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Masaru Katoh

Publications and source records attributed to Masaru Katoh.

At least 37 records · Page 2Linked to original sources
PubMed2006

NUMB is a break of WNT-Notch signaling cycle.

Notch, FGF and WNT signaling pathways cross-talk during embryogenesis, tissue regeneration and carcinogenesis. Notch-ligand binding to Notch receptors leads to the cleavage of Notch receptors and the following nuclear translocation of Notch intracellular domain (NICD) to induce transcriptional activation of Notch target genes. Notch signaling inhibitors, NUMB and NUMB-like (NUMBL), are docking proteins with PTB domain. We searched for the TCF/LEF-binding site within the promoter region of NUMB and NUMBL genes. Because two TCF/LEF-binding sites were identified within human NUMB promoter based on bioinformatics and human intelligence (Humint), comparative integromics analyses on NUMB orthologs were further performed. Chimpanzee NUBM gene, consisting of 13 exons, was identified within NW_115880.1 genome sequence. XM_510045.1 was not the correct coding sequence for chimpanzee NUMB. Chimpanzee NUMB gene was found to encode a 651-amino-acid protein showing 99.5, 93.9 and 82.6% total-amino-acid identity with human NUMB, mouse Numb and chicken numb, respectively. Human NUMB mRNA was expressed in placenta, ES cells, neural tissues, trachea, testis, uterus, thymus, coronary artery as well as in a variety of tumors, such as cervical cancer, tong tumor, brain tumor, colorectal and breast cancer. Although distal TCF/LEF-binding site within human NUMB promoter was conserved only among primate NUMB orthologs, proximal TCF/LEF-binding site was conserved among primate and rodent NUMB orthologs. NUMB, JAG1, FGF18, FGF20 and SPRY4 are potent targets of the canonical WNT signaling pathway in progenitor cells. NUMB inhibits Notch signaling in progenitor cells to induce differentiation, while JAG1 activates Notch signaling in stem cells to maintain self-renewal potential. Because Notch signaling inhibitor NUMB was identified as the safe apparatus for the WNT - Notch signaling cycle, epigenetic silencing, deletion and loss-of-function mutation of NUMB gene could lead to carcinogenesis through the dysregulation of the WNT - Notch signaling cycle.

Animals↗
PubMed2006

Comparative integromics on FAT1, FAT2, FAT3 and FAT4.

WNT5A, WNT5B, WNT11, FZD3, FZD6, VANGL1, VANGL2, DVL1, DVL2, DVL3, PRICKLE1, PRICKLE2, ANKRD6, NKD1, NKD2, DAAM1, DAAM2, CELSR1, CELSR2, CELSR3, ROR1 and ROR2 are planar cell polarity (PCP) signaling molecules implicated in the regulation of cellular polarity, convergent extension, and invasion. FAT1, FAT2, FAT3 and FAT4 are Cadherin superfamily members homologous to Drosophila Fat, functioning as a positive regulator of PCP in the Drosophila wing. Complete coding sequence (CDS) for human FAT1 (NM_005245.3) and FAT2 (NM_001447.1) are available, while artificial CDS for human FAT3 (XM_926199 and XM_936538) and partial CDS for FAT4 (NM_024582.2). Here, complete CDS of human FAT3 and FAT4 were determined by using bioinformatics and human intelligence (Humint). FAT3 gene, consisting of 26 exons, encoded a 4557-aa protein with extracellular 33 Cadherin repeats, one Laminin G (LamG) domain and two EGF domains. FAT4 gene encoded a 4924-aa protein with extracellular 34 Cadherin repeats, two LamG domains and three EGF domains. Cytoplasmic VCSVxPxLP and SDYxS motifs were identified as novel motifs conserved among FAT1, FAT2 and FAT3 orthologs. Domain architecture comparison and phylogenetic analysis revealed that FAT1, FAT2 and FAR3 were divergent from FAT4. FAT1-MTNR1A locus at 4q35.2 and FAT3-MTNR1B locus at 11q14.3-q21 were paralogous regions within the human genome. FAT1 mRNA was expressed in embryonic stem (ES) cells, neural tissues, gastric cancer, pancreatic cancer, colorectal cancer, breast cancer, lung cancer and brain tumors. FAT2 mRNA was expressed in infant brain, cerebellum, gastric cancer, pancreatic cancer, ovarian cancer, esophageal cancer, skin squamous cell carcinoma, head and neck cancer. FAT3 mRNA was expressed in ES cells, primitive neuroectoderm, fetal brain, infant brain, adult neural tissues and prostate. FAT4 mRNA was expressed in fetal brain, infant brain, brain tumor and colorectal cancer. FAT family members were revealed to be targets of systems medicine in the fields of oncology and neurology.

