Biology subjects

Tian, S.

Publications and source records attributed to Tian, S..

At least 55 records · Page 3Linked to original sources

bioRxiv2024

StrainR2 accurately deconvolutes strain-level abundances in synthetic microbial communities

BackgroundSynthetic microbial communities offer an opportunity to conduct reductionist research in tractable model systems. However, deriving abundances of highly related strains within these communities is currently unreliable. 16S rRNA gene sequencing does not resolve abundance at the strain level, standard methods for analysis of shotgun metagenomic sequencing do not account for ambiguous mapping between closely related strains, and other methods such as quantitative PCR (qPCR) scale poorly and are resource prohibitive for complex communities. We present StrainR2, which utilizes shotgun metagenomic sequencing paired with a k-mer-based normalization strategy to provide high accuracy strain-level abundances for all members of a synthetic community, provided their genomes. ResultsBoth in silico, and using sequencing data derived from gnotobiotic mice colonized with a synthetic fecal microbiota, StrainR2 resolves strain abundances with greater accuracy than other tools utilizing shotgun metagenomic sequencing reads and can resolve complex mixtures of highly related strains. Through experimental validation and benchmarking, we demonstrate that StrainR2s accuracy is comparable to that of qPCR on a subset of strains resolved using absolute quantification. Further, it is capable of scaling to communities of hundreds of strains and efficiently utilizes memory being capable of running both on personal computers and high-performance computing nodes. ConclusionsUsing shotgun metagenomic sequencing reads is a viable method for determining accurate strain-level abundances in synthetic communities using StrainR2.

bioinformatics↗

bioRxiv2024

Introducing identification probability for automated and transferable assessment of metabolite identification confidence in metabolomics and related studies

Methods for assessing compound identification confidence in metabolomics and related studies have been debated and actively researched for the past two decades. The earliest effort in 2007 focused primarily on mass spectrometry and nuclear magnetic resonance spectroscopy and resulted in four recommended levels of metabolite identification confidence - the Metabolite Standards Initiative (MSI) Levels. In 2014, the original MSI Levels were expanded to five levels (including two sublevels) to facilitate communication of compound identification confidence in high resolution mass spectrometry studies. Further refinement in identification levels have occurred, for example to accommodate use of ion mobility spectrometry in metabolomics workflows, and alternate approaches to communicate compound identification confidence also have been developed based on identification points schema. However, neither qualitative levels of identification confidence nor quantitative scoring systems address the degree of ambiguity in compound identifications in context of the chemical space being considered, are easily automated, or are transferable between analytical platforms. In this perspective, we propose that the metabolomics and related communities consider identification probability as an approach for automated and transferable assessment of compound identification and ambiguity in metabolomics and related studies. Identification probability is defined simply as 1/N, where N is the number of compounds in a reference library or chemical space that match to an experimentally measured molecule within user-defined measurement precision(s), for example mass measurement or retention time accuracy, etc. We demonstrate the utility of identification probability in an in silico analysis of multi-property reference libraries constructed from the Human Metabolome Database and computational property predictions, provide guidance to the community in transparent implementation of the concept, and invite the community to further evaluate this concept in parallel with their current preferred methods for assessing metabolite identification confidence.

biochemistry↗

bioRxiv2024

Stabilized dengue virus 2 envelope subunit vaccine redirects the neutralizing antibody response to all E-domains

