Biology subjects

Sato, K.

Publications and source records attributed to Sato, K..

At least 73 records · Page 4Linked to original sources

bioRxiv2025

Inferring context-specific site variation with evotuned protein language models

Multiple sequence alignments (MSAs) have been traditionally used for making inferences about site-specific diversity in proteins. Recent advancements in the field of artificial intelligence have highlighted the potential of protein language models (pLMs) to capture similar protein properties. Unlike MSAs, pLMs can make inferences from single sequences, without the need for a set of aligned sequences. In this study, we introduce a novel, pLM-based metric, termed pLM entropy, to assess protein site conservation and variability. We test this metric using versions of two popular pLMs (ESM-2 and protT5) fine-tuned on the diversity of different Influenza A virus serotype hemagglutinin proteins. Our study demonstrates how our pLM entropy metric can capture which sites are more likely to change in a specific sequence context and how fine-tuning pLMs on a set of evolutionarily related proteins (evotuning) can improve the models understanding of the groups diversity.

evolutionary biology↗

bioRxiv2025

Evolution of BA.2.86 to JN.1 reveals functional changes in non-structural viral proteins are required for fitness of SARS-CoV-2

Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), the causative agent of the coronavirus disease 2019 (COVID-19), is still circulating among humans, leading to the continuous evolution. SARS-CoV-2 Omicron JN.1 evolved from a distinct SARS-CoV-2 lineage, BA.2.86, spread rapidly worldwide. It is unclear why BA.2.86 did not become dominant and was quickly replaced by JN.1, which possesses one amino acid substitution in the spike protein (S:L455S) and two in the non-spike proteins NSP6 and ORF7b (NSP6:R252K and ORF7b:F19L) compared to BA.2.86. Here, we utilized recombinant viruses to elucidate the impact of these mutations on the virological characteristics of JN.1. We found that the mutation in the spike attenuated viral replication, but the non-spike mutations enhanced replication, suggesting the mutations in the non-spike proteins compensate for the one in the spike to improve viral fitness, as the mutations in the spike contribute to further immune evasion. Our findings suggest that functional changes in both the spike and non-spike proteins are necessary in the evolution of SARS-CoV-2 to enable evasion of adaptive immunity within the human population while sustaining replication. IMPORTANCEBecause the spike protein is strongly associated with certain virological properties of SARS-CoV-2, such as immune evasion and infectivity, most previous studies on SARS-CoV-2 variants have focused on spike protein mutations. However, the non-spike proteins also contribute to infectivity, as observed throughout the evolution of Omicron subvariants. In this study, we demonstrate a "trade-off" strategy in SARS-CoV-2 Omicron JN.1 in which the reduced infectivity caused by spike mutation is compensated by non-spike mutations. Our results provide insight into the evolutionary scenario of the emerging virus in the human population.

microbiology↗

bioRxiv2025

A trehalase-derived MAMP triggers LecRK-V-mediated immune responses in Arabidopsis

Plant-parasitic nematodes (PPNs) cause major agricultural losses worldwide, yet the molecular basis of plant immunity against these pathogens remains poorly understood. To investigate how plants recognize PPNs, we aimed to identify microbe-associated molecular patterns (MAMPs) from nematodes and the corresponding plant immune components. Due to the limited availability of material from obligate PPNs, we used Caenorhabditis elegans, a free-living nematode, as a MAMP source. C. elegans extracts activated MAMP-triggered immune responses in Arabidopsis Col-0. Through chromatography-based purification, we identified a secreted trehalase and pinpointed a conserved peptide region essential for its MAMP activity. A corresponding peptide from root-knot nematode trehalase enabled the identification of lectin receptor kinases LecRK-V.5 and LecRK-V.6 as key components in immune induction. Notably, this peptide region is conserved across insect and fungal pathogens, with LecRK-Vs required for immune responses to these peptides, highlighting the role of LecRK-V-mediated mechanism for broad-spectrum pathogen detection via trehalase-derived peptides. TeaserTrehalase-derived peptides trigger LecRK-V-mediated immune responses in plants, enabling broad detection of nematodes, insects, and fungi.

