Biology subjects

Peng, W.

Publications and source records attributed to Peng, W..

At least 55 records · Page 3Linked to original sources

bioRxiv2024

An emerging PB2-627 polymorphism increases the pandemic potential of avian influenza virus by breaking through ANP32 host restriction in mammalian and avian hosts

Alterations in the PB2-627 domain could substantially increase the risk of an avian influenza virus (AIV) pandemic. So far, a well-known mammalian mutation PB2-E627K has not been maintained in AIV in poultry, which limits the spread of AIVs from avian to humans. Here, we discovered a variant, PB2-627V, which combines the properties of avian-like PB2-627E and human-like PB2-627K, overcoming host restrictions and posing a risk for human pandemics. Specifically, by screening the global PB2 sequences, we discovered a new independent cluster with PB2-627V emerged in the 2010s, which is prevalent in various avian, mammalian, and human isolates of AIVs, including H9N2, H7N9, H3N8, 2.3.4.4b H5N1, and other subtypes. And, the increasing prevalence of PB2-627V in poultry is accompanied by a rise in human infection cases with this variant. Then we systematically assessed its host adaptation, fitness, and transmissibility across three subtypes of AIVs (H9N2, H7N9, and H3N8) in different host models, including avian and human cells, chickens, mice, and ferrets where infections naturally occur. We found that PB2-627V facilitates AIVs to efficiently infect and replicate in chickens and mice by utilizing both avian- and human-origin ANP32A proteins. Importantly, and like PB2-627K, PB2-627V promotes efficient transmission between ferrets through respiratory droplets. Deep sequencing in passaged chicken samples and transmitted ferret samples indicates that PB2-627V remains stable across the two distinct hosts and has a high potential for long-term prevalence in avian species. Therefore, the mutation has the ability to continue spreading among poultry and can also overcome the barrier between birds and humans, greatly enhancing the likelihood of AIVs infecting humans. Given the escalating global spread of AIVs, it is crucial to closely monitor influenza viruses carrying PB2-627V to prevent a pandemic.

microbiology↗

bioRxiv2024

Elucidating immune-related gene transcriptional programs via factorization of large-scale RNA-profiles

Recent developments in immunotherapy, including immune checkpoint blockade (ICB) and adoptive cell therapy, have encountered challenges such as immune-related adverse events and resistance, especially in solid tumors. To advance the field, a deeper understanding of the molecular mechanisms behind treatment responses and resistance is essential. However, the lack of functionally characterized immune-related gene sets has limited data-driven immunological research. To address this gap, we adopted non-negative matrix factorization on 83 human bulk RNA-seq datasets and constructed 28 immune-specific gene sets. After rigorous immunologist-led manual annotations and orthogonal validations across immunological contexts and functional omics data, we demonstrated that these gene sets can be applied to refine pan-cancer immune subtypes, improve ICB response prediction and functionally annotate spatial transcriptomic data. These functional gene sets, informing diverse immune states, will advance our understanding of immunology and cancer research.

bioinformatics↗

bioRxiv2024

High Frequency Terahertz Stimulation Alleviates Neuropathic Pain by Inhibiting the Pyramidal Neuron Activity in the Anterior Cingulate Cortex of mice

Neuropathic pain (NP) is caused by a lesion or disease of the somatosensory system and is characterized by abnormal hypersensitivity to stimuli and nociceptive responses to non-noxious stimuli, affecting approximately 7-10% of the general population. However, current first-line drugs like non-steroidal anti-inflammatory agents and opioids have limitations, including dose-limiting side effects, dependence, and tolerability issues. Therefore, developing new interventions for the management of NP is urgent. In this study, we discovered that the high-frequency terahertz stimulation (HFTS) at approximate 36 THz effectively alleviates NP symptoms in mice with spared nerve injury. Computational simulation suggests that the frequency resonates with the carbonyl group in the filter region of Kv1.2 channels, facilitating the translocation of potassium ions. In vivo and in vitro results demonstrate that HFTS reduces the excitability of pyramidal neurons in the anterior cingulate cortex through enhancing the voltage-gated K+ and also the leak K+ conductance. This research presents a novel optical intervention strategy with terahertz waves for the treatment of NP and holds promising application in other nervous system diseases.

