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Huang, M.

Publications and source records attributed to Huang, M..

At least 109 records · Page 6Linked to original sources
bioRxiv2024

Engineering customized viral receptors for various coronaviruses

Coronaviruses display versatile receptor usage, yet in-depth characterization of coronaviruses lacking known receptor identities has been impeded by the absence of feasible infection models1,2. Here, we developed an innovative strategy to engineer functional customized viral receptors (CVRs). The modular design relies on building receptor frameworks comprising various function modules and generating specific epitope-targeting viral binding domains. We showed the key factors for CVRs to efficiently facilitate spike cleavage, membrane fusion, pseudovirus entry, and authentic virus propagation for various coronaviruses, resembling their native receptors. Applying this strategy, we delineated the accessible receptor binding epitopes for functional SARS-CoV-2 CVR design and elucidated the mechanism of entry supported by an amino-terminus domain (NTD) targeting S2L20-CVR. Furthermore, we created CVR-expressing cells for assessing antibodies and inhibitors against 12 representative coronaviruses from six subgenera, most of which lacking known receptors. Notably, a pan-sarbecovirus CVR supported entry of various sarbecoviruses, as well as propagation of a replicable HKU3 pseudovirus and the authentic strain RsHuB2019A3. Through combining an HKU5-specific CVR with reverse genetics, we successfully rescued and cultured wild-type and fluorescence protein-incorporated HKU5, a receptor-unidentified merbecovirus. Our study demonstrated the great potential of CVR strategy in establishing native receptor-independent infection models, paving the way for studying various viruses that are challenging to culture due to the lack of susceptible cells. O_FIG O_LINKSMALLFIG WIDTH=200 HEIGHT=162 SRC="FIGDIR/small/583237v1_ufig1.gif" ALT="Figure 1"> View larger version (52K): org.highwire.dtl.DTLVardef@7cb9ccorg.highwire.dtl.DTLVardef@8a2855org.highwire.dtl.DTLVardef@5e14f0org.highwire.dtl.DTLVardef@b0b993_HPS_FORMAT_FIGEXP M_FIG O_FLOATNOGraphic abstractC_FLOATNO C_FIG

microbiology↗
bioRxiv2024

Characterization of the SARS-CoV-2 BA.5 Variants in H11-K18-hACE2 Hamsters

This study aims to comprehensively characterize the SARS-CoV-2 BA.5 variants using K18 hACE2 transgenic mice and golden hamsters as model organisms. Previous research on SARS-CoV-2 has utilized both mouse and hamster models, leading to conflicting results concerning the viruss lethality. In our study, the finding suggests that H11-K18 hACE2 golden hamsters closely mimic the disease progression observed in human COVID-19 cases caused by BA.5 variants, demonstrating consistent severity and symptoms comparable to severe infections. Additionally, hamsters exhibit heightened respiratory viral replication, accurately reflecting the clinical viral kinetics observed in humans. The study emphasizes the critical importance of selecting an appropriate animal model for SARS-CoV-2 research, while also providing robust support for the hypothesis that BA.5 variants contribute to fatal outcomes in COVID-19 cases. These findings highlight the pivotal role of the golden hamster model in advancing our understanding of the pathogenic mechanisms underlying SARS-CoV-2 variants, as well as in the development of targeted therapeutic strategies. Significance StatementOur research work explores groundbreaking insights that could reshape our understanding of COVID-19 and pave the way for targeted therapies. We use golden hamster models to express the possibility of different animal models could contribute to human diseases. We hope this finding could clarify some conflicts existed, and help further development of medication for COVID.

immunology↗
bioRxiv2024

Sarbecovirus RBD indels and specific residues dictating ACE2 multi-species adaptiveness

