Biology subjects

Lee, C.-H.

Publications and source records attributed to Lee, C.-H..

At least 37 records · Page 2Linked to original sources

bioRxiv2025

Interplay between Skin Sympathetic Nerve Activity and Gut Microbiota, the Neurocardiac Axis in Acute Coronary Syndrome

BACKGROUNDPrevious studies have linked gut dysbiosis to the acute coronary syndrome (ACS) and sympathetic nervous system disturbances. However, the relationship between skin sympathetic nerve activity (SKNA) and gut microbiota in ACS patients remains largely unexplored. We hypothesize that elevated SKNA may interact with specific microbial profiles in ACS. METHODS AND RESULTSFifteen ACS patients with age- and sex-matched controls were enrolled in the cross-sectional study. Subjects with type 2 diabetes or on antibiotics, proton pump inhibitors, or metformin were excluded. Demographic and clinical data were recorded, and SKNA was measured by neuECG. Gut microbial profiles were analyzed by sequencing the V3-V4 region of the 16S rRNA gene. Significant differences in alpha diversity, including Chao 1 index and Faiths phylogenetic diversity, were observed between the ACS and control groups (P<0.001). Distinct beta diversity between the two groups was also identified using unweighted normalized UniFrac analysis (P=0.001). Redundancy analysis and Mantel test revealed a significant relationship between SKNA and microbial profiles. Several butyrate-producing bacteria were decreased in the ACS group, while the genus Hungatella, a trimethylamine producer, showed a significant increase and was positively correlated with SKNA. Additionally, predicted microbial functional analysis indicated an elevation in branched-chain amino acid biosynthesis in the ACS group. CONCLUSIONSThis study is the first to establish an association between SKNA and gut microbial profiles in ACS patients. SKNA can serve as a biomarker for ACS, offering a simple and non-invasive tool to explore the interaction between the nervous system and gut microbiota in cardiovascular diseases. Clinical PerspectiveO_ST_ABSWHAT IS NEW?C_ST_ABSThe Skin sympathetic nerve activity (SKNA) is a novel and non-invasive recording of the sympathetic nervous system from the skin of patients. The NEW findings in our study from acute coronary syndrome (ACS) patients are (1) to establish the correlation between SKNA, heart rate variability and microbiota, (2) the Hungatella is correlated with SKNA and standard deviation of NN intervals (SDNN). WHAT ARE THE CLINICAL IMPLICATIONS?Since microbiota and sympathetic nervous system (SNS) might be essential factors of ACS, it is important to assess the abundance of microbiota and SNS activity for accurate management of ACS. The Hungatella, one of the microbiota involved in atherosclerotic cardiovascular disease, heart failure, inflammatory process, and anxiety disorder, might be the link between SNS and ACS. In our study, we prove the positive association between Hungatella and SKNA. Therefore, by checking the SKNA of patients with ACS, we might discover the SNS activity and also the underlying microbiota etiology of ACS. Then, it is critical and accurate to target Hungatella in ACS patients with high SKNA to reduce the risk of ACS.

microbiology↗

bioRxiv2024

A single-gene-based AI model to identify core and context-specific essential genes by biological interpretation from pooled genome-wide CRISPR and omics data

