Takashi Kodama - Academia.edu (original) (raw)

Papers by Takashi Kodama

Cell reports, Jan 3, 2017

γ-secretase inhibitors (GSI) are drugs developed to decrease amyloid-β peptide (Aβ) production by... more γ-secretase inhibitors (GSI) are drugs developed to decrease amyloid-β peptide (Aβ) production by inhibiting intramembranous cleavage of β-amyloid protein precursor (βAPP). However, a large phase 3 trial of semagacestat, a potential non-transition state analog (non-TSA) GSI, in patients with Alzheimer's disease (AD) was terminated due to unexpected aggravation of cognitive deficits and side effects. Here, we show that some semagacestat effects are clearly different from a phenotype caused by a loss of function of presenilins, core proteins in the γ-secretase complex. Semagacestat increases intracellular byproduct peptides, produced along with Aβ through serial γ-cleavage of βAPP, as well as intracellular long Aβ species, in cell-based and in vivo studies of AD model mice. Other potential non-TSA GSIs, but not L685,458, a TSA GSI, have similar effects. Furthermore, semagacestat inhibits release of de novo intramembranous γ-byproducts to the soluble space. Thus, semagacestat is a ...

Proceedings of the National Academy of Sciences of the United States of America, Jan 18, 2014

Alzheimer's disease (AD) is characterized by the accumulation of amyloid-β (Aβ). The genes th... more Alzheimer's disease (AD) is characterized by the accumulation of amyloid-β (Aβ). The genes that govern this process, however, have remained elusive. To this end, we combined distinct mouse strains with transcriptomics to directly identify disease-relevant genes. We show that AD model mice (APP-Tg) with DBA/2 genetic backgrounds have significantly lower levels of Aβ accumulation compared with SJL and C57BL/6 mice. We then applied brain transcriptomics to reveal the genes in DBA/2 that suppress Aβ accumulation. To avoid detecting secondarily affected genes by Aβ, we used non-Tg mice in the absence of Aβ pathology and selected candidate genes differently expressed in DBA/2 mice. Additional transcriptome analysis of APP-Tg mice with mixed genetic backgrounds revealed kinesin light chain-1 (Klc1) as an Aβ modifier, indicating a role for intracellular trafficking in Aβ accumulation. Aβ levels correlated with the expression levels of Klc1 splice variant E and the genotype of Klc1 in th...

EMBO Molecular Medicine, 2009

Surrogate markers for the Alzheimer disease (AD)-associated 42-amino acid form of amyloid-b (Ab42... more Surrogate markers for the Alzheimer disease (AD)-associated 42-amino acid form of amyloid-b (Ab42) have been sought because they may aid in the diagnosis of AD and for clarification of disease pathogenesis. Here, we demonstrate that human cerebrospinal fluid (CSF) contains three APLP1-derived Ab-like peptides (APL1b) that are generated by band g-cleavages at a concentration of $4.5 nM. These novel peptides, APL1b25, APL1b27 and APL1b28, were not deposited in AD brains. Interestingly, most g-secretase modulators (GSMs) and familial ADassociated presenilin1 mutants that up-regulate the relative production of Ab42 cause a parallel increase in the production of APL1b28 in cultured cells. Moreover, in CSF from patients with pathological mutations in presenilin1 gene, the relative APL1b28 levels are higher than in non-AD controls, while the relative Ab42 levels are unchanged or lower. Most strikingly, the relative APL1b28 levels are higher in CSF from sporadic AD patients (regardless of whether they are at mild cognitive impairment or AD stage), than those of non-AD controls. Based on these results, we propose the relative level of APL1b28 in the CSF as a candidate surrogate marker for the relative level of Ab42 production in the brain.

