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Tang YJ, Xu H, Hughes NW, Kim SH, Ruiz P, Shuldiner EG, Lopez SS, Hebert JD, Karmakar S, Andrejka L, Dolcen DN, Boross G, Chu P, Detrick C, Pierce S, Ashkin EL, Greenleaf WJ, Voss AK, Thomas T, van de Rijn M, Petrov DA, Winslow MM. Functional mapping of epigenetic regulators uncovers coordinated tumor suppression by the HBO1 and MLL1 complexes. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.08.19.607671. [PMID: 39229041 PMCID: PMC11370414 DOI: 10.1101/2024.08.19.607671] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 09/05/2024]
Abstract
Epigenetic dysregulation is widespread in cancer. However, the specific epigenetic regulators and the processes they control to drive cancer phenotypes are poorly understood. Here, we employed a novel, scalable and high-throughput in vivo method to perform iterative functional screens of over 250 epigenetic regulatory genes within autochthonous oncogenic KRAS-driven lung tumors. We identified multiple novel epigenetic tumor suppressor and tumor dependency genes. We show that a specific HBO1 complex and the MLL1 complex are among the most impactful tumor suppressive epigenetic regulators in lung. The histone modifications generated by the HBO1 complex are frequently absent or reduced in human lung adenocarcinomas. The HBO1 and MLL1 complexes regulate chromatin accessibility of shared genomic regions, lineage fidelity and the expression of canonical tumor suppressor genes. The HBO1 and MLL1 complexes are epistatic during lung tumorigenesis, and their functional correlation is conserved in human cancer cell lines. Together, these results demonstrate the value of quantitative methods to generate a phenotypic roadmap of epigenetic regulatory genes in tumorigenesis in vivo .
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Zhao Z, Shuai Y, Wu Y, Xu X, Li M, Wu D. Age-dependent functional development pattern in neonatal brain: An fMRI-based brain entropy study. Neuroimage 2024; 297:120669. [PMID: 38852805 DOI: 10.1016/j.neuroimage.2024.120669] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/11/2023] [Revised: 04/01/2024] [Accepted: 06/05/2024] [Indexed: 06/11/2024] Open
Abstract
The relationship between brain entropy (BEN) and early brain development has been established through animal studies. However, it remains unclear whether the BEN can be used to identify age-dependent functional changes in human neonatal brains and the genetic underpinning of the new neuroimaging marker remains to be elucidated. In this study, we analyzed resting-state fMRI data from the Developing Human Connectome Project, including 280 infants who were scanned at 37.5-43.5 weeks postmenstrual age. The BEN maps were calculated for each subject, and a voxel-wise analysis was conducted using a general linear model to examine the effects of age, sex, and preterm birth on BEN. Additionally, we evaluated the correlation between regional BEN and gene expression levels. Our results demonstrated that the BEN in the sensorimotor-auditory and association cortices, along the 'S-A' axis, was significantly positively correlated with postnatal age (PNA), and negatively correlated with gestational age (GA), respectively. Meanwhile, the BEN in the right rolandic operculum correlated significantly with both GA and PNA. Preterm-born infants exhibited increased BEN values in widespread cortical areas, particularly in the visual-motor cortex, when compared to term-born infants. Moreover, we identified five BEN-related genes (DNAJC12, FIG4, STX12, CETN2, and IRF2BP2), which were involved in protein folding, synaptic vesicle transportation and cell division. These findings suggest that the fMRI-based BEN can serve as an indicator of age-dependent brain functional development in human neonates, which may be influenced by specific genes.
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Affiliation(s)
- Zhiyong Zhao
- Department of Radiology, Children's Hospital, Zhejiang University School of Medicine, National Clinical Research Center for Child Health, Hangzhou, China
| | - Yifan Shuai
- Key Laboratory for Biomedical Engineering of Ministry of Education, Department of Biomedical Engineering, College of Biomedical Engineering & Instrument Science, Zhejiang University, Hangzhou, China
| | - Yihan Wu
- Department of Biomedical Engineering, Johns Hopkins University, Baltimore, MD, USA
| | - Xinyi Xu
- Key Laboratory for Biomedical Engineering of Ministry of Education, Department of Biomedical Engineering, College of Biomedical Engineering & Instrument Science, Zhejiang University, Hangzhou, China
| | - Mingyang Li
- Key Laboratory for Biomedical Engineering of Ministry of Education, Department of Biomedical Engineering, College of Biomedical Engineering & Instrument Science, Zhejiang University, Hangzhou, China
| | - Dan Wu
- Key Laboratory for Biomedical Engineering of Ministry of Education, Department of Biomedical Engineering, College of Biomedical Engineering & Instrument Science, Zhejiang University, Hangzhou, China.
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3
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Li J, Shyr Y, Liu Q. aKNNO: single-cell and spatial transcriptomics clustering with an optimized adaptive k-nearest neighbor graph. Genome Biol 2024; 25:203. [PMID: 39090647 PMCID: PMC11293182 DOI: 10.1186/s13059-024-03339-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/16/2023] [Accepted: 07/16/2024] [Indexed: 08/04/2024] Open
Abstract
Typical clustering methods for single-cell and spatial transcriptomics struggle to identify rare cell types, while approaches tailored to detect rare cell types gain this ability at the cost of poorer performance for grouping abundant ones. Here, we develop aKNNO to simultaneously identify abundant and rare cell types based on an adaptive k-nearest neighbor graph with optimization. Benchmarking on 38 simulated and 20 single-cell and spatial transcriptomics datasets demonstrates that aKNNO identifies both abundant and rare cell types more accurately than general and specialized methods. Using only gene expression aKNNO maps abundant and rare cells more precisely compared to integrative approaches.
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Affiliation(s)
- Jia Li
- Department of Biostatistics, Vanderbilt University Medical Center, Nashville, TN, 37203, USA
- Center for Quantitative Sciences, Vanderbilt University Medical Center, Nashville, TN, 37203, USA
| | - Yu Shyr
- Department of Biostatistics, Vanderbilt University Medical Center, Nashville, TN, 37203, USA.
- Center for Quantitative Sciences, Vanderbilt University Medical Center, Nashville, TN, 37203, USA.
| | - Qi Liu
- Department of Biostatistics, Vanderbilt University Medical Center, Nashville, TN, 37203, USA.
- Center for Quantitative Sciences, Vanderbilt University Medical Center, Nashville, TN, 37203, USA.
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Ye K, Chang W, Xu J, Guo Y, Qin Q, Dang K, Han X, Zhu X, Ge Q, Cui Q, Xu Y, Zhao X. Spatial transcriptomic profiling of isolated microregions in tissue sections utilizing laser-induced forward transfer. PLoS One 2024; 19:e0305977. [PMID: 39052564 PMCID: PMC11271912 DOI: 10.1371/journal.pone.0305977] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/29/2023] [Accepted: 06/07/2024] [Indexed: 07/27/2024] Open
Abstract
Profiling gene expression while preserving cell locations aids in the comprehensive understanding of cell fates in multicellular organisms. However, simple and flexible isolation of microregions of interest (mROIs) for spatial transcriptomics is still challenging. We present a laser-induced forward transfer (LIFT)-based method combined with a full-length mRNA-sequencing protocol (LIFT-seq) for profiling region-specific tissues. LIFT-seq demonstrated that mROIs from two adjacent sections could reliably and sensitively detect and display gene expression. In addition, LIFT-seq can identify region-specific mROIs in the mouse cortex and hippocampus. Finally, LIFT-seq identified marker genes in different layers of the cortex with very similar expression patterns. These genes were then validated using in situ hybridization (ISH) results. Therefore, LIFT-seq will be a valuable and efficient technique for profiling the spatial transcriptome in various tissues.
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Affiliation(s)
- Kaiqiang Ye
- State Key Laboratory of Digital Medical Engineering, School of Biological Science & Medical Engineering, Southeast University, Nanjing, Jiangsu, China
| | - Wanqing Chang
- State Key Laboratory of Digital Medical Engineering, School of Biological Science & Medical Engineering, Southeast University, Nanjing, Jiangsu, China
| | - Jitao Xu
- State Key Laboratory of Digital Medical Engineering, School of Biological Science & Medical Engineering, Southeast University, Nanjing, Jiangsu, China
| | - Yunxia Guo
- State Key Laboratory of Digital Medical Engineering, School of Biological Science & Medical Engineering, Southeast University, Nanjing, Jiangsu, China
| | - Qingyang Qin
- State Key Laboratory of Digital Medical Engineering, School of Biological Science & Medical Engineering, Southeast University, Nanjing, Jiangsu, China
| | - Kaitong Dang
- State Key Laboratory of Digital Medical Engineering, School of Biological Science & Medical Engineering, Southeast University, Nanjing, Jiangsu, China
| | - Xiaofeng Han
- State Key Laboratory of Digital Medical Engineering, School of Biological Science & Medical Engineering, Southeast University, Nanjing, Jiangsu, China
| | - Xiaolei Zhu
- Department of Neurology, Nanjing Drum Tower Hospital, Affiliated Hospital of Medical School, Nanjing University, Nanjing, Jiangsu, China
| | - Qinyu Ge
- State Key Laboratory of Digital Medical Engineering, School of Biological Science & Medical Engineering, Southeast University, Nanjing, Jiangsu, China
| | - Qiannan Cui
- State Key Laboratory of Digital Medical Engineering, School of Biological Science & Medical Engineering, Southeast University, Nanjing, Jiangsu, China
| | - Yun Xu
- Department of Neurology, Nanjing Drum Tower Hospital, Affiliated Hospital of Medical School, Nanjing University, Nanjing, Jiangsu, China
| | - Xiangwei Zhao
- State Key Laboratory of Digital Medical Engineering, School of Biological Science & Medical Engineering, Southeast University, Nanjing, Jiangsu, China
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Li Y, Cui Y, Song K, Shen L, Xiao L, Jin J, Zhao Y, Yan Y, Zhao S, Yao W, Wang S, Du Z, Yang R, Yi B, Song Y. TagP, a PAAR-domain containing protein, plays roles in the fitness and virulence of Acinetobacter baumannii. Front Cell Infect Microbiol 2024; 14:1379106. [PMID: 39193505 PMCID: PMC11348943 DOI: 10.3389/fcimb.2024.1379106] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/20/2024] [Accepted: 07/03/2024] [Indexed: 08/29/2024] Open
Abstract
Background Type VI secretion system (T6SS) is widely present in Gram-negative bacteria and directly mediates antagonistic prokaryote interactions. PAAR (proline-alanine-alanine-arginine repeats) proteins have been proven essential for T6SS-mediated secretion and target cell killing. Although PAAR proteins are commonly found in A. baumannii, their biological functions are not fully disclosed yet. In this study, we investigated the functions of a PAAR protein termed TagP (T6SS-associated-gene PAAR), encoded by the gene ACX60_RS09070 outside the core T6SS locus of A. baumannii strain ATCC 17978. Methods In this study, tagP null and complement A. baumannii ATCC 17978 strains were constructed. The influence of TagP on T6SS function was investigated through Hcp detection and bacterial competition assay; the influence on environmental fitness was studied through in vitro growth, biofilm formation assay, surface motility assay, survivability in various simulated environmental conditions; the influence on pathogenicity was explored through cell adhesion and invasion assays, intramacrophage survival assay, serum survival assay, and G. melonella Killing assays. Quantitative transcriptomic and proteomic analyses were utilized to observe the global impact of TagP on bacterial status. Results Compared with the wildtype strain, the tagP null mutant was impaired in several tested phenotypes such as surface motility, biofilm formation, tolerance to adverse environments, adherence to eukaryotic cells, endurance to serum complement killing, and virulence to Galleria melonella. Notably, although RNA-Seq and proteomics analysis revealed that many genes were significantly down-regulated in the tagP null mutant compared to the wildtype strain, there is no significant difference in their antagonistic abilities. We also found that Histone-like nucleoid structuring protein (H-NS) was significantly upregulated in the tagP null mutant at both mRNA and protein levels. Conclusions This study enriches our understanding of the biofunction of PAAR proteins in A. baumannii. The results indicates that TagP involved in a unique modulation of fitness and virulence control in A. baumannii, it is more than a classic PAAR protein involved in T6SS, while how TagP play roles in the fitness and virulence of A. baumannii needs further investigation to clarify.
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Affiliation(s)
- Yanbing Li
- State Key Laboratory of Pathogen and Biosecurity, Beijing Institute of Microbiology and Epidemiology, Beijing, China
- Department of Clinical Laboratory, Xiangya Hospital, Central South University, Changsha, Hunan, China
| | - Yiming Cui
- School of Life Sciences, Fujian Agriculture and Forestry University, Fuzhou, China
| | - Kai Song
- State Key Laboratory of Pathogen and Biosecurity, Beijing Institute of Microbiology and Epidemiology, Beijing, China
| | - Leiming Shen
- State Key Laboratory of Pathogen and Biosecurity, Beijing Institute of Microbiology and Epidemiology, Beijing, China
| | - Liting Xiao
- State Key Laboratory of Pathogen and Biosecurity, Beijing Institute of Microbiology and Epidemiology, Beijing, China
| | - Junyan Jin
- State Key Laboratory of Pathogen and Biosecurity, Beijing Institute of Microbiology and Epidemiology, Beijing, China
| | - Yanting Zhao
- State Key Laboratory of Pathogen and Biosecurity, Beijing Institute of Microbiology and Epidemiology, Beijing, China
| | - Yanfeng Yan
- State Key Laboratory of Pathogen and Biosecurity, Beijing Institute of Microbiology and Epidemiology, Beijing, China
| | - Shengyuan Zhao
- Department of Clinical Laboratory, Xiangya Hospital, Central South University, Changsha, Hunan, China
| | - Wenwu Yao
- State Key Laboratory of Pathogen and Biosecurity, Beijing Institute of Microbiology and Epidemiology, Beijing, China
| | - Shihua Wang
- School of Life Sciences, Fujian Agriculture and Forestry University, Fuzhou, China
| | - Zongmin Du
- State Key Laboratory of Pathogen and Biosecurity, Beijing Institute of Microbiology and Epidemiology, Beijing, China
| | - Ruifu Yang
- State Key Laboratory of Pathogen and Biosecurity, Beijing Institute of Microbiology and Epidemiology, Beijing, China
| | - Bin Yi
- Department of Clinical Laboratory, Xiangya Hospital, Central South University, Changsha, Hunan, China
| | - Yajun Song
- State Key Laboratory of Pathogen and Biosecurity, Beijing Institute of Microbiology and Epidemiology, Beijing, China
- School of Life Sciences, Fujian Agriculture and Forestry University, Fuzhou, China
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6
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Sun K, Liu X, Lan X. A single-cell atlas of chromatin accessibility in mouse organogenesis. Nat Cell Biol 2024; 26:1200-1211. [PMID: 38977846 DOI: 10.1038/s41556-024-01435-6] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/15/2022] [Accepted: 04/29/2024] [Indexed: 07/10/2024]
Abstract
Organogenesis is a highly complex and precisely regulated process. Here we profiled the chromatin accessibility in >350,000 cells derived from 13 mouse embryos at four developmental stages from embryonic day (E) 10.5 to E13.5 by SPATAC-seq in a single experiment. The resulting atlas revealed the status of 830,873 candidate cis-regulatory elements in 43 major cell types. By integrating the chromatin accessibility atlas with the previous transcriptomic dataset, we characterized cis-regulatory sequences and transcription factors associated with cell fate commitment, such as Nr5a2 in the development of gastrointestinal tract, which was preliminarily supported by the in vivo experiment in zebrafish. Finally, we integrated this atlas with the previous single-cell chromatin accessibility dataset from 13 adult mouse tissues to delineate the developmental stage-specific gene regulatory programmes within and across different cell types and identify potential molecular switches throughout lineage development. This comprehensive dataset provides a foundation for exploring transcriptional regulation in organogenesis.
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Affiliation(s)
- Keyong Sun
- School of Medicine, Tsinghua University, Beijing, China
- Peking-Tsinghua-NIBS Joint Graduate Program, Tsinghua University, Beijing, China
- Tsinghua-Peking Center for Life Sciences, Beijing, China
| | - Xin Liu
- Tsinghua-Peking Center for Life Sciences, Beijing, China
- School of Life Sciences, Tsinghua University, Beijing, China
| | - Xun Lan
- School of Medicine, Tsinghua University, Beijing, China.
- Peking-Tsinghua-NIBS Joint Graduate Program, Tsinghua University, Beijing, China.
- Tsinghua-Peking Center for Life Sciences, Beijing, China.
- MOE Key Laboratory of Bioinformatics, Tsinghua University, Beijing, China.
