Article
Multidisciplinary Sciences
Youjin Lee, Derek Bogdanoff, Yutong Wang, George C. Hartoularos, Jonathan M. Woo, Cody T. Mowery, Hunter M. Nisonoff, David S. Lee, Yang Sun, James Lee, Sadaf Mehdizadeh, Joshua Cantlon, Eric Shifrut, David N. Ngyuen, Theodore L. Roth, Yun S. Song, Alexander Marson, Eric D. Chow, Chun Jimmie Ye
Summary: Using the XYZeq workflow, spatial metadata can be encoded into scRNAseq libraries to analyze the transcriptome and spatial localization of individual cells, revealing the functional interactions within an anatomical space. Studies show that tumor-associated MSCs express different tumor suppressor genes at varying distances from the tumor core, highlighting the spatial distribution and functional characteristics of cells in pathological tissues.
Article
Cell Biology
Guizhen Zhao, Haocheng Lu, Yuhao Liu, Yang Zhao, Tianqing Zhu, Minerva T. Garcia-Barrio, Y. Eugene Chen, Jifeng Zhang
Summary: The study investigated the transcriptomic changes in endothelial cells (ECs) in diabetic atherosclerosis using single-cell RNA sequencing. It identified high heterogeneity and plasticity of ECs under normal and atherosclerotic conditions. Metabolic transcriptomic analysis showed that EndMT-derived fibroblast-like cells play a prominent role in atherosclerosis, with altered functions related to extracellular-matrix organization and apoptosis.
FRONTIERS IN CELL AND DEVELOPMENTAL BIOLOGY
(2021)
Article
Biochemistry & Molecular Biology
Guangxu Cao, Jiali Yue, Yetian Ruan, Ya Han, Yong Zhi, Jianqiao Lu, Min Liu, Xinxin Xu, Jin Wang, Quan Gu, Xuejun Wen, Jinli Gao, Qingfeng Zhang, Jiuhong Kang, Chenfei Wang, Fang Li
Summary: This study conducted single-cell RNA and TCR sequencing of cervical cancer tumors and adjacent normal tissues to map the immune landscape. The study revealed tumor-specific germinal center B cells associated with improved clinical outcomes and established a joint model of tumor and stromal cells to predict patients' prognosis. These findings provide information for future combinational immunotherapy.
Article
Biochemical Research Methods
Luca Rappez, Mira Stadler, Sergio Triana, Rose Muthoni Gathungu, Katja Ovchinnikova, Prasad Phapale, Mathias Heikenwalder, Theodore Alexandrov
Summary: SpaceM is an open-source method for in situ single-cell metabolomics that can detect a large number of metabolites per hour and predict and validate the cell types and metabolic states. By simulating different stimuli, SpaceM reveals the coexistence of different cellular metabolic states and the mechanisms of balance disruption.
Article
Immunology
Qi-Wen Man, Rui-Fang Li, Su-Ran Li, Jing Wang, Lin-Lin Bu, Yi Zhao, Bing Liu
Summary: The study identified different cell types with high intra-lesional heterogeneity in odontogenic keratocyst (OKC) and found that CXCL-enriched fibroblasts are crucial for angiogenesis of OKCs, which could be partially regulated by hydrostatic pressure.
JOURNAL OF INFLAMMATION RESEARCH
(2021)
Article
Obstetrics & Gynecology
Jyoti Goad, Joshua Rudolph, Mehrdad Zandigohar, Matthew Tae, Yang Dai, Jian-Jun Wei, Serdar E. Bulun, Debabrata Chakravarti, Aleksandar Rajkovic
Summary: This study explored the cellular composition and single-cell transcriptomic differences between myometrium and leiomyomas using single-cell RNA sequencing. The results revealed cellular heterogeneity in smooth muscle cells, fibroblast, and endothelial cell populations in both tissues.
HUMAN REPRODUCTION
(2022)
Article
Genetics & Heredity
Sai Batchu, Karan Patel, Siyuan Yu, Aleem T. Mohamed, Michael Karsy
Summary: This study characterized the metabolic differences between ependymoma subgroups at the single-cell level using gene expression profiles. The results showed that mitochondrial oxidative phosphorylation and drug metabolism pathways contribute significantly to the heterogeneity within subgroups.