Sarbecoviruses exhibit varying abilities in using angiotensin-converting enzyme 2 (ACE2) receptor1-3. However, a comprehensive understanding of their multi-species ACE2 adaptiveness and the underlying mechanism remains elusive, particularly for many sarbecoviruses with various receptor binding motif (RBM) insertions/deletions (indels)4-11. Here, we analyzed RBM sequences from 268 sarbecoviruses categorized into four RBM indel types. We extensively examined the capability of 14 representative sarbecoviruses and their derivatives in using ACE2 orthologues from 51 bats and five non-bat mammals. We revealed that most sarbecoviruses with longer RBMs (type-I), present broad ACE2 tropism, whereas viruses with single deletions in Region 1 (type-II) or Region 2 (type-III) generally exhibit narrow ACE2 tropism, typically favoring their hosts ACE2. Sarbecoviruses with double region deletions (type-IV) exhibit a complete loss of ACE2 usage. Subsequent investigations unveiled that both loop deletions and critical RBM residues significantly impact multi-species ACE2 tropism in different ways. Additionally, fine mapping based on type-IV sarbecoviruses elucidated the role of several clade-specific residues, both within and outside the RBM, in restricting ACE2 usage. Lastly, we hypothesized the evolution of sarbecovirus RBM indels and illustrated how loop length, disulfide, and adaptive mutations shape their multi-species ACE2 adaptiveness. This study provides profound insights into the mechanisms governing ACE2 usage and spillover risks of sarbecoviruses.

microbiology↗
bioRxiv2023

Quantification of cell phenotype transition manifolds with information geometry

Cell phenotype transition (CPT) is crucial in development and other biological processes. Advances in single-cell sequencing reveal that CPT dynamics are confined to low-dimensional manifolds, yet current methods cannot directly quantify these manifolds. We present SCIM (single cell information manifolds), a geometry-guided approach using information geometry. SCIM embeds single-cell gene expression profiles as Gaussian distributions, defining the Fisher metric naturally in this space. We compute each cells coarse Ricci curvature, finding that low-curvature cells mark critical transitions. By further calculating each cells information velocity from RNA velocity, we find that regions with high information velocity coincide with low curvature, suggesting that geometry guides cellular dynamics on CPT manifolds. SCIM uncovers invariant features of CPT manifolds and provides a general framework for quantifying dynamics on these manifolds.

biophysics↗
bioRxiv2023

A direct estrogenic involvement in the expression of human hypocretin

BackgroundHypocretin-1 may play an important role in depression, which was increased in female depression in LHA in our previous study. Estrogen acts through its nuclear transcriptional receptors. MethodsWe studied the possibility of a direct action of estrogen receptors on the expression of human hypocretin. To explore the activation of ERs by hypocretin, we first investigated the potential presence of co-localization of the estrogen receptors (ERs) in hypocretin-immunoreactive neurons in the lateral hypothalamic area (LHA) in human and nuclear ERs in hypocretin immunoreactive neuroblastoma SK-N-SH cells. We investigated the relationship between E2 and hypocretin in female rats. After we explored the regulating role of exogenous estrogen on hypocretin gene expression via ERs through Chromatin immunoprecipitation, Electrophoretic mobility shift assay and Luciferase assay. ResultsWe found that hypocretin-1 plasma level was significantly higher in female depression. Estrogen receptors (ER and ER{beta}) and hypocretin are co-localized in female depression LHA, PC12 and SK-N-SH cell lines. The estrogen receptor response elements (EREs) existing in the hypocretin promoter region may directly regulate the expression of hypocretin, the synchronicity of change of hypocretin and estradiol both in hypothalamus and plasma was verified in female rats. With the presence of estradiol, there is specific binding between human ER and the Hypocretin-ERE. Expression of ER combined with estradiol repressed hypocretin promoter activity through the ERE. Conclusionswe defined that estradiol may affect hypocretin neurons in the human hypothalamus via ER binding to the Hypocretin-ERE directly, which may thus lead to the sex-specific pathogenesis of depression.

neuroscience↗
bioRxiv2023

Activating SRC/MAPK signaling via 5-HT1A receptor contributes to the effect of vilazodone on improving thrombocytopenia

