Article
Immunology
Andrew D. Hildreth, Feiyang Ma, Yung Yu Wong, Ryan Sun, Matteo Pellegrini, Timothy E. O'Sullivan
Summary: This study provides a comprehensive analysis of the cellular composition in healthy and obese human white adipose tissue, revealing changes in immune cell populations and inflammatory pathways in obese individuals. The findings highlight the importance of immune cell regulation in metabolic diseases and offer insights into new cellular networks and differentiation trajectories in white adipose tissue.
Article
Multidisciplinary Sciences
Chia-Lung Wu, Amanda Dicks, Nancy Steward, Ruhang Tang, Dakota B. Katz, Yun-Rak Choi, Farshid Guilak
Summary: The study identified key genes such as WNT and MITF in off-target cell differentiation during chondrogenic differentiation using bulk and single cell RNA-sequencing; inhibiting these pathways can enhance cell homogeneity and yield.
NATURE COMMUNICATIONS
(2021)
Article
Multidisciplinary Sciences
Taghreed Hirz, Shenglin Mei, Hirak Sarkar, Youmna Kfoury, Shulin Wu, Bronte M. Verhoeven, Alexander O. Subtelny, Dimitar V. Zlatev, Matthew W. Wszolek, Keyan Salari, Evan Murray, Fei Chen, Evan Z. Macosko, Chin-Lee Wu, David T. Scadden, Douglas M. Dahl, Ninib Baryawno, Philip J. Saylor, Peter V. Kharchenko, David B. Sykes
Summary: The treatment of low-risk primary prostate cancer only requires active surveillance, while high-risk disease necessitates multimodal treatment including surgery, radiation therapy, and hormonal therapy. Recurrence and metastatic disease development remain clinical challenges due to immune escape and tumor progression mechanisms that are not well understood. Through single-cell RNA sequencing and spatial transcriptomic analyses, we comprehensively describe the tumor microenvironment in localized prostate cancer and its differences compared to adjacent normal samples and healthy controls. Our study reveals an immune suppressive tumor microenvironment characterized by suppressive myeloid populations, exhausted T-cells, and high stromal angiogenic activity. We also infer cell-to-cell relationships within undissociated tissue sections using ligand-receptor interaction measurements. Overall, our work provides a highly detailed and comprehensive resource on the prostate tumor microenvironment and tumor-stromal cell interactions.
NATURE COMMUNICATIONS
(2023)
Article
Multidisciplinary Sciences
Lei Han, Xiaoyu Wei, Chuanyu Liu, Giacomo Volpe, Zhenkun Zhuang, Xuanxuan Zou, Zhifeng Wang, Taotao Pan, Yue Yuan, Xiao Zhang, Peng Fan, Pengcheng Guo, Yiwei Lai, Ying Lei, Xingyuan Liu, Feng Yu, Shuncheng Shangguan, Guangyao Lai, Qiuting Deng, Ya Liu, Liang Wu, Quan Shi, Hao Yu, Yunting Huang, Mengnan Cheng, Jiangshan Xu, Yang Liu, Mingyue Wang, Chunqing Wang, Yuanhang Zhang, Duo Xie, Yunzhi Yang, Yeya Yu, Huiwen Zheng, Yanrong Wei, Fubaoqian Huang, Junjie Lei, Waidong Huang, Zhiyong Zhu, Haorong Lu, Bo Wang, Xiaofeng Wei, Fengzhen Chen, Tao Yang, Wensi Du, Jing Chen, Shibo Xu, Juan An, Carl Ward, Zongren Wang, Zhong Pei, Chi-Wai Wong, Xiaolei Liu, Huafeng Zhang, Mingyuan Liu, Baoming Qin, Axel Schambach, Joan Isern, Liqiang Feng, Yan Liu, Xiangyu Guo, Zhen Liu, Qiang Sun, Patrick H. Maxwell, Nick Barker, Pura Munoz-Canoves, Ying Gu, Jan Mulder, Mathias Uhlen, Tao Tan, Shiping Liu, Huanming Yang, Jian Wang, Yong Hou, Xun Xu, Miguel A. Esteban, Longqi Liu
Summary: Studying tissue composition and function in non-human primates is crucial for understanding the nature of human species. This study presents a large-scale cell transcriptomic atlas of the non-human primate Macaca fascicularis, providing a vast annotated resource for studying a species closely related to humans. The atlas has been used to reconstruct cell-cell interaction networks, map the distribution of receptors for viruses causing human infectious diseases, and establish potential clinical associations with human genetic diseases.
