Tsutomu Mori

A new D-stereospecific amino acid amidase from Ochrobactrum anthropi.

A new D-stereospecific amino acid amidase has been partially purified from Ochrobactrum anthropi SCRC SV3, which had been isolated and selected from soil. The Mr of the enzyme was estimated to be about 38,000, and its isoelectric point was 5.3. The enzyme catalyzes the stereospecific hydrolysis of D-amino acid amide to yield D-amino acid and ammonia. The major substrates included D-phenylalanine amide, D-tyrosine amide, D-tryptophan amide, D-leucine amide, and D-alanine amide.

NIRF, a novel RING finger protein, is involved in cell-cycle regulation

Through database mining, we found a novel PEST-containing nuclear protein (PCNP). To characterize PCNP, we carried out yeast two-hybrid screening for PCNP-interacting factors. A novel Np95/ICBP90-like RING finger protein (NIRF), which possessed a ubiquitin-like domain, a PHD finger, a YDG/SRA domain and a RING finger, was identified. Interaction between PCNP and NIRF was clarified by mammalian two-hybrid system, GST pull-down assay, and nuclear co-localization. RT-PCR showed that NIRF expression is high in proliferating phase but significantly low in G0/G1 phase in normal TIG-7 and WI-38 cells, while consistently high in tumoral HT-1080 and HepG2 cells, suggesting that NIRF is involved in cell-cycle regulation. The NIRF gene resides in 9p23-24.1 that is altered in numerous types of tumors at the top of frequency. Furthermore, the NIRF gene is just within small amplicons in some tumors, suggesting that PCNP and NIRF might be involved in some aspects of tumorigenesis.

NIRF is a ubiquitin ligase that is capable of ubiquitinating PCNP, a PEST-containing nuclear protein.

We previously reported the association of a novel Np95/ICBP90‐like RING finger protein (NIRF) with a novel PEST‐containing nuclear protein (PCNP). NIRF is a nuclear protein with a ubiquitin‐like domain, a PHD finger, a YDG/SRA domain, Rb‐binding motifs and a RING finger. In this study, we showed that NIRF has auto‐ubiquitination activity, the hallmark of a ubiquitin ligase. PCNP was readily ubiquitinated in 293 and COS‐7 cells, and NIRF ubiquitinated PCNP in vitro as well as in vivo. Considering that NIRF is implicated in cell cycle regulation, these findings suggest that NIRF and PCNP are a ubiquitin ligase and its substrate, respectively, and may constitute a novel signaling pathway with some relation to cell proliferation.

NIRF/UHRF2 occupies a central position in the cell cycle network and allows coupling with the epigenetic landscape

As predicted by systems biology, a paradigm shift will emerge through the integration of information about different layers of cellular processes. The cell cycle network is at the heart of the cellular computing system, and orchestrates versatile cellular functions. The NIRF/UHRF2 ubiquitin ligase is an “intermodular hub” that occupies a central position in the network, and facilitates coordination among the cell cycle machinery, the ubiquitin–proteasome system, and the epigenetic system. NIRF interacts with cyclins, CDKs, p53, pRB, PCNA, HDAC1, DNMTs, G9a, methylated histone H3 lysine 9, and methylated DNA. NIRF ubiquitinates cyclins D1 and E1, and induces G1 arrest. The NIRF gene is frequently lost in tumors and is a candidate tumor suppressor, while its paralog, the UHRF1 gene, is hardly altered. Thus, investigations of NIRF are essential to understand the entire biological systems. Through integration of the enormous information flows, NIRF may contribute to the coupling between the cell cycle network and the epigenetic landscape. We propose the new paradigm that NIRF produces the extreme diversity in the network wiring that helps the diversity of Waddingtons canals.

Immunohistochemical analysis‐based proteomic subclassification of newly diagnosed glioblastomas

Recent gene expression and copy number profilings of glioblastoma multiforme (GBM) by The Cancer Genome Atlas (TCGA) Research Network suggest the existence of distinct subtypes of this tumor. However, these approaches might not be easily applicable in routine clinical practice. In the current study, we aimed to establish a proteomics‐based subclassification of GBM by integrating their genomic and epigenomic profiles. We subclassified 79 newly diagnosed GBM based on expression patterns determined by comprehensive immunohistochemical observation in combination with their DNA copy number and DNA methylation patterns. The clinical relevance of our classification was independently validated in TCGA datasets. Consensus clustering identified the four distinct GBM subtypes: Oligodendrocyte Precursor (OPC) type, Differentiated Oligodendrocyte (DOC) type, Astrocytic Mesenchymal (AsMes) type and Mixed type. The OPC type was characterized by highly positive scores of Olig2, PDGFRA, p16, p53 and synaptophysin. In contrast, the AsMes type was strongly associated with strong expressions of nestin, CD44 and podoplanin, with a high glial fibrillary acidic protein score. The median overall survival of OPC‐type patients was significantly longer than that of the AsMes‐type patients (19.9 vs 12.8 months). This finding was in agreement with the Oncomine analysis of TCGA datasets, which revealed that PDGFRA and Olig2 were favorable prognostic factors and podoplanin and CD44 were associated with a poor clinical outcome. This is the first study to establish a subclassification of GBM on the basis of immunohistochemical analysis. Our study will shed light on personalized therapies that might be feasible in daily neuropathological practice. (Cancer Sci, doi: 10.1111/j.1349‐7006.2012.02377.x, 2012)

Autoantibodies of sera from patients with primary biliary cirrhosis recognize the α subunit of the decarboxylase component of human branched-chain 2-oxo acid dehydrogenase complex