Thrombocytopenia caused by long-term radiotherapy and chemotherapy exists in cancer treatment. Previous research demonstrates that 5-Hydroxtrayptamine (5-HT) and its receptors induces the formation of megakaryocytes (MKs) and platelets. However, the relationships between 5-HT1A receptor (5-HTR1A) and MKs is unclear so far. We screened and investigated the mechanism of vilazodone as a 5-HTR1A partial agonist in promoting MK differentiation and evaluated its therapeutic effect in thrombocytopenia. We employed a drug screening model based on machine learning (ML) to screen the megakaryocytopoiesis activity of VLZ. The effects of Vilazodone (VLZ) on megakaryocytopoiesis were verified in HEL and Meg-01 cells. Tg (itga2b: eGFP) zebrafish was performed to analyze the alterations in thrombopoiesis. Moreover, we established a thrombocytopenia mice model to investigate VLZ administration accelerates platelet recovery and function. We carried out network pharmacology, Western blot and immunofluorescence to demonstrate the potential targets and pathway of VLZ. VLZ has been predicted to have a potential biological action. Meanwhile, VLZ administration promotes MK differentiation and thrombopoiesis in cells and zebrafish models. Progressive experiments showed that VLZ has a potential therapeutic effect on radiation-induced thrombocytopenia in vivo. The network pharmacology and associated mechanism study indicated that SRC and MAPK signaling are both involved in the processes of megakaryopoiesis facilitated by VLZ. Furthermore, the expression of 5-HTR1A during megakaryocyte differentiation is closely related to the activation of SRC and MAPK. Our findings demonstrated that the expression of 5-HTR1A on MK, VLZ could bind to the 5-HTR1A receptor and further regulate the SRC/MAPK signaling pathway to facilitate megakaryocyte differentiation and platelet production, which provides new insights into the alternative therapeutic options for thrombocytopenia.

pharmacology and toxicology↗
bioRxiv2023

A genome-wide survey of DNA methylation in Panax notoginseng reveals CHH hyper-methylation regulates the after-ripening and dormancy of recalcitrant seeds

DNA methylation plays a crucial role in regulating fruit ripening and seed development. It remains unknown about the dynamic characteristics of DNA methylation and its regulation mechanisms in morpho-physiological dormancy (MPD)-typed seeds with recalcitrant characteristics. The P. notoginseng seeds are defined by the MPD and are characterized by a strong sensitivity to dehydration during the after-ripening process. We performed DNA methylomes, siRNA profiles, and transcriptomes of embryo and endosperm in P. notoginseng seeds at different after-ripening stages. Herein, we find that the CHH hyper-methylation contributes to the global increase in DNA methylation during the after-ripening process of P. notoginseng seeds. The endosperm genome is hyper-methylated compared to the embryo genome. The CHH hyper-methylation is caused by the high expression level of DNA methyltransferase PnCMT2 in the embryo, and PnDRM2 in the endosperm, respectively. The CHH hyper-methylation alters gene transcription levels to regulate the after-ripening and dormancy of recalcitrant seeds. For example, it inhibits the expression of genes in embryo development to make seeds maintain a dormant status, whereas it activates the expression of genes in the hormone-mediated signaling pathway, and energy metabolism to accomplish the MPD-typed seed after-ripening process. Together, our findings reveal a global increase in DNA methylation and its vital driver in gene expression, and thus elucidate how global CHH hyper-methylation regulates the after-ripening in recalcitrant MPD-typed seeds. This work establishes a key role for epigenetics in regulating the dormancy of MPD-typed seeds with recalcitrant characteristics.

developmental biology↗
bioRxiv2023

Identification of ACE2 as the Entry Receptor for Two Novel European Bat Merbecoviruses

