Article
Biochemistry & Molecular Biology
Yingxin Cao, Laiyi Fu, Jie Wu, Qinke Peng, Qing Nie, Jing Zhang, Xiaohui Xie
Summary: In this study, we propose a deep learning framework called SAILERX for efficient, robust, and flexible analysis of multi-modal single-cell data. SAILERX utilizes invariant representation learning and multimodal data alignment mechanism to handle noise, integrate information, and provide various downstream analysis functions.
NUCLEIC ACIDS RESEARCH
(2022)
Article
Genetics & Heredity
Jared Huzar, Hannah Kim, Sudhir Kumar, Sayaka Miura
Summary: This article introduces a software called MOCA, which can analyze gene expressions and genetic variations from single-cell RNA sequencing data to study the evolution of cancer cells and gene expression patterns.
FRONTIERS IN GENETICS
(2022)
Article
Biochemistry & Molecular Biology
Yuhan Hao, Stephanie Hao, Erica Andersen-Nissen, William M. I. I. I. I. I. I. Mauck, Shiwei Zheng, Andrew Butler, Maddie J. Lee, Aaron J. Wilk, Charlotte Darby, Michael Zager, Paul Hoffman, Marlon Stoeckius, Efthymia Papalexi, Eleni P. Mimitou, Jaison Jain, Avi Srivastava, Tim Stuart, Lamar M. Fleming, Bertrand Yeung, Angela J. Rogers, Juliana M. McElrath, Catherine A. Blish, Raphael Gottardo, Peter Smibert, Rahul Satija
Summary: The study introduces a weighted-nearest neighbor analysis framework to learn the relative utility of each data type in each cell, enabling integrative analysis of multiple modalities. Applied to a CITE-seq dataset, the method constructs a multimodal reference atlas of the circulating immune system and successfully identifies and validates previously unreported lymphoid subpopulations.
Article
Biochemical Research Methods
Haruki Odaka, Haruka Ozaki, Hiroaki Tateno
Summary: The article introduces a system for combined analysis of glycan and RNA in single cells, which can reveal the cellular heterogeneity of glycans in multicellular systems. The system combines glycan profiling by sequencing and single-cell transcriptome profiling.
Article
Cardiac & Cardiovascular Systems
Alma Zernecke, Florian Erhard, Tobias Weinberger, Christian Schulz, Klaus Ley, Antoine Emmanuel Saliba, Clement Cochain
Summary: This study aimed to refine the nomenclature of mononuclear phagocytes in atherosclerotic vessels and compare their transcriptomic profiles in mouse and human disease. The researchers integrated single-cell RNA-sequencing datasets from both mice and humans, identifying subpopulations and unique transcriptomic features. They found conserved transcriptomic features of macrophages and DCs in atherosclerosis, highlighting the relevance of mouse models in studying mononuclear phagocytes in this disease.
CARDIOVASCULAR RESEARCH
(2023)
Article
Immunology
Frederike Straeten, Jing Zhu, Anna-Lena Boersch, Baohong Zhang, Kejie Li, I-Na Lu, Catharina Gross, Michael Heming, Xiaolin Li, Rebekah Rubin, Zhengyu Ouyang, Heinz Wiendl, Michael Mingueneau, Gerd Meyer zu Hoerste
Summary: Multiple sclerosis (MS) is a chronic autoimmune disease of the central nervous system. Analysis of cerebrospinal fluid (CSF) can help diagnose and understand MS. Recent studies using single-cell RNA sequencing have identified changes in CSF cells associated with MS. However, not all changes were consistent across studies. This study integrated multiple datasets to validate the expansion of B cells and other cell alterations in the CSF of MS patients.
JOURNAL OF NEUROINFLAMMATION
(2022)
Article
Biochemistry & Molecular Biology
Mengwei Li, Xiaomeng Zhang, Kok Siong Ang, Jingjing Ling, Raman Sethi, Nicole Yee Shin Lee, Florent Ginhoux, Jinmiao Chen
Summary: DISCO is an integrated database of single-cell omics data, offering an integrated cell atlas and harmonized metadata that users can utilize for comprehensive single-cell data analysis and exploration.
NUCLEIC ACIDS RESEARCH
(2022)
Article
Biochemical Research Methods
Adam Gayoso, Philipp Weiler, Mohammad Lotfollahi, Dominik Klein, Justin Hong, Aaron Streets, Fabian J. Theis, Nir Yosef
Summary: RNA velocity analysis has been enhanced by veloVI, a deep generative modeling framework that provides gene-specific modeling of RNA metabolism and quantification of velocity uncertainty. It allows for assessment of whether velocity analysis is appropriate for a given dataset.
