4.5 Article

Application of high-mannose-type glycan-specific lectin from Oscillatoria Agardhii for affinity isolation of tumor-derived extracellular vesicles

期刊

ANALYTICAL BIOCHEMISTRY
卷 580, 期 -, 页码 21-29

出版社

ACADEMIC PRESS INC ELSEVIER SCIENCE
DOI: 10.1016/j.ab.2019.06.001

关键词

Extracellular vesicles; Exosomes; High-mannose-type glycans; Lectins; Tumor cells

向作者/读者索取更多资源

Tumor cells secrete membrane vesicles of various sizes, termed extracellular vesicles (EVs), which have gained increasing attention as potential tumor diagnostic markers. Tumor-derived EVs are enriched with high-mannose-type glycans. Here, we report the affinity isolation of EVs from human melanoma A375 cells by using high-mannose-type glycan-specific agglutinin from Oscillatoria Agardhii (OAA). Glycan analysis of melanoma EVs revealed the presence of high-mannose-type glycans with structural units preferred by OAA. We showed that in solution, OAA binds to melanoma EVs in a high-mannose-type glycan-dependent manner. Furthermore, OAA-immobilized beads were found to capture 60% of the particles and most proteinous components from melanoma EVs. Major EV glycoproteins that potentially interact with OAA were identified to be cluster of differentiation 109 (CD109), integrin alpha 6 and a disintegrin and metalloproteinase domain-containing protein 10 (ADAM10). In addition to melanoma EVs, OAA captured EVs from human lung cancer, glioblastoma and colon cancer cells, but not those from endothelial cells and fibroblasts. These results indicate that OAA-immobilized beads may serve as a novel platform for affinity-capture of tumor-derived EVs.

作者

我是这篇论文的作者
点击您的名字以认领此论文并将其添加到您的个人资料中。

评论

主要评分

4.5
评分不足

次要评分

新颖性
-
重要性
-
科学严谨性
-
评价这篇论文

推荐

Article Biochemistry & Molecular Biology

C-mannosylation regulates stabilization of RAMP1 protein and RMAP1-mediated cell migration

Hayato Mizuta, Ayane Takakusaki, Takehiro Suzuki, Keisuke Otake, Naoshi Dohmae, Siro Simizu

Summary: C-mannosylation is a unique type of protein glycosylation that affects protein functions, including secretion, intracellular localization, and stability. This study identifies a new C-mannosylated protein, RAMP1, and demonstrates that C-mannosylation enhances protein stability and cell migration activity.

FEBS JOURNAL (2023)

Article Biochemistry & Molecular Biology

Destabilization of vitelline membrane outer layer protein 1 homolog (VMO1) by C-mannosylation

Satoshi Yoshimoto, Takehiro Suzuki, Naoki Otani, Daisuke Takahashi, Kazunobu Toshima, Naoshi Dohmae, Siro Simizu

Summary: C-mannosylation is a rare type of protein glycosylation that affects protein secretion, intracellular localization, and stability. In this study, the VMO1 protein was found to be C-mannosylated at Trp(105), leading to destabilization and conformational changes in the protein.

FEBS OPEN BIO (2023)

Article Multidisciplinary Sciences

Cryo-EM structure of the transposon-associated TnpB enzyme

Ryoya Nakagawa, Hisato Hirano, Satoshi N. Omura, Suchita Nety, Soumya Kannan, Han Altae-Tran, Xiao Yao, Yuriko Sakaguchi, Takayuki Ohira, Wen Y. Wu, Hiroshi Nakayama, Yutaro Shuto, Tatsuki Tanaka, Fumiya K. Sano, Tsukasa Kusakizako, Yoshiaki Kise, Yuzuru Itoh, Naoshi Dohmae, John van der Oost, Tsutomu Suzuki, Feng Zhang, Osamu Nureki