The angiotensin-converting enzyme 2 (ACE2) receptor is shared by various coronaviruses with distinct receptor-binding domain (RBD) architectures, yet our understanding of these convergent acquisition events remains elusive. Here, we report that two European bat MERS-related coronaviruses (MERSr-CoVs) infecting Pipistrellus nathusii (P.nat), MOW15-22 and PnNL2018B, use ACE2 as their receptor, with narrow ortholog specificity. Cryo-electron microscopy structures of the MOW15-22 RBD-ACE2 complex unveil an unexpected and entirely distinct binding mode, mapping 50[A] away from that of any other known ACE2-using coronaviruses. Functional profiling of ACE2 orthologs from 105 mammalian species led to the identification of host tropism determinants, including an ACE2 N432-glycosylation restricting viral recognition, and the design of a soluble P.nat ACE2 mutant with potent viral neutralizing activity. Our findings reveal convergent acquisition of ACE2 usage for merbecoviruses found in European bats, underscoring the extraordinary diversity of ACE2 recognition modes among coronaviruses and the promiscuity of this receptor. Graphic abstract O_FIG O_LINKSMALLFIG WIDTH=200 HEIGHT=112 SRC="FIGDIR/small/560486v2_ufig1.gif" ALT="Figure 1"> View larger version (45K): org.highwire.dtl.DTLVardef@1967686org.highwire.dtl.DTLVardef@13f8c8borg.highwire.dtl.DTLVardef@1241e38org.highwire.dtl.DTLVardef@3bfd7a_HPS_FORMAT_FIGEXP M_FIG C_FIG

microbiology↗
bioRxiv2023

Oligodendroglia generate vascular mural cells and neurons in the adult mouse brain

BACKGROUNDOligodendroglia encompass oligodendrocyte precursor cells (OPCs) and oligodendrocytes (OLs). In the grey matter of the cortex, nearly all OPCs divide slowly, yet they dont differentiate solely into mature OLs, leaving the exact role of these OPCs in the grey matter enigmatic. METHODSOligodendroglia, including OPCs, were traced using the Sox10 Cre-ERT2 reporter mice. We compared the effect of tamoxifen dissolved in different solvents on the fate of Sox10 cells. We also compared the effect of tamoxifen dosage on the fate of Sox10 cells. The differentiation of labeled red fluorescent protein (RFP) cells was analyzed using immunofluorescence staining. RESULTSTwo groups of RFP cells, type A Sox10 (Sox10-A) cells, and type B Sox10 (Sox10-B) cells, were identified in the cortex, striatum, hippocampus, thalamus, and hypothalamus. Sox10-A cells differentiate into platelet-derived growth factor receptor-{beta} (PDGFR{beta})+, CD13+ pericytes, and smooth muscle myosin heavy chain 11 (MYH11) + smooth muscle cells when the mice received ethanol or high-dose tamoxifen. Sox10-B cells transform into glutamatergic neurons when the mice received high-dose tamoxifen. Sox10-B cells include perineurona OPCs and OLs. CONCLUSIONSThis investigation provides evidence that a substantial proportion of oligodendroglia in the grey matter serve as mural cell precursors and neuronal precursors. These two phenomena may contribute to our understanding of neurodegenerative diseases. Graphic abstract O_FIG O_LINKSMALLFIG WIDTH=200 HEIGHT=84 SRC="FIGDIR/small/549127v1_ufig1.gif" ALT="Figure 1"> View larger version (14K): org.highwire.dtl.DTLVardef@1b7bef9org.highwire.dtl.DTLVardef@5af54borg.highwire.dtl.DTLVardef@19e3d45org.highwire.dtl.DTLVardef@1c881f1_HPS_FORMAT_FIGEXP M_FIG C_FIG

neuroscience↗
bioRxiv2023

Network effects of traumatic brain injury: from infra slow to high frequency oscillations

