Biology subjects

Zhu, F.

Publications and source records attributed to Zhu, F..

At least 55 records · Page 3Linked to original sources

bioRxiv2023

OBMeta: a comprehensive web server to analyze and validate gut microbial features and biomarkers for obesity-associated metabolic diseases

Gut dysbiosis is closely associated with obesity and related metabolic diseases including type 2 diabetes (T2D) and non-alcoholic fatty liver disease (NAFLD). The gut microbial features and biomarkers have been increasingly investigated in recent studies, which require further validation due to the limited sample size and various confounding factors that may affect microbial compositions. So far, it lacks a comprehensive bioinformatics pipeline providing automated statistical analysis and integrating independent studies for cross validation simultaneously. OBMeta aims to streamline the standard metagenomics data analysis from diversity analysis, comparative analysis, functional analysis, to co-abundance network analysis. In addition, a curated database has been established with a total of 88 public research projects, covering three different phenotypes (Obesity, T2D, and NAFLD) and more than five different intervention strategies (exercise, diet, probiotics, medication, and surgery). With OBMeta, users can not only analyze their own research projects, but also search and match public datasets of interest for cross-project validation. Moreover, OBMeta provides cross-phenotype and cross-intervention-based advanced validation that maximally supports preliminary findings from an individual study. To summarize, OBMeta is a comprehensive web server to analyze and validate gut microbial features and biomarkers for obesity-associated metabolic diseases. OBMeta is freely available at: http://obmeta.met-bioinformatics.cn/. O_FIG O_LINKSMALLFIG WIDTH=200 HEIGHT=82 SRC="FIGDIR/small/552363v1_ufig1.gif" ALT="Figure 1"> View larger version (31K): org.highwire.dtl.DTLVardef@1b58a9borg.highwire.dtl.DTLVardef@19efa47org.highwire.dtl.DTLVardef@418597org.highwire.dtl.DTLVardef@1a9bc3c_HPS_FORMAT_FIGEXP M_FIG C_FIG

bioinformatics↗

bioRxiv2023

Patient-derived organoids assist personalized treatment for a patient with multiple metastatic neuroendocrine carcinoma of the cervix

Neuroendocrine carcinoma of the cervix (NECC) is a rare subtype of cervical cancer with rapid metastasis. Lack of treatment regimens for metastatic NECC highlights the need for preclinical models and personalized treatment. Here, we established two patient-derived NECC organoid lines from lung metastases from the same patient, one of which was drug-free and the other exhibited tolerance to carboplatin plus etoposide (EP). The two organoids recapitulated the histopathology and genomic spectrum of the original tumors. Whole-genome sequencing revealed genomic structural variations (SVs), including HPV16 infection, NEUROD2, and ERBB2 amplification. The sensitivity phenotype of organoids to ERBB2 inhibitors coincides with the genomic features of ERBB2 amplification. In addition, the patient after relapse responded well to the paclitaxel plus carboplatin (TC) regimen as recommended by organoid drug screening, underscoring the utility of organoids as preclinical models. We first provide two NECC organoids of lung metastases with comprehensive molecular characteristics as valuable resources for this rare cancer and give a typical application for personalized treatment based on organoids.

cancer biology↗

bioRxiv2023

Prominent contributions of selective neuronal subtypes to pediatric drug-resistant focal dysplasia

About 75% cases of epilepsy begin during childhood, and 10 - 30% of pediatric epilepsy patients are resistant to drug treatment. The predominant seizure type in children is focal cortical dysplasia (FCD) which is highly associated with drug-resistant epilepsy, but its underlying cause is poorly understood. We performed single-cell RNA sequencing and patch-clamp recording on fresh brain tissues obtained from pediatric FCD patients shortly after surgery to reveal critical factors contributing to FCD. We report that known epilepsy genes or significant transcriptomic alterations occur in only a few neuronal subgroups, suggesting that epilepsy-associated neurons cluster into only a few neuronal subtypes. These epilepsy-subtypes displayed significant epilepsy-related transcriptomic alterations, especially in the genes associated with excitation/inhibition balance and neuron functional signal pathways. Among eight epilepsy-subtypes, L2_4_CUX2_YWHAH and PVALB_RGS5 subtypes showed the most prominent alterations in FCD patient tissues. Supporting PV-neurons being important, recording from fast-spiking/parvalbumin-containing neurons in acute FCD patient brain slices revealed reduced excitatory synaptic inputs, implicating lower activity in these neurons and fewer synaptic inputs onto them. A higher percentage of mitochondria genes, and likely higher activity in the pathways associated with oxidative phosphorylation and ATP biosynthetic process, was observed in the epilepsy-subtypes, suggesting a high energy expenditure in them. Interestingly, the activity of the above two pathways in most epilepsy-subtypes was lower in the FCD patients, suggesting these subtypes may be more vulnerable to energy deficit in epilepsy. Altogether, transcriptomics is significantly altered in only a few neuronal subtypes in pediatric FCD patient brains. These selective epilepsy-subtypes may play prominent roles in the genesis of pediatric drug-resistant seizure and targeting them may provide new treatment options.