Summary: Researchers used cryo-electron microscopy to determine the structure of the complex formed by ISDra2 TnpB, its cognate.RNA, and target DNA. They found that the.RNA had an unexpected structure and formed a pseudoknot, which is a common feature among all guide RNAs of Cas12 enzymes. Furthermore, the structure revealed how the compact TnpB recognized the omega RNA and cleaved the target DNA complementary to the guide. Comparison with Cas12 enzymes suggested that CRISPR-Cas12 effectors acquired the ability to recognize the protospacer-adjacent motif-distal end of the guide RNA-target DNA heteroduplex, possibly through asymmetric dimer formation or diverse REC2 insertions, enabling engagement in CRISPR-Cas adaptive immunity. Overall, this study provides mechanistic insights into TnpB function and advances our understanding of the evolution from transposon-encoded TnpB proteins to CRISPR-Cas12 effectors.

NATURE (2023)

Article Cell Biology

STING signalling is terminated through ESCRT-dependent microautophagy of vesicles originating from recycling endosomes

Yoshihiko Kuchitsu, Kojiro Mukai, Rei Uematsu, Yuki Takaada, Ayumi Shinojima, Ruri Shindo, Tsumugi Shoji, Shiori Hamano, Emari Ogawa, Ryota Sato, Kensuke Miyake, Akihisa Kato, Yasushi Kawaguchi, Masahiko Nishitani-Isa, Kazushi Izawa, Ryuta Nishikomori, Takahiro Yasumi, Takehiro Suzuki, Naoshi Dohmae, Takefumi Uemura, Glen N. N. Barber, Hiroyuki Arai, Satoshi Waguri, Tomohiko Taguchi

Summary: Stimulator of interferon genes (STING) is crucial for the immune response against DNA pathogens, and its degradation is mediated by endosomal sorting complexes required for transport (ESCRT) proteins. STING-positive vesicles derived from recycling endosomes are encapsulated into lysosomes after STING ubiquitination. This study provides insights into the regulation of STING and prevents hyperactivation of the immune response.

NATURE CELL BIOLOGY (2023)

Article Biochemistry & Molecular Biology

Epigenetic plasticity safeguards heterochromatin configuration in mammals

Kei Fukuda, Takeshi Shimi, Chikako Shimura, Takao Ono, Takehiro Suzuki, Kenta Onoue, Satoko Okayama, Hisashi Miura, Ichiro Hiratani, Kazuho Ikeda, Yasushi Okada, Naoshi Dohmae, Shigenobu Yonemura, Azusa Inoue, Hiroshi Kimura, Yoichi Shinkai

Summary: Heterochromatin, a critical architectural feature of eukaryotic chromosomes, plays crucial roles in cell type-specific gene expression and genome stability. The spatial organization of heterochromatin is poorly understood, and this study investigates the role of H3K9 and H3K27 methylation in heterochromatin organization. The findings demonstrate that the loss of H3K9 methylation leads to the redistribution of H3K27me3 and impaired condensation and spatial organization of heterochromatin in mammalian cells.

NUCLEIC ACIDS RESEARCH (2023)

Article Cell Biology

Targeting transglutaminase 2 mediated exostosin glycosyltransferase 1 signaling in liver cancer stem cells with acyclic retinoid

Xian-Yang Qin, Yutaka Furutani, Kento Yonezawa, Nobutaka Shimizu, Miyuki Kato-Murayama, Mikako Shirouzu, Yali Xu, Yumiko Yamano, Akimori Wada, Luc Gailhouste, Rajan Shrestha, Masataka Takahashi, Jeffrey W. W. Keillor, Ting Su, Wenkui Yu, Shinya Fujii, Hiroyuki Kagechika, Naoshi Dohmae, Yohei Shirakami, Masahito Shimizu, Takahiro Masaki, Tomokazu Matsuura, Harukazu Suzuki, Soichi Kojima

Summary: This study examined the effects of ACR on TG2 activity at a structural level and its role in depleting liver cancer stem cells (CSCs). It was found that ACR directly binds to TG2, induces oligomer formation, and inhibits the transamidase activity of cytoplasmic TG2. The loss of TG2 function suppressed stemness-related genes, spheroid proliferation, and induced cell death in a liver CSC subpopulation. Proteome analysis revealed that TG2 inhibition suppressed the expression of EXT1 and heparan sulfate biosynthesis. ACR could act as a novel TG2 inhibitor and TG2-mediated EXT1 signaling is a promising therapeutic target.

