1,721,022 research outputs found
Glycobiology of selectin
No full textSelectins, carbohydrate-binding molecules, bind to fucosylated and sialylated glycoprotein ligands, and are found on endothelial cells, leukocytes and platelets. They can be classified into E-, L- and P-selectins, and are involved in trafficking of cells of the innate immune system, T lymphocytes and platelets via binding with specific ligands. An absence of selectins or selectin ligands has serious consequences in mice or humans, leadinq to recurrent bacterial infections and persistent disease. Selectins are involved in constitutive lymphocyte homing and chronic and acute inflammation processes, including post-ischemic inflammation in muscle, kidney, heart, skin inflammation, athero-sclerosis, glomerulonephritis and lupus erythematosus. Selectin-neutralizing monoclonal antibodies, recombinant soluble P-selectin glycoprotein ligand 1 and small-molecule inhibitors of selectins have been tested in clinical trials on patients with multiple trauma, cardiac indications and pediatric asthma, respectively. Anti-selectin antibodies have also been successfully used in preclinical models to deliver imaging contrast agents and therapeutics to sites of inflammation. The contributions of selectins and selectin ligands to signalling deserve further study, which will allow a much more detailed analysis of the contributions of selectins in models of inflammation, haemostasis, haematopoiesis, wound healing, atherogenesis, and tumor metastasis.open
Implication of aberrant glycosylation in cancer and use of lectin for cancer biomarker discovery
No full textAberrant glycosylation is frequently found in cancer, and efforts for biomarker discovery include the preparation of aberrant glycoproteins as promising analytes. Several lectins that bind to aberrant glycans and can be thus used to capture and enrich aberrant glycoproteins in the frontal stage during biomarker discovery are to be introduced.open
Application of cancer‐associated glycoforms and glycan‐binding probes to an in vitro diagnostic multivariate index assay for precise diagnoses of cancer
No full textPersonalized medicine has emerged as a widely accepted trend in medicine for the efficacious and safe treatment of various diseases. It covers every medical treatment tailored according to various properties of individuals. Cancer-associated glycosylation mirrors cancer states more precisely, and this “sweet side of cancer” is thus intended to spur the development of an advanced in vitro diagnostic system. The changes of glyco-codes are often subtle and thus not easy to trace, thereby making it difficult to discriminate changes from various compounding factors. Special glycan-binding probes, often lectins, can be paired with aglycosylated antibodies to enable quantitative and qualitative measurements of glycoforms. With the in vitro diagnosis multivariate index assay (IVDMIA) considered to be capable of yielding patient-specific results, the combinatorial use of multiple glycoproteins may be a good modality to ensure disease-specific, personalized diagnoses.open
Pros and cons of using aberrant glycosylation as companion biomarkers for therapeutics in cancer
No full textCancer treatment has been stratified by companion biomarker tests that serve to provide information on the genetic status of cancer patients and to identify patients who can be expected to respond to a given treatment. This stratification guarantees better efficiency and safety during treatment. Cancer patients, however, marginally benefit from the current companion biomarker-aided treatment regimens, presumably because companion biomarker tests are dependent solely on the mutation status of several genes status quo. In the true sense of the term, “personalized medicine”, cancer patients are deemed to be identified individually by their molecular signatures, which are not necessarily confined to genetic mutations. Glycosylation is tremendously dynamic and shows alterations in cancer. Evidence is accumulating that aberrant glycosylation contributes to the development and progression of cancer, holding the promise for use of glycosylation status as a companion biomarker in cancer treatment. There are, however, several challenges derived from the lack of a reliable detection system for aberrant glycosylation, and a limited library of aberrant glycosylation. The challenges should be addressed if glycosylation status is to be used as a companion biomarker in cancer treatment and contribute to the fulfillment of personalized medicine.open