Article
Genetics & Heredity
Yu-Mei Huang, Lin-Qian Wang, Ying Liu, Fa-Qing Tang, Wen-Ling Zhang
Summary: This study identified novel biomarkers involved in nasopharyngeal carcinoma (NPC) by integrating bulk and single-cell RNA sequencing data, and discovered that PKP1 and tumor-infiltrating lymphocyte-B cells (TIL-Bs) were promising therapeutic targets for NPC.
FRONTIERS IN GENETICS
(2022)
Article
Biology
Tongcui Ma, Matthew McGregor, Leila Giron, Guorui Xie, Ashley F. George, Mohamed Abdel-Mohsen, Nadia R. Roan
Summary: This study develops a method called CyTOF-Lec that allows for simultaneous characterization of protein and glycan features of human immune cells at the single-cell level. It finds that HIV infection not only remodels cellular proteins but also glycans, and that glycan expression can differentiate memory CD4+ T cells with varying susceptibility to HIV infection.
Article
Immunology
Lin Chen, Senjun Jin, Min Yang, Chunmei Gui, Yingpu Yuan, Guangtao Dong, Weizhong Zeng, Jing Zeng, Guoxin Hu, Lujun Qiao, Jinhua Wang, Yonglin Xi, Jian Sun, Nan Wang, Minmin Wang, Lifeng Xing, Yi Yang, Yan Teng, Junxia Hou, Qiaojie Bi, Huabo Cai, Gensheng Zhang, Yucai Hong, Zhongheng Zhang
Summary: This study systematically explored the potential mechanisms of the immunomodulatory effects of Ulinastatin (UTI) in sepsis by integrating bulk and single cell RNA-seq data. The results indicate that UTI regulates neutrophil activity to achieve immunomodulation and leads to significant expansion of Myeloid-derived suppressor cells (MDSC) in sepsis. Further analysis revealed signaling pathways that may be involved in the immunomodulatory effects of UTI.
FRONTIERS IN IMMUNOLOGY
(2022)
Article
Medicine, Research & Experimental
Wencong Song, Jie Qiu, Lianghong Yin, Xiaoping Hong, Weier Dai, Donge Tang, Dongzhou Liu, Yong Dai
Summary: Differential expression profiles of various ceRNAs related to SLE were identified, leading to the construction of ceRNA signalling networks. Key hub genes involved in ceRNA signalling pathways such as the IL-17 signalling pathway and type I interferon signalling pathway were discovered.
JOURNAL OF TRANSLATIONAL MEDICINE
(2021)
Article
Physiology
Vaibhav Jain, Wen-Hsuan Yang, Jianli Wu, John D. Roback, Simon G. Gregory, Jen-Tsan Chi
Summary: Phenotypic heterogeneity of red blood cells (RBCs) is important in the study of RBC diseases. This study used single cell RNA-Seq to analyze RBCs from three healthy adult donors stored in blood bank conditions, and identified multiple RBC sub-populations as well as the impact of storage on RBC populations.
FRONTIERS IN PHYSIOLOGY
(2022)
Article
Biochemistry & Molecular Biology
Roger Riera, Tim P. Hogervorst, Ward Doelman, Yan Ni, Silvia Pujals, Evangelia Bolli, Jeroen D. C. Codee, Sander van Kasteren, Lorenzo Albertazzi
Summary: Glyco-PAINT is introduced as a method to study weak glycan-lectin interactions on living cells using super-resolution microscopy. This method allows for the measurement of sugar-lectin complex densities, residence times, and diffusion on cell surfaces, revealing how sugar multivalency and presentation geometry can be optimized for binding and internalization.
NATURE CHEMICAL BIOLOGY
(2021)
Article
Immunology
David Gomez Jimenez, Can Altunbulakli, Sabine Swoboda, Aastha Sobti, David Askmyr, Ashfaq Ali, Lennart Greiff, Malin Lindstedt
Summary: The incidence of HPV+ tonsillar cancer has increased significantly in recent decades. This study used single-cell RNA-sequencing to investigate the myeloid compartment in HPV+ tonsillar cancer. The researchers observed an expansion of the myeloid compartment and interferon-induced cellular responses in dendritic cells and monocyte-macrophages. They discovered four dendritic cell lineages, two macrophage polarization processes, and identified biomarkers that correlate with patient survival. This study contributes to understanding the role of myeloid cells in HPV-driven tonsillar cancer and provides potential prognostic markers.