Article
Endocrinology & Metabolism
Zhenhui Li, Ming Zheng, Jiawei Mo, Kan Li, Xin Yang, Lijin Guo, Xiquan Zhang, Bahareldin Ali Abdalla, Qinghua Nie
Summary: This study identified different subpopulations of melatonin-treated preadipocytes, with the G0S2(-) cluster playing a crucial role in promoting lipolysis and inhibiting adipogenesis. Regulation of gene expression such as ATGL and PPARγ contributes to the weight-reducing effects observed in this study.
JOURNAL OF PINEAL RESEARCH
(2021)
Article
Biochemistry & Molecular Biology
Yu Zhou, Siyang Liu, Chao Liu, Jiabin Yang, Qing Lin, Shangyou Zheng, Changhao Chen, Quanbo Zhou, Rufu Chen
Summary: Utilizing single-cell RNA sequencing technology, this study uncovered both intra- and inter-tumor heterogeneities in pancreatic neuroendocrine tumors, identifying activation of cancer progression hallmarks at different stages, defining two dominant clones with metastatic potential, and developing a gene signature for predicting tumor metastatic potential validated in patient cohorts.
INTERNATIONAL JOURNAL OF BIOLOGICAL SCIENCES
(2021)
Article
Oncology
Wei Guo, Bolun Zhou, Fenglong Bie, Qilin Huai, Xuemin Xue, Lei Guo, Fengwei Tan, Qi Xue, Liang Zhao, Shugeng Gao
Summary: This study aims to comprehensively reveal the cellular characteristics and inter-cellular connections of MPLC. scRNA-seq was performed from 23 samples of six MPLC patients, combined with bulk whole-exome sequencing. Trajectory analysis was performed to investigate the transition of different cell types during the development of MPLC.
CLINICAL AND TRANSLATIONAL MEDICINE
(2023)
Article
Cardiac & Cardiovascular Systems
Luka Nicin, Wesley T. Abplanalp, Anne Schaenzer, Anke Sprengel, David John, Hannah Mellentin, Lukas Tombor, Matthias Keuper, Evelyn Ullrich, Karin Klingel, Reinhard B. Dettmeyer, Jedrzej Hoffmann, Hakan Akintuerk, Christian Jux, Dietmar Schranz, Andreas M. Zeiher, Stefan Rupp, Stefanie Dimmeler
Summary: Single nuclei RNA sequencing on pediatric DCM patients’ heart tissues revealed age-dependent changes in fibroblast and cardiomyocyte gene expression patterns, with older patients showing more fibrotic signatures and infants showing enriched proregenerative profiles. This study identified a population of cardiomyocytes with high proregenerative potential in infants but absent in older children, indicating potential targets for personalized therapy in pediatric heart failure treatment.
Article
Cell Biology
Li Zhang, Zhihuang Qiu, Hui Zheng, Xi Yang, Jianqiang Ye, Jian He, Yumei Li, Liangwan Chen
Summary: This study revealed the differences in cellular components and functions between hypertension and Marfan-induced aortic dissection through single-cell RNA analysis, providing insights into the mechanisms of disease development and intercellular communication in a new perspective.
FRONTIERS IN CELL AND DEVELOPMENTAL BIOLOGY
(2022)
Article
Cell Biology
Jincheng Wang, Yuchen Sang, Shengxian Jin, Xuezheng Wang, Gajendra Kumar Azad, Mark A. McCormick, Brian K. Kennedy, Qing Li, Jianbin Wang, Xiannian Zhang, Yi Zhang, Yanyi Huang
Summary: This study utilized single-cell transcriptomic sequencing to explore the early heterogeneity during aging in yeast, identifying key biological processes and cellular components, as well as the regulation of transcription factors on oxidative stress response and proteasome activity.
Article
Biochemistry & Molecular Biology
Xiaoyong Chen, Yue Chen, Xiangrong Chen, Penghui Wei, Yuanxiang Lin, Zanyi Wu, Zhangya Lin, Dezhi Kang, Chenyu Ding
Summary: This study comprehensively dissects the molecular landscape of glioblastoma (GBM) and highlights the heterogeneous distribution and potential role of Enhancer of zeste homolog 2 (EZH2) in the tumor microenvironment (TME). The researchers discovered a MES2-like GBM subcluster characterized by a glial-immune dual feature and identified a tumor-associated macrophages (TAMs) subset with EZH2 overexpression, which plays a pro-tumor role. These findings provide valuable insights into the complexity of GBM and potential therapeutic targets.
