Article
Biochemical Research Methods
Adam C. Swensen, Dusan Velickovic, Sarah M. Williams, Ronald J. Moore, Le Z. Day, Sherry Niessen, Sarah Hennessy, Camilo Posso, Mara Monetti, Wei-Jun Qian, Jon Jacobs, Laurence Whiteley, Ying Zhu, Paul D. Piehowski
Summary: Despite their small size, islets of Langerhans play a crucial role in maintaining systemic energy balance in the body. This study uses advanced technologies to investigate the protein profiles of different features within the islet, revealing unique protein signatures in the inner vasculature that indicate increased innervation and intra-islet neuron-like crosstalk. The data also prove useful in identifying localized structure-specific drug-target interactions.
MOLECULAR & CELLULAR PROTEOMICS
(2022)
Article
Hematology
Yuanliang Peng, Li Tang, Yanan Li, Jianhui Song, Hong Liu, Pan Wang, Zhizhou Zhong, Yifei Yang, Shihui Wang, Lixiang Chen, Ji Zhang, Shijie Zhang, Zi Wang, Min Li, Long Liang, Jing Liu
Summary: This study characterized the quantitative and qualitative analysis of phosphorylated proteins during human early erythropoiesis using tandem mass-tagging technology. The results revealed the important regulatory role of phosphorylated proteins in erythroid development and identified functional modules related to cell cycle and signaling pathways.
BRITISH JOURNAL OF HAEMATOLOGY
(2022)
Article
Cell Biology
Fabien Forest, David Laville, Cyril Habougit, Vanessa Da Cruz, Francois Casteillo, Violaine Yvorel, Sandrine Bard-Sorel, William Godard, Tiphanie Picot, Olivier Tiffet, Jean-Luc Perrot, Michel Peoc'h
Summary: The study analyzed 42 lung adenocarcinoma skin metastasis samples collected between 2010 and 2020 from a database of 2659 lung adenocarcinomas. The results showed that skin metastases of lung adenocarcinoma have a specific histopathological profile, indicating differences from other metastatic sites.
Article
Biochemistry & Molecular Biology
Qing Li, Jiong Zhang, Yi Fang, Yan Dai, Ping Jia, Ziyan Shen, Sujuan Xu, Xiaoqiang Ding, Feng Zhou
Summary: This study identified phosphorylated proteins in urinary extracellular vesicles (uEVs) as potential biomarkers for diabetic nephropathy (DN) using ultra-high-sensitivity quantitative phosphoproteomics. The researchers detected 233 phosphopeptides within the uEVs, with 47 phosphoproteins showing significant alterations in DN patients. Further validation experiments confirmed the importance of phosphorylated aquaporin-2 and phosphorylated glycogen synthase kinase-3 beta in DN.
Article
Multidisciplinary Sciences
Nikolas L. Jorstad, Janet H. T. Song, David Exposito-Alonso, Hamsini Suresh, Nathan Castro-Pacheco, Fenna M. Krienen, Anna Marie Yanny, Jennie Close, Emily Gelfand, Brian Long, Stephanie C. Seeman, Kyle J. Travaglini, Soumyadeep Basu, Marc Beaudin, Darren Bertagnolli, Megan Crow, Song-Lin Ding, Jeroen Eggermont, Alexandra Glandon, Jeff Goldy, Katelyn Kiick, Thomas Kroes, Delissa Mcmillen, Trangthanh Pham, Christine Rimorin, Kimberly Siletti, Saroja Somasundaram, Michael Tieu, Amy Torkelson, Guoping Feng, William D. Hopkins, Thomas Hollt, C. Dirk Keene, Sten Linnarsson, Steven A. Mccarroll, Boudewijn P. Lelieveldt, Chet C. Sherwood, Kimberly Smith, Christopher A. Walsh, Alexander Dobin, Jesse Gillis, Ed S. Lein, Rebecca D. Hodge, Trygve E. Bakken
Summary: Our study used snRNA-seq to analyze the transcriptome of the cerebral cortex in humans and four nonhuman primate species. We found that cell types in the cerebral cortex are highly conserved among great apes, with marmosets showing some unique cell type proportions. Profiling gorillas allowed us to identify expression differences between humans and chimpanzees that are specialized in humans. We also discovered that neuronal gene expression has evolved faster on the human lineage, while glial expression changes have occurred rapidly in all species. Human-specific DEGs are enriched near adaptive genomic changes and may contribute to specialized cortical function.