Article
Cell Biology
Oladapo Edward Olaniru, Ulrich Kadolsky, Shichina Kannambath, Heli Vaikkinen, Kathy Fung, Pawan Dhami, Shanta J. Persaud
Summary: Current differentiation protocols have not been successful in reproducibly generating fully functional human beta cells in vitro, partly due to incomplete understanding of human pancreas development. In this study, detailed transcriptomic analysis of the developing human pancreas was presented, revealing distinct temporal-spatial gene cascades. Integration of single-cell RNA sequencing with spatial transcriptomics identified endocrine progenitor populations and branch-specific genes as the progenitors differentiate. The study also provided insights into the spatial co-location of Schwann cells with endocrine progenitors and their potential interaction via L1CAM-EPHB2 signaling. A web resource for investigating human pancreas development was generated.
Article
Medicine, Research & Experimental
Akiko Yano, Shuang Liu, Yasuyuki Suzuki, Matome Imai, Masaki Mogi, Takashi Sugiyama
Summary: This study used single-cell RNA sequencing to uncover the cellular composition and functional shift in the adipose tissue during pregnancy. It identified unique properties of adipocytes in response to pregnancy processes and their potential contribution to maternal-fetal immune tolerance. The study also highlighted the role of adipocytes in pregnancy-induced vesicular remodeling.
Article
Chemistry, Multidisciplinary
Julia Rogal, Julia Roosz, Claudia Teufel, Madalena Cipriano, Raylin Xu, Wiebke Eisler, Martin Weiss, Katja Schenke-Layland, Peter Loskill
Summary: Obesity and associated diseases have become epidemic globally. Researchers have developed a microphysiological in vitro model of human white adipose tissue, leveraging Organ-on-Chip technology, which can recapitulate crucial adipose tissue functions and offers advantages such as low inter-donor variability and controllability, making it a valuable tool for metabolism research and personalized medicine applications.
Article
Immunology
Ines Felix, Heli Jokela, Joonas Karhula, Noora Kotaja, Eriika Savontaus, Marko Salmi, Pia Rantakari
Summary: This study reveals the diversity and developmental origin of resident adipose tissue macrophages through comprehensive single-cell mass cytometry analysis, as well as the functional differences in their in vitro and in vivo activities. A high-fat diet induces changes in the quantity and functionality of macrophages, which can be reversed by dietary intervention.
FRONTIERS IN IMMUNOLOGY
(2021)
Review
Endocrinology & Metabolism
Irem Altun, Xiaocheng Yan, Siegfried Ussar
Summary: Adipose tissue is important for energy storage and regulating metabolism. Obesity can lead to dysfunction in adipose tissue, affecting the composition and function of stromal cells. Immune cells in adipose tissue play essential roles in regulating adipocyte function. Macrophages, mast cells, innate lymphoid cells, and T cells all have a significant impact on adipocyte progenitor proliferation, differentiation, and lineage commitment.
FRONTIERS IN ENDOCRINOLOGY
(2022)
Article
Cell & Tissue Engineering
Rongmei Qu, Kai He, Tingyu Fan, Yuchao Yang, Liyao Mai, Zhiwei Lian, Zhitao Zhou, Yan Peng, Asmat Ullah Khan, Bing Sun, Xiaolan Huang, Jun Ouyang, Xinghua Pan, Jingxing Dai, Wenhua Huang
Summary: The study used single-cell RNA sequencing to investigate the chemically induced osteogenesis process of human adipose MSCs, identifying some cells intrinsically prepared for osteogenesis and a set of genes related to cell stress response.
Article
Multidisciplinary Sciences
Richard C. Tyser, Elmir Mahammadov, Shota Nakanoh, Ludovic Vallier, Antonio Scialdone, Shankar Srinivas
Summary: The single-cell transcriptional profile of a human embryo between 16 and 19 days after fertilization shows similarities and differences in gastrulation compared to mouse and non-human primate models. This study provides new insights into human development and offers valuable information for directed differentiation of human cells in vitro.
Article
Multidisciplinary Sciences
Xiaowei Xie, Mengyao Liu, Yawen Zhang, Bingrui Wang, Caiying Zhu, Chenchen Wang, Qing Li, Yingying Huo, Jiaojiao Guo, Changlu Xu, Linping Hu, Aiming Pang, Shihui Ma, Lina Wang, Wenbin Cao, Shulian Chen, Qiuling Li, Sudong Zhang, Xueying Zhao, Wen Zhou, Hongbo Luo, Guoguang Zheng, Erlie Jiang, Sizhou Feng, Lixiang Chen, Lihong Shi, Hui Cheng, Sha Hao, Ping Zhu, Tao Cheng
Summary: A single-cell transcriptional atlas of human blood cells was constructed, revealing transcriptional differences and regulatory networks among different cell types. The study identified putative lncRNAs and transcription factors regulating cell differentiation in hematopoiesis.
