Biology subjects

Hoshino, A.

Publications and source records attributed to Hoshino, A..

At least 19 recordsLinked to original sources

bioRxiv2026

Bioenergetic and Proteomic Profiling of ARID1A-Deficient Ovarian Clear Cell Carcinoma under Metabolic Challenge

ARID1A loss is associated with increased mitochondrial respiration in ovarian clear cell carcinoma (OCCC), but whether this phenotype is maintained under metabolic challenge remains unclear. Here, we examined mitochondrial function and electron transport chain (ETC) protein abundance in isogenic ARID1A wild-type (WT) and ARID1A-knockout (KO) OCCC cells cultured under physiological glucose, galactose, or the Complex I inhibitor IACS-010759. Across all conditions, KO cells maintained higher basal, ATP-linked, and maximal respiration, greater spare respiratory capacity, and higher coupling efficiency than WT cells, despite lower steady-state ATP levels. In human OCCC tumors, ARID1A-negative cases showed a higher bioenergetic cellular (BEC) index than ARID1A-positive cases, and high BEC was associated with poorer cancer-specific survival. Quantitative proteomics revealed a trend toward higher ETC complex abundance in KO cells, although whole-complex differences did not reach statistical significance. ARID1A loss was associated with selective increases in Complex III and V proteins, whereas metabolic challenge was associated with increases in Complex I and IV proteins. Together, these findings show that the ARID1A-associated mitochondrial phenotype persists across distinct metabolic challenges and is not explained simply by coordinated increases in ETC protein abundance. The association of mitochondrial bioenergetics with clinical outcomes further supports its relevance in human OCCC.

cancer biology↗

bioRxiv2026

Gut bacterial composition and predicted functional profiles associated with depressive symptom burden in Japanese adults recruited independently of depression diagnosis

Reported associations between depressive symptoms and the gut microbiota have been inconsistent, particularly with respect to predicted microbial function. We conducted an exploratory cross-sectional study of 17 adults to examine associations of depressive symptom burden with fecal bacterial composition and predicted functional potential. Depressive symptoms were assessed using the Japanese version of the Center for Epidemiologic Studies Depression Scale (CES-D); 13 participants scored <16 and 4 met the screening cutoff ([≥]16) for elevated depressive symptoms. Bacterial communities were profiled by 16S ribosomal RNA gene sequencing. Weighted UniFrac community structure differed between groups by permutational multivariate analysis of variance. Exploratory taxonomic analysis identified 31 features differentiating the groups. Among features enriched in the higher CES-D group, those assigned to Veillonella, Parabacteroides, and Porphyromonadaceae showed the highest linear discriminant analysis scores, whereas Firmicutes and several Lachnospiraceae- and Ruminococcaceae-related taxa were enriched in the lower CES-D group. PICRUSt2-predicted functional profiles differed between groups across four annotation systems. At the MetaCyc pathway level, the lower CES-D group showed nominally higher predicted purine salvage and several amino acid, phospholipid, and coenzyme A biosynthesis I pathways, whereas the higher CES-D group showed nominally higher predicted de novo pyrimidine deoxyribonucleotide biosynthesis, several TCA-cycle variants, glucose/xylose and N-acetylneuraminate degradation, the glycolysis/Entner-Doudoroff superpathway, and the urea cycle. These findings provide exploratory evidence that depressive symptom burden is associated with gut bacterial composition and predicted functional profiles among Japanese adults recruited independently of depression diagnosis.

microbiology↗

bioRxiv2026

Disruption of the single-copy GOLDEN2-like gene underlies the classical yellow and yellow-mutable mutations of Japanese morning glory

GOLDEN2-like (GLK) transcription factors are key regulators of chloroplast differentiation and photosynthetic gene expression. The classical yellow mutation in Japanese morning glory (Ipomoea nil) produces yellowish-green leaves, whereas an unstable allele, yellow-mutable, produces green somatic sectors on a yellowish-green background. The gene responsible for these mutations was identified as InGLK, which encodes a GOLDEN2-like transcription factor. The stable yellow mutant carried a 4-bp frameshift insertion in InGLK, whereas two yellow-mutable lines carried the Tpn1-family transposon Tpn12 in intron 5. Excision of Tpn12 in germinal revertants left short footprints and restored the green leaf phenotype. Genome searches identified InGLK as the sole GLK gene in I. nil. Pigment analysis of green somatic reversion sectors and yellowish-green background areas showed that most of the measured photosynthetic pigments were significantly reduced in the yellowish-green background, whereas the chlorophyll a/b ratio was unchanged. Chloroplasts in the yellowish-green tissue retained thylakoid-like membranes and starch granule-like structures but had less distinct grana-like stacks and sparse stromal lamellae-like structures. Wild-type-like chloroplast ultrastructure was restored in germinal revertants. These findings show that loss of function of a single-copy GLK gene broadly reduces photosynthetic pigment accumulation and alters chloroplast internal membrane organization. The yellow mutants of I. nil therefore provide a genetic system for examining non-redundant GLK function.

