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Chen W, Chen X, Yao L, Feng J, Li F, Shan Y, Ren L, Zhuo C, Feng M, Zhong S, He C. A global view of altered ligand-receptor interactions in bone marrow aging based on single-cell sequencing. Comput Struct Biotechnol J 2024; 23:2754-2762. [PMID: 39050783 PMCID: PMC11267010 DOI: 10.1016/j.csbj.2024.06.020] [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: 03/25/2024] [Revised: 06/17/2024] [Accepted: 06/18/2024] [Indexed: 07/27/2024] Open
Abstract
Altered cell-cell communication is a hallmark of aging, but its impact on bone marrow aging remains poorly understood. Based on a common and effective pipeline and single-cell transcriptome sequencing, we detected 384,124 interactions including 2575 ligand-receptor pairs and 16 non-adherent bone marrow cell types in old and young mouse and identified a total of 5560 significantly different interactions, which were then verified by flow cytometry and quantitative real-time PCR. These differential ligand-receptor interactions exhibited enrichment for the senescence-associated secretory phenotypes. Further validation demonstrated supplementing specific extracellular ligands could modify the senescent signs of hematopoietic stem cells derived from old mouse. Our work provides an effective procedure to detect the ligand-receptor interactions based on single-cell sequencing, which contributes to understand mechanisms and provides a potential strategy for intervention of bone marrow aging.
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Affiliation(s)
- Wenbo Chen
- School of Basic Medical Sciences, Taikang Medical School, Wuhan University, Wuhan 430071, China
| | - Xin Chen
- College of Biomedicine and Health, Huazhong Agricultural University, Wuhan 430070, China
| | - Lei Yao
- College of Biomedicine and Health, Huazhong Agricultural University, Wuhan 430070, China
| | - Jing Feng
- School of Computer Science, Wuhan University, Wuhan 430072, China
| | - Fengyue Li
- College of Biomedicine and Health, Huazhong Agricultural University, Wuhan 430070, China
| | - Yuxin Shan
- College of Biomedicine and Health, Huazhong Agricultural University, Wuhan 430070, China
| | - Linli Ren
- College of Biomedicine and Health, Huazhong Agricultural University, Wuhan 430070, China
| | - Chenjian Zhuo
- College of Biomedicine and Health, Huazhong Agricultural University, Wuhan 430070, China
| | - Mingqian Feng
- College of Biomedicine and Health, Huazhong Agricultural University, Wuhan 430070, China
| | - Shan Zhong
- School of Basic Medical Sciences, Taikang Medical School, Wuhan University, Wuhan 430071, China
| | - Chunjiang He
- College of Biomedicine and Health, Huazhong Agricultural University, Wuhan 430070, China
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Sun F, Li H, Sun D, Fu S, Gu L, Shao X, Wang Q, Dong X, Duan B, Xing F, Wu J, Xiao M, Zhao F, Han JDJ, Liu Q, Fan X, Li C, Wang C, Shi T. Single-cell omics: experimental workflow, data analyses and applications. SCIENCE CHINA. LIFE SCIENCES 2024:10.1007/s11427-023-2561-0. [PMID: 39060615 DOI: 10.1007/s11427-023-2561-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/07/2023] [Accepted: 04/18/2024] [Indexed: 07/28/2024]
Abstract
Cells are the fundamental units of biological systems and exhibit unique development trajectories and molecular features. Our exploration of how the genomes orchestrate the formation and maintenance of each cell, and control the cellular phenotypes of various organismsis, is both captivating and intricate. Since the inception of the first single-cell RNA technology, technologies related to single-cell sequencing have experienced rapid advancements in recent years. These technologies have expanded horizontally to include single-cell genome, epigenome, proteome, and metabolome, while vertically, they have progressed to integrate multiple omics data and incorporate additional information such as spatial scRNA-seq and CRISPR screening. Single-cell omics represent a groundbreaking advancement in the biomedical field, offering profound insights into the understanding of complex diseases, including cancers. Here, we comprehensively summarize recent advances in single-cell omics technologies, with a specific focus on the methodology section. This overview aims to guide researchers in selecting appropriate methods for single-cell sequencing and related data analysis.
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Affiliation(s)
- Fengying Sun
- Department of Clinical Laboratory, the Affiliated Wuhu Hospital of East China Normal University (The Second People's Hospital of Wuhu City), Wuhu, 241000, China
| | - Haoyan Li
- Pharmaceutical Informatics Institute, College of Pharmaceutical Sciences, Zhejiang University, Hangzhou, 310058, China
| | - Dongqing Sun
- Key Laboratory of Spine and Spinal Cord Injury Repair and Regeneration (Tongji University), Ministry of Education, Orthopaedic Department, Tongji Hospital, Bioinformatics Department, School of Life Sciences and Technology, Tongji University, Shanghai, 200082, China
- Frontier Science Center for Stem Cells, School of Life Sciences and Technology, Tongji University, Shanghai, 200092, China
| | - Shaliu Fu
- Key Laboratory of Spine and Spinal Cord Injury Repair and Regeneration (Tongji University), Ministry of Education, Orthopaedic Department, Tongji Hospital, Bioinformatics Department, School of Life Sciences and Technology, Tongji University, Shanghai, 200082, China
- Translational Medical Center for Stem Cell Therapy and Institute for Regenerative Medicine, Shanghai East Hospital, Bioinformatics Department, School of Life Sciences and Technology, Tongji University, Shanghai, 200082, China
- Research Institute of Intelligent Computing, Zhejiang Lab, Hangzhou, 311121, China
- Shanghai Research Institute for Intelligent Autonomous Systems, Shanghai, 201210, China
| | - Lei Gu
- Center for Single-cell Omics, School of Public Health, Shanghai Jiao Tong University School of Medicine, Shanghai, 200025, China
| | - Xin Shao
- Pharmaceutical Informatics Institute, College of Pharmaceutical Sciences, Zhejiang University, Hangzhou, 310058, China
- National Key Laboratory of Chinese Medicine Modernization, Innovation Center of Yangtze River Delta, Zhejiang University, Jiaxing, 314103, China
| | - Qinqin Wang
- Center for Single-cell Omics, School of Public Health, Shanghai Jiao Tong University School of Medicine, Shanghai, 200025, China
| | - Xin Dong
- Key Laboratory of Spine and Spinal Cord Injury Repair and Regeneration (Tongji University), Ministry of Education, Orthopaedic Department, Tongji Hospital, Bioinformatics Department, School of Life Sciences and Technology, Tongji University, Shanghai, 200082, China
- Frontier Science Center for Stem Cells, School of Life Sciences and Technology, Tongji University, Shanghai, 200092, China
| | - Bin Duan
- Key Laboratory of Spine and Spinal Cord Injury Repair and Regeneration (Tongji University), Ministry of Education, Orthopaedic Department, Tongji Hospital, Bioinformatics Department, School of Life Sciences and Technology, Tongji University, Shanghai, 200082, China
- Translational Medical Center for Stem Cell Therapy and Institute for Regenerative Medicine, Shanghai East Hospital, Bioinformatics Department, School of Life Sciences and Technology, Tongji University, Shanghai, 200082, China
- Research Institute of Intelligent Computing, Zhejiang Lab, Hangzhou, 311121, China
- Shanghai Research Institute for Intelligent Autonomous Systems, Shanghai, 201210, China
| | - Feiyang Xing
- Key Laboratory of Spine and Spinal Cord Injury Repair and Regeneration (Tongji University), Ministry of Education, Orthopaedic Department, Tongji Hospital, Bioinformatics Department, School of Life Sciences and Technology, Tongji University, Shanghai, 200082, China
- Frontier Science Center for Stem Cells, School of Life Sciences and Technology, Tongji University, Shanghai, 200092, China
| | - Jun Wu
- Center for Bioinformatics and Computational Biology, Shanghai Key Laboratory of Regulatory Biology, the Institute of Biomedical Sciences and School of Life Sciences, East China Normal University, Shanghai, 200241, China
| | - Minmin Xiao
- Department of Clinical Laboratory, the Affiliated Wuhu Hospital of East China Normal University (The Second People's Hospital of Wuhu City), Wuhu, 241000, China.
| | - Fangqing Zhao
- Beijing Institutes of Life Science, Chinese Academy of Sciences, Beijing, 100101, China.
| | - Jing-Dong J Han
- Peking-Tsinghua Center for Life Sciences, Academy for Advanced Interdisciplinary Studies, Center for Quantitative Biology (CQB), Peking University, Beijing, 100871, China.
| | - Qi Liu
- Key Laboratory of Spine and Spinal Cord Injury Repair and Regeneration (Tongji University), Ministry of Education, Orthopaedic Department, Tongji Hospital, Bioinformatics Department, School of Life Sciences and Technology, Tongji University, Shanghai, 200082, China.
- Translational Medical Center for Stem Cell Therapy and Institute for Regenerative Medicine, Shanghai East Hospital, Bioinformatics Department, School of Life Sciences and Technology, Tongji University, Shanghai, 200082, China.
- Research Institute of Intelligent Computing, Zhejiang Lab, Hangzhou, 311121, China.
- Shanghai Research Institute for Intelligent Autonomous Systems, Shanghai, 201210, China.
| | - Xiaohui Fan
- Pharmaceutical Informatics Institute, College of Pharmaceutical Sciences, Zhejiang University, Hangzhou, 310058, China.
- National Key Laboratory of Chinese Medicine Modernization, Innovation Center of Yangtze River Delta, Zhejiang University, Jiaxing, 314103, China.
- Zhejiang Key Laboratory of Precision Diagnosis and Therapy for Major Gynecological Diseases, Women's Hospital, Zhejiang University School of Medicine, Hangzhou, 310006, China.
| | - Chen Li
- Center for Single-cell Omics, School of Public Health, Shanghai Jiao Tong University School of Medicine, Shanghai, 200025, China.
| | - Chenfei Wang
- Key Laboratory of Spine and Spinal Cord Injury Repair and Regeneration (Tongji University), Ministry of Education, Orthopaedic Department, Tongji Hospital, Bioinformatics Department, School of Life Sciences and Technology, Tongji University, Shanghai, 200082, China.
- Frontier Science Center for Stem Cells, School of Life Sciences and Technology, Tongji University, Shanghai, 200092, China.
| | - Tieliu Shi
- Department of Clinical Laboratory, the Affiliated Wuhu Hospital of East China Normal University (The Second People's Hospital of Wuhu City), Wuhu, 241000, China.
- Center for Bioinformatics and Computational Biology, Shanghai Key Laboratory of Regulatory Biology, the Institute of Biomedical Sciences and School of Life Sciences, East China Normal University, Shanghai, 200241, China.
- Key Laboratory of Advanced Theory and Application in Statistics and Data Science-MOE, School of Statistics, East China Normal University, Shanghai, 200062, China.