BIOCHIMICA ET BIOPHYSICA ACTA-MOLECULAR BASIS OF DISEASE
(2022)
Article
Genetics & Heredity
Chen Zhang, Xueshuai Han, Jingkun Liu, Lei Chen, Ying Lei, Kunying Chen, Jia Si, Tian-yi Wang, Hui Zhou, Xiaoyun Zhao, Xiaohui Zhang, Yihua An, Yueying Li, Qian-Fei Wang
Summary: By single-cell RNA sequencing, this study identified five distinct subpopulations of ex vivo-expanded mesenchymal stem cells (MSCs). Among them, a stem-like subpopulation exhibited strong proliferation and stemness signatures, while another subpopulation of prechondrocytes played a role in immunoregulation. These findings contribute to a better understanding and application of MSCs.
GENOMICS PROTEOMICS & BIOINFORMATICS
(2022)
Article
Cardiac & Cardiovascular Systems
Laura P. M. H. de Rooij, Lisa M. Becker, Laure Anne Teuwen, Bram Boeckx, Sander Jansen, Simon Feys, Stijn Verleden, Laurens Liesenborghs, Anna K. Stalder, Sasha Libbrecht, Tina Van Buyten, Gino Philips, Abhishek Subramanian, Sebastien J. Dumas, Elda Meta, Mila Borri, Liliana Sokol, Amelie Dendooven, Anh Co K. Truong, Jan Gunst, Pierre Van Mol, Jasmin D. Haslbauer, Katerina Rohlenova, Thomas Menter, Robbert Boudewijns, Vincent Geldhof, Stefan Vinckier, Jacob Amersfoort, Wim Wuyts, Dirk Van Raemdonck, Werner Jacobs, Laurens J. Ceulemans, Birgit Weynand, Bernard Thienpont, Martin Lammens, Mark Kuehnel, Guy Eelen, Mieke Dewerchin, Luc Schoonjans, Danny Jonigk, Jo van Dorpe, Alexandar Tzankov, Els Wauters, Massimiliano Mazzone, Johan Neyts, Joost Wauters, Diether Lambrechts, Peter Carmeliet
Summary: This study provides new insights into the abundance, expression patterns, and interactomes of endothelial cell (EC) subtypes in COVID-19 and idiopathic pulmonary fibrosis (IPF). The findings suggest the importance of ECs in the pathophysiology of both conditions and may contribute to future investigations into the progression and treatment of COVID-19 and IPF.
CARDIOVASCULAR RESEARCH
(2023)
Article
Critical Care Medicine
Eilise M. Ryan, Pranvera Sadiku, Patricia Coelho, Emily R. Watts, Ailiang Zhang, Andrew J. M. Howden, Manuel A. Sanchez-Garcia, Martin Bewley, Joby Cole, Brian J. McHugh, Wesley Vermaelen, Bart Ghesquiere, Peter Carmeliet, Giovanny Rodriguez Blanco, Alex Von Kriegsheim, Yolanda Sanchez, William Rumsey, James F. Callahan, George Cooper, Nicholas Parkinson, Kenneth Baillie, Doreen A. Cantrell, John McCafferty, Gourab Choudhury, Dave Singh, David H. Dockrell, Moira K. B. Whyte, Sarah R. Walmsley
Summary: Chronic obstructive pulmonary disease (COPD) is characterized by persistent airway inflammation and impaired macrophage function. This study found that COPD alveolar macrophages (AMs) and peripheral monocyte-derived macrophages (MDMs) exhibit metabolic deficiencies and impairments in redox balance. Activation of the NRF2 pathway can rescue these defects and improve macrophage function in COPD.