neuroscience↗

bioRxiv2024

LRRK2 G2019S mutation suppresses differentiation of Th9 and Treg cells via JAK/STAT3

The Leucine-rich repeat kinase-2 (LRRK2) G2019S mutation, resulting in aberrantly enhanced kinase activity, is one of the well-recognized genetic risk factors in Parkinsons Disease (PD). Increased LRRK2 activity was also observed in immune cells from PD patients. Emerging results have also unveiled an upsurge in -synuclein (-syn)-specific CD4+ T cell responses in PD patients. Given that LRRK2 mutations in PD are germline mutations, there are unmet meets to explore whether LRRK2 G2019S mutation contributes to the pathogenesis of PD via altering CD4+ T-cell functions. To fill this knowledge gap, we generated a new T cell receptor (TCR) transgenic mouse strain bearing LRRK2 G2019S knock-in mutation, OT-II/LRRK2 (Refer to Mut). As CD4+ T cells from OT-II mice specifically recognize ovalbumin, this new strain enables us to explore the impact of LRRK2 G2019S mutation on T-cell functions in an antigen-specific manner. We found that the abundance and proliferation of major immune subsets in spleen tissue from Mut mice are comparable to wild-type (OT-II, Refer to WT) control. However, when we characterized T cell differentiation in these two strains, T cells derived from Mut mice displayed increased Th2 differentiation (IL-4) and decreased Th9 (IL-9) and Treg (Foxp3+ %) differentiation. LRRK2 G2019S mutation significantly altered the expression levels of master transcription factors (TFs) for T cell differentiation. Specifically, Mut T cells displayed an increase in mRNA expression of Gata3 (TF for Th2), a decrease in expression of Irf4 and Foxp3 (TFs for Th9 and Treg, respectively). Mechanistically, LRRK2 mutation decreased IL-9 production and Treg cell population through the JAK/STAT3 signaling. In conclusion, LRRK2 plays a critical role in regulating T cell differentiation, warranting further studies to evaluate the impacts of altered T cell differentiation led by LRRK2 mutation in dopaminergic neuron damages.

immunology↗

bioRxiv2024

Architecture of the spinach plastid-encoded RNA polymerase

The plastid-encoded RNA polymerase (PEP) serves as the principal transcription machinery within chloroplasts and is responsible for transcribing over 80% of primary plastid transcripts. Plant PEP is composed of a prokaryotic-like multisubunit core enzyme known as the PEP core, supplemented by newly evolved PEP-associated proteins (PAPs). In this study, we present the cryo-electron microscopy (cryo-EM) structure of a PEP complex derived from spinach (Spinacia oleracea). Our structural analysis unveils the presence of 14 PAPs closely associated with the PEP core complex consisting of 5 subunits, forming an irregular-shaped supercomplex. We provide a detailed depiction of the PEP core subunits and the 14 PAPs, elucidating their precise spatial arrangement and interactions. This research offers a crucial structural basis for future investigations into the functions and regulatory mechanisms governing plastid transcription.

biochemistry↗

bioRxiv2023

FASlpr gene dosage tunes the extent of lymphoproliferation and T cell differentiation in lupus

Sle1 and Faslpr are two lupus susceptibility loci that lead to manifestations of systemic lupus erythematosus. To evaluate dosage effects of FASlpr in determining cellular and serological phenotypes associated with lupus, we developed a new C57BL/6 (B6) congenic lupus strain, B6.Sle1/Sle1.Faslpr/+ (sle1homo.lprhet) and compared it with B6.Faslpr/lpr(lprhomo), B6.Sle1/Sle1 (sle1homo), and B6.Sle1/Sle1.Faslpr/lpr (sle1homo.lprhomo) strains. Whereas Sle1homo.lprhomo mice exhibited profound lymphoproliferation and early mortality, sle1homo.lprhet mice had a lifespan comparable to B6 mice, with no evidence of splenomegaly or lymphadenopathy. Compared to B6 monogenic lupus strains, sle1homo.lprhet mice exhibited significantly elevated serum anti-dsDNA antibodies and increased proteinuria. Additionally, Sle1homo.lprhet T cells had an increased propensity to differentiate into Th1 cells. Gene dose effects of Faslpr were noted in upregulating serum IL-1, IL-2, and IL-27. Taken together, sle1homo.lprhet mice emerge as a more faithful model of human SLE, ideal for genetic studies, autoantibody repertoire investigation, and for exploring Th1 effector cell skewing.

