Biology subjects

Imami, K.

Publications and source records attributed to Imami, K..

At least 19 recordsLinked to original sources

bioRxiv2026

Expanding N-terminomics Coverage by Extending N-terminal Peptide Length

In bottom-up proteomics, protease specificity determines peptide length and LC/MS/MS detectability; in N-terminomics, this is critical because each protein N-terminal peptide is unique and cannot be substituted by other peptides. CHromatographic AMplification of Protein N-terminal peptides (CHAMP-N) combines LysargiNase digestion with StageTip-based strong cation exchange chromatography (SCX), removing internal peptides by exploiting their newly generated N-terminal Lys/Arg residues and thereby selectively isolating protein N-terminal peptides. However, LysargiNase cleavage near the protein N-terminus can generate excessively short peptides. Here, we developed two complementary CHAMP-N approaches that modurate N-terminal peptide length while retaining the charge-based SCX separation principle. LysN digestion avoided cleavage at N-terminal-proximal Arg residues, whereas D3-acetylation blocked Lys cleavage by LysargiNase to produce ArgN-like specificity. Both approaches extended otherwise short N-terminal peptides while preserving N-terminal basic residues on internal peptides. Conventional LysargiNase, LysN, and ArgN-like CHAMP-N generated complementary sets of N-terminal peptides. Integration of the three workflows identified 2,552 protein N-termini, approximately twice the number identified by conventional CHAMP-N alone. The median relative standard deviations of N-terminal peptide intensities were approximately 15% for all three workflows, indicating comparable technical reproducibility. These results demonstrate that coordinating protease cleavage specificity with SCX selectivity reduces sequence-dependent losses and expands N-terminome coverage while preserving the simplicity and reproducibility of CHAMP-N.

biochemistry↗

bioRxiv2026

Recording proteome dynamics in the late-stage embryo at hour-timescale, spatial, and single-cell resolution with MEMBRYO

Cell fate during development is directed by new gene expression states that replace prior ones. When and where a protein is first translated, and how long it will remain in the cell, dictate the timing and extent of a gene's phenotypic effect. Accessing protein synthesis and turnover information in the rapidly developing embryo remains a major challenge. Here we present MEMBRYO: a method for continuous stable isotope labeling (SILAC) of newly synthesized proteins throughout the live embryo at the hour-timescales of developmental phenotypes. We extend embryo culture into the late stages of organogenesis, thereby accessing the proteome of neurogenesis in the forebrain ex utero. Variations in protein synthesis and turnover activity lead to expression patterns that diverge from the corresponding transcripts, impacting molecular pathways and key milestones of cortical neuron differentiation. The high labeling depth enabled both spatial and single-cell SILAC proteomics analysis of cortical cells, revealing distinct layers of post-transcriptional gene expression regulation in progenitors and neurons. By continuous metabolic labeling in the live embryo, MEMBRYO tracks the past, present, and future of the developmental proteome.

developmental biology↗

bioRxiv2026

SPIN1 selectively silences evolutionarily young transposable elements through chromatin regulation

Mammalian genomes encode multiple transposable element (TE) silencing pathways that distinguish their targets through different molecular features, with KRAB zinc finger proteins recognizing DNA sequence, the HUSH complex sensing intronless transcripts, and the PIWI-piRNA pathway using small RNA guides. How chromatin state itself contributes to TE recognition remains less defined. Here we identify Spindlin1 (SPIN1), a three-Tudor-domain histone reader implicated in germline piRNA-directed DNA methylation, as a transcriptional repressor of evolutionarily young TEs in mouse embryonic stem cells. SPIN1 selectively binds LINE and ERV loci carrying H3K4me3 and H3K9me3, a chromatin signature enriched at young, transcription-permissive elements, and recognition of these marks by Tudor domains 1 and 2 is required for TE targeting. SPIN1 engages SPINDOC as a Tudor 1 and 3-dependent cofactor whose loss phenocopies SPIN1 depletion, and associates with the H3K9 methyltransferases SETDB1 and G9a. SPIN1 loss reduces H3K9me3 and is accompanied by increased chromatin accessibility, without altering DNA methylation. Thus, SPIN1 uses a histone-state-based mechanism to identify and repress young TEs in pluripotent cells, mechanistically distinct from its germline mode in which SPIN1 cooperates with the PIWI-piRNA pathway to promote DNA methylation, illustrating how a single histone reader engages distinct silencing machineries across cellular contexts.