Traumatic brain injury (TBI) can have a multitude of effects on neural functioning. In extreme cases, TBI can lead to seizures both immediately following the injury as well as persistent epilepsy over years to a lifetime. However, mechanisms of neural dysfunctioning after TBI remain poorly understood. To address these questions, we analyzed experimental data and developed a biophysical network model implementing effects of ion concentration dynamics and homeostatic synaptic plasticity to test effects of TBI on the brain network dynamics. We focus on three primary phenomena that have been reported in vivo after TBI: an increase in infra slow oscillations (<0.1 Hz), increase in delta (0.1 - 4 Hz) power, and the emergence of high frequency oscillations (HFOs) in the gamma range (30 - 100 Hz). We show that the infra slow oscillations can be directly attributed to extracellular potassium fluctuations, while the existence and characterization of HFOs is related to the increase in strength of synaptic weights from homeostatic synaptic scaling. The experimentally found transient increase in delta power can be attributed to the inter-HFO timings. We then show that buildup of high frequency oscillations in the injured region can lead to seizure-like events that span all neurons in the network; additional seizures can then be initiated in previously healthy regions. This study brings greater understanding of network effects of TBI, and how they can give rise to epileptic activity. This lays the foundation to begin investigating how injured networks can be healed and seizures prevented. Significance StatementThis project delineates and attempts to explain abnormalities seen in human brain following traumatic brain injury (TBI). TBI can lead to the development of seizures, which may last a lifetime and often become resistant to pharmaceutical treatments. The study identified key mechanisms responsible for occurrence of three characteristic changes in spatio-temporal network dynamics following TBI. This model provides predictions that can serve as a testing ground for potential therapeutic approaches.

neuroscience↗
bioRxiv2023

SNAP-25, but not SNAP-23, is essential for photoreceptor function and survival in mice

Vesicular transport plays critical roles in photopigment delivery at photoreceptor outer segments and glutamate exocytosis at photoreceptor synapses. Previous studies into the role of photoreceptor SNAP proteins are limited in their characterizations into only gene/protein expression and do not delve further into their functional role. Here, we examine the expression and localization of SNAP-23 and SNAP-25 mRNA and protein. Using SNAP-23 and SNAP-25 conditional knockout mice, we further evaluated the morphological and functional consequences that the absence of these proteins has on vision. Although we found that the ubiquitously expressed SNAP-23 showed weak mRNA expression in photoreceptors, removal of SNAP-23 did not result in any observable phenotype. We found that neuronal SNAP-25 is developmentally regulated and SNAP-25 mRNA undergoes mRNA trafficking to the photoreceptor inner segments coinciding with the development of photoreceptor outer segments. Removal of SNAP-25 in photoreceptor cells led to changes in both outer segment protein trafficking and synaptic integrity, resulting in a complete loss of vision in SNAP-25 cKO mice. Our results conclude that SNAP-25, but not SNAP-23, is the essential isoform for photoreceptor survival and function.

neuroscience↗
bioRxiv2023

Mouse model of multiple sclerosis induced by disrupting vesicular transport in oligodendrocytes

Multiple Sclerosis is an autoimmune demyelination disorder with unknown etiology. Despite the myelin damage, the roles of myelinating oligodendrocytes in driving disease progression remain unknown. We hypothesize that disrupting vesicular transport in oligodendrocytes during adolescence will disrupt myelin integrity and causes neuroinflammation. By creating a mouse model of SNAP-23 conditional knockout in mature oligodendrocytes, we showed that impairment in vesicular trafficking in oligodendrocytes causes demyelination. Neuroinflammation with infiltration of peripheral immune T cells into the central nervous system was observed accompanied by demyelination. Mechanistically, SNAP-23 removal in oligodendrocytes caused abnormal axon-myelin structures and impaired myelin protein trafficking, both can contribute to autoimmune activation and demyelination. With our novel animal model, we propose that oligodendrocyte injury is an endogenous early event in triggering Multiple Sclerosis. One-Sentence SummaryImpaired vesicular transport in oligodendrocytes in adults caused demyelination and inflammation driving Multiple Sclerosis

neuroscience↗
bioRxiv2023

Differential Regulation of Excitatory vs Inhibitory Synaptic Release by Complexin/CPX-1 and CAPS/UNC-31 at the C. elegans Neuromuscular Junctions