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7
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Han Z, Yang C, He H, Huang T, Yin Q, Tian G, Wu Y, Hu W, Lu L, Bajpai AK, Mi J, Xu F. Systems Genetics Analyses Reveals Key Genes Related to Behavioral Traits in the Striatum of CFW Mice. J Neurosci 2024; 44:e0252242024. [PMID: 38777602 PMCID: PMC11211725 DOI: 10.1523/jneurosci.0252-24.2024] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/06/2024] [Revised: 04/10/2024] [Accepted: 05/06/2024] [Indexed: 05/25/2024] Open
Abstract
The striatum plays a central role in directing many complex behaviors ranging from motor control to action choice and reward learning. In our study, we used 55 male CFW mice with rapid decay linkage disequilibrium to systematically mine the striatum-related behavioral functional genes by analyzing their striatal transcriptomes and 79 measured behavioral phenotypic data. By constructing a gene coexpression network, we clustered the genes into 13 modules, with most of them being positively correlated with motor traits. Based on functional annotations as well as Fisher's exact and hypergeometric distribution tests, brown and magenta modules were identified as core modules. They were significantly enriched for striatal-related functional genes. Subsequent Mendelian randomization analysis verified the causal relationship between the core modules and dyskinesia. Through the intramodular gene connectivity analysis, Adcy5 and Kcnma1 were identified as brown and magenta module hub genes, respectively. Knock outs of both Adcy5 and Kcnma1 lead to motor dysfunction in mice, and KCNMA1 acts as a risk gene for schizophrenia and smoking addiction in humans. We also evaluated the cellular composition of each module and identified oligodendrocytes in the striatum to have a positive role in motor regulation.
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Affiliation(s)
- Zhe Han
- School of Pharmacy, Binzhou Medical University, Yantai 264003, Shandong Province, China
- Shandong Technology Innovation Center of Molecular Targeting and Intelligent Diagnosis and Treatment, Yantai 264003, Shandong Province, China
| | - Chunhua Yang
- School of Pharmacy, Binzhou Medical University, Yantai 264003, Shandong Province, China
- Shandong Technology Innovation Center of Molecular Targeting and Intelligent Diagnosis and Treatment, Yantai 264003, Shandong Province, China
| | - Hongjie He
- School of Pharmacy, Binzhou Medical University, Yantai 264003, Shandong Province, China
- Shandong Technology Innovation Center of Molecular Targeting and Intelligent Diagnosis and Treatment, Yantai 264003, Shandong Province, China
| | - Tingting Huang
- School of Pharmacy, Binzhou Medical University, Yantai 264003, Shandong Province, China
- Shandong Technology Innovation Center of Molecular Targeting and Intelligent Diagnosis and Treatment, Yantai 264003, Shandong Province, China
| | - Quanting Yin
- School of Pharmacy, Binzhou Medical University, Yantai 264003, Shandong Province, China
- Shandong Technology Innovation Center of Molecular Targeting and Intelligent Diagnosis and Treatment, Yantai 264003, Shandong Province, China
| | - Geng Tian
- School of Pharmacy, Binzhou Medical University, Yantai 264003, Shandong Province, China
- Shandong Technology Innovation Center of Molecular Targeting and Intelligent Diagnosis and Treatment, Yantai 264003, Shandong Province, China
| | - Yuyong Wu
- School of Pharmacy, Binzhou Medical University, Yantai 264003, Shandong Province, China
| | - Wei Hu
- School of Pharmacy, Binzhou Medical University, Yantai 264003, Shandong Province, China
| | - Lu Lu
- Department of Genetics, Genomics and Informatics, University of Tennessee Health Science Center, Memphis, Tennessee 38163
| | - Akhilesh Kumar Bajpai
- Department of Genetics, Genomics and Informatics, University of Tennessee Health Science Center, Memphis, Tennessee 38163
| | - Jia Mi
- School of Pharmacy, Binzhou Medical University, Yantai 264003, Shandong Province, China
- Shandong Technology Innovation Center of Molecular Targeting and Intelligent Diagnosis and Treatment, Yantai 264003, Shandong Province, China
| | - Fuyi Xu
- School of Pharmacy, Binzhou Medical University, Yantai 264003, Shandong Province, China
- Shandong Technology Innovation Center of Molecular Targeting and Intelligent Diagnosis and Treatment, Yantai 264003, Shandong Province, China
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8
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Teschendorff AE. Computational single-cell methods for predicting cancer risk. Biochem Soc Trans 2024; 52:1503-1514. [PMID: 38856037 DOI: 10.1042/bst20231488] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/29/2024] [Revised: 05/22/2024] [Accepted: 05/24/2024] [Indexed: 06/11/2024]
Abstract
Despite recent biotechnological breakthroughs, cancer risk prediction remains a formidable computational and experimental challenge. Addressing it is critical in order to improve prevention, early detection and survival rates. Here, I briefly summarize some key emerging theoretical and computational challenges as well as recent computational advances that promise to help realize the goals of cancer-risk prediction. The focus is on computational strategies based on single-cell data, in particular on bottom-up network modeling approaches that aim to estimate cancer stemness and dedifferentiation at single-cell resolution from a systems-biological perspective. I will describe two promising methods, a tissue and cell-lineage independent one based on the concept of diffusion network entropy, and a tissue and cell-lineage specific one that uses transcription factor regulons. Application of these tools to single-cell and single-nucleus RNA-seq data from stages prior to invasive cancer reveal that they can successfully delineate the heterogeneous inter-cellular cancer-risk landscape, identifying those cells that are more likely to turn cancerous. Bottom-up systems biological modeling of single-cell omic data is a novel computational analysis paradigm that promises to facilitate the development of preventive, early detection and cancer-risk prediction strategies.
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Affiliation(s)
- Andrew E Teschendorff
- CAS Key Laboratory of Computational Biology, Shanghai Institute of Nutrition and Health, University of Chinese Academy of Sciences, Chinese Academy of Sciences, Shanghai 200031, China
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9
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Baig MS, Ahmad A, Pathan RR, Mishra RK. Precision Nanomedicine with Bio-Inspired Nanosystems: Recent Trends and Challenges in Mesenchymal Stem Cells Membrane-Coated Bioengineered Nanocarriers in Targeted Nanotherapeutics. J Xenobiot 2024; 14:827-872. [PMID: 39051343 PMCID: PMC11270309 DOI: 10.3390/jox14030047] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/17/2024] [Revised: 05/09/2024] [Accepted: 06/15/2024] [Indexed: 07/27/2024] Open
Abstract
In the recent past, the formulation and development of nanocarriers has been elaborated into the broader fields and opened various avenues in their preclinical and clinical applications. In particular, the cellular membrane-based nanoformulations have been formulated to surpass and surmount the limitations and restrictions associated with naïve or free forms of therapeutic compounds and circumvent various physicochemical and immunological barriers including but not limited to systemic barriers, microenvironmental roadblocks, and other cellular or subcellular hinderances-which are quite heterogeneous throughout the diseases and patient cohorts. These limitations in drug delivery have been overcome through mesenchymal cells membrane-based precision therapeutics, where these interventions have led to the significant enhancements in therapeutic efficacies. However, the formulation and development of nanocarriers still focuses on optimization of drug delivery paradigms with a one-size-fits-all resolutions. As mesenchymal stem cell membrane-based nanocarriers have been engineered in highly diversified fashions, these are being optimized for delivering the drug payloads in more and better personalized modes, entering the arena of precision as well as personalized nanomedicine. In this Review, we have included some of the advanced nanocarriers which have been designed and been utilized in both the non-personalized as well as precision applicability which can be employed for the improvements in precision nanotherapeutics. In the present report, authors have focused on various other aspects of the advancements in stem cells membrane-based nanoparticle conceptions which can surmount several roadblocks and barriers in drug delivery and nanomedicine. It has been suggested that well-informed designing of these nanocarriers will lead to appreciable improvements in the therapeutic efficacy in therapeutic payload delivery applications. These approaches will also enable the tailored and customized designs of MSC-based nanocarriers for personalized therapeutic applications, and finally amending the patient outcomes.
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Affiliation(s)
- Mirza Salman Baig
- Anjuman-I-Islam Kalsekar Technical Campus School of Pharmacy, Sector-16, Near Thana Naka, Khandagao, New Panvel, Navi Mumbai 410206, Maharashtra, India;
| | - Anas Ahmad
- Julia McFarlane Diabetes Research Centre (JMDRC), Department of Microbiology, Immunology and Infectious Diseases, Snyder Institute for Chronic Diseases, Hotchkiss Brain Institute, Cumming School of Medicine, Foothills Medical Centre, University of Calgary, Calgary, AB T2N 4N1, Canada
| | | | - Rakesh Kumar Mishra
- School of Health Sciences and Technology, University of Petroleum and Energy Studies (UPES), Bidholi, Dehradun 248007, Uttarakhand, India;
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10
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Miyamoto Y, Kikuta J, Matsui T, Hasegawa T, Fujii K, Okuzaki D, Liu YC, Yoshioka T, Seno S, Motooka D, Uchida Y, Yamashita E, Kobayashi S, Eguchi H, Morii E, Tryggvason K, Shichita T, Kayama H, Atarashi K, Kunisawa J, Honda K, Takeda K, Ishii M. Periportal macrophages protect against commensal-driven liver inflammation. Nature 2024; 629:901-909. [PMID: 38658756 DOI: 10.1038/s41586-024-07372-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/15/2022] [Accepted: 04/02/2024] [Indexed: 04/26/2024]
Abstract
The liver is the main gateway from the gut, and the unidirectional sinusoidal flow from portal to central veins constitutes heterogenous zones, including the periportal vein (PV) and the pericentral vein zones1-5. However, functional differences in the immune system in each zone remain poorly understood. Here intravital imaging revealed that inflammatory responses are suppressed in PV zones. Zone-specific single-cell transcriptomics detected a subset of immunosuppressive macrophages enriched in PV zones that express high levels of interleukin-10 and Marco, a scavenger receptor that sequesters pro-inflammatory pathogen-associated molecular patterns and damage-associated molecular patterns, and consequently suppress immune responses. Induction of Marco+ immunosuppressive macrophages depended on gut microbiota. In particular, a specific bacterial family, Odoribacteraceae, was identified to induce this macrophage subset through its postbiotic isoallolithocholic acid. Intestinal barrier leakage resulted in inflammation in PV zones, which was markedly augmented in Marco-deficient conditions. Chronic liver inflammatory diseases such as primary sclerosing cholangitis (PSC) and non-alcoholic steatohepatitis (NASH) showed decreased numbers of Marco+ macrophages. Functional ablation of Marco+ macrophages led to PSC-like inflammatory phenotypes related to colitis and exacerbated steatosis in NASH in animal experimental models. Collectively, commensal bacteria induce Marco+ immunosuppressive macrophages, which consequently limit excessive inflammation at the gateway of the liver. Failure of this self-limiting system promotes hepatic inflammatory disorders such as PSC and NASH.
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Affiliation(s)
- Yu Miyamoto
- Department of Immunology and Cell Biology, Graduate School of Medicine and Frontier Biosciences, Osaka University, Osaka, Japan
- WPI-Immunology Frontier Research Center, Osaka University, Osaka, Japan
- Life-omics Research Division, Institute for Open and Transdisciplinary Research Initiative, Osaka University, Osaka, Japan
| | - Junichi Kikuta
- Department of Immunology and Cell Biology, Graduate School of Medicine and Frontier Biosciences, Osaka University, Osaka, Japan
- WPI-Immunology Frontier Research Center, Osaka University, Osaka, Japan
- Life-omics Research Division, Institute for Open and Transdisciplinary Research Initiative, Osaka University, Osaka, Japan
- Laboratory of Bioimaging and Drug Discovery, National Institutes of Biomedical Innovation, Health and Nutrition, Osaka, Japan
| | - Takahiro Matsui
- Department of Immunology and Cell Biology, Graduate School of Medicine and Frontier Biosciences, Osaka University, Osaka, Japan
- Department of Pathology, Graduate School of Medicine, Osaka University, Osaka, Japan
| | - Tetsuo Hasegawa
- Department of Immunology and Cell Biology, Graduate School of Medicine and Frontier Biosciences, Osaka University, Osaka, Japan
| | - Kentaro Fujii
- Department of Immunology and Cell Biology, Graduate School of Medicine and Frontier Biosciences, Osaka University, Osaka, Japan
- WPI-Immunology Frontier Research Center, Osaka University, Osaka, Japan
- Life-omics Research Division, Institute for Open and Transdisciplinary Research Initiative, Osaka University, Osaka, Japan
| | - Daisuke Okuzaki
- WPI-Immunology Frontier Research Center, Osaka University, Osaka, Japan
- Genome Information Research Center, Research Institute for Microbial Diseases, Osaka University, Osaka, Japan
| | - Yu-Chen Liu
- WPI-Immunology Frontier Research Center, Osaka University, Osaka, Japan
- Genome Information Research Center, Research Institute for Microbial Diseases, Osaka University, Osaka, Japan
| | - Takuya Yoshioka
- Laboratory of Vaccine Materials, Center for Vaccine and Adjuvant Research, National Institutes of Biomedical Innovation, Health and Nutrition, Osaka, Japan
| | - Shigeto Seno
- Department of Bioinformatic Engineering, Graduate School of Information Science and Technology, Osaka University, Osaka, Japan
| | - Daisuke Motooka
- WPI-Immunology Frontier Research Center, Osaka University, Osaka, Japan
- Genome Information Research Center, Research Institute for Microbial Diseases, Osaka University, Osaka, Japan
| | - Yutaka Uchida
- Department of Immunology and Cell Biology, Graduate School of Medicine and Frontier Biosciences, Osaka University, Osaka, Japan
- WPI-Immunology Frontier Research Center, Osaka University, Osaka, Japan
- Life-omics Research Division, Institute for Open and Transdisciplinary Research Initiative, Osaka University, Osaka, Japan
- Laboratory of Bioimaging and Drug Discovery, National Institutes of Biomedical Innovation, Health and Nutrition, Osaka, Japan
| | - Erika Yamashita
- Department of Immunology and Cell Biology, Graduate School of Medicine and Frontier Biosciences, Osaka University, Osaka, Japan
- WPI-Immunology Frontier Research Center, Osaka University, Osaka, Japan
- Life-omics Research Division, Institute for Open and Transdisciplinary Research Initiative, Osaka University, Osaka, Japan
| | - Shogo Kobayashi
- Department of Gastroenterological Surgery, Graduate School of Medicine, Osaka University, Osaka, Japan
| | - Hidetoshi Eguchi
- Department of Gastroenterological Surgery, Graduate School of Medicine, Osaka University, Osaka, Japan
| | - Eiichi Morii
- Department of Pathology, Graduate School of Medicine, Osaka University, Osaka, Japan
| | - Karl Tryggvason
- Cardiovascular and Metabolic Disorders Program, Duke-NUS, Duke-NUS Medical School, Singapore, Singapore
| | - Takashi Shichita
- Laboratory for Neuroinflammation and Repair, Medical Research Institute, Tokyo Medical and Dental University, Tokyo, Japan
| | - Hisako Kayama
- WPI-Immunology Frontier Research Center, Osaka University, Osaka, Japan
- Department of Microbiology and Immunology, Graduate School of Medicine, Osaka University, Osaka, Japan
| | - Koji Atarashi
- Department of Microbiology and Immunology, School of Medicine, Keio University, Tokyo, Japan
| | - Jun Kunisawa
- Laboratory of Vaccine Materials, Center for Vaccine and Adjuvant Research, National Institutes of Biomedical Innovation, Health and Nutrition, Osaka, Japan
| | - Kenya Honda
- Department of Microbiology and Immunology, School of Medicine, Keio University, Tokyo, Japan
| | - Kiyoshi Takeda
- WPI-Immunology Frontier Research Center, Osaka University, Osaka, Japan
- Department of Microbiology and Immunology, Graduate School of Medicine, Osaka University, Osaka, Japan
| | - Masaru Ishii
- Department of Immunology and Cell Biology, Graduate School of Medicine and Frontier Biosciences, Osaka University, Osaka, Japan.
- WPI-Immunology Frontier Research Center, Osaka University, Osaka, Japan.
- Life-omics Research Division, Institute for Open and Transdisciplinary Research Initiative, Osaka University, Osaka, Japan.
- Laboratory of Bioimaging and Drug Discovery, National Institutes of Biomedical Innovation, Health and Nutrition, Osaka, Japan.