The four-dengue virus (DENV) serotypes cause several hundred million infections annually. Several live-attenuated tetravalent dengue vaccines (LAVs) are at different stages of clinical testing and regulatory approval. A major hurdle faced by the two leading LAVs is uneven replication of vaccine serotypes stimulating a dominant response to one serotype at the expense of the other three, leading to the potential for vaccine antibody (Ab) enhanced more severe infections by wild type DENV serotypes that fail to replicate in the vaccine. Protein subunit vaccines are a promising alternative since antigen dosing can be precisely controlled. However, DENV envelope (E) protein subunit vaccines have not performed well to date, possibly due to differences between the monomeric structure of soluble E and the E homodimer of the viral surface. Previously, we have combined structure-guided computational and experimental approaches to design and produce DENV2 E antigens that are stable homodimers at 37 and stimulate higher levels of neutralizing Abs (NAbs) than the WT E antigen in mice. The goal of this study was to evaluate if DENV2 E homodimers stimulate NAbs that target different epitopes on E protein compared to the WT E monomer. Using DENV4/2 chimeric viruses and Ab depletion methods, we mapped the WT E-elicited NAbs to simple epitopes on domain III of E. In contrast, the stable E homodimer stimulated a more complex response towards all three surface-exposed domains of the E protein. Our findings highlight the impact of DENV2 E oligomeric state on the quality and specificity of DENV NAbs, and the promise of DENV E homodimers as subunit vaccines. ImportanceThe ideal dengue virus (DENV) vaccine should elicit a balanced and highly protective immune response against all 4 DENV serotypes. Current tetravalent live-attenuated DENV vaccines have faced challenges due to uneven replication of vaccine virus strains stimulating a strong immune response to one serotype and weak responses to the other three. Protein subunit vaccines provide novel opportunities to stimulate a balanced response because dosing can be precisely controlled and independent of vaccine virus replication. Here, we compare immune responses elicited by a new DENV serotype 2 protein vaccine designed to match the structure of proteins on the viral surface. We find that proteins designed to match the viral surface stimulate better immune responses targeting multiple sites on the viral surface compared to previous protein vaccines. Our results justify further testing and development of these second-generation DENV protein subunit vaccines.

microbiology↗

bioRxiv2024

Single-cell resolved differentiation of pre-Kranz anatomy in maize leaf primordia

Typical C4 plants such as maize possess highly optimized Kranz-type leaf anatomy, whereby concentric wreaths of mesophyll and bundle sheath cells surround closely spaced veins. The veins and the cells that surround them are derived from the middle ground meristem (mGM) through processes that are as yet undefined. Here we distinguished the active zone of vascular development within early leaf primordia, and used comparative transcriptomics of sub-sectioned maize and rice primordia to identify cohorts of genes likely involved in early Kranz development. Leveraging single-nucleus RNA sequencing (snRNA-seq) we then explored the cell heterogeneity and developmental trajectories within single maize leaf primordia. Assisted by in situ hybridization, cell clusters of mGM and procambium were identified, with candidate marker genes showing different yet inter-related expression patterns. Localization of the vascular marker ZmSHR1 was preceded by that of ZmEREB161 and ZmEREB114 in terms of procambium initiation. Potential subclusters of bundle sheath cells and different layer of mesophyll cells were depicted from developing cells toward the tip of sub-sectioned maize primordia. Collectively our results identify potential mGM derived or procambium localized Kranz regulators and provide resources for investigating leaf vein development in maize and rice, at sub-primordium and single-cell resolution.

plant biology↗

bioRxiv2024

The Folding of Germ Granule mRNAs Controls Intermolecular Base Pairing in Germ Granules and Maintains Normal Fly Development

Drosophila germ granules enrich mRNAs critical for fly development. Within germ granules, mRNAs form multi-transcript clusters marked by increased mRNA concentration, creating an elevated potential for intermolecular base pairing. However, the type and abundance of intermolecular base pairing in mRNA clusters is poorly characterized. Using single-molecule super-resolution microscopy, chemical probing for base accessibility, phase separation assays, and simulations, we demonstrated that mRNAs remain well-folded upon localization to germ granules. While most base pairing is intramolecular, mRNAs still display the ability for intermolecular base pairing, facilitating clustering without high sequence complementarity or significant melting of secondary structure. This base pairing among mRNAs is driven by scattered and discontinuous stretches of bases appearing on the surface of folded RNAs, providing multivalency to clustering but exhibits low probability for sustained interactions. Notably, engineered germ granule mRNAs with exposed GC-rich complementary sequences (CSs) presented within stable stem loops induce sustained base pairing in vitro and enhanced intermolecular interactions in vivo. However, the presence of these stem loops alone disrupts fly development, and the addition of GC-rich CSs exacerbates this phenotype. Although germ granule mRNAs contain numerous GC-rich CSs capable of stable intermolecular base pairing, they are primarily embedded by RNA folding. This study emphasizes the role of RNA folding in controlling the type and abundance of intermolecular base pairing, thereby preserving the functional integrity of mRNAs within the germ granules.