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Zhang Y, Yang Y, Ren L, Zhan M, Sun T, Zou Q, Zhang Y. Predicting intercellular communication based on metabolite-related ligand-receptor interactions with MRCLinkdb. BMC Biol 2024; 22:152. [PMID: 38978014 PMCID: PMC11232326 DOI: 10.1186/s12915-024-01950-w] [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: 03/16/2024] [Accepted: 07/03/2024] [Indexed: 07/10/2024] Open
Abstract
BACKGROUND Metabolite-associated cell communications play critical roles in maintaining human biological function. However, most existing tools and resources focus only on ligand-receptor interaction pairs where both partners are proteinaceous, neglecting other non-protein molecules. To address this gap, we introduce the MRCLinkdb database and algorithm, which aggregates and organizes data related to non-protein L-R interactions in cell-cell communication, providing a valuable resource for predicting intercellular communication based on metabolite-related ligand-receptor interactions. RESULTS Here, we manually curated the metabolite-ligand-receptor (ML-R) interactions from the literature and known databases, ultimately collecting over 790 human and 670 mouse ML-R interactions. Additionally, we compiled information on over 1900 enzymes and 260 transporter entries associated with these metabolites. We developed Metabolite-Receptor based Cell Link Database (MRCLinkdb) to store these ML-R interactions data. Meanwhile, the platform also offers extensive information for presenting ML-R interactions, including fundamental metabolite information and the overall expression landscape of metabolite-associated gene sets (such as receptor, enzymes, and transporter proteins) based on single-cell transcriptomics sequencing (covering 35 human and 26 mouse tissues, 52 human and 44 mouse cell types) and bulk RNA-seq/microarray data (encompassing 62 human and 39 mouse tissues). Furthermore, MRCLinkdb introduces a web server dedicated to the analysis of intercellular communication based on ML-R interactions. MRCLinkdb is freely available at https://www.cellknowledge.com.cn/mrclinkdb/ . CONCLUSIONS In addition to supplementing ligand-receptor databases, MRCLinkdb may provide new perspectives for decoding the intercellular communication and advancing related prediction tools based on ML-R interactions.
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Affiliation(s)
- Yuncong Zhang
- Guangdong Provincial Key Laboratory of Tumor Interventional Diagnosis and Treatment, Zhuhai Institute of Translational Medicine, Zhuhai People's Hospital (Zhuhai Clinical Medical College of Jinan University), Jinan University, Zhuhai, Guangdong, China
| | - Yu Yang
- Innovative Institute of Chinese Medicine and Pharmacy, Academy for Interdiscipline, Chengdu University of Traditional Chinese Medicine, Chengdu, China
- School of Healthcare Technology, Chengdu Neusoft University, Chengdu, China
| | - Liping Ren
- School of Healthcare Technology, Chengdu Neusoft University, Chengdu, China
| | - Meixiao Zhan
- Guangdong Provincial Key Laboratory of Tumor Interventional Diagnosis and Treatment, Zhuhai Institute of Translational Medicine, Zhuhai People's Hospital (Zhuhai Clinical Medical College of Jinan University), Jinan University, Zhuhai, Guangdong, China
| | - Taoping Sun
- Guangdong Provincial Key Laboratory of Tumor Interventional Diagnosis and Treatment, Zhuhai Institute of Translational Medicine, Zhuhai People's Hospital (Zhuhai Clinical Medical College of Jinan University), Jinan University, Zhuhai, Guangdong, China.
| | - Quan Zou
- Institute of Fundamental and Frontier Sciences, University of Electronic Science and Technology of China, Chengdu, China.
| | - Yang Zhang
- Innovative Institute of Chinese Medicine and Pharmacy, Academy for Interdiscipline, Chengdu University of Traditional Chinese Medicine, Chengdu, China.
- Institute of Fundamental and Frontier Sciences, University of Electronic Science and Technology of China, Chengdu, China.
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4
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Sarkar H, Chitra U, Gold J, Raphael BJ. A count-based model for delineating cell-cell interactions in spatial transcriptomics data. Bioinformatics 2024; 40:i481-i489. [PMID: 38940134 PMCID: PMC11211854 DOI: 10.1093/bioinformatics/btae219] [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] [Indexed: 06/29/2024] Open
Abstract
MOTIVATION Cell-cell interactions (CCIs) consist of cells exchanging signals with themselves and neighboring cells by expressing ligand and receptor molecules and play a key role in cellular development, tissue homeostasis, and other critical biological functions. Since direct measurement of CCIs is challenging, multiple methods have been developed to infer CCIs by quantifying correlations between the gene expression of the ligands and receptors that mediate CCIs, originally from bulk RNA-sequencing data and more recently from single-cell or spatially resolved transcriptomics (SRT) data. SRT has a particular advantage over single-cell approaches, since ligand-receptor correlations can be computed between cells or spots that are physically close in the tissue. However, the transcript counts of individual ligands and receptors in SRT data are generally low, complicating the inference of CCIs from expression correlations. RESULTS We introduce Copulacci, a count-based model for inferring CCIs from SRT data. Copulacci uses a Gaussian copula to model dependencies between the expression of ligands and receptors from nearby spatial locations even when the transcript counts are low. On simulated data, Copulacci outperforms existing CCI inference methods based on the standard Spearman and Pearson correlation coefficients. Using several real SRT datasets, we show that Copulacci discovers biologically meaningful ligand-receptor interactions that are lowly expressed and undiscoverable by existing CCI inference methods. AVAILABILITY AND IMPLEMENTATION Copulacci is implemented in Python and available at https://github.com/raphael-group/copulacci.
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Affiliation(s)
- Hirak Sarkar
- Department of Computer Science, Princeton University, Princeton, NJ, 08540, United States
- Ludwig Cancer Institute, Princeton Branch, Princeton University, Princeton, NJ, 08540, United States
| | - Uthsav Chitra
- Department of Computer Science, Princeton University, Princeton, NJ, 08540, United States
| | - Julian Gold
- Department of Computer Science, Princeton University, Princeton, NJ, 08540, United States
- Center for Statistics and Machine Learning, Princeton University, Princeton, NJ, 08540, United States
| | - Benjamin J Raphael
- Department of Computer Science, Princeton University, Princeton, NJ, 08540, United States
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5
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Qian J, Bao H, Shao X, Fang Y, Liao J, Chen Z, Li C, Guo W, Hu Y, Li A, Yao Y, Fan X, Cheng Y. Simulating multiple variability in spatially resolved transcriptomics with scCube. Nat Commun 2024; 15:5021. [PMID: 38866768 PMCID: PMC11169532 DOI: 10.1038/s41467-024-49445-0] [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: 09/28/2023] [Accepted: 06/03/2024] [Indexed: 06/14/2024] Open
Abstract
A pressing challenge in spatially resolved transcriptomics (SRT) is to benchmark the computational methods. A widely-used approach involves utilizing simulated data. However, biases exist in terms of the currently available simulated SRT data, which seriously affects the accuracy of method evaluation and validation. Herein, we present scCube ( https://github.com/ZJUFanLab/scCube ), a Python package for independent, reproducible, and technology-diverse simulation of SRT data. scCube not only enables the preservation of spatial expression patterns of genes in reference-based simulations, but also generates simulated data with different spatial variability (covering the spatial pattern type, the resolution, the spot arrangement, the targeted gene type, and the tissue slice dimension, etc.) in reference-free simulations. We comprehensively benchmark scCube with existing single-cell or SRT simulators, and demonstrate the utility of scCube in benchmarking spot deconvolution, gene imputation, and resolution enhancement methods in detail through three applications.
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Affiliation(s)
- Jingyang Qian
- College of Pharmaceutical Sciences, Zhejiang University, Hangzhou, 310058, China
- National Key Laboratory of Chinese Medicine Modernization, Innovation Center of Yangtze River Delta, Zhejiang University, 314100, Jiaxing, China
| | - Hudong Bao
- College of Pharmaceutical Sciences, Zhejiang University, Hangzhou, 310058, China
| | - Xin Shao
- College of Pharmaceutical Sciences, Zhejiang University, Hangzhou, 310058, China
- National Key Laboratory of Chinese Medicine Modernization, Innovation Center of Yangtze River Delta, Zhejiang University, 314100, Jiaxing, China
| | - Yin Fang
- College of Computer Science and Technology, Zhejiang University, Hangzhou, 310013, China
| | - Jie Liao
- College of Pharmaceutical Sciences, Zhejiang University, Hangzhou, 310058, China
- National Key Laboratory of Chinese Medicine Modernization, Innovation Center of Yangtze River Delta, Zhejiang University, 314100, Jiaxing, China
| | - Zhuo Chen
- College of Computer Science and Technology, Zhejiang University, Hangzhou, 310013, China
| | - Chengyu Li
- College of Pharmaceutical Sciences, Zhejiang University, Hangzhou, 310058, China
- National Key Laboratory of Chinese Medicine Modernization, Innovation Center of Yangtze River Delta, Zhejiang University, 314100, Jiaxing, China
| | - Wenbo Guo
- College of Pharmaceutical Sciences, Zhejiang University, Hangzhou, 310058, China
- National Key Laboratory of Chinese Medicine Modernization, Innovation Center of Yangtze River Delta, Zhejiang University, 314100, Jiaxing, China
| | - Yining Hu
- College of Pharmaceutical Sciences, Zhejiang University, Hangzhou, 310058, China
- National Key Laboratory of Chinese Medicine Modernization, Innovation Center of Yangtze River Delta, Zhejiang University, 314100, Jiaxing, China
| | - Anyao Li
- College of Pharmaceutical Sciences, Zhejiang University, Hangzhou, 310058, China
- National Key Laboratory of Chinese Medicine Modernization, Innovation Center of Yangtze River Delta, Zhejiang University, 314100, Jiaxing, China
| | - Yue Yao
- College of Pharmaceutical Sciences, Zhejiang University, Hangzhou, 310058, China
- National Key Laboratory of Chinese Medicine Modernization, Innovation Center of Yangtze River Delta, Zhejiang University, 314100, Jiaxing, China
| | - Xiaohui Fan
- College of Pharmaceutical Sciences, Zhejiang University, Hangzhou, 310058, China.
- National Key Laboratory of Chinese Medicine Modernization, Innovation Center of Yangtze River Delta, Zhejiang University, 314100, Jiaxing, China.
- Zhejiang Key Laboratory of Precision Diagnosis and Therapy for Major Gynecological Diseases, Women's Hospital, Zhejiang University School of Medicine, Hangzhou, 310006, China.
| | - Yiyu Cheng
- College of Pharmaceutical Sciences, Zhejiang University, Hangzhou, 310058, China.
- National Key Laboratory of Chinese Medicine Modernization, Innovation Center of Yangtze River Delta, Zhejiang University, 314100, Jiaxing, China.