Genome-wide Clustered Regularly Interspaced Short Palindromic Repeats (CRISPR) is a powerful tool for screening essential genes (EGs) and studying gene function by systematically knocking out individual genes. EGs are essential for the survival of organisms and can be divided into core EGs (CEGs) and context-specific EGs, which are crucial for the development of drugs. Although a variety of CEGs have been identified using knockout technology, the concordance among these CEG sets is extremely low; there is a lack of studies on the EG mechanisms. Therefore, developing systematic methods to identify CEGs and reveal corresponding mechanisms are important biological issues. To address these issues, we propose a comprehensive ensembled-based model utilizing gene community-regulated pathways to decipher pan-cancer CEGs and context-specific EGs across 29 cancer types and provide insights into their regulatory abilities for each pathway. The project aims include developing a model with Systematic Identification of Essential Gene (SIEG) scores for CEGs and Context-Specific Enrichment (CSE) scores for context-specific EGs. Subsequently, we assess the regulated pathways and mechanisms of these identified EGs by integrating diverse data sources such as genome-wide CRISPR/Cas9 knockout screens, multiple omics data, KEGG pathways, and Gene Ontology. Ultimately, we aim to establish a user-friendly web service. In our preliminary results, we gathered 1,845 genome-wide CRISPR datasets and various omics datasets, including 8,941 clinical samples and 1,346 cell lines, leading to the identification of 3,213 CEGs. By employing the SIEG score, we found that 1,178 of these pan-cancer CEGs overlapped with previously defined CEGs, reflecting a 60% similarity rate. These 3,213 CEGs play crucial roles in regulating pathways associated with cell viability, expansion, and proliferation. Additionally, they exhibit characteristics typical of CEGs, showing less favorable as therapeutic targets and centralizing within protein-protein interaction networks. Moreover, we delineated six pathway signatures of pan-cancer CEGs, encompassing transcription, translation, protein folding, replication and repair, cell growth and death, as well as energy. We anticipate that these signatures will contribute to the future redefinition of CEGs.

bioinformatics↗

bioRxiv2024

Inhibiting EZH2 complements steroid effects in Duchenne muscular dystrophy

Duchenne muscular dystrophy (DMD) is a devastating X-linked disorder caused by mutations in the dystrophin gene. Despite recent advances in understanding the disease etiology and applying emerging treatment methodologies, glucocorticoid derivatives remain the only general therapeutic option that can slow disease development. However, the precise molecular mechanism of glucocorticoid action remains unclear, and there is still need for additional remedies to complement the treatment. Here, using single-nucleus RNA-sequencing and spatial transcriptome analyses of human and mouse muscles, we investigated pathogenic features in DMD patients and palliative effects of glucocorticoids. Our approach further illuminated the importance of proliferating satellite cells, and revealed increased activity of a signal transduction pathway involving EZH2 in the patient cells. Subsequent administration of EZH2 inhibitors to Dmd mutant mice resulted in improved muscle phenotype through maintaining the immune-suppressing effect but overriding the muscle weakness and fibrogenic effects exerted by glucocorticoids. Our analysis reveals pathogenic mechanisms that can be readily targeted by extant therapeutic options for DMD. TeaserA survey of DMD tissues in human and mouse suggests EZH2 as a critical factor in DMD satellite cells; its inhibition resulted in better prognosis.

genetics↗

bioRxiv2023

PET imaging of fibroblast activation protein alpha (FAP) detects incipient cardiotoxicity due to anthracycline chemotherapy