Cell Death & Differentiation, 2000

The SMN gene is implicated in spinal muscular atrophy (SMA), and its product has been shown to in... more The SMN gene is implicated in spinal muscular atrophy (SMA), and its product has been shown to interact with Bcl-2 protein to enhance its anti-apoptotic activity. In this study, we determined the regions that were essential for the interaction of Bcl-2 and SMN by co-immunoprecipitation of deletion mutants. Bcl-2 lacking its amino-terminal 20 amino acid residues or its carboxyl-terminal membrane-anchoring domain showed no or greatly reduced binding with SMN, respectively. However, Bcl-2 lacking other regions could still bind to SMN. Because Bcl-2 lacking the membrane-anchoring domain could bind to SMN in a yeast two-hybrid system, the amino-terminal region of Bcl-2 seems to be the most important domain for binding with SMN. A fragment of SMN encoded by exon 6 could bind to Bcl-2, but SMN lacking this region could not. From these results, we concluded that Bcl-2 and SMN proteins bound with each other at the amino-terminal region near the BH4 domain of Bcl-2 and the region encoded by exon 6 of SMN, both regions known to be important for their function. Cell Death and Differentiation (2000) 7, 374 ± 383.

Genes & Development, 1999

Induction of heat shock proteins in Escherichia coli is primarily caused by increased cellular le... more Induction of heat shock proteins in Escherichia coli is primarily caused by increased cellular levels of the heat shock-factor 32 encoded by the rpoH gene. Increased 32 levels result from both enhanced synthesis and stabilization. Previous work indicated that 32 synthesis is induced at the translational level and is mediated by the mRNA secondary structure formed within the 5-coding sequence of rpoH, including the translation initiation region. To understand the mechanism of heat induction of 32 synthesis further, we analyzed expression of rpoH-lacZ gene fusions with altered stability of mRNA structure before and after heat shock. A clear correlation was found between the stability and expression or the extent of heat induction. Temperature-melting profiles of mRNAs with or without mutations correlated well with the expression patterns of fusion genes carrying the corresponding mutations in vivo. Furthermore, temperature dependence of mRNA-30S ribosome-tRNA f Met complex formation with wild-type or mutant mRNAs in vitro agreed well with that of the expression of gene fusions in vivo. Our results support a novel mechanism in which partial melting of mRNA secondary structure at high temperature enhances ribosome entry and translational initiation without involvement of other cellular components, that is, intrinsic mRNA stability controls synthesis of a transcriptional regulator.

Seibutsu Butsuri, 2006

We have develeped the full-autematic classifieatlen system of PDB and a scries of programs that c... more We have develeped the full-autematic classifieatlen system of PDB and a scries of programs that can generute empirical rules of ligu]d-pretein interaction from the classified complex stmctures.

Nucleic Acids Research, 2001

Fluorescence resonance energy transfer (FRET) experiments have been performed to elucidate the st... more Fluorescence resonance energy transfer (FRET) experiments have been performed to elucidate the structural features of oligonucleotide duplexes containing the pyrimidine(6-4)pyrimidone photoproduct, which is one of the major DNA lesions formed at dipyrimidine sites by UV light. Synthetic 32mer duplexes with and without the (6-4) photoproduct were prepared and fluorescein and tetramethylrhodamine were attached, as a donor and an acceptor, respectively, to the aminohexyl linker at the C5 position of thymine in each strand. Steadystate and time-resolved analyses revealed that both the FRET efficiency and the fluorescence lifetime of the duplex containing the (6-4) photoproduct were almost identical to those of the undamaged duplex, while marked differences were observed for a cisplatin-modified duplex, as a model of kinked DNA. Lifetime measurements of a series of duplexes containing the (6-4) photoproduct, in which the fluorescein position was changed systematically, revealed a small unwinding at the damage site, but did not suggest a kinked structure. These results indicate that formation of the (6-4) photoproduct induces only a small change in the DNA structure, in contrast to the large kink at the (6-4) photoproduct site reported in an NMR study.