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6
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Armingol E, Baghdassarian HM, Lewis NE. The diversification of methods for studying cell-cell interactions and communication. Nat Rev Genet 2024; 25:381-400. [PMID: 38238518 PMCID: PMC11139546 DOI: 10.1038/s41576-023-00685-8] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 12/01/2023] [Indexed: 05/20/2024]
Abstract
No cell lives in a vacuum, and the molecular interactions between cells define most phenotypes. Transcriptomics provides rich information to infer cell-cell interactions and communication, thus accelerating the discovery of the roles of cells within their communities. Such research relies heavily on algorithms that infer which cells are interacting and the ligands and receptors involved. Specific pressures on different research niches are driving the evolution of next-generation computational tools, enabling new conceptual opportunities and technological advances. More sophisticated algorithms now account for the heterogeneity and spatial organization of cells, multiple ligand types and intracellular signalling events, and enable the use of larger and more complex datasets, including single-cell and spatial transcriptomics. Similarly, new high-throughput experimental methods are increasing the number and resolution of interactions that can be analysed simultaneously. Here, we explore recent progress in cell-cell interaction research and highlight the diversification of the next generation of tools, which have yielded a rich ecosystem of tools for different applications and are enabling invaluable discoveries.
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Affiliation(s)
- Erick Armingol
- Bioinformatics and Systems Biology Graduate Program, University of California, San Diego, La Jolla, CA, USA.
- Department of Paediatrics, University of California, San Diego, La Jolla, CA, USA.
| | - Hratch M Baghdassarian
- Bioinformatics and Systems Biology Graduate Program, University of California, San Diego, La Jolla, CA, USA
- Department of Paediatrics, University of California, San Diego, La Jolla, CA, USA
| | - Nathan E Lewis
- Department of Paediatrics, University of California, San Diego, La Jolla, CA, USA.
- Department of Bioengineering, University of California, San Diego, La Jolla, CA, USA.
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7
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Feng J, Song H, Province M, Li G, Payne PRO, Chen Y, Li F. PathFinder: a novel graph transformer model to infer multi-cell intra- and inter-cellular signaling pathways and communications. Front Cell Neurosci 2024; 18:1369242. [PMID: 38846640 PMCID: PMC11155453 DOI: 10.3389/fncel.2024.1369242] [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: 01/11/2024] [Accepted: 04/30/2024] [Indexed: 06/09/2024] Open
Abstract
Recently, large-scale scRNA-seq datasets have been generated to understand the complex signaling mechanisms within the microenvironment of Alzheimer's Disease (AD), which are critical for identifying novel therapeutic targets and precision medicine. However, the background signaling networks are highly complex and interactive. It remains challenging to infer the core intra- and inter-multi-cell signaling communication networks using scRNA-seq data. In this study, we introduced a novel graph transformer model, PathFinder, to infer multi-cell intra- and inter-cellular signaling pathways and communications among multi-cell types. Compared with existing models, the novel and unique design of PathFinder is based on the divide-and-conquer strategy. This model divides complex signaling networks into signaling paths, which are then scored and ranked using a novel graph transformer architecture to infer intra- and inter-cell signaling communications. We evaluated the performance of PathFinder using two scRNA-seq data cohorts. The first cohort is an APOE4 genotype-specific AD, and the second is a human cirrhosis cohort. The evaluation confirms the promising potential of using PathFinder as a general signaling network inference model.
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Affiliation(s)
- Jiarui Feng
- Institute for Informatics (I2), Washington University School of Medicine, Washington University in St. Louis, St. Louis, MO, United States
- Department of Computer Science and Engineering, Washington University in St. Louis, St. Louis, MO, United States
| | - Haoran Song
- Institute for Informatics (I2), Washington University School of Medicine, Washington University in St. Louis, St. Louis, MO, United States
- Department of Computer Science and Engineering, Washington University in St. Louis, St. Louis, MO, United States
| | - Michael Province
- Division of Statistical Genomics, Department of Genetics, Washington University in St. Louis, St. Louis, MO, United States
| | - Guangfu Li
- Department of Surgery, University of Missouri-Columbia, Columbia, MO, United States
- Department of Molecular Microbiology and Immunology, University of Missouri-Columbia, Columbia, MO, United States
- NextGen Precision Health Institute, University of Missouri-Columbia, Columbia, MO, United States
| | - Philip R. O. Payne
- Institute for Informatics (I2), Washington University School of Medicine, Washington University in St. Louis, St. Louis, MO, United States
| | - Yixin Chen
- Department of Computer Science and Engineering, Washington University in St. Louis, St. Louis, MO, United States
| | - Fuhai Li
- Institute for Informatics (I2), Washington University School of Medicine, Washington University in St. Louis, St. Louis, MO, United States
- Department of Pediatrics, Washington University School of Medicine, Washington University in St. Louis, St. Louis, MO, United States
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8
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Pavlicev M, Wagner GP. Reading the palimpsest of cell interactions: What questions may we ask of the data? iScience 2024; 27:109670. [PMID: 38665209 PMCID: PMC11043885 DOI: 10.1016/j.isci.2024.109670] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 04/28/2024] Open
Abstract
Biological function depends on the composition and structure of the organism, the latter describing the organization of interactions between parts. While cells in multicellular organisms are capable of a remarkable degree of autonomy, most functions do require cell communication: the coordination of functions (growth, differentiation, and apoptosis), the compartmentalization of cellular processes, and the integration of cells into higher levels of structural organization. A wealth of data on putative cell interactions has become available, yet its biological interpretation depends on our expectations about the structure of interaction networks. Here, we attempt to formulate basic questions to ask when interpreting cell interaction data. We build on the understanding that cells fulfill two general functions: the integrity-maintaining and the organismal service function. We derive the expected patterns of cell interactions considering two intertwined aspects: the functional and the evolutionary. Based on these, we propose guidelines for analysis and interpretation of transcriptional cell-interactome data.
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Affiliation(s)
- Mihaela Pavlicev
- Unit for Theoretical Biology, Department for Evolutionary Biology, University of Vienna, Vienna 1030, Austria
- Complexity Science Hub, Vienna 1090, Austria
| | - Günter P. Wagner
- Unit for Theoretical Biology, Department for Evolutionary Biology, University of Vienna, Vienna 1030, Austria
- Yale University, New Haven, CT 06520, USA
- Texas A&M University, College Station, TX 77843, USA
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9
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Nathans JF, Ayers JL, Shendure J, Simpson CL. Genetic Tools for Cell Lineage Tracing and Profiling Developmental Trajectories in the Skin. J Invest Dermatol 2024; 144:936-949. [PMID: 38643988 PMCID: PMC11034889 DOI: 10.1016/j.jid.2024.02.006] [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: 12/19/2023] [Revised: 01/28/2024] [Accepted: 02/08/2024] [Indexed: 04/23/2024]
Abstract
The epidermis is the body's first line of protection against dehydration and pathogens, continually regenerating the outermost protective skin layers throughout life. During both embryonic development and wound healing, epidermal stem and progenitor cells must respond to external stimuli and insults to build, maintain, and repair the cutaneous barrier. Recent advances in CRISPR-based methods for cell lineage tracing have remarkably expanded the potential for experiments that track stem and progenitor cell proliferation and differentiation over the course of tissue and even organismal development. Additional tools for DNA-based recording of cellular signaling cues promise to deepen our understanding of the mechanisms driving normal skin morphogenesis and response to stressors as well as the dysregulation of cell proliferation and differentiation in skin diseases and cancer. In this review, we highlight cutting-edge methods for cell lineage tracing, including in organoids and model organisms, and explore how cutaneous biology researchers might leverage these techniques to elucidate the developmental programs that support the regenerative capacity and plasticity of the skin.
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Affiliation(s)
- Jenny F Nathans
- Medical Scientist Training Program, University of Washington, Seattle, Washington, USA; Department of Genome Sciences, University of Washington, Seattle, Washington, USA
| | - Jessica L Ayers
- Molecular Medicine and Mechanisms of Disease PhD Program, Department of Laboratory Medicine and Pathology, University of Washington, Seattle, Washington, USA; Department of Dermatology, University of Washington, Seattle, Washington, USA
| | - Jay Shendure
- Department of Genome Sciences, University of Washington, Seattle, Washington, USA; Institute for Stem Cell & Regenerative Medicine, University of Washington, Seattle, Washington, USA
| | - Cory L Simpson
- Department of Dermatology, University of Washington, Seattle, Washington, USA; Institute for Stem Cell & Regenerative Medicine, University of Washington, Seattle, Washington, USA.
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10
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Konecny AJ, Huang Y, Setty M, Prlic M. Signals that control MAIT cell function in healthy and inflamed human tissues. Immunol Rev 2024; 323:138-149. [PMID: 38520075 DOI: 10.1111/imr.13325] [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] [Indexed: 03/25/2024]
Abstract
Mucosal-associated invariant T (MAIT) cells have a semi-invariant T-cell receptor that allows recognition of antigen in the context of the MHC class I-related (MR1) protein. Metabolic intermediates of the riboflavin synthesis pathway have been identified as MR1-restricted antigens with agonist properties. As riboflavin synthesis occurs in many bacterial species, but not human cells, it has been proposed that the main purpose of MAIT cells is antibacterial surveillance and protection. The majority of human MAIT cells secrete interferon-gamma (IFNg) upon activation, while some MAIT cells in tissues can also express IL-17. Given that MAIT cells are present in human barrier tissues colonized by a microbiome, MAIT cells must somehow be able to distinguish colonization from infection to ensure effector functions are only elicited when necessary. Importantly, MAIT cells have additional functional properties, including the potential to contribute to restoring tissue homeostasis by expression of CTLA-4 and secretion of the cytokine IL-22. A recent study provided compelling data indicating that the range of human MAIT cell functional properties is explained by plasticity rather than distinct lineages. This further underscores the necessity to better understand how different signals regulate MAIT cell function. In this review, we highlight what is known in regards to activating and inhibitory signals for MAIT cells with a specific focus on signals relevant to healthy and inflamed tissues. We consider the quantity, quality, and the temporal order of these signals on MAIT cell function and discuss the current limitations of computational tools to extrapolate which signals are received by MAIT cells in human tissues. Using lessons learned from conventional CD8 T cells, we also discuss how TCR signals may integrate with cytokine signals in MAIT cells to elicit distinct functional states.
