Biology subjects

Wang, Q.

Publications and source records attributed to Wang, Q..

At least 415 records · Page 23Linked to original sources

bioRxiv2023

Deep spatial proteomic exploration of severe COVID-19-related pulmonary injury in post-mortem specimens

The lung, as a primary target of SARS-CoV-2, exhibits heterogeneous microenvironment accompanied by various histopathological changes following virus infection. However, comprehensive insight into the protein basis of COVID-19-related pulmonary injury with spatial resolution is currently deficient. Here, we generated a region-resolved quantitative proteomic atlas of seven major pathological structures within the lungs of COVID-19 victims by integrating histological examination, laser microdissection, and ultrasensitive proteomic technologies. Over 10,000 proteins were quantified across 71 dissected FFPE post-mortem specimens. By comparison with control samples, we identified a spectrum of COVID-19-induced protein and pathway dysregulations in alveolar epithelium, bronchial epithelium, and pulmonary blood vessels, providing evidence for the proliferation of transitional-state pneumocytes. Additionally, we profiled the region-specific proteomes of hallmark COVID-19 pulmonary injuries, including bronchiole mucus plug, pulmonary fibrosis, airspace inflammation, and hyperplastic alveolar type 2 cells. Bioinformatic analysis revealed the enrichment of cell-type and functional markers in these regions (e.g. enriched TGFBI in fibrotic region). Furthermore, we identified the up-regulation of proteins associated with viral entry, host restriction, and inflammatory response in COVID-19 lungs, such as FURIN and HGF. Collectively, this study provides spatial proteomic insights for understanding COVID-19-caused pulmonary injury, and may serve as a valuable reference for improving therapeutic intervention for severe pneumonia.

systems biology↗

bioRxiv2023

Improving the Circularization Efficiency, Stability and Translatability of Circular RNA by circDesign

Synthetic circular RNA (circRNA) has emerged as a promising platform for vaccine and therapeutic development, featuring its uniqueness in a closed-loop structure, cap-independent translation mechanism, and prolonged expression. However, the rational design of a circRNA sequence to jointly improve its stability and protein coding potential remains challenging. In this study, we present circDesign, an efficient algorithm to achieve the optimal design of circRNA by ensuring optimized folding of each segment, which leads to enhanced circularization efficiency, stability, and translatability. Using rabies virus glycoprotein (RABV-G) as the model antigen, we demonstrated that circDesign-generated circRNAs exhibited higher stability and protein translation efficiency in vitro and in vivo compared to other codon adaptation index (CAI)-optimized sequences, thus leading to enhanced in vivo immunogenicity. Ribosome and polysome profiling further revealed that an intact internal ribosome entry site (IRES) structure is critical for efficient translation. By intentionally disrupting the IRES motifs, we observed that the resulting circRNA sequences had lower translatability compared to circDesign-generated sequences. Taken together, our circular RNA design algorithm provides a general strategy to leverage the capability of circRNA as next-generation vaccines or therapeutics.

bioengineering↗

bioRxiv2023

Transcriptome brings variations of gene expression, alternative splicing, and structural variations into gene-scale trait dissection in soybean

Genome-wide association study (GWAS) identifies trait-associated loci, but due in part to slow decay of linkage disequilibrium (LD), identifying the causal genes can be a bottleneck. Transcriptome-wide association study (TWAS) addresses this by identifying gene expression-phenotype associations or integrating gene expression quantitative trait loci (eQTLs) with GWAS results. Here, we used self-pollinated soybean as a model to evaluate the application of TWAS in the genetic dissection of traits in plant species that exhibit slow LD decay. The first RNA-Seq analysis of a soybean diversity panel was conducted, which identified the genetic regulation of 29,286 genes. Different TWAS solutions were less affected by LD and robust with source of expression that identified known genes related to traits from different development stages and tissues. A novel gene named pod color L2 was identified via TWAS and functionally validated by genome editing. Our introduction of the new exon proportion feature significantly improves the capture of expression variations resulting from structural variations and alternative splicing. As a result, the genes identified by our TWAS approach exhibited a diverse range of causal variations, including SNP, insertion/deletion, gene fusion, copy number variation, and alternative splicing. Using our TWAS approach, we identified genes associated with flowering time, including both previously known candidates and novel genes that had not been linked to this trait before, providing complementary insights with GWAS. In summary, this study supports the application of TWAS for candidate gene identification in species with low rates of LD decay.