Amino Acid Sequence↗
PubMed2006

Hedgehog signaling pathway and gastrointestinal stem cell signaling network (review).

Hedgehog, BMP/TGFbeta, FGF, WNT and Notch signaling pathways constitute the stem cell signaling network, which plays a key role in a variety of processes, such as embryogenesis, maintenance of adult tissue homeostasis, tissue repair during chronic persistent inflammation, and carcinogenesis. Sonic hedgehog (SHH), Indian hedgehog (IHH) and Desert hedgehog (DHH) bind to PTCH1/PTCH or PTCH2 receptor to release Smoothened (SMO) signal transducer from Patched-dependent suppression. SMO then activates STK36 serine/threonine kinase to stabilize GLI family members and to phosphorylate SUFU for nuclear accumulation of GLI. Hedgehog signaling activation leads to GLI-dependent transcriptional activation of target genes, such as GLI1, PTCH1, CCND2, FOXL1, JAG2 and SFRP1. GLI1-dependent positive feedback loop combined with PTCH1-dependent negative feedback loop gives rise to transient proliferation of Hedgehog target cells. Iguana homologs (DZIP1 and DZIP1L) and Costal-2 homologs (KIF7 and KIF27) are identified by comparative integromics. SHH-dependent parietal cell proliferation is implicated in gastric mucosal repair during chronic Helicobacter pylori infection. BMP-RUNX3 signaling induces IHH expression in surface differentiated epithelial cells of stomach and intestine. Hedgehog signals from epithelial cells then induces FOXL1-mediated BMP4 upregulation in mesenchymal cells. Hedgehog signaling is frequently activated in esophageal cancer, gastric cancer and pancreatic cancer due to transcriptional upregulation of Hedgehog ligands and epigenetic silencing of HHIP1/HHIP gene, encoding the Hedgehog inhibitor. However, Hedgehog signaling is rarely activated in colorectal cancer due to negative regulation by the canonical WNT signaling pathway. Hedgehog signaling molecules or targets, such as SHH, IHH, HHIP1, PTCH1 and GLI1, are applied as biomarkers for cancer diagnostics, prognostics and therapeutics. Small-molecule inhibitors for SMO or STK36 are suitable to be used for treatment of Hedgehog-dependent cancer.

Animals↗
PubMed2005

Xenopus frizzled-4S, a splicing variant of Xfz4 is a context-dependent activator and inhibitor of Wnt/beta-catenin signaling.

BACKGROUND: Secreted Frizzled related proteins (SFRPs) are extracellular regulators of Wnt signaling. These proteins contain an N-terminal cysteine rich domain (CRD) highly similar to the CRDs of the Frizzled family of seven-transmembrane proteins that act as Wnt receptors. SFRPs can bind to Wnts and prevent their interaction with the Frizzled receptor. Recently it has been reported that a splice variant of human Frizzled-4 (FZD4S) lacking the transmembrane and the cytoplasmic domains of Frizzled-4 can activate rather than inhibit Wnt-8 activity in Xenopus embryos. This indicates that secreted CRD containing proteins such as Frizzled ecto-domains and SFRPs may not always act as Wnt inhibitors. It is not known how FZD4S can activate Wnt/beta-catenin signaling and what biological role this molecule plays in vivo. RESULTS: Here we report that the Xenopus frizzled-4 is alternatively spliced to give rise to a putative secreted protein that lacks the seven-transmembrane and the cytoplasmic domains. We performed functional experiments in Xenopus embryos to investigate how this novel splicing variant, Xfz4S, can modulate the Wnt/beta-catenin pathway. We show that Xfz4S as well as the extracellular domain of Xfz8 (ECD8) can act as both activators and inhibitors of Wnt/beta-catenin signaling dependent on the Wnt ligand presented. The positive regulation of Wnt/beta-catenin signaling by the extracellular domains of Frizzled receptors is mediated by the members of low density lipoprotein receptor-related protein (LRP-5/6) that act as Wnt coreceptors. CONCLUSION: This work provides evidence that the secreted extracellular domains of Frizzled receptors may act as both inhibitors and activators of Wnt signaling dependent on the Wnt ligand presented.