AMERICAN JOURNAL OF RESPIRATORY AND CRITICAL CARE MEDICINE
(2023)
Article
Oncology
Monica Fernandez-Cortes, Daniel Delgado-Bellido, Eloisa Bermudez-Jimenez, Jesus M. Paramio, Francisco O'Valle, Stefan Vinckier, Peter Carmeliet, Angel Garcia-Diaz, F. Javier Oliver
Summary: Vasculogenic mimicry (VM) refers to the ability of aggressive tumor cells to develop pseudovascular structures without endothelial cells. This study investigated the role of hypoxia and PARP inhibition in VM. Results showed that the PARP inhibitor olaparib improved pericyte coverage and reduced metastasis in uveal melanoma xenografts with VM. PARP inhibition and hypoxia induced changes in melanoma tube formation and gene expression related to vasculogenesis, enhancing the endothelial-like phenotype of VM+ melanoma cells. Overall, PARP inhibitors have the potential to modulate VM characteristics and reduce metastatic spread in melanoma.
JOURNAL OF PATHOLOGY
(2023)
Article
Endocrinology & Metabolism
Lushun Yuan, Ruifang Li-Gao, Aswin Verhoeven, Huub J. van Eyk, Maurice B. Bizino, Patrick C. N. Rensen, Martin Giera, Ingrid M. Jazet, Hildo J. Lamb, Ton J. Rabelink, Bernard M. van den Berg
Summary: This study aimed to investigate the association between changes in HDL composition and increased microvascular risk in individuals with type 2 diabetes mellitus. Differences in HDL composition were found between Dutch South Asian and Dutch white Caucasian individuals with diabetes, and these differences were associated with the incidence of microvascular complications. These HDL compositional differences could serve as ethnicity-specific biomarkers for type 2 diabetes.
DIABETES OBESITY & METABOLISM
(2023)
Review
Neurosciences
Thomas Waelchli, Jeroen Bisschop, Peter Carmeliet, Gelareh Zadeh, Philippe P. Monnier, Katrien De Bock, Ivan Radovanovic
Summary: This review examines the mechanisms of angiogenesis in brain development, brain vascular malformations, and brain tumors. The CNS critically relies on the formation and proper function of its vasculature during different stages, and angiogenesis plays a key role in vascular-dependent brain diseases. However, the exact molecular pathways and mechanisms underlying angiogenesis in the CNS are not fully understood.
NATURE REVIEWS NEUROSCIENCE
(2023)
Correction
Neurosciences
Carmen Ruiz de Almodovar, Pierre J. Fabre, Ellen Knevels, Cathy Coulon, Inmaculada Segura, Patrick C. G. Haddick, Liesbeth Aerts, Nicolas Delattin, Geraldine Strasser, Won-Jong Oh, Christian Lange, Stefan Vinckier, Jody Haigh, Coralie Fouquet, Chengua Gu, Kari Alitalo, Valerie Castellani, Marc Tessier-Lavigne, Alain Chedotal, Frederic Charron, Peter Carmeliet
Article
Multidisciplinary Sciences
Stefania Crotta, Matteo Villa, Jack Major, Katja Finsterbusch, Miriam Llorian, Peter Carmeliet, Joerg Buescher, Andreas Wack
Summary: Airway epithelial repair requires a shift from glycolysis to fatty acid oxidation. Promoting fatty acid oxidation enhances epithelial differentiation, offering potential therapeutic options. Defects in mucociliary clearance or barrier integrity lead to recurrent infections and chronic inflammation in the airway epithelium.
NATURE COMMUNICATIONS
(2023)
Article
Cell Biology
Bin Liu, Ran Chen, Yidan Zhang, Jinrong Huang, Yonglun Luo, Susanne Rosthoj, Chenyang Zhao, Marja Jaattela
Summary: Commonly used antihistamines and other cationic amphiphilic drugs (CADs) have emerged as potential cancer drugs due to their ability to alter lysosomal pH and inhibit STAT3 signaling, leading to cancer cell apoptosis and inhibition of tumor growth. The rapid elevation of lysosomal pH induced by CADs is caused by lysosomal H+ efflux mediated by P2RX4 and precedes lysosomal membrane permeabilization. These findings highlight the anticancer mechanisms of CADs and support their repurposing as cheap and safe cancer drugs, especially in combination with STAT3 inhibition.
Article
Neurosciences
Hankui Liu, Liping Guan, Min Deng, Lars Bolund, Karsten Kristiansen, Jianguo Zhang, Yonglun Luo, Zhanchi Zhang
Summary: By analyzing the expression of ALS-related genes in different cell types using single-cell transcriptomics data, we found that alpha- and gamma-motor neurons are associated with ALS susceptibility and pathogenicity genes, respectively, indicating differences in biological processes between sporadic and familial ALS.