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Affiliation(s)
- Andrew J Konecny
- Vaccine and Infectious Disease Division, Fred Hutchinson Cancer Center, Seattle, Washington, USA
- Department of Immunology, University of Washington, Seattle, Washington, USA
| | - Yin Huang
- Basic Sciences Division, Fred Hutchinson Cancer Center, Seattle, Washington, USA
- Herbold Computational Biology Program, Public Health Sciences Division, Fred Hutchinson Cancer Center, Seattle, Washington, USA
- Molecular and Cellular Biology Program, University of Washington, Seattle, Washington, USA
| | - Manu Setty
- Basic Sciences Division, Fred Hutchinson Cancer Center, Seattle, Washington, USA
- Herbold Computational Biology Program, Public Health Sciences Division, Fred Hutchinson Cancer Center, Seattle, Washington, USA
| | - Martin Prlic
- Vaccine and Infectious Disease Division, Fred Hutchinson Cancer Center, Seattle, Washington, USA
- Department of Immunology, University of Washington, Seattle, Washington, USA
- Department of Global Health, University of Washington, Seattle, Washington, USA
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11
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Zhou L, Wang X, Peng L, Chen M, Wen H. SEnSCA: Identifying possible ligand-receptor interactions and its application in cell-cell communication inference. J Cell Mol Med 2024; 28:e18372. [PMID: 38747737 PMCID: PMC11095317 DOI: 10.1111/jcmm.18372] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/06/2024] [Revised: 04/10/2024] [Accepted: 04/18/2024] [Indexed: 05/18/2024] Open
Abstract
Multicellular organisms have dense affinity with the coordination of cellular activities, which severely depend on communication across diverse cell types. Cell-cell communication (CCC) is often mediated via ligand-receptor interactions (LRIs). Existing CCC inference methods are limited to known LRIs. To address this problem, we developed a comprehensive CCC analysis tool SEnSCA by integrating single cell RNA sequencing and proteome data. SEnSCA mainly contains potential LRI acquisition and CCC strength evaluation. For acquiring potential LRIs, it first extracts LRI features and reduces the feature dimension, subsequently constructs negative LRI samples through K-means clustering, finally acquires potential LRIs based on Stacking ensemble comprising support vector machine, 1D-convolutional neural networks and multi-head attention mechanism. During CCC strength evaluation, SEnSCA conducts LRI filtering and then infers CCC by combining the three-point estimation approach and single cell RNA sequencing data. SEnSCA computed better precision, recall, accuracy, F1 score, AUC and AUPR under most of conditions when predicting possible LRIs. To better illustrate the inferred CCC network, SEnSCA provided three visualization options: heatmap, bubble diagram and network diagram. Its application on human melanoma tissue demonstrated its reliability in CCC detection. In summary, SEnSCA offers a useful CCC inference tool and is freely available at https://github.com/plhhnu/SEnSCA.
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Affiliation(s)
- Liqian Zhou
- School of Life Sciences and ChemistryHunan University of TechnologyHunanChina
| | - Xiwen Wang
- School of Life Sciences and ChemistryHunan University of TechnologyHunanChina
| | - Lihong Peng
- School of Life Sciences and ChemistryHunan University of TechnologyHunanChina
| | - Min Chen
- School of Computer ScienceHunan Institute of TechnologyHengyangChina
| | - Hong Wen
- School of Computer ScienceHunan University of TechnologyHunanChina
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12
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Tian J, Bai X, Quek C. Single-Cell Informatics for Tumor Microenvironment and Immunotherapy. Int J Mol Sci 2024; 25:4485. [PMID: 38674070 PMCID: PMC11050520 DOI: 10.3390/ijms25084485] [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: 03/08/2024] [Revised: 04/12/2024] [Accepted: 04/16/2024] [Indexed: 04/28/2024] Open
Abstract
Cancer comprises malignant cells surrounded by the tumor microenvironment (TME), a dynamic ecosystem composed of heterogeneous cell populations that exert unique influences on tumor development. The immune community within the TME plays a substantial role in tumorigenesis and tumor evolution. The innate and adaptive immune cells "talk" to the tumor through ligand-receptor interactions and signaling molecules, forming a complex communication network to influence the cellular and molecular basis of cancer. Such intricate intratumoral immune composition and interactions foster the application of immunotherapies, which empower the immune system against cancer to elicit durable long-term responses in cancer patients. Single-cell technologies have allowed for the dissection and characterization of the TME to an unprecedented level, while recent advancements in bioinformatics tools have expanded the horizon and depth of high-dimensional single-cell data analysis. This review will unravel the intertwined networks between malignancy and immunity, explore the utilization of computational tools for a deeper understanding of tumor-immune communications, and discuss the application of these approaches to aid in diagnosis or treatment decision making in the clinical setting, as well as the current challenges faced by the researchers with their potential future improvements.
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Affiliation(s)
| | | | - Camelia Quek
- Faculty of Medicine and Health, The University of Sydney, Sydney, NSW 2006, Australia; (J.T.); (X.B.)
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13
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Yuan Q, Duren Z. Inferring gene regulatory networks from single-cell multiome data using atlas-scale external data. Nat Biotechnol 2024:10.1038/s41587-024-02182-7. [PMID: 38609714 DOI: 10.1038/s41587-024-02182-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/04/2023] [Accepted: 02/26/2024] [Indexed: 04/14/2024]
Abstract
Existing methods for gene regulatory network (GRN) inference rely on gene expression data alone or on lower resolution bulk data. Despite the recent integration of chromatin accessibility and RNA sequencing data, learning complex mechanisms from limited independent data points still presents a daunting challenge. Here we present LINGER (Lifelong neural network for gene regulation), a machine-learning method to infer GRNs from single-cell paired gene expression and chromatin accessibility data. LINGER incorporates atlas-scale external bulk data across diverse cellular contexts and prior knowledge of transcription factor motifs as a manifold regularization. LINGER achieves a fourfold to sevenfold relative increase in accuracy over existing methods and reveals a complex regulatory landscape of genome-wide association studies, enabling enhanced interpretation of disease-associated variants and genes. Following the GRN inference from reference single-cell multiome data, LINGER enables the estimation of transcription factor activity solely from bulk or single-cell gene expression data, leveraging the abundance of available gene expression data to identify driver regulators from case-control studies.
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Affiliation(s)
- Qiuyue Yuan
- Center for Human Genetics, Department of Genetics and Biochemistry, Clemson University, Greenwood, SC, USA
| | - Zhana Duren
- Center for Human Genetics, Department of Genetics and Biochemistry, Clemson University, Greenwood, SC, USA.
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14
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Li R, Chen X, Yang X. Navigating the landscapes of spatial transcriptomics: How computational methods guide the way. WILEY INTERDISCIPLINARY REVIEWS. RNA 2024; 15:e1839. [PMID: 38527900 DOI: 10.1002/wrna.1839] [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: 11/23/2023] [Revised: 02/24/2024] [Accepted: 03/04/2024] [Indexed: 03/27/2024]
Abstract
Spatially resolved transcriptomics has been dramatically transforming biological and medical research in various fields. It enables transcriptome profiling at single-cell, multi-cellular, or sub-cellular resolution, while retaining the information of geometric localizations of cells in complex tissues. The coupling of cell spatial information and its molecular characteristics generates a novel multi-modal high-throughput data source, which poses new challenges for the development of analytical methods for data-mining. Spatial transcriptomic data are often highly complex, noisy, and biased, presenting a series of difficulties, many unresolved, for data analysis and generation of biological insights. In addition, to keep pace with the ever-evolving spatial transcriptomic experimental technologies, the existing analytical theories and tools need to be updated and reformed accordingly. In this review, we provide an overview and discussion of the current computational approaches for mining of spatial transcriptomics data. Future directions and perspectives of methodology design are proposed to stimulate further discussions and advances in new analytical models and algorithms. This article is categorized under: RNA Methods > RNA Analyses in Cells RNA Evolution and Genomics > Computational Analyses of RNA RNA Export and Localization > RNA Localization.
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Affiliation(s)
- Runze Li
- MOE Key Laboratory of Bioinformatics, Center for Synthetic & Systems Biology, School of Life Sciences, Tsinghua University, Beijing, China
| | - Xu Chen
- MOE Key Laboratory of Bioinformatics, Center for Synthetic & Systems Biology, School of Life Sciences, Tsinghua University, Beijing, China
| | - Xuerui Yang
- MOE Key Laboratory of Bioinformatics, Center for Synthetic & Systems Biology, School of Life Sciences, Tsinghua University, Beijing, China
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15
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Peng L, Gao P, Xiong W, Li Z, Chen X. Identifying potential ligand-receptor interactions based on gradient boosted neural network and interpretable boosting machine for intercellular communication analysis. Comput Biol Med 2024; 171:108110. [PMID: 38367445 DOI: 10.1016/j.compbiomed.2024.108110] [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: 10/30/2023] [Revised: 01/24/2024] [Accepted: 02/04/2024] [Indexed: 02/19/2024]
Abstract
Cell-cell communication is essential to many key biological processes. Intercellular communication is generally mediated by ligand-receptor interactions (LRIs). Thus, building a comprehensive and high-quality LRI resource can significantly improve intercellular communication analysis. Meantime, due to lack of a "gold standard" dataset, it remains a challenge to evaluate LRI-mediated intercellular communication results. Here, we introduce CellGiQ, a high-confident LRI prediction framework for intercellular communication analysis. Highly confident LRIs are first inferred by LRI feature extraction with BioTriangle, LRI selection using LightGBM, and LRI classification based on ensemble of gradient boosted neural network and interpretable boosting machine. Subsequently, known and identified high-confident LRIs are filtered by combining single-cell RNA sequencing (scRNA-seq) data and further applied to intercellular communication inference through a quartile scoring strategy. To validation the predictions, CellGiQ exploited several evaluation strategies: using AUC and AUPR, it surpassed six competing LRI prediction models on four LRI datasets; through Venn diagrams and molecular docking, its predicted LRIs were validated by five other popular intercellular communication inference methods; based on the overlapping LRIs, it computed high Jaccard index with six other state-of-the-art intercellular communication prediction tools within human HNSCC tissues; by comparing with classical models and literature retrieve, its inferred HNSCC-related intercellular communication results was further validated. The novelty of this study is to identify high-confident LRIs based on machine learning as well as design several LRI validation ways, providing reference for computational LRI prediction. CellGiQ provides an open-source and useful tool to decompose LRI-mediated intercellular communication at single cell resolution. CellGiQ is freely available at https://github.com/plhhnu/CellGiQ.
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Affiliation(s)
- Lihong Peng
- College of Life Science and Chemistry, Hunan University of Technology, Zhuzhou, 412007, Hunan, China
| | - Pengfei Gao
- College of Life Science and Chemistry, Hunan University of Technology, Zhuzhou, 412007, Hunan, China
| | - Wei Xiong
- College of Life Science and Chemistry, Hunan University of Technology, Zhuzhou, 412007, Hunan, China
| | - Zejun Li
- School of Computer Science and Engineering, Hunan Institute of Technology, Hengyang, 421002, Hunan, China.
| | - Xing Chen
- School of Science, Jiangnan University, Wuxi, 214122, Jiangsu, China.