CELL DEATH & DISEASE (2023)

Article Multidisciplinary Sciences

Structure of a monomeric photosystem I core associated with iron-stress-induced-A proteins from Anabaena sp. PCC 7120

Ryo Nagao, Koji Kato, Tasuku Hamaguchi, Yoshifumi Ueno, Naoki Tsuboshita, Shota Shimizu, Miyu Furutani, Shigeki Ehira, Yoshiki Nakajima, Keisuke Kawakami, Takehiro Suzuki, Naoshi Dohmae, Seiji Akimoto, Koji Yonekura, Jian-Ren Shen

Summary: By using cryo-EM, the authors determined the structure of a PSI monomer associated with six IsiA proteins in Anabaena, providing insights into the diversity and functions of IsiAs. IsiAs are expressed in cyanobacteria under iron-deficient conditions, and the binding properties and functional roles of IsiAs in PSI were still unknown in Anabaena. The cryo-EM structure of a PSI-IsiA supercomplex isolated from iron-deficient Anabaena revealed the association of six IsiA subunits with a PSI core monomer, and the absence of a PsaL subunit due to the occupation of its position by the C-terminal domain of IsiA2.

NATURE COMMUNICATIONS (2023)

Article Cell Biology

Lysine long-chain fatty acylation regulates the TEAD transcription factor

Kota Noritsugu, Takehiro Suzuki, Kosuke Dodo, Kenji Ohgane, Yasue Ichikawa, Kota Koike, Satoshi Morita, Takashi Umehara, Kenji Ogawa, Mikiko Sodeoka, Naoshi Dohmae, Minoru Yoshida, Akihiro Ito

Summary: TEAD transcription factors regulate the transcriptional output of Hippo signaling by phosphorylating YAP and TAZ as coactivators. Recent studies have shown that cysteine palmitoylation also plays a role in regulating TEAD activity. This study discovers lysine long-chain fatty acylation as another post-translational modification of TEADs. Lysine fatty acylation enhances the interaction between TEADs and YAP/TAZ, contributing to their transcriptional activity. Interestingly, lysine fatty acylation of TEADs increases upon Hippo signaling activation, despite a decrease in cysteine acylation. These findings provide new insights into the regulation of TEAD activity through fatty-acyl modifications.

CELL REPORTS (2023)

Article Biochemical Research Methods

Comparative proteomic analysis of glomerular proteins in IgA nephropathy and IgA vasculitis with nephritis

Hajime Kaga, Hirotoshi Matsumura, Ayano Saito, Masaya Saito, Fumito Abe, Takehiro Suzuki, Naoshi Dohmae, Masafumi Odaka, Atsushi Komatsuda, Hideki Wakui, Naoto Takahashi

Summary: A comparative proteomic analysis of glomerular proteins was performed in IgAN and IgAVN patients, revealing shared molecular mechanisms for glomerular injury in both diseases except for enhanced glomerular complement activation in IgAN.

CLINICAL PROTEOMICS (2023)

Article Biochemistry & Molecular Biology

The two-step cargo recognition mechanism of heterotrimeric kinesin

Xuguang Jiang, Tadayuki Ogawa, Kento Yonezawa, Nobutaka Shimizu, Sotaro Ichinose, Takayuki Uchihashi, Wataru Nagaike, Toshio Moriya, Naruhiko Adachi, Masato Kawasaki, Naoshi Dohmae, Toshiya Senda, Nobutaka Hirokawa

Summary: This study reveals the molecular mechanism of specific and dynamic cargo-binding of kinesin complexes. The two-step cargo recognition and stabilization mechanism of kinesins provides novel insights into intracellular trafficking machinery.