molecular biology↗

bioRxiv2024

Unified somatic calling and machine learning-based classification enhance the discovery of clonal hematopoiesis of indeterminate potential

Clonal hematopoiesis (CH) of indeterminate potential (CHIP), driven by somatic mutations in leukemia-associated genes, confers increased risk of hematologic malignancies, cardiovascular disease and all-cause mortality. In blood of healthy individuals, small CH clones can expand over time to reach 2% variant allele frequency (VAF), the current threshold for CHIP. Nevertheless, reliable detection of low-VAF CHIP mutations is challenging, often relying on deep targeted sequencing. Here, we present UNISOM, a streamlined workflow for CHIP detection from whole-genome and whole-exome sequencing data that are underpowered, especially for low VAFs. UNISOM utilizes a meta-caller for variant detection, in couple with machine learning models which classify variants into CHIP, germline and artifact. In whole-exome data, UNISOM recovered nearly 80% of the CHIP mutations identified via deep targeted sequencing in the same cohort. Applied to whole-genome data from Mayo Clinic Biobank, it recapitulated the patterns previously established in much larger cohorts, including the most frequently mutated CHIP genes, predominant mutation types and signatures, as well as strong associations of CHIP with age and smoking status. Notably, 30% of the identified CHIP mutations had <5% VAFs, demonstrating its high sensitivity toward small mutant clones. This workflow is applicable to CHIP screening in population genomic studies.

bioinformatics↗

bioRxiv2024

Metastatic site influences driver gene function in pancreatic cancer

Driver gene mutations can increase the metastatic potential of the primary tumor1-3, but their role in sustaining tumor growth at metastatic sites is poorly understood. A paradigm of such mutations is inactivation of SMAD4 - a transcriptional effector of TGF{beta} signaling - which is a hallmark of multiple gastrointestinal malignancies4,5. SMAD4 inactivation mediates TGF{beta}s remarkable anti-to pro-tumorigenic switch during cancer progression and can thus influence both tumor initiation and metastasis6-14. To determine whether metastatic tumors remain dependent on SMAD4 inactivation, we developed a mouse model of pancreatic ductal adenocarcinoma (PDAC) that enables Smad4 depletion in the pre-malignant pancreas and subsequent Smad4 reactivation in established metastases. As expected, Smad4 inactivation facilitated the formation of primary tumors that eventually colonized the liver and lungs. By contrast, Smad4 reactivation in metastatic disease had strikingly opposite effects depending on the tumors organ of residence: suppression of liver metastases and promotion of lung metastases. Integrative multiomic analysis revealed organ-specific differences in the tumor cells epigenomic state, whereby the liver and lungs harbored chromatin programs respectively dominated by the KLF and RUNX developmental transcription factors, with Klf4 depletion being sufficient to reverse Smad4s tumor-suppressive activity in liver metastases. Our results show how epigenetic states favored by the organ of residence can influence the function of driver genes in metastatic tumors. This organ-specific gene-chromatin interplay invites consideration of anatomical site in the interpretation of tumor genetics, with implications for the therapeutic targeting of metastatic disease.

cancer biology↗

bioRxiv2024

A micro-RNA drives a 100-million-year adaptive evolution of melanic patterns in butterflies and moths