plant biology↗

bioRxiv2025

Allometric studies on human- and pig-sized Delphinidae to understand resting metabolic rates with respiratory measurements

Exponential relationships between basal metabolic rate (BMR) and body mass are known in both terrestrial and marine mammals, with elevated BMR in the latter. However, it remains unclear whether the exponential relationship in marine mammals is different from that in terrestrial mammals. Metabolic rates of animals while resting at the water surface (resting metabolic rates: RMRs) were measured by breath-by-breath respirometry in two species of Delphinidae from temperate regions to elucidate the relationship between RMR and body mass in pantropical spotted dolphins (Stenella attenuate) and Rissos dolphins (Grampus griseus) with body masses ranging from 71 to 386 kg. The RMRs of rough-toothed dolphins (83-123 kg), common bottlenose dolphins (143-220 kg), and killer whales (3,364-5,318 kg) were obtained from the literature for allometric analyses. Measured RMRs were 344 {+/-} 39 and 1398 {+/-} 160 ml O2 min-1, respectively, which were 1.2-2.1 times higher than those predicted for similar-sized terrestrial mammals. A linear mixed-effects model showed the allometric mass exponent of 0.65 (95% CI: 0.54-0.76), which was closer to the 2/3-power of body mass than that of the widely observed 3/4-power commonly reported across a broad range of taxa. The new scaling relationship observed in the Delphinidae indicates that larger dolphins require less energy in aquatic environments, which is consistent with the theory of heat loss associated with a narrower surface area relative to larger volumes. This study suggested a different scaling relationship between aquatic and terrestrial mammals.

zoology↗

bioRxiv2025

Modeling the human limb skeletal development using human pluripotent stem cell-derived skeletal assembloid

Despite recent advances in pluripotent stem cell-based approaches to induce skeletal cells, recapitulating human limb skeletal development in terms of structure and longitudinally oriented growth remains an unresolved challenge. Here, we report a method to differentiate human pluripotent stem cells into region-specific skeletal organoids harboring GDF5+PRG4+ interzone/articular chondrocyte progenitors (IZ/ACPs) and SP7+ growth plate chondrocytes (GPCs) via PRRX1+ limb-bud mesenchymal cells. Comparative analysis demonstrated marked similarities of IZ/ACP and GPC organoids to the human embryonic limb, and graft fate and regenerative capacity in vivo were further characterized. We also mimicked the limb skeletal developmental process in a spatially structured manner by vertically positioning two IZ/ACP organoids at both ends of a GPC organoid to generate a human skeletal assembloid. Notably, this human skeletal assembloid recapitulated endochondral ossification with longitudinal skeletal growth upon transplantation. In summary, our study provides a novel research platform for human limb skeletal development and disease.

bioengineering↗

bioRxiv2024

Hyperactive PLCG1 drives non-canonical signaling to promote cell survival

One of the long-standing questions in cell signaling field to identify and characterize key signaling nodes out of a complex network. Phospholipase C{gamma}1 (PLCG1) was identified as the most frequently mutated gene in adult T-cell leukemia/lymphoma, suggesting a critical function of PLCG1 in driving T cell activation. However, it remains unclear how these mutations regulate T cell physiology and pathology. Here we investigated three common leukemia/lymphoma associated mutations (R48W, S345F, and D1165H). We discovered that these mutations induced hyperactive T cell signaling and caused pro-survival phenotypes. PLCG1 mutants enhanced LAT condensation, calcium influx, and ERK activation. They promoted T cell proliferation, induced cell aggregation, and rendered resistance to vorinostat, an FDA-approved drug for cutaneous T-cell lymphoma. The resistance to vorinostat depended on ERK signaling and can be reversed with an ERK inhibitor. Mechanistically, alpha smooth muscle actin, which was specifically induced by PLCG1 mutants, directly bound PLCG1 to promote its activation. Together, these results demonstrated that hyperactive PLCG1 promoted T cell survival and drug resistance through inducing non-canonical signaling.