genetics↗

bioRxiv2023

Decapitated body intelligence (DBI) in cricket Gryllodes sigillatus

Backgroundintelligence is a highly complex problem. The decapitated insect exhibits various behaviors, indicating that they may have intelligence. Recent studies have reported organoid intelligence (OI) that lab-grown organoids also possess intelligence. This study investigated the response of decapitated crickets to different chemical stimuli to determine whether decapitated crickets have intelligence. MethodsWe used deionized water, NaCl, sucrose, and sodium hypochlorite to stimulate the front legs of the decapitated crickets and lesion the T1-T2 nerve connection of the thoracic ganglia. The behavioral response types of their forelegs were recorded. Reaction time, incidence rate, and total number of responses were calculated and analyzed. ResultsThe decapitated crickets exhibit four types of responses: leg extension, leg withdrawal, leg lift, and jump. The reaction time and incidence rate varied depending on the type and concentration of the stimulant solution. The total number of responses gradually increased with deionized water, NaCl, sucrose, and sodium hypochlorite. The lesion experiments further revealed that the only T1 thoracic ganglion can control stimulating behavior. ConclusionThe decapitated crickets possess the intelligence of perceiving stimuli and taking corresponding action. We called it decapitated body intelligence (DBI) or extrabrain intelligence (EI), which suggests that intelligence is not localized exclusively in the brain but also resides in insect ganglia. This finding opens up new ideas and avenues for the study of intelligence and the brain.

neuroscience↗

bioRxiv2023

Lysine vitcylation is a novel vitamin C-derived protein modification that enhances STAT1-mediated immune response

Vitamin C (vitC) is a vital nutrient for health and also used as a therapeutic agent in diseases such as cancer. However, the mechanisms underlying vitCs effects remain elusive. Here we report that vitC directly modifies lysine without enzymes to form vitcyl-lysine, termed "vitcylation", in a dose-, pH-, and sequence-dependent manner across diverse proteins in cells. We further discover that vitC vitcylates K298 site of STAT1, which impairs its interaction with the phosphatase PTPN2, preventing STAT1 Y701 dephosphorylation and leading to increased STAT1-mediated IFN pathway activation in tumor cells. As a result, these cells have increased MHC/HLA class-I expression and activate immune cells in co-cultures. Tumors collected from vitC-treated tumor-bearing mice have enhanced vitcylation, STAT1 phosphorylation and antigen presentation. The identification of vitcylation as a novel PTM and the characterization of its effect in tumor cells opens a new avenue for understanding vitC in cellular processes, disease mechanisms, and therapeutics.

biochemistry↗

bioRxiv2023

Modeling of mitochondrial genetic polymorphisms reveals induction of heteroplasmy by pleiotropic disease locus MT:10398A>G