FRONTIERS IN IMMUNOLOGY
(2023)
Article
Biochemistry & Molecular Biology
Shin Irumagawa, Keiko Hiemori, Sayoko Saito, Hiroaki Tateno, Ryoichi Arai
Summary: Lectins are proteins that have the ability to bind carbohydrates and they have multiple carbohydrate recognition domains and multivalent binding effects. This study developed functional protein nano-building blocks by fusing lectins to oligomeric proteins, which can self-assemble into various nanostructures. The binding avidity of the lectin nano-blocks to glycans was significantly increased through multivalent effects.
INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES
(2022)
Article
Biotechnology & Applied Microbiology
Lalhaba Oinam, Ryoma Hayashi, Keiko Hiemori, Kayo Kiyoi, Kimiyo Sage-Ono, Kenji Miura, Michiyuki Ono, Hiroaki Tateno
Summary: In this study, recombinant Concanavalin A (ConA) was successfully produced in lettuce using the Agrobacterium tumefaciens-mediated transient expression system. The recombinant ConA showed similar glycan-binding specificity and affinity to the native ConA. This study provides a new approach for the recombinant expression of ConA.
BIOTECHNOLOGY AND BIOENGINEERING
(2022)
Article
Gastroenterology & Hepatology
Haruki Odaka, Keiko Hiemori, Asako Shimoda, Kazunari Akiyoshi, Hiroaki Tateno
Summary: In this study, it was found that serum levels of CD63(+)-EVs and platelet-derived EVs (CD41(+)-EVs, CD61(+)-EVs) were significantly increased in patients with PDAC compared to healthy controls. CD63(+)-EVs showed high diagnostic performance in discriminating patients with PDAC from healthy controls and could be potential biomarkers for PDAC.
BMC GASTROENTEROLOGY
(2022)
Article
Biochemistry & Molecular Biology
Yuta Hayashi, Dilimulati Yimiti, Yohei Sanada, Chenyang Ding, Takenori Omoto, Toshihiko Ogura, Tomoyuki Nakasa, Masakazu Ishikawa, Keiko Hiemori, Hiroaki Tateno, Shigeru Miyaki, Nobuo Adachi
Summary: The therapeutic potential of MSC-derived EVs for tissue repair is being explored. The study found that early passaged MSC-EVs accelerate Achilles tendon healing compared with senescent MSC-EVs. Glycans on MSC-EVs may be useful for quality control and isolation of therapeutic MSC-EVs in regenerative medicine.
Article
Urology & Nephrology
Masayuki Tasaki, Hiroaki Tateno, Takashi Sato, Hisashi Narimatsu, Kazuhide Saito, Yuki Nakagawa, Toshinari Aoki, Masami Kamimura, Takashi Ushiki, Kota Takahashi, Yoshihiko Tomita
Summary: The study investigated the reactivity of anti-ABO antibodies detected after ABO-incompatible kidney transplantation with stable graft function to the renal graft endothelial cells, and found that the antibody reactivity was low.
CLINICAL AND EXPERIMENTAL NEPHROLOGY
(2023)
Article
Biochemistry & Molecular Biology
Kazuhiko Yamasaki, Naruhiko Adachi, Mya Myat Ngwe Tun, Akihito Ikeda, Toshio Moriya, Masato Kawasaki, Tomoko Yamasaki, Tomomi Kubota, Izuru Nagashima, Hiroki Shimizu, Hiroaki Tateno, Kouichi Morita
Summary: The N-glycosylation sites on the spike protein of SARS-CoV-2 are relatively invariant and play a crucial role in infection. Core-fucosylated N-glycans have a high affinity for the spike protein and can inhibit viral infection across different variants. Cryogenic electron microscopy revealed that the multivalence of core-fucosylated N-glycans leads to the aggregation of the spike protein. This study highlights the potential for developing specific binders targeted at the spike protein.
Article
Oncology
Yukihito Kuroda, Tatsuya Oda, Osamu Shimomura, Shinji Hashimoto, Yoshimasa Akashi, Yoshihiro Miyazaki, Kinji Furuya, Tomoaki Furuta, Hiromitsu Nakahashi, Pakavarin Louphrasitthiphol, Bryan J. Mathis, Takahito Nakajima, Hiroaki Tateno
Summary: Pancreatic ductal adenocarcinoma (PDAC) is resistant to current treatments but lectin-based phototherapy (Lec-PT) targeting cell surface glycans shows promise as a new therapy. The study combines a PDAC targeting lectin with a photoabsorber to create a near-infrared light-activated therapy. In vitro and in vivo experiments demonstrate cytotoxicity and tumor growth inhibition upon exposure to near-infrared light.