cell biology↗

bioRxiv2024

Robust antiviral humoral immunity induced by JN.1 monovalent mRNA vaccines against a broad range of SARS-CoV-2 Omicron subvariants including JN.1, KP.3.1.1 and XEC

As of November 2024, SARS-CoV-2 Omicron JN.1 subvariants, such as KP.2 (JN.1.11.1.2), KP.3 (JN.1.11.1.3), KP.3.1.1 (JN.1.11.1.3.1.1), and XEC -- a recombinant lineage between KS.1.1 (JN.13.1.1.1) and KP.3.3 (JN.1.11.1.3.3) -- have been circulating in several countries. To control the infection with SARS-CoV-2 Omicron JN.1 subvariants, JN.1 monovalent mRNA vaccines have been developed. Some previous reports showed that the JN.1 monovalent mRNA vaccine of Pfizer/BioNTech (US/Germany) increased antiviral humoral immunity against JN.1 subvariants and XEC. However, the efficacy of other available JN.1 monovalent mRNA vaccines (e.g., Daiichi-Sankyo, Japan) remains unassessed. To validate the antiviral efficacy induced by JN.1 mRNA vaccines, sera were collected from individuals vaccinated with Pfizer/BioNTech JN.1 mRNA vaccine (N=15) or Daiichi-Sankyo JN.1 mRNA vaccine (N=19) before and 3-4 weeks after vaccination. We then performed a neutralization assay using these sera and pseudoviruses. Both Pfizer/BioNTech JN.1 vaccine (2.4-to 8.0-fold, P=0.0001) and Daiichi-Sankyo JN.1 vaccine (2.3-to 13-fold, P=0.0001) boosted antiviral humoral immunity against all variants tested with statistical significance. While the Pfizer/BioNTech mRNA vaccine encodes the full-length JN.1 spike (S), the Daiichi-Sankyo mRNA vaccine encodes the receptor-binding domain of JN.1 S. Our data suggest that the receptor-binding domain of JN.1 S can effectively induce antiviral humoral immunity against JN.1 subvariants and XEC comparable to the full-length JN.1 S. However, it should be considered that the sizes of our cohorts are relatively small (<20 donors per cohort), and donor characteristics, such as age, sex, underlying disease status, and previous SARS-CoV-2 infection, may critically affect the experimental results. Future investigations with larger cohorts will address this concern. When compared to vaccination with JN.1 mRNA vaccines, our previous investigations showed that the natural infection of JN.1 and KP.3.3 elicited poorer antiviral humoral immunity against JN.1 and its subvariants. Our results suggest that the JN.1 mRNA vaccination more robustly induces antiviral humoral immunity against recent JN.1 subvariants than the natural infection of JN.1 subvariants regardless of manufacturer. Moreover, as we reported last year, the humoral immunity induced by XBB.1.5 monovalent mRNA vaccine against XBB.1.5 was weaker than that against ancestral B.1.1. However, in the case of JN.1 monovalent mRNA vaccine, here we showed that the 50% neutralization titer against XBB.1.5 is greater than that against ancestral B.1.1. These observations imply that immune imprinting has shifted from that biased toward pre-Omicron to that biased toward Omicron, depending on the time and/or number of immune stimuli (e.g., infection and/or vaccination).