In Lepidoptera (butterflies and moths), the genomic region around the gene cortex is a hotspot locus, repeatedly used to generate intraspecific melanic wing color polymorphisms across 100-million-years of evolution. However, the identity of the effector gene regulating melanic wing color within this locus remains unknown. Here, we show that none of the four candidate protein-coding genes within this locus, including cortex, serve as major effectors. Instead, a micro-RNA (miRNA), mir-193, serves as the major effector across three deeply diverged lineages of butterflies, and its function is conserved in Drosophila. In Lepidoptera, mir-193 is derived from a gigantic long non-coding RNA, ivory, and it functions by directly repressing multiple pigmentation genes. We show that a miRNA can drive repeated instances of adaptive evolution in animals.

genetics↗

bioRxiv2024

Transient BRD4 degradation improves cardiac reprogramming by inhibiting macrophage/Oncostatin M induced JAK/STAT pathway

Reprogramming fibroblasts into induced cardiomyocytes (iCMs) holds great potential for cardiac regeneration. However, low conversion rate both in vitro and in vivo remains a significant challenge. To address this challenge, we focused on potential epigenetic barriers and screened 33 small-molecule inhibitors/degraders targeting histone acetyl post-translational modifications and related epigenetic factors. BET degraders were found to enhance cardiac reprogramming efficiency by degrading BRD4 and repressing genes involved in immune response, particularly those in the JAK/STAT pathway. We further identified that macrophage/oncostatin M activated the JAK/STAT pathway to repress cardiac reprogramming. BRD4 degrader treatment improved iCMs formation by inhibiting macrophage/oncostatin M-induced activation of the JAK/STAT pathway. Moreover, BRD4 degrader treatment enhanced MGT-mediated cardiac regeneration in vivo and improved myocardial performance post-myocardial infarction. These findings provide new insights into BRD4, macrophage/oncostatin M and JAK/STAT pathway in fibroblast to cardiomyocyte-like cell conversion and offer promising targets and small molecules to improve iCM reprogramming for clinical applications. HighlightsO_LIScreen of histone acetylation modifiers identified BRD4, a histone acetylation reader, as an important regulator in cardiac reprogramming. C_LIO_LIBRD4 degradation promoted cardiac reprogramming by repressing inflammation and the JAK-STAT pathway. C_LIO_LIBRD4 degradation inhibited macrophage/oncostatin M-induced activation of the JAK/STAT pathway. C_LIO_LIBRD4 degradation enhanced MGT-mediated cardiac regeneration in vivo and improved myocardial performance post-myocardial infarction. C_LI

cell biology↗

bioRxiv2023

Conformational Space Profile Enhances Generic Molecular Representation Learning

The molecular representation model is a neural network that converts molecular representations (SMILES, Graph) into feature vectors, that carries the potential to be applied across a wide scope of drug discovery scenarios. However, current molecular representation models have been limited to 2D or static 3D structures, overlooking the dynamic nature of small molecules in solution and their ability to adopt flexible conformational changes crucial for drug-target interactions. To address this limitation, we propose a novel strategy that incorporates the conformational space profile into molecular representation learning. By capturing the intricate interplay between molecular structure and conformational space, our strategy enhances the representational capacity of our model named GeminiMol. Consequently, when pre-trained on a miniaturized molecular dataset, the GeminiMol model demonstrates a balanced and superior performance not only on traditional molecular property prediction tasks but also on zero-shot learning tasks, including virtual screening and target identification. By capturing the dynamic behavior of small molecules, our strategy paves the way for rapid exploration of chemical space, facilitating the transformation of drug design paradigms.

bioinformatics↗

bioRxiv2023

EPAS1 Attenuates Atherosclerosis Initiation at Disturbed Flow Sites through Endothelial Fatty Acid Uptake