BackgroundAnthracycline chemotherapy is associated with a risk of cardiotoxicity leading to heart disease, particularly in pediatric cancer patients. Gold standard methods of detecting cardiotoxicity are insufficiently sensitive to early damage and specific pathophysiologies driving disease. Positron emission tomography (PET) couples anatomical resolution with biochemical mechanistic selectivity and potentially addresses the current diagnostic limitations in cardio-oncology. We aimed to validate PET imaging biomarkers targeting fibroblast activation protein alpha (FAP), Translocator protein (TSPO), and norepinephrine receptor (NET) for detection of incipient anthracycline-induced cardiotoxicity. MethodsCardiotoxicity was established in male C57BL/6J mice by a cumulative dose of 24 mg/kg doxorubicin (DOX) over 2 weeks. DOX mice and their age-matched controls were imaged with echocardiography and PET, using [68Ga]Ga-FAPI-04, [18F]DPA-714, and [18F]MFBG, over 12 weeks. Fractional shortening (FS) was determined from the echocardiograms, and cardiac uptake of the radioligands was quantified from the PET images. Heart sections were collected and used for the analysis of bulk RNA-seq, RT-qPCR, Western blot, in situ hybridization (ISH), and histopathological analysis. ResultsDOX mice exhibited cardiotoxicity and cardiac atrophy. Cardiac [68Ga]Ga-FAPI-04 PET signal was significantly higher in DOX mice from 2 weeks through the study endpoint. By contrast, no cardiac dysfunction was evident by echocardiography until 10 weeks, at which point FS was significantly reduced in DOX mice. There were no differences in [18F]DPA-714 and [18F]MFBG signals. Transcription and translation of FAP, but not TSPO or NET, was detected in cardiomyocytes and were elevated in the DOX hearts, in agreement with the PET data. Genes related to cell adhesion and extracellular remodeling were significantly upregulated in the DOX mice relative to controls. ConclusionsFAP is a sensitive and selective imaging biomarker for incipient cardiotoxicity and FAPI PET is a promising non-invasive imaging tool for identifying patients at risk of cardiotoxicity during or after anthracycline chemotherapy. GRAPHICAL ABSTRACT O_FIG O_LINKSMALLFIG WIDTH=200 HEIGHT=150 SRC="FIGDIR/small/556130v1_ufig1.gif" ALT="Figure 1"> View larger version (38K): org.highwire.dtl.DTLVardef@1d9e717org.highwire.dtl.DTLVardef@d2bde8org.highwire.dtl.DTLVardef@1b1f2c5org.highwire.dtl.DTLVardef@1b99bc6_HPS_FORMAT_FIGEXP M_FIG C_FIG NOVELTY AND SIGNIFICANCEO_ST_ABSWhat is Known?C_ST_ABSO_LIAnthracycline chemotherapy results in cardiotoxicity for a sizeable population of treated patients. Cardiotoxocity manifests as cardiac dysfunction, and may result in long-term cardiac disease and heart failure, particularly in survivors of pediatric cancer. C_LIO_LICardiotoxicity is typically defined in terms of left ventricular ejection fraction (LVEF) deficits, as measured by echocardiography. However, this metric is often poorly sensitive to early disease and agnostic to underlying pathophysiology. C_LIO_LIEarly treatment of cardiotoxicity improves recovery and long-term survival, emphasizing the need for accurate diagnostics in incipient disease. C_LI What New Information Does This Article Contain?O_LI[68Ga]Ga-FAPI-04 accumulates in the hearts of mice experiencing doxorubicin-induced cardiotoxicity as a function of fibroblast activation protein alpha (FAP) expression and activity. By contrast, cardiac uptake of radioligands targeting the translocator protein 18-kDa (TSPO) and the norepinephrine transporter (NET) do not differ between DOX animals and controls. C_LIO_LIPositron emission tomography (PET) imaging following administration of [68Ga]Ga-FAPI-04 detects abnormal cardiac remodeling significantly earlier than LVEF decrease is observed, indicating that it may be more sensitive to incipient disease. C_LI Our study identifies fibroblast activation protein alpha (FAP) as a promising diagnostic imaging biomarker in anthracycline-induced cardiotoxicity. We show that cardiac PET signal increases immediately after doxorubicin treatment, and the signal increase is sustained for at least 10 weeks. In addition, we demonstrate that FAP inhibitor (FAPI) PET correlates with expression of FAP protein and gene. Thus, we provide mechanistic insight into potentially-treatable pathophysiologies driving cardiac atrophy and toxicity, and have identified a translational PET tracer that can image the activation of these processes at an early stage.

cancer biology↗

bioRxiv2023

Epidermal Growth Factor potentiates EGFR(Y992/1173)-mediated therapeutic response of triple negative breast cancer cells to cold atmospheric plasma-activated medium

Cold atmospheric plasma (CAP) holds promise as a cancer-specific treatment that selectively kills basal-like breast cancer cells. We used CAP-activated media (PAM) to capture the multi-modal chemical species of CAP. Specific antibodies, small molecule inhibitors and CRISPR/Cas9 gene-editing approaches showed an essential role for receptor tyrosine kinases, especially epidermal growth factor (EGF) receptor, in mediating triple negative breast cancer (TNBC) cell responses to PAM. EGF also dramatically enhanced the sensitivity and specificity of PAM against TNBC cells. Site-specific phospho-EGFR analysis, signal transduction inhibitors and reconstitution of EGFR-depleted cells with EGFR-mutants confirmed the role of phospho-tyrosines 992/1173 and phospholipase C gamma signaling in upregulating levels of reactive oxygen species above the apoptotic threshold. EGF-triggered EGFR activation enhanced the sensitivity and selectivity of PAM effects on TNBC cells, such that a strategy based on the synergism of CAP and EGF therapy may provide new opportunities to improve the clinical management of TNBC.