immunology↗

bioRxiv2023

HIV-1 binds dynein directly to hijack microtubule transport machinery

Viruses exploit host cytoskeletal elements and motor proteins for trafficking through the dense cytoplasm. Yet the molecular mechanism that describes how viruses connect to the motor machinery is unknown. Here, we demonstrate the first example of viral microtubule trafficking from purified components: HIV-1 hijacking microtubule transport machinery. We discover that HIV-1 directly binds to the retrograde microtubule-associated motor, dynein, and not via a cargo adaptor, as previously suggested. Moreover, we show that HIV-1 motility is supported by multiple, diverse dynein cargo adaptors as HIV-1 binds to dynein light and intermediate chains on dyneins tail. Further, we demonstrate that multiple dynein motors tethered to rigid cargoes, like HIV-1 capsids, display reduced motility, distinct from the behavior of multiple motors on membranous cargoes. Our results introduce a new model of viral trafficking wherein a pathogen opportunistically hijacks the microtubule transport machinery for motility, enabling multiple transport pathways through the host cytoplasm.

microbiology↗

bioRxiv2023

Cell-type specific optogenetic fMRI on basal forebrain reveals functional network basis of behavioral preference

The basal forebrain (BF) is a complex structure that plays key roles in regulating various brain functions. However, it remains unclear how cholinergic and non-cholinergic BF neurons modulate large-scale functional networks and their relevance in intrinsic and extrinsic behaviors. With optimized awake mouse optogenetic fMRI approach, we revealed optogenetic stimulations of four BF neuron types evoked distinct cell-type specific whole-brain BOLD activations, which could attribute to BF-originated low dimensional structural networks. Additionally, optogenetic activation of VGLUT2, ChAT and PV neurons in BF modulated the preference of locomotion, exploration and grooming, respectively. Furthermore, we uncovered the functional network basis of the above BF-modulated behavioral preference, through a decoding model linking the BF-modulated BOLD activations, low dimensional structural networks, and behavioral preference. To summarize, we decoded functional network basis of differential behavioral preference with cell-type specific optogenetic fMRI on BF, and provided an avenue for investigating mouse behaviors from a whole-brain view.

neuroscience↗

bioRxiv2023

Reverse engineering the anti-MUC1 hybridoma antibody 139H2 by mass spectrometry-based de novo sequencing

Mucin 1 (MUC1) is a transmembrane mucin expressed at the apical surface of epithelial cells at different mucosal surfaces including breast and intestine. In the gastrointestinal tract, MUC1 has a barrier function against bacterial invasion, but can also serve as an entry receptor for pathogenic Salmonella bacteria. Moreover, MUC1 is well known for its aberrant expression and glycosylation in adenocarcinomas The MUC1 extracellular domain contains a variable number of tandem repeats (VNTR) of 20 amino acids, which are heavily O-linked glycosylated.. Monoclonal antibodies against the MUC1 VNTR can be powerful tools because of their multiplicity of binding and possible applications in the diagnosis and treatment of MUC1-expressing cancers. One such antibody is the hybridoma mouse monoclonal 139H2, which is also widely used as a research tool to study non-cancer MUC1. Here we report direct mass spectrometry-based sequencing of hybridoma-derived 139H2 IgG, which enabled reverse engineering of a recombinant 139H2. The performance of the reverse engineered 139H2 IgG and its Fab fragment were validated by comparison to the hybridoma-derived product in Western blot and immunofluorescence microscopy. The reverse engineering of 139H2 allowed us to characterize binding to the VNTR peptide epitope by surface plasmon resonance (SPR) and solve the crystal structure of the 139H2 Fab fragment in complex with the MUC1 VNTR peptide. These analyses reveal the molecular basis for 139H2 binding specificity to MUC1 and its tolerance to O-glycosylation of the VNTR. The available sequence of 139H2 will allow further development of MUC1-related diagnostics, targeting and treatment strategies.