molecular biology↗

bioRxiv2026

Elucidation of the anti-inflammatory mechanism of isoliquiritigenin from Glycyrrhiza uralensis using activity-based protein profiling

Glycyrrhiza uralensis is a widely used medicinal plant present in more than 70% of Kampo formulations in Japan owing to its diverse pharmacological activities, including immunomodulatory, antitumor, and antioxidant effects. Isoliquiritigenin (ILG), a major chalcone constituent of G. uralensis, exhibits anti-inflammatory activity; however, its molecular mechanism remains unclear. Here, we employed an activity-based protein profiling approach to identify the molecular targets of ILG. Given that the ,{beta}-unsaturated carbonyl moiety of ILG can covalently react with reactive cysteine residues via nucleophilic addition, we used an iodoacetamide-based probe to globally profile cysteine-reactive proteomes. The comparative analysis between ILG- and vehicle-treated RAW 264.7 macrophages identified cysteine 65 (Cys65) of lipocalin-type prostaglandin D2 synthase (L-PGDS) as a potential covalent target. ILG treatment did not alter L-PGDS expression levels, indicating that reduced probe labeling reflects direct covalent competition rather than changes in expression. Consistently, ILG significantly suppressed prostaglandin D2 (PGD2) production, comparable to the selective L-PGDS inhibitor AT-56. Although both ILG and AT-56 reduced interleukin-6 expression, ILG exerted a stronger inhibitory effect. Our results demonstrate that covalent inhibition of L-PGDS and subsequent suppression of PGD2 production represent a key mechanism underlying the anti-inflammatory activity of ILG.

biochemistry↗

bioRxiv2026

Seamless workflow of hydroxy acid-modified metal oxide chromatography for rapid and sensitive phosphoproteomics sample preparation

Phosphoproteomics by liquid chromatography/tandem mass spectrometry requires efficient phosphopeptide enrichment, but conventional workflows are often time-consuming and prone to sample loss, particularly at low input. Here, we present Rapid Hydroxy Acid-Modified Metal Oxide Chromatography (Rapid HAMMOC), a streamlined, TiO2-based enrichment workflow that features three key improvements. First, we optimized the TiO2 column loading conditions and found that alternative pH-buffering agents and organic solvents, such as sodium bicarbonate combined with ethyl acetate, outperformed the commonly used Tris-based buffer with isopropanol. Second, to minimize sample loss and manual handling in desalting, phosphopeptides eluted under basic conditions were directly loaded onto a dual-membrane StageTip composed of stacked strong anion exchange (SAX) and reversed-phase styrene-divinylbenzene (SDB) membranes (SAX-SDB StageTip). Third, the addition of lauryl maltose neopentyl glycol (LMNG), which is readily removed during desalting, suppressed nonspecific adsorption. Rapid HAMMOC provided markedly improved sensitivity, identifying approximately 5,000 class I phosphosites from 5 g of K562 cell digests, with a median 7.9-fold increase in intensity compared to the original workflow. Rapid HAMMOC also identified, on average, approximately 8,000 class I phosphosites from as little as 0.5 g input from HeLa, A549, and HCT116 cells. Furthermore, coupling Rapid HAMMOC with anti-puromycin immunoprecipitation enabled single-day profiling of nascent polypeptides from ultra-low input samples, yielding 2,310 high-confidence co-translational phosphosites. Beyond providing a practical enrichment workflow, this study offers broadly applicable insights that can be extended to other TiO2-based phosphoproteomic methods.

biochemistry↗

bioRxiv2025

Primary Cilium-dependent Humoral Bioactive Factors Acts in a Paracrine Manner to Control Fibroblast Cell Migration