Journal Article↗
PubMed2005

Hedgehog signaling pathway and gastric cancer.

Hedgehog, WNT, FGF and BMP signaling pathways network together during embryogenesis, tissue regeneration, and carcinogenesis. Aberrant activation of Hedgehog signaling pathway leads to pathological consequences in a variety of human tumors, such as gastric cancer and pancreatic cancer. Endoscopic mucosal resection (EMR), endoscopic submucosal dissection (ESD), surgical gastrectomy and chemotherapy are therapeutic options for gastric cancer; however, prognosis of advanced gastric cancer patient is still poor. Here, Hedgehog signaling pathway in human gastric cancer and its clinical applications will be reviewed. Human SHH, IHH, DHH (Hedgehog homologs), HHAT (Hedgehog acyltransferase), HHIP (Hedgehog-interacting protein), DISP1, DISP2, DISP3 (Dispatched homologs), PTCH1, PTCH2 (Patched homologs), SMO (Smoothened homolog), KIF27, KIF7 (Costal-2 homologs), STK36 (Fused homolog), SUFU (SuFu homolog), DZIP1 (Iguana homolog), GLI1, GLI2 and GLI3 (Cubitus interruptus homologs) are implicated in the Hedgehog signaling. PTCH1, FOXM1 and CCND2 are direct transcriptional targets of Hedgehog signaling. Hedgehog signaling activation leads to cell proliferation through cell cycle regulation. SHH regulates growth and differentiation within gastric mucosa through autocrine loop and FOXL1-mediated epithelial-mesenchymal interaction. SHH is implicated in stem/progenitor cell restitution of damaged gastric mucosa during chronic infection with Helicobacter pylori. SHH up-regulation, IHH upregulation and HHIP down-regulation lead to aberrant activation of Hedgehog signaling through PTCH1 to GLI1 in gastric cancer. Small molecule compounds targeted to SMO (KADD-cyclopamine, SANT1-4, Cur61414) as well as humanized anti-SHH antibodies are potent anti-cancer drugs for gastric cancer. Cocktail of Hedgehog inhibitors would be developed as novel therapeutics for gastric cancer. Single nucleotide polymorphism (SNP) and copy number polymorphism (CNP) of Hedgehog signaling genes would be utilized for genetic screening of gastric cancer, while cDNA-PCR, microarray and ELISA detecting aberrant Hedgehog signaling activation would be utilized for therapeutic optional choice. Genetic screening and precise selection of therapeutic options would contribute to the realization of personalized medicine.

Animals↗
PubMed2005

Comparative genomics on ROR1 and ROR2 orthologs.

Transmembrane proteins with extracellular Frizzled domain, such as ROR1, ROR2, MUSK, MFRP, FZD1, FZD2, FZD3, FZD4, FZD5, FZD6, FZD7, FZD8, FZD9 and FZD10, are key molecules for WNT signaling network. Here, comparative integromics analyses on ROR1 and ROR2 orthologs were performed by using bioinformatics. Zebrafish ror2 gene, consisting of nine exons, was identified within CR-450684.3 genome sequence. CV490605.1 EST corresponded to the 5'-end of zebrafish ror2 mRNA, and BM533602.1 EST corresponded to the 3'-end. Zebrafish ror2 gene was found to encode a 939-aa transmembrane protein, showing 71.7% and 56.2% total amino-acid identity with human ROR2 and ROR1, respectively. Immunoglobulin-like domain, Frizzled domain, Kringle domain within the extracellular region, tyrosine kinase domain, Ror homology C-terminal (RORHC) domain and juxta-C-terminal LLGD motif within the cytoplasmic region were conserved among vertebrate ROR1 and ROR2 orthologs. SH2 binding site within the RORHC domain was conserved among vertebrate ROR2 orthologs, but not among vertebrate ROR1 orthologs. ROR1 mRNA was expressed in embryonic stem (ES) cells, infant brain, renal cancer, and colon cancer. ROR2 mRNA was expressed in parathyroid, testis, uterus, and also in diffuse type gastric cancer with signet ring cell features. ROR2 promoter rather than ROR1 promoter was more evolutionarily conserved. WNT5A and ROR family receptors, co-expressed in ES cells and gastric cancer, are implicated in the planar cell polarity (PCP) pathway. ROR1 and ROR2 are the pharmacogenomics targets in the fields of stem cell biology and oncology.