microbiology↗

bioRxiv2024

Evolution and functioning of an X-A balance sex determination system in hops

Chromosomal sex determining systems with male heterogamety include actively male-determining-Y and X-A balance systems, both of which are found in animals and plants. The sex-determining genes have been identified in several active-Y plant systems, but the evolution and functioning of X-A balance systems remains mysterious. To study this, we sequenced and compared the genomes of two hop species. The evolution of the hop X-A balance system involved an ancient recombination suppression event across a large X chromosome region shared by both species. In one species, an autosome fused to this ancestral sex chromosome, and recombination was subsequently suppressed again. The two evolutionary strata created in this neo-X have degenerated to different degrees, and evolved correspondingly different dosage compensation levels that correlate with histone modification patterns. Finally, we identified an X-specific ETR1-like ethylene receptor in the ancestral X region. Its dosage may affect sex determination, as part of the counting mechanism of this X-A balance system. One sentence summaryBased on whole genome sequences of the cultivated hop, Humulus lupulus, and its wild relative H. japonicus, we describe the evolution of sex chromosomal regions, three of which that evolved region-specific dosage compensation, and identify a candidate gene involved in their X-A balance sex determining system.

evolutionary biology↗

bioRxiv2024

Data driven refinement of gene expression signatures for enrichment analysis

Gene set enrichment methods measure biological process or pathway activation in gene expression data by testing coordinate up- or down-regulation of pathway members in a ranked list of genes. These methods rely on curated, annotated gene sets whose members coordinate expression is an indicator of a process or state. We therefore developed the Molecular Signatures Database (MSigDB), a collection of expertly annotated gene sets. While using, enhancing, and expanding MSigDB, we have observed that some gene sets can lack coordinate expression, especially those derived from canonical pathways. To address this challenge, we developed gene set refinement (GSR), a data-driven approach leveraging large-scale multi-omics compendia to extract context-specific sets, deconvolve heterogeneity, and reveal multiple downstream signaling. We applied this method to address cancer biology questions, and demonstrated successful, targeted refinement of existing MSigDB gene sets.

bioinformatics↗

bioRxiv2024

Virological characteristics of the SARS-CoV-2 XEC variant

The SARS-CoV-2 JN.1 variant (BA.2.86.1.1), arising from BA.2.86.1 with spike protein (S) substitution S:L455S, outcompeted the previously predominant XBB lineages by the beginning of 2024. Subsequently, JN.1 subvariants including KP.2 (JN.1.11.1.2) and KP.3 (JN.1.11.1.3), which acquired additional S substitutions (e.g., S:R346T, S:F456L, and S:Q493E), have emerged concurrently. As of October 2024, KP.3.1.1 (JN.1.11.1.3.1.1), which acquired S:31del, outcompeted other JN.1 subvariants including KP.2 and KP.3 and is the most predominant SARS-CoV-2 variant in the world. Thereafter, XEC, a recombinant lineage of KS.1.1 (JN.13.1.1.1) and KP.3.3 (JN.1.11.1.3.3), was first identified in Germany on August 7, 2024. XEC acquired two S substitutions, S:T22N and S:F59S, compared with KP.3 through recombination, with a breakpoint at genomic position 21,738-22,599. We estimated the relative effective reproduction number (Re) of XEC using a Bayesian multinomial logistic model based on genome surveillance data from the USA, the United Kingdom, France, Canada, and Germany, where this variant has spread as of August 2024. In the USA, the Re of XEC is 1.13-fold higher than that of KP.3.1.1. Additionally, the other countries under investigation herein showed higher Re for XEC. These results suggest that XEC has the potential to outcompete the other major lineage including KP.3.1.1. We then assessed the virological properties of XEC using pseudoviruses. Pseudovirus infection assay showed that the infectivity of KP.3.1.1 and XEC was significantly higher than that of KP.3. Although S:T22N did not affect the infectivity of the pseudovirus based on KP.3, S:F59S significantly increased it. Neutralization assay was performed using three types of human sera: convalescent sera after breakthrough infection (BTI) with XBB.1.5 or KP.3.3, and convalescent sera after JN.1 infection. In all serum groups, XEC as well as KP.3.1.1 showed immune resistance when compared to KP.3 with statistically significant differences. In the cases of XBB.1.5 BTI sera and JN.1 infection sera, the 50% neutralization titers (NT50s) of XEC and KP.3.1.1 were comparable. However, we revealed that the NT50 of XEC was significantly (1.3-fold) lower than that of KP.3.1.1. Moreover, both S:T22N and S:F59S significantly (1.5-fold and 1.6-fold) increased the resistance to KP.3.3 BTI sera. Here we showed that XEC exhibited higher pseudovirus infectivity and higher immune evasion than KP.3. Particularly, XEC exhibited more robust immune resistance to KP.3.3 BTI sera than KP.3.1.1. Our data suggest that the higher Re of XEC than KP.3.1.1 is attributed to this property and XEC will be a predominant SARS-CoV-2 variant in the world in the near future.

