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Kengo Kinoshita

Publications and source records attributed to Kengo Kinoshita.

12 recordsLinked to original sources
PubMed2026

Seafood and polyunsaturated fatty acid intake and age-related hearing loss: a cross-sectional study conducted in Japan.

BACKGROUND: Age-related hearing loss (ARHL) is a common condition associated with dementia, social isolation, and reduced quality of life. N-3 polyunsaturated fatty acids (N-3 PUFAs), mainly derived from seafood, have been hypothesized to protect against ARHL through anti-inflammatory and antioxidant effects. However, evidence remains inconsistent. This cross-sectional study examined the association of seafood and dietary fatty acid intakes with ARHL in a Japanese population with high seafood consumption. METHODS: A total of 13,908 adults aged 50-79 years from the Tohoku Medical Megabank Project Cohort Study were included. Hearing thresholds were measured by pure-tone audiometry at 500, 1,000, 2,000, and 4,000 Hz. Dietary intake was assessed using a validated food frequency questionnaire. Seafood, N-3 PUFA, and saturated fatty acid (SFA) intakes were categorized into quartiles. Multivariable linear regression was used to estimate adjusted mean differences in hearing thresholds. RESULTS: In men, higher SFA intake was significantly associated with lower hearing thresholds at 1,000 Hz (Q4 vs. Q1: β = -2.23 dB HL, 95% CI: -3.437 to -1.023) and for pure-tone average (β = -1.704 dB HL; 95% CI, -2.872 to -0.536). Seafood and N-3 PUFA intakes were not significantly associated with hearing thresholds. In women, no significant associations were observed. CONCLUSION: In this population with high seafood consumption, seafood and N-3 PUFA intakes were not associated with hearing thresholds. Low SFA intake may be associated with higher hearing thresholds in Japanese men, suggesting that the relationship between dietary fatty acids and ARHL may be complex and may differ by sex.

Age-related hearing loss↗
PubMed2026

BCL11B enhancer hijacking by t(14;16)(q32;q24) translocation defines a novel high-risk subtype of T-ALL.

The molecular classification of T-cell acute lymphoblastic leukemia (T-ALL) remains incomplete, limiting risk stratification and the development of targeted therapies. Enhancer hijacking is a critical oncogenic mechanism that deregulates proto-oncogenes by repositioning cisregulatory regions via structural variants. Here, we performed an integrated analysis of pediatric and adult T-ALL and mixed-phenotype acute leukemias (MPALs), using whole-genome and whole-transcriptome sequencing. This analysis identified a group of 14 patients with predominantly T-lineage neoplasms driven by a t(14;16)(q32;q24) translocation, harboring universal GATA3 mutations and CDKN2A/B deletions. Mechanistically, this translocation repositions the ThymoD locus downstream of BCL11B, causing monoallelic, ectopic overexpression of FENDRR and mesenchymal transcription factor genes FOXF1 and FOXC2 and activating epithelial-mesenchymal transition transcription signatures. Immunophenotypic and single-cell RNA sequencing analyses revealed marked lineage ambiguity with myeloid and B-cell differentiation potentials specific to this subtype. Furthermore, functional analyses in CD34+ cord blood cells demonstrated that FOXF1 overexpression promotes myeloid differentiation while suppressing T-cell differentiation, serving as a key factor for lineage specification. Clinically, this subtype was detected in 0.15% to 4.0% of T-ALL/MPAL cases depending on the cohort, showing a median age of 15 years and enrichment in adolescents and young adults. Importantly, patients with t(14;16)(q32;q24) have an extremely poor prognosis, showing a trend toward worse outcomes than high-risk groups such as KMT2A-rearranged early T-cell progenitor-like, SPI1-rearranged, and LMO2 γδ-like T-ALLs. The unique molecular landscape and poor prognosis of patients with the t(14;16)(q32;q24) translocation underscore the need for the development of novel subtype-specific therapeutic approaches.

Humans↗
PubMed2025

JG2: an updated version of the Japanese population-specific reference genome.