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16
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Sharma V, Singh A, Chauhan S, Sharma PK, Chaudhary S, Sharma A, Porwal O, Fuloria NK. Role of Artificial Intelligence in Drug Discovery and Target Identification in Cancer. Curr Drug Deliv 2024; 21:870-886. [PMID: 37670704 DOI: 10.2174/1567201821666230905090621] [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: 10/31/2022] [Revised: 03/08/2023] [Accepted: 03/24/2023] [Indexed: 09/07/2023]
Abstract
Drug discovery and development (DDD) is a highly complex process that necessitates precise monitoring and extensive data analysis at each stage. Furthermore, the DDD process is both timeconsuming and costly. To tackle these concerns, artificial intelligence (AI) technology can be used, which facilitates rapid and precise analysis of extensive datasets within a limited timeframe. The pathophysiology of cancer disease is complicated and requires extensive research for novel drug discovery and development. The first stage in the process of drug discovery and development involves identifying targets. Cell structure and molecular functioning are complex due to the vast number of molecules that function constantly, performing various roles. Furthermore, scientists are continually discovering novel cellular mechanisms and molecules, expanding the range of potential targets. Accurately identifying the correct target is a crucial step in the preparation of a treatment strategy. Various forms of AI, such as machine learning, neural-based learning, deep learning, and network-based learning, are currently being utilised in applications, online services, and databases. These technologies facilitate the identification and validation of targets, ultimately contributing to the success of projects. This review focuses on the different types and subcategories of AI databases utilised in the field of drug discovery and target identification for cancer.
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Affiliation(s)
- Vishal Sharma
- Department of Pharmacy, Galgotias University, Greater Noida, Uttar Pradesh, 201310, India
| | - Amit Singh
- Department of Pharmacy, Galgotias University, Greater Noida, Uttar Pradesh, 201310, India
| | - Sanjana Chauhan
- Department of Pharmacy, Galgotias University, Greater Noida, Uttar Pradesh, 201310, India
| | - Pramod Kumar Sharma
- Department of Pharmacy, Galgotias University, Greater Noida, Uttar Pradesh, 201310, India
| | - Shubham Chaudhary
- Department of Pharmacy, Galgotias University, Greater Noida, Uttar Pradesh, 201310, India
| | - Astha Sharma
- Department of Pharmacy, Galgotias University, Greater Noida, Uttar Pradesh, 201310, India
| | - Omji Porwal
- Department of Pharmacognosy, Faculty of Pharmacy, Tishk International University, Erbil 44001, Iraq
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17
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Dai Q, Epstein MP, Yang J. STACCato: Supervised Tensor Analysis tool for studying Cell-cell Communication using scRNA-seq data across multiple samples and conditions. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.12.15.571918. [PMID: 38168391 PMCID: PMC10760171 DOI: 10.1101/2023.12.15.571918] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/05/2024]
Abstract
Research on cell-cell communication (CCC) is crucial for understanding biology and diseases. Many existing CCC inference tools neglect potential confounders, such as batch and demographic variables, when analyzing multi-sample, multi-condition scRNA-seq datasets. To address this significant gap, we introduce STACCato, a Supervised Tensor Analysis tool for studying Cell-cell Communication, that identifies CCC events and estimates the effects of biological conditions (e.g., disease status, tissue types) on such events, while adjusting for potential confounders. Application of STACCato to both simulated data and real scRNA-seq data of lupus and autism studies demonstrate that incorporating sample-level variables into CCC inference consistently provides more accurate estimations of disease effects and cell type activity patterns than existing methods that ignore sample-level variables. A computational tool implementing the STACCato framework is available on GitHub.
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Affiliation(s)
- Qile Dai
- Department of Biostatistics and Bioinformatics, Emory University School of Public Health, Atlanta, Georgia 30322, United States of America
- Center for Computational and Quantitative Genetics, Department of Human Genetics, Emory University School of Medicine, Atlanta, Georgia 30322, United States of America
| | - Michael P. Epstein
- Center for Computational and Quantitative Genetics, Department of Human Genetics, Emory University School of Medicine, Atlanta, Georgia 30322, United States of America
| | - Jingjing Yang
- Center for Computational and Quantitative Genetics, Department of Human Genetics, Emory University School of Medicine, Atlanta, Georgia 30322, United States of America
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18
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Tsuyuzaki K, Ishii M, Nikaido I. Sctensor detects many-to-many cell-cell interactions from single cell RNA-sequencing data. BMC Bioinformatics 2023; 24:420. [PMID: 37936079 PMCID: PMC10631077 DOI: 10.1186/s12859-023-05490-y] [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: 07/05/2023] [Accepted: 09/21/2023] [Indexed: 11/09/2023] Open
Abstract
BACKGROUND Complex biological systems are described as a multitude of cell-cell interactions (CCIs). Recent single-cell RNA-sequencing studies focus on CCIs based on ligand-receptor (L-R) gene co-expression but the analytical methods are not appropriate to detect many-to-many CCIs. RESULTS In this work, we propose scTensor, a novel method for extracting representative triadic relationships (or hypergraphs), which include ligand-expression, receptor-expression, and related L-R pairs. CONCLUSIONS Through extensive studies with simulated and empirical datasets, we have shown that scTensor can detect some hypergraphs that cannot be detected using conventional CCI detection methods, especially when they include many-to-many relationships. scTensor is implemented as a freely available R/Bioconductor package.
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Affiliation(s)
- Koki Tsuyuzaki
- Laboratory for Bioinformatics Research RIKEN Center for Biosystems Dynamics Research, 2-1 Hirosawa, Wako, Saitama, 351-0198, Japan.
- Japan Science and Technology Agency, PRESTO, 7 Gobancho, Chiyoda-ku, Tokyo, 102-0076, Japan.
| | - Manabu Ishii
- Laboratory for Bioinformatics Research RIKEN Center for Biosystems Dynamics Research, 2-1 Hirosawa, Wako, Saitama, 351-0198, Japan
| | - Itoshi Nikaido
- Laboratory for Bioinformatics Research RIKEN Center for Biosystems Dynamics Research, 2-1 Hirosawa, Wako, Saitama, 351-0198, Japan.
- Department of Functional Genome Informatics, Division of Biological Data Science, Medical Research Institute, Tokyo Medical and Dental University (TMDU), 1-5-45 Yushima, Bunkyo-ku, Tokyo, 113-8510, Japan.
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19
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Moratalla-Navarro F, Moreno V, Sanz-Pamplona R. TALKIEN: crossTALK IntEraction Network. A web-based tool for deciphering molecular communication through ligand-receptor interactions. Mol Omics 2023; 19:688-696. [PMID: 37403821 DOI: 10.1039/d3mo00049d] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 07/06/2023]
Abstract
Molecular crosstalk, the dialogue between different cell types, is attracting more attention in cancer research. On the one hand, the communication between tumor and non-tumor cells in the microenvironment or between different tumor clones has influential consequences for the progression and spread of tumors and response to treatment. On the other hand, novel techniques such as single-cell sequencing or spatial transcriptomics provide detailed information that needs to be interpreted. TALKIEN: crossTALK IntEraction Network is a simple and intuitive online R/shiny application to visualize molecular crosstalk information through the construction and analysis of a protein-protein interaction network. Taking two or more lists of genes or proteins as input, which are representative of cell lineages, TALKIEN extracts information about ligand-receptor interactions, builds a network and analyzes it using systems biology techniques such as centrality measures and component analysis, among others. Moreover, it expands the network displaying pathways downstream receptors. The application allows users to select different graphical layouts, performs functional analysis and gives information about drugs targeting receptors. In conclusion, TALKIEN allows users to detect ligand-receptor interactions generating new in silico predictions of cell-cell communication thus providing a translational rationale for future experiments. It is freely available at https://www.odap-ico.org/talkien.
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Affiliation(s)
- Ferran Moratalla-Navarro
- Unit of Biomarkers and Susceptibility, Oncology Data Analytics Program (ODAP), Catalan Institute of Oncology (ICO), Colorectal Cancer Group, ONCOBELL Program, Bellvitge Biomedical Research Institute (IDIBELL), L'Hospitalet de Llobregat, Barcelona, Spain
- Centro de Investigación Biomédica en Red de Epidemiologia y Salud Pública (CIBERESP), Spain
- Department of Clinical Sciences, Faculty of Medicine and Health Sciences, University of Barcelona, Barcelona, Spain
| | - Víctor Moreno
- Unit of Biomarkers and Susceptibility, Oncology Data Analytics Program (ODAP), Catalan Institute of Oncology (ICO), Colorectal Cancer Group, ONCOBELL Program, Bellvitge Biomedical Research Institute (IDIBELL), L'Hospitalet de Llobregat, Barcelona, Spain
- Centro de Investigación Biomédica en Red de Epidemiologia y Salud Pública (CIBERESP), Spain
- Department of Clinical Sciences, Faculty of Medicine and Health Sciences, University of Barcelona, Barcelona, Spain
| | - Rebeca Sanz-Pamplona
- Unit of Biomarkers and Susceptibility, Oncology Data Analytics Program (ODAP), Catalan Institute of Oncology (ICO), Colorectal Cancer Group, ONCOBELL Program, Bellvitge Biomedical Research Institute (IDIBELL), L'Hospitalet de Llobregat, Barcelona, Spain
- Centro de Investigación Biomédica en Red de Epidemiologia y Salud Pública (CIBERESP), Spain
- University Hospital Lozano Blesa, Aragon Health Research Institute (IISA), ARAID Foundation, Aragon Government, Zaragoza, Spain.
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20
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Wang X, Almet AA, Nie Q. The promising application of cell-cell interaction analysis in cancer from single-cell and spatial transcriptomics. Semin Cancer Biol 2023; 95:42-51. [PMID: 37454878 PMCID: PMC10627116 DOI: 10.1016/j.semcancer.2023.07.001] [Citation(s) in RCA: 6] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/31/2022] [Revised: 03/02/2023] [Accepted: 07/13/2023] [Indexed: 07/18/2023]
Abstract
Cell-cell interactions instruct cell fate and function. These interactions are hijacked to promote cancer development. Single-cell transcriptomics and spatial transcriptomics have become powerful new tools for researchers to profile the transcriptional landscape of cancer at unparalleled genetic depth. In this review, we discuss the rapidly growing array of computational tools to infer cell-cell interactions from non-spatial single-cell RNA-sequencing and the limited but growing number of methods for spatial transcriptomics data. Downstream analyses of these computational tools and applications to cancer studies are highlighted. We finish by suggesting several directions for further extensions that anticipate the increasing availability of multi-omics cancer data.
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Affiliation(s)
- Xinyi Wang
- Department of Mathematics, University of California, Irvine, Irvine, CA, United States
| | - Axel A Almet
- Department of Mathematics, University of California, Irvine, Irvine, CA, United States; The NSF-Simons Center for Multiscale Cell Fate Research, University of California, Irvine, Irvine, CA, United States.
| | - Qing Nie
- Department of Mathematics, University of California, Irvine, Irvine, CA, United States; The NSF-Simons Center for Multiscale Cell Fate Research, University of California, Irvine, Irvine, CA, United States; Department of Developmental and Cell Biology, University of California, Irvine, Irvine, CA, United States.