cancer biology↗

bioRxiv2023

Finite Element Modeling of Residual Hearing after Cochlear Implant Surgery in Chinchillas

Cochlear implant (CI) surgery is one of the most utilized treatments for severe hearing loss. However, the effects of a successful scala tympani insertion on the mechanics of hearing are not yet fully understood. This paper presents a finite element (FE) model of the chinchilla inner ear for studying the interrelationship between the mechanical function and the insertion angle of a CI electrode. This FE model includes a three-chambered cochlea and full vestibular system, accomplished using -MRI and -CT scanning technology. This models first application found minimal loss of residual hearing due to insertion angle after CI surgery and indicates that it is a reliable and helpful tool for future application in CI design, surgical planning, and stimuli setup.

bioengineering↗

bioRxiv2022

Molecular mechanism of substrate recognition by folate transporter SLC19A1

Folate (vitamin B9) is the coenzyme involved in one-carbon transfer biochemical reactions essential for cell survival and proliferation, with its inadequacy causing developmental defects or severe diseases. Notably, mammalian cells lack the ability to de novo synthesize folate but instead rely on its intake from extracellular sources via specific transporters or receptors, among which SLC19A1 is the ubiquitously expressed one in tissues. However, the mechanism of substrate recognition by SLC19A1 has been unclear. Here we report the cryo-EM structures of human SLC19A1 and its complex with 5-methyltetrahydrofolate at 3.5-3.6 [A] resolution and elucidate the critical residues for substrate recognition. In particular, we reveal that two variant residues among SLC19 subfamily members would designate the specificity for folate. Moreover, we identify intracellular thiamine pyrophosphate as the favorite coupled substrate for folate transport by SLC19A1. Together, this work has established the molecular basis of substrate recognition by this central folate transporter.

biochemistry↗

bioRxiv2022

EZH2/ hSULF1 axis mediates receptor tyrosine kinase signaling to shape cartilage tumor progression

BackgroundChondrosarcomas are primary cancers of cartilaginous tissue and capable of alteration to highly aggressive, metastatic, and treatment-refractory states, leading to a poor prognosis with a five-year survival rate at 11 months for the dedifferentiated subtype. At present, the surgical resection of chondrosarcoma is the only effective treatment, and no other treatment options including targeted therapies, conventional chemotherapies, or immunotherapies are available for these patients. MethodsA non-biased ChIP sequence, cDNA microarray analysis, and validation of chondrosarcoma cell lines identified sulfatase 1(SULF1) as the top EZH2-targeted gene to regulate chondrosarcoma progression. Receptor tyrosine kinase (RTK) array of chondrosarcoma cells with vector control or ectopically expressed SULF1 revealed that cMET was the downstream signal. The regulation of the EZH2/SULF1/cMET axis was further validated in mice and patient samples with mice models and chondrosarcoma tissue array, respectively. ResultsThe EZH2/SULF1/cMET axis is identified, which contributes to the malignancy of chondrosarcoma and provides a potential therapeutic option for the disease. Ectopically expressed SULF1 or pharmaceutical inhibition of the cMET pathway significantly retards the chondrosarcoma growth and extends mice survival. ConclusionsThe results not only established a signal pathway promoting the malignancy of chondrosarcoma but also provided a therapeutic potential for further development of effective target therapy to treat chondrosarcoma.

cancer biology↗

bioRxiv2022

Molecular Characterization of the Tumor Microenvironment in Renal Medullary Carcinoma