bioinformatics↗

bioRxiv2023

Contribution of the delta-class glutathione S-transferase to agrochemical adaptation in Apis mellifera

The European honey bee, Apis mellifera, serves as the principle managed pollinator species globally. In recent decades, honey bee populations have been facing serious health threats from combined biotic and abiotic stressors, including diseases, limited nutrition, and agrochemical exposure. Understanding the molecular mechanisms underlying xenobiotic adaptation of A. mellifera is critical, considering its extensive exposure to phytochemicals and agrochemicals present in flowers, propolis, hives, and the environment. In this study, we conducted a comprehensive structural and functional characterization of AmGSTD1, a delta class glutathione S-transferase (GST) enzyme, to unravel its roles in agrochemical detoxification and antioxidative stress responses. Significantly, we determined the 3D structure of a honey bee GST using protein crystallography for the first time, providing new insights into its molecular structure. Our investigations revealed that AmGSTD1 efficiently metabolizes model substrates, including 1-chloro-2,4-dinitrobenzene (CDNB), p-nitrophenyl acetate (PNA), phenylethyl isothiocyanate (PEITC), propyl isothiocyanate (PITC), and the oxidation byproduct 4-hydroxynonenal (4-HNE). Moreover, we discovered that AmGSTD1 exhibits binding affinity with the fluorophore 8-Anilinonaphthalene-1-sulfonic acid (ANS), which can be inhibited with various herbicides, fungicides, insecticides, and their metabolites. These findings highlight the potential contribution of AmGSTD1 in safeguarding honey bee health against various agrochemicals and their metabolites, while also mitigating oxidative stress resulting from exposure to these substances.

pharmacology and toxicology↗

bioRxiv2023

Genomic context sensitizes regulatory elements to genetic disruption

Enhancer function is frequently investigated piecemeal using truncated reporter assays or single deletion analysis. Thus it remains unclear to what extent enhancer function at native loci relies on surrounding genomic context. Using the Big-IN technology for targeted integration of large DNAs, we analyzed the regulatory architecture of the murine Igf2/H19 locus, a paradigmatic model of enhancer selectivity. We assembled payloads containing a 157-kb functional Igf2/H19 locus and engineered mutations to genetically direct CTCF occupancy at the imprinting control region (ICR) that switches the target gene of the H19 enhancer cluster. Contrasting activity of payloads delivered at the endogenous Igf2/H19 locus or ectopically at Hprt revealed that the Igf2/H19 locus includes additional, previously unknown long-range regulatory elements. Exchanging components of the Igf2/H19 locus with the well-studied Sox2 locus showed that the H19 enhancer cluster functioned poorly out of context, and required its native surroundings to activate Sox2 expression. Conversely, the Sox2 locus control region (LCR) could activate both Igf2 and H19 outside its native context, but its activity was only partially modulated by CTCF occupancy at the ICR. Analysis of regulatory DNA actuation across different cell types revealed that, while the H19 enhancers are tightly coordinated within their native locus, the Sox2 LCR acts more independently. We show that these enhancer clusters typify broader classes of loci genome-wide. Our results show that unexpected dependencies may influence even the most studied functional elements, and our synthetic regulatory genomics approach permits large-scale manipulation of complete loci to investigate the relationship between locus architecture and function. HIGHLIGHTSO_LIComposite enhancer elements are subject to genomic context effects mapped to a specific architecture of their endogenous loci. C_LIO_LIIgf2/H19 expression is affected by long-range regulatory elements beyond the canonically defined locus, and the H19 enhancer cluster in particular relies on the surrounding context at its endogenous locus. C_LIO_LIThe Sox2 LCR functions as an autonomous enhancer without requiring additional surrounding context. C_LIO_LIThe influence of genomic context is buffered at intact loci, but manifests more strongly as key regulatory elements are deleted or repositioned. C_LI