plant biology↗

bioRxiv2026

InMYB21B Promotes Petal Cell Expansion and Flower Opening in Japanese Morning Glory (Ipomoea nil)

Flower opening is a complex developmental process involving coordinated changes in cell proliferation and cell expansion. Although several regulators of flower opening have been identified, how transcriptional programs are coordinated with the cellular and metabolic changes underlying petal expansion immediately before flower opening remains incompletely understood. Japanese morning glory (Ipomoea nil) is a suitable model for investigating these processes because its flowers open synchronously at a predictable time. This study aimed to identify transcriptional regulators involved in petal development and flower opening in Japanese morning glory. Temporal analyses of petal growth, sugar metabolism, and gene expression revealed that petal development was driven by both cell proliferation and cell expansion until approximately 48 h before flower opening, whereas cell expansion predominated thereafter. Weighted gene co-expression network analysis identified two genes encoding R2R3-MYB subgroup 19 transcription factors, InMYB21A and InMYB21B, as candidate regulators associated with petal development. CRISPR/Cas9-mediated knockout analysis revealed a prominent role for InMYB21B, whose loss markedly impaired petal cell expansion and prevented flower opening. InMYB21B knockout also impaired stamen and pistil development, resulting in male and female sterility. Starch degradation and glucose accumulation were impaired in InMYB21B knockout petals. Transcriptome analysis revealed delayed transcriptomic progression during petal development and reduced expression of genes associated with starch degradation, sucrose metabolism, cell wall remodeling, and water transport. These findings identify InMYB21B as a key regulator of petal cell expansion and flower opening in Japanese morning glory and show that loss of InMYB21B disrupts both metabolic and transcriptomic progression during late petal development.

plant biology↗

bioRxiv2025

G3BP1 Maintains Lysosomal Homeostasis to Limit Tau Aggregate Accumulation

Tau aggregation is a pathological hallmark of a group of neurodegenerative diseases collectively termed tauopathies. While impaired proteostasis is known to drive the accumulation of abnormal proteins, the molecular factors influencing Tau aggregate clearance remain incompletely understood. In this study, we employed a cell-based Tau reporter assay combined with a lentivirus-based pooled CRISPR-Cas9 loss-of-function library to identify genes that regulate Tau aggregation. Genome-wide screening revealed that candidate genes were significantly enriched in categories related to mRNA metabolic processes and autophagy. Among them, we focused on the RNA-binding protein G3BP1, which is functionally associated with both processes. Detailed analyses showed that G3BP1 deficiency promoted the accumulation of Tau aggregates without affecting stress granule formation or autophagic flux. Instead, G3BP1 dysfunction resulted in impaired lysosomal homeostasis, as evidenced by reduced lysosomal abundance and acidification. Furthermore, lysosomal damage induced by L-leucyl-L-leucine methyl ester (LLOMe) enhanced Tau aggregation, particularly in G3BP1-deficient cells. Conversely, pharmacological activation of TFEB by the curcumin analog C1 restored lysosomal function and suppressed Tau aggregate accumulation to wild-type levels. These findings highlight a role of G3BP1 in maintaining lysosomal homeostasis and promoting Tau clearance. Our results further suggest that therapeutic strategies aimed at enhancing lysosomal biogenesis, such as TFEB activation, may hold promise for the treatment of tauopathies.

cell biology↗

bioRxiv2025

Parasitism-mediated horizontal transfer of a functional cytochrome P450 gene entails transposon colonization in newly gained introns