BackgroundAtherosclerotic plaques form unevenly due to disturbed blood flow, causing localized endothelial cell (EC) dysfunction. Obesity exacerbates this process, but the underlying molecular mechanisms are unclear. The transcription factor EPAS1 (HIF2A) has regulatory roles in endothelium, but its involvement in atherosclerosis remains unexplored. This study investigates the potential interplay between EPAS1, obesity, and atherosclerosis. MethodsResponses to shear stress were analysed using cultured porcine aortic EC exposed to flow in vitro coupled with metabolic and molecular analyses, and by en face immunostaining of murine aortic EC exposed to disturbed flow in vivo. Obesity and dyslipidemia were induced in mice via exposure to high-fat diet or through Leptin gene deletion. The role of Epas1 in atherosclerosis was evaluated by inducible endothelial Epas1 deletion, followed by hypercholesterolemia induction (AAV-PCSK9; high-fat diet). ResultsEn face staining revealed EPAS1 enrichment at sites of disturbed blood flow that are prone to atherosclerosis initiation. Obese mice exhibited substantial reduction in endothelial EPAS1 expression, correlating with hyperlipidaemia. Sulforaphane, a compound with known atheroprotective effects, restored EPAS1 expression and concurrently reduced plasma triglyceride levels in obese mice. Consistently, triglyceride derivatives (free fatty acids) suppressed EPAS1 in cultured EC by upregulating the negative regulator PHD3. Clinical observations revealed that reduced plasma EPAS1 correlated with increased endothelial PHD3 in obese individuals. Functionally, endothelial EPAS1 deletion increased lesion formation in hypercholesterolemic mice, indicating an atheroprotective function. Mechanistic insights revealed that EPAS1 protects arteries by maintaining endothelial proliferation by positively regulating CD36 and LIPG expression to increase fatty acid beta-oxidation. ConclusionsEndothelial EPAS1 attenuates atherosclerosis at sites of disturbed flow by maintaining EC proliferative via fatty acid uptake and metabolism. This endothelial repair pathway is inhibited in obesity, suggesting a novel triglyceride-PHD3 modulation pathway suppressing EPAS1 expression. These findings have implications for therapeutic strategies addressing vascular dysfunction in obesity.

physiology↗

bioRxiv2023

14-3-3 binding motif phosphorylation disrupts Hdac4 organized condensates to stimulate cardiacreprogramming

Cell fate conversion is associated with extensive epigenetic and post translational modifications (PTMs) and architectural changes of sub-organelles and organelles, yet how these events are interconnected remains unknown. We report here the identification of a phosphorylation code in 14-3-3 binding motifs (PC14-3-3) that greatly stimulates induced cardiomyocyte (iCM) formation from fibroblasts. PC14-3-3 was identified in pivotal functional proteins for iCM reprogramming, including transcription factors and epigenetic factors. Akt1 kinase and PP2A phosphatase were a key writer and eraser of the PC14-3-3 code, respectively. PC14-3-3 activation induces iCM formation with the presence of only Tbx5. In contrast, PC14-3-3 inhibition by mutagenesis or inhibitor-mediated code removal abolished reprogramming. We discovered that key PC14-3-3 embedded factors, such as Hdac4, Mef2c, Nrip1, and Foxo1, formed Hdac4 organized inhibitory nuclear condensates. Notably, PC14-3-3 activation disrupted Hdac4 condensates to promote cardiac gene expression. Our study suggests that sub-organelle dynamics regulated by a post-translational modification code could be a general mechanism for stimulating cell reprogramming and organ regeneration. HighlightsO_LIA PC14-3-3 (phosphorylation code in 14-3-3 binding motifs) is identified in pivotal functional proteins, such as HDAC4 and Mef2c, that stimulates iCM formation. C_LIO_LIAkt1 kinase and PP2A phosphatase are a key writer and a key eraser of the PC14-3-3 code, respectively, and PC14-3-3 code activation can replace Mef2c and Gata4 in cardiac reprogramming. C_LIO_LIPC14-3-3 activation disrupts Hdac4 organized condensates which results in releasing multiple 14-3-3 motif embedded proteins from the condensates to stimulate cardiac reprogramming. C_LIO_LISub-organelle dynamics and function regulated by a post-translational modification code could be a general mechanism in stimulating cell reprogramming and organ regeneration. C_LI Graphic abstract O_FIG O_LINKSMALLFIG WIDTH=200 HEIGHT=150 SRC="FIGDIR/small/567913v1_ufig1.gif" ALT="Figure 1"> View larger version (52K): org.highwire.dtl.DTLVardef@1fec3aforg.highwire.dtl.DTLVardef@e13b16org.highwire.dtl.DTLVardef@ee354borg.highwire.dtl.DTLVardef@ecd58e_HPS_FORMAT_FIGEXP M_FIG C_FIG

