Masatsugu Moriyama

Genome-wide microRNA expression profiling in renal cell carcinoma: significant down-regulation of miR-141 and miR-200c.

We investigated expression profiles of microRNA (miRNA) in renal cell carcinoma [clear cell carcinomas (CCC) and chromophobe renal cell carcinomas (ChCC)] and in normal kidneys by using a miRNA microarray platform which covers a total of 470 human miRNAs (Sanger miRBase release 9.1). Unsupervised hierarchical cluster analysis revealed that CCC and ChCC were separable and that no subgroups were identified in CCCs. We found that 43 miRNAs were differentially expressed between CCC and normal kidney, of which 37 were significantly down‐regulated in CCC and the other 6 were up‐regulated. We also found that 57 miRNAs were differentially expressed between ChCC and normal kidney, of which 51 were significantly down‐regulated in ChCC and the other 6 were up‐regulated. Together, these observations indicate that expression of miRNAs tends to be down‐regulated in both CCC and ChCC compared with normal kidney. We observed that miR‐141 and miR‐200c were the most significantly down‐regulated miRNAs in CCCs. Indeed, in all cases of CCC analysed, both miR‐141 and miR‐200c were down‐regulated in comparison with normal kidney. Microarray data and quantitative RT–PCR showed that these two miRNAs were expressed concordantly. TargetScan algorithm revealed that ZFHX1B mRNA is a hypothetical target of both miR‐141 and ‐200c. We established by quantitative RT–PCR that, in CCCs in which miR‐141 and miR‐200c were down‐regulated, ZFHX1B, a transcriptional repressor for CDH1/E‐cadherin, tended to be up‐regulated. Furthermore, we found that overexpression of miR‐141 and miR‐200c caused down‐regulation of ZFHX1B and up‐regulation of E‐cadherin in two renal carcinoma cell lines, ACHN and 786‐O. On the basis of these findings, we suggest that down‐regulation of miR‐141 and miR‐200c in CCCs might be involved in suppression of CDH1/E‐cadherin transcription via up‐regulation of ZFHX1B. Copyright

Expression of C-ERBB-2 Gene Product in Urinary Bladder Cancer

Expression of the c-erbB-2 gene product and the epidermal growth factor receptor (EGF-R) was investigated in 54 cases of human bladder cancer immunohistologically and by Western blot analysis. For detection of the c-erbB-2 product, two specific antibodies, a rabbit polyclonal antibody directed to the intracellular domain and a murine monoclonal antibody recognizing an epitope in the extracellular domain, were used. Seventeen cases of bladder cancer were stained by the anti-c-erbB-2 polyclonal antibody, while 20 cases were stained by the monoclonal antibody, with good correlation on both stainings (p less than 0.01). There were four c-erbB-2 positive cases in 26 G1 tumors, four in 15 G2 tumors, and nine in 13 G3 tumors. There were also eight erbB-2 positive cases in nine muscle-invasive tumors, nine of 45 superficial tumors, four of five with lymph node metastasis, and seven of 14 without metastasis, as revealed by staining with the polyclonal antibody. Thus, the c-erbB-2 gene product was more frequently expressed in high grade tumors (p less than 0.01), in high stage tumors (p less than 0.01), and nodal metastatic tumors (N.S. by Chi-square test). Twenty-two of the 54 tumors were stained by an anti-EGF-R monoclonal antibody, 528 IgG. The expression of EGF-R was independent of histological grading, tumor stage, and nodal status, and no correlation was observed between expression of the c-erbB-2 product and EGF-R. The c-erbB-2 product may be applicable as a tumor marker for evaluation of malignant potential, invasiveness, and probably metastatic potential of human bladder cancer.

Genome-wide analysis of DNA copy number alterations and gene expression in gastric cancer.

Genomic copy number aberrations (CNAs) are believed to play a major role in the development and progression of human cancers. Although many CNAs have been reported in gastric cancer, their genome‐wide transcriptional consequences are poorly understood. In this study, to reveal the impact of CNAs on genome‐wide expression in gastric cancer, we analysed 30 cases of gastric cancers for their CNAs by array comparative genomic hybridization (array CGH) and 24 of these 30 cases for their expression profiles by oligonucleotide‐expression microarray. We found that with the application of laser microdissection, most CNAs were detected at higher frequency than in previous studies. Notably, gain at 20q13 was detected in almost all cases (97%), suggesting that this may play an important role in the pathogenesis of gastric cancer. By comparing the array CGH data with expression profiles of the same samples, we showed that both genomic amplification and deletion strongly influence the expression of genes in altered genomic regions. Furthermore, we identified 125 candidate genes, consisting of 114 up‐regulated genes located in recurrent regions (>10%) of amplification and 11 down‐regulated genes located in recurrent regions of deletion. Up‐regulation of several candidate genes, such as CDC6, SEC61G, ANP32E, BYSL and FDFT1, was confirmed by immunohistochemistry. Interestingly, some candidate genes were localized at genomic loci adjacent to well‐known genes such as EGFR, ERBB2 and SMAD4, and concordantly deregulated by genomic alterations. Based on these results, we propose that our list of candidate genes may contain novel genes involved in the pathogenesis of advanced gastric cancer. Copyright