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11
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Ning Y, Duo S, Lin X, Zhang H, Fei J, Zhang B, Zeng Y, Xie D, Chen J, Liu X, Han C. Transcription factor PBX4 regulates limb development and haematopoiesis in mice. Cell Prolif 2024; 57:e13580. [PMID: 38230761 PMCID: PMC11056705 DOI: 10.1111/cpr.13580] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/01/2023] [Revised: 10/25/2023] [Accepted: 11/07/2023] [Indexed: 01/18/2024] Open
Abstract
The mammalian Pre-B cell leukaemia transcription factors 1-4 (PBX1-4) constitutes the PBC class of the homeodomain (HD)-containing proteins, which play important roles in diverse developmental processes. The functions and the underlying molecular mechanisms of PBX1-3 but not PBX4 have been extensively studied, and they have been reported to direct essential morphogenetic processes and organogenesis. In the present study, we generated knockin mice of FLAG-tagged PBX4 and the Pbx4 knockout (KO) mice and carried out in-depth characterisation of PBX4 expression and function. PBX4 was initially detected only in the testis among several organs of the adult mice and was expressed in spermatocytes and spermatids. However, no abnormality in spermatogenesis, but growth retardation and premature death after birth were observed in most adult Pbx4 KO mice. These animals were inactive and had shorter hindlimbs and lower numbers of reticulocytes and lymphocytes, probably caused by abnormalities at earlier developmental stages. Pbx4 mRNAs were indeed detected in several embryonic cell types related to limb development by in situ hybridisation and single-cell RNA-sequencing analysis. Pbx4 protein was also detected in the bone marrow of adult mice with a lower level compared with that in the testis. PBX4 preferentially binds to the promoters of a large number of genes including those for other HD-containing proteins and ribosomal proteins whose mutations are related to anaemia. PBX4-binding sites are enriched in motifs similar to those of other HD-containing proteins such as PKNOX1 indicating that PBX4 may also act as a co-transcription factor like other PBC proteins. Together, these results show that PBX4 participates in limb development and haematopoiesis while its function in spermatogenesis has not been revealed by gene KO probably due to the complementary effects of other genes.
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Affiliation(s)
- Yan Ning
- State Key Laboratory of Stem Cell and Reproductive Biology, Institute of ZoologyChinese Academy of SciencesBeijingChina
- Institute for Stem Cell and RegenerationChinese Academy of SciencesBeijingChina
- Beijing Institute for Stem Cell and Regenerative MedicineBeijingChina
- Savaid Medical SchoolUniversity of Chinese Academy of SciencesBeijingChina
| | - Shuguang Duo
- State Key Laboratory of Stem Cell and Reproductive Biology, Institute of ZoologyChinese Academy of SciencesBeijingChina
- Institute for Stem Cell and RegenerationChinese Academy of SciencesBeijingChina
- Beijing Institute for Stem Cell and Regenerative MedicineBeijingChina
| | - Xiwen Lin
- State Key Laboratory of Stem Cell and Reproductive Biology, Institute of ZoologyChinese Academy of SciencesBeijingChina
- Institute for Stem Cell and RegenerationChinese Academy of SciencesBeijingChina
- Beijing Institute for Stem Cell and Regenerative MedicineBeijingChina
| | - Hongbo Zhang
- The Key Laboratory for Stem Cells and Tissue Engineering, Ministry of Education, Zhongshan School of MedicineSun Yat‐sen UniversityGuangzhouChina
| | - Jifeng Fei
- Department of Pathology, Guangdong Provincial People's HospitalGuangdong Academy of Medical SciencesGuangzhouChina
| | - Bao Zhang
- The Key Laboratory for Stem Cells and Tissue Engineering, Ministry of Education, Zhongshan School of MedicineSun Yat‐sen UniversityGuangzhouChina
- Medical College of Jiaying UniversityMeizhouChina
| | - Yanyun Zeng
- Department of Pathology, Guangdong Provincial People's HospitalGuangdong Academy of Medical SciencesGuangzhouChina
| | - Dan Xie
- State Key Laboratory of Stem Cell and Reproductive Biology, Institute of ZoologyChinese Academy of SciencesBeijingChina
- Institute for Stem Cell and RegenerationChinese Academy of SciencesBeijingChina
- Beijing Institute for Stem Cell and Regenerative MedicineBeijingChina
- Savaid Medical SchoolUniversity of Chinese Academy of SciencesBeijingChina
| | - Jian Chen
- State Key Laboratory of Stem Cell and Reproductive Biology, Institute of ZoologyChinese Academy of SciencesBeijingChina
- Institute for Stem Cell and RegenerationChinese Academy of SciencesBeijingChina
- Beijing Institute for Stem Cell and Regenerative MedicineBeijingChina
| | - Xiaowei Liu
- State Key Laboratory of Stem Cell and Reproductive Biology, Institute of ZoologyChinese Academy of SciencesBeijingChina
- Institute for Stem Cell and RegenerationChinese Academy of SciencesBeijingChina
- Beijing Institute for Stem Cell and Regenerative MedicineBeijingChina
- Savaid Medical SchoolUniversity of Chinese Academy of SciencesBeijingChina
| | - Chunsheng Han
- State Key Laboratory of Stem Cell and Reproductive Biology, Institute of ZoologyChinese Academy of SciencesBeijingChina
- Institute for Stem Cell and RegenerationChinese Academy of SciencesBeijingChina
- Beijing Institute for Stem Cell and Regenerative MedicineBeijingChina
- Savaid Medical SchoolUniversity of Chinese Academy of SciencesBeijingChina
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12
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Wang K, Hou L, Wang X, Zhai X, Lu Z, Zi Z, Zhai W, He X, Curtis C, Zhou D, Hu Z. PhyloVelo enhances transcriptomic velocity field mapping using monotonically expressed genes. Nat Biotechnol 2024; 42:778-789. [PMID: 37524958 DOI: 10.1038/s41587-023-01887-5] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/24/2022] [Accepted: 06/28/2023] [Indexed: 08/02/2023]
Abstract
Single-cell RNA sequencing (scRNA-seq) is a powerful approach for studying cellular differentiation, but accurately tracking cell fate transitions can be challenging, especially in disease conditions. Here we introduce PhyloVelo, a computational framework that estimates the velocity of transcriptomic dynamics by using monotonically expressed genes (MEGs) or genes with expression patterns that either increase or decrease, but do not cycle, through phylogenetic time. Through integration of scRNA-seq data with lineage information, PhyloVelo identifies MEGs and reconstructs a transcriptomic velocity field. We validate PhyloVelo using simulated data and Caenorhabditis elegans ground truth data, successfully recovering linear, bifurcated and convergent differentiations. Applying PhyloVelo to seven lineage-traced scRNA-seq datasets, generated using CRISPR-Cas9 editing, lentiviral barcoding or immune repertoire profiling, demonstrates its high accuracy and robustness in inferring complex lineage trajectories while outperforming RNA velocity. Additionally, we discovered that MEGs across tissues and organisms share similar functions in translation and ribosome biogenesis.
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Affiliation(s)
- Kun Wang
- CAS Key Laboratory of Quantitative Engineering Biology, Shenzhen Institute of Synthetic Biology, Shenzhen Institute of Advanced Technology, Chinese Academy of Sciences, Shenzhen, China
- School of Mathematical Sciences, Xiamen University, Xiamen, China
| | - Liangzhen Hou
- CAS Key Laboratory of Quantitative Engineering Biology, Shenzhen Institute of Synthetic Biology, Shenzhen Institute of Advanced Technology, Chinese Academy of Sciences, Shenzhen, China
- Faculty of Health Sciences, University of Macau, Taipa, Macau, China
| | - Xin Wang
- CAS Key Laboratory of Quantitative Engineering Biology, Shenzhen Institute of Synthetic Biology, Shenzhen Institute of Advanced Technology, Chinese Academy of Sciences, Shenzhen, China
| | - Xiangwei Zhai
- MOE Key Laboratory of Gene Function and Regulation, State Key Laboratory of Biocontrol, School of Life Sciences, Sun Yat-Sen University, Guangzhou, China
| | - Zhaolian Lu
- CAS Key Laboratory of Quantitative Engineering Biology, Shenzhen Institute of Synthetic Biology, Shenzhen Institute of Advanced Technology, Chinese Academy of Sciences, Shenzhen, China
| | - Zhike Zi
- CAS Key Laboratory of Quantitative Engineering Biology, Shenzhen Institute of Synthetic Biology, Shenzhen Institute of Advanced Technology, Chinese Academy of Sciences, Shenzhen, China
| | - Weiwei Zhai
- CAS Key Laboratory of Zoological Systematics and Evolution, Institute of Zoology, Chinese Academy of Sciences, Beijing, China
- Center for Excellence in Animal Evolution and Genetics, Chinese Academy of Sciences, Kunming, China
| | - Xionglei He
- MOE Key Laboratory of Gene Function and Regulation, State Key Laboratory of Biocontrol, School of Life Sciences, Sun Yat-Sen University, Guangzhou, China
| | - Christina Curtis
- Department of Medicine, Division of Oncology, Stanford University School of Medicine, Stanford, CA, USA
- Department of Genetics, Stanford University School of Medicine, Stanford, CA, USA
- Stanford Cancer Institute, Stanford University School of Medicine, Stanford, CA, USA
| | - Da Zhou
- School of Mathematical Sciences, Xiamen University, Xiamen, China.
- National Institute for Data Science in Health and Medicine, Xiamen University, Xiamen, China.
| | - Zheng Hu
- CAS Key Laboratory of Quantitative Engineering Biology, Shenzhen Institute of Synthetic Biology, Shenzhen Institute of Advanced Technology, Chinese Academy of Sciences, Shenzhen, China.
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13
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Huang D, Li Y, Han J, Zuo H, Liu H, Chen Z. Xbp1 promotes odontoblastic differentiation through modulating mitochondrial homeostasis. FASEB J 2024; 38:e23600. [PMID: 38572599 DOI: 10.1096/fj.202400186r] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/23/2024] [Revised: 03/05/2024] [Accepted: 03/25/2024] [Indexed: 04/05/2024]
Abstract
Odontoblast differentiation depends on the orderly recruitment of transcriptional factors (TFs) in the transcriptional regulatory network. The depletion of crucial TFs disturbs dynamic alteration of the chromatin landscape and gene expression profile, leading to developmental defects. Our previous studies have revealed that the basic leucine zipper (bZIP) TF family is crucial in odontoblastic differentiation, but the function of bZIP TF family member XBP1 is still unknown. Here, we showed the stage-specific expression patterns of the spliced form Xbp1s during tooth development. Elevated Xbp1 expression and nuclear translocation of XBP1S in mesenchymal stem cells (MSCs) were induced by differentiation medium in vitro. Diminution of Xbp1 expression impaired the odontogenic differentiation potential of MSCs. The further integration of ATAC-seq and RNA-seq identified Hspa9 as a direct downstream target, an essential mitochondrial chaperonin gene that modulated mitochondrial homeostasis. The amelioration of mitochondrial dysfunction rescued the impaired odontogenic differentiation potential of MSCs caused by the diminution of Xbp1. Furthermore, the overexpression of Hspa9 rescued Xbp1-deficient defects in odontoblastic differentiation. Our study illustrates the crucial role of Xbp1 in odontoblastic differentiation via modulating mitochondrial homeostasis and brings evidence to the therapy of mitochondrial diseases caused by genetic defects.
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Affiliation(s)
- Delan Huang
- State Key Laboratory of Oral & Maxillofacial Reconstruction and Regeneration, Key Laboratory of Oral Biomedicine Ministry of Education, Hubei Key Laboratory of Stomatology, School & Hospital of Stomatology, Wuhan University, Wuhan, China
| | - Yuanyuan Li
- State Key Laboratory of Oral & Maxillofacial Reconstruction and Regeneration, Key Laboratory of Oral Biomedicine Ministry of Education, Hubei Key Laboratory of Stomatology, School & Hospital of Stomatology, Wuhan University, Wuhan, China
| | - Jiahao Han
- State Key Laboratory of Oral & Maxillofacial Reconstruction and Regeneration, Key Laboratory of Oral Biomedicine Ministry of Education, Hubei Key Laboratory of Stomatology, School & Hospital of Stomatology, Wuhan University, Wuhan, China
| | - Huanyan Zuo
- State Key Laboratory of Oral & Maxillofacial Reconstruction and Regeneration, Key Laboratory of Oral Biomedicine Ministry of Education, Hubei Key Laboratory of Stomatology, School & Hospital of Stomatology, Wuhan University, Wuhan, China
- Department of Cariology and Endodontics, School of Stomatology, Wuhan University, Wuhan, China
| | - Huan Liu
- State Key Laboratory of Oral & Maxillofacial Reconstruction and Regeneration, Key Laboratory of Oral Biomedicine Ministry of Education, Hubei Key Laboratory of Stomatology, School & Hospital of Stomatology, Wuhan University, Wuhan, China
- Department of Periodontology, School of Stomatology, Wuhan University, Wuhan, China
- TaiKang Center for Life and Medical Sciences, Wuhan University, Wuhan, China
| | - Zhi Chen
- State Key Laboratory of Oral & Maxillofacial Reconstruction and Regeneration, Key Laboratory of Oral Biomedicine Ministry of Education, Hubei Key Laboratory of Stomatology, School & Hospital of Stomatology, Wuhan University, Wuhan, China
- Department of Cariology and Endodontics, School of Stomatology, Wuhan University, Wuhan, China
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14
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Veland N, Gleneadie HJ, Brown KE, Sardini A, Pombo J, Dimond A, Burns V, Sarkisyan K, Schiering C, Webster Z, Merkenschlager M, Fisher AG. Bioluminescence imaging of Cyp1a1-luciferase reporter mice demonstrates prolonged activation of the aryl hydrocarbon receptor in the lung. Commun Biol 2024; 7:442. [PMID: 38600349 PMCID: PMC11006662 DOI: 10.1038/s42003-024-06089-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/30/2023] [Accepted: 03/21/2024] [Indexed: 04/12/2024] Open
Abstract
Aryl hydrocarbon receptor (AHR) signalling integrates biological processes that sense and respond to environmental, dietary, and metabolic challenges to ensure tissue homeostasis. AHR is a transcription factor that is inactive in the cytosol but upon encounter with ligand translocates to the nucleus and drives the expression of AHR targets, including genes of the cytochrome P4501 family of enzymes such as Cyp1a1. To dynamically visualise AHR activity in vivo, we generated reporter mice in which firefly luciferase (Fluc) was non-disruptively targeted into the endogenous Cyp1a1 locus. Exposure of these animals to FICZ, 3-MC or to dietary I3C induced strong bioluminescence signal and Cyp1a1 expression in many organs including liver, lung and intestine. Longitudinal studies revealed that AHR activity was surprisingly long-lived in the lung, with sustained Cyp1a1 expression evident in discrete populations of cells including columnar epithelia around bronchioles. Our data link diet to lung physiology and also reveal the power of bespoke Cyp1a1-Fluc reporters to longitudinally monitor AHR activity in vivo.
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Affiliation(s)
- Nicolas Veland
- Epigenetic Memory Group, MRC Laboratory of Medical Sciences, Imperial College London Hammersmith Hospital Campus, Du Cane Road, London, W12 OHS, UK
| | - Hannah J Gleneadie
- Epigenetic Memory Group, MRC Laboratory of Medical Sciences, Imperial College London Hammersmith Hospital Campus, Du Cane Road, London, W12 OHS, UK
| | - Karen E Brown
- Epigenetic Memory Group, MRC Laboratory of Medical Sciences, Imperial College London Hammersmith Hospital Campus, Du Cane Road, London, W12 OHS, UK
| | - Alessandro Sardini
- Whole Animal Physiology and Imaging, MRC Laboratory of Medical Sciences, Imperial College London, Hammersmith Hospital Campus, Du Cane Road, London, W12 0HS, UK
| | - Joaquim Pombo
- Senescence Group, MRC Laboratory of Medical Sciences, Imperial College London Hammersmith Hospital Campus, Du Cane Road, London, W12 0HS, UK
| | - Andrew Dimond
- Epigenetic Memory Group, MRC Laboratory of Medical Sciences, Imperial College London Hammersmith Hospital Campus, Du Cane Road, London, W12 OHS, UK
- Department of Biochemistry, University of Oxford, Oxford, OX1 3QU, UK
| | - Vanessa Burns
- Epigenetic Memory Group, MRC Laboratory of Medical Sciences, Imperial College London Hammersmith Hospital Campus, Du Cane Road, London, W12 OHS, UK
| | - Karen Sarkisyan
- Synthetic Biology Group, MRC Laboratory of Medical Sciences, Imperial College London Hammersmith Hospital Campus, Du Cane Road, London, W12 0HS, UK
| | - Chris Schiering
- Inflammation and Obesity Group, MRC Laboratory of Medical Sciences, Imperial College London Hammersmith Hospital Campus, Du Cane Road, London, W12 0HS, UK
| | - Zoe Webster
- Transgenics & Embryonic Stem Cell Facility, MRC Laboratory of Medical Sciences, Imperial College London Hammersmith Hospital Campus, Du Cane Road, London, W12 0HS, UK
| | - Matthias Merkenschlager
- Lymphocyte Development Group, MRC Laboratory of Medical Sciences, Imperial College London Hammersmith Hospital Campus, Du Cane Road, London, W12 0HS, UK
| | - Amanda G Fisher
- Epigenetic Memory Group, MRC Laboratory of Medical Sciences, Imperial College London Hammersmith Hospital Campus, Du Cane Road, London, W12 OHS, UK.