NATIONAL SCIENCE REVIEW
(2021)
Article
Biotechnology & Applied Microbiology
T. Lohoff, S. Ghazanfar, A. Missarova, N. Koulena, N. Pierson, J. A. Griffiths, E. S. Bardot, C. -H. L. Eng, R. C. V. Tyser, R. Argelaguet, C. Guibentif, S. Srinivas, J. Briscoe, B. D. Simons, A. -K. Hadjantonakis, B. Gottgens, W. Reik, J. Nichols, L. Cai, J. C. Marioni
Summary: Improved integration of spatial and single-cell transcriptomic data through the seqFISH method provides insights into mouse development, revealing cell types across the embryo and uncovering axes of cell differentiation that are not apparent from scRNA-seq data. This approach offers a high-resolution spatial map for studying cell fate decisions in complex tissues and development.
NATURE BIOTECHNOLOGY
(2022)
Article
Multidisciplinary Sciences
Karolina Hanna Prazanowska, Su Bin Lim
Summary: As the importance of single-cell RNA sequencing (scRNA-seq) in studying cellular heterogeneity grows, the number of available scRNA-seq datasets has also increased rapidly. However, reusing such data is often difficult due to small cohort size, limited cell types, and insufficient information on cell type classification. Here, we present a large integrated scRNA-seq dataset containing 224,611 cells from human primary non-small cell lung cancer (NSCLC) tumors. We preprocess and integrate seven independent scRNA-seq datasets using an anchor-based approach, with validation using two additional datasets. This integrated data serves as a valuable resource for studying NSCLC transcriptome at the single cell level.
Article
Dermatology
Kim Thrane, Marten C. G. Winge, Hongyu Wang, Larry Chen, Margaret G. Guo, Alma Andersson, Xesus M. Abalo, Xue Yang, Daniel S. Kim, Sophia K. Longo, Brian Y. Soong, Jordan M. Meyers, David L. Reynolds, Aaron McGeever, Deniz Demircioglu, Dan Hasson, Reza Mirzazadeh, Adam J. Rubin, Gordon H. Bae, Jim Karkanias, Kerri Rieger, Joakim Lundeberg, Andrew L. Ji
Summary: This study integrates human and mouse skin data to explore the relationship between epidermal homeostasis, skin diseases, and cellular subpopulations, and identifies potential therapeutic targets.
JOURNAL OF INVESTIGATIVE DERMATOLOGY
(2023)
Article
Endocrinology & Metabolism
Enrichetta Mileti, Kelvin H. M. Kwok, Daniel P. Andersson, Anthony Mathelier, Amitha Raman, Jesper Backdahl, Jutta Jalkanen, Lucas Massier, Anders Thorell, Hui Gao, Peter Arner, Niklas Mejhert, Carsten O. Daub, Mikael Ryden
Summary: Selective hepatic insulin resistance is a feature of obesity and type 2 diabetes. This study showed that white adipose tissue in obese individuals also displays a selective insulin response, which is normalized by weight loss in most genes.
Article
Endocrinology & Metabolism
Alyssa Imbert, Nathalie Vialaneix, Julien Marquis, Julie Vion, Aline Charpagne, Sylviane Metairon, Claire Laurens, Cedric Moro, Nathalie Boulet, Ondine Walter, Gregory Lefebvre, Jorg Hager, Dominique Langin, Wim H. M. Saris, Arne Astrup, Nathalie Viguerie, Armand Valsesia
Summary: This study investigated the relationship between changes in bioclinical parameters and gene expression in adipose tissue during a weight loss intervention. The results revealed that changes in body mass index were associated with changes in the expression of genes related to inflammatory response. Additionally, several genes specific to macrophages were found to be connected to changes in GDF15 expression throughout the dietary intervention.
JOURNAL OF CLINICAL ENDOCRINOLOGY & METABOLISM
(2022)
Article
Endocrinology & Metabolism
Peter Arner, Daniel P. Andersson, Erik Arner, Mikael Ryden, Alastair G. Kerr
Summary: Early onset overweight/obesity leads to a faster and more pronounced accumulation of subcutaneous adipose tissue, but the mechanisms of growth in terms of adipocyte structure, morphology, and lipolysis do not significantly differ between early/juvenile and late onset overweight/obesity.
INTERNATIONAL JOURNAL OF OBESITY
(2022)
Article
Multidisciplinary Sciences
Alastair G. Kerr, Zuoneng Wang, Na Wang, Kelvin H. M. Kwok, Jutta Jalkanen, Alison Ludzki, Simon Lecoutre, Dominique Langin, Martin O. Bergo, Ingrid Dahlman, Carsten Mim, Peter Arner, Hui Gao
Summary: The study identifies ADIPINT, a human adipocyte-specific lncRNA, as a regulator of lipid metabolism in white adipocytes. ADIPINT interacts with pyruvate carboxylase and affects its abundance and enzymatic activity, which in turn influences adipocyte lipid synthesis and breakdown. ADIPINT expression is increased in obesity and is associated with adipose insulin resistance and pyruvate carboxylase activity.