Amino Acid Sequence↗
PubMed2005

Characterization of KIF12 gene in silico.

Kinesin family (KIF) proteins with Kinesin motor catalytic (KISc) domain and Coiled-coil domain are micro-tubule-dependent molecular motors. KIF proteins produce forces by using the energy from ATP hydrolysis within the KISc domain. We have recently identified that KIF27 is one of mammalian orthologs for Drosophila Costal-2 (Cos2), functioning as regulator of Hedgehog signaling pathway. Mouse Kif12 RefSeq (NM_010616.1) contains the complete coding sequence (CDS); however, human KIF12 Refseq (NM_138424.1) encodes an N-terminally truncated KIF12 protein corresponding to codon 134-642 of mouse Kif12. Here, we characterized the human KIF12 gene by using bioinformatics. Complete CDS of human KIF12 was determined by assembling nucleotide sequences of BQ129377.1 EST, CD358781.1 EST and NM_138424.1 RefSeq. KIF12 gene at human chromosome 9q32 consists of 19 exons. NM_138424.1 RefSeq was a variant KIF12 cDNA with alternative transcription start site (TSS) and skipping of exon 4. NM_138424.1 RefSeq encoded a 513-amino-acid aberrant KIF7 protein with N-terminal-truncation, while KIF12 complete CDS encoded a 651-amino-acid full-length KIF12 protein. Representative human KIF12 and mouse Kif12 proteins with 80.8% total-amino-acid identity shared the common domain architecture, consisting of KISc domain, Coiled-coil domain with internal hinge region, and C-terminal tail domain. KIF12 mRNA was expressed in fetal liver, adult brain and pancreatic islet as well as in kidney tumors, uterus cancer and pancreatic cancer. This is the first report on comprehensive characterization of the human KIF12 gene.

Amino Acid Sequence↗
PubMed2005

Identification and characterization of rat Desert hedgehog and Indian hedgehog genes in silico.

Sonic hedgehog (SHH), Desert hedgehog (DHH) and Indian hedgehog (IHH) bind to Patched family receptors (PTCH1 and PTCH2) to transduce signals to GLI1, GLI2 and GLI3. GLI family transcription factors then activate transcription of Hedgehog target genes, such as FOXE1 and FOXM1 encoding Forkhead-box transcription factors. Hedgehog signaling pathway plays a pivotal role in a variety of human tumors, such as gastric cancer, pancreatic cancer, colorectal cancer, breast cancer, prostate cancer, basal cell carcinoma and brain tumors. Rat orthologs for human DHH and IHH remain to be identified. Here, we identified and characterized rat Dhh and Ihh genes by using bioinformatics. Rat Dhh complete coding sequence (CDS) was determined by assembling nucleotide positions 426397-426963, 429715-429976 and 430244-430898 of the AC114446.3 genome sequence. Rat Ihh complete CDS was determined by assembling nucleotide positions 63433-64033, 66432-66693 and 68242-69169 of AC095777.6 genome sequence. Rat Dhh mRNA was expressed in prostate, duodenum and dorsal root ganglia, while rat Ihh mRNA was expressed in cartilage. Rat Dhh showed 99.7% total-amino-acid identity with mouse Dhh, and 96.5% total-amino-acid identity with human DHH. Rat Ihh and human IHH were shorter than mouse Ihh by 38 amino acids. Rat Ihh showed 97.6% total-amino-acid identity with mouse Ihh and 94.4% total-amino-acid identity with human IHH. Hedgehog family proteins consist of signal peptide, Hedgehog ligand peptide and C-terminal peptide. Hedgehog ligand peptides derived from mammalian Hedgehog family proteins were conserved well, while C-terminal peptides were relatively divergent. The HPLGMXXXXS motif in the C-terminus was conserved in Shh orthologs and Ihh orthologs, but not in Dhh orthologs.

