Proteomic analysis of adult T-cell leukemia/lymphoma: A biomarker identification strategy based on preparation and in-solution digestion methods of total proteins.

Adult T-cell leukemia/lymphoma (ATL), caused by human T-cell leukemia virus type-1 (HTLV-1) infection, is a malignant hematologic cancer that remains difficult to cure. We herein established a biomarker identification strategy based on the total cell proteomics of cultured ATL cells to search for novel ATL biomarkers. Four protocols with a combination of selected conditions based on lysis buffers and addition agents for total cell proteomics were used for a differential analysis between the ATL cell group (consisting of 11 cell lines), HTLV-1-infected cell group (consisting of 6 cell lines), and HTLV-1-negative cell group (consisting of 6 cell lines). In the analysis, we identified 24 and 27 proteins that were significantly increased (ratio ≥2.0, p < 0.05) and decreased (ratio ≤ 0.5, p < 0.05), respectively, in the ATL group. Previously reported CCL3 and CD30/TNFRSF8 were confirmed to be among significantly increased proteins. Furthermore, correlation analysis between identified proteins and Tax suggested that RASSF2 and GORASP2 were candidates of novel Tax-regulated factors. The biomarker identification strategy established herein is expected to contribute to the identification of biomarkers for ATL and other diseases.

Establishment of a quantitative in vivo method for estimating adipose tissue volumes and the effects of dietary soy sauce oil on adipogenesis in medaka, Oryzias latipes.

Adipose tissue, which is conserved in higher eukaryotes, plays central roles in controlling the body's energy balance, including excess energy storage and energy expenditure during starvation. In adipogenesis, intranuclear receptor, peroxisome proliferator-activated receptor gamma (PPARγ) is a key molecule, and PPARγ agonists can promote adipogenesis. Many studies on the in vitro screening of PPARγ agonists with compounds derived from various materials have been reported; however, in vivo assays for quick examination of these feeding effects have not been established. In this study, we developed a technique using a lipophilic fluorescent reagent, Nile red to quantitatively estimate the adipose tissue volumes by using Japanese rice fish, medaka (Oryzias latipes) and studied effects of dietary soy sauce oil (SSO), which is a discarded by-product from Japanese traditional food and is known to have PPARγ-agonistic activity, on adipogenesis. We found that SSO feeding increased the adipose tissue volumes, and the expression levels of adipogenesis-related genes increased in these medaka larvae. These results suggest that SSO feeding increases the adipose tissue volumes through adipogenesis promotion by PPARγ-agonistic activity in medaka, and medaka is a powerful model for studying adipogenesis. Furthermore, our study also demonstrates the availability of SSO as a dietary additive for farmed fish.

Abnormal nuclear morphology is independent of longevity in a zmpste24-deficient fish model of Hutchinson-Gilford progeria syndrome (HGPS).

Lamin is an intermediate protein underlying the nuclear envelope and it plays a key role in maintaining the integrity of the nucleus. A defect in the processing of its precursor by a metalloprotease, ZMPSTE24, results in the accumulation of farnesylated prelamin in the nucleus and causes various diseases, including Hutchinson-Gilford progeria syndrome (HGPS). However, the role of lamin processing is unclear in fish species. Here, we generated zmpste24-deficient medaka and evaluated their phenotype. Unlike humans and mice, homozygous mutants did not show growth defects or lifespan shortening, despite lamin precursor accumulation. Gonadosomatic indices, blood glucose levels, and regenerative capacity of fins were similar in 1-year-old mutants and their wild-type (WT) siblings. Histological examination showed that the muscles, subcutaneous fat tissues, and gonads were normal in the mutants at the age of 1 year. However, the mutants showed hypersensitivity to X-ray irradiation, although p53target genes, p21 and mdm2, were induced 6 h after irradiation. Immunostaining of primary cultured cells from caudal fins and visualization of nuclei using H2B-GFP fusion proteins revealed an abnormal nuclear shape in the mutants both in vitro and in vivo. The telomere lengths were significantly shorter in the mutants compared to WT. Taken together, these results suggest that zmpste24-deficient medaka phenocopied HGPS only partially and that abnormal nuclear morphology and lifespan shortening are two independent events in vertebrates.

Ligation-based assembly for constructing mouse synthetic scFv libraries by chain shuffling with in vivo-amplified VH and VL fragments.