The primary cilium is classically recognized as a signal-reception hub, yet its role in mediating cell-to-cell communication via signal spread remains poorly defined. Here, we uncover a previously unrecognized paracrine function of the primary cilium in fibroblasts. Conditioned medium from ciliated wild-type NIH/3T3 cells enhanced wound healing in primary cilium-deficient fibroblasts, in contrast to conditioned medium derived from primary cilium-deficient NIH/3T3-Kif3a-KO or NIH/3T3-Dync2h1-KO cells. Fractionation of conditioned medium revealed that the wound healing activity resided predominantly in the 100K x g soluble supernatant (Sup-100K), rather than in extracellular vesicle (EV) fractions. Untargeted metabolomic analysis identified lysophosphatidylcholine (LPC) (14:0) as a key bioactive metabolite enriched in WT-Sup-100K secretome. Supplementation of LPC(14:0) restored wound healing capacity in NIH/3T3-Kif3a-KO cells to levels comparable to WT-Sup-100K treatment. Transcriptomic profiling of target cells revealed that WT-Sup-100K upregulated expression of extracellular matrix (ECM)-associated genes, including Ogn, Igf2, and Mfap4, while EVs modestly enhanced early ECM remodeling via induction of Nid2. Together, these findings demonstrate that the primary cilium coordinates a wound healing secretome in fibroblasts through the regulated release of LPC(14:0) and other soluble factors that activate ECM-remodeling pathways in recipient cells. This work expands the functional repertoire of the primary cilium and establishes its critical role in coordinating paracrine regenerative signaling.

cell biology↗

bioRxiv2025

Systemic Inflammation Modulates Clearance and drives Extra-Hepatic Distribution of Extracellular Vesicles

Extracellular vesicles (EVs) are promising vehicles for targeted therapeutic delivery, capable of encapsulating and transporting biomolecules to specific cells and tissues. Given that inflammation is central to many acute and chronic diseases, understanding EV biodistribution under inflammatory conditions is essential for therapeutic optimization. This study examines how acute systemic inflammation influences EV biodistribution, clearance, and plasma half-life, with a focus on the role of macrophages and their polarization states. Using a lipopolysaccharide (LPS)-induced inflammation model in wild-type mice and bioluminescent and fluorescent labelling of EVs, we observed that inflammation extends the plasma half-life of EVs by over 600-fold within 2 hours and 900-fold at 24 hours post-administration, leading to significant enrichment in inflamed organs, particularly the liver and spleen. Enhanced accumulation in specific tissues translated to increased targeting of immune- and epithelial cells within those organs, with notable uptake by hepatocytes in the liver. This prolonged half-life was attributed to the altered EV protein corona in inflamed tissues, which facilitates cellular association. These findings underscore the complex dynamics between EVs and immune cells under inflammatory conditions and provide critical insights for advancing EV-based therapies in chronic inflammatory diseases.

bioengineering↗

bioRxiv2025

SETD2 methyltransferase activity aids gene definition by promoting correct transcription initiation and termination

SETD2 is a methyltransferase responsible for depositing histone H3 lysine 36 trimethylation (H3K36me3). Loss of its enzymatic activity occurs in some cancers, including renal cell carcinoma (RCC). In RCC, SETD2 mutations have been linked to delayed transcription termination, but not explored in depth. Here, using nascent transcriptomics in SETD2 knockout and patient-derived cells, we reveal a dichotomy in SETD2 functions depending on the affected protein-coding gene. Majority of genes, named class I, are dependent on SETD2 function for transcription initiation, yet terminate transcription in the usual locations. In contrast, for class II genes, corresponding to 15-25% of active protein-coding genes, transcription initiation is robust in absence of SETD2 activity, however widespread transcriptional readthrough occurs. Defective termination following SETD2 loss/mutation is associated with increased cryptic transcription initiation and impaired 3' pre-mRNA cleavage. Additionally, alternative polyadenylation upon SETD2 activity loss is highly cell type specific, and unrelated to transcription readthrough. In summary, we demonstrate that methyltransferase activity of SETD2 regulates transcriptional integrity by stimulating proper initiation, preventing cryptic initiation and promoting efficient 3' end processing.

molecular biology↗

bioRxiv2025

Storage Protein-Mediated Translation Control Links Juvenile Diet to Longevity in Drosophila