Article
Multidisciplinary Sciences
Caitriona M. McEvoy, Julia M. Murphy, Lin Zhang, Sergi Clotet-Freixas, Jessica A. Mathews, James An, Mehran Karimzadeh, Delaram Pouyabahar, Shenghui Su, Olga Zaslaver, Hannes Roest, Rangi Arambewela, Lewis Y. Liu, Sally Zhang, Keith A. Lawson, Antonio Finelli, Bo Wang, Sonya A. MacParland, Gary D. Bader, Ana Konvalinka, Sarah Q. Crome
Summary: This study presents a detailed cellular map of healthy human kidney and explores the complexity of kidney-resident immune cells using single cell RNA sequencing. Sex-based differences in gene expression of kidney parenchymal cells were observed.
NATURE COMMUNICATIONS
(2022)
Article
Chemistry, Analytical
Luyan Meng, Bing Wang, Baichun Wang, Quanshou Feng, Sijia Zhang, Zi Xiong, Shun Zhang, Ting Cai, Chuan-Fan Ding, Yinghua Yan
Summary: A Ti4+-functionalized magnetic covalent organic framework material, mCOF@epsilon-PL@THBA-Ti4+, was proposed for efficient phosphopeptide enrichment. The material was built through post-synthesis modification using immobilized metal ion affinity chromatography (IMAC) enrichment strategy. The magnetic nanocomposite showed excellent performance in phosphopeptide enrichment, with good selectivity, low detection limit, and high loading capacity.
Editorial Material
Cell Biology
Susanne Zellner, Christian Behrends
Summary: Selective autophagy receptors play a role in degrading cellular components of different sizes and rigidity. By combining various techniques, the study identified new autophagy substrates and found that some substrates are degraded through endosomal microautophagy instead of canonical autophagy pathways.
Article
Chemistry, Multidisciplinary
Dustin T. King, Jesus E. Serrano-Negron, Yanping Zhu, Christopher L. Moore, Matthew D. Shoulders, Leonard J. Foster, David J. Vocadlo
Summary: Posttranslational modifications can alter protein stability and cellular physiology. This study presents an unbiased proteome-wide approach to explore the influence of protein modifications on thermodynamic stability. Using this approach, the authors identify a set of proteins that are destabilized by O-GlcNAc modification and form distinct macromolecular complexes.
JOURNAL OF THE AMERICAN CHEMICAL SOCIETY
(2022)
Article
Biochemistry & Molecular Biology
Benjamin Ober-Reynolds, Winston R. Becker, Karina Jouravleva, Samson M. Jolly, Phillip D. Zamore, William J. Greenleaf
Summary: Studies have shown that TtAgo uses biophysical adaptations similar to those of eukaryotic Argonautes for rapid association but requires more extensive complementarity to achieve high-affinity target binding. The cleavage rates of TtAgo vary widely based on the DNA guide, suggesting that only a subset of guides cleaves targets on physiologically relevant timescales.
Article
Multidisciplinary Sciences
Andrew M. M. Hogan, A. S. M. Zisanur Rahman, Anna Motnenko, Aakash Natarajan, Dustin T. T. Maydaniuk, Beltina Leon, Zayra Batun, Armando Palacios, Alejandra Bosch, Silvia T. T. Cardona
Summary: This study systematically investigated the effects of antibiotics on the cell envelope of Burkholderia cepacia complex, and identified resistance and susceptibility determinants associated with the cell envelope. The findings provide insights into new drug targets and potential antibiotic combination strategies, which can contribute to improving antibacterial therapies.
NATURE COMMUNICATIONS
(2023)
Article
Biochemical Research Methods
Raiha Tahir, Santosh Renuse, Savita Udainiya, Anil K. Madugundu, Jevon A. Cutler, Raja Sekhar Nirujogi, Chan Hyun Na, Yaoyu Xu, Xinyan Wu, Akhilesh Pandey
Summary: This study reveals significant signaling differences between two common KRAS mutations, highlighting distinct signaling mechanisms implicated in G12D and G13D mutations. By targeting a cell surface molecule MPZL1 and confirming its impact on proliferation of G12D cells, the study underscores the potential for individualized treatments based on subtle differences between related oncogenic mutants.