NATURE COMMUNICATIONS
(2022)
Article
Genetics & Heredity
Peiyao Mao, Yinchen Shen, Xun Xu, Jiawei Zhong
Summary: Retinoblastoma is a common pediatric intraocular cancer that can be treated with immunotherapies without vision loss. This study investigated the immune cell infiltrative landscape of retinoblastoma and found that patients with high immune cell infiltration scores had increased expression levels of late cone markers, while those with low scores had larger tumor size and metastasis propensity. The hypermethylated genes in the high-ICI subgroup were associated with immune regulation in the tumor microenvironment. This study provides a comprehensive framework for understanding the influence of epigenetic events on the tumor immune microenvironment and identifies potential immunotherapy targets for retinoblastoma.
FRONTIERS IN GENETICS
(2022)
Article
Endocrinology & Metabolism
Julie Pires Da Silva, Matthieu Wargny, Jeremy Raffin, Mikael Croyal, Thibaut Duparc, Guillaume Combes, Annelise Genoux, Bertrand Perret, Bruno Vellas, Sophie Guyonnet, Claire Thalamas, Dominique Langin, Cedric Moro, Nathalie Viguerie, Yves Rolland, Philipe de Souto Barreto, Bertrand Cariou, Laurent O. Martinez
Summary: This study analyzed the association between plasma ATPase inhibitory factor 1 (IF1) levels and markers of glucose homeostasis as well as the development of new-onset diabetes (NOD) in individuals with prediabetes. The results showed that IF1 levels were negatively correlated with clinical variables associated with obesity and insulin resistance, and positively correlated with markers of cardiometabolic health. Furthermore, the study found a significant association between IF1 levels and the risk of type 2 diabetes mellitus (T2DM).
DIABETES & METABOLISM
(2023)
Article
Endocrinology & Metabolism
Daniel P. Andersson, Alastair G. Kerr, Ingrid Dahlman, Mikael Ryden, Peter Arner
Summary: Insulin sensitivity for antilipolysis and lipogenesis is decreased in sedentary individuals, but only the association between antilipolysis sensitivity and physical activity remains significant. Fatty acid levels decrease following hyperinsulinemia, but remain higher in sedentary women. mRNA expression of insulin receptor and its substrates 1 and 2 is decreased in sedentary individuals.
Article
Hematology
Alastair G. Kerr, Daniel P. Andersson, Ingrid Dahlman, Mikael Ryden, Peter Arner
Summary: This study found that insulin resistance is closely associated with abnormal blood lipids and is independent of resistance in adipose tissue and liver. Insulin resistance is associated with antilipolysis and lipogenesis in adipocytes, which may be related to the expression of insulin receptor signaling pathways in adipose tissue.
ARTERIOSCLEROSIS THROMBOSIS AND VASCULAR BIOLOGY
(2023)
Article
Ophthalmology
Peiyao Mao, Yinchen Shen, Xiying Mao, Kun Liu, Jiawei Zhong
Summary: In this study, the researchers used 5'-tag-based single-cell RNA sequencing to identify cell type-specific alternative transcription start site events and key transcription factors in the retina. They found elevated apoptosis signal in Muller glia and microglia in diabetic retina, which may serve as an early sign of diabetic retinopathy. By measuring 5'UTR isoforms in retinal single-cell dataset, the study provides a comprehensive panorama of alternative transcription start sites and their potential consequences related to post-transcriptional regulation.
EXPERIMENTAL EYE RESEARCH
(2023)
Article
Endocrinology & Metabolism
Salwan Maqdasy, Simon Lecoutre, Gianluca Renzi, Scott Frendo-Cumbo, David Rizo-Roca, Thomas Moritz, Marta Juvany, Ondrej Hodek, Hui Gao, Morgane Couchet, Michael Witting, Alastair Kerr, Martin O. Bergo, Robin P. Choudhury, Myriam Aouadi, Juleen R. Zierath, Anna Krook, Niklas Mejhert, Mikael Ryden
Summary: This study reveals that an increased phosphocreatine/creatine ratio in white adipocytes contributes to AMP-activated protein kinase activity changes and promotes inflammation in obesity. Metabolomic and transcriptomic analysis of white adipose tissue samples from clinical cohorts and in vitro and in vivo models show that decreased phosphocreatine metabolism alters AMP-activated protein kinase activity by affecting ATP/ADP levels in white adipocytes. This disturbance leads to a pro-inflammatory profile characterized by increased production of chemokine (C-C motif) ligand 2 (CCL2). These findings provide new insights into the mechanisms driving white adipose tissue inflammation in obesity.