The excitation and inhibition (E/I) balance at neuromuscular junctions plays a crucial role in coordinating animal motor behavior. Prominent synaptic vesicle secretory regulatory proteins, specifically complexin and CAPS (Calcium-dependent Activator Protein for Secretion), have not garnered sufficient attention for E/I balance regulation. Here, we investigate the roles of complexin/CPX-1 and CAPS/UNC-31 in excitatory vs inhibitory synapses of C. elegans neuromuscular junctions. In our study, cpx-1 null mutants displayed remarkable reduction evoked release in both excitatory and inhibitory synapses. Intriguingly, these mutants exhibited an enhanced level of spontaneous release, particularly within the context of excitatory synapse. This enhancement aligns with its "clamp" role that preventing SV from fusing with the presynaptic membrane. Additionally, a clamping-specific knockin mutant cpx-1({Delta}12), which displayed no alterations in evoked release at either type of synapse, also revealed a biased substantial increase in excitatory spontaneous release. In contrast, unc-31 null mutation, with normal spontaneous release, led to a more pronounced decreased evoked release in the excitatory synapse independent of dense-core vesicle regulation. Intriguingly, we found that the enhanced excitatory spontaneous release observed in cpx-1 mutants was abolished by unc-31 in a Ca2+-dependent manner, implying that UNC-31 is essential for maintaining a high level of spontaneous fusion events. Collectively, our findings unveil a distinct regulatory pattern governing excitatory and inhibitory synaptic release, orchestrated by the interplay of CPX-1 and UNC-31. Notably, we uncover an unforeseen role of UNC-31 in influencing CPX-1s "clamp" function, further adding complexity to the neural dynamics, which may underlie complex behavioral phenotypes observed in C. elegans.

neuroscience↗
bioRxiv2023

Unravelling cancer subtype-specific driver genes in single-cell transcriptomics data with CSDGI

Cancer is known as a heterogeneous disease. Cancer driver genes (CDGs) need to be inferred for understanding tumor heterogeneity in cancer. However, the existing computational methods have identified many common CDGs. A key challenge exploring cancer progression is to infer cancer subtype-specific driver genes (CSDGs), which provides guidane for the diagnosis, treatment and prognosis of cancer. The significant advancements in single-cell RNA-sequencing (scRNA-seq) technologies have opened up new possibilities for studying human cancers at the individual cell level. In this study, we develop a novel unsupervised method, CSDGI (Cancer Subtype-specific Driver Gene Inference), which applies Encoder-Decoder-Framework consisting of low-rank residual neural networks to inferring driver genes corresponding to potential cancer subtypes at single-cell level. To infer CSDGs, we apply CSDGI to the tumor single-cell transcriptomics data. To filter the redundant genes before driver gene inference, we perform the differential expression genes (DEGs). The experimental results demonstrate CSDGI is effective to infer driver genes that are cancer subtype-specific. Functional and disease enrichment analysis shows these inferred CSDGs indicate the key biological processes and disease pathways. CSDGI is the first method to explore cancer driver genes at the cancer subtype level. We believe that it can be a useful method to understand the mechanisms of cell transformation driving tumours. Author summaryCancer is recognized as a complex disease with diverse characteristics. In order to comprehend the diversity within tumors, it is essential to infer cancer subtype-specific driver genes (CSDGs), which offer valuable insights for investigating cancer progression and treatment. The remarkable progress made in single-cell RNA-sequencing (scRNA-seq) technologies has ushered in new prospects for studying human cancers at the cellular level. Cancer Subtype-specific Driver Gene Inference (CSDGI) is a novel unsupervised method proposed. In our study, we use Encoder-Decoder-Framework to infer driver genes specific to cancer subtypes in the CSDGI. We apply CSDGI to three tumor single-cell transcriptomics data. The experimental results have shown the effectiveness of CSDGI. Furthermore, functional and disease enrichment analyses illustrate that these inferred CSDGs shed light on crucial biological processes and disease pathways. Our collection of driver genes will serve as a valuable resource in unraveling the mechanisms driving cell transformation in tumors.