Cloning and characterization of a gene encoding ABP57, a soluble auxin-binding protein
No full textAuxin-binding protein 57 (ABP57), a soluble auxin-binding protein, acts as a receptor to activate plasma membrane (PM) H+-ATPase. Here, we report the cloning of abp57 and the biochemical characterization of its protein expressed in E. coli. The analysis of internal amino acid sequences of ABP57 purified from rice shoots enabled us to search for the corresponding gene in protein DB of NCBI. Further BLAST analysis showed that rice has four abp57-like genes and maize has at least one homolog. Interestingly, Arabidopsis seems to have no homolog. Recombinant ABP57 expressed in E. coli caused the activation of PM H+-ATPase regardless of the existence of IAA. Scatchard analysis showed that the recombinant protein has relatively low affinity to IAA as compared to natural ABP57. These results collectively support the notion that the cloned gene is responsible for ABP57.open
Expression level and glycan dynamics determine the net effects of TIMP-1 on cancer progression
No full textTissue inhibitor of metalloproteinases (TIMPs; TIMP-1, -2, -3 and -4) are endogenous inhibitor for matrix metalloproteinases (MMPs) that are responsible for remodeling the extracellular matrix (ECM) and involved in migration, invasion and metastasis of tumor cells. Unlike under normal conditions, the imbalance between MMPs and TIMPs is associated with various diseased states. Among TIMPs, TIMP-1, a 184-residue protein, is the only N-linked glycoprotein with glycosylation sites at N30 and N78. The structural analysis of the catalytic domain of human stromelysin-1 (MMP-3) and human TIMP-1 suggests new possibilities of the role of TIMP-1 glycan moieties as a tuner for the proteolytic activities by MMPs. Because the TIMP-1 glycosylation participate in the interaction, aberrant glycosylation of TIMP-1 presumably affects the interaction, thereby leading to pathogenic dysfunction in cancer cells. TIMP-1 has not only the cell proliferation activities but also anti-oncogenic properties. Cancer cells appear to utilize these bilateral aspects of TIMP-1 for cancer progression; an elevated TIMP-1 level exerts to cancer development via MMP-independent pathway during the early phase of tumor formation, whereas it is the aberrant glycosylation of TIMP-1 that overcome the high anti-proteolytic burden. The aberrant glycosylation of TIMP-1 can thus be used as staging and/or prognostic biomarker in colon cancer.open
Quantitative analysis of an aberrant glycoform of TIMP1 from colon cancer serum by L-PHA-enrichment and SISCAPA with MRM mass spectrometry
No full textVariations in glycosylation levels or in the glycoprofile of a certain glycoprotein in tumor-related sera have been widely reported and can be used as a means of differentiation. However, quantitative mass analysis of glycoproteins is difficult because of their high structural complexity and low mass sensitivity of glycopeptides. Therefore, more powerful technologies are required for the discovery of these potential biomarkers. Tissue inhibitor of metalloproteinase 1 (TIMP1), a glycoprotein typically present at a low concentration in serum, is known to be aberrantly glycosylated in colorectal cancer cell lines as a result of the terminal addition of β-1,6-N- acetylglucosamine (β-1,6-GlcNAc) by N-acetylglucosaminyltransferase-V (GnT-V), which is reportedly up-regulated in invasive/metastatic cancer cells. In this report, a highly sensitive method is presented for the quantitative analysis of aberrant GlcNAcylated TIMP1 in the serum of colorectal cancer (CRC) patients. Glycoproteins having an N-linked glycan terminating with β-1,6-GlcNAc were enriched by phytohemagglutinin-L4 (L-PHA), a lectin that specifically recognizes the β-1,6-GlcNAc moiety of N-linked glycan. The L-PHA-enriched glycoproteins were digested in solution with trypsin. With the use of a monoclonal anti-peptide TIMP1 antibody linked covalently to magnetic beads, a unique target peptide (antigen) of TIMP1 was immuno-enriched from the L-PHA-enriched tryptic digests and analyzed quantitatively by multiple reaction monitoring (MRM) mass analysis. The systematic coupling of L-PHA lectin enrichment followed by stable isotope standards and capture by anti-peptide antibodies (SISCAPA) with MRM mass analysis afforded quantitation of TIMP1 at attomolar (10-18) concentrations. An aberrantly GlcNAcylated substoichiometric TIMP1 isoform was quantified at approximately 0.8 ng/mL serum, using sample equivalent to only 1.7 μL of serum from a CRC patient. This approach provides a useful tool for the quantitation of a specific aberrant glycoform from human serum containing a variety of protein isoforms and may be helpful in studies of biological function as it pertains to protein glycan heterogeneity.open