JOURNAL OF PROTEOME RESEARCH
(2021)
Article
Biochemical Research Methods
Xu Yan, Xinbao Gong, Tao Lin, Maosen Lin, Ping Qin, Jing Ye, Hailing Li, Qiwen Hong, Mengxian Li, Ya Liu, Yunsheng Li, Xiujuan Wang, Yunhai Zhang, Yinghui Ling, Hongguo Cao, Xiaorong Zhang, Fugui Fang
Summary: The study investigates the molecular changes controlling the onset of puberty in goats by identifying differentially phosphorylated proteins (DPPs) and phosphorylation sites (DPSs). The results provide evidence for a complex interaction network in goat hypothalamus proteins that affects puberty. This data may help identify new puberty-regulating candidates and contribute to understanding the physiological mechanism of puberty onset in mammals.
JOURNAL OF PROTEOMICS
(2022)
Article
Developmental Biology
Teresa Rayon, Rory J. Maizels, Christopher Barrington, James Briscoe
Summary: By using single-cell mRNA sequencing, we investigated the cellular diversity and complexity in the developing human neural tube, identifying dozens of distinct cell types and reconstructing differentiation pathways of specific neuronal subtypes. Comparison with mouse neural tube development showed overall similarity with some highlighted human-specific features. This data provides a catalog of gene expression and cell type identity in the human neural tube, supporting future studies of sensory and motor control systems. The data can be explored at https://shiny.crick.ac.uk/scviewer/neuraltube/.
Article
Chemistry, Multidisciplinary
Dongxue Zhang, Qin Qin, Liang Qiao
Summary: Bacterial antimicrobial resistance (AMR) poses a severe threat to global health and development. Current research on AMR mechanism focuses on bacterial cell populations, but fails to account for the heteroresistance exhibited by individual cells. This study developed a method using mass spectrometry to analyze the metabolic profiles of single bacterial cells and investigate AMR at the individual cell level. The results showed heterogeneity among ESBL-E. coli cells and revealed the involvement of metabolic pathways in bacterial filamentation against antibiotics. This single bacterial cell analysis method has promising applications in studying various AMR mechanisms and uncovering the heterogeneity of bacterial AMR.
CHINESE CHEMICAL LETTERS
(2023)
Article
Chemistry, Analytical
Hiroshi Nishida, Yasushi Ishihama
Summary: A one-step method using MOLEX chromatography was developed to isolate protein C-terminal peptides from V8 protease-digested proteins, achieving high coverage and purity in human HeLa cells.
ANALYTICAL CHEMISTRY
(2022)
Article
Biochemical Research Methods
Kazuya Tsumagari, Tomoya Niinae, Akira Otaka, Yasushi Ishihama
Summary: The study showed that peptide probes containing F(2)Pmp can effectively enrich different PTPs for tyrosine phosphatome analysis, while probes containing phosphotyrosine are ineffective due to dephosphorylation.
Article
Chemistry, Multidisciplinary
Eisuke Kanao, Katsuya Nakano, Ryoma Kamei, Takuro Hosomi, Yasushi Ishihama, Jun Adachi, Takuya Kubo, Koji Otsuka, Takeshi Yanagida
Summary: In this study, the hidden molecular recognition abilities of ZnO nanowires were explored via liquid chromatography. The results showed that ZnO nanowires exhibited a stronger intermolecular interaction with phenylphosphoric acid and specifically recognized the phosphate groups in nucleotides, with the interaction increasing with the number of phosphate groups. This unique molecular selectivity was attributed to the surface properties of ZnO nanowires.
NANOSCALE ADVANCES
(2022)
Article
Biochemistry & Molecular Biology
Yutaka Shinkawa, Koshi Imami, Yasuhiro Fuseya, Katsuhiro Sasaki, Koichiro Ohmura, Yasushi Ishihama, Akio Morinobu, Kazuhiro Iwai
Summary: This study reveals the important roles of linear ubiquitin chains and ABIN1 in immune signaling, particularly in regulating cell death and NF-kappa B signaling. The researchers also discovered that phosphorylated ABIN1 functions as a selective autophagy receptor in TLR signaling, leading to the degradation of signaling proteins and attenuation of NF-kappa B signaling.