INTERNATIONAL JOURNAL OF CANCER
(2023)
Article
Biochemical Research Methods
Shodai Taguchi, Yasuyuki Suda, Kenji Irie, Haruka Ozaki
Summary: In this study, the plate-based yeast spot assay of budding yeast was automated using an affordable liquid-handling robot and a flatbed scanner, enabling reproducible spot assays and subsequent quantification of cell density. This research will contribute to the introduction of automated spot assays in conventional laboratories.
Article
Oncology
Yukihito Kuroda, Tatsuya Oda, Osamu Shimomura, Pakavarin Louphrasitthiphol, Bryan J. Mathis, Hiroaki Tateno, Kentaro Hatano
Summary: By targeting cell surface glycans, a novel class of tumor-specific probes for positron emission tomography (PET) has been developed to improve the early detection of pancreatic ductal adenocarcinoma (PDAC). The PDAC-targeting ability of [F-18]FB-rBC2LCN allows for high-contrast PET imaging of tumors in a mouse model, providing an accurate and sensitive tool for early-stage pancreatic cancer detection.
Article
Cell & Tissue Engineering
Tianwei Huang, Yuya Sato, Akiko Kuramochi, Yoshio Ohba, Masayuki Sano, Makoto Miyagishi, Hiroaki Tateno, Renu Wadhwa, Kazunori Kawasaki, Takeyuki Uchida, Kristina N. Ekdahl, Bo Nilsson, Ung-il Chung, Yuji Teramura
Summary: This study aimed to improve intracellular delivery to endothelial cells by modifying the exosome surface with Tat peptide (YGRKKRRQRRR)-PEG-lipids. Tat-conjugated PEG-lipids with different spacer molecular weights and lipid types were incorporated into exosomes using fluorescein isothiocyanate labeling to optimize the number of Tat-PEG-lipids immobilized on the exosome surface. The exosomes modified with Tat-PEG-lipids showed high detection inside human umbilical vein endothelial cells (HUVECs), indicating improved intracellular delivery.
REGENERATIVE THERAPY
(2023)
Article
Biochemical Research Methods
Yuya Arai, Ko Takahashi, Takaaki Horinouchi, Koichi Takahashi, Haruka Ozaki
Summary: During laboratory automation of life science experiments, it is important to coordinate specialized instruments and human experimenters to minimize execution time. Existing scheduling methods for large-scale scheduling problems have difficulties in obtaining feasible solutions in real-time. In this study, we proposed a fast schedule-finding method called SAGAS, which combines simulated annealing and the greedy algorithm to find the shortest execution time for life science experiments.
Article
Biochemistry & Molecular Biology
Shuuji Mawaribuchi, Osamu Shimomura, Tatsuya Oda, Keiko Hiemori, Kayoko Shimizu, Kenya Yamase, Mutsuhiro Date, Hiroaki Tateno
Summary: Early detection for improving the survival of patients with pancreatic ductal adenocarcinoma (PDAC) is urgently needed. We identified SERPINA3 as a glycoprotein (BC2-S3) secreted from PDAC cells into the blood, which is reactive to rBC2LCN lectin. BC2-S3 exhibited higher levels in PDAC patients and showed a significantly higher detection rate for early stage PDAC than CA19-9.
Article
Surgery
Masayuki Tasaki, Hiroaki Tateno, Takashi Sato, Azusa Tomioka, Hiroyuki Kaji, Hisashi Narimatsu, Kazuhide Saito, Yuki Nakagawa, Toshinari Aoki, Masami Kamimura, Takashi Ushiki, Manabu Okada, Yuko Miwa, Kiyohiko Hotta, Yutaka Yoshida, Kota Takahashi, Yoshihiko Tomita
Summary: In this study, a new method to measure antibody titer using a microarray of recombinant CD31 linked to ABO antigens was developed. The results showed that this method had higher sensitivity and specificity in predicting antibody-mediated rejection in kidney transplantation compared to traditional isohemagglutinin assays.
TRANSPLANT INTERNATIONAL
(2022)
Meeting Abstract
Oncology
Yukihito Kuroda, Osamu Shimomura, Hiromitsu Nakahashi, Tomoaki Furuta, Yoshihiro Miyazaki, Takahito Nakajima, Hiroaki Tateno, Tatsuya Oda
Article
Biochemical Research Methods
Haruki Odaka, Haruka Ozaki, Hiroaki Tateno
Summary: The article introduces a system for combined analysis of glycan and RNA in single cells, which can reveal the cellular heterogeneity of glycans in multicellular systems. The system combines glycan profiling by sequencing and single-cell transcriptome profiling.