microbiology↗

bioRxiv2024

Virological characteristics of the SARS-CoV-2 KP.3.1.1 variant

The SARS-CoV-2 JN.1 variant (BA.2.86.1.1), arising from BA.2.86.1 with spike protein (S) substitution S:L455S, outcompeted the previously predominant XBB lineages by the beginning of 2024. Subsequently, JN.1 subvariants including KP.2 (JN.1.11.1.2) and KP.3 (JN.1.11.1.3), which acquired additional S substitutions e.g., S:R346T, S:F456L, and S:Q493E, have emerged concurrently. Thereafter, JN.1 subvariants, such as LB.1 (JN.1.9.2.1), KP.2.3 (JN.1.11.1.2.3), and KP.3.1.1 (JN.1.11.1.3.1.1), which convergently acquired a deletion of Serine at the 31st position in S (S:S31del) in addition to the above substitutions, have emerged and spread as of June 2024. We recently reported the virological features of JN.1 subvariants including KP.2, KP.3, LB.1, and KP.2.3.2,3 Here, we investigated the virological properties of KP.3.1.1. First, we estimated the relative effective reproduction number (Re) of KP.3.1.1 using a Bayesian multinomial logistic model4 based on genome surveillance data from Spain, the USA, France, Canada, and the UK, where this variant has spread as of June 2024. In Spain, the Re of KP.3.1.1 is over 1.2-fold higher than that of JN.1 and even higher than those of KP.2, KP.3, LB.1, and KP.2.3. Additionally, the other countries under investigation herein show higher Re for KP.3.1.1. However, it must be noted there is the possibility of overestimation in these countries due to more limited KP.3.1.1 sequence numbers. These results suggest that KP.3.1.1 will spread worldwide along with other JN.1 sublineages. We then assessed the virological properties of KP.3.1.1 using pseudoviruses. The pseudovirus of KP.3.1.1 had significantly higher infectivity than that of KP.3. Neutralization of KP.3.1.1 was tested using i) convalescent sera after breakthrough infection (BTI) with XBB.1.5 or EG.5, ii) convalescent sera after the infection with HK.3 or JN.1, and iii) sera after monovalent XBB.1.5 vaccination. The 50% neutralization titer (NT50) against KP.3.1.1 was significantly lower than KP.3 (1.4-1.6-fold) in all four groups of convalescent sera tested. KP.3.1.1 also showed a 1.3-fold lower NT50 against XBB.1.5 vaccine sera than KP.3. Moreover, KP.3.1.1 showed stronger resistance with a 1.3-fold lower NT50 with statistical significances to the convalescent sera infected with EG.5 and HK.3 than KP.2.3. Altogether, KP.3.1.1 exhibited a higher Re, higher pseudovirus infectivity, and higher neutralization evasion than KP.3. These results align with our recent report that the JN.1 subvariants with S:S31del (e.g., KP.2.3 and LB.1) exhibited enhanced Re and immune evasion compared to the other JN.1 subvariants without S:S31del (e.g., JN.1, KP.2, and KP.3), highlighting the evolutionary significance of S:S31del in the JN.1 lineages.