Dietary restriction (DR), whether applied during adulthood or juvenile stages, extends lifespan across diverse species. However, the mechanisms by which early-life dietary interventions influence adult physiology and longevity remain poorly understood. Here, using Drosophila as a model, we demonstrate that protein restriction during the larval stage (early-life protein restriction, ePR) promotes adult lifespan by reducing storage protein levels. Stable isotope tracing reveals that dietary amino acids obtained in the larval stage are retained into adulthood, especially incorporated into ribosomal proteins. This is mediated by larval serum protein 2 (Lsp2), a major storage protein, whose expression is durably downregulated by ePR. Both dietary (ePR) and genetic (Lsp2-RNAi) reduction of the protein storage lead to decreased ribosomal protein levels and translation activity in early adulthood. Notably, these storage proteins are enriched in aromatic amino acids such as tyrosine, and larval tyrosine restriction alone is sufficient to suppress translation and promote longevity. These findings show that storage proteins mediate the effect of larval nutrition on adult longevity via controlling translation. Our study uncovers a previously unrecognised mechanism of nutritional memory that links early-life diet to life-long organismal health.

physiology↗

bioRxiv2025

Unraveling anti-inflammatory metabolic signatures of Glycyrrhiza uralensis and isoliquiritigenin through multiomics

Glycyrrhiza uralensis, known for its diverse pharmacological effects, including immunoregulation, anti-tumor, and antioxidant properties, is a widely used medicinal plant found in more than 70% of traditional herbal medicines (Kampo) in Japan. Although over 300 compounds have been discovered in G. uralensis, the molecular mechanisms underlying its bioactivity remain largely unknown due to the chemical diversity of its compounds. Here, we performed a multiomics analysis incorporating untargeted hydrophilic metabolomics, lipidomics, and phosphoproteomics to elucidate the molecular mechanisms distinguishing the effects of a single bioactive compound, isoliquiritigenin (ILG), and the extract of G. uralensis (GU). Multiomics time-course data were obtained for lipopolysaccharide (LPS)-stimulated RAW264.7 cells under four experimental conditions: control, LPS(+), LPS(+)/ILG(+), and LPS(+)/GU(+), where 182 hydrophilic metabolites, 381 lipids, and 13,211 phosphopeptides were characterized. The metabolic signatures of inflammatory macrophages, including increased levels of glycolytic intermediates, succinate, citrulline, triacylglycerols, and cholesteryl esters, were attenuated in both the GU(+) and ILG(+) groups. Using a multivariate approach based on a partial least squares algorithm with an imposed inflammation level order information, we identified upregulated phosphorylation of sirtuin 1 and 2 (SIRT1/2) along with alterations in nicotinamide adenine dinucleotide metabolism in the ILG(+) group. The inhibition of SIRT2 suppressed the anti-inflammatory effect of ILG, as indicated by a reduction in interleukin-6 (IL-6) levels. Furthermore, we discovered a substantial increase in {gamma}-aminobutyric acid (GABA) and its downstream metabolite, 4-guanidinobutyric acid, in the GU(+) group. These increases were attributed to endogenous GABA production through glutamic acid decarboxylase rather than uptake via GABA transporters. Exogenous GABA administration significantly suppressed IL-6 and IL-1{beta} expression in LPS-stimulated cells, and the simultaneous administration of GABA and ILG enhanced the anti-inflammatory effects. Consequently, this study presents an approach to elucidating the importance of traditional herbal formulations and demonstrates the utility of multiomics in uncovering that endogenous GABA production would facilitate anti-inflammatory effects with ILG in GU administration.

systems biology↗

bioRxiv2024

Surface display of proximity labeling enzymes on extracellular vesicles for surfaceome and target cell mapping

Extracellular vesicles (EV) surface proteins have important extracellular functions and determine cellular tropism; however, characterizing the EV surfaceome remains challenging with available methods. EV-mediated intercellular communication takes place primarily through interactions at the recipient cell membrane, underscoring the importance of methodological advances to map this interplay. Here, we leverage the proximity labeling enzyme APEX2 (Apurinic/Apyrimidinic Endodeoxyribonuclease 2) for high-fidelity analysis of the EV surfaceome and cellular tropism. Surface display of APEX2 on EVs is achieved through its genetic fusion with EV-sorting domains, such as CD63 and TSPAN2. Upon adding the substrates biotin-phenol and hydrogen peroxide, vesicle surface APEX2 enables biotinylation of EV integral and corona proteins as well as target cells in vitro. Further data mining of the EV surfaceome reveals potential scaffolds for the bioengineering of EVs. Altogether, we introduce a robust tool for EV surfaceome and target cell mapping and uncover novel EV-sorting domains for bioengineering.