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21
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Luo J, Deng M, Zhang X, Sun X. ESICCC as a systematic computational framework for evaluation, selection, and integration of cell-cell communication inference methods. Genome Res 2023; 33:1788-1805. [PMID: 37827697 PMCID: PMC10691505 DOI: 10.1101/gr.278001.123] [Citation(s) in RCA: 6] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/22/2023] [Accepted: 09/21/2023] [Indexed: 10/14/2023]
Abstract
Cell-cell communication (CCC) is critical for determining cell fates and functions in multicellular organisms. With the advent of single-cell RNA-sequencing (scRNA-seq) and spatial transcriptomics (ST), an increasing number of CCC inference methods have been developed. Nevertheless, a thorough comparison of their performances is yet to be conducted. To fill this gap, we developed a systematic benchmark framework called ESICCC to evaluate 18 ligand-receptor (LR) inference methods and five ligand/receptor-target inference methods using a total of 116 data sets, including 15 ST data sets, 15 sets of cell line perturbation data, two sets of cell type-specific expression/proteomics data, and 84 sets of sampled or unsampled scRNA-seq data. We evaluated and compared the agreement, accuracy, robustness, and usability of these methods. Regarding accuracy evaluation, RNAMagnet, CellChat, and scSeqComm emerge as the three best-performing methods for intercellular ligand-receptor inference based on scRNA-seq data, whereas stMLnet and HoloNet are the best methods for predicting ligand/receptor-target regulation using ST data. To facilitate the practical applications, we provide a decision-tree-style guideline for users to easily choose best tools for their specific research concerns in CCC inference, and develop an ensemble pipeline CCCbank that enables versatile combinations of methods and databases. Moreover, our comparative results also uncover several critical influential factors for CCC inference, such as prior interaction information, ligand-receptor scoring algorithm, intracellular signaling complexity, and spatial relationship, which may be considered in the future studies to advance the development of new methodologies.
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Affiliation(s)
- Jiaxin Luo
- Zhongshan School of Medicine, Sun Yat-sen University, Guangzhou 510080, China
- School of Mathematics, Sun Yat-sen University, Guangzhou 510275, China
| | - Minghua Deng
- School of Mathematical Sciences, Peking University, Beijing, 100871, China
| | - Xuegong Zhang
- Bioinformatics Division of BNRIST and Department of Automation, MOE Key Lab of Bioinformatics, Tsinghua University, Beijing, 100084, China
| | - Xiaoqiang Sun
- School of Mathematics, Sun Yat-sen University, Guangzhou 510275, China;
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22
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Li H, Ma T, Hao M, Guo W, Gu J, Zhang X, Wei L. Decoding functional cell-cell communication events by multi-view graph learning on spatial transcriptomics. Brief Bioinform 2023; 24:bbad359. [PMID: 37824741 DOI: 10.1093/bib/bbad359] [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: 07/12/2023] [Revised: 08/25/2023] [Accepted: 09/18/2023] [Indexed: 10/14/2023] Open
Abstract
Cell-cell communication events (CEs) are mediated by multiple ligand-receptor (LR) pairs. Usually only a particular subset of CEs directly works for a specific downstream response in a particular microenvironment. We name them as functional communication events (FCEs) of the target responses. Decoding FCE-target gene relations is: important for understanding the mechanisms of many biological processes, but has been intractable due to the mixing of multiple factors and the lack of direct observations. We developed a method HoloNet for decoding FCEs using spatial transcriptomic data by integrating LR pairs, cell-type spatial distribution and downstream gene expression into a deep learning model. We modeled CEs as a multi-view network, developed an attention-based graph learning method to train the model for generating target gene expression with the CE networks, and decoded the FCEs for specific downstream genes by interpreting trained models. We applied HoloNet on three Visium datasets of breast cancer and liver cancer. The results detangled the multiple factors of FCEs by revealing how LR signals and cell types affect specific biological processes, and specified FCE-induced effects in each single cell. We conducted simulation experiments and showed that HoloNet is more reliable on LR prioritization in comparison with existing methods. HoloNet is a powerful tool to illustrate cell-cell communication landscapes and reveal vital FCEs that shape cellular phenotypes. HoloNet is available as a Python package at https://github.com/lhc17/HoloNet.
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Affiliation(s)
- Haochen Li
- School of Medicine, Tsinghua University, Beijing 100084, China
| | - Tianxing Ma
- MOE Key Lab of Bioinformatics, Bioinformatics Division of BNRIST and Department of Automation, Tsinghua University, Beijing 100084, China
| | - Minsheng Hao
- MOE Key Lab of Bioinformatics, Bioinformatics Division of BNRIST and Department of Automation, Tsinghua University, Beijing 100084, China
| | - Wenbo Guo
- MOE Key Lab of Bioinformatics, Bioinformatics Division of BNRIST and Department of Automation, Tsinghua University, Beijing 100084, China
| | - Jin Gu
- MOE Key Lab of Bioinformatics, Bioinformatics Division of BNRIST and Department of Automation, Tsinghua University, Beijing 100084, China
| | - Xuegong Zhang
- School of Medicine, Tsinghua University, Beijing 100084, China
- MOE Key Lab of Bioinformatics, Bioinformatics Division of BNRIST and Department of Automation, Tsinghua University, Beijing 100084, China
| | - Lei Wei
- MOE Key Lab of Bioinformatics, Bioinformatics Division of BNRIST and Department of Automation, Tsinghua University, Beijing 100084, China
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23
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Zhang C, Hu Y, Gao L. Defining and identifying cell sub-crosstalk pairs for characterizing cell-cell communication patterns. Sci Rep 2023; 13:15746. [PMID: 37735248 PMCID: PMC10514069 DOI: 10.1038/s41598-023-42883-8] [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: 03/13/2023] [Accepted: 09/15/2023] [Indexed: 09/23/2023] Open
Abstract
Current cell-cell communication analysis focuses on quantifying intercellular interactions at cell type level. In the tissue microenvironment, one type of cells could be divided into multiple cell subgroups that function differently and communicate with other cell types or subgroups via different ligand-receptor-mediated signaling pathways. Given two cell types, we define a cell sub-crosstalk pair (CSCP) as a combination of two cell subgroups with strong and similar intercellular crosstalk signals and identify CSCPs based on coupled non-negative matrix factorization. Using single-cell spatial transcriptomics data of mouse olfactory bulb and visual cortex, we find that cells of different types within CSCPs are significantly spatially closer with each other than those in the whole single-cell spatial map. To demonstrate the utility of CSCPs, we apply 13 cell-cell communication analysis methods to sampled single-cell transcriptomics datasets at CSCP level and reveal ligand-receptor interactions masked at cell type level. Furthermore, by analyzing single-cell transcriptomics data from 29 breast cancer patients with different immunotherapy responses, we find that CSCPs are useful predictive features to discriminate patients responding to anti-PD-1 therapy from non-responders. Taken together, partitioning a cell type pair into CSCPs enables fine-grained characterization of cell-cell communication in tissue and tumor microenvironments.
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Affiliation(s)
- Chenxing Zhang
- School of Computer Science and Technology, Xidian University, Xi'an, 710071, China
| | - Yuxuan Hu
- School of Computer Science and Technology, Xidian University, Xi'an, 710071, China
| | - Lin Gao
- School of Computer Science and Technology, Xidian University, Xi'an, 710071, China.
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24
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Li H, Zhang Z, Squires M, Chen X, Zhang X. scMultiSim: simulation of single cell multi-omics and spatial data guided by gene regulatory networks and cell-cell interactions. RESEARCH SQUARE 2023:rs.3.rs-3301625. [PMID: 37790516 PMCID: PMC10543280 DOI: 10.21203/rs.3.rs-3301625/v1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 10/05/2023]
Abstract
Simulated single-cell data is essential for designing and evaluating computational methods in the absence of experimental ground truth. Existing simulators typically focus on modeling one or two specific biological factors or mechanisms that affect the output data, which limits their capacity to simulate the complexity and multi-modality in real data. Here, we present scMultiSim, an in silico simulator that generates multi-modal single-cell data, including gene expression, chromatin accessibility, RNA velocity, and spatial cell locations while accounting for the relationships between modalities. scMultiSim jointly models various biological factors that affect the output data, including cell identity, within-cell gene regulatory networks (GRNs), cell-cell interactions (CCIs), and chromatin accessibility, hile also incorporating technical noises. Moreover, it allows users to adjust each factor's effect easily. We validated scMultiSim's simulated biological effects and demonstrated its applications by benchmarking a wide range of computational tasks, including multi-modal and multi-batch data integration, RNA velocity estimation, GRN inference and CCI inference using spatially resolved gene expression data, many of them were not benchmarked before due to the lack of proper tools. Compared to existing simulators, scMultiSim can benchmark a much broader range of existing computational problems and even new potential tasks.
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Affiliation(s)
- Hechen Li
- Georgia Institute of Technology, Atlanta, USA
| | - Ziqi Zhang
- Georgia Institute of Technology, Atlanta, USA
| | | | - Xi Chen
- Southern University of Science and Technology, Shenzhen, China
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25
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Peng L, Tan J, Xiong W, Zhang L, Wang Z, Yuan R, Li Z, Chen X. Deciphering ligand-receptor-mediated intercellular communication based on ensemble deep learning and the joint scoring strategy from single-cell transcriptomic data. Comput Biol Med 2023; 163:107137. [PMID: 37364528 DOI: 10.1016/j.compbiomed.2023.107137] [Citation(s) in RCA: 17] [Impact Index Per Article: 17.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/26/2023] [Revised: 05/18/2023] [Accepted: 06/04/2023] [Indexed: 06/28/2023]
Abstract
BACKGROUND Cell-cell communication in a tumor microenvironment is vital to tumorigenesis, tumor progression and therapy. Intercellular communication inference helps understand molecular mechanisms of tumor growth, progression and metastasis. METHODS Focusing on ligand-receptor co-expressions, in this study, we developed an ensemble deep learning framework, CellComNet, to decipher ligand-receptor-mediated cell-cell communication from single-cell transcriptomic data. First, credible LRIs are captured by integrating data arrangement, feature extraction, dimension reduction, and LRI classification based on an ensemble of heterogeneous Newton boosting machine and deep neural network. Next, known and identified LRIs are screened based on single-cell RNA sequencing (scRNA-seq) data in certain tissues. Finally, cell-cell communication is inferred by incorporating scRNA-seq data, the screened LRIs, a joint scoring strategy that combines expression thresholding and expression product of ligands and receptors. RESULTS The proposed CellComNet framework was compared with four competing protein-protein interaction prediction models (PIPR, XGBoost, DNNXGB, and OR-RCNN) and obtained the best AUCs and AUPRs on four LRI datasets, elucidating the optimal LRI classification ability. CellComNet was further applied to analyze intercellular communication in human melanoma and head and neck squamous cell carcinoma (HNSCC) tissues. The results demonstrate that cancer-associated fibroblasts highly communicate with melanoma cells and endothelial cells strong communicate with HNSCC cells. CONCLUSIONS The proposed CellComNet framework efficiently identified credible LRIs and significantly improved cell-cell communication inference performance. We anticipate that CellComNet can contribute to anticancer drug design and tumor-targeted therapy.