EMBO REPORTS (2023)

Article Biochemistry & Molecular Biology

Biogenesis of fibrils requires C-mannosylation of PMEL

Ryota Kawahara, Tomoko Usami, Satoko Arakawa, Hiroki Kamo, Takehiro Suzuki, Ryosuke Komatsu, Hiroyuki Hara, Yuki Niwa, Erina Shimizu, Naoshi Dohmae, Shigeomi Shimizu, Siro Simizu

Summary: PMEL is a melanocyte-specific glycoprotein involved in melanosome maturation. It undergoes C-mannosylation at multiple tryptophan residues in its core amyloid fragment and N-terminal fragment. The C-mannosylation of PMEL is required for proper melanosome development and fibril formation.

FEBS JOURNAL (2023)

Article Multidisciplinary Sciences

Epigenetic mechanisms to propagate histone acetylation by p300/CBP

Masaki Kikuchi, Satoshi Morita, Masatoshi Wakamori, Shin Sato, Tomomi Uchikubo-Kamo, Takehiro Suzuki, Naoshi Dohmae, Mikako Shirouzu, Takashi Umehara

Summary: In this study, the authors discovered that p300/CBP recognizes and acetylates histone H4 N-terminal tail (NT) acetylation (ac) in a nucleosome, and also acetylates non-H4 histone NTs within the same nucleosome. The authors propose a model in which p300/CBP replicates histone N-terminal tail acetylation within the H3-H4 tetramer and transfers it to the H2B-H2A dimers to activate context-dependent gene transcription through local nucleosome destabilization.

NATURE COMMUNICATIONS (2023)

Article Cell Biology

A non-nucleotide agonist that binds covalently to cysteine residues of STING

Kentaro Matsumoto, Shenwei Ni, Hiroyuki Arai, Takashi Toyama, Yoshiro Saito, Takehiro Suzuki, Naoshi Dohmae, Kojiro Mukai, Tomohiko Taguchi

Summary: Phenylarsine oxide (PAO) can activate mouse STING by covalently binding to cysteine residues, independent of cGAS or cGAMP. STING activation with PAO requires ER-to-Golgi trafficking and palmitoylation of STING. The study reveals that cysteine residues in STING can serve as a novel target for the development of STING agonists.

CELL STRUCTURE AND FUNCTION (2023)

Article Biochemistry & Molecular Biology

Substrate complex structure, active site labeling and catalytic role of the zinc ion in cysteine glycosidase

Shun Maruyama, Kota Sawano, Satoko Amaki, Takehiro Suzuki, Satoru Narita, Kenta Kimura, Takatoshi Arakawa, Chihaya Yamada, Yukishige Ito, Naoshi Dohmae, Kiyotaka Fujita, Akihiro Ishiwata, Shinya Fushinobu

Summary: This study investigated the catalytic mechanism and substrate binding structure of the beta-l-arabinofuranosidase HypBA1 from Bifidobacterium longum. Zn2+ ion and cysteine were found to play key roles in catalysis, and the mode of substrate binding affected the catalytic activity.

GLYCOBIOLOGY (2022)

Article Biochemistry & Molecular Biology

Splicing modulators elicit global translational repression by condensate-prone proteins translated from introns

Jagat K. Chhipi-Shrestha, Tilman Schneider-Poetsch, Takehiro Suzuki, Mari Mito, Khalid Khan, Naoshi Dohmae, Shintaro Iwasaki, Minoru Yoshida

Summary: Splicing modulators induce the translation of intron-retained mRNAs, generating truncated proteins. These truncated proteins have intrinsically disordered regions, form insoluble cellular condensates, and trigger the proteotoxic stress response, thereby inhibiting protein synthesis in cells.