genomics↗

bioRxiv2023

Deciphering the role of the OmpC-Mla system in bile salt resistance

The outer membrane (OM) of Gram-negative bacteria presents a formidable barrier against external insults, in part contributing to the survival of Enterobacteriaceae in the mammalian gut. The lipid asymmetry of the OM, where lipopolysaccharides (LPS) form a tight outer layer of low permeability, effectively restricts the passage of toxic substances across the bilayer. In the gut, however, bile salts pose a unique challenge to the bacterial cell due to their ability to form micelles and solubilize membranes; yet, mechanisms to prevent dissolution of the OM by such detergents are not well understood. In this study, we define a distinct role in bile salt resistance for the OmpC-Mla system in Escherichia coli, which is better known for its function in maintaining OM lipid asymmetry. We show that cells lacking a functional OmpC-Mla system are sensitive to bile salts, but only at or above critical micellar concentrations. Furthermore, we observe that these cells still exhibit bile salt sensitivity even when defects in OM lipid asymmetry have been corrected, suggesting that the OmpC-Mla system contributes to bile salt resistance independent of its role in lipid asymmetry. Finally, we demonstrate that MlaD, one of the key lipid-binding components of the system, displays specific binding to bile salts in vitro. Since the OmpC-Mla system maintains OM lipid asymmetry by transporting mislocalized PLs, our findings here support a model where this system also additionally removes bile salts that have intercalated into the OM, to ultimately prevent dissolution and disruption of this important barrier. IMPORTANCEBile salts are important components secreted into the human gut to help solubilize fats from our diet, yet they also possess anti-microbial properties due to their corresponding ability to dissolve bacterial membranes. For Enterobacteriaceae to survive in the gut environment, these bacterial cells must prevent intracellular build-up of bile salts by either restricting entry or by pumping out these molecules. Ultimately, they must resist bile salt-mediated dissolution of their membranes, particularly their outer membranes, which serve as a protective barrier against toxic substances. In this study, we reveal that a known lipid transport system in Escherichia coli has a distinct role in bile salt resistance independent of its role in maintaining outer membrane lipid asymmetry; it does so likely by removing bile salts from the outer membrane, thus preventing dissolution. Our work highlights the possibility of targeting this lipid transport system for the treatment of Enterobacteriaceae infections.

microbiology↗

bioRxiv2023

A pseudovirus-based method to dynamically mimic SARS-CoV-2-associated cell-to-cell fusion and transmission

SARS-CoV-2 has caused the global tremendous loss and continues to evolve to generate variants. Entry of SARS-CoV-2 into the host cells is primarily mediated by Spike (S), which binds to the host receptor hACE2 and initiates virus-cell membrane fusion. Cell fusion contributes to viral entry, cell-to-cell transmission and tissue damage in COVID-19 patients. Many reporter assays have been developed to study S-mediated cell fusion by equally coculturing S-expressing cells and hACE2-positive cells. However, these strategies cannot fully simulate cell-to-cell fusion and transmission of SARS-CoV-2 infection, in which virions from a single target cell transmit to the neighbor cells and induce syncytia formation. Here, we design a pseudovirus-based method to dynamically mimic cell-to-cell fusion and transmission of SARS-CoV-2. We coculture a small number of pseudovirus-producing 293FT cells and a large number of hACE2-expressing 293T cells, and demonstrate that a single cell producing S-pseudotyped virions can induce significant syncytia of hACE2-positive cells. This pseudovirus-based method is a powerful tool to screen and estimate potential inhibitors of S-driven syncytia. Moreover, this strategy can also be utilized to explore fusogenic ability of SARS-CoV-2 variants. Together, the pseudovirus-based method we report here will be beneficial to drug screening and scientific research against SARS-CoV-2 or future emerging coronavirus.