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Affiliation(s)
- Lihong Peng
- School of Computer Science, Hunan University of Technology, Zhuzhou, 412007, Hunan, China; College of Life Sciences and Chemistry, Hunan University of Technology, Zhuzhou, 412007, Hunan, China
| | - Jingwei Tan
- School of Computer Science, Hunan University of Technology, Zhuzhou, 412007, Hunan, China
| | - Wei Xiong
- School of Computer Science, Hunan University of Technology, Zhuzhou, 412007, Hunan, China
| | - Li Zhang
- School of Information and Control Engineering, China University of Mining and Technology, Xuzhou, 221116, Jiangsu, China
| | - Zhao Wang
- School of Computer Science, Hunan University of Technology, Zhuzhou, 412007, Hunan, China
| | - Ruya Yuan
- School of Computer Science, Hunan University of Technology, Zhuzhou, 412007, Hunan, China
| | - Zejun Li
- School of Computer Science, Hunan Institute of Technology, Hengyang, 421002, Hunan, China.
| | - Xing Chen
- School of Science, Jiangnan University, Wuxi, 214122, Jiangsu, China.
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26
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Yuan Q, Duren Z. Continuous lifelong learning for modeling of gene regulation from single cell multiome data by leveraging atlas-scale external data. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.08.01.551575. [PMID: 37577525 PMCID: PMC10418251 DOI: 10.1101/2023.08.01.551575] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 08/15/2023]
Abstract
Accurate context-specific Gene Regulatory Networks (GRNs) inference from genomics data is a crucial task in computational biology. However, existing methods face limitations, such as reliance on gene expression data alone, lower resolution from bulk data, and data scarcity for specific cellular systems. Despite recent technological advancements, including single-cell sequencing and the integration of ATAC-seq and RNA-seq data, learning such complex mechanisms from limited independent data points still presents a daunting challenge, impeding GRN inference accuracy. To overcome this challenge, we present LINGER (LIfelong neural Network for GEne Regulation), a novel deep learning-based method to infer GRNs from single-cell multiome data with paired gene expression and chromatin accessibility data from the same cell. LINGER incorporates both 1) atlas-scale external bulk data across diverse cellular contexts and 2) the knowledge of transcription factor (TF) motif matching to cis-regulatory elements as a manifold regularization to address the challenge of limited data and extensive parameter space in GRN inference. Our results demonstrate that LINGER achieves 2-3 fold higher accuracy over existing methods. LINGER reveals a complex regulatory landscape of genome-wide association studies, enabling enhanced interpretation of disease-associated variants and genes. Additionally, following the GRN inference from a reference sc-multiome data, LINGER allows for the estimation of TF activity solely from bulk or single-cell gene expression data, leveraging the abundance of available gene expression data to identify driver regulators from case-control studies. Overall, LINGER provides a comprehensive tool for robust gene regulation inference from genomics data, empowering deeper insights into cellular mechanisms.
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Affiliation(s)
- Qiuyue Yuan
- Center for Human Genetics, Department of Genetics and Biochemistry, Clemson University, Greenwood, SC 29646, USA
| | - Zhana Duren
- Center for Human Genetics, Department of Genetics and Biochemistry, Clemson University, Greenwood, SC 29646, USA
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27
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Xie Z, Li X, Mora A. A Comparison of Cell-Cell Interaction Prediction Tools Based on scRNA-seq Data. Biomolecules 2023; 13:1211. [PMID: 37627276 PMCID: PMC10452151 DOI: 10.3390/biom13081211] [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: 06/18/2023] [Revised: 07/29/2023] [Accepted: 07/31/2023] [Indexed: 08/27/2023] Open
Abstract
Computational prediction of cell-cell interactions (CCIs) is becoming increasingly important for understanding disease development and progression. We present a benchmark study of available CCI prediction tools based on single-cell RNA sequencing (scRNA-seq) data. By comparing prediction outputs with a manually curated gold standard for idiopathic pulmonary fibrosis (IPF), we evaluated prediction performance and processing time of several CCI prediction tools, including CCInx, CellChat, CellPhoneDB, iTALK, NATMI, scMLnet, SingleCellSignalR, and an ensemble of tools. According to our results, CellPhoneDB and NATMI are the best performer CCI prediction tools, among the ones analyzed, when we define a CCI as a source-target-ligand-receptor tetrad. In addition, we recommend specific tools according to different types of research projects and discuss the possible future paths in the field.
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Affiliation(s)
- Zihong Xie
- Joint School of Life Sciences, Guangzhou Medical University and Guangzhou Institutes of Biomedicine and Health (Chinese Academy of Sciences), Guangzhou 511436, China;
| | - Xuri Li
- State Key Laboratory of Ophthalmology, Zhongshan Ophthalmic Center, Sun Yat-Sen University, Guangdong Provincial Key Laboratory of Ophthalmology and Visual Science, Guangzhou 510060, China
| | - Antonio Mora
- Joint School of Life Sciences, Guangzhou Medical University and Guangzhou Institutes of Biomedicine and Health (Chinese Academy of Sciences), Guangzhou 511436, China;
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28
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Marku M, Pancaldi V. From time-series transcriptomics to gene regulatory networks: A review on inference methods. PLoS Comput Biol 2023; 19:e1011254. [PMID: 37561790 PMCID: PMC10414591 DOI: 10.1371/journal.pcbi.1011254] [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] [Indexed: 08/12/2023] Open
Abstract
Inference of gene regulatory networks has been an active area of research for around 20 years, leading to the development of sophisticated inference algorithms based on a variety of assumptions and approaches. With the ever increasing demand for more accurate and powerful models, the inference problem remains of broad scientific interest. The abstract representation of biological systems through gene regulatory networks represents a powerful method to study such systems, encoding different amounts and types of information. In this review, we summarize the different types of inference algorithms specifically based on time-series transcriptomics, giving an overview of the main applications of gene regulatory networks in computational biology. This review is intended to give an updated reference of regulatory networks inference tools to biologists and researchers new to the topic and guide them in selecting the appropriate inference method that best fits their questions, aims, and experimental data.
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Affiliation(s)
- Malvina Marku
- CRCT, Université de Toulouse, Inserm, CNRS, Université Toulouse III-Paul Sabatier, Centre de Recherches en Cancérologie de Toulouse, Toulouse, France
| | - Vera Pancaldi
- CRCT, Université de Toulouse, Inserm, CNRS, Université Toulouse III-Paul Sabatier, Centre de Recherches en Cancérologie de Toulouse, Toulouse, France
- Barcelona Supercomputing Center, Barcelona, Spain
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29
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Heumos L, Schaar AC, Lance C, Litinetskaya A, Drost F, Zappia L, Lücken MD, Strobl DC, Henao J, Curion F, Schiller HB, Theis FJ. Best practices for single-cell analysis across modalities. Nat Rev Genet 2023; 24:550-572. [PMID: 37002403 PMCID: PMC10066026 DOI: 10.1038/s41576-023-00586-w] [Citation(s) in RCA: 161] [Impact Index Per Article: 161.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 02/14/2023] [Indexed: 04/03/2023]
Abstract
Recent advances in single-cell technologies have enabled high-throughput molecular profiling of cells across modalities and locations. Single-cell transcriptomics data can now be complemented by chromatin accessibility, surface protein expression, adaptive immune receptor repertoire profiling and spatial information. The increasing availability of single-cell data across modalities has motivated the development of novel computational methods to help analysts derive biological insights. As the field grows, it becomes increasingly difficult to navigate the vast landscape of tools and analysis steps. Here, we summarize independent benchmarking studies of unimodal and multimodal single-cell analysis across modalities to suggest comprehensive best-practice workflows for the most common analysis steps. Where independent benchmarks are not available, we review and contrast popular methods. Our article serves as an entry point for novices in the field of single-cell (multi-)omic analysis and guides advanced users to the most recent best practices.
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Affiliation(s)
- Lukas Heumos
- Institute of Computational Biology, Department of Computational Health, Helmholtz Munich, Munich, Germany
- Institute of Lung Health and Immunity and Comprehensive Pneumology Center, Helmholtz Munich; Member of the German Center for Lung Research (DZL), Munich, Germany
- TUM School of Life Sciences Weihenstephan, Technical University of Munich, Munich, Germany
| | - Anna C Schaar
- Institute of Computational Biology, Department of Computational Health, Helmholtz Munich, Munich, Germany
- Department of Mathematics, School of Computation, Information and Technology, Technical University of Munich, Garching, Germany
- Munich Center for Machine Learning, Technical University of Munich, Garching, Germany
| | - Christopher Lance
- Institute of Computational Biology, Department of Computational Health, Helmholtz Munich, Munich, Germany
- Department of Paediatrics, Dr von Hauner Children's Hospital, University Hospital, Ludwig-Maximilians-Universität München, Munich, Germany
| | - Anastasia Litinetskaya
- Institute of Computational Biology, Department of Computational Health, Helmholtz Munich, Munich, Germany
- Department of Mathematics, School of Computation, Information and Technology, Technical University of Munich, Garching, Germany
| | - Felix Drost
- Institute of Computational Biology, Department of Computational Health, Helmholtz Munich, Munich, Germany
- TUM School of Life Sciences Weihenstephan, Technical University of Munich, Munich, Germany
| | - Luke Zappia
- Institute of Computational Biology, Department of Computational Health, Helmholtz Munich, Munich, Germany
- Department of Mathematics, School of Computation, Information and Technology, Technical University of Munich, Garching, Germany
| | - Malte D Lücken
- Institute of Computational Biology, Department of Computational Health, Helmholtz Munich, Munich, Germany
- Institute of Lung Health and Immunity, Helmholtz Munich, Munich, Germany
| | - Daniel C Strobl
- Institute of Computational Biology, Department of Computational Health, Helmholtz Munich, Munich, Germany
- TUM School of Life Sciences Weihenstephan, Technical University of Munich, Munich, Germany
- Institute of Clinical Chemistry and Pathobiochemistry, School of Medicine, Technical University of Munich, Munich, Germany
- TranslaTUM, Center for Translational Cancer Research, Technical University of Munich, Munich, Germany
| | - Juan Henao
- Institute of Computational Biology, Department of Computational Health, Helmholtz Munich, Munich, Germany
| | - Fabiola Curion
- Institute of Computational Biology, Department of Computational Health, Helmholtz Munich, Munich, Germany
- Department of Mathematics, School of Computation, Information and Technology, Technical University of Munich, Garching, Germany
| | - Herbert B Schiller
- Institute of Lung Health and Immunity and Comprehensive Pneumology Center, Helmholtz Munich; Member of the German Center for Lung Research (DZL), Munich, Germany
| | - Fabian J Theis
- Institute of Computational Biology, Department of Computational Health, Helmholtz Munich, Munich, Germany.