CELL CHEMICAL BIOLOGY (2022)

Article Biochemical Research Methods

Cationic and anionic detergent buffers in sequence yield high-quality genomic DNA from diverse plant species

Saranya Krishnan, Shina Sasi, Preshobha Kodakkattumannil, Salima Al Senaani, Geetha Lekshmi, Martin Kottackal, Khaled M. A. Amiri

Summary: This study aimed to develop an efficient DNA extraction protocol suitable for diverse plant species and tissues. A reliable and consistent protocol was described for the extraction of high-quality DNA from difficult-to-extract plant species. The optimized protocol was successful in extracting high-quality DNA from various plant species and tissues, making it useful for genomic studies of recalcitrant plants.

ANALYTICAL BIOCHEMISTRY (2024)

Article Biochemical Research Methods

Pyrophosphate detection method using 5-Br-PAPS to detect nucleic acid amplification - Application to LAMP method

Eisaku Hokazono, Saori Fukumoto, Takeshi Uchiumi, Susumu Osawa

Summary: This study proposes a method for detecting nucleic acid amplification using pyrophosphate, which requires only two reagents and an automated analyzer. The technique has high sensitivity and reproducibility, and can detect pyrophosphate within 10 minutes. Therefore, this method has the potential to be a new, rapid, and simple detection technique for amplified nucleic acids.

ANALYTICAL BIOCHEMISTRY (2024)

Article Biochemical Research Methods

SURE gel electrophoresis: A method for improved detection and purification of dilute nucleic acid samples

Drew S. Sowersby, L. Kevin Lewis

Summary: SURE electrophoresis is a new method for concentrating samples in gels, which allows efficient detection of highly dilute DNA samples. This approach generates single bands with enhanced signal intensities and minimal band broadening.

ANALYTICAL BIOCHEMISTRY (2024)

Article Biochemical Research Methods

Echinacoside regulates PI3K/AKT/HIF-1α/VEGF cross signaling axis in proliferation and apoptosis of breast cancer

Hongyi Liang, Guoliang Yin, Guangxi Shi, Zhiyong Liu, Xiaofei Liu, Jingwei Li

Summary: The mechanism of Echinacoside (ECH) in treating breast cancer (BC) was explored through network pharmacology and experimental validation. It was found that ECH plays an important role in anti-BC by regulating the PI3K/AKT/HIF-1 alpha/VEGF signaling pathway, and it exhibits multi-target and multi-pathway effects.

ANALYTICAL BIOCHEMISTRY (2024)

Article Biochemical Research Methods

Comparison of colorimetric, fluorometric, and liquid chromatography-mass spectrometry assays for acetyl-coenzyme A

Daniel S. Kantner, Emily Megill, Anna Bostwick, Vicky Yang, Carmen Bekeova, Alexandria Van Scoyk, Erin L. Seifert, Michael W. Deininger, Nathaniel W. Snyder

Summary: This study compared the results of different methods for measuring the amount of acetyl-Coenzyme A. The colorimetric ELISA kit did not produce interpretable results, while the fluorometric enzymatic kit showed comparable results to the LC-MS-based methods depending on the matrix and extraction conditions. LC-MS/MS and LC-HRMS methods produced well-aligned results, especially when using stable isotope-labeled internal standards.

ANALYTICAL BIOCHEMISTRY (2024)

Article Biochemical Research Methods

Synergistic co-catalytic nanozyme system for highly efficient one-pot colorimetric sensing at neutral pH: Combining molybdenum trioxide and Fe (III)-Modified covalent triazine framework

Jingyan Xu, Hanying Tan, Xionghui Ma, Linjing Su, Zhi Zhang, Yuhao Xiong

Summary: This study investigates the co-catalytic capabilities of MoO3 nanosheets in enhancing the enzyme-like catalytic activity of a two-dimensional ultrathin Fe(III)-modified covalent triazine framework (Fe-CTF) under neutral pH conditions. The Fe-CTF/MoO3 co-catalytic system exhibits enzyme-mimicking activity and enables the development of a colorimetric method for glucose detection. Furthermore, a straightforward one-pot colorimetric method is established for screening XOD inhibitors.