microbiology↗

bioRxiv2023

Astrocytes gate long-term potentiation in hippocampal interneurons

Long-term potentiation is involved in physiological processes such as learning and memory, motor learning and sensory processing, and pathological conditions such as addiction. In contrast to the extensive studies on the mechanism of long-term potentiation on excitatory glutamatergic synapses onto excitatory neurons (LTPE[->]E), the mechanism of LTP on excitatory glutamatergic synapses onto inhibitory neurons (LTPE[->]I) remains largely unknown. In the central nervous system, astrocytes play an important role in regulating synaptic activity and participate in the process of LTPE[->]E, but their functions in LTPE[->]I remain incompletely defined., We studied the role of astrocytes in regulating LTPE[->]I in the hippocampal CA1 region and their impact on cognitive function using electrophysiological, pharmacological, confocal calcium imaging, chemogenetics and behavior tests. We showed that LTPE[->]I in the stratum oriens of hippocampal CA1 is astrocyte independent. However, in the stratum radiatum, synaptically released endocannabinoids increase astrocyte Ca2+ via type-1 cannabinoid receptors, stimulate D-serine release, and potentiate excitatory synaptic transmission on inhibitory neurons through the activation of (N-methyl-D-aspartate) NMDA receptors. We also revealed that chemogenetic activation of astrocytes is sufficient for inducing NMDA-dependent de novo LTPE[->]I in the stratum radiatum of the hippocampus. Furthermore, we found that disrupting LTPE[->]I by knocking down {gamma}CaMKII in interneurons of the stratum radiatum resulted in dramatic memory impairment. Our findings suggest that astrocytes release D-serine, which activates NMDA receptors to regulate LTPE[->]I, and that cognitive function is intricately linked with the proper functioning of this LTPE[->]I pathway.

neuroscience↗

bioRxiv2023

Integrative Multi-omic Profiling of Two Human Decedents Receiving Pig Heart Xenografts Reveals Strong Perturbations in Early Immune-Cell and Cellular Metabolism Responses.

BackgroundRecent advances in xenotransplantation in living and decedent humans using pig xenografts have laid promising groundwork towards future emergency use and first in human trials. Major obstacles remain though, including a lack of knowledge of the genetic incompatibilities between pig donors and human recipients which may led to harmful immune responses against the xenograft or dysregulation of normal physiology. In 2022 two pig heart xenografts were transplanted into two brain-dead human decedents with a minimized immunosuppression regime, primarily to evaluate onset of hyper-acute antibody mediated rejection and sustained xenograft function over 3 days. MethodsWe performed multi-omic profiling to assess the dynamic interactions between the pig and human genomes in the first two pig heart-xenografts transplants into human decedents. To assess global and specific biological changes that may correlate with immune-related outcomes and xenograft function, we generated transcriptomic, lipidomic, proteomic and metabolomics datasets, across blood and tissue samples collected every 6 hours over the 3-day procedures. ResultsSingle-cell datasets in the 3-day pig xenograft-decedent models show dynamic immune activation processes. We observe specific scRNA-seq, snRNA-seq and geospatial transcriptomic changes of early immune-activation leading to pronounced downstream T-cell activity and hallmarks of early antibody mediated rejection (AbMR) and/or ischemia reperfusion injury (IRI) in the first xenograft recipient. Using longitudinal multiomic integrative analyses from blood in addition to antigen presentation pathway enrichment, we also observe in the first xeno-heart recipient significant cellular metabolism and liver damage pathway changes that correlate with profound physiological dysfunction whereas, these signals are not present in the other xenograft recipient. ConclusionsSingle-cell and multiomics approaches reveal fundamental insights into early molecular immune responses indicative of IRI and/or early AbMR in the first human decedent, which was not evident in the conventional histological evaluations.

systems biology↗

bioRxiv2023

AnnoPRO: an innovative strategy for protein function annotation based on image-like protein representation and multimodal deep learning

Protein function annotation has been one of the longstanding issues, which is key for discovering drug targets and understanding physiological or pathological process. A variety of computational methods have therefore been constructed to facilitate the research developments in this particular direction. However, the annotation of protein function based on computational methods has been suffering from the serious "long-tail problem", and it remains extremely challenging for existing methods to improve the prediction accuracies for protein families in tail label levels. In this study, an innovative strategy, entitled AnnoPRO, for protein function annotation was thus constructed. First, a novel method enabling image-like protein representations was proposed. This method is unique in capturing the intrinsic correlations among protein features, which can greatly favor the application of the state-of-the-art deep learning methods popular in image classification. Second, a multimodal framework integrating multichannel convolutional neural network and long short-term memory neural network was constructed to realize a deep learning-based protein functional annotation. Since this framework was inspired by a reputable method used in image classification for dealing with its long-tail problem, our AnnoPRO was expected to significantly improve the annotation performance of the protein families in tail label level. Multiple case studies based on benchmark were also conducted, which confirmed the superior performance of AnnoPRO among the existing methods. All source codes and models of AnnoPRO were freely available to all users at https://github.com/idrblab/AnnoPRO, and would be essential complement to existing methods.