FRONTIERS IN NEUROSCIENCE
(2023)
Article
Medicine, General & Internal
Zuzana Bielcikova, Jan Stursa, Ludmila Krizova, Lanfeng Dong, Jan Spacek, Stanislav Hlousek, Michal Vocka, Katerina Rohlenova, Olga Bartosova, Vladimir Cerny, Tomas Padrta, Michal Pesta, Pavel Michalek, Sona Stemberkova Hubackova, Katarina Kolostova, Eliska Pospisilova, Vladimir Bobek, Peter Klezl, Renata Zobalova, Berwini Endaya, Jakub Rohlena, Lubos Petruzelka, Lukas Werner, Jiri Neuzil
Summary: MitoTam, a mitochondria-targeted anti-cancer agent, was tested in a phase I/Ib trial with 75 metastatic cancer patients. The study found that MitoTam showed high efficacy against renal cell carcinoma.
Article
Biochemistry & Molecular Biology
Aikaterini Skorda, Anna Rossberg Lauridsen, Chengnan Wu, Jinrong Huang, Monika Mrackova, Nuggi Ingholt Winther, Vanessa Jank, Zsofia Sztupinszki, Robert Strauss, Mesut Bilgin, Kenji Maeda, Bin Liu, Yonglun Luo, Marja Jaattela, Tuula Kallunki
Summary: Cancer cells depend on cholesterol and have mechanisms for controlling its homeostasis. They can switch between cholesterol synthesis and uptake depending on their needs and environmental changes. Through oncogenic growth factor signaling, cancer cells promote the uptake and utilization of extracellular cholesterol, which is facilitated by Myeloid Zinc Finger 1 (MZF1)-mediated Niemann Pick C1 (NPC1) expression and increased macropinocytosis. This process allows cancer cells to obtain cholesterol for their energy-consuming activities, such as invasion.
Article
Multidisciplinary Sciences
Cecilia Fahlquist-Hagert, Thomas R. Wittenborn, Ewa Terczynska-Dyla, Kristian Savstrup Kastberg, Emily Yang, Alysa Nicole Rallistan, Quinton Raymond Markett, Gudrun Winther, Sofie Fonager, Lasse F. Voss, Mathias K. Pedersen, Nina van Campen, Alexey Ferapontov, Lisbeth Jensen, Jinrong Huang, John D. Nieland, Cees E. van der Poel, Johan Palmfeldt, Michael C. Carroll, Paul J. Utz, Yonglun Luo, Lin Lin, Soren E. Degn
Summary: Circumstantial evidence suggests that B cells may instruct T cells to break tolerance. A murine model experiment demonstrated that the autoimmune response can be initiated outside of germinal centers. B cells can directly relay autoreactivity between different compartments of MHC-restricted T cells and propagate the autoimmune response.
NATURE COMMUNICATIONS
(2023)
Article
Chemistry, Multidisciplinary
Jingyu Xiao, Fei Wang, Xiaoyan Hu, Dongli Li, Geng Liu, Qumiao Xu, Chao Chen, Haitao Xiang, Xuan Dong, Linnan Zhu, Dishuang Yang, Yanan Gao, Meijuan Wang, Yonglun Luo, Cheng-Chi Chao, Guanglei Li, Qiongyu Guo
Summary: Researchers used a 3D tumor model based on recellularized liver matrix to investigate T-cell immune response to HCC neoantigens. They collected whole exome sequencing data of 364 HCC patients and predicted 25 highly potential immunogenic neoantigens in silico. Six of the HCC neoantigen candidates were functionally validated and their minigenes were constructed. The 3D RLM HCC tumor model showed a specific immune response to the minigene-modified GFP-HepG2 cells.
ADVANCED MATERIALS INTERFACES
(2023)
Letter
Urology & Nephrology
Jolijn R. van Leeuwen, Ton J. Rabelink, Y. K. Onno Teng
KIDNEY INTERNATIONAL REPORTS
(2023)
Article
Medicine, Research & Experimental
Jolijn R. van Leeuwen, Tamara Popov, Achim Obergfell, Ton J. Rabelink, Y. K. Onno Teng
BIOLOGICS-TARGETS & THERAPY
(2023)