Amino Acid Motifs↗
PubMed2005

Identification and characterization of DISP3 gene in silico.

Lipid-modified soluble proteins Hedgehog (SHH, DHH and IHH) and WNT (WNT1, WNT2, WNT2B, WNT3, etc.) share distantly related mechanisms for ligand modification as well as for signaling through seven-transmembrane protein with Frizzled domain. Hedgehog and WNT signaling pathways network together during embryogenesis and carcinogenesis. Dispatched 1 (DISP1) and Dispatched 2 (DISP2) are human homologs for Drosophila Dispatched implicated in the release of lipid-anchored Hedgehog from producing cells. Here, we identified and characterized Dispatched 3 (DISP3) gene by using bioinformatics. DISP3 complete coding sequence was determined by assembling BU170953 EST and KIAA1337 uncharacterized cDNA. DISP3 gene at human chromosome 1p36.22 was linked to D1S2667 microsatellite maker and TERE1 gene, whose locus is associated with prostate cancer, bladder cancer, and liver cancer. DISP3 mRNA was expressed in human embryonic stem (ES) cells, brain, testis, lung carcinoid, neuroblastoma, retinoblastoma and brain tumor. DISPH1 domain with five transmembrane regions (codon 452-637 of DISP3) and DISPH2 domain with four transmembrane regions (codon 1116-1319 of DISP3) were identified as novel domains conserved between DISP3 (1392 aa) and DISP1. The region around DISPH1 and DISPH2 domains of DISP3 protein was the Patched homologous region conserved among Patched family members and DISP family members. Because DISP3 and DISP1 are multi-span transmembrane proteins with the Patched homologous region, DISP3 is predicted to be implicated in the release of lipid-anchored secreted proteins. This is the first report on identification and characterization of the DISP3 gene.

Amino Acid Sequence↗
PubMed2005

Identification and characterization of TMEM16H gene in silico.

TMEM16A gene is located within the CCND1-ORAOV1-FGF19-FGF4-FGF3-TMEM16A-FADD-PPFIA1-CTTN (cortactin or EMS1) amplicon at human chromosome 11q13.3. TMEM16A, TMEM16B, TMEM16C, TMEM16D, TMEM16E (GDD1), TMEM16F, TMEM16G and TP53I5 are TMEM16 family proteins with TM16H1, TM16H2 and TM16H3 domains. Here, we identified and characterized TMEM16H gene by using bioinformatics. Human TMEM16H gene, consisting of 18 exons, was located at human chromosome 19p13.11. AB046843.2 cDNA corresponded to TMEM16H isoform 1 without intron 17, while CR616031.1 cDNA corresponded to TMEM16H isoform 2 with retained intron 17. TMEM16H isoforms were eight-transmembrane proteins with TM16H3 domain. The last exon of isoforms 1 and 2 corresponded to C-terminal 122 and 227 aa, respectively. Human TMEM16H isoform 1 was the major transcript, while isoform 2 was the minor transcript prone to non-sense mediated mRNA decay (NMD). TMEM16H mRNA was expressed in embryonic stem (ES) cells, fetal brain, and neural tissues. Mouse Tmem16h representative cDNA was determined by assembling BC027735.1 and BC059855.1 cDNAs. Mouse and rat Tmem16h genes encoded Tmem16h proteins similar to human TMEM16H isoform 2. The regions corresponding to exons 17 and 18 of human TMEM16H gene were not separated by intron within mouse and rat Tmem16h genes. Insertion of intron 17 into human TMEM16H gene during evolution resulted in the generation of TMEM16H isoform 1. This is the first report on identification and characterization of the TMEM16H gene as well as on the molecular evolution of TMEM16H.

Amino Acid Sequence↗
PubMed2005

Identification and characterization of rat Ankrd6 gene in silico.