Evi9 Encodes a Novel Zinc Finger Protein That Physically Interacts with BCL6, a Known Human B-Cell Proto-Oncogene Product

ABSTRACT Evi9 is a common site of retroviral integration in BXH2 murine myeloid leukemias. Here we show that Evi9 encodes a novel zinc finger protein with three tissue-specific isoforms: Evi9a (773 amino acids [aa]) contains two C2H2-type zinc finger motifs, a proline-rich region, and an acidic domain; Evi9b (486 aa) lacks the first zinc finger motif and part of the proline-rich region; Evi9c (239 aa) lacks all but the first zinc finger motif. Proviral integration sites are located in the first intron of the gene and lead to increased gene expression. Evi9a and Evi9c, but not Evi9b, show transforming activity for NIH 3T3 cells, suggesting thatEvi9 is a dominantly acting proto-oncogene. Immunolocalization studies show that Evi9c is restricted to the cytoplasm whereas Evi9a and Evi9b are located in the nucleus, where they form a speckled localization pattern identical to that observed for BCL6, a human B-cell proto-oncogene product. Coimmunoprecipitation and glutathione S-transferase pull-down experiments show that Evi9a and Evi9b, but not Evi9c, physically interact with BCL6, while deletion mutagenesis localized the interaction domains in or near the second zinc finger and POZ domains of Evi9 and BCL6, respectively. These results suggest that Evi9 is a leukemia disease gene that functions, in part, through its interaction with BCL6.

Arpp, a New Homolog of Carp, Is Preferentially Expressed in Type 1 Skeletal Muscle Fibers and Is Markedly Induced by Denervation

In this study, we isolated and characterized a murine counterpart of the human Arpp (hArpp) gene. Sequence analysis revealed that the murine Arpp (mArpp) gene is almost identical to the Ankrd2 gene, which has recently been isolated as a mouse gene induced in stretched skeletal muscle. The mArpp gene encodes a protein of 332 amino acids that contains four well-conserved ankyrin-repeat domains in the central portion of the protein. The amino acid sequence of mArpp protein (mArpp) is highly homologous to that of mouse cardiac-restricted ankyrin-repeat protein (Carp), which is proposed to be a putative genetic marker for cardiac hypertrophy. Immunohistochemical analysis revealed that mArpp is preferentially expressed in type 1 skeletal muscle fibers, and that mArpp is localized in both the nucleus and the sarcomeric I-band of muscle fibers, suggesting that Arpp may function as a nuclear and sarcomeric protein. Furthermore, mArpp was also expressed in neurons of the cerebellum and cerebrum, the islets of Langerhans in the pancreas, and the esophageal epithelium, suggesting that mArpp may play a functional physiologic role in brain, pancreas, and esophagus as well as in type 1 muscle fibers. Interestingly, although mArpp was localized in both nucleus and cytoplasm in neurons, its localization was restricted to nucleus in pancreas and esophagus, suggesting that intracellular localization of mArpp is regulated in a tissue-specific manner. Furthermore, we found that mArpp- and Carp-expression in skeletal muscle were markedly up-regulated after denervation. Although the elevated expression level of Carp was kept only for two weeks after denervation, that of Arpp was kept at least for 4 weeks, suggesting that mArpp and Carp may play distinct functional roles in denervated skeletal muscle.

High-resolution analysis of DNA copy number alterations and gene expression in renal clear cell carcinoma†

We analysed chromosomal copy number aberrations (CNAs) in renal cell carcinomas by array‐based comparative genomic hybridization, using a genome‐wide scanning array with 2304 BAC and PAC clones covering the whole human genome at a resolution of roughly 1.3 Mb. A total of 30 samples of renal cell carcinoma were analysed, including 26 cases of clear cell carcinoma (CCC) and four cases of chromophobe renal cell carcinoma (ChCC). In CCCs, gains of chromosomes 5q33.1‐qter (58%), 7q11.22‐q35 (35%) and 16p12.3‐p13.12 (19%), and losses of chromosomes 3p25.1‐p25.3 (77%), 3p21.31‐p22.3 (81%), 3p14.1‐p14.2 (77%), 8p23.3 (31%), 9q21.13‐qter (19%) and 14q32.32‐qter (38%) were detected. On the other hand, the patterns of CNAs differed markedly between CCCs and ChCCs. Next, we examined the correlation of CNAs with expression profiles in the same tumour samples in 22/26 cases of CCC, using oligonucleotide microarray. We extracted genes that were differentially expressed between cases with and without CNAs, and found that significantly more up‐regulated genes were localized on chromosomes 5 and 7, where recurrent genomic gains have been detected. Conversely, significantly more down‐regulated genes were localized on chromosomes 14 and 3, where recurrent genomic losses have been detected. These results revealed that CNAs were correlated with deregulation of gene expression in CCCs. Furthermore, we compared the patterns of genomic imbalance with histopathological features, and found that loss of 14q appeared to be a specific and additional genetic abnormality in high‐grade CCC. When we compared the expression profiles of low‐grade CCCs with those of high‐grade CCCs, differentially down‐regulated genes tended to be localized on chromosomes 14 and 9. Thus, it is suggested that copy number loss at 14q in high‐grade CCC may be involved in the down‐regulation of genes located in this region. Copyright