Plants produce a wide variety of specialized metabolites that are typically present only in specific lineages. However, some specialized metabolites are found sporadically across distantly related plant species. While the latter cases have been explained as outcomes of convergent evolution, the molecular mechanism behind such metabolic evolution has remained largely elusive. Here, we report that parasitic dodders belonging to the genus Cuscuta accumulate sesamin, and that this accumulation may be attributed to the acquisition of enzymatically active homologs of Sesamum indicum CYP81Q1, which encodes piperitol/sesamin synthase (PSS). Phylogenetic analysis of CYP81Q homologs in Cuscuta and Grammica subgenera supports a trajectory in which ancestral Cuscuta species acquired CYP81Q from an ancestral host plant of Lamiales through horizontal gene transfer (HGT), and that the gene has been maintained during the speciation of Cuscuta. The evolution of the CYP81Q genes was accompanied by sequential intron gains, which likely involved the colonization of transposons. Experiments involving C. campestris and S. indicum suggested that expression of the host CYP81Q gene could be induced by parasitism, and physical connection to the host plant allowed the transfer of genetic elements to Cuscuta. These data suggest that parasitism-mediated HGT contributed to the transfer of a gene encoding a key enzyme in specialized lignan metabolism to Cuscuta, and that the acquired metabolic gene underwent structural modification while retaining its enzymatic function in dodders.

plant biology↗

bioRxiv2025

UNC-45A Drives ATP-Independent Microtubule Destabilization via Defect Recognition and Repair Inhibition Contributing to Neurite Dystrophy

UNC-45A is the only known ATP-independent microtubule severing protein. Using in vitro reconstitution and TIRF microscopy, we show that, unlike canonical severing enzymes such as katanin, spastin, and fidgetin, which hydrolyze ATP to remove tubulin dimers and promote lattice repair, UNC-45A selectively binds to pre-existing microtubule defects and inhibits GTP-tubulin incorporation. This mechanism prevents the formation of stabilized hot spots that typically protect microtubules from disassembly, resulting in persistent lattice damage and net microtubule loss, even in the presence of physiological levels of free GTP-tubulin. We further demonstrate that UNC-45A localizes near amyloid deposits in both mouse models and human cases of Alzheimers disease (AD). In cultured neurons, UNC-45A accumulates in axonal swellings--regions of pronounced microtubule disruption and experimental surrogates for dystrophic neurites in AD--and exacerbates their size and number, particularly under conditions mimicking microtubule damage. Notably, this is the first report of a microtubule severing protein that both localizes near amyloid plaques in tissue and accumulates in neurite swellings in cultured neurons, where it modulates their pathology. Together, our findings establish the mechanism of ATP-independent, damage-responsive severing pathway that couple defects recognition to repair inhibition, defining a new paradigm in microtubule quality control with broad implications for cytoskeletal integrity and remodeling in health and disease.

cell biology↗

bioRxiv2025

Therapeutic Knock-in Genome Editing Using Single AAV Vectors in Mouse Models of Inherited Liver Disease

Gene knock-in therapy has the potential to cure inherited liver diseases but is limited by low efficiency and delivery complexity. Here, we developed a single adeno-associated virus (AAV) vector system comprising a compact CRISPR effector, enAsCas12f, a guide RNA, and a donor template to enable therapeutic genome editing via non-homologous end joining (NHEJ). We targeted the system to the murine Alb locus and applied it to mouse models of hemophilia B, protein C (PC) deficiency, and ornithine transcarbamylase (OTC) deficiency. NHEJ-mediated knock-in showed higher efficiency than homology-directed repair, with successful therapeutic gene insertion in both neonatal and adult mice. The strategy restored plasma factor IX activity in hemophilia B (F9-/-) mice, prolonged survival of PC-deficient (Proc-/-) mice, and prevented hyperammonemia and weight loss in OTC-deficient (Otcspf-ash) mice upon high protein challenge. Importantly, gene integration was restricted to the liver, with no evidence of germline transmission. This compact, all-in-one AAV knock-in platform simplifies vector production, enables efficient delivery, and achieves reliable transgene expression in vivo. Our findings highlight the potential of liver-targeted knock-in genome editing as a transplant-independent treatment for neonatal-onset metabolic diseases, offering a clinically feasible path towards curative gene therapies for a wide range of monogenic liver disorders.