Article
Biochemistry & Molecular Biology
Jun-Yi Liu, Tsuyoshi Inoshita, Kahori Shiba-Fukushima, Shigeharu Yoshida, Kosuke Ogata, Yasushi Ishihama, Yuzuru Imai, Nobutaka Hattori
Summary: The mitochondrial kinase PINK1 and cytosolic ubiquitin ligase Parkin are involved in mitochondrial quality control. This study reveals the importance of ubiquitination of the Parkin Ubl domain and the phosphorylation of ubiquitin at K27 in Parkin activation.
HUMAN MOLECULAR GENETICS
(2022)
Article
Biochemistry & Molecular Biology
Yee Kien Chong, Sarang Tartey, Yuki Yoshikawa, Koshi Imami, Songling Li, Masanori Yoshinaga, Ai Hirabayashi, Guohao Liu, Alexis Vandenbon, Fabian Hia, Takuya Uehata, Takashi Mino, Yutaka Suzuki, Takeshi Noda, Dominique Ferrandon, Daron M. Standley, Yasushi Ishihama, Osamu Takeuchi
Summary: Cyclin J reduces cytokine production in macrophages by controlling glycolysis and mitochondrial functions. In mice, macrophage-specific cyclin J limits tumor growth, protects against LPS-induced shock, but increases susceptibility to bacterial infection.
Article
Biochemical Research Methods
Teck Yew Low, Yu-Ju Chen, Yasushi Ishihama, Max Ching Ming Chung, Stuart Cordwell, Terence Chuen Wai Poon, Ho Jeong Kwon
Summary: The AOHUPO Online Education Series aims to promote scientific education and collaboration among young scientists in the Asia-Oceania region. The second series focused on the renaissance of clinical proteomics and attracted over 300 participants from 29 countries/regions.
MOLECULAR & CELLULAR PROTEOMICS
(2022)
Article
Multidisciplinary Sciences
Hiroki Takahashi, Ge Yang, Takeshi Yoneshiro, Yohei Abe, Ryo Ito, Chaoran Yang, Junna Nakazono, Mayumi Okamoto-Katsuyama, Aoi Uchida, Makoto Arai, Hitomi Jin, Hyunmi Choi, Myagmar Tumenjargal, Shiyu Xie, Ji Zhang, Hina Sagae, Yanan Zhao, Rei Yamaguchi, Yu Nomura, Yuichi Shimizu, Kaito Yamada, Satoshi Yasuda, Hiroshi Kimura, Toshiya Tanaka, Youichiro Wada, Tatsuhiko Kodama, Hiroyuki Aburatani, Min-Sheng Zhu, Takeshi Inagaki, Timothy F. Osborne, Takeshi Kawamura, Yasushi Ishihama, Yoshihiro Matsumura, Juro Sakai
Summary: Protein kinase A promotes beige adipogenesis by phosphorylating proteins, including histone H3 lysine 9 demethylase JMJD1A. This process needs to be reversible and is regulated by MYPT1-PP1β phosphatase activity. This study uncovers regulatory cross-talk involved in beige adipogenesis that coordinates epigenetic regulation with direct activation of YAP/TAZ transcriptional co-activators.
NATURE COMMUNICATIONS
(2022)
Article
Chemistry, Analytical
Kosuke Ogata, Yasushi Ishihama
Summary: This study investigates the retention behavior of phosphorylated peptides in ion-pair reversed-phase liquid chromatography. The results indicate that the retention behavior of phosphorylated peptides is relatively predictable in the trifluoroacetic acid system but more diverse in the acetic acid system, requiring further data accumulation.