Mitochondrial (MT) dysfunction has been associated with several neurodegenerative diseases including Alzheimers disease (AD). While MT-copy number differences have been implicated in AD, the effect of MT heteroplasmy on AD has not been well characterized. Here, we analyzed over 1,800 whole genome sequencing data from four AD cohorts in seven different tissue types to determine the extent of MT heteroplasmy present. While MT-heteroplasmy was present throughout the entire MT genome for blood samples, we detected MT-heteroplasmy only within the MT control region for brain samples. We observed that an MT variant 10398A>G (rs2853826) was significantly associated with overall MT-heteroplasmy in brain tissue while also being linked with the largest number of distinct disease phenotypes of all annotated MT variants in MitoMap. Using gene-expression data from our brain samples, our modeling discovered several gene networks involved in mitochondrial respiratory chain and Complex I function associated with 10398A>G. The variant was also found to be an expression quantitative trait loci (eQTL) for the gene MT-ND3. We further characterized the effect of 10398A>G by phenotyping a population of lymphoblastoid cell-lines (LCLs) with and without the variant allele. Examination of RNA sequence data from these LCLs reveal that 10398A>G was an eQTL for MT-ND4. We also observed in LCLs that 10398A>G was significantly associated with overall MT-heteroplasmy within the MT control region, confirming the initial findings observed in post-mortem brain tissue. These results provide novel evidence linking MT SNPs with MT heteroplasmy and open novel avenues for the investigation of pathomechanisms that are driven by this pleiotropic disease associated loci.

genomics↗

bioRxiv2023

Pan-genome analysis highlights the role of structural variation in the evolution and environmental adaptation of Asian honeybees

The Asian honeybee, Apis cerana, is an ecologically and economically important pollinator. Mapping its genetic variation is key to understanding population-level health, histories, and potential capacities to respond to environmental changes. However, most efforts to date were focused on single nucleotide polymorphisms (SNPs) based on a single reference genome, thereby ignoring larger-scale genomic variation. We employed long-read sequencing technologies to generate a chromosome-scale reference genome for the ancestral group of A. cerana. Integrating this with 525 resequencing datasets, we constructed the first pan-genome of A. cerana, encompassing almost the entire gene content. We found that 31.32% of genes in the pan-genome were variably present across populations, providing a broad gene pool for environmental adaptation. We identified and characterized structural variations (SVs) and found that they were not closely linked with SNP distributions, however, the formation of SVs was closely associated with transposable elements. Furthermore, phylogenetic analysis using SVs revealed a novel A. cerana ecological group not recoverable from the SNP data. Performing environmental association analysis identified a total of 44 SVs likely to be associated with environmental adaptation. Verification and analysis of one of these, a 330 bp deletion in the Atpalpha gene, indicated that this SV may promote the cold adaptation of A. cerana by altering gene expression. Taken together, our study demonstrates the feasibility and utility of applying pan-genome approaches to map and explore genetic feature variations of honeybee populations, and in particular to examine the role of SVs in the evolution and environmental adaptation of A. cerana.

genomics↗

bioRxiv2023

CHPF boosts proliferation and invasion of clear cell renal cell carcinoma

BackgroundClear cell renal cell carcinoma (ccRCC) is a malignant tumor most commonly seen in the urinary system, featuring quick progression, invasive behavior, frequent recrudesce, and bad prognosis, whereas Chondroitin polymerizing factor (CHPF) is an essential glycosyl transferase of biosynthesis involved chondroitin sulphate. But the relationship between the two has not been fully understood so far. The present research will probe into the relationship between CHPF and ccRCC. MethodsExplore the CHPF expression level in renal ccRCC tissues through bioinformatics analysis of The Cancer Genome Atlas (TCGA) and the real-time quantitative polymerase chain reaction detection system (qPCR); acquire relevant clinical data from the TCGA data-base and use Kaplan-Meier survival analysis to verify the relevance of CHPF expression to the clinical prognosis of ccRCC patients; then, effectively silence CHPF in ccRCC 786-O cells by a lentivirus-mediated approach; next, observe the effects of CHPF on tumor cell proliferation, cell cycle progression, and apoptosis. ResultsIn ccRCC tissues, CHPF expression has been significantly upregulated; the higher expression, the shorter survival of ccRCC patients. CHPF downregulation in the 786-O cell can effectively hold back the proliferation, apoptosis and cycle of cancer cells. ConclusionBased on the above results, we arrive at a conclusion that CHPF expression contributes markedly to the development of human ccRCC cells. Therefore, CHPF may act as a potential prognostic marker of ccRCC and provide a new target for ccRCC treatment. Simple SummaryChondroitin polymerizing factor (CHPF) is an important glycosyltransferase involved in the biosynthesis of chondroitin sulfate, which is thought to have some pro-carcinogenic effects. However, the role and mechanism of CHPF in clear cell renal cell carcinoma (ccRCC) have not been reported. The aim of this study was to investigate the relationship between CHPF and ccRCC. In this study, we found that CHPF was highly expressed in ccRCC and knocking out CHPF can greatly inhibit the proliferation and cell cycle progression of ccRCC and accelerate its apoptosis, suggesting that CHPF can predict the prognosis of ccRCC and a potential target for treatment.