Here we present the construction of JG2, an updated population-specific reference genome for the Japanese population. Utilizing data from three individuals previously used in the construction of JG1, several methodologies were employed to enhance genomic coverage and assembly quality. Hi-C sequencing technology facilitated phase-aware assembly, generating two haploid assemblies per individual and enabling improved representation of genetic variation. A meta-assembly strategy and a majority decision approach further refined assembly quality by combining the best sequences from multiple assemblies and minimizing the inclusion of rare variants. The resulting JG2 genome comprises chromosome-level sequences, mitochondrial chromosomes and unplaced scaffolds, offering more comprehensive coverage of the Japanese genome. Comparative analyses with other reference genomes demonstrated the accuracy and representativeness of JG2, highlighting its utility for genetic research involving the Japanese population. Overall, by adopting the phased assembly technique, JG2 represents a substantial advancement over the collapsed assembly-based JG1, with improvements including a greater number of identified variants (3,115,695 variants, of which 298,644 had an allele frequency (AF) of 1.0 in the 3.5KJPNv2 AF panel) and a higher N50 value (152,668,378 bp). These enhancements provide researchers with a more precise and comprehensive resource for understanding the genetic landscape of the Japanese population. The sequences and annotations are available on the jMorp website ( https://jmorp.megabank.tohoku.ac.jp/ ).

Journal Article↗
PubMed2003

Prediction of catalytic residues in enzymes based on known tertiary structure, stability profile, and sequence conservation.

The catalytic or functionally important residues of a protein are known to exist in evolutionarily constrained regions. However, the patterns of residue conservation alone are sometimes not very informative, depending on the homologous sequences available for a given query protein. Here, we present an integrated method to locate the catalytic residues in an enzyme from its sequence and structure. Mutations of functional residues usually decrease the activity, but concurrently often increase stability. Also, catalytic residues tend to occupy partially buried sites in holes or clefts on the molecular surface. After confirming these general tendencies by carrying out statistical analyses on 49 representative enzymes, these data together with amino acid conservation were evaluated. This novel method exhibited better sensitivity in the prediction accuracy than traditional methods that consider only the residue conservation. We applied it to some so-called "hypothetical" proteins, with known structures but undefined functions. The relationships among the catalytic, conserved, and destabilizing residues in enzymatic proteins are discussed.

Amino Acid Sequence↗
PubMed2003

Ring and zipper formation is the key to understanding the structural variety in all-beta proteins.

A novel structural classification of beta proteins is presented from the viewpoint of the ring-shaped structure and the zipper-like contact pattern, based on the fact that 92% and 60% of beta proteins have the ring topology and the zippered contact pattern, respectively. We discuss the implication of the unexpectedly high preference for the ring and zippered structures in connection with the folding process of beta proteins.

Models, Molecular↗
PubMed2003

Protein informatics towards function identification.

The study of structural genomics and structural proteomics has determined the tertiary structures of many hypothetical proteins, whose molecular functions could not be understood using conventional methods. In order to infer the geometrical location of the functional site, the biochemical function and the biological function of the hypothetical protein, much effort has been made in protein informatics. The importance of heterogeneous databases and various descriptors of amino acid sequences, tertiary structures and pathways on the proteome scale has been emphasised.

Binding Sites↗
PubMed2003

Crystal structure of the conserved protein TT1542 from Thermus thermophilus HB8.

The TT1542 protein from Thermus thermophilus HB8 is annotated as a conserved hypothetical protein, and belongs to the DUF158 family in the Pfam database. A BLAST search revealed that homologs of TT1542 are present in a wide range of organisms. The TT1542 homologs in eukaryotes, PIG-L in mammals, and GPI12 in yeast and protozoa, have N-acetylglucosaminylphosphatidylinositol (GlcNAc-PI) de-N-acetylase activity. Although most of the homologs in prokaryotes are hypothetical and have no known function, Rv1082 and Rv1170 from Mycobacterium tuberculosis are enzymes involved in the mycothiol detoxification pathway. Here we report the crystal structure of the TT1542 protein at 2.0 A resolution, which represents the first structure for this superfamily of proteins. The structure of the TT1542 monomer consists of a twisted beta-sheet composed of six parallel beta-strands and one antiparallel beta-strand (with the strand order 3-2-1-4-5-7-6) sandwiched between six alpha-helices. The N-terminal five beta-strands and four alpha-helices form an incomplete Rossmann fold-like structure. The structure shares some similarity to the sugar-processing enzymes with Rossmann fold-like domains, especially those of the GPGTF (glycogen phosphorylase/glycosyl transferase) superfamily, and also to the NAD(P)-binding Rossmann fold domains. TT1542 is a homohexamer in the crystal and in solution, the six monomers forming a cylindrical structure. Putative active sites are suggested by the structure and conserved amino acid residues.

Amino Acid Sequence↗
PubMed2003

Identification of protein biochemical functions by similarity search using the molecular surface database eF-site.