Renal medullary carcinoma (RMC) is a highly aggressive disease associated with sickle hemoglobinopathies and universal loss of the tumor suppressor gene SMARCB1. RMC has a relatively low rate of incidence compared with other renal cell carcinomas (RCCs) that has hitherto made molecular profiling difficult. To probe this rare disease in detail we performed an in-depth characterization of the RMC tumor microenvironment using a combination of genomic, metabolic and single-cell RNA-sequencing experiments on tissue from a representative untreated RMC patient, complemented by retrospective analyses of archival tissue and existing published data. Our study of the tumor identifies a heterogenous population of malignant cell states originating from the thick ascending limb of the Loop of Henle within the renal medulla, displaying the hallmarks of increased resistance to cell death by ferroptosis and proteotoxic stress driven by MYC-induced proliferative signals. Specifically, genomic characterization of RMC tumors provides substantiating evidence for the recently proposed dependence of SMARCB1-difficient cancers on an intact CDKN2A-p53 pathway and we suggest increased cystine-mTORC-GPX4 signaling also plays a role within transformed RMC cells. We further propose that RMC has an immune landscape comparable to that of untreated RCCs, including heterogenous expression of the immune ligand CD70 within a sub-population of tumor cells, which could provide an immune-modulatory role that serves as a viable candidate for therapeutic targeting.

cancer biology↗

bioRxiv2021

A protocol for the reduction of applied torque on parent vessel duringelastase-induced aneurysm formation using rabbit animal models

Endovascular therapies for intracranial aneurysms requires animal models for testing the safety and effectiveness prior to translation to the clinic. Rabbits combined with the elastase and right common carotid artery (RCCA) ligation methods is currently a widely used animal model for endovascular device testing. However, the injection of elastase utilizing angiocatheters may potentially exerts adverse torque to the parent vessel and the optimal aneurysm creation period has not been well investigated. In this study, we present a modification to the elastase/RCCA-ligation method by replacing the angio-catheter with a butterfly catheter. Formation of saccular aneurysms was introduced in New Zealand white rabbits (n = 6), and were maintained for 2, 4 and 6 weeks. The formed aneurysms exhibited an elongated geometry and were stable during the study period. We found that the modification in the animal surgery procedure provides improved manipulation of the surgical area, prolonged injection of elastase, and effective degradation of the vascular elastic lamina. Compared to the traditional elastase/RCCA-ligation method, the present technique can more effectively reduce unwanted injury to the parent vessel and, therefore, improved stability of the vasculature for testing the efficacy of newly developed endovascular embolization devices.