genetics↗

bioRxiv2023

A Gpr35 tuned gut-brain metabolic axis regulates depressive-like behavior

Gene-environment interactions shape animal behavior and the susceptibility to neurobehavioral symptoms such as depression. However, little is known about the signaling pathway that integrates genetic and environmental inputs with neurobehavioral outcomes, preventing the development of targeted therapies. Here we report that Gpr35 engages a gut microbe-to-brain metabolic pathway to modulate neuronal plasticity and depressive behavior in mice. Chronic stress decreases gut epithelial Gpr35, the genetic deletion of which induces despair and social impairment in a microbiome-dependent manner. We identify a dominant role for the imbalance of microbe-derived indole-3-carboxaldehyde (IAld) and indole-3-lactate (ILA) in the behavioral symptoms with Gpr35 deficiency. Mechanistically, these bacterial metabolites counteractively modulate dendritic spine density and synaptic transmission in the nucleus accumbens. Supplementation of IAld, which is similarly decreased in depressive patients, produce anti-depressant effects in mice with stress or gut epithelial Gpr35 deficiency. Together, these findings identify a genetics-shaped gut-brain connection underlying the susceptibility to depression and suggest a microbial metabolite-based therapeutic strategy to genetic predisposition.

animal behavior and cognition↗

bioRxiv2023

Activation of Multiple Eph Receptors on Neuronal Membranes Correlates with The Onset of Traumatic Optic Neuropathy

BackgroundOptic neuropathy (ON) is a major cause of irreversible blindness, yet the molecular determinants that contribute to neuronal demise have not been fully elucidated. Several studies have identified ephrin signaling as one of the most dysregulated pathways in the early pathophysiology of ON with varied etiologies. Developmentally, gradients in ephrin signaling coordinate retinotopic mapping via repulsive modulation of cytoskeletal dynamics in neuronal membranes. Little is known about the role ephrin signaling played in the post-natal visual system and its correlation with the onset of optic neuropathy. MethodsPostnatal mouse retinas were collected for mass spectrometry analysis for Eph receptors. Optic nerve crush (ONC) model was employed to induce optic neuropathy, and proteomic changes during the acute phase of neuropathic onset were analyzed. Confocal and super-resolution microscopy determined the cellular localization of activated Eph receptors after ONC injury. Eph receptor inhibitors assessed the neuroprotective effect of ephrin signaling modulation. ResultsMass spectrometry revealed expression of seven Eph receptors (EphA2, A4, A5, B1, B2, B3, and B6) in postnatal mouse retinal tissue. Immunoblotting analysis indicated a significant increase in phosphorylation of these Eph receptors 48 hours after ONC. Confocal microscopy demonstrated the presence of both subclasses of Eph receptors in the inner retinal layers. STORM super-resolution imaging combined with optimal transport colocalization analysis revealed a significant co-localization of activated Eph receptors with injured neuronal processes, compared to uninjured neuronal and/or injured glial cells, 48 hours post-ONC. Eph receptor inhibitors displayed notable neuroprotective effects after 6 days of ONC injury. ConclusionsOur findings demonstrate the functional presence of diverse Eph receptors in the postnatal mammalian retina, capable of modulating multiple biological processes. Pan-Eph receptor activation contributes to the onset of neuropathy in ONs, with preferential activation of Eph receptors on neuronal processes in the inner retina following optic nerve injury. Notably, Eph receptor activation precedes neuronal loss. We observed neuroprotective effects upon inhibiting Eph receptors. Our study highlights the importance of investigating this repulsive pathway in early optic neuropathies and provides a comprehensive characterization of the receptors present in the developed retina of mice, relevant to both homeostasis and disease processes.