In vitro assembly of two or three PCR fragments using primers is a common method of constructing scFv fragments for display on the surface of phage. However, mismatch annealing often occurs during in this step, leading to cloning and display of incomplete Fab or scFv fragments. To overcome this limitation, we developed a ligation-based two-fragment assembly (LTFA) protocol that involved separately cloning VH and Vκ fragments into the high-copy-number plasmid pUC18. The VH and Vκ fragments had randomized complementarity-determining region 3 (CDR3) and were joined with a peptidyl linker composed of (G4S)3. Using this approach, complete sequences of scFv fragments were successfully constructed, and the sequencing of 83 scFv clones revealed that none of the sequences, including the linker region, contained deletions or mutations. In contrast, linker sequences generated using a conventional two-fragment PCR assembly (TFPA) protocol often contained sequence anomalies, including large truncations. Using the LTFA protocol, a final library size of 1.0×10(8)cfu was achieved. Examination of the amino acid profiles of the generated scFv fragments within the randomized regions introduced using degenerate codons did not detect any bias from that expected based on stochastic distribution. After several cycles of panning with this library, antigen-specific scFvs against two reference antigens, hen egg lysozyme and streptavidin were detected. In addition, scFvs with specificity against peptidyl antigens in the loop region of the Medaka ortholog of human C6orf89, which encodes a histone deacetylase enhancer that interacts with the bombesin receptor, were also obtained. The LTFA protocol developed here is robust and allows for the easy construction of integral scFv fragments compared with conventional TFPA. Utilizing LTFA, other CDRs can be readily combined. This approach also allows for the in vitro maturation of scFv fragments by separately introducing randomization in CDRs or using error-prone PCR for the amplification of pre-selected sequences as a template scaffold.

Structural and biochemical characterization of O-mannose-linked human natural killer-1 glycan expressed on phosphacan in developing mouse brains.

The human natural killer-1 (HNK-1) carbohydrate comprising a sulfated trisaccharide (HSO3-3GlcAß1-3Galß1-4GlcNAc-) is expressed on N-linked and O-mannose-linked glycans in the nervous system and involved in learning and memory functions. Although whole/core glycan structures and carrier glycoproteins for the N-linked HNK-1 epitope have been studied, carrier glycoproteins and the biosynthetic pathway of the O-mannose-linked HNK-1 epitope have not been fully characterized. Here, using mass spectrometric analyses, we identified the major carrier glycoprotein of the O-linked HNK-1 as phosphacan in developing mouse brains and determined the major O-glycan structures having the terminal HNK-1 epitope from partially purified phosphacan. The O-linked HNK-1 epitope on phosphacan almost disappeared due to the knockout of protein O-mannose ß1,2-N-acetylglucosaminyltransferase 1, an N-acetylglucosaminyltransferase essential for O-mannose-linked glycan synthesis, indicating that the reducing terminal of the O-linked HNK-1 is mannose. We also showed that glucuronyltransferase-P (GlcAT-P) was involved in the biosynthesis of O-mannose-linked HNK-1 using the gene-deficient mice of GlcAT-P, one of the glucuronyltransferases for HNK-1 synthesis. Consistent with this result, we revealed that GlcAT-P specifically synthesized O-linked HNK-1 onto phosphacan using cultured cells. Furthermore, we characterized the as-yet-unknown epitope of the 6B4 monoclonal antibody (mAb), which was thought to recognize a unique phosphacan glycoform. The reactivity of the 6B4 mAb almost completely disappeared in GlcAT-P-deficient mice, and exogenously expressed phosphacan was selectively recognized by the 6B4 mAb when co-expressed with GlcAT-P, suggesting that the 6B4 mAb preferentially recognizes O-mannose-linked HNK-1 on phosphacan. This is the first study to show that 6B4 mAb-reactive O-mannose-linked HNK-1 in the brain is mainly carried by phosphacan.

Regulated expression of the HNK-1 carbohydrate is essential for medaka (Oryzias latipes) embryogenesis.

Carbohydrates are known to play essential roles in various biological processes including development. However, it remains largely unknown which carbohydrate structure takes part in each biological event. Here, we examined the roles of the human natural killer-1 (HNK-1) carbohydrate in medaka embryogenesis. We first cloned two medaka glucuronyltransferases, GlcAT-P and GlcAT-S, key enzymes for HNK-1 biosynthesis. Overexpression of these glucuronyltransferases affected morphogenetic processes. In addition, loss-of-function experiments revealed that GlcAT-P is physiologically indispensable for head morphogenesis and GlcAT-P depletion also led to markedly increased apoptosis. However, even when the apoptosis was blocked, abnormal head morphogenesis caused by GlcAT-P depletion was still observed, indicating that apoptosis was not the main cause of the abnormality. Moreover, in situ hybridization analyses indicated that GlcAT-P depletion resulted in the abnormal formation of the nervous system but not in cell specification. These results suggest that tight regulation of HNK-1 expression is essential for proper morphogenesis of medaka embryos.

Essential role of beta-1,4-galactosyltransferase 2 during medaka (Oryzias latipes) gastrulation.