cell biology↗

bioRxiv2023

BioKG: a comprehensive, high-quality biomedical knowledge graph for AI-powered, data-driven biomedical research

To address the rapid growth of scientific publications and data in biomedical research, knowledge graphs (KGs) have become a critical tool for integrating large volumes of heterogeneous data to enable efficient information retrieval and automated knowledge discovery (AKD). However, transforming unstructured scientific literature into KGs remains a significant challenge, with previous methods unable to achieve human-level accuracy. In this study, we utilized an information extraction pipeline that won first place in the LitCoin NLP Challenge (2022) to construct a large-scale KG named iKraph using all PubMed abstracts. The extracted information matches human expert annotations and significantly exceeds the content of manually curated public databases. To enhance the KGs comprehensiveness, we integrated relation data from 40 public databases and relation information inferred from high-throughput genomics data. This KG facilitates rigorous performance evaluation of AKD, which was infeasible in previous studies. We designed an interpretable, probabilistic-based inference method to identify indirect causal relations and applied it to real-time COVID-19 drug repurposing from March 2020 to May 2023. Our method identified 600-1400 candidate drugs per month, with one-third of those discovered in the first two months later supported by clinical trials or PubMed publications. These outcomes are very challenging to attain through alternative approaches that lack a thorough understanding of the existing literature. A cloud-based platform (https://biokde.insilicom.com) was developed for academic users to access this rich structured data and associated tools.

bioinformatics↗

bioRxiv2023

SRSF1-mediated alternative splicing of Tial1/Tiar is essential for homing and self-renewal in mouse spermatogonial stem cells

AbstractSpermatogonial stem cells (SSCs) are essential for continuous spermatogenesis and male fertility. The underlying mechanisms of alternative splicing (AS) in mouse SSCs are still largely unclear. We demonstrated that SRSF1 is essential for gene expression and splicing in mouse SSCs. Crosslinking immunoprecipitation and sequencing (CLIP-seq) data revealed that spermatogonia-related genes (e.g., Plzf, Id4, Setdb1, Stra8, Tial1/Tiar, Bcas2, Ddx5, Srsf10, Uhrf1, and Bud31) were bound by SRSF1 in the mouse testes. Specific deletion of Srsf1 in mouse germ cells impairs homing of precursor SSCs leading to male infertility. Whole-mount staining data showed the absence of germ cells in the testes of adult conditional knockout (cKO) mice, which indicates Sertoli cell-only syndrome (SCOS) in cKO mice. The expression of spermatogonia-related genes (Gfra1, Pou5f1, Plzf, Dnd1, Stra8, and Taf4b) was significantly reduced in the testes of cKO mice. Moreover, multiomics analysis suggests that SRSF1 may affect survival of spermatogonia by directly binding and regulating Tial1/Tiar expression through AS. In addition, immunoprecipitation mass spectrometry (IP-MS) and co-immunoprecipitation (Co-IP) data showed that SRSF1 interacts with RNA splicing-related proteins (SART1, RBM15, and SRSF10). Collectively, our data reveal the critical role of SRSF1 in spermatogonia survival, which may provide a framework to elucidate the molecular mechanisms of the posttranscriptional network underlying homing of precursor SSCs.