ANALYTICAL BIOCHEMISTRY (2024)

Article Biochemical Research Methods

A novel fusion technology utilizing complex network and sequence information for FAD-binding site identification

Lichao Zhang, Kang Xiao, Xueting Wang, Liang Kong

Summary: A novel fusion technology was designed to identify FAD-binding sites, achieving the best results on two independent test datasets and outperforming existing methods significantly. The high performance and certainty of the method were demonstrated through statistical tests and cross-entropy loss analysis.

ANALYTICAL BIOCHEMISTRY (2024)

Article Biochemical Research Methods

Investigation of the electrochemical properties of edoxaban using glassy carbon and boron-doped diamond electrodes and development of an eco-friendly and cost effective voltammetric method for its determination

Abdulkadir Kilic, Mehmet Aslan, Abdulkadir Levent

Summary: This study developed a simple, rapid, sensitive, and selective voltammetric technique for the electrochemical characterization and detection of the highly risky drug Edoxaban. The optimized voltammetric method showed good analytical working range and was successfully applied to urine and tablet samples.

ANALYTICAL BIOCHEMISTRY (2024)

Article Biochemical Research Methods

Application of liquid-based colorimetric method for high throughput screening of bioplastic-degrading strains using esterase assay

Su Hyun Kim, Nara Shin, Jong-Min Jeon, Jeong-Jun Yoon, Jeong Chan Joo, Hee Taek Kim, Shashi Kant Bhatia, Yung-Hun Yang

Summary: To address environmental issues caused by traditional plastics, bioplastics have gained attention as alternatives. Although bioplastics have better degradability, their degradation still takes longer than anticipated. This study proposes a novel screening method to identify bioplastic degraders faster, saving time and providing more quantitative data.

ANALYTICAL BIOCHEMISTRY (2024)

Article Biochemical Research Methods

Disposable biosensor based on ionic liquid, carbon nanofiber and poly (glutamic acid) for tyramine determination

Irem Okman Kocoglu, Pinar Esra Erden, Esma Kilic

Summary: In this study, an electrochemical biosensor based on carbon nanofibers and ionic liquid modification was constructed for tyramine detection. The biosensor showed linear response, low detection limit, high sensitivity, and exhibited good reproducibility, stability, and anti-interference ability.

ANALYTICAL BIOCHEMISTRY (2024)

Article Biochemical Research Methods

LAMPrimers iQ: New primer design software for loop-mediated isothermal amplification (LAMP)

Liana U. Akhmetzianova, Timur M. Davletkulov, Assol R. Sakhabutdinova, Alexey Chemeris, Irek M. Gubaydullin, Ravil R. Garafutdinov

Summary: A new program called LAMPrimers iQ has been developed for high-quality LAMP primer design, and its advantages in providing higher specificity and reliable detection of viral RNA were validated using SARS-CoV-2 coronavirus RNA as a model target.

ANALYTICAL BIOCHEMISTRY (2024)

Article Biochemical Research Methods

Direct competitive assay for HER2 detection in human plasma using Bloch surface wave-based biosensors

Tommaso Pileri, Alberto Sinibaldi, Agostino Occhicone, Norbert Danz, Elena Giordani, Matteo Allegretti, Frank Sonntag, Peter Munzert, Patrizio Giacomini, Francesco Michelotti

Summary: This study developed a biosensing device based on one-dimensional photonic crystal to detect HER2 in breast cancer. The device combines label-free and fluorescence operation modes, allowing for real-time and accurate detection in less than 20 minutes. It offers a promising technique for combined label-free and fluorescence detection in disease diagnosis and therapeutic monitoring.

ANALYTICAL BIOCHEMISTRY (2024)