Biology subjects

Huang, W.

Publications and source records attributed to Huang, W..

At least 163 records · Page 9Linked to original sources

bioRxiv2024

From Sight to Insight: A Multi-task Approach with the Visual Language Decoding Model

Visual neural decoding aims to unlock the mysteries of how the human brain interprets the visual world. While early studies made some progress in decoding visual activity for singular type of information, they failed to concurrently reveal the multi-level interweaving linguistic information in the brain. Here, we developed a novel Visual Language Decoding Model (VLDM) capable of decoding categories, semantic labels, and textual descriptions from visual perceptual activities simultaneously. We selected the large-scale NSD dataset to ensure the efficiency of the decoding model in joint training and evaluation across multiple tasks. For category decoding, we achieved the effective classification of 12 categories with an accuracy of nearly 70%, significantly surpassing the chance level. For label decoding, we attained the precise prediction of 80 specific semantic labels with a 16-fold improvement over the chance level. For text decoding, the scores of the decoded text surpassed the corresponding baseline levels by remarkable margins on six evaluation metrics. This study contributes significantly to extensive applications in multi-layered brain-computer interfaces, potentially leading to more natural and efficient human-computer interaction experiences.

neuroscience↗

bioRxiv2024

Mendelian segregation and high recombination rates facilitate genetic analyses in Cryptosporidium parvum

Very little is known about the process of meiosis in the apicomplexan parasite Cryptosporidium despite the essentiality of sex in its life cycle. Most cell lines only support asexual growth of Cryptosporidium parvum (C. parvum), but stem cell derived intestinal epithelial cells grown under air-liquid interface (ALI) conditions support the sexual cycle. To examine chromosomal dynamics during meiosis in C. parvum, we generated two transgenic lines of parasites that were fluorescently tagged with mCherry or GFP on chromosomes 1 or 5, respectively. Infection of ALI cultures or Ifngr1-/- mice with mCherry and GFP parasites produced "yellow" oocysts generated by cross-fertilization. Outcrossed oocysts from the F1 generation were purified and used to infect HCT-8 cultures, and phenotypes of the progeny were observed by microscopy. All possible phenotypes predicted by independent segregation were represented equally ([~]25%) in the population, indicating that C. parvum chromosomes exhibit a Mendelian inheritance pattern. Unexpectedly, the most common pattern observed from the outgrowth of single oocysts included all possible parental and recombinant phenotypes derived from a single meiotic event, suggesting a high rate of crossover. To estimate the frequency of crossover, additional loci on chromosomes 1 and 5 were tagged and used to monitor intrachromosomal crosses in Ifngr1-/- mice. Both chromosomes showed a high frequency of crossover compared to other apicomplexans with map distances (i.e., 1% recombination) of 3-12 kb. Overall, a high recombination rate may explain many unique characteristics observed in Cryptosporidium spp. such as high rates of speciation, wide variation in host range, and rapid evolution of host-specific virulence factors. AUTHOR SUMMARYAlthough sex is essential for the transmission and maintenance of infection of Cryptosporidium, it has been historically challenging to study the process of meiosis in this medically relevant protist. We utilize recent methodological advances such as a specialized in vitro culture system, cell sorting, and the generation of transgenic parasites to cross identical strains of parasites in the absence of selection pressure to identify intrinsic chromosome behavior during meiosis. By specifically examining the phenotypes from the first generation of parasites, we reveal that cross-fertilization frequently occurs in parasite populations, chromosomes segregate in a Mendelian manner, and the rate of crossover is high on Chromosomes 1 and 5. Understanding these baseline meiotic mechanisms is essential for planning and interpreting future genetic studies of Cryptosporidium seeking to identify genes associated with phenotypes of interest.