microbiology↗

bioRxiv2024

Virological characteristics of the SARS-CoV-2 KP.3, LB.1 and KP.2.3 variants

The SARS-CoV-2 JN.1 variant, arising from BA.2.86.1 with a substitution in the spike (S) protein, S:L455S, exhibited increased fitness and outcompeted the previously predominant XBB lineages by the beginning of 2024. Subsequently, JN.1 subvariants including KP.2 and KP.3, which convergently acquired S protein substitutions such as S:R346T, S:F456L, and S:Q493E, have emerged concurrently. Furthermore, JN.1 subvariants such as LB.1 and KP.2.3, which convergently acquired S:S31del in addition to the above substitutions, have emerged and spread as of June 2024. Here we investigated the virological properties of KP.3, LB.1 and KP.2.3. We estimated the relative effective reproduction number (Re) of KP.3, LB.1, and KP.2.3 using a Bayesian multinomial logistic model based on the genome surveillance data from Canada, the UK, and the USA, where these variants have spread from March to April 2024. The Re of KP.3 is more than 1.2-fold higher than that of JN.1 and higher than or comparable to that of KP.2 in these countries. Importantly, the Re values of LB.1 and KP.2.3 are even higher than those of KP.2 and KP.3. These results suggest that the three variants we investigated herein, particularly LB.1, and KP.2.3, will become major circulating variants worldwide in addition to KP.2 and KP.3. The pseudovirus infectivity of KP.2 and KP.3 was significantly lower than that of JN.1. On the other hand, the pseudovirus infectivity of LB.1 and KP.2.3 was comparable to that of JN.1. Neutralization assay was conducted by using four types of breakthrough infection (BTI) sera with XBB.1.5, EG.5, HK.3 and JN.1 infections as well as monovalent XBB.1.5 vaccine sera. In all four groups of BTI sera tested, the 50% neutralization titers (NT50) against LB.1 and KP.2.3 were significantly lower than those against JN.1 (2.2-3.3-fold and 2.0-2.9-fold) and even lower than those against KP.2 (1.6-1.9-fold and 1.4-1.7 fold). Although KP.3 exhibited neutralization resistance against all BTI sera tested than JN.1 (1.6-2.2-fold) with statistical significance, there were no significant differences between KP.3 and KP.2. In the case of infection-naive XBB.1.5 vaccine sera, the NT50 values of JN.1 subvariants were very low. In the case of XBB.1.5 vaccine sera after natural XBB infection, the NT50 values against KP.3, LB.1 and KP.2.3 were significantly lower than those of JN.1 (2.1-2.8-fold) and even lower than KP.2 after infection (1.4-2.0-fold). Overall, our results suggest that the S substitutions convergently acquired in the JN.1 subvariants contribute to immune evasion, and therefore, increase their Re when compared to parental JN.1. More importantly, LB.1 and KP.2.3 exhibited higher pseudovirus infectivity and more robust immune resistance than KP.2. These data suggest that S:S31del is critical to exhibit increased infectivity, increased immune evasion, and therefore, potentially contributes to increased Re.

microbiology↗

bioRxiv2024

A single-cell atlas characterizes dysregulation of the bone marrow immune microenvironment associated with outcomes in multiple myeloma

Multiple Myeloma (MM) remains incurable despite advances in treatment options. Although tumor subtypes and specific DNA abnormalities are linked to worse prognosis, the impact of immune dysfunction on disease emergence and/or treatment sensitivity remains unclear. We established a harmonized consortium to generate an Immune Atlas of MM aimed at informing disease etiology, risk stratification, and potential therapeutic strategies. We generated a transcriptome profile of 1,149,344 single cells from the bone marrow of 263 newly diagnosed patients enrolled in the CoMMpass study and characterized immune and hematopoietic cell populations. Associating cell abundances and gene expression with disease progression revealed the presence of a proinflammatory immune senescence-associated secretory phenotype in rapidly progressing patients. Furthermore, signaling analyses suggested active intercellular communication involving APRIL-BCMA, potentially promoting tumor growth and survival. Finally, we demonstrate that integrating immune cell levels with genetic information can significantly improve patient stratification.