- Department of Biochemistry, University of Oxford, Oxford, OX1 3QU, UK.
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15
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Zhang G, Fu Y, Yang L, Ye F, Zhang P, Zhang S, Ma L, Li J, Wu H, Han X, Wang J, Guo G. Construction of single-cell cross-species chromatin accessibility landscapes with combinatorial-hybridization-based ATAC-seq. Dev Cell 2024; 59:793-811.e8. [PMID: 38330939 DOI: 10.1016/j.devcel.2024.01.015] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/01/2023] [Revised: 11/03/2023] [Accepted: 01/18/2024] [Indexed: 02/10/2024]
Abstract
Despite recent advances in single-cell genomics, the lack of maps for single-cell candidate cis-regulatory elements (cCREs) in non-mammal species has limited our exploration of conserved regulatory programs across vertebrates and invertebrates. Here, we developed a combinatorial-hybridization-based method for single-cell assay for transposase-accessible chromatin using sequencing (scATAC-seq) named CH-ATAC-seq, enabling the construction of single-cell accessible chromatin landscapes for zebrafish, Drosophila, and earthworms (Eisenia andrei). By integrating scATAC censuses of humans, monkeys, and mice, we systematically identified 152 distinct main cell types and around 0.8 million cell-type-specific cCREs. Our analysis provided insights into the conservation of neural, muscle, and immune lineages across species, while epithelial cells exhibited a higher organ-origin heterogeneity. Additionally, a large-scale gene regulatory network (GRN) was constructed in four vertebrates by integrating scRNA-seq censuses. Overall, our study provides a valuable resource for comparative epigenomics, identifying the evolutionary conservation and divergence of gene regulation across different species.
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Affiliation(s)
- Guodong Zhang
- Bone Marrow Transplantation Center of the First Affiliated Hospital, and Center for Stem Cell and Regenerative Medicine, Zhejiang University School of Medicine, Hangzhou 310000, China; Liangzhu Laboratory, Zhejiang University, Hangzhou 311121, China
| | - Yuting Fu
- Bone Marrow Transplantation Center of the First Affiliated Hospital, and Center for Stem Cell and Regenerative Medicine, Zhejiang University School of Medicine, Hangzhou 310000, China
| | - Lei Yang
- Bone Marrow Transplantation Center of the First Affiliated Hospital, and Center for Stem Cell and Regenerative Medicine, Zhejiang University School of Medicine, Hangzhou 310000, China
| | - Fang Ye
- Bone Marrow Transplantation Center of the First Affiliated Hospital, and Center for Stem Cell and Regenerative Medicine, Zhejiang University School of Medicine, Hangzhou 310000, China; Liangzhu Laboratory, Zhejiang University, Hangzhou 311121, China
| | - Peijing Zhang
- Bone Marrow Transplantation Center of the First Affiliated Hospital, and Center for Stem Cell and Regenerative Medicine, Zhejiang University School of Medicine, Hangzhou 310000, China
| | - Shuang Zhang
- Bone Marrow Transplantation Center of the First Affiliated Hospital, and Center for Stem Cell and Regenerative Medicine, Zhejiang University School of Medicine, Hangzhou 310000, China
| | - Lifeng Ma
- Bone Marrow Transplantation Center of the First Affiliated Hospital, and Center for Stem Cell and Regenerative Medicine, Zhejiang University School of Medicine, Hangzhou 310000, China
| | - Jiaqi Li
- Bone Marrow Transplantation Center of the First Affiliated Hospital, and Center for Stem Cell and Regenerative Medicine, Zhejiang University School of Medicine, Hangzhou 310000, China
| | - Hanyu Wu
- Bone Marrow Transplantation Center of the First Affiliated Hospital, and Center for Stem Cell and Regenerative Medicine, Zhejiang University School of Medicine, Hangzhou 310000, China
| | - Xiaoping Han
- Bone Marrow Transplantation Center of the First Affiliated Hospital, and Center for Stem Cell and Regenerative Medicine, Zhejiang University School of Medicine, Hangzhou 310000, China; Zhejiang Provincial Key Laboratory for Tissue Engineering and Regenerative Medicine, Dr. Li Dak Sum & Yip Yio Chin Center for Stem Cell and Regenerative Medicine, Hangzhou 310058, China.
| | - Jingjing Wang
- Bone Marrow Transplantation Center of the First Affiliated Hospital, and Center for Stem Cell and Regenerative Medicine, Zhejiang University School of Medicine, Hangzhou 310000, China; Liangzhu Laboratory, Zhejiang University, Hangzhou 311121, China.
| | - Guoji Guo
- Bone Marrow Transplantation Center of the First Affiliated Hospital, and Center for Stem Cell and Regenerative Medicine, Zhejiang University School of Medicine, Hangzhou 310000, China; Liangzhu Laboratory, Zhejiang University, Hangzhou 311121, China; Zhejiang Provincial Key Laboratory for Tissue Engineering and Regenerative Medicine, Dr. Li Dak Sum & Yip Yio Chin Center for Stem Cell and Regenerative Medicine, Hangzhou 310058, China; Institute of Hematology, Zhejiang University, Hangzhou, China.
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16
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Becker PB. Cell-free genomics: transcription factor interactions in reconstituted naïve embryonic chromatin. Biochem Soc Trans 2024; 52:423-429. [PMID: 38329186 DOI: 10.1042/bst20230878] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/02/2023] [Revised: 01/26/2024] [Accepted: 01/30/2024] [Indexed: 02/09/2024]
Abstract
Extracts from Drosophila preblastoderm embryos (DREX) form the basis of a powerful in vitro chromatin reconstitution system that assembles entire genomes into complex chromatin with physiological nucleosome spacing and polymer condensation. As the zygotic genome has not yet been activated in preblastoderm embryos, the reconstitution extract lacks endogenous transcription factors (TFs) and the RNA polymerase machinery. At the same time, it contains high levels of ATP-dependent nucleosome sliding enzymes that render the reconstituted chromatin dynamic. The naïve chromatin can be used to determine the intrinsic DNA binding properties of exogenous, usually recombinant TFs (or DNA binding proteins in general) in a complex chromatin context. Recent applications of the system include the description of cooperation and competition of Drosophila pioneer TFs for composite binding sites, and the characterization of nucleosome interactions of mammalian pioneer TFs in the heterologous system.
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Affiliation(s)
- Peter B Becker
- Biomedical Center, Molecular Biology Division, Faculty of Medicine, LMU, Munich, Germany
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17
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Ye F, Wang J, Li J, Mei Y, Guo G. Mapping Cell Atlases at the Single-Cell Level. ADVANCED SCIENCE (WEINHEIM, BADEN-WURTTEMBERG, GERMANY) 2024; 11:e2305449. [PMID: 38145338 PMCID: PMC10885669 DOI: 10.1002/advs.202305449] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/07/2023] [Revised: 12/01/2023] [Indexed: 12/26/2023]
Abstract
Recent advancements in single-cell technologies have led to rapid developments in the construction of cell atlases. These atlases have the potential to provide detailed information about every cell type in different organisms, enabling the characterization of cellular diversity at the single-cell level. Global efforts in developing comprehensive cell atlases have profound implications for both basic research and clinical applications. This review provides a broad overview of the cellular diversity and dynamics across various biological systems. In addition, the incorporation of machine learning techniques into cell atlas analyses opens up exciting prospects for the field of integrative biology.
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Affiliation(s)
- Fang Ye
- Bone Marrow Transplantation Center of the First Affiliated Hospital, and Center for Stem Cell and Regenerative MedicineZhejiang University School of MedicineHangzhouZhejiang310000China
- Liangzhu LaboratoryZhejiang UniversityHangzhouZhejiang311121China
| | - Jingjing Wang
- Bone Marrow Transplantation Center of the First Affiliated Hospital, and Center for Stem Cell and Regenerative MedicineZhejiang University School of MedicineHangzhouZhejiang310000China
- Liangzhu LaboratoryZhejiang UniversityHangzhouZhejiang311121China
| | - Jiaqi Li
- Bone Marrow Transplantation Center of the First Affiliated Hospital, and Center for Stem Cell and Regenerative MedicineZhejiang University School of MedicineHangzhouZhejiang310000China
| | - Yuqing Mei
- Bone Marrow Transplantation Center of the First Affiliated Hospital, and Center for Stem Cell and Regenerative MedicineZhejiang University School of MedicineHangzhouZhejiang310000China
| | - Guoji Guo
- Bone Marrow Transplantation Center of the First Affiliated Hospital, and Center for Stem Cell and Regenerative MedicineZhejiang University School of MedicineHangzhouZhejiang310000China
- Liangzhu LaboratoryZhejiang UniversityHangzhouZhejiang311121China
- Zhejiang Provincial Key Lab for Tissue Engineering and Regenerative MedicineDr. Li Dak Sum & Yip Yio Chin Center for Stem Cell and Regenerative MedicineHangzhouZhejiang310058China
- Institute of HematologyZhejiang UniversityHangzhouZhejiang310000China
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18
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Peng Y, Kenney HM, de Mesy Bentley KL, Xing L, Ritchlin CT, Schwarz EM. Distinct mast cell subpopulations within and around lymphatic vessels regulate lymph flow and progression of inflammatory-erosive arthritis in TNF-transgenic mice. Front Immunol 2023; 14:1275871. [PMID: 38155962 PMCID: PMC10752982 DOI: 10.3389/fimmu.2023.1275871] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/10/2023] [Accepted: 11/20/2023] [Indexed: 12/30/2023] Open
Abstract
Objective Inflammatory-erosive arthritis is exacerbated by dysfunction of joint-draining popliteal lymphatic vessels (PLVs). Synovial mast cells are known to be pro-inflammatory in rheumatoid arthritis (RA). In other settings they have anti-inflammatory and tissue reparative effects. Herein, we elucidate the role of mast cells on PLV function and inflammatory-erosive arthritis in tumor necrosis factor transgenic (TNF-tg) mice that exhibit defects in PLVs commensurate with disease progression. Methods Whole mount immunofluorescent microscopy, toluidine blue stained histology, scanning electron microscopy, and in silico bioinformatics were performed to phenotype and quantify PLV mast cells. Ankle bone volumes were assessed by μCT, while corresponding histology quantified synovitis and osteoclasts. Near-infrared indocyanine green imaging measured lymphatic clearance as an outcome of PLV draining function. Effects of genetic MC depletion were assessed via comparison of 4.5-month-old WT, TNF-tg, MC deficient KitW-sh/W-sh (cKit-/-), and TNF-tg x cKit-/- mice. Pharmacological inhibition of mast cells was assessed by treating TNF-tg mice with placebo or cromolyn sodium (3.15mg/kg/day) for 3-weeks. Results PLVs are surrounded by MCT+/MCPT1+/MCPT4+ mast cells whose numbers are increased 2.8-fold in TNF-tg mice. The percentage of peri-vascular degranulating mast cells was inversely correlated with ICG clearance. A population of MCT+/MCPT1-/MCPT4- mast cells were embedded within the PLV structure. In silico single-cell RNA-seq (scRNAseq) analyses identified a population of PLV-associated mast cells (marker genes: Mcpt4, Cma1, Cpa3, Tpsb2, Kit, Fcer1a & Gata2) with enhanced TGFβ-related signaling that are phenotypically distinct from known MC subsets in the Mouse Cell Atlas. cKit-/- mice have greater lymphatic defects than TNF-tg mice with exacerbation of lymphatic dysfunction and inflammatory-erosive arthritis in TNF-tg x cKit-/- vs. TNF-Tg mice. Cromolyn sodium therapy stabilized PLV mast cells, increased TNF-induced bone loss, synovitis, and osteoclasts, and decreased ICG clearance. Conclusions Mast cells are required for normal lymphatic function. Genetic ablation and pharmacological inhibition of mast cells exacerbates TNF-induced inflammatory-erosive arthritis with decreased lymphatic clearance. Together, these findings support an inflammatory role of activated/degranulated peri-PLV mast cells during arthritic progression, and a homeostatic role of intra-PLV mast cells, in which loss of the latter dominantly exacerbates arthritis secondary to defects in joint-draining lymphatics, warranting investigation into specific cellular mechanisms.
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Affiliation(s)
- Yue Peng
- Center for Musculoskeletal Research, University of Rochester Medical Center, Rochester, NY, United States
- Department of Pathology & Laboratory Medicine, University of Rochester Medical Center, Rochester, NY, United States
| | - H. Mark Kenney
- Center for Musculoskeletal Research, University of Rochester Medical Center, Rochester, NY, United States
- Department of Pathology & Laboratory Medicine, University of Rochester Medical Center, Rochester, NY, United States
| | - Karen L. de Mesy Bentley
- Center for Musculoskeletal Research, University of Rochester Medical Center, Rochester, NY, United States
- Department of Pathology & Laboratory Medicine, University of Rochester Medical Center, Rochester, NY, United States
| | - Lianping Xing
- Center for Musculoskeletal Research, University of Rochester Medical Center, Rochester, NY, United States
- Department of Pathology & Laboratory Medicine, University of Rochester Medical Center, Rochester, NY, United States
| | - Christopher T. Ritchlin
- Center for Musculoskeletal Research, University of Rochester Medical Center, Rochester, NY, United States
- Department of Medicine, Division of Allergy, Immunology, Rheumatology, University of Rochester Medical Center, Rochester, NY, United States
| | - Edward M. Schwarz
- Center for Musculoskeletal Research, University of Rochester Medical Center, Rochester, NY, United States
- Department of Pathology & Laboratory Medicine, University of Rochester Medical Center, Rochester, NY, United States
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19
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Liu D, Fu Y, Wang X, Wang X, Fang X, Zhou Y, Wang R, Zhang P, Jiang M, Jia D, Wang J, Chen H, Guo G, Han X. Characterization of human pluripotent stem cell differentiation by single-cell dual-omics analyses. Stem Cell Reports 2023; 18:2464-2481. [PMID: 37995704 PMCID: PMC10724075 DOI: 10.1016/j.stemcr.2023.10.018] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/13/2023] [Revised: 10/24/2023] [Accepted: 10/26/2023] [Indexed: 11/25/2023] Open
Abstract
In vivo differentiation of human pluripotent stem cells (hPSCs) has unique advantages, such as multilineage differentiation, angiogenesis, and close cell-cell interactions. To systematically investigate multilineage differentiation mechanisms of hPSCs, we constructed the in vivo hPSC differentiation landscape containing 239,670 cells using teratoma models. We identified 43 cell types, inferred 18 cell differentiation trajectories, and characterized common and specific gene regulation patterns during hPSC differentiation at both transcriptional and epigenetic levels. Additionally, we developed the developmental single-cell Basic Local Alignment Search Tool (dscBLAST), an R-based cell identification tool, to simplify the identification processes of developmental cells. Using dscBLAST, we aligned cells in multiple differentiation models to normally developing cells to further understand their differentiation states. Overall, our study offers new insights into stem cell differentiation and human embryonic development; dscBLAST shows favorable cell identification performance, providing a powerful identification tool for developmental cells.