BACKGROUND/AIMS The major antigens for anti-mitochondrial autoantibodies in primary biliary cirrhosis (PBC) are the lipoyl-containing components of 2-oxo acid dehydrogenase complexes. Autoantibodies against the E1alpha subunit of the pyruvate dehydrogenase complex (PDH) also have been found, but those against the E1alpha subunit of branched-chain 2-oxo acid dehydrogenase complex (BCKADH) have not been detected. We investigated the occurrence of BCKADH-E1alpha-specific autoantibodies by employing the purified human antigen. METHODS The reactivities of PBC sera against purified antigens were assessed by ELISA and by immunoblotting analysis. The specificity of immunoreactivity was confirmed by absorption tests and affinity-purified antibodies. RESULTS Fourteen out of 27 PBC sera reacted with BCKADH-E1alpha, and these same sera also reacted with BCKADH-E2. No PBC sera reacted with BCKADH-E1beta. The reactivity of PBC sera with BCKADH-E1alpha was removed only when the sera were pre-absorbed with this antigen. However, reactivities to BCKADH-E2 and PDH-E1alpha were retained. Affinity-purified antibodies to BCKADH-E1alpha reacted with BCKADH-E1alpha, but not PDH-E1alpha. Thus, it was confirmed that anti-BCKADH-Elalpha did not cross-react with either BCKADH-E2 or PDH-E1alpha. CONCLUSIONS BCKADH-E1alpha-specific autoantibodies were found in the sera of PBC patients. The antibodies seem to occur subsequent to the anti-BCKADH-E2 antibody production, supporting the concept of intermolecular determinant spreading.

Regulation by induction of branched-chain 2-oxo acid dehydrogenase complex in clofibrate-fed rat liver

The activity of branched-chain 2-oxo acid dehydrogenase complex increased 3.0-fold in liver of rats fed on 0.1%(w/w) clofibrate. Immunotitration experiments with antibodies against the constituent enzymes of the complex revealed that this increase resulted mainly from the increased amounts of only two(a decarboxylase and a lipoate acyltransferase) of three components of the complex and that the other component(dihydrolipoamide dehydrogenase) remained unchanged in its content, irrespective of clofibrate administration. The increases of both enzyme components were associated with increases in their mRNA levels which were estimated by in vitro translation with poly(A)+ RNA.

Epitope mapping on E1α subunit of pyruvate dehydrogenase complex with autoantibodies of patients with primary biliary cirrhosis

Background: A major mitochondrial autoantigen recognized by sera of patients with primary biliary cirrhosis (PBC) is dihydrolipoamide acetyltransferase (E2) of the pyruvate dehydrogenase complex (PDH). The α subunit of pyruvate decarboxylase (E1α) of PDH is also recognized in some E2‐reactive PBC sera, suggesting that the occurrence of autoimmunity against E1α is subsequent to that against E2.

Expression of activation-induced cytidine deaminase enhances the clearance of pneumococcal pneumonia: evidence of a subpopulation of protective anti-pneumococcal B1a cells.

We describe a protective early acquired immune response to pneumococcal pneumonia that is mediated by a subset of B1a cells. Mice deficient in B1 cells (xid), or activation‐induced cytidine deaminase (AID−/−), or invariant natural killer T (iNKT) cells (Jα18−/−), or interleukin‐13 (IL‐13−/−) had impaired early clearance of pneumococci in the lung, compared with wild‐type mice. In contrast, AID−/− mice adoptively transferred with AID+/+ B1a cells, significantly cleared bacteria from the lungs as early as 3 days post infection. We show that this early bacterial clearance corresponds to an allergic contact sensitivity‐like cutaneous response, probably due to a subpopulation of initiating B1a cells. In the pneumonia model, these B1a cells were found to secrete higher affinity antigen‐specific IgM. In addition, as in contact sensitivity, iNKT cells were required for the anti‐pneumococcal B1a cell initiating response, probably through early production of IL‐13, given that IL‐13−/− mice also failed to clear infection. Our study is the first to demonstrate the importance of AID in generating an appropriate B1a cell response to pathogenic bacteria. Given the antibody affinity and pneumonia resistance data, natural IgM produced by conventional B1a cells are not responsible for pneumonia clearance compared with the AID‐dependent subset.

Characterization of Autoantibodies against the E1α Subunit of Branched-Chain 2-Oxoacid Dehydrogenase in Patients with Primary Biliary Cirrhosis

Primary biliary cirrhosis (PBC) is characterized by antimitochondrial antibodies (AMAs) that react with the lipoyl-containing E2 subunits of 2-oxoacid dehydrogenase complexes such as BCOADC and PDC. The lipoyl domains of E2 contain the major epitopes essential for immunopathology. However, the non-lipoyl-containing E1 subunits are also frequently targeted. Since anti-E1 antibodies always appear in combination with anti-E2 antibodies, the mechanisms underlying the autoimmunity against E1 may be linked to, but distinct from, those against E2. Here, we demonstrate that intermolecular and intramolecular determinant spreading underlies the autoimmunity against E1. We performed characterizations and epitope mapping for anti-BCOADC-E1α antibodies from both the intermolecular and intramolecular points of view. The antibody reactivities form a cluster against the BCOADC complex that is distinct from that against the PDC complex, and the anti-BCOADC-E1α antibodies arise as part of the cluster against the BCOADC complex. Multiple epitopes are present on the surface of the BCOADC-E1α molecule, and the major epitope overlaps with the active center. Sera with anti-BCOADC-E1α antibodies strongly inhibited the enzyme activity. These findings suggest that the E1α subunit as part of the native BCOADC complex is an immunogen, and that determinant spreading is involved in the pathogenesis of AMA production.