The identification of protein biochemical functions based on their three-dimensional structures is strongly required in the post-genome-sequencing era. We have developed a new method to identify and predict protein biochemical functions using the similarity information of molecular surface geometries and electrostatic potentials on the surfaces. Our prediction system consists of a similarity search method based on a clique search algorithm and the molecular surface database eF-site (electrostatic surface of functional-site in proteins). Using this system, functional sites similar to those of phosphoenoylpyruvate carboxy kinase were detected in several mononucleotide-binding proteins, which have different folds. We also applied our method to a hypothetical protein, MJ0226 from Methanococcus jannaschii, and detected the mononucleotide binding site from the similarity to other proteins having different folds.

Algorithms↗
PubMed2002

Intramolecular interaction of SUR2 subtypes for intracellular ADP-Induced differential control of K(ATP) channels.

ATP-sensitive K+ (K(ATP)) channels are composed of sulfonylurea receptors (SURs) and inwardly rectifying Kir6.2-channels. The C-terminal 42 amino acid residues (C42) of SURs are responsible for ADP-induced differential activation of K(ATP) channels in SUR-subtypes. By examining ADP-effect on K(ATP) channels containing various chimeras of SUR2A and SUR2B, we identified a segment of 7 residues at central portion of C42 critical for this phenomenon. A 3-D structure model of the region containing the second nucleotide-binding domain (NBD2) of SUR and C42 was developed based on the structure of HisP, a nucleotide-binding protein forming the bacterial Histidine transporter complex. In the model, the polar and charged residues in the critical segment located within a distance that allows their electrostatic interaction with Arg1344 at the Walker-A loop of NBD2. Therefore, the interaction might be involved in the control of ADP-induced differential activation of SUR2-subtype K(ATP) channels.

ATP-Binding Cassette Transporters↗
PubMed2002

Identification of protein functions from a molecular surface database, eF-site.

A bioinformatics method was developed to identify the protein surface around the functional site and to estimate the biochemical function, using a newly constructed molecular surface database named the eF-site (electrostatic surface of Functional site. Molecular surfaces of protein molecules were computed based on the atom coordinates, and the eF-site database was prepared by adding the physical properties on the constructed molecular surfaces. The electrostatic potential on each molecular surface was individually calculated solving the Poisson-Boltzmann equation numerically for the precise continuum model, and the hydrophobicity information of each residue was also included. The eF-site database is accessed by the internet (http://pi.protein.osaka-u.ac.jp/eF-site/). We have prepared four different databases, eF-site/antibody, eF-site/prosite, eF-site/P-site, and eF-site/ActiveSite, corresponding to the antigen binding sites of antibodies with the same orientations, the molecular surfaces for the individual motifs in PROSITE database, the phosphate binding sites, and the active site surfaces for the representatives of the individual protein family, respectively. An algorithm using the clique detection method as an applied graph theory was developed to search of the eF-site database, so as to recognize and discriminate the characteristic molecular surfaces of the proteins. The method identifies the active site having the similar function to those of the known proteins.

Antibodies↗
PubMed2002

Key amino acid residues required for aryl migration catalysed by the cytochrome P450 2-hydroxyisoflavanone synthase.

Isoflavonoids are distributed predominantly in leguminous plants, and play pivotal roles in the interaction of host plants with biological environments. Isoflavones in the diet also have beneficial effects on human health as phytoestrogens. The isoflavonoid skeleton is constructed by the CYP93C subfamily of cytochrome P450s in plant cells. The reaction consists of hydroxylation of the flavanone molecule at C-2 and an intramolecular 1,2-aryl migration from C-2 to C-3 to yield 2-hydroxyisoflavanone. In this study, with the aid of alignment of amino acid sequences of CYP93 family P450s and a computer-generated putative stereo structure of the protein, candidates for key amino acid residues in CYP93C2 responsible for the unique aryl migration in 2-hydroxyisoflavanone synthase reaction were identified. Microsomes of recombinant yeast cells expressing mutant proteins of CYP93C2 were prepared, and their catalytic activities tested. The reaction with the mutant in which Ser 310 in the centre of the I-helix was converted to Thr yielded increased formation of 3-hydroxyflavanone, a by-product of the 2-hydroxyisoflavanone synthase reaction, in addition to the major isoflavonoid product. More dramatically, the mutant in which Lys 375 in the end of beta-sheet 1-4 was replaced with Thr produced only 3-hydroxyflavanone and did not yield the isoflavonoid any longer. The roles of these amino acid residues in the catalysis and evolution of isoflavonoid biosynthesis are discussed.

Amino Acid Sequence↗