neuroscience↗

bioRxiv2023

Peripheral death by neglect and limited clonal deletion during physiologic B lymphocyte development

Autoreactive B cells generated during B cell development are inactivated by clonal deletion, receptor editing or anergy. Up to 97% of immature B cells appear to die before completing maturation, but the anatomic sites and reasons underlying this massive cell loss are not fully understood. Here, we directly quantitated apoptosis and clonal deletion during physiologic B lymphocyte development using Rosa26INDIA apoptosis indicator mice. Immature B cells displayed low levels of apoptosis in the bone marrow but started dying at high levels in the periphery upon release from bone marrow sinusoids into the blood circulation. Clonal deletion of self-reactive B cells was neither a major contributor to apoptosis in the bone marrow nor the periphery. Instead, most peripheral transitional 1 B cells did not encounter the signals required for positive selection into the mature B cell compartments. This study sheds new light on B cell development and suggests that receptor editing and/or anergy efficiently control most primary autoreactivity in mice. SummaryThe large amount of cell loss predicted during B lymphocyte development is unexplained by clonal deletion of self-reactive cells. Many transitional 1 B cells die in the periphery due to failed selection in the mature B cell compartments.

immunology↗

bioRxiv2023

The Structural Role of N170 in Substrate-assisted Deacylation in KPC-2 β-Lactamase

The amino acid substitutions in Klebsiella pneumoniae carbapenemase 2 (KPC-2) that have arisen in the clinic are observed to lead to the development of resistance to ceftazidime-avibactam, a preferred treatment for KPC bearing Gram-negative bacteria. Specific substitutions in the omega loop (R164-D179) results in changes in the structure and function of the enzyme, leading to alterations in substrate specificity, decreased stability, and more recently observed, increased resistance to ceftazidime/avibactam. Using accelerated rare-event sampling well-tempered metadynamics simulations, we explored in detail the structural role of R164 and D179 variants that are described to confer ceftazidime/avibactam resistance. The buried conformation of D179 substitutions produce a pronounced structural disorder in the omega loop - more than R164 mutants, where the crystallographic omega loop structure remains mostly intact. Our findings also reveal that the conformation of N170 plays an underappreciated role impacting drug binding and restricting deacylation. The results further support the hypothesis that KPC-2 D179 variants employ substrate-assisted catalysis for ceftazidime hydrolysis, involving the ring amine of the aminothiazole group to promote deacylation and catalytic turnover. Moreover, the shift in the WT conformation of N170 contributes to reduced deacylation and altered spectrum of enzymatic activity.

biophysics↗

bioRxiv2023

Stanniocalcin 2 (STC2) is a potent biomarker of hepatocellular carcinoma with its expression being augmented in Nrf1α-deficient cells, but diminished in Nrf2-deficient cells