bioinformatics↗

bioRxiv2023

Spatiotemporal Genomic Profiling of Intestinal Metaplasia Reveals Clonal Dynamics of Gastric Cancer Progression

Intestinal metaplasia (IM) is a pre-malignant condition of the gastric mucosa associated with increased gastric cancer (GC) risk. We analyzed 1256 gastric samples (1152 IMs) from 692 subjects through a prospective 10-year study. We identified 26 IM driver genes in diverse pathways including chromatin regulation (ARID1A) and intestinal homeostasis (SOX9), largely occurring as small clonal events. Analysis of clonal dynamics between and within subjects, and also longitudinally across time, revealed that IM clones are likely transient but increase in size upon progression to dysplasia, with eventual transmission of somatic events to paired GCs. Single-cell and spatial profiling highlighted changes in tissue ecology and lineage heterogeneity in IM, including an intestinal stem-cell dominant cellular compartment linked to early malignancy. Expanded transcriptome profiling revealed expression-based molecular subtypes of IM, including a body-resident "pseudoantralized" subtype associated with incomplete histology, antral/intestinal cell types, ARID1A mutations, inflammation, and microbial communities normally associated with the healthy oral tract. We demonstrate that combined clinical- genomic models outperform clinical-only models in predicting IMs likely to progress. Our results raise opportunities for GC precision prevention and interception by highlighting strategies for accurately identifying IM patients at high GC risk and a role for microbial dysbiosis in IM progression.

cancer biology↗

bioRxiv2023

In vitro screening of non-antibiotic alternative growth promoter combinations in broilers

Available research on non-antibiotic alternative growth promoter (NAGPs) mainly focuses on the effect of a single preparation on the substitution effect of antibiotics. However, different NAGP might work together in harmony. Studies related to NAGP combinations are lacking. This study aimed to screen six non-antibiotic alternative growth promoter combinations (NAGPCs) in vitro so as to find a better alternative method to ensure feed efficiency and the broiler health. Pepsin and 42-d broiler ileal fluid were used for the in vitro digestion test, and the optimal addition levels of NAGPs and NAGPCs were selected based on dry matter (DM) and organic matter (OM) digestibility, microbiota of digestive fluid, and antioxidant capacity of digestive fluid. Results showed the optimum addition amount of Mannose oligosaccharide (MOS), fruit oligosaccharide (FOS), mannanase (MAN), Bacillus subtilis (BS), sodium butyrate (SB), guanidinoacetic acid (CA), xylanase (XYL), glucose oxidase (GO), and phytase (PT) were 0.2%, 0.9%, 0.03%, 0.05%, 0.08%, 0.002%, 0.008%, and 0.004%. The six best combinations were 0.2%MOS + 0.03%MAN + 0.15%SB, 0.2%MOS + 0.03%MAN + 0.05%BS, 0.2%MOS + 0.9%FOS + 0.15%SB, 0.2%MOS + 0.9%FOS + 0.05%BS, 0.2%MOS + 0.9%FOS + 0.03%MAN, and 0.2%MOS + 0.05%BS + 0.004%PT. In conclusion, NAGPCs improved the apparent digestibility of ileal DM and OM, intestinal flora and antioxidant capacity. Comparatively, under this condition, using NAGPC has more beneficial effects than using non-antibiotic alternative growth promoter.

zoology↗

bioRxiv2023

iTie controls intestinal tolerance through suppressing the NLRP6 inflammasome

Intestines are full of commensal bacteria that possess numerous pathogen-associated molecular patterns. How the intestinal epithelial cells are tolerant to these stimuli under normal conditions is still elusive. Here we show that iTie is expressed in small intestinal enterocytes and its deficiency leads to body weight loss in mice, accompanied by length reduce of small intestines and intestinal villi. The activation of NLRP6 inflammasome is exacerbated upon iTie deletion. iTie has a higher binding affinity for NLRP6 than NLRP6s physiological ligand LTA does. iTie deficiency gives rise to uncontrolled GSDMD activation and pyroptosis of small intestinal enterocytes. Inhibition of GSDMD permeabilization on cell membrane ameliorates the damage caused by iTie deficiency. iTes expression is diminished in small intestines of patients with Crohns disease. Our results uncover a self-control system for mouse intestine to tolerate commensal bacteria which might shed new light on the treatment of bowel diseases.