bioengineering↗

bioRxiv2021

Genomic and Metabolic Hallmarks of SDH- and FH-Deficient Renal Cell Carcinomas

PurposeSuccinate dehydrogenase-deficient and fumarate hydratase-deficient renal cell carcinomas (SDHRCC and FHRCC) are rare kidney cancers driven by loss of metabolically proximal enzymes. We sought to define and compare the genomic and metabolomic hallmarks of these entities. Experimental DesignWe analyzed SDHRCC and FHRCC tumors with either immunohistochemical evidence of loss of protein expression or genomically-confirmed biallelic inactivation of SDHA/B/C/D/AF2 or FH. Somatic alterations were identified using clinical pipelines, and allele-specific copy number changes were identified using FACETS. Mass-spectrometry-based metabolomic profiling was performed on available SDHRCC and FHRCC tumors. ResultsForty two patients were analyzed (25 FHRCC, 17 SDHRCC). In the germline analysis, 16/17 SDHRCC harbored a germline alteration in SDHB, whereas only 17/22 FHRCC had pathogenic germline FH variants. SDHRCC had a lower mutation burden (p = 0.02) and copy number alteration burden (p = 0.0002) than FHRCC. All SDHRCC presented with deletion of chromosome 1p (overlapping SDHB), whereas FHRCC demonstrated high but not ubiquitous loss of 1q (FH locus). Both SDHRCC and FHRCC demonstrated significant, idiopathic accumulation of the metabolite guanine. FHRCC tumors had elevated levels of urea cycle metabolites (argininosuccinate, citrulline, and fumarate), whereas SDHRCC had elevation of numerous acylcarnitines. These characteristic metabolic changes enabled the identification of a previously unrecognized SDH-deficient RCC. ConclusionDespite sharing similar genetic etiology, SDHRCC and FHRCC represent distinct molecular entities with unique genetic and metabolic abnormalities. Translational RelevanceMutations to the TCA cycle enzymes Succinate Dehydrogenase (SDH) and Fumarate Hydratase (FH) predispose individuals to unique subtypes of renal cell carcinoma (SDHRCC and FHRCC, respectively). Defining the genetic and metabolic hallmarks of these diseases is critical for advancing new diagnostic and therapeutic approaches for these rare but biologically intriguing entities. Despite a superficially similar genetic etiology, SDHRCC and FHRCC demonstrated significantly fewer secondary mutations to other cancer-associated genes and copy number aberrations than FHRCC, and was distinguished by universal loss-of-heterozygosity of chromosome 1p. Metabolomic analysis identified pathways disrupted in both SDHRCC and FHRCC, including the massive accumulation of free guanine, as well as pathways uniquely disrupted in each of the two entities. These metabolomic findings enabled the identification of a previously unidentified case of unclassified RCC with SDH deficiency, suggesting that metabolomic profiling may aid in phenotypic classification of tumors and uncover novel therapeutic targets.

cancer biology↗

bioRxiv2021

Binocular Mirror-Symmetric Microsaccadic Sampling of Hyperacute 3D-Vision

Neural mechanisms behind stereopsis, which requires simultaneous disparity inputs from two eyes, have remained mysterious. Here we show how ultrafast mirror-symmetric photomechanical contractions in the frontal forward-facing left and right eye photoreceptors give Drosophila super-resolution 3D-vision. By interlinking multiscale in vivo assays with multiscale simulations, we reveal how these photoreceptor microsaccades - by verging, diverging and narrowing the eyes overlapping receptive fields - channel depth information, as phasic binocular image motion disparity signals in time. We further show how peripherally, outside stereopsis, microsaccadic sampling tracks a flying flys optic flow field to better resolve the world in motion. These results change our understanding of how insect compound eyes work and suggest a general dynamic stereo-information sampling strategy for animals, robots and sensors. Significance statementTo move efficiently, animals must continuously work out their x,y,z-positions in respect to real-world objects, and many animals have a pair of eyes to achieve this. How photoreceptors actively sample the eyes optical image disparity is not understood because this fundamental information-limiting step has not been investigated in vivo over the eyes whole sampling matrix. This integrative multiscale study will advance our current understanding of stereopsis from static image disparity comparison to a new morphodynamic active sampling theory. It shows how photomechanical photoreceptor microsaccades enable Drosophila super-resolution 3D-vision and proposes neural computations for accurately predicting these flies depth-perception dynamics, limits, and visual behaviors.

neuroscience↗

bioRxiv2021

Nuclear HMGB1 protects from non-alcoholic fatty liver diseases through negative regulation of liver X receptor

Dysregulations of lipid metabolism in the liver may trigger steatosis progression leading to potentially severe clinical consequences such as non-alcoholic fatty liver diseases (NAFLD). Molecular mechanisms underlying liver lipogenesis are very complex and fine-tuned by chromatin dynamics and the activity of multiple key transcription factors. Here, we demonstrate that the nuclear factor HMGB1 acts as a strong repressor of liver lipogenesis during metabolic stress in NAFLD. Mice with liver-specific Hmgb1-deficiency display exacerbated liver steatosis and hepatic insulin resistance when subjected to a high-fat diet or after fasting/refeeding. Global transcriptome and functional analysis revealed that the deletion of Hmgb1 gene enhances LXR activity resulting in increased lipogenesis. HMGB1 repression is not mediated through nucleosome landscape re-organization but rather via a preferential DNA occupation in region carrying genes regulated by LXR. Together these findings suggest that hepatocellular HMGB1 protects from liver steatosis development. HMGB1 may constitute a new attractive option to therapeutically target LXR axis during NAFLD.

pathology↗

bioRxiv2020

Human cytomegalovirus evades ZAP detection by suppressing CpG dinucleotides in the major immediate early genes.