Intronic U50 small-nucleolar-RNA (snoRNA) host gene of no protein-coding potential is mapped at the chromosome breakpoint t(3;6)(q27;q15) of human B-cell lymphoma

In eukaryotic cells, nucleolar processing of preribosomal RNAs (prerRNAs) is assisted by a large number of small nucleolar RNAs (snoRNAs) that function in the 2′‐O‐methylation or the pseudouridylation of rRNAs. Most snoRNAs so far characterized are encoded and processed from introns of premRNAs.

Carp, a Cardiac Ankyrin-Repeated Protein, and Its New Homologue, Arpp, Are Differentially Expressed in Heart, Skeletal Muscle, and Rhabdomyosarcomas

Arpp, a protein containing an ankyrin repeat domain, PEST sequence, and proline-rich region, is a novel ankyrin-repeated protein highly homologous to Carp, which is proposed to be the putative genetic marker for cardiac hypertrophy. In this study, we comparatively analyzed expression of Arpp and Carp protein in skeletal and cardiac muscles and rhabdomyosarcomas (RMSs). In adult skeletal muscle, Arpp was preferentially expressed in the nucleus and cytoplasm of type I fibers, whereas Carp was barely detectable in skeletal muscle. On the other hand, in adult cardiac muscle, interestingly, Arpp was expressed in ventricles mostly, whereas Carp was expressed throughout the atrium and ventricle. Furthermore, although Carp was identified in fetal heart at 11 developmental weeks, Arpp was very low or undetectable in these fetal hearts. These results suggest that Arpp and Carp are differentially expressed and function in both skeletal and cardiac muscle of fetus and adult. We found that Arpp expression was induced during the differentiation of C2C12 cells in vitro, suggesting that Arpp-expression may be associated with the differentiation stage during myogenesis. Both Arpp and Carp were found to be expressed in all of the RMS cases studied. Because the expression patterns of Arpp in RMS were different from those of muscle actin or desmin, Arpp may be detectable in RMS cases that do not express other existing RMS markers.

Adenovirus-mediated high expression of BCL-6 in CV-1 cells induces apoptotic cell death accompanied by down-regulation of BCL-2 and BCL-X L

The BCL-6 proto-oncogene encodes a 92- to 98-kDa transcriptional repressor containing the BTB/POZ domain at its N-terminal region and the zinc finger domain at its C-terminal region, respectively. In the present study, we examined the function of BCL-6 by using a recombinant adenovirus expressing BCL-6 (Ax1CA-BCL-6) and the lacZ reporter gene (Ax1CA-lacZ). Viability of CV-1 and HeLa cells infected with Ax1CA-BCL-6 was markedly reduced due to apoptosis, suggesting that BCL-6-overexpression induces apoptosis in CV-1 and HeLa cells. FACS analysis revealed that BCL-6-overexpressing cells are accumulated not only at the sub-G1 but also at G2/M phase. Induction of apoptosis by BCL-6 was preceded by down-regulation of apoptosis repressors BCL-2 and BCL-XL. These results suggest that BCL-6 induces apoptosis by regulating the expression of these apoptosis-regulating genes.

Identification of heterologous translocation partner genes fused to the BCL6 gene in diffuse large B-cell lymphomas: 5′-RACE and LA – PCR analyses of biopsy samples

In order to elucidate the molecular mechanism(s) for BCL6 translocation, we identified translocational partner genes by subjecting clinical biopsy samples from patients with non-Hodgkins lymphoma to 5′-rapid amplification of cDNA ends (5′-RACE). Sequence analysis of the 5′-RACE product revealed that the BCL6 gene was fused to the J segment of the immunoglobulin heavy chain (IgH) gene in about half of the cases, but in the other half, it was fused to heterologous partners, including the MHC class II transactivator (CIITA), pim-1, eukaryotic initiation factor 4AII (eif4AII), transferrin receptor (TFRR) and ikaros genes. Since analyses using genomic long and accurate (LA) – PCR revealed that the breakpoints in the partner gene were confined to the first intron or the second exon in all cases, the promoter and the first exon of the BCL6 gene were replaced by the promoter and the first or both the first and second exon of the partner gene. The breakpoint flanking sequences had no recombination signal sequences (RSSs) or chi sequences and were homologous with the switch region only when the BCL6 gene was fused to the IgH gene, suggesting that BCL6 translocation cannot be explained solely by mistakes of V(D)J, or chi-mediated or class-switch recombination, but rather another mechanism may also be required to explain the molecular mechanism for the promiscuous BCL6 translocation.