Glycans are known to play important roles in vertebrate development; however, it is difficult to analyze in mammals because it takes place in utero. Therefore, we used medaka (Oryzias latipes) to clarify the roles of glycans during vertebrate development. beta-1,4-Galactosyltransferase is one of the key enzymes in the biosynthesis of the lactosamine structures that are commonly found on glycoproteins and glycolipids. Here, we show the essential role of beta4GalT2 during medaka development. Depletion of beta4GalT2 by morpholino antisense oligonucleotide injection resulted in significant morphological defects, such as shortening of the anterior-posterior axis, cyclopia, impaired somite segmentation, and head hypoplasia. In situ hybridization analyses revealed that the loss of beta4GalT2 led to defective anterior-posterior axis elongation during gastrulation without affecting organizer formation. Furthermore, a cell tracing experiment demonstrated that beta4GalT2 knockdown mainly affects mediolateral cell intercalation, which contributes to anterior-posterior axis elongation. A cell transplantation experiment indicated that glycans are produced by beta4GalT2 cell-autonomously during gastrulation. beta4GalT2 depletion also led to enhanced apoptosis; however, this does not account for the phenotypic abnormalities, as blockade of apoptosis failed to compensate for the beta4GalT2 depletion. Our data suggest that beta4GalT2 activity is cell-autonomously required in cells undergoing mediolateral cell intercalation, which drives extension movements during medaka gastrulation.

Distinct transport and intracellular activities of two GlcAT-P isoforms.

A neural glycotope, human natural killer-1 carbohydrate, is involved in synaptic plasticity. The key biosynthetic enzyme is a glucuronyltransferase, GlcAT-P, a type II membrane protein comprising an N-terminal cytoplasmic tail, transmembrane domain, stem region, and C-terminal catalytic domain. Previously, we reported that GlcAT-P has two isoforms differing in only the presence or absence of the N-terminal 13 amino acids (P-N13) in the cytoplasmic tail, but the functional distinction of these two isoforms has not been reported. Herein, we show that when expressed in Neuro2A cells, short form GlcAT-P (sGlcAT-P) exhibited significantly higher glucuronylation activity than the longer form (lGlcAT-P), despite their comparable specific activities in vitro. In addition, sGlcAT-P was strictly localized in Golgi apparatus, whereas lGlcAT-P was mainly localized in Golgi but partly in the endoplasmic reticulum. We demonstrated that the small GTPase, Sar1, recognized a dibasic motif in the cytoplasmic tail near P-N13 that was important for exiting the endoplasmic reticulum, and Sar1 interacted with sGlcAT-P more strongly than lGlcAT-P. Finally, the attachment of P-N13 to another glycosyltransferase, polysialyltransferase-I (ST8Sia-IV), had similar effects, such as reduced activity and entrapment within endoplasmic reticulum. These results suggest that P-N13 can control glycosyltransferase transport through Sar1 binding interference.

Different acceptor specificities of two glucuronyltransferases involved in the biosynthesis of HNK-1 carbohydrate.

The biosynthesis of HNK-1 carbohydrate is mainly regulated by two glucuronyltransferases (GlcAT-P and GlcAT-S) and a sulfotransferase (HNK-1 ST). To determine how the two glucuronyltransferases are involved in the biosynthesis of the HNK-1 carbohydrate, we prepared soluble forms of GlcAT-P and GlcAT-S fused with the IgG-binding domain of protein A and then compared the enzymatic properties of the two enzymes. Both GlcAT-P and GlcAT-S transferred glucuronic acid (GlcA) not only to a glycoprotein acceptor, asialoorosomucoid (ASOR), but also to a glycolipid acceptor, paragloboside. The activity of GlcAT-P toward ASOR was enhanced fivefold in the presence of sphingomyelin, but there were no effects on that of GlcAT-S. The activities of the two enzymes toward paragloboside were only detected in the presence of phospholipids such as phosphatidylinositol. Kinetic analysis revealed that the K(m) value of GlcAT-P for ASOR was 10 times lower than that for paragloboside. Furthermore, acceptor specificity analysis involving various oligosaccarides revealed that GlcAT-P specifically recognized N-acetyllactosamine (Galbeta1-4GlcNAc) at the nonreducing terminals of acceptor substrates. In contrast, GlcAT-S recognized not only the terminal Galbeta1-4GlcNAc structure but also the Galbeta1-3GlcNAc structure and showed the highest activity toward triantennary N-linked oligosaccharides. GlcAT-P transferred GlcA to NCAM about twice as much as to ASOR, whereas GlcAT-S did not show any activity toward NCAM. These lines of evidence indicate that these two enzymes have significantly different acceptor specificities, suggesting that they may synthesize functionally and structurally different HNK-1 carbohydrates in the nervous system.