microbiology↗

bioRxiv2024

Emotional prosody modulates visual mental imagery

Perceptual stimulis emotional properties are vital for human evolution and adaptation. While visual imagery is predominantly regarded as a weak form of perception, the influence of cross-modal emotional features on imagery is still unknown. The present study aims to investigate how emotional prosody modulates imagery quality (i.e., accuracy and clarity) and neural mechanisms using a combination of behavioral tasks and functional magnetic resonance imaging (fMRI). At the behavioral level, our results showed that frustrated conditions induced significant prosody effects on visual mental imagery quality measures, and the effects were particularly pronounced in individuals with lower imagery use tendency. At the neural level, compared with the neutral condition, the emotional prosody conditions (both happy and frustrated) showed stronger activation in various regions including the middle occipital gyrus, supporting the critical role of primary visual system in imagery. Moreover, compared to the frustrated prosody condition, the happy prosody showed stronger activation in the precuneus and anterior cingulate cortex, which are core components of the default mode network. A machine learning prediction analysis with a random forest model identified a significant brain-behavioral correlation between prosody-linked neural activity and individual imagery use tendency. A subsequent Shapley Additive exPlanations (SHAP) analysis further highlighted the primary visual and default mode regions as top contributors to this prediction. Taken together, these results provide new insights for the understanding of how emotional prosody modulates visual mental imagery, considering individual differences, and provide compelling evidence for incorporating emotion as important shaping factor in more general model for imagery.

neuroscience↗

bioRxiv2024

Multi-omic characterization of allele-specific regulatory variation in hybrid pigs

Genetic variation in the regulation of gene expression contributes substantially to phenotypic variation. Understanding how variation in DNA sequences and epigentic modifications leads to gene expression variation remains a challenging task. In hybrid animals where cellular environments are homogeneous, differences between the expression of paternal and maternal alleles must be due to cis sequence or epigenic differences. Therefore, hybrid mapping is a powerful approach to efficiently identify and characterize genes under regulation through mechanisms in cis. In this study, using reciprocal crosses of the phenotypically divergent Duroc and Lulai pig breeds, we performed a comprehensive multi-omic characterization of regulatory variation across brain, liver, muscle, and placenta in four developmental stages. We produced one of the largest multi-omic datasets to date in pigs, including 16 whole genome sequenced genomes, 48 whole genome bisulfite sequencing, 168 ATAC-Seq and 168 RNA-Seq samples. We developed a novel read count-based method to reliably assess allele-specific methylation, chromatin accessibility, and RNA expression. We showed that tissue specificity was much stronger than developmental stage specificity in all of DNA methylation, chromatin accessibility, and gene expression. We identified 573 genes showing allele specific expression, including those influenced by parent-of-origin as well as allele genotype effects. By integrating methylation, chromatin accessibility, and gene expression data, many of these allele specific expression can be explained by allele specific methylation and/or chromatin accessibility. This study provides one of the most comprehensive characterizations of regulatory variation across multiple tissues and developmental stages in pigs and offers new opportunity of genetic improvement for this important food animal species.

developmental biology↗

bioRxiv2023

Complex life cycles and parasite-mediated trophic cascades drive species coexistence and the maintenance of genetic diversity

Ecological and evolutionary processes shape the dynamics of species interactions, yet the drivers of eco-evolutionary feedback remain elusive. Here, we developed an individual-based model of a coevolving predator-prey-parasite system, in which predators can be infected by trophically transmitted parasites. We combined host-parasite coevolution with prey-predator interactions at an individual level, hence integrating evolutionary and ecological processes. We show that species coexist more when parasite-mediated selection is weak on both the predator and the prey. Population size and genotypic diversity of the parasite are highest at intermediate parasite-mediated selection on the predator and no parasite-mediated selection on the prey. Interestingly, we show that the evolution of super-resistant genotypes, where host genotypes have resistant alleles in all loci, is driven by interspecific interactions rather than by the population size of the host species. Overall, host-parasite coevolution shapes the direction of interspecific ecological interactions which, in turn, determine species coexistence and community diversity in a complex system.

ecology↗

bioRxiv2023

Chloroplast Methyltransferase Homolog RMT2 is Involved in Photosystem I Biogenesis