bioengineering↗

bioRxiv2025

The glare illusion in individuals with schizophrenia

Individuals with schizophrenia are known to demonstrate unique reactions to visual illusions, and prior research has indicated a potential link between their increased susceptibility to geometric illusions and specific symptom profiles. While various illusory experiences have been examined among individuals with schizophrenia, their responses to brightness-related illusions remain poorly understood. In this study, we investigated how individuals with schizophrenia perceive the glare illusion, in which the apparent brightness of the central region is increased. A total of 30 patients with schizophrenia and 34 control participants were recruited. During each trial, a glare or control image (standard stimulus) was presented alongside a control image (comparison stimulus) with one of seven luminance levels. In the glare condition, the standard stimulus was a glare image; in the control condition, two control images were presented, but only the luminance of the comparison stimulus varied. The participants were asked to judge which central region appeared brighter. The results revealed that the individuals with schizophrenia exhibited greater susceptibility to the glare illusion than did the control participants. However, no significant associations were found between susceptibility to the glare illusion and scores assessing symptom severity. These findings suggest that differences in visual processing in patients with schizophrenia may increase their susceptibility to brightness illusions, although this phenomenon is independent of symptom characteristics. Understanding these perceptual alterations may aid in the development of objective measures of visual cognition for patients with schizophrenia.

neuroscience↗

bioRxiv2024

Universal base editing for hemophilia B

The repair of pathological gene variants is an ultimate aim for treating genetic diseases; however, it is not practical to develop different therapeutic reagents for each of the many variants that can occur in a gene. Here, we investigated whether base editing to induce a gain-of-function variant in blood coagulation factor IX (FIX) can increase FIX activity as a treatment strategy for hemophilia B. We engineered a G:C to A:T substitution at c.1151 of F9 by cytosine base editing to generate R338Q, known as the Shanghai F9 variant, which markedly potentiates coagulation factor activity. An adeno-associated virus vector harboring the base editor converted more than 60% of the target G:C to A:T and increased FIX activity in HEK293 cells harboring patient-derived F9 variants, as well as in knock-in mice harboring a human F9 cDNA. Furthermore, administration of lipid nanoparticles embedded with the base editor mRNA and gRNA increased FIX activity in mice. These data indicate that cytosine base editing to generate R338Q in FIX can become a universal genome editing strategy for hemophilia B.

bioengineering↗

bioRxiv2024

Labor- and cost-effective long-read amplicon sequencing using a plasmid analysis service: Application to transposon-inserted alleles in Japanese morning glory

The sequencing of PCR fragments amplified from specific regions of genomes is a fundamental technique in molecular genetics. Sanger sequencing is commonly used for this analysis; however, amplicon sequencing utilizing next-generation sequencing has become widespread. In addition, long-read amplicon sequencing, using Nanopore or PacBio sequencers to analyze long PCR fragments, has emerged, although it is often more expensive than Sanger sequencing. Recently, low-cost commercial services for full-length plasmid DNA sequencing using Nanopore sequencers have been launched in several countries, including Japan. This study explored the potential of these services to sequence long PCR fragments without the need for cloning into plasmid DNA. PCR fragments of 4-11 kb, amplified from the DFR-B gene involved in the biosynthesis of anthocyanin, with or without Tpn1 transposons in Japanese morning glory (Ipomoea nil), were circularized using T4 ligase and analyzed as templates. Although some inaccuracies in the length of homopolymer stretches were observed, the remaining sequences were obtained without significant errors. This method could potentially reduce the labor and costs associated with cloning, primer synthesis, and sequence assembly, thus making it a viable option for the analysis of long PCR fragment sequences. Moreover, this study reconfirmed that Tpn1 transposons are major mutagens in I. nil and demonstrated their transposition in the Violet line, a long-used standard in plant physiology.

genetics↗

bioRxiv2024

Frame-shift mutation of InCO might cause early flowering of Japanese morning glory and might have contributed to northward expansion

Japanese morning glory (Ipomoea nil), a short day plant, has been used for studying flowering times. Here, quantitative trait loci (QTL) analysis for days from sowing to flowering (DTF) of F2 between I. nil var. Tokyo Kokei Standard (TKS) and I. hederacea line var. Q65, an early flowering variety, revealed four QTLs: QTL Ipomoea Flowering 1-4 (qIF1-4). The position of qIF3, which had the most significant effect among the four QTLs, corresponds with that of I. nil (or I. hederacea) CONSTANS (InCO/IhCO) in the linkage map. There is a single-base In/Del in the coding sequence of InCO/IhCO. The single-base deletion (SBD) causes a frame-shift mutation and loss of function in TKS allele (inco-1). I. nil accessions bearing inco-1 tend to flower early, similarly to rice varieties bearing the loss of function allele of CO ortholog, hd1. Consequently, inco-1 was inferred to reduce DTF. This inferred effect of inco-1 corresponds with the effect of the TKS allele of qIF3. Because inco-1 is found exclusively in Asian accessions, the SBD in inco-1 might have played an important role in the expansion of Japanese morning glories, originally native to the tropical regions of the Americas, into temperate Asia.