WNT signals are transduced to the beta-catenin pathway or the planar cell polarity (PCP) pathway. Drosophila Frizzled (Fz), Starry night (Stan), Van Gogh (Vang), Prickle (Pk) and Diego (Dgo) are PCP signaling molecules. Human FZD1, FZD2, FZD3, FZD4, FZD5, FZD6, FZD7, FZD8, FZD9 and FZD10 are Fz homologs. Human CELSR1, CELSR2 and CELSR3 are Stan homologs. Human VANGL1 and VANGL2 are Vang homologs. Human PRICKLE1 and PRICKLE2 are Pk homologs. Human ANKRN6 is a Dgo homolog. Here, we identified and characterized rat Ankrd6 gene by using bioinformatics. Ankrd6 gene, consisting of 15 exons, was located within AC105547.5 genome sequence derived from rat chromosome 5q21. Rat Ankrd6 mRNA was expressed in corpus-striatum, eye, lung, and kidney. Rat Ankrd6 (714 aa) with six ankyrin (Ank) repeats and two coiled-coil regions showed 95.0, 84.2 and 53.4% total-amino-acid identity with mouse, human and zebrafish orthologs, respectively. Ser 340 of rat Ankrd6, conserved among mammalian Ankrd6 orthologs, was a protein kinase A (PKA) phosphotylation and 14-3-3 interaction site. Ank repeats are putative binding domains for Prickle1, Prickle2, Vangl1, and Vangl2. Central coiled-coil region is located within binding domain for Casein kinase I epsilon (CkIe). C-terminal coiled-coil region is located within binding domain for Axin1 and Axin2. Fourth to sixth Ank repeats of vertebrate Ankrd6 orthologs (codon 141-239) were highly conserved in Drosophila Dgo; however, two coiled-coil regions of vertebrate Ankrd6 orthologs were absent in Drosophila Dgo. Due to the molecular evolution, functions of vertebrate Ankrd6 orthologs were predicted to partially differ from those of Drosophila Dgo.

14-3-3 Proteins↗
PubMed2005

Identification and characterization of rat Wnt6 and Wnt10a genes in silico.

WNT and Hedgehog signaling pathways are implicated in various types of human cancer, such as gastric and pancreatic cancer. WNT1, WNT2, WNT2B (WNT13), WNT3, WNT3A, WNT4, WNT5A, WNT5B, WNT6, WNT7A, WNT7B, WNT8A, WNT8B, WNT9A (WNT14), WNT9B (WNT14B). WNT10A, WNT10B, WNT11 and WNT16 genes encode WNT family glycoproteins, which transduce signals through Frizzled (FZD) family receptors with extracellular WNT-binding and cytoplasmic Dishevelled-binding domains. WNT6 and WNT10A genes at human chromosome 2q35 are clustered in tail-to-head manner with an interval of <7 kb. Here, we identified and characterized rat Wnt6 and Wnt10a genes by using bioinformatics. Wnt6 and Wnt10a genes were clustered in tail-to-head manner with an interval of about 7 kb within AC127107.3 and AC132020.3 genome sequences. Rat Wnt6 gene, consisting of four exons, encoded a 365-aa protein with signal peptide, 24 conserved Cys residues, two Asn-linked glycosylation sites and an RGD motif. Rat Wnt10a gene, consisting of four exons, encoded a 417-aa protein with 24 conserved Cys residues, two Asn-linked glycosylation sites and an RGD motif. Rat Wnt6 and human WNT6 showed 97.8% total-amino-acid identity, while rat Wnt10a and human WNT10A showed 95.4% total-amino-acid identity. Promoter region was conserved between rat Wnt6 and human WNT6 genes. GATA, FOXA2, and TGIF binding sites were located within the conserved region of rat Wnt6 and human WNT6 promoters. This is the first report on rat Wnt6 and Wnt10a genes as well as on the conserved promoter region of Wnt6 orthologs.

Amino Acid Sequence↗
PubMed2005

Identification and characterization of rat Ror1 and Ror2 genes in silico.