For insights into the fact that liver-specific knockout of Nrf1 leads to development of non-alcoholic steatohepatitis and spontaneous hepatoma, we previously found that loss of Nrf1 (i.e., a full-length isoform encoded by Nfe2l1) promotes HepG2-derived tumor growth in xenograft mice, but malgrowth of the xenograft tumor is significantly suppressed by knockout of Nrf2 (encoded by Nfe2l2). The mechanism underlying such marked distinctions in their pathologic phenotypes remains elusive, however, to date. Herein, we mined the transcriptome data of liver cancer from the TCGA database to establish a prognostic model of liver cancer and then calculated the predicted risk score of each cell line. The results indicated that knockout of Nrf1 significantly increased the risk score in HepG2 cells, whereas the risk score was reduced by knockout of Nrf2. Of note, stanniocalcin 2 (STC2, a biomarker of liver cancer, that is up-expressed in hepatocellular carcinoma (HCC) tissues with a reduction in the overall survival ratio of those patients) was augmented in Nrf1Nrf2-/- cells, but diminished in Nrf2-/- cells. Thereby, it is inferable that STC2 is likely involved in mediating the distinction between Nrf1Nrf2-/- and Nrf2-/-. Further investigation revealed that HIF1A is an upstream regulator of STC2 in caNrf2{Delta}N, rather than Nrf1Nrf2-/-, cells, and regulation of STC2 and HIF1A in Nrf1Nrf2-/- is determined by Nrf2, but the regulation of STC2 by Nrf2 may be independent on HIF1A. In turn, STC2 can regulate Nrf2 via the putative calcium-mediated Keap1-p62 signaling so to form a feedback regulatory loop. Such potential function of STC2 was further corroborated by a series of experiments combined with transcriptomic sequencing. The results unraveled that STC2 manifests as a dominant tumor-promoter, because the STC2-leading increases in clonogenicity of hepatoma cells and malgrowth of relevant xenograft tumor were almost completely abolished in STC2-/-cells. Together, these demonstrate that STC2 could be paved as a novel potent therapeutic target, albeit as a diagnostic marker, for hepatocellular carcinoma.

cell biology↗

bioRxiv2023

BiATNovo: A Self-Attention based Bidirectional Peptide Sequencing Method

De novo sequencing from tandem mass spectra (MS/MS) data is a key technique for identifying novel peptides. In theory, the Data-Independent Acquisition (DIA) method can fragment all precursor ions in an unbiased and non-targeted fashion. However, each spectrum contains fragments from multiple precursor ions, and the unclear relationship between these ions and their fragments poses a significant challenge to the accuracy of de novo sequencing algorithms. Here we present BiATNovo, an attention-based bidirectional de novo peptide sequencing framework. BiATNovo comprises a bidirectional attention-based model and a bidirectional fusion-reranking post-processing module, which enables efficient capture of relationships between tandem mass spectra, fragment ions, and peptide patterns, while also expanding the candidate set to select the optimal sequence. This framework improves peptide prediction accuracy, particularly for long peptide sequences, and mitigates the imbalance where the initial amino acids are predicted more accurately than the last ones. Evaluation results demonstrate that BiATNovo outperforms existing algorithms, including DeepNovo-DIA and PepNet, in both peptid-level and amino acid-level. Furthermore, when extended to DDA datasets, BiATNovo achieves comparable performance to state-of-the-art models.

bioinformatics↗

bioRxiv2023

Dynamics of Single-Base Editing: Theoretical Analysis

Recent experimental advances led to the development of DNA base editors (BEs) with a single-nucleotide precision that is critical for future progress in various scientific and technological fields. The molecular mechanisms of single-base discrimination, however, remain not well understood. Using a recently developed stochastic approach, we theoretically investigated the dynamics of single-base editing. More specifically, transient and mean times to edit "TC" motifs by cytosine BEs are explicitly evaluated for correct (target) and incorrect (bystander) locations on DNA. In addition, the effect of mutations on the dynamics of the single-base edition is also analyzed. It is found that for most ranges of parameters, it is possible to temporarily separate target and bystander products of base editing, supporting the idea of dynamic selectivity as a method of improving the precision of single-base editing. We conclude that to improve the efficiency of single-base editing, selecting the probability or selecting the time requires different strategies. Physical-chemical arguments to explain the observed dynamic properties are presented. The theoretical analysis clarifies some important aspects of molecular mechanisms of selective base editing.

biophysics↗

bioRxiv2023

Population genomics reveals extensive inbreeding and purging of mutational load in wild Amur tigers