plant biology↗

bioRxiv2024

Transcriptomic dynamics of petal development in the one-day flower species, Japanese morning glory (Ipomoea nil)

Various aspects of Japanese morning glory (Ipomoea nil) petals, such as color, pattern, shape, flower opening time, and senescence, have been extensively studied. To facilitate such studies, transcriptome data were collected from flower petals at 3-h intervals over 3.5 days; the data was collected from 72 h before and 12 h after flower opening, accounting for 29 timepoints. Data analysis revealed substantial transcriptomic changes before and after flower opening. The expression patterns of cell division marker genes indicated that cell division practically stops at approximately 48 h before flower opening. Furthermore, the increased expression of genes encoding transporters for sugars, amino acids, nucleic acids, and autophagy-related genes was observed after flower opening, indicating the translocation of nutrients from senescing petal cells to other developing tissues. Correlations were found between the temporal expression patterns of the three transcriptional regulators and expression patterns of different sets of structural genes within the anthocyanin biosynthesis pathway, indicating differential reliance on each regulator for the activation of specific structural genes. Furthermore, clock genes were identified. Three copies of the clock gene ELF3 did not exhibit circadian rhythms, potentially allowing I. nil to adapt to high-latitude regions. The temporal transcriptome data and interactive database (https://ipomoeanil.nibb.ac.jp/fpkm/) offer valuable insights into gene expression dynamics, periodicity, and correlations and provide a crucial resource for further research on I. nil and other plant species.

plant biology↗

bioRxiv2024

The uptake of small extracellular vesicles by recipient cells is facilitated by paracrine adhesion signaling

Small extracellular vesicles (sEVs) play crucial roles in intercellular communication. However, the internalization of individual sEVs by recipient cells has not yet been directly observed. Here, we examined these mechanisms using state-of-the-art imaging techniques. Single-molecule imaging showed that tumor-derived sEVs can be classified into several subtypes. Simultaneous single-sEV particle tracking and observation of super-resolution movies of membrane invaginations in living cells revealed that all sEV subtypes were internalized via clathrin-independent endocytosis mediated by galectin-3 and LAMP-2C, while some subtypes that recruited raft markers were internalized through caveolae. Integrin {beta}1 and talin-1 accumulated in recipient cell plasma membranes beneath all sEV subtypes. Paracrine, but not autocrine, sEV binding triggered Ca2+ mobilization induced by the activation of Src family kinases and PLC{gamma}. Subsequent Ca2+-induced activation of calcineurin-dynamin promoted sEV internalization, leading to the recycling pathway. Thus, we have clarified the detailed mechanisms of sEV internalization driven by paracrine adhesion signaling.

cell biology↗

bioRxiv2023

Fibroblast Nrf2 inhibits profibrotic transcription with Ddx54 and mitigates pathological fibrosis in the mouse heart and kidney

BackgroundTissue fibrosis is a common feature of many organ dysfunctions, such as heart failure and chronic kidney disease. However, no fundamental treatment has been developed. This study aims to identify novel molecular mechanisms for antifibrotic intervention, focusing on fibroblast activation. MethodsWe performed a forward genetic screen using a genome-wide CRISPR library in the context of transforming growth factor {beta} (TGF-{beta})-mediated connective tissue growth factor (CTGF) expression, and used unbiased techniques such as Cleavage Under Targets and Tagmentation (CUT&Tag) and proximity-dependent biotin labeling by TurboID to reveal the detailed molecular mechanisms. ResultsCRISPR library screening identified a number of players in both the canonical Smad pathway and the non-canonical pathway. In addition to the known factors, the Keap1-Nrf2 pathway was identified as a predominant regulator of TGF-{beta}-mediated CTGF expression. Keap1 deletion and consequent Nrf2 activation broadly suppressed profibrotic gene expression, independently of conventional antioxidant effects. CUT&Tag revealed that Nrf2 bound to the proximity of fibrosis-related genes including Ctgf and Fn1. Subsequent individual analysis revealed Smad3 and RNA polymerase II binding to the Nrf2 peak site, which was attenuated by Keap1 deletion. TurboID experiments further discovered that Nrf2 interacts with Ddx54, which acts as a corepressor. Consistently, Keap1 deletion-mediated repression of profibrotic gene expression was reversed by additional Ddx54 deletion. The impact of the Keap1-Nrf2 pathway on pathological fibrosis was examined using tamoxifen-inducible fibroblast-specific Keap1 knockout mice. Pressure overload for 4 weeks robustly induced cardiac hypertrophy, fibrosis and contractile dysfunction. However, deletion of Keap1 in the Postn lineage attenuated these cardiac pathologies. The anti-fibrotic effects of Keap1 deletion were also confirmed in renal fibrosis in the unilateral ureteral obstruction (UUO) model. ConclusionsFibroblast Nrf2 transcriptionally represses fibrosis-related genes in cooperation with the corepressor Ddx54. Fibroblast-specific deletion of Keap1 attenuated pathological fibrosis in pressure overload heart failure and renal fibrosis.