immunology↗

bioRxiv2022

Effects of nonantibiotic alternative growth promoter combinations on nutrient utilization, digestive enzyme activity, intestinal morphology, and cecal microflora of broilers

Given the ban on antibiotic growth promoters, six nonantibiotic alternative growth promoter combinations (NAGPCs) for broilers were evaluated. All birds were fed pellets of two basal diets--starter (0-21 d) and grower (22-42 d)--with either enramycin (ENR) or NAGPC supplemented. 1) control + 100 mg/kg ENR; 2) control diet (CON, basal diet); 3) control + 2,000 mg/kg mannose oligosaccharide (MOS) + 300 mg/kg mannanase (MAN) + 1,500 mg/kg sodium butyrate (SB) (MMS); 4) control + 2,000 mg/kg MOS + 300 mg/kg MAN + 500 mg/kg Bacillus subtilis (BS) (MMB); 5) control + 2,000 mg/kg MOS + 9,000 mg/kg fruit oligosaccharide (FOS) + 1,500 mg/kg SB (MFS); 6) control + 9,000 mg/kg FOS + 500 mg/kg BS (MFS) (MBP). The experiment used a completely random block design with six replicates per group: 50 Ross 308 broilers in the starter phase and 16 in the grower phase. All the NAGPCs significantly improved (P < 0.01) utilization of dry matter (DM), organic matter (OM), crude protein (CP), and crude fat (CF) on d 21, significantly increased DM, OM (P < 0.01), and CP (P < 0.05) on d 42, and significantly increased (P < 0.01) villus height, crypt depth, and the villus height to crypt depth ratio in the jejunum and ileum compared with CON and ENR. On d 21 and 42, trypsin, lipase, and amylase activity of the duodenum significantly increased in the MMS, MMB, MFB, and MFM groups. Compared with ENR and CON, MMS, MMB, and MBP increased the abundance of Firmicutes at d 21 and of Bacteroides at d 42 whereas MMB, MFB, and MBP decreased the abundance of Proteobacteria at d 21 and 42. Overall, the NAGPCs were found to have some beneficial effects and may be used as effective antibiotic replacements in broilers.

biophysics↗

bioRxiv2022

Identification of S1PR4 as an immune modulator for favorable prognosis in HNSCC through unbiased machine learning

As the largest family of membrane proteins, G protein-coupled receptors (GPCRs) are the most prominent family of pharmacological targets. However, only a few GPCRs have been well-defined in terms of their physiological and pathological functions. Thus, an efficient way to identify key GPCRs involved in tumour formation is urgently needed. In this study, patients with head and neck squamous cell carcinoma (HNSCC) were classified into two different subtypes based on the characteristics of GPCRs using an unbiased machine learning method. Notably, these two subtypes showed significant differences in prognosis, gene expression, and immune microenvironment, especially in the infiltration of CD8+ T cells. Based on these differences, we screened three potential key regulators (S1PR4, S1PR5, and GPR87) from all GPCRs and constructed a prognostic nomogram for patients with HNSCC. We identified S1PR4 as the key GPCR in determining the two subtypes for positive correlation with the proportion and cytotoxicity of CD8+ T cells in HNSCC and was mainly expressed in a subset of CX3CR1+CD8+ T cells. We also demonstrated that S1PR4 is an immune modulator for the favourable prognosis of HNSCC patients. We found that S1PR4 was highly expressed in CD8+ T cells from the tumours of HNSCC patients, which was significantly associated with better prognosis, and S1PR4 expression was accompanied by higher T cell cytotoxic marker expression (IFNG and GZMB). Notably, S1PR4 co-localised with CX3CR1, which has been identified as the most cytotoxic marker of CD8+ T cells. Furthermore, S1PR4 upregulation could significantly increase T cell function in CAR-T cell therapy, indicating its great potential in cancer immunotherapy. Therefore, these results identified S1PR4 as a key indicator of cytotoxicity and the proportion of tumour-infiltrating CD8+ T cells and confirmed the prognostic value of S1PR4 in HNSCC. Our findings contribute to the knowledge of S1PR4 in anti-tumour immunity, providing a potential GPCR-targeted therapeutic option for future HNSCC treatment.

cancer biology↗

bioRxiv2022

Ratio-based quantitative multiomics profiling using universal reference materials empowers data integration