genomics↗

bioRxiv2024

The Continuous Language of Protein Structure

Just as language is composed of sublexical tokens that combine to form words, sentences, and paragraphs, protein backbones are composed of sub-structural elements that combine to form helices, sheets, folds, domains, and chains. Autoregressive language models operate on discrete tokens, whereas protein structure is inherently continuous, and generative approaches to protein design have borrowed more from image generation than language modeling. But autoregressive models do not inherently require their inputs and outputs to be discrete. Here we describe a generative autoregressive language model over the continuous space of protein backbones, where the distribution over the placement of each successive amino acid is conditioned on all preceding residues, and can be sampled from one residue after another. We show that this approach can learn to sample diverse and realistic protein chains, opening a new potential avenue for in silico protein design.

bioinformatics↗

bioRxiv2024

Bioinformatic evaluation of the potential oral-gut translocation of periodontal pathogens in patients with colorectal polyps

ObjectiveThis study aimed to characterize the profiles of the oral and gut microbiota of patients with colorectal polyps using 16S rRNA gene sequencing and bioinformatic approaches. BackgroundPrevious studies have shown microbial translocation from the oral cavity to the gut, implying pathogenic impacts on gastroesophageal disease, including colorectal cancer (CRC). However, its details remain unclear. MethodsTwenty patients scheduled for endoscopic colorectal polypectomy were enrolled in this study. Oral samples (saliva and subgingival dental plaque) and intestinal samples (feces and swab of intestinal mucosa) were collected during preoperative and 6-month-postoperative reassessment periods. After sequencing the V3-V4 region of the bacterial 16S rRNA gene, several bioinformatic analyses (bacterial composition, diversity, core microbiome, and shared ASV) were performed on pre- and postoperative samples for each subject. ResultsThe bacterial composition was dominated by Bacteroides, Streptococcus, Fusobacterium, Veillonella, and Prevotella_7 in all four samples. Beta diversity analysis using weighted UniFrac distance distinctly segregated the samples between oral and intestinal environments in the principal coordinate analysis plot. Core microbiome analysis revealed that Streptococcus and Porphyromonas were dominantly shared in intra-oral environments. Additionally, alongside Streptococcus, periodontitis-related bacteria, such as Veillonella, Fusobacterium, Porphyromonas, Prevotella_7, Haemophilus, and Prevotella, were identified as shared genera between oral and intestinal environments. Finally, shared ASV analysis demonstrated that Streptococcus was shared in the oral and intestinal environments of most patients, while periodontal pathogens were shared in some patients. ConclusionsThe core microbiome and shared ASV analyses revealed that several genes are shared between oral and intestinal environments in patients with colorectal polyps, indicating the oral-gut translocation of periodontitis-related bacteria. Further large-scale studies are needed to elucidate their involvement in CRC.

bioinformatics↗

bioRxiv2024

Virological characteristics of the SARS-CoV-2 KP.2 variant

The JN.1 variant (BA.2.86.1.1), arising from BA.2.86(.1) with the S:L455S substitution, exhibited increased fitness and outcompeted the previous dominant XBB lineage by the biggening of 2024. JN.1 subsequently diversified, leading to the emergence of descendants with spike (S) protein substitutions such as S:R346T and S:F456L. Particularly, the KP.2 (JN.1.11.1.2) variant, a descendant of JN.1 bearing both S:R346T and S:F456L, is rapidly spreading in multiple regions as of April 2024. Here, we investigated the virological properties of KP.2. KP.2 has three substitutions in the S protein including the two above and additional one substitution in non-S protein compared with JN.1. We estimated the relative effective reproduction number (Re) of KP.2 based on the genome surveillance data from the USA, United Kingdom, and Canada where >30 sequences of KP.2 has been reported, using a Bayesian multinomial logistic model. The Re of KP.2 is 1.22-, 1.32-, and 1.26-times higher than that of JN.1 in USA, United Kingdom, and Canada, respectively. These results suggest that KP.2 has higher viral fitness and potentially becomes the predominant lineage worldwide. Indeed, as of the beginning of April 2024, the estimated variant frequency of KP.2 has already reached 20% in United Kingdom. The pseudovirus assay showed that the infectivity of KP.2 is significantly (10.5-fold) lower than that of JN.1. We then performed a neutralization assay using monovalent XBB.1.5 vaccine sera and breakthrough infection (BTI) sera with XBB.1.5, EG.5, HK.3 and JN.1 infections. In all cases, the 50% neutralization titer (NT50) against KP.2 was significantly lower than that against JN.1. Particularly, KP.2 shows the most significant resistance to the sera of monovalent XBB.1.5 vaccinee without infection (3.1-fold) as well as those who with infection (1.8-fold). Altogether, these results suggest that the increased immune resistance ability of KP.2 partially contributes to the higher Re more than previous variants including JN.1.