biochemistry↗

bioRxiv2023

Shortcut barcoding and early pooling for scalable multiplex single-cell reduced-representation CpG methylation sequencing at single nucleotide resolution

DNA methylation is essential for a wide variety of biological processes, yet the development of a highly efficient and robust technology remains a challenge for routine single-cell analysis. We developed a multiplex scalable single-cell reduced representation bisulfite sequencing (msRRBS) technology with off-the-shelf reagents and equipment. It allows cell-specific barcoded DNA fragments of individual cells to be pooled before bisulfite conversion, free of enzymatic modification or physical capture of the DNA ends, and achieves unparalleled read mapping rates of 62.51%, covering 59.95% of CpG islands and 71.62% of promoters in K562 cells on average. Its reproducibility is shown in duplicates of bulk cells with near perfect correlation (R=0.97-99). At a low 1 Mb of clean reads, msRRBS provides consistent coverage of CpG islands and promoters, outperforming the conventional methods with orders of magnitude reduction in cost. Here, we use this method to characterize the distinct methylation patterns and cellular heterogeneity of 6 cell lines, and leukemia and hepatocellular carcinoma models. Taking 4 hours of hands-on time, msRRBS offers a unique, highly efficient approach for dissecting methylation heterogeneity in a variety of multicellular systems.

genomics↗

bioRxiv2023

Direct mass spectrometry-based detection and antibody sequencing of Monoclonal Gammopathy of Undetermined Significance from patient serum - a case study.

Monoclonal gammopathy of undetermined significance (MGUS) is a plasma cell disorder, characterized by the presence of a predominant monoclonal antibody (i.e., M-protein) in serum, without clinical symptoms. Here we present a case study in which we detect MGUS by liquid-chromatography coupled with mass spectrometry (LC-MS) profiling of IgG1 in human serum. We detected a Fab-glycosylated M-protein and determined the full heavy and light chain sequences by bottom-up proteomics techniques using multiple proteases, further validated by top-down LC-MS. Moreover, the composition and location of the Fab-glycan could be determined in CDR1 of the heavy chain. The outlined approach adds to an expanding mass spectrometry-based toolkit to characterize monoclonal gammopathies such as MGUS and multiple myeloma, with fine molecular detail. The ability to detect monoclonal gammopathies and determine M-protein sequences straight from blood samples by mass spectrometry provides new opportunities to understand the molecular mechanisms of such diseases.

immunology↗

bioRxiv2023

Using macromolecular electron densities to improve the enrichment of active compounds in virtual screening

The quest for more effective virtual screening algorithms is hindered by the scarcity of training data, calling for innovative approaches. This study presents the first use of experimental electron density (ED) data for improving active compound enrichment in virtual screening, supported by EDs ability to reflect the time-averaged behavior of ligands and solvents in the binding pocket. Experimental ED-based grid matching score (ExptGMS) was developed to score compounds by measuring the degree of matching between their binding conformations and a series of multi-resolution experimental ED grids. The efficiency of ExptGMS was validated using both in-silico tests with the Directory of Useful Decoys-Enhanced dataset and wet-lab tests on Covid-19 3CLpro-inhibitors. ExptGMS improved the active compound enrichment in top-ranked molecules by approximately 20%. Furthermore, ExptGMS helped identify four new and active inhibitors of 3CLpro, with the top showing an IC50 value of 1.9 {micro}M. To facilitate the use of ExptGMS, we developed an online database containing experimental ED grids for over 17,000 proteins.

bioinformatics↗

bioRxiv2023

The lung employs an intrinsic surfactant-mediated inflammatory response for viral defense

