabetes.

genetics↗

bioRxiv2019

Study of the AMP-activated protein kinase role in energy metabolism changes during the postmortem aging of yak longissimus lumborum

To explore the postmortem physiological mechanism of muscle, activity of adenosine monophosphate activated protein kinase (AMPK) as well as its role in energy metabolism of postmortem yaks were studied. In this experiment, we injected 5-amino-1-beta-d-furanonyl imidazole-4-formamide (AICAR), a specific activator of AMPK, and the specific AMPK inhibitor STO-609, to observe the changes in glycolysis, energy metabolism, AMPK activity and AMPK gene expression (PRKA1 and PRKA2) in postmortem yaks during maturation. The results showed that AICAR could increase the expression of the PRKKA1 and PRKAA2 genes, activate AMPK and increase its activity. The effects of AICAR include a lower concentration of ATP, an increase in AMP production, an acceleration of glycolysis, an increase in the lactic acid concentration, and a decrease in the pH value. In contrast, STO-609 had the opposite effect. Under hypoxic adaptation, the activity of the meat AMPK increased, which accelerated glycolysis and metabolism, and more effectively regulated energy production.

biochemistry↗

bioRxiv2019

Inhibition of GMP synthesis extends yeast replicative lifespan

Aging, the time-dependent accumulation of molecular damage, is the primary limiting factor of human lifespan. Slowing down damage accumulation or its prevention therefore represents a promising therapeutic paradigm to combat aging-related disease and death. While several chemical compounds extend lifespan in model organisms, their mechanism of action is often unknown, reducing their therapeutic potential. Using a systematic approach, here we show that inhibition of GMP synthesis is a novel lifespan extension mechanism in yeast. We further discover that proteasome activation extends lifespan in part through GMP insufficiency. GMP synthesis inhibition exerts its lifespan extension effect independently of the canonical nutrient-sensing and sirtuin pathways regulating lifespan. Exposing longitudinally aging yeast cells to GMP synthesis inhibition in an age-dependent manner, we demonstrate that the lifespan extension by GMP insufficiency is facilitated by slowing, rather than reversing, the aging process in cells. While GMP and its downstream metabolites are involved in many cellular processes in cells, our results rule out the combined effect of global transcription and translation on cellular lifespan. These findings elucidate the involvement of nucleotide metabolism in the aging process. The existence of clinically-approved GMP synthesis inhibitors elicits the potential of a new class of therapeutics for aging-related disorders.

systems biology↗

bioRxiv2019

Stochastic modeling of aging cells reveals how damage accumulation, repair, and cell-division asymmetry affect clonal senescence and population fitness

BackgroundAsymmetry during cellular division, both in the uneven partitioning of damaged cellular components and of cell volume, is a cell biological phenomenon experienced by many unicellular organisms. Previous work based on a deterministic model claimed that such asymmetry in the partitioning of cell volume and of aging-associated damage confers a fitness benefit in avoiding clonal senescence, primarily by diversifying the cellular population. However, clonal populations of unicellular organisms are already naturally diversified due to the inherent stochasticity of biological processes.\n\nResultsApplying a model of aging cells that accounts for natural cell-to-cell variations across a broad range of parameter values, here we show that the parameters directly controlling the accumulation and repair of damage are the most important factors affecting fitness and clonal senescence, while the effects of both segregation of damaged components and division asymmetry are frequently minimal and generally context-dependent.\n\nConclusionsWe conclude that damage segregation and division asymmetry, perhaps counterintuitively, are not necessarily beneficial from an evolutionary perspective.

systems biology↗

bioRxiv2019

Defining the dynamic chromatin landscape of nephron progenitors

Six2+ cap mesenchyme cells, also called nephrons progenitor cells (NPC), are precursors of all epithelial cell types of the nephron, the filtering unit of the kidney. Current evidence indicates that perinatal \"old\" NPC have a greater tendency to exit the progenitor niche and differentiate into nascent nephrons than their embryonic \"young\" counterpart. Understanding the underpinnings of NPC aging may offer insights to rejuvenate old NPC and expand the progenitor pool. Here, we compared the chromatin landscape of young and old NPC and found common features reflecting their shared lineage but also intrinsic differences in chromatin accessibility and enhancer landscape supporting the view that old NPC are epigenetically poised for differentiation. Annotation of open chromatin regions and active enhancers uncovered the transcription factor Bach2 as a potential link between the pro-renewal MAPK/AP1 and pro-differentiation Six2/b-catenin pathways that might be of critical importance in regulation of NPC fate. Our data provide the first glimpse of the dynamic chromatin landscape of NPC and serve as a platform for future studies of the impact of genetic or environmental perturbations on the epigenome of NPC.\n\nSummary statementHilliard et al. investigated the chromatin landscape of native Six2+ nephron progenitors across their lifespan. They identified age-dependent changes in accessible chromatin and regulatory regions supporting the view that old nephron progenitors are epigenetically poised for differentiation.

developmental biology↗

bioRxiv2019

Setting off the Alarms: Candida albicans Elicits Pro-Inflammatory Differential Gene Expression in Intestinal Peyer’s Patches

Candida albicans has been associated with a number of human diseases that pertain to the gastrointestinal (GI) tract. However, the details of how gut-associated lymphoid tissues (GALT) such as Peyers patches (PPs) in the small intestine play a role in immune surveillance and microbial differentiation, and what mechanisms PP use to protect the mucosal barrier in response to fungal organisms such as C. albicans, are still unclear. We particularly focus on PPs as they are the immune sensors and inductive sites of the gut that influence inflammation and tolerance. We have previously demonstrated that CD11c+ phagocytes located in the sub-epithelial dome (SED) within PPs sample C. albicans. To gain insight on how specific cells within PPs sense and respond to the sampling of fungi, we gavaged mice with C. albicans strains ATCC 18804 and SC5314 as well as Saccharomyces cerevisiae. We measured the differential gene expression of sorted CD45+ B220+ B-cells, CD3+ T-cells, and CD11c+ DCs within the first 24 hrs post-gavage using nanostring nCounter(R) technology. The results reveal that at 24 hrs, PP phagocytes were the cell type that displayed differential gene expression. These phagocytes were both able to sample C. albicans and able to discriminate between strains. In particular, strain ATCC 18804 upregulated fungal specific pro-inflammatory genes in CD11c+ phagocytes pertaining to innate and adaptive immune responses. Interestingly, PP CD11c+ phagocytes differentially expressed genes in response to C. albicans that were important in the protection of the mucosal barrier. These results highlight that the mucosal barrier not only responds to C. albicans, but also aids in the protection of the host.\n\nImportanceThe specific gene expression changes within PPs that send the warning signals when encountering fungi, and how PPs can discriminate between innocuous S. cerevisiae or different strains of C. albicans during early stages of sampling, have not been elucidated. Here we show that within the first 24 hours of sampling, CD11c+ phagocytes were not only important in sampling, but they were the cell type that exhibited clear differential gene expression. These differentially expressed genes play important dual roles in inflammation, chemotaxis, and fungal specific recognition, as well as maintaining homeostasis and protection of the mucosal barrier. Using nanostring technology, we were also able to demonstrate that PPs can distinguish between different strains of C. albicans and can \"set off the alarms\" when necessary.

microbiology↗