developmental biology↗

bioRxiv2023

A regulatory circuit involving the NADH dehydrogenase-like complex balances C4 photosynthetic carbon flow and cellular redox in maize

O_LIC4 plants typically operate a CO2 concentration mechanism from mesophyll (M) cells into bundle sheath (BS) cells. NADH dehydrogenase-like (NDH) complex is enriched in the BS cells of many NADP-ME type C4 plants, and is more abundant in C4 than in C3 plants, but to what extent it is involved in the CO2 concentration mechanism remains to be experimentally investigated. C_LIO_LIWe created maize and rice mutants deficient in NDH function, and used a combination of transcriptomic, proteomic, and metabolomic approaches for comparative analysis. C_LIO_LIConsiderable decrease in growth, photosynthetic activities, and levels of key photosynthetic proteins were observed in maize but not rice mutants. However, gene expression for many cyclic electron transport and Calvin-Benson cycle components plus BS specific C4 enzymes, was up-regulated in maize mutants. Metabolite analysis of the maize ndh mutants revealed increased NADPH/NADP ratio, as well as malate, RuBP, FBP, and photorespiration components. C_LIO_LIWe suggest that by optimizing NADPH and malate levels, adjusting NADP-ME activity, NDH functions to balance metabolic and redox states in the BS cells of maize, coordinating photosynthetic gene expression and protein content, thus directly regulating the carbon flow in the two-celled C4 system of maize. C_LI

plant biology↗

bioRxiv2022

Structural and Computational Design of a SARS-CoV-2 Spike Antigen with Increased Receptor Binding Domain Exposure and Improved Immunogenicity

Emerging SARS-CoV-2 variants of concern challenge the efficacy of approved vaccines and emphasize the need for improved antigens. Using an evolutionary-based design approach starting from the widely used engineered Spike antigen, S-2P, we sought to increase antigen production levels and the exposure of highly conserved and neutralization sensitive receptor-binding domain (RBD) epitopes. Thirty-six prototypes were generated in silico, of which fifteen were produced and tested in biochemical assays. Design S2D14, which contains 20 mutations within the Spike S2 domain, showed a 6-fold increase in expression while preserving similar thermal stability and antigenicity as S-2P. Cryo-EM structures indicate that the dominant populations of S2D14 particles have RBDs in exposed states, and analysis of these structures revealed how modifications within the S2 domain balance trimer stability and RBD accessibility through formation and removal of hydrogen bonds and surface charge alterations. Importantly, vaccination of mice with adjuvanted S2D14 resulted in higher levels of neutralizing antibodies than adjuvanted S-2P against SARS-CoV-2 Wuhan strain and four variants of concern. These results can guide the design of next generation vaccines to combat current, and future coronaviruses and the approaches used may be broadly applicable to streamline the successful design of vaccine antigens.

immunology↗

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

Quartet protein reference materials and datasets for multi-platform assessment of label-free proteomics

Quantitative proteomics is an indispensable tool in life science research. However, there is a lack of reference materials for evaluating the reproducibility of label-free liquid chromatography-tandem mass spectrometry (LC-MS/MS)-based measurements among different instruments and laboratories. We developed the Quartet as a proteome reference material with built-in truths, and distributed the same aliquots to 15 laboratories with nine conventional LC-MS/MS platforms across six cities in China. Relative abundance of over 12,000 proteins on 816 MS files were obtained and compared for reproducibility among the instruments and laboratories to ultimately generate proteomics benchmark datasets. There was a wide dynamic range of proteomes spanning ~7 orders of magnitude (101-108 copies/cell), and the injection order had marked effects on quantitative instead of qualitative. Overall, the Quartet offers valuable standard materials and data resources for improving the quality control of proteomic analyses as well as the reproducibility and reliability of research findings.

molecular biology↗