cell biology↗

bioRxiv2023

Advancement in Cellular Topographic and Nanoparticle Capture Imaging by High Resolution Microscopy Incorporating a Freeze-Drying and Gaseous Nitrogen-based Approach

Scanning electron microscopy (SEM) offers an unparalleled view of the membrane topography of mammalian cells by using a conventional osmium (OsO4) and ethanol-based tissue preparation. However, conventional SEM methods limit optimal resolution due to ethanol and lipid interactions and interfere with visualization of fluorescent reporter proteins. Therefore, SEM correlative light and electron microscopy (CLEM) has been hindered by the adverse effects of ethanol and OsO4 on retention of fluorescence signals. To overcome this technological gap in achieving high-resolution SEM and retain fluorescent reporter signals, we developed a freeze-drying method with gaseous nitrogen (FDGN). We demonstrate that FDGN preserves cyto-architecture to allow visualization of detailed membrane topography while retaining fluorescent signals and that FDGN processing can be used in conjunction with a variety of high-resolution imaging systems to enable collection and validation of unique, high-quality data from these approaches. In particular, we show that FDGN coupled with high resolution microscopy provided detailed insight into viral or tumor-derived extracellular vesicle (TEV)-host cell interactions and may aid in designing new approaches to intervene during viral infection or to harness TEVs as therapeutic agents.

cell biology↗

bioRxiv2023

The Microtubule Severing Protein UNC-45A Counteracts the Microtubule Straightening Effects of Taxol

UNC-45A is the only known ATP-independent microtubule (MT) severing protein. Thus, it severs MTs via a novel mechanism. In vitro and in cells UNC-45A-mediated MT severing is preceded by the appearance of MT bends. While MTs are stiff biological polymers, in cells, they often curve, and the result of this curving can be breaking off. The contribution of MT severing proteins on MT lattice curvature is largely undefined. Here we show that UNC-45A curves MTs. Using in vitro biophysical reconstitution and TIRF microscopy analysis, we show that UNC-45A is enriched in the areas where MTs are curved versus the areas where MTs are straight. In cells, we show that UNC-45A overexpression increases MT curvature and its depletion has the opposite effect. We also show that this effect occurs is independent of actomyosin contractility. Lastly, we show for the first time that in cells, Paclitaxel straightens MTs, and that UNC-45A can counteracts the MT straightening effects of the drug. Significance: Our findings reveal for the first time that UNC-45A increases MT curvature. This hints that UNC-45A-mediated MT severing could be due to the worsening of MT curvature and provide a mechanistic understanding of how this MT-severing protein may act. UNC-45A is the only MT severing protein expressed in human cancers, including paclitaxel-resistant ovarian cancer. Our finding that UNC-45A counteracts the paclitaxel-straightening effects of MTs in cells suggests an additional mechanism through which cancer cells escape drug treatment.

cell biology↗

bioRxiv2023

Deep mutational scanning of whole SARS-CoV-2 spike in an inverted infection system

In order to investigate SARS-CoV-2 mutations and their impact on immune evasion and infectivity, we developed a Deep Mutational Scanning (DMS) platform utilizing an inverted infection assay to measure spike expression, ACE2 affinity, and viral infectivity in human cells. Surprisingly, our analysis reveals that spike protein expression, rather than ACE2 affinity, is the primary factor affecting viral infectivity and correlated with SARS-CoV-2 evolution. Notably, within the N-terminal domain (NTD), spike expression and infectivity-enhancing mutations are concentrated in flexible loops. We also observed that Omicron variants BA.1 and BA.2 exhibit immune evasion through receptor binding domain (RBD) mutations, although these mutations reduce structural stability. Interestingly, the NTD has evolved to increase stability, compensating for the RBD instability and resulting in heightened overall infectivity. Our findings, available in SpikeScanDB, emphasize the importance of spike expression levels and compensatory mutations in both the NTD and RBD domains for shaping Omicron variant infectivity.

microbiology↗