Oxygen (O2), a dominant element in the atmosphere and essential for most life on Earth, is produced by the photosynthetic oxidation of water. However, metabolic activity can cause accumulation of reactive O2 species (ROS) and severe cell damage. To identify and characterize mechanisms enabling cells to cope with ROS, we performed a high-throughput O2 sensitivity screen on a genome-wide insertional mutant library of the unicellular alga Chlamydomonas reinhardtii. This screen led to identification of a gene encoding a protein designated Rubisco methyltransferase 2 (RMT2). Although homologous to methyltransferases, RMT2 has not been experimentally demonstrated to have methyltransferase activity. Furthermore, the rmt2 mutant was not compromised for Rubisco (first enzyme of Calvin-Benson Cycle) levels but did exhibit a marked decrease in accumulation/activity of photosystem I (PSI), which causes light sensitivity, with much less of an impact on other photosynthetic complexes. This mutant also shows increased accumulation of Ycf3 and Ycf4, proteins critical for PSI assembly. Rescue of the mutant phenotype with a wild-type (WT) copy of RMT2 fused to the mNeonGreen fluorophore indicates that the protein localizes to the chloroplast and appears to be enriched in/around the pyrenoid, an intrachloroplast compartment present in many algae that is packed with Rubisco and potentially hypoxic. These results indicate that RMT2 serves an important role in PSI biogenesis which, although still speculative, may be enriched around or within the pyrenoid. Significance StatementA high-throughput genetic screen was used to identify O2 sensitive mutants of Chlamydomonas reinhardtii (Chlamydomonas throughout) that experience elevated oxidative stress in the light relative to WT cells. Identification of genes altered in these mutants offers opportunities to discover activities that a) protect photosynthetic cells from oxidative damage, b) participate in rapid assembly of photosynthetic complexes, which would limit accessibility of intermediates to O2, and/or c) facilitate repair of damaged cellular complexes. A mutant from this screen disrupted for RMT2, originally described as encoding a Rubisco methyltransferase, was defective for PSI biogenesis. Additionally, RMT2 appears to be enriched in/around the pyrenoid, a chloroplast localized compartment harboring much of the Chlamydomonas Rubisco, raising the possibility that this compartment plays a role in PSI biogenesis.

plant biology↗

bioRxiv2023

Climate change has desynchronized insect and vegetation phenologies across Europe

Climate change is drastically affecting the phenologies of species worldwide, including shifts in development1-3. The potential impact of climate change on the synchronicity of plant-insect phenology is particularly concerning since the stability of pollination networks and food chains depends on their tight temporal dependencies4-6. Furthermore, the recently reported "insect armageddon"7 makes it urgent to establish trends and identify primary drivers of plant-insect phenological synchrony. Here, coupling high-resolution remote sensing and citizen science data across Europe over 34 years, we examine the differences in occurrence dates of 1,584 herbivorous insects across four orders and the corresponding dates of leaf unfolding. We find that 61.2% of the vegetation and insect phenologies have become highly asynchronous, with vegetation phenology advancing four-fold faster than insect phenology. These trends were modulated by insects life-cycles and taxonomic order. A primary driver of this phenological mismatch is the higher sensitivity of vegetation phenology than insect phenology to climate, which has prevented insects from matching the pace of plant phenological advance in the growing season. Our analyses provide a unique continental overview and underlying mechanisms of the asynchronicity between vegetation and insect phenologies, thus enhancing our ability to predict and manage its potential cascading ecological effects.

ecology↗

bioRxiv2023

The Arabidopsis PPR protein EMB1006 interacts with both EMB1270 and CFM2 to facilitate plastid clpP1 intron2 splicing

Plastid intron splicing is an essential step for gene expression. Although many nucleus-encoded splicing factors have been identified for plastid intron splicing, how these proteins coordinately regulate intron splicing is unclear. Here we found that EMB1006, an Arabidopsis P-type PPR protein, is required for splicing several plastid introns including clpP1 intron 2 by analyzing the level of intron retention in its knockdown lines and RIP-qPCR (RNA immunoprecipitation and quantitative PCR) assay. In addition, RNA electrophoretic mobility shift assay (REMSA) showed that EMB1006 specifically binds to the sequence UUACCAAACGU close to the 3 end of clpP1 exon 2 in vitro. Furthermore, yeast two hybrid (Y2H), split luciferase complementation (Split-LUC) and semi-in vivo pull-down assays showed that EMB1006 interacts with both EMB1270 and CFM2, which also interact each other. Taken together, our data indicate that EMB1006 forms a complex with EMB1270 and CFM2 to facilitate clpP1 intron 2 splicing in chloroplasts.

plant biology↗

bioRxiv2023

Cultivation of host-adapted Cryptosporidium parvum and Cryptosporidium hominis using enteroids for cryopreservation of isolates and transcriptomic studies of infection