synthetic biology↗

bioRxiv2024

Prediction of Protein Half-lives from Amino Acid Sequences by Protein Language Models

We developed a protein half-life prediction model, PLTNUM, based on a protein language model using an extensive dataset of protein sequences and protein half-lives from the NIH3T3 mouse embryo fibroblast cell line as a training set. PLTNUM achieved an accuracy of 71% on validation data and showed robust performance with an ROC of 0.73 when applied to a human cell line dataset. By incorporating Shapley Additive Explanations (SHAP) into PLTNUM, we identified key factors contributing to shorter protein half-lives, such as cysteine-containing domains and intrinsically disordered regions. Using SHAP values, PLTNUM can also predict potential degron sequences that shorten protein half-lives. This model provides a platform for elucidating the sequence dependency of protein half-lives, while the uncertainty in predictions underscores the importance of biological context in influencing protein half-lives.

bioinformatics↗

bioRxiv2024

Proteomic analysis to classify extracellular vesicles and plasmodesmata in Arabidopsis cell culture supernatants

The plant apoplast contains diverse proteins. In this study, we analyzed the extracellular vesicle proteome using cell culture supernatants. Unexpectedly, many plasmodesmata proteins were identified in the extracellular vesicle fraction. The comparison between the cell culture EV proteome and the plasmodesmata proteome revealed that EV and plasmodesmata proteins were indistinguishable. Highly sensitive imaging analyses showed that PDLP3-GFP, a representative plasmodesmata marker, was localized to plasmodesmata, but it was also present as small granules in apoplast regions. Next, we attempted to distinguish EV proteins from plasmodesmata proteins. The step-wise density gradient ultracentrifugation and clustering analysis separated EV protein clusters (represented by tetraspanins and membrane trafficking proteins) from plasmodesmata clusters (represented by PDLPs and PDCBs). These results provide the basis for future explorations of plant plasmodesmata and EVs.

plant biology↗

bioRxiv2024

One-step N-terminomics based on isolation of protein N-terminal peptides from LysargiNase digests by tip-based strong cation exchange chromatography

We have developed a one-step isolation method for protein N-terminal peptides from LysargiNase digests by pipette tip-based strong cation exchange (SCX) chromatography. This CHAMP-N (CHromatographic AMplification of Protein N-terminal peptides) method using disposable and parallel-processable SCX tips instead of conventional HPLC SCX columns facilitates simple, sensitive and high-throughput N-terminomic profiling without sacrificing the high identification numbers and selectivity achieved by the HPLC-based method. By applying the CHAMP-N method to HEK293T cells, we identified novel cleavage sites for signal and transit peptides, and non-canonical translation initiation sites. Finally, for proteome-wide terminomics, we present a simple and comprehensive N-and C-terminomics platform employing three different tip-based approaches, including CHAMP-N, in which protease digestion and one-step isolation by tip LC are commonly used to achieve complementary terminome coverages.

biochemistry↗

bioRxiv2023

Mapping adipocyte interactome networks by HaloTag enrichment mass-spectrometry

Mapping protein interaction complexes in their natural state in vivo represents the holy grail of protein network analysis. Detection of protein interaction stoichiometry has been an important technical challenge, as few studies have focused this, yet this may be solved by artificial intelligence and proteomics. Here, we describe the development of HaloMS, a high-throughput HaloTag-based affinity purification-mass spectrometry assay for protein interaction discovery. The approach enables the rapid capture of newly expressed proteins, eliminating tedious conventional one-by-one assay. As a proof-of-principle, we used HaloMS to evaluate protein complex interactions of 17 regulatory proteins in human adipocytes. The adipocyte interactome network was validated using an in vitro pull-down assay and artificial intelligence-based prediction tools. The application of HaloMS to probe adipocyte differentiation facilitated the identification of previously unknown transcription factor-protein complexes, revealing proteome-wide human adipocyte transcription factor networks, and shedding light on how different pathways are integrated.