bioinformatics↗
bioRxiv2023

Double open syntaxin and UNC-18 P334A mutation leads to excitatory-inhibitory imbalance and impairs multiple aspects of C. elegans behavior

SNARE and Sec/Munc18 proteins are essential in synaptic vesicle exocytosis. Open form t-SNARE syntaxin and UNC-18 P334A are well-studied exocytosis-enhancing mutants. Here we investigate the interrelationship between the two mutations by generating double mutants in various genetic backgrounds in C. elegans. While each single mutation rescued the motility of CAPS/unc-31 and synaptotagmin/snt-1 mutants significantly, double mutations unexpectedly worsened motility or lost their rescuing effects. Electrophysiological analyses revealed that simultaneous mutations of open syntaxin and gain-of-function P334A UNC-18 induces a strong imbalance of excitatory over inhibitory transmission. In liposome fusion assays performed with mammalian proteins, the enhancement of fusion caused by the two mutations individually was abolished when the two mutations were introduced simultaneously, consistent with what we observed in C. elegans. We conclude that open syntaxin and P334A UNC-18 do not have additive beneficial effects, and this extends to C. elegans characteristics such as motility, growth, offspring bared, body size, and exocytosis, as well as liposome fusion in vitro. Our results also reveal unexpected differences between the regulation of exocytosis in excitatory versus inhibitory synapses.

neuroscience↗
bioRxiv2023

weIMPUTE: A User-Friendly Web-Based Genotype Imputation Platform

Genotype imputation is a critical preprocessing step in genome-wide association studies (GWAS), enhancing statistical power for detecting associated single nucleotide polymorphisms (SNPs) by increasing marker size. In response to the needs of researchers seeking user-friendly graphical tools for imputation without requiring informatics or computer expertise, we have developed weIMPUTE, a web-based imputation graphical user interface (GUI). Unlike existing genotype imputation software, weIMPUTE supports multiple imputation software, including SHAPEIT, Eagle, Minimac4, Beagle, and IMPUTE2, while encompassing the entire workflow, from quality control to data format conversion. This comprehensive platform enables both novices and experienced users to readily perform imputation tasks. For reference genotype data owners, weIMPUTE can be installed on a server or workstation, facilitating web-based imputation services without data sharing. weIMPUTE represents a versatile imputation solution for researchers across various fields, offering the flexibility to create personalized imputation servers on different operating systems.

bioinformatics↗
bioRxiv2023

DePARylation is critical for S phase progression and cell survival

Poly(ADP-ribose)ylation or PARylation by PAR polymerase 1 (PARP1) and dePARylation by poly(ADP-ribose) glycohydrolase (PARG) are equally important for the dynamic regulation of DNA damage response. PARG, the most active dePARylation enzyme, is recruited to sites of DNA damage via pADPr-dependent and PCNA-dependent mechanisms. Targeting dePARylation is considered an alternative strategy to overcome PARP inhibitor resistance. However, precisely how dePARylation functions in normal unperturbed cells remains elusive. To address this challenge, we conducted multiple CRISPR screens and revealed that dePARylation of S phase pADPr by PARG is essential for cell viability. Loss of dePARylation activity initially induced S phase-specific pADPr signaling, which resulted from unligated Okazaki fragments and eventually led to uncontrolled pADPr accumulation and PARP1/2-dependent cytotoxicity. Moreover, we demonstrated that proteins involved in Okazaki fragment ligation and/or base excision repair regulate pADPr signaling and cell death induced by PARG inhibition. In addition, we determined that PARG expression is critical for cellular sensitivity to PARG inhibition. Additionally, we revealed that PARG is essential for cell survival by suppressing pADPr. Collectively, our data not only identify an essential role for PARG in normal proliferating cells but also provide a potential biomarker for the further development of PARG inhibitors in cancer therapy.

cancer biology↗