Cryptosporidium hominis and Cryptosporidium parvum are major causes of severe diarrhea in humans. Comparative studies of them are hampered by the lack of effective cultivation and cryopreservation methods, especially for C. hominis. Here, we described adapted murine enteroids for the cultivation of one C. parvum IId subtype and nonhuman primate-adapted C. hominis Ib, Im, and In subtypes, which allowed the complete development of the pathogens, producing oocysts infectious to mice. Using the system, we developed a novel cryopreservation method for Cryptosporidium isolates. In comparative RNA-seq analyses of C. hominis cultures, the enteroid system generated significantly more transcriptomic responses of both pathogen and host genes than the conventional HCT-8 cell system. In particular, the infection was shown to upregulate PI3K-Akt, Wnt, Ras,TNF, NF-{kappa}B, IL-17, MAPK, and innate immunity signaling pathways and downregulate Wnt and Hippo signaling pathways, host cell metabolism, and parasites in enteroid cultures had significantly higher expression of genes involved in oocyst formation. Therefore, the new culture model provides a valuable tool for comparative studies of the biology of divergent Cryptosporidium species. IMPORTANCE The two dominant species for human cryptosporidiosis, Cryptosporidium hominis and Cryptosporidium parvum, differ significantly in host range and virulence. Up to date, biological studies of Cryptosporidium spp. are almost exclusively done with bovine-adapted IIa subtypes of C. parvum, which is the species with effective laboratory animal models and in vitro cultivation methods. Here, we describe modified procedures for the generation of murine enteroids for successful cultivation of both nonhuman primate-adapted C. hominis subtypes and a C. parvum IId subtype, producing oocysts infective to mice. In addition, we have developed a novel cryopreservation method using the system for long-term storage of Cryptosporidium isolates. RNA-seq analyses of C. hominis cultures indicate that the enteroid culture system generates host and pathogen transcriptomic responses similar to those in natural infection. This new development alleviates a technical bottleneck in cryptosporidiosis research, and provides an example for other difficult-to-culture pathogens of major public health importance.

microbiology↗

bioRxiv2023

Gain of function in linc-133 compensates for daf-18/PTEN loss and rescues survival

DAF-18, homology of PTEN, possess tumor suppressor activity. Loss of daf-18 causes cell growth in L1 diapause C. elegans is well studied; however, the reason why survival is dramatically shortened is not well elaborated. We found that linc-133 gain of function can fully restore the shortened survival caused by daf-18 loss. When lipid phosphatase activity of DAF-18 is defective, the linc-133 gain of function interacts with 14-3-3 proteins to obstruct DAF-16 translocation from the nucleus to the cytoplasm. However, the dysfunction of protein phosphatase activity of DAF-18 caused high levels of aggregated proteins. The linc-133 gain of function can induce HSP chaperones to select and process the aggregated proteins for degradation through ubiquitination. Our work demonstrates that protein homeostasis controlled by the protein phosphatase activity of DAF-18 is the main factor affecting survival and identifies a new function of the linc-133 gene, which can compensate for the loss of daf-18.

genetics↗

bioRxiv2023

Screening and characterization of aging regulators using synthesized yeast chromosome XIII

Yeast, a single eukaryotic cell model organism, demonstrates a progressive aging process. In the era of synthetic biology, study of the impact of synthetic chromosomes and aging is urgent and intriguing. Herein, we successfully constructed the 884 Kb synXIII of Saccharomyces cerevisiae and conducted replicative aging studies using the synthetic strains. We verified that the rRNA-related transcriptional factor RRN9 is a major positive controller of replicative lifespan. Using SCRaMbLE and an HSP104 reporter as a biomarker for mutant discovery, we screened 135 SCRaMbLEd synXIII strains with extended lifespan and identified 10 genes on synXIII that potentially serve as aging regulators. In addition, the genome-scale regression analysis of long-replicative lifespan SCRaMbLEd strains revealed distinct dysregulation of nucleus, ribosome, and mitochondrion function networks. Our findings suggest that Sc2.0 yeast has potential for unveiling new aging-related genes and gene-gene interactions underlying replicative lifespan.

synthetic biology↗

bioRxiv2023

PARP knockdown promotes synapse reformation after axon injury

Injured nervous systems are often incapable of self-repairing, resulting in permanent loss of function and disability. To restore function, a severed axon must not only regenerate, but must also reform synapses with target cells. Together, these processes beget functional axon regeneration. Progress has been made towards a mechanistic understanding of axon regeneration. However, the molecular mechanisms that determine whether and how synapses are formed by a regenerated motor axon are not well understood. Using a combination of in vivo laser axotomy, genetics, and high-resolution imaging, we find that poly (ADP-ribose) polymerases (PARPs) inhibit synapse reformation in regenerating axons. As a result, regenerated parp(-) axons regain more function than regenerated wild-type axons, even though both have reached their target cells. We find that PARPs regulate both axon regeneration and synapse reformation in coordination with proteolytic calpain CLP-4. These results indicate approaches to functionally repair the injured nervous system must specifically target synapse reformation, in addition to other components of the injury response.