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Affiliation(s)
- Daiyuan Liu
- Center for Stem Cell and Regenerative Medicine, and Bone Marrow Transplantation Center of the First Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, Zhejiang 310058, China
| | - Yuting Fu
- Center for Stem Cell and Regenerative Medicine, and Bone Marrow Transplantation Center of the First Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, Zhejiang 310058, China
| | - Xinru Wang
- Center for Stem Cell and Regenerative Medicine, and Bone Marrow Transplantation Center of the First Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, Zhejiang 310058, China
| | - Xueyi Wang
- Center for Stem Cell and Regenerative Medicine, and Bone Marrow Transplantation Center of the First Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, Zhejiang 310058, China
| | - Xing Fang
- Center for Stem Cell and Regenerative Medicine, and Bone Marrow Transplantation Center of the First Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, Zhejiang 310058, China; Zhejiang Provincial Key Laboratory for Tissue Engineering and Regenerative Medicine, Dr. Li Dak Sum & Yip Yio Chin Center for Stem Cell and Regenerative Medicine, Hangzhou, Zhejiang 310058, China
| | - Yincong Zhou
- College of Life Sciences, Zhejiang University, Hangzhou 310058, China
| | - Renying Wang
- Center for Stem Cell and Regenerative Medicine, and Bone Marrow Transplantation Center of the First Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, Zhejiang 310058, China
| | - Peijing Zhang
- Center for Stem Cell and Regenerative Medicine, and Bone Marrow Transplantation Center of the First Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, Zhejiang 310058, China; Zhejiang Provincial Key Laboratory for Tissue Engineering and Regenerative Medicine, Dr. Li Dak Sum & Yip Yio Chin Center for Stem Cell and Regenerative Medicine, Hangzhou, Zhejiang 310058, China
| | - Mengmeng Jiang
- Liangzhu Laboratory, Zhejiang University, 1369 West Wenyi Road, Hangzhou 311121, China
| | - Danmei Jia
- Center for Stem Cell and Regenerative Medicine, and Bone Marrow Transplantation Center of the First Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, Zhejiang 310058, China
| | - Jingjing Wang
- Liangzhu Laboratory, Zhejiang University, 1369 West Wenyi Road, Hangzhou 311121, China
| | - Haide Chen
- Center for Stem Cell and Regenerative Medicine, and Bone Marrow Transplantation Center of the First Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, Zhejiang 310058, China; Liangzhu Laboratory, Zhejiang University, 1369 West Wenyi Road, Hangzhou 311121, China; M20 Genomics, Hangzhou, China
| | - Guoji Guo
- Center for Stem Cell and Regenerative Medicine, and Bone Marrow Transplantation Center of the First Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, Zhejiang 310058, China; Zhejiang Provincial Key Laboratory for Tissue Engineering and Regenerative Medicine, Dr. Li Dak Sum & Yip Yio Chin Center for Stem Cell and Regenerative Medicine, Hangzhou, Zhejiang 310058, China; Liangzhu Laboratory, Zhejiang University, 1369 West Wenyi Road, Hangzhou 311121, China
| | - Xiaoping Han
- Center for Stem Cell and Regenerative Medicine, and Bone Marrow Transplantation Center of the First Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, Zhejiang 310058, China; Zhejiang Provincial Key Laboratory for Tissue Engineering and Regenerative Medicine, Dr. Li Dak Sum & Yip Yio Chin Center for Stem Cell and Regenerative Medicine, Hangzhou, Zhejiang 310058, China.
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20
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Li J, Shyr Y, Liu Q. Single-cell and Spatial Transcriptomics Clustering with an Optimized Adaptive K-Nearest Neighbor Graph. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.10.13.562261. [PMID: 37905097 PMCID: PMC10614787 DOI: 10.1101/2023.10.13.562261] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/02/2023]
Abstract
Single-cell and spatial transcriptomics have been widely used to characterize cellular landscape in complex tissues. To understand cellular heterogeneity, one essential step is to define cell types through unsupervised clustering. While typical clustering methods have difficulty in identifying rare cell types, approaches specifically tailored to detect rare cell types gain their ability at the cost of poorer performance for grouping abundant ones. Here, we developed aKNNO, a method to identify abundant and rare cell types simultaneously based on an adaptive k-nearest neighbor graph with optimization. Benchmarked on 38 simulated and 20 single-cell and spatial transcriptomics datasets, aKNNO identified both abundant and rare cell types accurately. Without sacrificing performance for clustering abundant cell types, aKNNO discovered known and novel rare cell types that those typical and even specifically tailored methods failed to detect. aKNNO, using transcriptome alone, stereotyped fine-grained anatomical structures more precisely than those integrative approaches combining expression with spatial locations and histology image.
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Affiliation(s)
- Jia Li
- Department of Biostatistics, Vanderbilt University Medical Center, Nashville, TN, 37203, USA
- Center for Quantitative Sciences, Vanderbilt University Medical Center, Nashville, TN, 37232, USA
| | - Yu Shyr
- Department of Biostatistics, Vanderbilt University Medical Center, Nashville, TN, 37203, USA
- Center for Quantitative Sciences, Vanderbilt University Medical Center, Nashville, TN, 37232, USA
| | - Qi Liu
- Department of Biostatistics, Vanderbilt University Medical Center, Nashville, TN, 37203, USA
- Center for Quantitative Sciences, Vanderbilt University Medical Center, Nashville, TN, 37232, USA
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21
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Wang L, Li W, Xie W, Wang R, Yu K. Dual-GCN-based deep clustering with triplet contrast for ScRNA-seq data analysis. Comput Biol Chem 2023; 106:107924. [PMID: 37487251 DOI: 10.1016/j.compbiolchem.2023.107924] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/01/2023] [Revised: 06/08/2023] [Accepted: 07/12/2023] [Indexed: 07/26/2023]
Abstract
Single-cell RNA sequencing (ScRNA-seq) technology reveals gene expression information at the cellular level. The critical tasks in ScRNA-seq data analysis are clustering and dimensionality reduction. Recent deep clustering algorithms are used to optimize the two tasks jointly, and their variations, graph-based deep clustering algorithms, are used to capture and preserve topological information in the process. However, the existing graph-based deep clustering algorithms ignore the distribution information of nodes when constructing cell graphs which leads to incomplete information in the embedding representation; and graph convolutional networks (GCN), which are most commonly used, often suffer from over-smoothing that leads to high sample similarity in the embedding representation and then poor clustering performance. Here, the dual-GCN-based deep clustering with Triplet contrast (scDGDC) is proposed for dimensionality reduction and clustering of scRNA-seq data. Two critical components are dual-GCN-based encoder for capturing more comprehensive topological information and triplet contrast for reducing GCN over-smoothing. The two components improve the dimensionality reduction and clustering performance of scDGDC in terms of information acquisition and model optimization, respectively. The experiments on eight real ScRNA-seq datasets showed that scDGDC achieves excellent performance for both clustering and dimensionality reduction tasks and is high robustness to parameters.
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Affiliation(s)
- LinJie Wang
- School of Computer Science and Engineering, Northeastern University, Shenyang 110819, China.
| | - Wei Li
- Key Laboratory of Intelligent Computing in Medical Image (MIIC), Northeastern University, Ministry of Education, Shenyang 110000, China.
| | - WeiDong Xie
- School of Computer Science and Engineering, Northeastern University, Shenyang 110819, China.
| | - Rui Wang
- School of Computer Science and Engineering, Northeastern University, Shenyang 110819, China.
| | - Kun Yu
- College of Medicine and Bioinformation Engineering, Northeastern University, Shenyang 110819, China.
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22
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Kafai NM, Janova H, Cain MD, Alippe Y, Muraro S, Sariol A, Elam-Noll M, Klein RS, Diamond MS. Entry receptor LDLRAD3 is required for Venezuelan equine encephalitis virus peripheral infection and neurotropism leading to pathogenesis in mice. Cell Rep 2023; 42:112946. [PMID: 37556325 PMCID: PMC10529316 DOI: 10.1016/j.celrep.2023.112946] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/14/2023] [Revised: 07/03/2023] [Accepted: 07/21/2023] [Indexed: 08/11/2023] Open
Abstract
Venezuelan equine encephalitis virus (VEEV) is an encephalitic alphavirus responsible for epidemics of neurological disease across the Americas. Low-density lipoprotein receptor class A domain-containing 3 (LDLRAD3) is a recently reported entry receptor for VEEV. Here, using wild-type and Ldlrad3-deficient mice, we define a critical role for LDLRAD3 in controlling steps in VEEV infection, pathogenesis, and neurotropism. Our analysis shows that LDLRAD3 is required for efficient VEEV infection and pathogenesis prior to and after central nervous system invasion. Ldlrad3-deficient mice survive intranasal and intracranial VEEV inoculation and show reduced infection of neurons in different brain regions. As LDLRAD3 is a determinant of pathogenesis and an entry receptor required for VEEV infection of neurons of the brain, receptor-targeted therapies may hold promise as countermeasures.
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Affiliation(s)
- Natasha M Kafai
- Department of Medicine, Washington University School of Medicine, St. Louis, MO 63110, USA; Department of Pathology and Immunology, Washington University School of Medicine, St. Louis, MO 63110, USA
| | - Hana Janova
- Department of Medicine, Washington University School of Medicine, St. Louis, MO 63110, USA
| | - Matthew D Cain
- Department of Medicine, Washington University School of Medicine, St. Louis, MO 63110, USA
| | - Yael Alippe
- Department of Medicine, Washington University School of Medicine, St. Louis, MO 63110, USA
| | - Stefanie Muraro
- Department of Medicine, Washington University School of Medicine, St. Louis, MO 63110, USA
| | - Alan Sariol
- Department of Medicine, Washington University School of Medicine, St. Louis, MO 63110, USA
| | - Michelle Elam-Noll
- Department of Medicine, Washington University School of Medicine, St. Louis, MO 63110, USA
| | - Robyn S Klein
- Department of Medicine, Washington University School of Medicine, St. Louis, MO 63110, USA; Department of Pathology and Immunology, Washington University School of Medicine, St. Louis, MO 63110, USA; Department of Neuroscience, Washington University School of Medicine, St. Louis, MO 63110, USA
| | - Michael S Diamond
- Department of Medicine, Washington University School of Medicine, St. Louis, MO 63110, USA; Department of Pathology and Immunology, Washington University School of Medicine, St. Louis, MO 63110, USA; Department of Molecular Microbiology, Washington University School of Medicine, St. Louis, MO 63110, USA; The Andrew M. and Jane M. Bursky Center for Human Immunology and Immunotherapy Programs, Washington University School of Medicine, St. Louis, MO 63110, USA.
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23
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Guldenpfennig C, Teixeiro E, Daniels M. NF-kB's contribution to B cell fate decisions. Front Immunol 2023; 14:1214095. [PMID: 37533858 PMCID: PMC10391175 DOI: 10.3389/fimmu.2023.1214095] [Citation(s) in RCA: 13] [Impact Index Per Article: 13.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/28/2023] [Accepted: 07/03/2023] [Indexed: 08/04/2023] Open
Abstract
NF-κB signaling is essential to an effective innate and adaptive immune response. Many immune-specific functional and developmental outcomes depend in large on NF-κB. The formidable task of sorting out the mechanisms behind the regulation and outcome of NF-κB signaling remains an important area of immunology research. Here we briefly discuss the role of NF-κB in regulating cell fate decisions at various times in the path of B cell development, activation, and the generation of long-term humoral immunity.
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Affiliation(s)
- Caitlyn Guldenpfennig
- Molecular Microbiology and Immunology, University of Missouri, Columbia, MO, United States
- NextGen Precision Health, University of Missouri, Columbia, MO, United States
| | - Emma Teixeiro
- Molecular Microbiology and Immunology, University of Missouri, Columbia, MO, United States
- NextGen Precision Health, University of Missouri, Columbia, MO, United States
| | - Mark Daniels
- Molecular Microbiology and Immunology, University of Missouri, Columbia, MO, United States
- NextGen Precision Health, University of Missouri, Columbia, MO, United States
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24
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Lee J, Kim H, Kang YW, Kim Y, Park MY, Song JH, Jo Y, Dao T, Ryu D, Lee J, Oh CM, Park S. LY6D is crucial for lipid accumulation and inflammation in nonalcoholic fatty liver disease. Exp Mol Med 2023:10.1038/s12276-023-01033-w. [PMID: 37394588 PMCID: PMC10394021 DOI: 10.1038/s12276-023-01033-w] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/08/2023] [Revised: 02/07/2023] [Accepted: 04/17/2023] [Indexed: 07/04/2023] Open
Abstract
Nonalcoholic fatty liver disease (NAFLD) is a serious metabolic disorder characterized by excess fat accumulation in the liver. Over the past decade, NAFLD prevalence and incidence have risen globally. There are currently no effective licensed drugs for its treatment. Thus, further study is required to identify new targets for NAFLD prevention and treatment. In this study, we fed C57BL6/J mice one of three diets, a standard chow diet, high-sucrose diet, or high-fat diet, and then characterized them. The mice fed a high-sucrose diet had more severely compacted macrovesicular and microvesicular lipid droplets than those in the other groups. Mouse liver transcriptome analysis identified lymphocyte antigen 6 family member D (Ly6d) as a key regulator of hepatic steatosis and the inflammatory response. Data from the Genotype-Tissue Expression project database showed that individuals with high liver Ly6d expression had more severe NAFLD histology than those with low liver Ly6d expression. In AML12 mouse hepatocytes, Ly6d overexpression increased lipid accumulation, while Ly6d knockdown decreased lipid accumulation. Inhibition of Ly6d ameliorated hepatic steatosis in a diet-induced NAFLD mouse model. Western blot analysis showed that Ly6d phosphorylated and activated ATP citrate lyase, which is a key enzyme in de novo lipogenesis. In addition, RNA- and ATAC-sequencing analyses revealed that Ly6d drives NAFLD progression by causing genetic and epigenetic changes. In conclusion, Ly6d is responsible for the regulation of lipid metabolism, and inhibiting Ly6d can prevent diet-induced steatosis in the liver. These findings highlight Ly6d as a novel therapeutic target for NAFLD.
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Affiliation(s)
- Jibeom Lee
- Department of Biomedical Science and Engineering, Gwangju Institute of Science and Technology, Gwangju, Korea
| | - Hyeonhui Kim
- Graduate School of Medical Science, Brain Korea 21 Project, Yonsei University College of Medicine, Seoul, Korea
| | - Yun-Won Kang
- Department of Biomedical Science and Engineering, Gwangju Institute of Science and Technology, Gwangju, Korea
| | - Yumin Kim
- Department of Biomedical Science and Engineering, Gwangju Institute of Science and Technology, Gwangju, Korea
| | - Moon-Young Park
- Department of Biomedical Science and Engineering, Gwangju Institute of Science and Technology, Gwangju, Korea
| | - Ji-Hong Song
- Department of Biomedical Science and Engineering, Gwangju Institute of Science and Technology, Gwangju, Korea
| | - Yunju Jo
- Department of Molecular Cell Biology, Sungkyunkwan University (SKKU) School of Medicine, Suwon, Korea
| | - Tam Dao
- Department of Molecular Cell Biology, Sungkyunkwan University (SKKU) School of Medicine, Suwon, Korea
| | - Dongryeol Ryu
- Department of Molecular Cell Biology, Sungkyunkwan University (SKKU) School of Medicine, Suwon, Korea
| | - Junguee Lee
- Department of Pathology, St Mary's Hospital, the Catholic University of Korea, Daejeon, Korea
| | - Chang-Myung Oh
- Department of Biomedical Science and Engineering, Gwangju Institute of Science and Technology, Gwangju, Korea.
| | - Sangkyu Park
- Department of Precision Medicine, Yonsei University Wonju College of Medicine, Wonju, Korea.
- Mitohormesis Research Center, Yonsei University Wonju College of Medicine, Wonju, Gangwon-do, Korea.
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25
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Zhao R, Cheng W, Shen J, Liang W, Zhang Z, Sheng Y, Chai T, Chen X, Zhang Y, Huang X, Yang H, Song C, Pang L, Nan C, Zhang Y, Chen R, Mei J, Wei H, Fang X. Single-cell and spatiotemporal transcriptomic analyses reveal the effects of microorganisms on immunity and metabolism in the mouse liver. Comput Struct Biotechnol J 2023; 21:3466-3477. [PMID: 38152123 PMCID: PMC10751235 DOI: 10.1016/j.csbj.2023.06.020] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/17/2023] [Revised: 06/28/2023] [Accepted: 06/28/2023] [Indexed: 12/29/2023] Open
Abstract
The gut-liver axis is a complex bidirectional communication pathway between the intestine and the liver in which microorganisms and their metabolites flow from the intestine through the portal vein to the liver and influence liver function. In a sterile environment, the phenotype or function of the liver is altered, but few studies have investigated the specific cellular and molecular effects of microorganisms on the liver. To this end, we constructed single-cell and spatial transcriptomic (ST) profiles of germ-free (GF) and specific-pathogen-free (SPF) mouse livers. Single-cell RNA sequencing (scRNA-seq) and single-nucleus RNA sequencing (snRNA-seq) revealed that the ratio of most immune cells was altered in the liver of GF mice; in particular, natural killer T (NKT) cells, IgA plasma cells (IgAs) and Kupffer cells (KCs) were significantly reduced in GF mice. Spatial enhanced resolution omics sequencing (Stereo-seq) confirmed that microorganisms mediated the accumulation of Kupffer cells in the periportal zone. Unexpectedly, IgA plasma cells were more numerous and concentrated in the periportal vein in liver sections from SPF mice but less numerous and scattered in GF mice. ST technology also enables the precise zonation of liver lobules into eight layers and three patterns based on the gene expression level in each layer, allowing us to further investigate the effects of microbes on gene zonation patterns and functions. Furthermore, untargeted metabolism experiments of the liver revealed that the propionic acid levels were significantly lower in GF mice, and this reduction may be related to the control of genes involved in bile acid and fatty acid metabolism. In conclusion, the combination of sc/snRNA-seq, Stereo-seq, and untargeted metabolomics revealed immune system defects as well as altered bile acid and lipid metabolic processes at the single-cell and spatial levels in the livers of GF mice. This study will be of great value for understanding host-microbiota interactions.