Article
Chemistry, Analytical
Eisuke Kanao, Shuntaro Wada, Hiroshi Nishida, Takuya Kubo, Tetsuya Tanigawa, Koshi Imami, Asako Shimoda, Kaori Umezaki, Yoshihiro Sasaki, Kazunari Akiyoshi, Jun Adachi, Koji Otsuka, Yasushi Ishihama
Summary: Extracellular vesicles (EVs) are lipid bilayer vesicles enclosing various biomolecules, showing potential as sensitive biomarkers for disease detection. A novel lectin-based affinity chromatography method is demonstrated to classify EVs based on their glycan structures, utilizing a spongy-like monolithic polymer that allows efficient in situ protein reaction. This approach helps to overcome the obstacle of differing molecular compositions of EVs from same donor cells, showing promise for elucidating their biological functions objectively.
ANALYTICAL CHEMISTRY
(2022)
Article
Biochemical Research Methods
Taylor Battellino, Kosuke Ogata, Victor Spicer, Yasushi Ishihama, Oleg Krokhin
Summary: In this study, the sensitivity of peptide analysis and chromatographic behavior were compared between formic acid and acetic acid in reversed-phase liquid chromatography-tandem mass spectrometry (LC-MS/MS) applications. The results showed that acetic acid resulted in a 2.2-2.5 times increase in MS signal and a slight decrease in retention compared to formic acid. The number of identified peptides was up to 60% higher under acetic acid conditions, depending on the sample type. The retention shift was found to be dependent on peptide net charge and demonstrated the hydrophilicity of acetic acid.
JOURNAL OF PROTEOME RESEARCH
(2023)
Article
Biochemistry & Molecular Biology
Eric W. Deutsch, Nuno Bandeira, Yasset Perez-Riverol, Vagisha Sharma, Jeremy J. Carver, Luis Mendoza, Deepti J. Kundu, Shengbo Wang, Chakradhar Bandla, Selvakumar Kamatchinathan, Suresh Hewapathirana, Benjamin S. Pullman, Julie Wertz, Zhi Sun, Shin Kawano, Shujiro Okuda, Yu Watanabe, Brendan MacLean, Michael J. MacCoss, Yunping Zhu, Yasushi Ishihama, Juan Antonio Vizcaino
Summary: This article describes the recent developments in the ProteomeXchange (PX) consortium, which aims to standardize data submission and dissemination of MS proteomics data. The article highlights the increase in the number of datasets submitted to PX resources and the growing data re-use activities.
NUCLEIC ACIDS RESEARCH
(2023)
Article
Rheumatology
Koji Kitagori, Takuma Oku, Masaki Wakabayashi, Tomoya Nakajima, Ran Nakashima, Kosaku Murakami, Yoshitaka Hirayama, Yasushi Ishihama, Koichiro Ohmura, Akio Morinobu, Tsuneyo Mimori, Hajime Yoshifuji
Summary: In this study, the expression of S100A8 protein and mRNA was found to be significantly upregulated in B cells of SLE patients. Flow cytometry results showed that S100A8 was highly expressed on the surface of B cells in active SLE patients, and its surface expression decreased after treatment, suggesting that S100A8 may be a marker for disease activity. The mRNA expression of S100A8 was particularly upregulated in memory B cells of SLE, indicating that S100A8 may be mainly secreted by memory B cells in the pathogenesis of SLE.
ARTHRITIS RESEARCH & THERAPY
(2023)
Article
Oncology
Kosuke Ogata, Shunsuke Takagi, Naoyuki Sugiyama, Yasushi Ishihama
Summary: Phosphoproteomics is crucial for understanding cell biology, but comprehensive analysis of the phosphoproteome is still lacking. Therefore, we introduced a new method to enrich a subset of the phosphoproteome and broaden the scope of analysis using in vitro kinase reactions. Our approach identified and quantified previously unobserved phosphopeptides and effectively profiled kinase inhibitors. This workflow can be easily adapted to target different subsets of the phosphoproteome and applied to various samples.
Article
Biochemical Research Methods
Chia-Feng Tsai, Kosuke Ogata, Naoyuki Sugiyama, Yasushi Ishihama
Summary: Identifying cellular phosphorylation pathways based on kinase-substrate relationships is critical for understanding the regulation of physiological functions. This study presents a motif-centric phosphoproteomics approach combined with multiplexed isobaric labeling, allowing for quantitative analysis of multiple phosphorylation pathways in cells.
CELL REPORTS METHODS
(2022)