neuroscience↗

bioRxiv2023

Adenosine triggers astrocyte reactivity to drive the pathogenesis of sepsis-associated encephalopathy

Molecular pathways mediating systemic inflammation entering the brain parenchyma to induce sepsis-associated encephalopathy (SAE) remain elusive. Here, we report that in mice during the first 6 hours of peripheral lipopolysaccharide (LPS)-evoked systemic inflammation (6 hpi), the plasma level of adenosine quickly increased and enhanced the tone of central extracellular adenosine which then provoked neuroinflammation by triggering early astrocyte reactivity. Specific ablation of astrocytic A1 adenosine receptors (A1ARs) prevented this early reactivity and reduced the levels of inflammatory factors (e.g., CCL2, CCL5, and CXCL1) in astrocytes, thereby alleviating microglial activation, ameliorating blood-brain barrier disruption, neuronal dysfunction, and depression-like behaviour in the mice. Chemogenetic stimulation of Gi signaling in A1AR-deficent astrocytes at 2 and 4 hpi of LPS injection could restore neuroinflammation and depression-like behaviour, highlighting astrocytes rather than microglia as early drivers of neuroinflammation. Our results identify early astrocyte reactivity towards peripheral and central levels of adenosine as a novel pathway driving SAE.

neuroscience↗

bioRxiv2023

Parasite-mediated predation determines the infection in a complex predator-prey system

The interplay of host-parasite and predator-prey interactions is critical in ecological dynamics because both predators and parasites play an important role in regulating populations and communities. But what is the prevalence of infected prey and predators when a parasite is transmitted through trophic interactions, particularly when stochastic fluctuations of demographical changes are allowed arising from individual-level dynamics? Here, we analysed the system stability and the frequency of infected and uninfected host subpopulations in a complex predator-prey-parasite system, where infection happens through trophic interactions transmitting parasites from prey to predators. We varied the parasite virulence implemented as reproductive costs imposed on infected hosts and the probabilities of parasites infecting the hosts per encounter, to investigate how those important evolutionary factors will determine the species coexistence and population composition. We further explored the role of stochasticity in our system by comparing our deterministic analysis with stochastic simulations. Our results show that parasites go extinct when the infection probabilities of either host are small. The success in infecting the final host (the predator) is more critical for the survival of the parasite species, as the threshold for infection probability of the predator is higher than that of the prey for three-species coexistence. While our stochastic simulations agree with deterministic predictions well in most parameter regions. However, in the border parameter regions between coexistence and extinction typically with high infection probabilities, while only one possible outcome in deterministic dynamics, both coexistence and extinction can happen in stochastic repeats under the same parameter values. This illustrates the importance of stochasticity and demographic fluctuations in species coexistence. In addition, the proportion of infected individuals increases with the infection probabilities in our deterministic analysis and stochastic simulations as expected. Interestingly, we found that in some parameter space, the relative frequencies of infected and uninfected individuals are different between the intermediate host (prey) and the final host (predator) populations. This counterintuitive observation shows that the interplay of host-parasite and predator-prey interactions lead to more complex dynamics than a simple resource-consumer relationship.

ecology↗

bioRxiv2023

The GIAB genomic stratifications resource for human reference genomes

Stratification of the genome into different genomic contexts is useful when developing bioinformatics software like variant callers, to assess performance in difficult regions in the human genome. Here we describe a set of genomic stratifications for the human reference genomes GRCh37, GRCh38, and T2T-CHM13v2.0. Generating stratifications for the new complete CHM13 reference genome is critical to understanding improvements in variant caller performance when using this new complete reference. The GIAB stratifications can be used when benchmarking variant calls to analyze difficult regions of the human genome in a standardized way. Here we present stratifications in the CHM13 genome in comparison to GRCh37 and GRCh38, highlighting expansions in hard-to-map and GC-rich stratifications which provide useful insight for accuracy of variants in these newly-added regions. To evaluate the reliability and utility of the new stratifications, we used the stratifications of the three references to assess accuracy of variant calls in diverse, challenging genomic regions. The means to generate these stratifications are available as a snakemake pipeline at https://github.com/ndwarshuis/giab-stratifications.

genomics↗

bioRxiv2023

Immune Epitopes of SARS-CoV-2 Spike Protein and Considerations for Universal Vaccine Development