microbiology↗

bioRxiv2024

Structural basis for bispecific antibody design: arrangement of domain linkage produces activity enhancement

A bispecific antibody (BsAb) is a protein genetically engineered from two different antibodies, allowing simultaneous binding to two kinds of antigen to bring them into close proximity. BsAbs have been developed as anti-cancer drugs that accumulate lymphocytes onto cancer cells by bridging antigens present on each. Ex3 is a bispecific diabody composed of the two fused variable regions (Fvs) of an anti-epidermal growth factor receptor (EGFR) antibody and an anti-CD3 antibody with potent cancer cytotoxic activity. In Ex3, the LH-type, in which the variable regions of the light chain (VLs) are located at the N-terminus of those of the heavy chain (VHs), exerted 1000-fold greater anticancer activity than the HL-type, in which the VHs are located at the N-terminus of the VLs. This effect (termed activity enhancement), in which the activity is greatly enhanced by domain rearrangement, has been reported not only for Ex3 but also for several other BsAbs. However, the molecular details of this activity enhancement have yet to be elucidated. In this study, we determined the cryo-EM structures of Ex3 LH- and HL-types in complex with CD3 and EGFR. Structural comparison of the LH- and HL-types showed that rearrangement of the domain linkage produces drastic structural differences in the overall shape of these complexes, and dynamics attributed to the flexibility between the two Fvs. These findings provide valuable insights into the molecular mechanism for the activity enhancement of BsAbs. This study will be a stepping stone towards establishing a design foundation for BsAb development.

biochemistry↗

bioRxiv2024

Fragility of ER homeostatic regulation underlies haploid instability in human somatic cells

Mammalian somatic cells are generally unstable in the haploid state, resulting in haploid-to-diploid conversion within a short time frame. However, cellular and molecular principles that limit the sustainability of somatic haploidy remain unknown. In this study, we found the haploidy-linked vulnerability to ER stress as a critical cause of haploid intolerance in human somatic cells. Pharmacological induction of ER stress selectively induced apoptosis in haploid cells, facilitating the replacement of haploids by co-existing diploidized cells in a caspase-dependent manner. Biochemical analyses revealed that unfolded protein response (UPR) was activated with similar dynamics between haploids and diploids upon ER stress induction. However, haploids were less efficient in solving proteotoxic status, resulting in a bias toward a proapoptotic mode of UPR signaling. Artificial replenishment of chaperone function or inhibition of a UPR signal transducer ATF6 substantially alleviated the haploidy-linked upregulation of proapoptotic signaling and improved haploid cell retention under ER stress. These data demonstrate that the ER stress-driven haploid instability stems from inefficient proteostatic control that alters the functionality of UPR to cause apoptosis selectively in haploids. Interestingly, haploids suffered a higher level of protein aggregation even in unperturbed conditions, and the long-term stability of the haploid state was significantly improved by alleviating their natural proteotoxicity. Based on these results, we propose that the haploidy-specific vulnerability to ER stress creates a fundamental cause of haploid intolerance in mammalian somatic cells. Our findings provide new insight into the principle that places a stringent restriction on the evolution of animal life cycles.

biochemistry↗