The inbreeding is a big threat for the persistence of genetic diversity in small and isolated populations of endangered species. The homozygous genome could exacerbate inbreeding depression by introducing homozygous deleterious alleles in the population. However, purging of inbreeding loads as they become homozygotes in small populations could alleviate the depression. The Amur tiger (Panthera tigris altaica) is typically exists in small population living in forests in Northeast Asia and is among the most endangered animals on the planet with great symbolic significance of conservation. By comparing with captive individuals, we revealed substantially higher and more extensive inbreeding in the wild Amur tiger population (FROH=0.51) than in captive Amur tigers (FROH=0.26). We further found much less mutational loads in wild populations when compared with captive Amur tigers. However, the frequency of loss of function and deleterious nonsynonymous mutations inside ROH regions are much lower than that in non-ROH regions in both wild and captive Amur tigers, indicating the purging may had occurred in both populations but much effective in the wild population. In addition, we found the average frequency of deleterious alleles was much lower than that of neutral alleles in the wild population, indicating that the purifying selection contributed to the purging of mutational loads in the wild Amur tigers. These findings provide valuable genome-wide evidence to support the making of future conservation plans of wild Amur tigers.

genomics↗

bioRxiv2023

Neural response properties predict perceived contents and locations elicited by intracranial electrical stimulation of human auditory cortex

Intracranial electrical stimulation (iES) of auditory cortex can elicit sound experiences with a variety of perceived contents (hallucination or illusion) and locations (contralateral or bilateral side), independent of actual acoustic inputs. However, the neural mechanisms underlying this elicitation heterogeneity remain undiscovered. Here, we collected subjective reports following iES at 3062 intracranial sites in 28 patients and identified 113 auditory cortical sites with iES-elicited sound experiences. We then decomposed the sound-induced intracranial electroencephalogram (iEEG) signals recorded from all 113 sites into time-frequency features. We found that the iES-elicited perceived contents can be predicted by the early high-{gamma} features extract from sound-induced iEEG. In contrast, the perceived locations elicited by stimulating hallucination sites and illusion sites are determined by the late high-{gamma} and long-lasting features, respectively. Our study unveils the crucial neural signatures of iES-elicited sound experiences in human and presents a new strategy to hearing restoration for individuals suffering from deafness.

neuroscience↗

bioRxiv2023

Deep immunological imprinting due to the ancestral spike in the current bivalent COVID-19 vaccine

With the aim of broadening immune responses against the evolving SARS-CoV-2 Omicron variants, bivalent COVID-19 mRNA vaccines that encode the ancestral and Omicron BA.5 spike proteins have been authorized for clinical use, supplanting the original monovalent counterpart in numerous countries. However, recent studies have demonstrated that administering either a monovalent or bivalent vaccine as a fourth vaccine dose results in similar neutralizing antibody titers against the latest Omicron subvariants, raising the possibility of immunological imprinting. Utilizing binding immunoassays, pseudotyped virus neutralization assays, and antigenic mapping, we investigated antibody responses from 72 participants who received three monovalent mRNA vaccine doses followed by either a bivalent or monovalent booster, or who experienced breakthrough infections with the BA.5 or BQ subvariant after vaccinations with an original monovalent vaccine. Compared to a monovalent booster, the bivalent booster did not yield noticeably higher binding titers to D614G, BA.5, and BQ.1.1 spike proteins, nor higher virus-neutralizing titers against SARS-CoV-2 variants including the predominant XBB.1.5 and the emergent XBB.1.16. However, sera from breakthrough infection cohorts neutralized Omicron subvariants significantly better. Multiple analyses of these results, including antigenic mapping, made clear that inclusion of the ancestral spike prevents the broadening of antibodies to the BA.5 component in the bivalent vaccine, thereby defeating its intended goal. Our findings suggest that the ancestral spike in the current bivalent COVID-19 vaccine is the cause of deep immunological imprinting. Its removal from future vaccine compositions is therefore strongly recommended.

microbiology↗