Frizzled-1 (FZD1), FZD2, FZD3, FZD4, FZD5, FZD6, FZD7, FZD8, FZD9 and FZD10 are seven-transmembrane-type WNT receptors with extracellular Frizzled (Fz) domain. ROR1, ROR2 and MUSK are receptor-type tyrosine kinases with extracellular Fz domain, while MFRP is type II transmembrane protein with extracellular Fz domain. ROR1, ROR2, MUSK and MFRP are predicted to transduce or regulate WNT signaling. Here, we identified and characterized rat Ror1 and Ror2 genes by using bioinformatics. Rat Ror1 gene was located within AC108320.4, AC098031.5 and AC129856.4 genome sequences, while rat Ror2 gene was located within AC139870.3 and AC123431.4 genome sequences. Exon-intron structure was conserved between rat Ror1 and Ror2 genes, consisting of nine exons. Rat Ror1 mRNA was expressed in fetal ventricle, while rat Ror2 mRNA was expressed in cerebral cortex, hypothalamus, dorsolateral prostate, and chondrosarcoma. Rat Ror1 (937 aa) and Ror2 (943 aa) showed 56.5% total-amino-acid identity. Rat Ror1 and Ror2 were type I transmembrane proteins with extracellular Immunoglobulin-like (Ig), Fz, Kringle (KR) domains, and cytoplasmic Juxta-membrane (JM), Tyrosine kinase (TK), and Ror homology C-terminal (RORHC) domains. Casein kinase Iepsilon-binding RORHC domain was conserved among vertebrate Ror1 and Ror2 homologs, but not in Drosophila Ror. Thr 582 within TK domain was conserved among mammalian Ror family members, and was predicted as Casein kinase I phosphorylation site. This is the first report on rat Ror1 and Ror2 genes as well as on molecular evolution of Ror1 and Ror2 homologs.

Amino Acid Sequence↗
PubMed2005

Identification and characterization of rat Bcl9l gene in silico.

Drosophila wingless (wg), shaggy (sgg), armadillo (arm), legless (lgs), pygopus (pygo), pangolin (pan), and engrailed (en) are segment polarity genes implicated in Wg-Arm (WNT-beta-catenin) pathway. Drosophila lgs encodes nuclear scaffold protein functioning as positive regulator for Wg-Arm pathway. Cancer-associated genes BCL9 and BCL9L are human homologs for Drosophila lgs. Here, we identified and characterized rat Bcl9l gene by using bioinformatics. Rat Bcl9l gene, consisting of eight exons, was located within AC124034.4 and AC105645.5 genome sequences. Bcl9l gene was linked to Blr1 gene at rat chromosome 8q22 in the tail-to-tail manner with an interval less than 2 kb. Rat Bcl9l gene was found to encode a 1494-aa Bcl9l protein, which showed 97.7% and 94.2% total-amino-acid identity with mouse Bcl9l and human BCL9L, respectively. B9H1-B9H6 domains, originally identified as conserved regions among mammalian BCL9 and BCL9L homologs, were also identified within rat Bcl9l. B9H1 and B9H2 domains corresponded to HD1 and HD2 domains of Drosophila lgs, functioning as binding regions for Pygo and Arm, respectively. B9H4 domain was characterized by multiple Ser-Pro repeats. Thr 954 within B9H4 domain of rat Bcl9l was conserved in mammalian BCL9 and BCL9L homologs. Phylogenetic analysis revealed that mammalian Bcl9l homologs were more related to human BCL9 than to Drosophila lgs. This is the first report on rat Bcl9l gene.

Amino Acid Sequence↗
PubMed2005

Identification and characterization of rat Wnt1 and Wnt10b genes in silico.

WNT family genes encode WNT family glycoproteins, while Frizzled (FZD) family genes encode seven-transmembrane-type receptors with extracellular WNT-binding domain and cytoplasmic Dishevelled-binding domain. WNT signaling pathway is implicated in carcinogenesis and embryogenesis. WNT1-WNT10B, WNT6-WNT10A, WNT3-WNT9B (WNT14B), WNT3A-WNT9A (WNT14) gene clusters exist within the human genome. Here, we identified and characterized rat Wnt1 and Wnt10b genes by using bioinformatics. Rat Wnt1 gene, consisting of four exons, encoded a 370-aa protein with signal peptide, 22 conserved Cys residues and four Asn-linked glycosylation sites. Rat Wnt10b gene, consisting of five exons, encoded a 389-aa protein with signal peptide, 24 conserved Cys residues and two Asn-linked glycosylation sites. Wnt1 and Wnt10b genes at rat chromosome 7q36 were clustered in head-to-head manner with an interval of about 10 kb within AC096835.4 or AC118760.4 genome sequences. Promoter region, exon 1 and 5'-part of intron 1 were conserved between rat and human Wnt1 orthologs. Intergenic conserved region (IGCR) was identified within the Wnt1-Wnt10b gene cluster. GC content of rat Wnt1-Wnt10b IGCR (nucleotide position 14962-15875 of AC096835.4 genome sequence) was 59.4%. Rat Wnt1-Wnt10b IGCR showed 92.5 and 74.4% nucleotide identity with mouse Wnt1-Wnt10b IGCR and human WNT1-WNT10B IGCR, respectively. Wnt1-Wnt10b IGCR was predicted as regulatory element rather than gene because cDNA or EST derived from Wnt1-Wnt10b IGCR was not identified. This is the first report on rat Wnt1 and Wnt10b genes as well as on Wnt1-Wnt10b IGCR.