biochemistry↗

bioRxiv2023

UGGT1/2-mediated reglucosylation of N-glycan competes with ER-associated degradation of unstable and misfolded glycoproteins

How the fate (folding versus degradation) of glycoproteins is determined in the endoplasmic reticulum (ER) is an intriguing question. Monoglucosylated glycoproteins are recognized by lectin chaperones to facilitate their folding, whereas glycoproteins exposing well-trimmed mannoses are subjected to glycoprotein ER-associated degradation (gpERAD); we have elucidated how mannoses are sequentially trimmed by EDEM family members (George et al., 2020, 2021 eLife). Although reglucosylation by UGGT was previously reported to have no effect on substrate degradation, here we directly tested this notion using cells with genetically disrupted UGGT1/2. Strikingly, the results showed that UGGT1 delayed the degradation of misfolded substrates and unstable glycoproteins including ATF6. An experiment with a point mutant of UGGT1 indicated that the glucosylation activity of UGGT1 was required for the inhibition of early glycoprotein degradation. These and overexpression-based competition experiments suggested that the fate of glycoproteins is determined by a tug-of-war between structure formation by UGGT1 and degradation by EDEMs. We further demonstrated the physiological importance of UGGT1, since ATF6 cannot function properly without UGGT1. Thus, our work strongly suggests that UGGT1 is a central factor in ER protein quality control via regulation of both glycoprotein folding and degradation.

cell biology↗

bioRxiv2023

Pathogenic mutations of human phosphorylation sites affect protein-protein interactions

Despite their lack of a defined 3D structure, intrinsically disordered regions (IDRs) of proteins play important biological roles. Many IDRs contain short linear motifs (SLiMs) that mediate protein-protein interactions (PPIs), which can be regulated by post-translational modifications like phosphorylation. 20% of pathogenic missense mutations are found in IDRs, and understanding how such mutations affect PPIs is essential for unraveling disease mechanisms. Here, we employed peptide-based interaction proteomics to investigate 36 disease-causing mutations affecting phosphorylation sites. Our results unveiled significant differences in interactomes between phosphorylated and non-phosphorylated peptides, often due to disrupted phosphorylation-dependent SLiMs. We focused on a mutation of a serine phosphorylation site in the transcription factor GATAD1, which causes dilated cardiomyopathy. We found that this phosphorylation site mediates interaction with 14-3-3 family proteins. Follow-up experiments revealed the structural basis of this interaction and suggest that 14-3-3 binding affects GATAD1 nucleocytoplasmic transport by masking a nuclear localisation signal. Our results demonstrate that pathogenic mutations of human phosphorylation sites can significantly impact protein-protein interactions, offering fresh insights into potential molecular mechanisms underlying pathogenesis.

systems biology↗

bioRxiv2023

One thousand samples per day capillary-flow LC/MS/MS for high-speed, high-sensitivity and in-depth proteomics

We developed a capillary-flow LC/MS/MS system with ultrahigh speed, enabling a throughput of 1,000 samples per day while maintaining high sensitivity and depth of analysis. In targeted LC/MS mode, 36 endogenous phosphopeptides in HeLa cells, including EphA2- derived phosphopeptide isomers, were successfully quantified with high selectivity and linearity by combining ion mobility separation. When 500 ng of HeLa cell digest was measured 100 times repeatedly in data-dependent acquisition mode, the coefficient of variation of retention time, peak intensity and number of identified peptides were on average 3.4%, 19.8%, and 6.0%, respectively. In data-independent acquisition mode, this system achieved the identification and quantification of 3,139 protein groups from a 100 ng HeLa cell digest and 2,145 protein groups from a sample of only 10 ng. The coefficient of variation of protein commonly quantified in the triplicate analysis ranged from 12 to 24% for HeLa digest samples ranging from 10 to 1000 ng. Finally, we applied this high-speed system to the spatial proteomics of the mouse brain, and succeeded in capturing the proteome distribution along a 96-sectioned brain structure in 135 minutes. This is the first LC/MS/MS system to achieve both more than 500 samples per day and more than 3000 identified protein groups ID with less than 100 ng human cultured cells simultaneously.

systems biology↗