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Affiliation(s)
- Ruizhen Zhao
- College of Life Sciences, University of Chinese Academy of Sciences, Beijing 100049, China
- BGI-Shenzhen, Shenzhen 518083, China
| | - Wei Cheng
- College of Animal Sciences and Technology, Huazhong Agricultural University, Wuhan 430070, China
| | - Juan Shen
- BGI-Shenzhen, Shenzhen 518083, China
| | | | - Zhao Zhang
- College of Life Sciences, University of Chinese Academy of Sciences, Beijing 100049, China
- BGI-Shenzhen, Shenzhen 518083, China
| | - Yifei Sheng
- College of Life Sciences, University of Chinese Academy of Sciences, Beijing 100049, China
- BGI-Shenzhen, Shenzhen 518083, China
| | - Tailiang Chai
- College of Life Sciences, University of Chinese Academy of Sciences, Beijing 100049, China
- BGI-Shenzhen, Shenzhen 518083, China
| | - Xueting Chen
- College of Life Sciences, University of Chinese Academy of Sciences, Beijing 100049, China
- BGI-Shenzhen, Shenzhen 518083, China
| | - Yin Zhang
- College of Life Sciences, University of Chinese Academy of Sciences, Beijing 100049, China
- BGI-Shenzhen, Shenzhen 518083, China
| | - Xiang Huang
- College of Life Sciences, University of Chinese Academy of Sciences, Beijing 100049, China
| | | | - Chunqing Song
- Key Laboratory of Growth Regulation and Translational Research of Zhejiang Province, School of Life Sciences, Westlake University, Hangzhou, Zhejiang 310024, China
| | - Li Pang
- BGI-Qingdao, BGI-Shenzhen, Qingdao 266555, China
| | - Cuoji Nan
- BGI-Shenzhen, Shenzhen 518083, China
| | | | - Rouxi Chen
- BGI-Sanya, BGI-Shenzhen, Sanya 572025, China
| | - Junpu Mei
- BGI-Shenzhen, Shenzhen 518083, China
- BGI-Sanya, BGI-Shenzhen, Sanya 572025, China
| | - Hong Wei
- Precision Medicine Institute, The First Affiliated Hospital, Sun Yat-sen University, Guangzhou, Guangdong 510080, China
| | - Xiaodong Fang
- BGI-Shenzhen, Shenzhen 518083, China
- BGI-Sanya, BGI-Shenzhen, Sanya 572025, China
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26
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Wang Z, Ou Q, Gao L. The increased cfRNA of TNFSF4 in peripheral blood at late gestation and preterm labor: its implication as a noninvasive biomarker for premature delivery. Front Immunol 2023; 14:1154025. [PMID: 37275889 PMCID: PMC10232964 DOI: 10.3389/fimmu.2023.1154025] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/30/2023] [Accepted: 04/27/2023] [Indexed: 06/07/2023] Open
Abstract
Introduction Given the important roles of immune tolerance and inflammation in both preterm and term labor, some inflammation-related genes could be related to the initiation of labor, even preterm labor. Inspection of cell-free RNA (cfRNA) engaged in inflammation in maternal blood may represent the varied gestational age and may have significant implications for the development of noninvasive diagnostics for preterm birth. Methods To identify potential biomarkers of preterm birth, we investigated the cfRNA and exosomal miRNA in the peripheral blood of pregnant women at different gestational ages that undergo term labor or preterm labor. 17 inflammatory initiation-related cfRNAs were screened by overlapping with the targets of decreasing miRNAs during gestation and highly expressed cfRNAs at late gestation in maternal blood. To reveal the origins and mechanisms of these screened cfRNAs, the datasets of single-cell RNA sequencing from peripheral blood mononuclear cells of pregnant women, the fetal lung, and the placenta across different gestational ages were analyzed. Results During late gestation, TNFSF4 expression increased exclusively in pro-inflammatory macrophages of maternal blood, whereas its receptor, TNFRSF4, increased expression in T cells from the decidua, which suggested the potential cell-cell communication of maternally-originated pro-inflammatory macrophages with the decidual T cells and contributed to the initiation of labor. Additionally, the cfRNA of TNFSF4 was also increased in preterm labor compared to term labor in the validation cohorts. The EIF2AK2 and TLR4 transcripts were increased in pro-inflammatory macrophages from both fetal lung and placenta but not in those from maternal mononuclear cells at late gestation, suggesting these cfRNAs are possibly derived from fetal tissues exclusively. Moreover, EIF2AK2 and TLR4 transcripts were found highly expressed in the pro-inflammatory macrophages from decidua as well, which suggested these specific fetal-origin macrophages may function at the maternal-fetal interface to stimulate uterine contractions, which have been implicated as the trigger of parturition and preterm labor. Discussion Taken together, our findings not only revealed the potential of peripheral TNFSF4 as a novel cfRNA biomarker for noninvasive testing of preterm labor but further illustrated how maternal and fetal signals coordinately modulate the inflammatory process at the maternal-fetal interface, causing the initiation of term or preterm labor.
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Affiliation(s)
- Zhe Wang
- Department of Physiology, College of Basic Medical Sciences, Naval Medical University, Shanghai, China
| | - Qingjian Ou
- Department of Ophthalmology of Tongji Hospital, School of Medicine, Tongji University, Shanghai, China
| | - Lu Gao
- Department of Physiology, College of Basic Medical Sciences, Naval Medical University, Shanghai, China
- Shanghai Key Laboratory for Assisted Reproduction and Reproductive Genetics, Shanghai Jiaotong University, Shanghai, China
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27
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Czárán D, Sasvári P, Horváth ÁI, Ella K, Sűdy ÁR, Borbély É, Rusznák K, Czéh B, Mócsai A, Helyes Z, Csépányi-Kömi R. Lacking ARHGAP25 mitigates the symptoms of autoantibody-induced arthritis in mice. Front Immunol 2023; 14:1182278. [PMID: 37234175 PMCID: PMC10208528 DOI: 10.3389/fimmu.2023.1182278] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/08/2023] [Accepted: 04/24/2023] [Indexed: 05/27/2023] Open
Abstract
Objective Despite intensive research on rheumatoid arthritis, the pathomechanism of the disease is still not fully understood and the treatment has not been completely resolved. Previously we demonstrated that the GTPase-activating protein, ARHGAP25 has a crucial role in the regulation of basic phagocyte functions. Here we investigate the role of ARHGAP25 in the complex inflammatory process of autoantibody-induced arthritis. Methods Wild-type and ARHGAP25 deficient (KO) mice on a C57BL/6 background, as well as bone marrow chimeric mice, were treated i.p. with the K/BxN arthritogenic or control serum, and the severity of inflammation and pain-related behavior was measured. Histology was prepared, leukocyte infiltration, cytokine production, myeloperoxidase activity, and superoxide production were determined, and comprehensive western blot analysis was conducted. Results In the absence of ARHGAP25, the severity of inflammation, joint destruction, and mechanical hyperalgesia significantly decreased, similarly to phagocyte infiltration, IL-1β, and MIP-2 levels in the tibiotarsal joint, whereas superoxide production or myeloperoxidase activity was unchanged. We observed a significantly mitigated phenotype in KO bone marrow chimeras as well. In addition, fibroblast-like synoviocytes showed comparable expression of ARHGAP25 to neutrophils. Significantly reduced ERK1/2, MAPK, and I-κB protein signals were detected in the arthritic KO mouse ankles. Conclusion Our findings suggest that ARHGAP25 has a key role in the pathomechanism of autoantibody-induced arthritis in which it regulates inflammation via the I-κB/NF-κB/IL-1β axis with the involvement of both immune cells and fibroblast-like synoviocytes.
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Affiliation(s)
- Domonkos Czárán
- Department of Physiology, Semmelweis University, Budapest, Hungary
| | - Péter Sasvári
- Department of Physiology, Semmelweis University, Budapest, Hungary
| | - Ádám István Horváth
- Department of Pharmacology and Pharmacotherapy, Medical School, University of Pécs, Pécs, Hungary
- National Laboratory for Drug Research and Development, Budapest, Hungary
| | - Krisztina Ella
- Department of Physiology, Semmelweis University, Budapest, Hungary
| | - Ágnes Réka Sűdy
- Department of Physiology, Semmelweis University, Budapest, Hungary
| | - Éva Borbély
- Department of Pharmacology and Pharmacotherapy, Medical School, University of Pécs, Pécs, Hungary
- National Laboratory for Drug Research and Development, Budapest, Hungary
| | - Kitti Rusznák
- Histology and Light Microscopy Core Facility, Szentágothai Research Centre, University of Pécs, Pécs, Hungary
- Department of Laboratory Medicine, Medical School, University of Pécs, Pécs, Hungary
| | - Boldizsár Czéh
- Histology and Light Microscopy Core Facility, Szentágothai Research Centre, University of Pécs, Pécs, Hungary
- Department of Laboratory Medicine, Medical School, University of Pécs, Pécs, Hungary
| | - Attila Mócsai
- Department of Physiology, Semmelweis University, Budapest, Hungary
| | - Zsuzsanna Helyes
- Department of Pharmacology and Pharmacotherapy, Medical School, University of Pécs, Pécs, Hungary
- National Laboratory for Drug Research and Development, Budapest, Hungary
- Chronic Pain Research Group, Eötvös Loránd Research Network, University of Pécs, Pécs, Hungary
- PharmInVivo Ltd., Pécs, Hungary
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28
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Verwilligen RAF, Mulder L, Araújo PM, Carneiro M, Bussmann J, Hoekstra M, Van Eck M. Zebrafish as outgroup model to study evolution of scavenger receptor class B type I functions. Biochim Biophys Acta Mol Cell Biol Lipids 2023; 1868:159308. [PMID: 36931457 DOI: 10.1016/j.bbalip.2023.159308] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/30/2022] [Revised: 01/26/2023] [Accepted: 02/25/2023] [Indexed: 03/17/2023]
Abstract
BACKGROUND AND AIMS Scavenger receptor class B1 (SCARB1) - also known as the high-density lipoprotein (HDL) receptor - is a multi-ligand scavenger receptor that is primarily expressed in liver and steroidogenic organs. This receptor is known for its function in reverse cholesterol transport (RCT) in mammals and hence disruption leads to a massive increase in HDL cholesterol in these species. The extracellular domain of SCARB1 - which is important for cholesterol handling - is highly conserved across multiple vertebrates, except in zebrafish. METHODS To examine the functional conservation of SCARB1 among vertebrates, two stable scarb1 knockout zebrafish lines, scarb1 715delA (scarb1 -1 nt) and scarb1 715_716insGG (scarb1 +2 nt), were created using CRISPR-Cas9 technology. RESULTS We demonstrate that, in zebrafish, SCARB1 deficiency leads to disruption of carotenoid-based pigmentation, reduced fertility, and a decreased larvae survival rate, whereas steroidogenesis was unaltered. The observed reduced fertility is driven by defects in female fertility (-50 %, p < 0.001). Importantly, these alterations were independent of changes in free (wild-type 2.4 ± 0.2 μg/μl versus scarb1-/- 2.0 ± 0.1 μg/μl) as well as total (wild-type 4.2 ± 0.4 μg/μl versus scarb1-/- 4.0 ± 0.3 μg/μl) plasma cholesterol levels. Uptake of HDL in the liver of scarb1-/- zebrafish larvae was reduced (-86.7 %, p < 0.001), but this coincided with reduced perfusion of the liver. No effect was observed on lipoprotein uptake in the caudal vein. SCARB1 deficient canaries, which also lack carotenoids in their plumage, similarly as scarb1-/- zebrafish, failed to show an increase in plasma free- and total cholesterol levels. CONCLUSION Our findings suggest that the specific function of SCARB1 in maintaining plasma cholesterol could be an evolutionary novelty that became prominent in mammals, while other known functions were already present earlier during vertebrate evolution.
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Affiliation(s)
- Robin A F Verwilligen
- Division of BioTherapeutics, Leiden Academic Centre for Drug Research (LACDR), Leiden University, Leiden, the Netherlands.
| | - Lindsay Mulder
- Division of BioTherapeutics, Leiden Academic Centre for Drug Research (LACDR), Leiden University, Leiden, the Netherlands
| | - Pedro M Araújo
- University of Coimbra, MARE - Marine and Environmental Sciences Centre, Department Life Sciences, Coimbra, Portugal; CIBIO, Centro de Investigação em Biodiversidade e Recursos Genéticos, InBIO, Universidade do Porto, Vairão, Portugal; BIOPOLIS Program in Genomics, Biodiversity and Land Planning, CIBIO, Vairão, Portugal
| | - Miguel Carneiro
- CIBIO, Centro de Investigação em Biodiversidade e Recursos Genéticos, InBIO, Universidade do Porto, Vairão, Portugal; BIOPOLIS Program in Genomics, Biodiversity and Land Planning, CIBIO, Vairão, Portugal
| | - Jeroen Bussmann
- Division of BioTherapeutics, Leiden Academic Centre for Drug Research (LACDR), Leiden University, Leiden, the Netherlands
| | - Menno Hoekstra
- Division of BioTherapeutics, Leiden Academic Centre for Drug Research (LACDR), Leiden University, Leiden, the Netherlands; Division of Systems Pharmacology and Pharmacy, Leiden Academic Centre for Drug Research (LACDR), Leiden University, Leiden, the Netherlands; Pharmacy Leiden, Leiden, the Netherlands
| | - Miranda Van Eck
- Division of BioTherapeutics, Leiden Academic Centre for Drug Research (LACDR), Leiden University, Leiden, the Netherlands; Division of Systems Pharmacology and Pharmacy, Leiden Academic Centre for Drug Research (LACDR), Leiden University, Leiden, the Netherlands; Pharmacy Leiden, Leiden, the Netherlands
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29
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Wang R, Zhang P, Wang J, Ma L, E W, Suo S, Jiang M, Li J, Chen H, Sun H, Fei L, Zhou Z, Zhou Y, Chen Y, Zhang W, Wang X, Mei Y, Sun Z, Yu C, Shao J, Fu Y, Xiao Y, Ye F, Fang X, Wu H, Guo Q, Fang X, Li X, Gao X, Wang D, Xu PF, Zeng R, Xu G, Zhu L, Wang L, Qu J, Zhang D, Ouyang H, Huang H, Chen M, NG SC, Liu GH, Yuan GC, Guo G, Han X. Construction of a cross-species cell landscape at single-cell level. Nucleic Acids Res 2023; 51:501-516. [PMID: 35929025 PMCID: PMC9881150 DOI: 10.1093/nar/gkac633] [Citation(s) in RCA: 32] [Impact Index Per Article: 32.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/01/2022] [Revised: 06/30/2022] [Accepted: 07/20/2022] [Indexed: 02/06/2023] Open
Abstract
Individual cells are basic units of life. Despite extensive efforts to characterize the cellular heterogeneity of different organisms, cross-species comparisons of landscape dynamics have not been achieved. Here, we applied single-cell RNA sequencing (scRNA-seq) to map organism-level cell landscapes at multiple life stages for mice, zebrafish and Drosophila. By integrating the comprehensive dataset of > 2.6 million single cells, we constructed a cross-species cell landscape and identified signatures and common pathways that changed throughout the life span. We identified structural inflammation and mitochondrial dysfunction as the most common hallmarks of organism aging, and found that pharmacological activation of mitochondrial metabolism alleviated aging phenotypes in mice. The cross-species cell landscape with other published datasets were stored in an integrated online portal-Cell Landscape. Our work provides a valuable resource for studying lineage development, maturation and aging.