Amino Acid Sequence↗
PubMed2005

Comparative genomics on Wnt8a and Wnt8b genes.

WNT family ligands transduce signals through FZD1, FZD2, FZD3, FZD4, FZD5, FZD6, FZD7, FZD8, FZD9, FZD10, LRP5, LRP6, ROR1, ROR2 and RYK. WNT1, WNT2, WNT2B, WNT3, WNT3A, WNT8A, WNT8B, WNT10A and WNT10B are canonical WNTs to activate WNT - beta-catenin pathway. Human WNT8A mRNA is expressed in NT2 cells with neuronal differentiation potential, while human WNT8B mRNA in diffuse type gastric cancer. Here, we identified and characterized the rat Wnt8a and Wnt8b genes by using bioinformatics. The rat Wnt8a gene, consisting of six exons, was located within AC134361.2 genome sequence. The rat Wnt8b gene, consisting of six exons, was located within AC105487.6 and AC103018.7 genome sequences. The rat Wnt8a (355 aa) and Wnt8b (350 aa) with 60.0% total-amino-acid identity were secreted-type proteins with 22 conserved Cys residues and two Asn-linked glycosylation sites. Wnt8b orthologs were more conserved than Wnt8a orthologs. GATA-binding site was located within conserved region of rat Wnt8b and human WNT8B promoters. GATA6 ESTs were expressed in diffuse type gastric cancer, and FGFR2 gene is reported preferentially amplified in diffuse type gastric cancer. KGF-FGFR2-PI3K-GATA6-WNT8B signaling cascade is predicted to play important roles in diffuse type gastric cancer. This is the first report on the rat Wnt8a and Wnt8b genes as well as on the conserved GATA-binding site within rat Wnt8b and human WNT8B promoters.

Amino Acid Sequence↗
PubMed2005

Molecular evolution of Wnt2b orthologs.

WNT family proteins transduce signals through Frizzled (FZD) receptors with extracellular WNT-binding domain and cytoplasmic Dishevelled-binding domain. WNT2B-ST7L and WNT2-ST7 loci are paralogous regions within the human genome. WNT2B isoform 2 and WNT2 are canonical WNTs to activate the beta-catenin - TCF pathway in human cancer, especially in gastric cancer. Here, the rat Wnt2b gene was identified and characterized by using bioinformatics. The rat Wnt2b gene, consisting of five exons, was located within AC106372.5 genome sequence. Wnt2b core promoter region (nucleotide position 234449-233652 of AC106372.5 rat genome sequence) was identified as an evolutionarily conserved region. GC content of rat Wnt2b promoter was 71.8%. Nucleotide identity between human and rat Wnt2b promoters was 71.2%. E box, CP2-binding site, CCAAT box and ZNFN1A1 (IKAROS)-binding site were located within the conserved region of rat Wnt2b, mouse Wnt2b, and human WNT2B promoters. Rat Wnt2b (391 aa), human WNT2B isoform 2 and other vertebrate Wnt2b orthologs were type II transmembrane proteins with cleavable extracellular WNT domain, while vertebrate Wnt2 orthologs were secreted proteins. Twenty-four Cys residues were conserved among vertebrate Wnt2b and Wnt2 orthologs. Glycosylation sites at Asn 283 of rat Wnt2b and RGD motif were identified within mammalian Wnt2b orthologs, but not within vertebrate Wnt2 orthologs and zebrafish wnt2b. Zebrafish wnt2b acquired N-terminal cytoplasmic region to evolve into type II transmembrane protein, and then mammalian Wnt2b orthologs acquired integrin-targeting RGD motif within the extracellular WNT domain. This is the first report on the rat Wnt2b gene as well as on molecular evolution of the Wnt2b orthologs.

Amino Acid Sequence↗