The genomes of RNA and small DNA viruses of vertebrates display significant suppression of CpG dinucleotide frequencies. Artificially increasing dinucleotide frequencies results in substantial attenuation of virus replication, suggesting that these compositional changes may facilitate recognition of non-self RNA sequences. Recently, the interferon inducible protein ZAP, was identified as the host factor responsible for sensing CpG in viral RNA, through direct binding and possibly downstream targeting for degradation. Using an arrayed interferon stimulated gene expression library screen, we identified ZAPS, and its associated factor TRIM25, as direct inhibitors of human cytomegalovirus (HCMV) replication. Exogenous expression of ZAPS and TRIM25 significantly reduced virus replication while knockdown resulted in increased virus replication. HCMV displays a strikingly heterogeneous pattern of CpG representation with a specific suppression of CpGs within the IE1 major immediate early transcript which is absent in subsequently expressed genes. We demonstrated that suppression of CpG dinucleotides in the IE1 gene allows evasion of inhibitory effects of ZAP. During HCMV infection, expression of ZAP and TRIM25 are rapidly reduced, removing pressure to suppress dinucleotide frequencies in viral genes expressed after the immediate early genes, while acute virus replication and high levels of ZAP are mutually exclusive. Finally, we show that TRIM25 regulates alternative splicing between the ZAP short and long isoforms during HCMV infection and interferon induction, with knockdown of TRIM25 resulting in decreased ZAPS and corresponding increased ZAPL expression. These results demonstrate for the first time that ZAP is a potent host restriction factor against large DNA viruses and that HCMV evades ZAP detection through suppression of CpG dinucleotides within the major immediate early transcripts. Furthermore, TRIM25 is required for efficient upregulation of the interferon inducible short isoform of ZAP through regulation of alternative splicing.

microbiology↗

bioRxiv2019

Bmal1 integrates mitochondrial metabolism and macrophage activation

Metabolic pathways and inflammatory processes are under circadian regulation. While rhythmic immune cell recruitment is known to impact infection outcomes, whether the circadian clock modulates immunometabolism remains unclear. We find the molecular clock Bmal1 is induced by inflammatory stimulants, including Ifn-{gamma}/lipopolysaccharide (M1) and tumor conditioned medium, to maintain mitochondrial metabolism under these metabolically stressed conditions in mouse macrophages. Upon M1 stimulation, myeloid-specific Bmal1 knockout (M-BKO) renders macrophages unable to sustain mitochondrial function, enhancing succinate dehydrogenase (SDH)-mediated mitochondrial ROS production and Hif-1-dependent metabolic reprogramming and inflammatory damage. In tumor-associated macrophages, the aberrant Hif-1 activation and metabolic dysregulation by M-BKO contribute to an immunosuppressive tumor microenvironment. Consequently, M-BKO increases melanoma tumor burden, while administrating an SDH inhibitor dimethyl malonate suppresses tumor growth. Therefore, Bmal1 functions as a metabolic checkpoint integrating macrophage mitochondrial metabolism, redox homeostasis and effector functions. This Bmal1-Hif-1 regulatory loop may provide therapeutic opportunities for inflammatory diseases and immunotherapy.

cell biology↗

bioRxiv2019

Structure-function analyses of a keratin heterotypic complex identify specific keratin regions involved in intermediate filament assembly

Intermediate filaments (IFs) provide vital mechanical support in a broad array of cell types. Interference with this role causes cell fragility and accounts for a large number of human diseases. Gaining an understanding IF structure is paramount to understanding their function and designing therapeutic agents for relevant diseases. Here, we report the 2.6 [A] resolution crystal structure of a complex of interacting 2B domains of keratin 5 (K5) and K14. K5 and K14 form a long-range, left-handle coiled coil, with participating -helices aligned in parallel and in register. Follow-up mutagenesis revealed that specific contacts between interacting 2B domains play a crucial role during 10-nm IF assembly, likely at the step of octamer-octamer association. The resulting structural model represents the first atomic-resolution visualization of 2B-2B interactions consistent with the A22 dimer alignment and provide insight into the defects introduced by mutations in IF genes associated with human skin diseases.