Nucleic acids symposium series (2004), 2004

We have found that distamycin A can bind to DNA duplexes containing the (6-4) photoproduct, one o... more We have found that distamycin A can bind to DNA duplexes containing the (6-4) photoproduct, one of the major UV lesions in DNA, in spite of the changes caused by photoproduct formation in the chemical structure of the base moiety and the local tertiary structure of the duplex. Distamycin binding was analyzed in detail using 14-mer duplexes. Curve fitting of the CD titration data and induced CD difference Spectra revealed that the binding stoichiometry changed from 1:1 to 2:1 with the photoproduct formation. Melting curves of the drug-DNA complexes also supported this stoichiometry.

Proteins, 2005

The peroxisome proliferator-activated receptor gamma (PPARgamma) is important to adipocyte differ... more The peroxisome proliferator-activated receptor gamma (PPARgamma) is important to adipocyte differentiation and glucose homeostasis, and mutations in the gene have been observed in type 2 diabetes mellitus. The mutated residues, V290 and P467, bind to neither ligands nor a coactivator peptide in the reported crystal structures of the PPARgamma ligand binding domain. To understand the mechanism of type 2 diabetes mellitus caused by germline mutations in the PPARgamma ligand-binding domain, theoretical models of the PPARgamma-ligand-coactivator complex were built at an atomic resolution. In the models, the secondary coactivator peptide was docked next to the conventional coactivator peptide, which both contain the LXXLL motif. The secondary interface in PPARgamma for the secondary coactivator peptide has not been demonstrated by experiments. Binding energy calculations of the complex, considering the solvent effect, revealed that the secondary coactivator peptide, derived from nuclear ...

Journal of Biological Chemistry, 2005

Peroxisome proliferator-activated receptor ␥ (PPAR␥) functions in various biological processes, i... more Peroxisome proliferator-activated receptor ␥ (PPAR␥) functions in various biological processes, including macrophage and adipocyte differentiation. Several natural lipid metabolites have been shown to activate PPAR␥. Here, we report that some PPAR␥ ligands, including 15-deoxy-⌬ 12,14-prostaglandin J 2 , covalently bind to a cysteine residue in the PPAR␥ ligand binding pocket through a Michael addition reaction by an ␣,␤unsaturated ketone. Using rhodamine-maleimide as well as mass spectroscopy, we showed that the binding of these ligands is covalent and irreversible. Consistently, mutation at the cysteine residue abolished abilities of these ligands to activate PPAR␥, but not of BRL49653, a non-covalent synthetic agonist, indicating that covalent binding of the ␣,␤-unsaturated ketone in the natural ligands was required for their transcriptional activities. Screening of lipid metabolites containing the ␣,␤-unsaturated ketone revealed that several other oxidized metabolites of hydroxyeicosatetraenoic acid, hydroxyeicosadecaenoic acid, and prostaglandins can also function as novel covalent ligands for PPAR␥. We propose that PPAR␥ senses oxidation of fatty acids by recognizing such an ␣,␤-unsaturated ketone as a common moiety.

Journal of Biological Chemistry, 2004

Biochemical Journal, 2006

PPARγ (peroxisome proliferator-activated receptor γ) is a nuclear receptor that is activated by n... more PPARγ (peroxisome proliferator-activated receptor γ) is a nuclear receptor that is activated by natural lipid metabolites, including 15d-PGJ2 (15-deoxy-Δ12,14-prostaglandin J2). We previously reported that several oxidized lipid metabolites covalently bind to PPARγ through a Michael-addition to activate transcription. To separate the ligand-entering (dock) and covalent-binding (lock) steps in PPARγ activation, we investigated the binding kinetics of 15d-PGJ2 to the PPARγ LBD (ligand-binding domain) by stopped-flow spectroscopy. We analysed the spectral changes of 15d-PGJ2 by multi-wavelength global fitting based on a two-step chemical reaction model, in which an intermediate state represents the 15d-PGJ2–PPARγ complex without covalent binding. The extracted spectrum of the intermediate state in wild-type PPARγ was quite similar to the observed spectrum of 15d-PGJ2 in the C285S mutant, which cannot be activated by 15d-PGJ2, indicating that the complex remains in the inactive, interme...