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Affiliation(s)
- Renying Wang
- Center for Stem Cell and Regenerative Medicine, and Bone Marrow Transplantation Center of the First Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, Zhejiang 310000, China
| | - Peijing Zhang
- Center for Stem Cell and Regenerative Medicine, and Bone Marrow Transplantation Center of the First Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, Zhejiang 310000, China
- Liangzhu Laboratory, Zhejiang University Medical Center, Hangzhou, 311121, China
| | - Jingjing Wang
- Center for Stem Cell and Regenerative Medicine, and Bone Marrow Transplantation Center of the First Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, Zhejiang 310000, China
- Liangzhu Laboratory, Zhejiang University Medical Center, Hangzhou, 311121, China
| | - Lifeng Ma
- Center for Stem Cell and Regenerative Medicine, and Bone Marrow Transplantation Center of the First Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, Zhejiang 310000, China
| | - Weigao E
- Center for Stem Cell and Regenerative Medicine, and Bone Marrow Transplantation Center of the First Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, Zhejiang 310000, China
| | | | - Mengmeng Jiang
- Center for Stem Cell and Regenerative Medicine, and Bone Marrow Transplantation Center of the First Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, Zhejiang 310000, China
- Liangzhu Laboratory, Zhejiang University Medical Center, Hangzhou, 311121, China
| | - Jiaqi Li
- Center for Stem Cell and Regenerative Medicine, and Bone Marrow Transplantation Center of the First Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, Zhejiang 310000, China
| | - Haide Chen
- Center for Stem Cell and Regenerative Medicine, and Bone Marrow Transplantation Center of the First Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, Zhejiang 310000, China
- Liangzhu Laboratory, Zhejiang University Medical Center, Hangzhou, 311121, China
| | - Huiyu Sun
- Center for Stem Cell and Regenerative Medicine, and Bone Marrow Transplantation Center of the First Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, Zhejiang 310000, China
| | - Lijiang Fei
- Center for Stem Cell and Regenerative Medicine, and Bone Marrow Transplantation Center of the First Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, Zhejiang 310000, China
| | - Ziming Zhou
- Center for Stem Cell and Regenerative Medicine, and Bone Marrow Transplantation Center of the First Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, Zhejiang 310000, China
| | - Yincong Zhou
- College of Life Sciences, Zhejiang University, Hangzhou 310058, China
| | - Yao Chen
- Key Laboratory of Reproductive Genetics (Ministry of Education), Department of Reproductive Endocrinology, Women's Hospital, Zhejiang University School of Medicine, Hangzhou, Zhejiang 310006, PR China
| | - Weiqi Zhang
- CAS Key Laboratory of Genomic and Precision Medicine, Beijing Institute of Genomics, Chinese Academy of Sciences, China National Center for Bioinformation, Beijing 100101, China
| | - Xinru Wang
- Center for Stem Cell and Regenerative Medicine, and Bone Marrow Transplantation Center of the First Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, Zhejiang 310000, China
| | - Yuqing Mei
- Center for Stem Cell and Regenerative Medicine, and Bone Marrow Transplantation Center of the First Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, Zhejiang 310000, China
| | - Zhongyi Sun
- Center for Stem Cell and Regenerative Medicine, and Bone Marrow Transplantation Center of the First Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, Zhejiang 310000, China
| | - Chengxuan Yu
- Center for Stem Cell and Regenerative Medicine, and Bone Marrow Transplantation Center of the First Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, Zhejiang 310000, China
| | - Jikai Shao
- Center for Stem Cell and Regenerative Medicine, and Bone Marrow Transplantation Center of the First Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, Zhejiang 310000, China
| | - Yuting Fu
- Center for Stem Cell and Regenerative Medicine, and Bone Marrow Transplantation Center of the First Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, Zhejiang 310000, China
| | - Yanyu Xiao
- Center for Stem Cell and Regenerative Medicine, and Bone Marrow Transplantation Center of the First Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, Zhejiang 310000, China
| | - Fang Ye
- Center for Stem Cell and Regenerative Medicine, and Bone Marrow Transplantation Center of the First Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, Zhejiang 310000, China
| | - Xing Fang
- Center for Stem Cell and Regenerative Medicine, and Bone Marrow Transplantation Center of the First Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, Zhejiang 310000, China
| | - Hanyu Wu
- Center for Stem Cell and Regenerative Medicine, and Bone Marrow Transplantation Center of the First Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, Zhejiang 310000, China
| | - Qile Guo
- Zhejiang University-University of Edinburgh Institute, Zhejiang University School of Medicine, Zhejiang University, Hangzhou 314400, China
| | - Xiunan Fang
- Center for Stem Cell and Regenerative Medicine, and Bone Marrow Transplantation Center of the First Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, Zhejiang 310000, China
| | - Xia Li
- Center for Stem Cell and Regenerative Medicine, and Bone Marrow Transplantation Center of the First Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, Zhejiang 310000, China
| | - Xianzhi Gao
- Institute of Immunology and Bone Marrow Transplantation Center, First Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou 310058, China
| | - Dan Wang
- Women's Hospital, and Institute of Genetics, Zhejiang University School of Medicine, Hangzhou 310058, China
| | - Peng-Fei Xu
- Women's Hospital, and Institute of Genetics, Zhejiang University School of Medicine, Hangzhou 310058, China
| | - Rui Zeng
- Division of Nephrology, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan 430030, China
| | - Gang Xu
- Division of Nephrology, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan 430030, China
| | - Lijun Zhu
- Zhejiang Provincial Key Laboratory for Diagnosis and Treatment of Aging and Physic-chemical Injury Diseases, The First Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou 310058, China
| | - Lie Wang
- Institute of Immunology and Bone Marrow Transplantation Center, First Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou 310058, China
| | - Jing Qu
- Institute for Stem Cell and Regeneration, Chinese Academy of Sciences, Beijing 100101, China
| | - Dan Zhang
- Key Laboratory of Reproductive Genetics (Ministry of Education), Department of Reproductive Endocrinology, Women's Hospital, Zhejiang University School of Medicine, Hangzhou, Zhejiang 310006, PR China
| | - Hongwei Ouyang
- Zhejiang University-University of Edinburgh Institute, Zhejiang University School of Medicine, Zhejiang University, Hangzhou 314400, China
- Zhejiang Provincial Key Lab for Tissue Engineering and Regenerative Medicine, Dr. Li Dak Sum & Yip Yio Chin Center for Stem Cell and Regenerative Medicine, Hangzhou, Zhejiang 310058, China
| | - He Huang
- Center for Stem Cell and Regenerative Medicine, and Bone Marrow Transplantation Center of the First Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, Zhejiang 310000, China
| | - Ming Chen
- College of Life Sciences, Zhejiang University, Hangzhou 310058, China
| | - Shyh-Chang NG
- Institute for Stem Cell and Regeneration, Chinese Academy of Sciences, Beijing 100101, China
| | - Guang-Hui Liu
- Institute for Stem Cell and Regeneration, Chinese Academy of Sciences, Beijing 100101, China
| | - Guo-Cheng Yuan
- Department of Genetics and Genomic Sciences, Charles Bronfman Institute for Personalized Medicine, Icahn School of Medicine at Mount Sinai, NY, NY 10029, USA
| | - Guoji Guo
- Center for Stem Cell and Regenerative Medicine, and Bone Marrow Transplantation Center of the First Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, Zhejiang 310000, China
- Liangzhu Laboratory, Zhejiang University Medical Center, Hangzhou, 311121, China
- Zhejiang University-University of Edinburgh Institute, Zhejiang University School of Medicine, Zhejiang University, Hangzhou 314400, China
- Zhejiang Provincial Key Lab for Tissue Engineering and Regenerative Medicine, Dr. Li Dak Sum & Yip Yio Chin Center for Stem Cell and Regenerative Medicine, Hangzhou, Zhejiang 310058, China
| | - Xiaoping Han
- Center for Stem Cell and Regenerative Medicine, and Bone Marrow Transplantation Center of the First Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, Zhejiang 310000, China
- Zhejiang Provincial Key Lab for Tissue Engineering and Regenerative Medicine, Dr. Li Dak Sum & Yip Yio Chin Center for Stem Cell and Regenerative Medicine, Hangzhou, Zhejiang 310058, China
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30
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Gu Y, Zhou Y, Ju S, Liu X, Zhang Z, Guo J, Gao J, Zang J, Sun H, Chen Q, Wang J, Xu J, Xu Y, Chen Y, Guo Y, Dai J, Ma H, Wang C, Jin G, Li C, Xia Y, Shen H, Yang Y, Guo X, Hu Z. Multi-omics profiling visualizes dynamics of cardiac development and functions. Cell Rep 2022; 41:111891. [PMID: 36577384 DOI: 10.1016/j.celrep.2022.111891] [Citation(s) in RCA: 17] [Impact Index Per Article: 8.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/28/2022] [Revised: 09/14/2022] [Accepted: 12/05/2022] [Indexed: 12/29/2022] Open
Abstract
Cardiogenesis is a tightly regulated dynamic process through a continuum of differentiation and proliferation events. Key factors and pathways governing this process remain incompletely understood. Here, we investigate mice hearts from embryonic day 10.5 to postnatal week 8 and dissect developmental changes in phosphoproteome-, proteome-, metabolome-, and transcriptome-encompassing cardiogenesis and cardiac maturation. We identify mitogen-activated protein kinases as core kinases involved in transcriptional regulation by mediating the phosphorylation of chromatin remodeling proteins during early cardiogenesis. We construct the reciprocal regulatory network of transcription factors (TFs) and identify a series of TFs controlling early cardiogenesis involved in cycling-dependent proliferation. After birth, we identify cardiac resident macrophages with high arachidonic acid metabolism activities likely involved in the clearance of injured apoptotic cardiomyocytes. Together, our comprehensive multi-omics data offer a panoramic view of cardiac development and maturation that provides a resource for further in-depth functional exploration.
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Affiliation(s)
- Yayun Gu
- State Key Laboratory of Reproductive Medicine, Nanjing Medical University, Nanjing, Jiangsu 211100, China; School of Public Health, Center for Global Health, Nanjing Medical University, Nanjing, Jiangsu 211100, China
| | - Yan Zhou
- State Key Laboratory of Reproductive Medicine, Nanjing Medical University, Nanjing, Jiangsu 211100, China; School of Public Health, Center for Global Health, Nanjing Medical University, Nanjing, Jiangsu 211100, China
| | - Sihan Ju
- State Key Laboratory of Reproductive Medicine, Nanjing Medical University, Nanjing, Jiangsu 211100, China; Department of Neurosurgery, Huashan Hospital, Fudan University, Shanghai 200040, China
| | - Xiaofei Liu
- State Key Laboratory of Reproductive Medicine, Nanjing Medical University, Nanjing, Jiangsu 211100, China
| | - Zicheng Zhang
- State Key Laboratory of Reproductive Medicine, Nanjing Medical University, Nanjing, Jiangsu 211100, China
| | - Jia Guo
- State Key Laboratory of Reproductive Medicine, Nanjing Medical University, Nanjing, Jiangsu 211100, China
| | - Jimiao Gao
- State Key Laboratory of Reproductive Medicine, Nanjing Medical University, Nanjing, Jiangsu 211100, China; School of Public Health, Center for Global Health, Nanjing Medical University, Nanjing, Jiangsu 211100, China
| | - Jie Zang
- School of Public Health, Center for Global Health, Nanjing Medical University, Nanjing, Jiangsu 211100, China
| | - Hao Sun
- State Key Laboratory of Reproductive Medicine, Nanjing Medical University, Nanjing, Jiangsu 211100, China
| | - Qi Chen
- State Key Laboratory of Reproductive Medicine, Nanjing Medical University, Nanjing, Jiangsu 211100, China; School of Public Health, Center for Global Health, Nanjing Medical University, Nanjing, Jiangsu 211100, China
| | - Jinghan Wang
- State Key Laboratory of Reproductive Medicine, Nanjing Medical University, Nanjing, Jiangsu 211100, China; School of Public Health, Center for Global Health, Nanjing Medical University, Nanjing, Jiangsu 211100, China
| | - Jiani Xu
- School of Public Health, Center for Global Health, Nanjing Medical University, Nanjing, Jiangsu 211100, China
| | - Yiqun Xu
- State Key Laboratory of Reproductive Medicine, Nanjing Medical University, Nanjing, Jiangsu 211100, China; School of Public Health, Center for Global Health, Nanjing Medical University, Nanjing, Jiangsu 211100, China
| | - Yingjia Chen
- State Key Laboratory of Reproductive Medicine, Nanjing Medical University, Nanjing, Jiangsu 211100, China
| | - Yueshuai Guo
- State Key Laboratory of Reproductive Medicine, Nanjing Medical University, Nanjing, Jiangsu 211100, China
| | - Juncheng Dai
- State Key Laboratory of Reproductive Medicine, Nanjing Medical University, Nanjing, Jiangsu 211100, China; School of Public Health, Center for Global Health, Nanjing Medical University, Nanjing, Jiangsu 211100, China
| | - Hongxia Ma
- State Key Laboratory of Reproductive Medicine, Nanjing Medical University, Nanjing, Jiangsu 211100, China; School of Public Health, Center for Global Health, Nanjing Medical University, Nanjing, Jiangsu 211100, China
| | - Cheng Wang
- State Key Laboratory of Reproductive Medicine, Nanjing Medical University, Nanjing, Jiangsu 211100, China
| | - Guangfu Jin
- State Key Laboratory of Reproductive Medicine, Nanjing Medical University, Nanjing, Jiangsu 211100, China; School of Public Health, Center for Global Health, Nanjing Medical University, Nanjing, Jiangsu 211100, China
| | - Chaojun Li
- State Key Laboratory of Reproductive Medicine, Nanjing Medical University, Nanjing, Jiangsu 211100, China
| | - Yankai Xia
- State Key Laboratory of Reproductive Medicine, Nanjing Medical University, Nanjing, Jiangsu 211100, China; School of Public Health, Center for Global Health, Nanjing Medical University, Nanjing, Jiangsu 211100, China
| | - Hongbing Shen
- State Key Laboratory of Reproductive Medicine, Nanjing Medical University, Nanjing, Jiangsu 211100, China; School of Public Health, Center for Global Health, Nanjing Medical University, Nanjing, Jiangsu 211100, China
| | - Yang Yang
- State Key Laboratory of Reproductive Medicine, Nanjing Medical University, Nanjing, Jiangsu 211100, China
| | - Xuejiang Guo
- State Key Laboratory of Reproductive Medicine, Nanjing Medical University, Nanjing, Jiangsu 211100, China
| | - Zhibin Hu
- State Key Laboratory of Reproductive Medicine, Nanjing Medical University, Nanjing, Jiangsu 211100, China; School of Public Health, Center for Global Health, Nanjing Medical University, Nanjing, Jiangsu 211100, China.
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31
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Xie W, Cheng J, Hong Z, Cai W, Zhuo H, Hou J, Lin L, Wei X, Wang K, Chen X, Song Y, Wang Z, Cai J. Multi-Transcriptomic Analysis Reveals the Heterogeneity and Tumor-Promoting Role of SPP1/CD44-Mediated Intratumoral Crosstalk in Gastric Cancer. Cancers (Basel) 2022; 15:cancers15010164. [PMID: 36612160 PMCID: PMC9818284 DOI: 10.3390/cancers15010164] [Citation(s) in RCA: 15] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/21/2022] [Revised: 12/20/2022] [Accepted: 12/25/2022] [Indexed: 12/29/2022] Open
Abstract
GC is a fatal disease with high heterogeneity and invasiveness. Recently, SPP1 has been reported to be involved in the tumor progression of multiple human cancers; however, the role of SPP1 in GC heterogeneity and whether it is associated with the invasiveness and mortality of GC remain unclear. Here, we combined multiple RNA sequencing approaches to evaluate the impact of SPP1 on GC. Through bulk RNA sequencing (bulk RNA-seq) and immunohistochemistry (IHC), we found that SPP1 was highly expressed in GC, and high levels of SPP1 were associated with macrophage infiltration, an advanced tumor stage, and higher mortality for advanced GC patients. Furthermore, through simultaneous single-cell and spatial analysis, we demonstrated that SPP1+ macrophages are tumor-specific macrophages unique to cancer and enriched in the deep layer of GC tissue. Cell-cell communication analysis revealed that SPP1/CD44 interactions between SPP1+ macrophages and their localized tumor epithelial cells could activate downstream target genes in epithelial cells to promote dynamic changes in intratumor heterogeneity. Moreover, these activated genes were found to be closely associated with poor clinical GC outcomes and with cancer-related pathways that promote GC progression, as shown by survival analysis and enrichment analysis, respectively. Collectively, our study reveals that tumor-specific SPP1+ macrophages drive the architecture of intratumor heterogeneity to evolve with tumor progression and that SPP1 may serve as a prognostic marker for advanced GC patients, as well as a potential therapeutic target for GC.