Severe Acute Respiratory Syndrome Coronavirus-2 (SARS-CoV-2) causes an acute respiratory distress syndrome (ARDS) that resembles surfactant deficient RDS. Using a novel multi-cell type, human induced pluripotent stem cell (hiPSC)-derived lung organoid (LO) system, validated against primary lung cells, we found that inflammatory cytokine/chemokine production and interferon (IFN) responses are dynamically regulated autonomously within the lung following SARS-CoV-2 infection, an intrinsic defense mechanism mediated by surfactant proteins (SP). Single cell RNA sequencing revealed broad infectability of most lung cell types through canonical (ACE2) and non-canonical (endocytotic) viral entry routes. SARS-CoV-2 triggers rapid apoptosis, impairing viral dissemination. In the absence of surfactant protein B (SP-B), resistance to infection was impaired and cytokine/chemokine production and IFN responses were modulated. Exogenous surfactant, recombinant SP-B, or genomic correction of the SP-B deletion restored resistance to SARS-CoV-2 and improved viability.

immunology↗

bioRxiv2022

Octopamine metabolically reprograms astrocytes to confer neuroprotection against α-synuclein

Octopamine is a well-established invertebrate neurotransmitter involved in fight-or-flight responses. In mammals, its function was replaced by norepinephrine. Nevertheless, it is present at trace amounts and can modulate the release of monoamine neurotransmitters by a yet unidentified mechanism. Here, through a multidisciplinary approach utilizing in vitro and in vivo models of -synucleinopathy, we uncovered an unprecedented role for octopamine in driving the conversion from toxic to neuroprotective astrocytes in the cerebral cortex by fostering aerobic glycolysis. Physiological levels of neuron-derived octopamine act on astrocytes via a TAAR1-Orai1-Ca2+-calcineurin-mediated signaling pathway to stimulate lactate secretion. Lactate uptake in neurons via the MCT2-calcineurin-dependent pathway increases ATP and prevents neurodegeneration. Pathological increases of octopamine caused by -synuclein halts lactate production in astrocytes and short-circuits the metabolic communication to neurons. Our work provides a novel function of octopamine as a modulator of astrocyte metabolism and subsequent neuroprotection with implications to -synucleinopathies.

neuroscience↗

bioRxiv2022

pCMLM: Genome Wide Association Study of Body Size Traits in Multiple Regions of Yak Based on the Provided Compressed Mixed Linear Model

ObjectiveYak is a unique large animal species living in the Qinghai-Tibet Plateau and the surrounding Hengduan Mountains, and has evolved several regional variety resources due to the special geographical and ecological environment in which it lives. Therefore, it is of great importance to investigate the genetic composition of body size traits among breeds in multiple regions for yak breeding and production. MethodA genome-wide association analysis was performed on 94 yak individuals (a total of 31 variety resources) for five body size traits (body height, body weight, body length, chest circumference, and circumference of cannon bone). The individuals were clustered following known population habitat. The kinship of grouping individuals was used in the CMLM. This provided compressed mixed linear model was named pCMLM method. ResultTotal of 3,584,464 high-quality SNP markers were obtained on 30 chromosomes. Principal component analysis using the whole SNPs do not accurately classify all populations into multiple subpopulations, a result that is not the same as the population habitat. Six SNP loci were identified in the pCMLM-based GWAS with statistically significant correlation with body height, and four candidate genes (FXYD6, SOHLH2, ADGRB2, and OSBPL6), which in the vicinity of the variant loci, were screened and annotated. Two of these genes, ADGRB2 and OSBPL6, are involved in biological regulatory processes such as body height regulation, adipocyte proliferation and differentiation. ConclusionBased on the previous population information, the pCMLM can provide more sufficient associated results when the conventional CMLM can not catch optimum clustering groups. The fundamental information for quantitative trait gene localization or candidate gene cloning in the mechanism of yak body size trait formation.