Multiomics profiling is a powerful tool to characterize the same samples with complementary features orchestrating the genome, epigenome, transcriptome, proteome, and metabolome. However, the lack of ground truth hampers the objective assessment of and subsequent choice from a plethora of measurement and computational methods aiming to integrate diverse and often enigmatically incomparable omics datasets. Here we establish and characterize the first suites of publicly available multiomics reference materials of matched DNA, RNA, proteins, and metabolites derived from immortalized cell lines from a family quartet of parents and monozygotic twin daughters, providing built-in truth defined by family relationship and the central dogma. We demonstrate that the "ratio"-based omics profiling data, i.e., by scaling the absolute feature values of a study sample relative to those of a concurrently measured universal reference sample, were inherently much more reproducible and comparable across batches, labs, platforms, and omics types, thus empower the horizontal (within-omics) and vertical (cross-omics) data integration in multiomics studies. Our study identifies "absolute" feature quantitation as the root cause of irreproducibility in multiomics measurement and data integration, and urges a paradigm shift from "absolute" to "ratio"-based multiomics profiling with universal reference materials.

systems biology↗

bioRxiv2022

Computationally restoring the potency of a clinical antibody against SARS-CoV-2 Omicron subvariants

The COVID-19 pandemic underscored the promise of monoclonal antibody-based prophylactic and therapeutic drugs1-3, but also revealed how quickly viral escape can curtail effective options4, 5. With the emergence of the SARS-CoV-2 Omicron variant in late 2021, many clinically used antibody drug products lost potency, including EvusheldTM and its constituent, cilgavimab4, 6. Cilgavimab, like its progenitor COV2-2130, is a class 3 antibody that is compatible with other antibodies in combination4 and is challenging to replace with existing approaches. Rapidly modifying such high-value antibodies with a known clinical profile to restore efficacy against emerging variants is a compelling mitigation strategy. We sought to redesign COV2-2130 to rescue in vivo efficacy against Omicron BA.1 and BA.1.1 strains while maintaining efficacy against the contemporaneously dominant Delta variant. Here we show that our computationally redesigned antibody, 2130-1-0114-112, achieves this objective, simultaneously increases neutralization potency against Delta and many variants of concern that subsequently emerged, and provides protection in vivo against the strains tested, WA1/2020, BA.1.1, and BA.5. Deep mutational scanning of tens of thousands pseudovirus variants reveals 2130-1-0114-112 improves broad potency without incurring additional escape liabilities. Our results suggest that computational approaches can optimize an antibody to target multiple escape variants, while simultaneously enriching potency. Because our approach is computationally driven, not requiring experimental iterations or pre-existing binding data, it could enable rapid response strategies to address escape variants or pre-emptively mitigate escape vulnerabilities.

microbiology↗

bioRxiv2022

Synaptic Expression of TAR-DNA-Binding Protein 43 in the Mouse Spinal Cord Determined Using Super-Resolution Microscopy

Cellular inclusions of hyperphosphorylated TAR-DNA-Binding Protein 43 (TDP-43) are a key hallmark of neurodegenerative diseases such as Amyotrophic Lateral Sclerosis (ALS). ALS is characterised by a loss of motor neurons in the brain and spinal cord that is preceded by early-stage changes in synaptic function that may be associated with TDP-43 pathology. However, there has been little characterisation of the synaptic expression of TDP-43 in spinal cord synapses. This study utilises a range of high-resolution and super-resolution microscopy techniques with immunolabelling, as well as an aptamer-based TDP-43 labelling strategy visualised with single-molecule localisation microscopy, to characterise and quantify the presence of phosphorylated TDP-43 (pTDP-43) in spinal cord synapses. We observe that TDP-43 is expressed in the majority of spinal cord synapses as nanoscale clusters as small as 60 nm in diameter. Synaptic TDP-43 expression is more frequently associated with presynaptic terminals than postsynaptic densities, and is more enriched in VGLUT1-associated synapses, compared to VGLUT2-associated synapses. Our nanoscopy techniques showed no difference in the subsynaptic expression of pTDP-43 in the ALS mouse model, SOD1G93a compared to healthy controls. This research characterizes the basic synaptic expression of TDP-43 with nanoscale precision and provides a framework with which to investigate the potential relationship between TDP-43 pathology and synaptic pathology in neurodegenerative diseases.

neuroscience↗