Despite the success of global vaccination programs in slowing the spread of COVID-19, these efforts have been hindered by the emergence of new SARS-CoV-2 strains capable of evading prior immunity. The mutation and evolution of SARS-CoV-2 have created a demand for persistent efforts in vaccine development. SARS-CoV-2 Spike protein has been the primary target for COVID-19 vaccine development, but it is also the hotspot of mutations directly involved in host susceptibility and immune evasion. Our ability to predict emerging mutants and select conserved epitopes is critical for the development of a broadly neutralizing therapy or a universal vaccine. In this article, we review the general paradigm of immune responses to COVID-19 vaccines, highlighting the immunological epitopes of Spike protein that are likely associated with eliciting protective immunity resulting from vaccination. Specifically, we analyze the structural and evolutionary characteristics of the SARS-CoV-2 Spike protein related to immune activation and function via the toll-like receptors (TLRs), B cells, and T cells. We aim to provide a comprehensive analysis of immune epitopes of Spike protein, thereby contributing to the development of new strategies for broad neutralization or universal vaccination.

immunology↗

bioRxiv2023

Unveiling the A-to-I mRNA editing machinery and its regulation and evolution in fungi

A-to-I mRNA editing occurs during fungal sexual reproduction with an unknown mechanism. Here, we demonstrated that the eukaryotic tRNA-specific heterodimeric deaminase FgTad2-FgTad3, not typically associated with mRNA editing, is responsible for A-to-I mRNA editing in Fusarium graminearum. This editing capacity relies on the interaction between FgTad3 and a sexual stage-specific protein called Ame1. The interaction emerged in Sordariomycetes. Key residues involved in the interaction have been identified. Expression and activity of FgTad2-FgTad3 are regulated through alternative promoters, alternative translation initiation, and post-translational modifications. FgTad2-FgTad3-Ame1 efficiently edits target mRNAs in yeasts, bacteria, and human cells, with significant implications for developing base editors in therapy and agriculture. This study reveals mechanisms, regulation, and evolution of RNA editing in fungi, emphasizing protein-protein interactions in controlling enzyme function.

molecular biology↗

bioRxiv2023

Th2 and Th17-Associated Immunopathology Following SARS-CoV-2 Breakthrough Infection in Spike-vaccinated ACE2-humanized Mice

Vaccines have demonstrated remarkable effectiveness in protecting against COVID-19; however, concerns regarding vaccine-associated enhanced respiratory diseases (VAERD) following breakthrough infections have emerged. Spike protein subunit vaccines for SARS-CoV-2 induce VAERD in hamsters, where aluminum adjuvants promote a Th2-biased immune response, leading to increased type 2 pulmonary inflammation in animals with breakthrough infections. To gain a deeper understanding of the potential risks and the underlying mechanisms of VAERD, we immunized ACE2-humanized mice with SARS-CoV-2 Spike protein adjuvanted with aluminum and CpG-ODN. Subsequently, we exposed them to increasing doses of SARS-CoV-2 to establish a breakthrough infection. The vaccine elicited robust neutralizing antibody responses, reduced viral titers, and enhanced host survival. However, following a breakthrough infection, vaccinated animals exhibited severe pulmonary immunopathology, characterized by a significant perivascular infiltration of eosinophils and CD4+ T cells, along with increased expression of Th2/Th17 cytokines. Intracellular flow cytometric analysis revealed a systemic Th17 inflammatory response, particularly pronounced in the lungs. Our data demonstrate that aluminum/CpG adjuvants induce strong antibody and Th1-associated immunity against COVID-19 but also prime a robust Th2/Th17 inflammatory response, which may contribute to the rapid onset of T cell-mediated pulmonary immunopathology following a breakthrough infection. These findings underscore the necessity for further research to unravel the complexities of VAERD in COVID-19 and to enhance vaccine formulations for broad protection and maximum safety. Significance statementThis research investigates the safety and efficacy of a Spike protein subunit vaccine adjuvanted with Alum and CpG in an ACE2-humanized mouse model, simulating SARS-CoV-2 breakthrough infections. The study reveals that despite robust protection against severe COVID-19, vaccinated mice exhibit substantial pulmonary immunopathology, including eosinophilia and enhanced Th2 effector immunity, following breakthrough infections. Surprisingly, the study also uncovers a significant systemic Th17 inflammatory response in vaccinated mice. This research sheds light on the potential risks associated with COVID-19 vaccine breakthrough infections and the need for a comprehensive understanding of vaccine-induced immune responses, emphasizing the importance of ongoing research, surveillance, and careful vaccine development for both protection and safety in the fight against the COVID-19 pandemic.

immunology↗