bioinformatics↗

bioRxiv2022

Engineering non-cytotoxic delivery of proteins by T cells via fusion to NPC2

Engineering cellular therapeutics by programming T cells has great potential in immunology. The primary mechanism employed by T cells for the specific transfer of proteins at the immunological synapse is via the lysosomal perforin pathway that facilitates the transfer of cytotoxic granzymes leading to apoptosis in target cells. Facilitating the delivery of non-cytotoxic proteins through perforin oligomers will dramatically expand the range of protein cargos that T cells can traffic to the target cells. Here, we have identified the intralysosomal protein, NPC2, as a chaperone that can facilitate the delivery of T-cell derived reporter proteins through perforin pores at the immunological synapse. Structural and biophysical considerations suggested that NPC2 could traverse through perforin pores and in vitro experiments confirmed the transport of purified NPC2 through perforin pores on cell membranes. To characterize the ability of NPC2 to facilitate the transfer of payloads in T cells, we constructed NPC2-mCherry fusion proteins in T cells. Using confocal microscopy and flow cytometry, we confirmed the colocalization of the NPC2 fused protein with lytic granules and the transfer of the fluorescent protein payload from T cells to target cells in co-culture experiments. The NPC2 fusion enabled the localization of mCherry to secretory lysosomes in mouse TCR CD8+ T cells and human CD4+ and CD8+ chimeric antigen receptor (CAR) T cells. These results illustrate that by using NPC2 as a molecular chaperone, the NPC2-perforin pathway can be exploited as a programmable molecular delivery system for cell-based therapies.

immunology↗

bioRxiv2022

The ChlorON Series: Turn-on fluorescent protein sensors for imaging labile chloride in living cells

Beyond its role as the queen electrolyte, chloride can also serve as an allosteric regulator or even a signaling ion. To illuminate this essential anion across such a spectrum of biological processes, researchers have relied on fluorescence imaging with genetically encoded sensors. In large part, these have been derived from the green fluorescent protein found in the jellyfish Aequorea victoria. However, a standalone sensor with a turn-on intensiometric response at physiological pH has yet to be reported. Here, we address this technology gap by building on our discovery of mNeonGreen (mNG) derived from lanYFP found in the cephalochordate Branchiostoma lanceolatum. Targeted engineering of two non-coordinating residues in the chloride binding pocket of mNG unlocks the ChlorON series. In vitro spectroscopy reveals that the binding of chloride tunes the chromophore environment to give rise to the turn-on response. We further showcase how this unique sensing mechanism can be exploited for directly imaging labile chloride in living cells with spatial and temporal resolution, accelerating the path forward for fundamental and translational aspects of chloride biology. O_FIG O_LINKSMALLFIG WIDTH=200 HEIGHT=61 SRC="FIGDIR/small/503807v2_ufig1.gif" ALT="Figure 1"> View larger version (23K): org.highwire.dtl.DTLVardef@36cc4org.highwire.dtl.DTLVardef@d9dccborg.highwire.dtl.DTLVardef@12ec0fforg.highwire.dtl.DTLVardef@80c9db_HPS_FORMAT_FIGEXP M_FIG C_FIG

biochemistry↗

bioRxiv2022

Loss of aquaporin-4 results in glymphatic system dysfunction via brain-wide interstitial fluid stagnation

The glymphatic system is a fluid transport network of cerebrospinal fluid (CSF) entering the brain along arterial perivascular spaces, exchanging with interstitial fluid (ISF), ultimately establishing directional clearance of interstitial solutes. CSF transport is facilitated by the expression of aquaporin-4 (AQP4) water channels on the perivascular endfeet of astrocytes. Mice with genetic deletion of AQP4 (AQP4 KO) exhibit abnormalities in the brain structure and molecular water transport. Yet, no studies have systematically examined how these abnormalities in structure and water transport correlate with glymphatic function. Here we used high-resolution 3D magnetic resonance (MR) non-contrast cisternography, diffusion-weighted MR imaging (MR-DWI) along with intravoxel-incoherent motion (IVIM) DWI, while evaluating glymphatic function using a standard dynamic contrast-enhanced MR imaging to better understand how water transport and glymphatic function is disrupted after genetic deletion of AQP4. AQP4 KO mice had larger interstitial spaces and total brain volumes resulting in higher water content and reduced CSF space volumes, despite similar CSF production rates and vascular density compared to wildtype mice. The larger interstitial fluid volume likely resulted in increased slow but not fast MR diffusion scores and coincided with reduced glymphatic influx. This markedly altered brain fluid transport in AQP4 KO mice may result from a reduction in glymphatic clearance, leading to stagnation of ISF movement and enlargement of the interstitial space. Overall, diffusion MR is a useful tool to evaluate glymphatic function and may serve as valuable translational biomarker to study glymphatics in human disease.

neuroscience↗