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Affiliation(s)
- Wen Xie
- Department of Gastrointestinal Surgery, Zhongshan Hospital of Xiamen University, School of Medicine, Xiamen University, Xiamen 361001, China
- Xiamen Municipal Key Laboratory of Gastrointestinal Oncology, Xiamen 361001, China
| | - Jia Cheng
- Department of Gastrointestinal Surgery, Zhongshan Hospital of Xiamen University, School of Medicine, Xiamen University, Xiamen 361001, China
- Xiamen Municipal Key Laboratory of Gastrointestinal Oncology, Xiamen 361001, China
| | - Zhijun Hong
- Department of Gastrointestinal Surgery, Zhongshan Hospital of Xiamen University, School of Medicine, Xiamen University, Xiamen 361001, China
- Xiamen Municipal Key Laboratory of Gastrointestinal Oncology, Xiamen 361001, China
| | - Wangyu Cai
- Department of Gastrointestinal Surgery, Zhongshan Hospital of Xiamen University, School of Medicine, Xiamen University, Xiamen 361001, China
- Xiamen Municipal Key Laboratory of Gastrointestinal Oncology, Xiamen 361001, China
| | - Huiqin Zhuo
- Department of Gastrointestinal Surgery, Zhongshan Hospital of Xiamen University, School of Medicine, Xiamen University, Xiamen 361001, China
- Xiamen Municipal Key Laboratory of Gastrointestinal Oncology, Xiamen 361001, China
| | - Jingjing Hou
- Department of Gastrointestinal Surgery, Zhongshan Hospital of Xiamen University, School of Medicine, Xiamen University, Xiamen 361001, China
- Xiamen Municipal Key Laboratory of Gastrointestinal Oncology, Xiamen 361001, China
| | - Lingyun Lin
- Department of Gastrointestinal Surgery, Zhongshan Hospital of Xiamen University, School of Medicine, Xiamen University, Xiamen 361001, China
- Xiamen Municipal Key Laboratory of Gastrointestinal Oncology, Xiamen 361001, China
| | - Xujin Wei
- The Graduate School of Fujian Medical University, Fuzhou 350004, China
| | - Kang Wang
- Department of Gastrointestinal Surgery, Zhongshan Hospital of Xiamen University, School of Medicine, Xiamen University, Xiamen 361001, China
- Xiamen Municipal Key Laboratory of Gastrointestinal Oncology, Xiamen 361001, China
| | - Xin Chen
- The Graduate School of Fujian Medical University, Fuzhou 350004, China
| | - Yucheng Song
- The Graduate School of Fujian Medical University, Fuzhou 350004, China
| | - Zhenfa Wang
- Department of Gastrointestinal Surgery, Zhongshan Hospital of Xiamen University, School of Medicine, Xiamen University, Xiamen 361001, China
- Xiamen Municipal Key Laboratory of Gastrointestinal Oncology, Xiamen 361001, China
| | - Jianchun Cai
- Department of Gastrointestinal Surgery, Zhongshan Hospital of Xiamen University, School of Medicine, Xiamen University, Xiamen 361001, China
- Xiamen Municipal Key Laboratory of Gastrointestinal Oncology, Xiamen 361001, China
- The Graduate School of Fujian Medical University, Fuzhou 350004, China
- Correspondence:
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Secuer: Ultrafast, scalable and accurate clustering of single-cell RNA-seq data. PLoS Comput Biol 2022; 18:e1010753. [DOI: 10.1371/journal.pcbi.1010753] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/04/2022] [Revised: 12/15/2022] [Accepted: 11/22/2022] [Indexed: 12/12/2022] Open
Abstract
Identifying cell clusters is a critical step for single-cell transcriptomics study. Despite the numerous clustering tools developed recently, the rapid growth of scRNA-seq volumes prompts for a more (computationally) efficient clustering method. Here, we introduce Secuer, a Scalable and Efficient speCtral clUstERing algorithm for scRNA-seq data. By employing an anchor-based bipartite graph representation algorithm, Secuer enjoys reduced runtime and memory usage over one order of magnitude for datasets with more than 1 million cells. Meanwhile, Secuer also achieves better or comparable accuracy than competing methods in small and moderate benchmark datasets. Furthermore, we showcase that Secuer can also serve as a building block for a new consensus clustering method, Secuer-consensus, which again improves the runtime and scalability of state-of-the-art consensus clustering methods while also maintaining the accuracy. Overall, Secuer is a versatile, accurate, and scalable clustering framework suitable for small to ultra-large single-cell clustering tasks.
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Li J, Diamante G, Ahn IS, Wijaya D, Wang X, Chang CH, Ha SM, Immadisetty K, Meng H, Nel A, Yang X, Xia T. Determination of the nanoparticle- and cell-specific toxicological mechanisms in 3D liver spheroids using scRNAseq analysis. NANO TODAY 2022; 47:101652. [PMID: 36911538 PMCID: PMC10004129 DOI: 10.1016/j.nantod.2022.101652] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 06/18/2023]
Abstract
Engineered nanomaterials (ENMs) are commonly used in consumer products, allowing exposure to target organs such as the lung, liver, and skin that could lead to adverse health effects in humans. To better reflect on toxicological effects in liver cells, it is important to consider the contribution of hepatocyte morphology, function, and intercellular interactions in a dynamic 3D microenvironment. Herein, we used a 3D liver spheroid model containing hepatocyte and Kupffer cells (KCs) to study the effects of three different material compositions, namely vanadium pentoxide (V2O5), titanium dioxide (TiO2), or graphene oxide (GO). Additionally, we used single-cell RNA sequencing (scRNAseq) to determine the nanoparticle (NP) and cell-specific toxicological responses. A general finding was that hepatocytes exhibit more variation in gene expression and adaptation of signaling pathways than KCs. TNF-α production tied to the NF-κB pathway was a commonly affected pathway by all NPs while impacts on the metabolic function of hepatocytes were unique to V2O5. V2O5 NPs also showed the largest number of differentially expressed genes in both cell types, many of which are related to pro-inflammatory and apoptotic response pathways. There was also evidence of mitochondrial ROS generation and caspase-1 activation after GO and V2O5 treatment, in association with cytokine production. All considered, this study provides insight into the impact of nanoparticles on gene responses in key liver cell types, providing us with a scRNAseq platform that can be used for high-content screening of nanomaterial impact on the liver, for use in biosafety and biomedical applications.
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Affiliation(s)
- Jiulong Li
- Center of Environmental Implications of Nanotechnology (UC CEIN), California Nanosystems Institute, University of California, Los Angeles, CA 90095, USA
- Division of NanoMedicine, Department of Medicine, California Nanosystems Institute, University of California, Los Angeles, CA 90095, USA
| | - Graciel Diamante
- Department of Integrative Biology and Physiology, University of California, Los Angeles (UCLA), Los Angeles, CA 90095, USA
| | - In Sook Ahn
- Department of Integrative Biology and Physiology, University of California, Los Angeles (UCLA), Los Angeles, CA 90095, USA
| | - Darren Wijaya
- Department of Integrative Biology and Physiology, University of California, Los Angeles (UCLA), Los Angeles, CA 90095, USA
| | - Xiang Wang
- Center of Environmental Implications of Nanotechnology (UC CEIN), California Nanosystems Institute, University of California, Los Angeles, CA 90095, USA
- Division of NanoMedicine, Department of Medicine, California Nanosystems Institute, University of California, Los Angeles, CA 90095, USA
| | - Chong Hyun Chang
- Center of Environmental Implications of Nanotechnology (UC CEIN), California Nanosystems Institute, University of California, Los Angeles, CA 90095, USA
- Division of NanoMedicine, Department of Medicine, California Nanosystems Institute, University of California, Los Angeles, CA 90095, USA
| | - Sung-min Ha
- Department of Integrative Biology and Physiology, University of California, Los Angeles (UCLA), Los Angeles, CA 90095, USA
| | - Kavya Immadisetty
- Department of Integrative Biology and Physiology, University of California, Los Angeles (UCLA), Los Angeles, CA 90095, USA
| | - Huan Meng
- Center of Environmental Implications of Nanotechnology (UC CEIN), California Nanosystems Institute, University of California, Los Angeles, CA 90095, USA
- Division of NanoMedicine, Department of Medicine, California Nanosystems Institute, University of California, Los Angeles, CA 90095, USA
| | - André Nel
- Center of Environmental Implications of Nanotechnology (UC CEIN), California Nanosystems Institute, University of California, Los Angeles, CA 90095, USA
- Division of NanoMedicine, Department of Medicine, California Nanosystems Institute, University of California, Los Angeles, CA 90095, USA
| | - Xia Yang
- Molecular Toxicology Interdepartmental Program, University of California, Los Angeles (UCLA), Los Angeles, CA 90095, USA
- Department of Integrative Biology and Physiology, University of California, Los Angeles (UCLA), Los Angeles, CA 90095, USA
| | - Tian Xia
- Center of Environmental Implications of Nanotechnology (UC CEIN), California Nanosystems Institute, University of California, Los Angeles, CA 90095, USA
- Division of NanoMedicine, Department of Medicine, California Nanosystems Institute, University of California, Los Angeles, CA 90095, USA
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Zhou Z, Tan C, Chau M, Jiang X, Ke Z, Chen X, Cao Y, Kwok YK, Bellgard M, Leung T, Choy K, Dong Z. TEDD: a database of temporal gene expression patterns during multiple developmental periods in human and model organisms. Nucleic Acids Res 2022; 51:D1168-D1178. [PMID: 36350663 PMCID: PMC9825605 DOI: 10.1093/nar/gkac978] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/09/2022] [Revised: 10/06/2022] [Accepted: 10/15/2022] [Indexed: 11/10/2022] Open
Abstract
Characterization of the specific expression and chromatin profiles of genes enables understanding how they contribute to tissue/organ development and the mechanisms leading to diseases. Whilst the number of single-cell sequencing studies is increasing dramatically; however, data mining and reanalysis remains challenging. Herein, we systematically curated the up-to-date and most comprehensive datasets of sequencing data originating from 2760 bulk samples and over 5.1 million single-cells from multiple developmental periods from humans and multiple model organisms. With unified and systematic analysis, we profiled the gene expression and chromatin accessibility among 481 cell-types, 79 tissue-types and 92 timepoints, and pinpointed cells with the co-expression of target genes. We also enabled the detection of gene(s) with a temporal and cell-type specific expression profile that is similar to or distinct from that of a target gene. Additionally, we illustrated the potential upstream and downstream gene-gene regulation interactions, particularly under the same biological process(es) or KEGG pathway(s). Thus, TEDD (Temporal Expression during Development Database), a value-added database with a user-friendly interface, not only enables researchers to identify cell-type/tissue-type specific and temporal gene expression and chromatin profiles but also facilitates the association of genes with undefined biological functions in development and diseases. The database URL is https://TEDD.obg.cuhk.edu.hk/.
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Affiliation(s)
| | | | - Matthew Hoi Kin Chau
- Department of Obstetrics and Gynaecology, The Chinese University of Hong Kong, Hong Kong, China,Shenzhen Research Institute, The Chinese University of Hong Kong, Shenzhen 518057, China,Hong Kong Hub of Paediatric Excellence, The Chinese University of Hong Kong, Hong Kong, China,The Chinese University of Hong Kong-Baylor College of Medicine Joint Center for Medical Genetics, Hong Kong, China
| | - Xiaosen Jiang
- BGI-Shenzhen, Shenzhen 518083, China,College of Life Sciences, University of Chinese Academy of Sciences, Beijing 100049, China
| | - Ziyuan Ke
- BGI-Shenzhen, Shenzhen 518083, China
| | - Xiaoyan Chen
- Department of Obstetrics and Gynaecology, The Chinese University of Hong Kong, Hong Kong, China,Maternal-Fetal Medicine Institute, Shenzhen Baoan Women's and Children's Hospital, Shenzhen University, Shenzhen, China
| | - Ye Cao
- Department of Obstetrics and Gynaecology, The Chinese University of Hong Kong, Hong Kong, China,Shenzhen Research Institute, The Chinese University of Hong Kong, Shenzhen 518057, China,Hong Kong Hub of Paediatric Excellence, The Chinese University of Hong Kong, Hong Kong, China,The Fertility Preservation Research Center, Department of Obstetrics and Gynaecology, The Chinese University of Hong Kong, Hong Kong, China
| | - Yvonne K Kwok
- Department of Obstetrics and Gynaecology, The Chinese University of Hong Kong, Hong Kong, China
| | - Matthew Bellgard
- eResearch Office, Queensland University of Technology, Brisbane, QLD, Australia
| | - Tak Yeung Leung
- Department of Obstetrics and Gynaecology, The Chinese University of Hong Kong, Hong Kong, China,Shenzhen Research Institute, The Chinese University of Hong Kong, Shenzhen 518057, China,Hong Kong Hub of Paediatric Excellence, The Chinese University of Hong Kong, Hong Kong, China,The Chinese University of Hong Kong-Baylor College of Medicine Joint Center for Medical Genetics, Hong Kong, China,The Fertility Preservation Research Center, Department of Obstetrics and Gynaecology, The Chinese University of Hong Kong, Hong Kong, China
| | - Kwong Wai Choy
- Correspondence may also be addressed to Kwong Wai Choy. Tel: +852 3505 3099; Fax: +852 2636 0008;
| | - Zirui Dong
- To whom correspondence should be addressed. Tel: +852 3505 3099; Fax: +852 2636 0008;
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35
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Yan H, Wang R, Ma S, Huang D, Wang S, Ren J, Lu C, Chen X, Lu X, Zheng Z, Zhang W, Qu J, Zhou Y, Liu GH. Lineage Landscape: a comprehensive database that records lineage commitment across species. Nucleic Acids Res 2022; 51:D1061-D1066. [PMID: 36305824 PMCID: PMC9825468 DOI: 10.1093/nar/gkac951] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/16/2022] [Revised: 09/23/2022] [Accepted: 10/11/2022] [Indexed: 01/30/2023] Open
Abstract
Commitment to specific cell lineages is critical for mammalian embryonic development. Lineage determination, differentiation, maintenance, and organogenesis result in diverse life forms composed of multiple cell types. To understand the formation and maintenance of living individuals, including human beings, a comprehensive database that integrates multi-omic information underlying lineage differentiation across multiple species is urgently needed. Here, we construct Lineage Landscape, a database that compiles, analyzes and visualizes transcriptomic and epigenomic information related to lineage development in a collection of species. This landscape draws together datasets that capture the ongoing changes in cell lineages from classic model organisms to human beings throughout embryonic, fetal, adult, and aged stages, providing comprehensive, open-access information that is useful to researchers of a broad spectrum of life science disciplines. Lineage Landscape contains single-cell gene expression and bulk transcriptomic, DNA methylation, histone modifications, and chromatin accessibility profiles. Using this database, users can explore genes of interest that exhibit dynamic expression patterns at the transcriptional or epigenetic levels at different stages of lineage development. Lineage Landscape currently includes over 6.6 million cells, 15 million differentially expressed genes and 36 million data entries across 10 species and 34 organs. Lineage Landscape is free to access, browse, search, and download at http://data.iscr.ac.cn/lineage/#/home.
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Affiliation(s)
| | | | | | | | | | | | - Changfa Lu
- Computer Network Information Center, Chinese Academy of Sciences, Beijing 100190, China
| | - Xin Chen
- Computer Network Information Center, Chinese Academy of Sciences, Beijing 100190, China
| | - Xiaoyong Lu
- University of Chinese Academy of Sciences, Beijing 100049, China,China National Center for Bioinformation, Beijing 100101, China,CAS Key Laboratory of Genomic and Precision Medicine, Beijing Institute of Genomics, Chinese Academy of Sciences, Beijing 100101, China
| | - Zikai Zheng
- University of Chinese Academy of Sciences, Beijing 100049, China,China National Center for Bioinformation, Beijing 100101, China,CAS Key Laboratory of Genomic and Precision Medicine, Beijing Institute of Genomics, Chinese Academy of Sciences, Beijing 100101, China
| | - Weiqi Zhang
- Correspondence may also be addressed to Weiqi Zhang. Tel: +86 10 8409 7838;
| | - Jing Qu
- Correspondence may also be addressed to Jing Qu. Tel: +86 10 6480 7768;
| | - Yuanchun Zhou
- Correspondence may also be addressed to Yuanchun Zhou. Tel: +86 10 5881 2561;
| | - Guang-Hui Liu
- To whom correspondence should be addressed. Tel: +86 10 6480 7583;
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36
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Kim SH, Cho SY. Single-cell transcriptomics to understand the cellular heterogeneity in toxicology. Mol Cell Toxicol 2022. [DOI: 10.1007/s13273-022-00304-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/07/2022]
Abstract
Abstract
Background
Identification of molecular signatures from omics studies is widely applied in toxicological studies, and the evaluation of potential toxic effects provides novel insights into molecular resolution.
Objective
The prediction of toxic effects and drug tolerance provides important clues regarding the mode of action of target compounds. However, heterogeneity within samples makes toxicology studies challenging because the purity of the target cell in the samples remains unknown until their actual utilization.
Result
Single-cell resolution studies have been suggested in toxicogenomics, and several studies have explained toxic effects and drug tolerance using heterogeneous cells in both in vivo and in vitro conditions. In this review, we presented an understanding of single-cell transcriptomes and their applications in toxicogenomics.
Conclusion
The most toxicological mechanism in organisms occurs through intramolecular combinations, and heterogeneity issues have reached a surmountable level. We hope this review provides insights to successfully conduct future studies on toxicology.
Purpose of the review
Toxicogenomics is an interdisciplinary field between toxicology and genomics that was successfully applied to construct molecular profiles in a broad spectrum of toxicology. However, heterogeneity within samples makes toxicology studies challenging because the purity of target cell in the samples remains unknown until their actual utilisation. In this review, we presented an understanding of single-cell transcriptomes and their applications in toxicogenomics.
Recent findings
A high-throughput techniques have been used to understand cellular heterogeneity and molecular mechanisms at toxicogenomics. Single-cell resolution analysis is required to identify biomarkers of explain toxic effect and in order to understand drug tolerance.
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