biochemistry↗

bioRxiv2019

Diversity and complexity of the large surface protein family in the compacted genomes of various Pneumocystis species

Pneumocystis, a major opportunistic pathogen in patients with a broad range of immunodeficiencies, contains abundant surface proteins encoded by a multi-copy gene family, termed the major surface glycoprotein (Msg) gene superfamily. This superfamily has been identified in all Pneumocystis species characterized to date, highlighting its important role in Pneumocystis biology. In this report, through a comprehensive and in-depth characterization of 459 msg genes from 7 Pneumocystis species, we demonstrate, for the first time, the phylogeny and evolution of conserved domains in Msg proteins, and provide detailed description of the classification, unique characteristics and phylogenetic relatedness of five Msg families. We further describe the relative expression levels of individual msg families in two rodent Pneumocystis species, the substantial variability of the msg repertoires in P. carinii from laboratory and wild rats, and the distinct features of the expression site for the classic msg genes in Pneumocystis from 8 mammalian host species. Our analysis suggests a wide variety of functions for this superfamily, not only conferring antigenic variation to allow immune evasion but also mediating life-stage development, optimizing cell mobility and adhesion, and adapting to specific host niches or environmental conditions. This study provides a rich source of information that lays the foundation for the continued experimental exploration of the functions of the Msg superfamily in Pneumocystis biology.

molecular biology↗

bioRxiv2019

Asparagine deprivation causes a reversible inhibition of Human Cytomegalovirus acute virus replication

As obligate intracellular pathogens, viruses rely on the host cell machinery to replicate efficiently, with the host metabolism extensively manipulated for this purpose. High throughput siRNA screens provide a systematic approach for the identification of novel host-virus interactions. Here, we report a large-scale screen for host factors important for human cytomegalovirus (HCMV), consisting of 6,881 siRNAs. We identified 47 proviral factors and 68 antiviral factors involved in a wide range of cellular processes including the mediator complex, proteasome function and mRNA splicing. Focused characterisation of one of the hits, asparagine synthetase (ASNS), demonstrated a strict requirement for asparagine for HCMV replication which leads to an early block in virus replication before the onset of DNA amplification. This effect is specific to HCMV, as knockdown of ASNS had little effect on herpes simplex virus-1 or influenza A virus replication, suggesting the restriction is not simply due to a failure in protein production. Remarkably, virus replication could be completely rescued seven days post-infection with addition of exogenous asparagine, indicating that while virus replication is restricted at an early stage, it maintains the capacity for full replication days after initial infection. This study represents the most comprehensive siRNA screen for the identification of host factors involved in HCMV replication and identifies the non-essential amino acid, asparagine as a critical factor in regulating HCMV virus replication. These results have implications for control of viral latency and the clinical treatment of HCMV in patients.\n\nImportanceHCMV accounts for more than 60% of complications associated with solid organ transplant patients. Prophylactic or preventative treatment with antivirals, such as ganciclovir, reduces the occurrence of early onset HCMV disease. However, late onset disease remains a significant problem and prolonged treatment, especially in patients with suppressed immune systems, greatly increases the risk of antiviral resistance. Very few antivirals have been developed for use against HCMV since the licensing of ganciclovir, and of these, the same viral genes are often targeted, reducing the usefulness of these drugs against resistant strains. An alternative approach is to target host genes essential for virus replication. Here we demonstrate that HCMV replication is highly dependent on levels of the amino acid asparagine and knockdown of a critical enzyme involved in asparagine synthesis results in severe attenuation of virus replication. These results suggest that reducing asparagine levels through dietary restriction or chemotherapeutic treatment could limit HCMV replication in patients.

microbiology↗