One-step genotyping method in CRISPR based on short inner primer-assisted, tetra primer-paired amplifications
No full textBase editors and prime editors induce precise DNA modifications over one or several nucleotides in eukaryotic cells. The T7E1 assay has been widely adopted for the assessment of genome editing, but it has several limitations in the applications for prime editing and base editing due to low sensitivity, inaccuracy and additional disadvantages. Here, we propose a short inner primer-assisted, tetra primer-paired amplification (SIPATA) method as an alternative to T7E1 analysis. SIPATA is a PCR-based method in which two long outer and two short (15 nt) inner primers are used for the amplification of a specific genotype in the presence of Hot start-Taq. One of the inner primers carries a 3'-terminally wild-type nucleotide sequence, and the other carries a post-editing sequence. Under optimized conditions, SIPATA enabled sensitive and accurate genotyping of single-nucleotide conversions by base editors and prime editors. Furthermore, SIPATA could be applied to trace low levels of DNA modifications achieved by HDR-mediated gene correction or chimerism during the generation of model animals. Multiplexed genotyping was also possible without compromising those multifaceted analytical advantages of SIPATA. Our findings demonstrate that SIPATA offers a robust, fast and sensitive genotyping platform for single-nucleotide variations in a variety of CRISPR applications.
Unbiased investigation of specificities of prime editing systems in human cells
No full textPrime editors (PEs) enable targeted precise editing, including the generation of substitutions, insertions and deletions, in eukaryotic genomes. However, their genome-wide specificity has not been explored. Here, we developed Nickase-based Digenome-seq (nDigenome-seq), an in vitro assay that uses whole-genome sequencing to identify single-strand breaks induced by CRISPR (clustered regularly interspaced short palindromic repeats)-Cas9 (CRISPR-associated protein 9) nickase. We used nDigenome-seq to screen for potential genome-wide off-target sites of Cas9 H840A nickase, a PE component, targeted to nine human genomic sites. Then, using targeted amplicon sequencing of off-target candidates identified by nDigenome-seq, we showed that only five off-target sites showed detectable PE-induced modifications in cells, at frequencies ranging from 0.1 to 1.9%, suggesting that PEs provide a highly specific method of precise genome editing. We also found that PE specificity in human cells could be further improved by incorporating mutations from engineered Cas9 variants, particularly eSpCas9 and Sniper Cas9, into PE.
Depletion of BIS sensitizes A549 cells to treatment with cisplatin
No full textBcl-2 interacting cell death suppressor (BIS), an anti-stress and ant-apoptotic protein, has been reported to be expressed at high levels in various cancers. In a previous study, we reported on a high level of expression of BIS in non small cell lung cancer tissues. To explore the significance this finding in lung cancer, in this study, we investigated the effect of BIS depletion on the survival of A549 cells upon treatment with anti-tumor agents. BIS knock out A549 cells, prepared by the CRISPR/Cas9 system, revealed a substantial decrease in survival to cisplatin treatment. Western blotting and quantitative real time PCR assays indicated that, among the anti-apoptotic Bcl-2 family proteins, the expression of Mcl-1 was decreased by BIS depletion at the protein level not at the mRNA level. Since BIS expression has been shown to be regulated by HSF1, we subsequently illustrated the sensitization effect of KRIBB11, a HSF1 inhibitor, on cisplatin-induced toxicity in A549 cells, accompanied by a decrease in both BIS and Mcl-1 expression. Our results suggest that BIS-mediated Mcl-1 stabilization represents a potential therapeutic target for cancer therapy.open
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