- TUM School of Life Sciences Weihenstephan, Technical University of Munich, Munich, Germany.
- Department of Mathematics, School of Computation, Information and Technology, Technical University of Munich, Garching, Germany.
- Munich Center for Machine Learning, Technical University of Munich, Garching, Germany.
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30
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Cheng C, Chen W, Jin H, Chen X. A Review of Single-Cell RNA-Seq Annotation, Integration, and Cell-Cell Communication. Cells 2023; 12:1970. [PMID: 37566049 PMCID: PMC10417635 DOI: 10.3390/cells12151970] [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: 06/13/2023] [Revised: 07/10/2023] [Accepted: 07/21/2023] [Indexed: 08/12/2023] Open
Abstract
Single-cell RNA sequencing (scRNA-seq) has emerged as a powerful tool for investigating cellular biology at an unprecedented resolution, enabling the characterization of cellular heterogeneity, identification of rare but significant cell types, and exploration of cell-cell communications and interactions. Its broad applications span both basic and clinical research domains. In this comprehensive review, we survey the current landscape of scRNA-seq analysis methods and tools, focusing on count modeling, cell-type annotation, data integration, including spatial transcriptomics, and the inference of cell-cell communication. We review the challenges encountered in scRNA-seq analysis, including issues of sparsity or low expression, reliability of cell annotation, and assumptions in data integration, and discuss the potential impact of suboptimal clustering and differential expression analysis tools on downstream analyses, particularly in identifying cell subpopulations. Finally, we discuss recent advancements and future directions for enhancing scRNA-seq analysis. Specifically, we highlight the development of novel tools for annotating single-cell data, integrating and interpreting multimodal datasets covering transcriptomics, epigenomics, and proteomics, and inferring cellular communication networks. By elucidating the latest progress and innovation, we provide a comprehensive overview of the rapidly advancing field of scRNA-seq analysis.
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Affiliation(s)
- Changde Cheng
- Department of Computational Biology, St. Jude Children’s Research Hospital, Memphis, TN 38105, USA;
| | - Wenan Chen
- Center for Applied Bioinformatics, St. Jude Children’s Research Hospital, Memphis, TN 38105, USA; (W.C.); (H.J.)
| | - Hongjian Jin
- Center for Applied Bioinformatics, St. Jude Children’s Research Hospital, Memphis, TN 38105, USA; (W.C.); (H.J.)
| | - Xiang Chen
- Department of Computational Biology, St. Jude Children’s Research Hospital, Memphis, TN 38105, USA;
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31
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Zhang C, Gao L, Hu Y, Huang Z. RobustCCC: a robustness evaluation tool for cell-cell communication methods. Front Genet 2023; 14:1236956. [PMID: 37547470 PMCID: PMC10400800 DOI: 10.3389/fgene.2023.1236956] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/08/2023] [Accepted: 07/11/2023] [Indexed: 08/08/2023] Open
Abstract
Cell-cell communication (CCC) inference has become a routine task in single-cell data analysis. Many computational tools are developed for this purpose. However, the robustness of existing CCC methods remains underexplored. We develop a user-friendly tool, RobustCCC, to facilitate the robustness evaluation of CCC methods with respect to three perspectives, including replicated data, transcriptomic data noise and prior knowledge noise. RobustCCC currently integrates 14 state-of-the-art CCC methods and 6 simulated single-cell transcriptomics datasets to generate robustness evaluation reports in tabular form for easy interpretation. We find that these methods exhibit substantially different robustness performances using different simulation datasets, implying a strong impact of the input data on resulting CCC patterns. In summary, RobustCCC represents a scalable tool that can easily integrate more CCC methods, more single-cell datasets from different species (e.g., mouse and human) to provide guidance in selecting methods for identification of consistent and stable CCC patterns in tissue microenvironments. RobustCCC is freely available at https://github.com/GaoLabXDU/RobustCCC.
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32
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Yang Y, Li G, Zhong Y, Xu Q, Lin YT, Roman-Vicharra C, Chapkin RS, Cai JJ. scTenifoldXct: A semi-supervised method for predicting cell-cell interactions and mapping cellular communication graphs. Cell Syst 2023; 14:302-311.e4. [PMID: 36787742 PMCID: PMC10121998 DOI: 10.1016/j.cels.2023.01.004] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/29/2022] [Revised: 08/22/2022] [Accepted: 01/20/2023] [Indexed: 02/16/2023]
Abstract
We present scTenifoldXct, a semi-supervised computational tool for detecting ligand-receptor (LR)-mediated cell-cell interactions and mapping cellular communication graphs. Our method is based on manifold alignment, using LR pairs as inter-data correspondences to embed ligand and receptor genes expressed in interacting cells into a unified latent space. Neural networks are employed to minimize the distance between corresponding genes while preserving the structure of gene regression networks. We apply scTenifoldXct to real datasets for testing and demonstrate that our method detects interactions with high consistency compared with other methods. More importantly, scTenifoldXct uncovers weak but biologically relevant interactions overlooked by other methods. We also demonstrate how scTenifoldXct can be used to compare different samples, such as healthy vs. diseased and wild type vs. knockout, to identify differential interactions, thereby revealing functional implications associated with changes in cellular communication status.
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Affiliation(s)
- Yongjian Yang
- Department of Electrical and Computer Engineering, Texas A&M University, College Station, TX 77843, USA
| | - Guanxun Li
- Department of Statistics, Texas A&M University, College Station, TX 77843, USA
| | - Yan Zhong
- Key Laboratory of Advanced Theory and Application in Statistics and Data Science-MOE, School of Statistics, East China Normal University, 3663 North Zhongshan Road, Shanghai 200062, China
| | - Qian Xu
- Department of Veterinary Integrative Biosciences, Texas A&M University, College Station, TX 77843, USA
| | - Yu-Te Lin
- Graduate Institute of Biomedical Electronics and Bioinformatics, National Taiwan University, Taipei, Taiwan
| | - Cristhian Roman-Vicharra
- Department of Veterinary Integrative Biosciences, Texas A&M University, College Station, TX 77843, USA
| | - Robert S Chapkin
- Department of Nutrition and the Program in Integrative Nutrition & Complex Diseases, Texas A&M University, College Station, TX 77843, USA.
| | - James J Cai
- Department of Electrical and Computer Engineering, Texas A&M University, College Station, TX 77843, USA; Department of Veterinary Integrative Biosciences, Texas A&M University, College Station, TX 77843, USA; Interdisciplinary Program of Genetics, Texas A&M University, College Station, TX 77843, USA.
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33
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Li H, Zhang Z, Squires M, Chen X, Zhang X. scMultiSim: simulation of multi-modality single cell data guided by cell-cell interactions and gene regulatory networks. RESEARCH SQUARE 2023:rs.3.rs-2675530. [PMID: 36993284 PMCID: PMC10055660 DOI: 10.21203/rs.3.rs-2675530/v1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Indexed: 06/19/2023]
Abstract
Simulated single-cell data is essential for designing and evaluating computational methods in the absence of experimental ground truth. Existing simulators typically focus on modeling one or two specific biological factors or mechanisms that affect the output data, which limits their capacity to simulate the complexity and multi-modality in real data. Here, we present scMultiSim, an in silico simulator that generates multi-modal single-cell data, including gene expression, chromatin accessibility, RNA velocity, and spatial cell locations while accounting for the relationships between modalities. scMultiSim jointly models various biological factors that affect the output data, including cell identity, within-cell gene regulatory networks (GRNs), cell-cell interactions (CCIs), and chromatin accessibility, while also incorporating technical noises. Moreover, it allows users to adjust each factor's effect easily. We validated scMultiSim's simulated biological effects and demonstrated its applications by benchmarking a wide range of computational tasks, including cell clustering and trajectory inference, multi-modal and multi-batch data integration, RNA velocity estimation, GRN inference and CCI inference using spatially resolved gene expression data. Compared to existing simulators, scMultiSim can benchmark a much broader range of existing computational problems and even new potential tasks.
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Affiliation(s)
- Hechen Li
- Georgia Institute of Technology, Atlanta, USA
| | - Ziqi Zhang
- Georgia Institute of Technology, Atlanta, USA
| | | | - Xi Chen
- Southern University of Science and Technology, China
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34
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Cang Z, Zhao Y, Almet AA, Stabell A, Ramos R, Plikus MV, Atwood SX, Nie Q. Screening cell-cell communication in spatial transcriptomics via collective optimal transport. Nat Methods 2023; 20:218-228. [PMID: 36690742 PMCID: PMC9911355 DOI: 10.1038/s41592-022-01728-4] [Citation(s) in RCA: 43] [Impact Index Per Article: 43.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/08/2021] [Accepted: 11/21/2022] [Indexed: 01/24/2023]
Abstract
Spatial transcriptomic technologies and spatially annotated single-cell RNA sequencing datasets provide unprecedented opportunities to dissect cell-cell communication (CCC). However, incorporation of the spatial information and complex biochemical processes required in the reconstruction of CCC remains a major challenge. Here, we present COMMOT (COMMunication analysis by Optimal Transport) to infer CCC in spatial transcriptomics, which accounts for the competition between different ligand and receptor species as well as spatial distances between cells. A collective optimal transport method is developed to handle complex molecular interactions and spatial constraints. Furthermore, we introduce downstream analysis tools to infer spatial signaling directionality and genes regulated by signaling using machine learning models. We apply COMMOT to simulation data and eight spatial datasets acquired with five different technologies to show its effectiveness and robustness in identifying spatial CCC in data with varying spatial resolutions and gene coverages. Finally, COMMOT identifies new CCCs during skin morphogenesis in a case study of human epidermal development.
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Affiliation(s)
- Zixuan Cang
- Department of Mathematics and Center for Research in Scientific Computation, North Carolina State University, Raleigh, NC, USA
| | - Yanxiang Zhao
- Department of Mathematics, The George Washington University, Washington, DC, USA
| | - Axel A Almet
- Department of Mathematics, University of California, Irvine, Irvine, CA, USA
- The NSF-Simons Center for Multiscale Cell Fate Research, University of California, Irvine, Irvine, CA, USA
| | - Adam Stabell
- The NSF-Simons Center for Multiscale Cell Fate Research, University of California, Irvine, Irvine, CA, USA
- Department of Developmental and Cell Biology, University of California, Irvine, Irvine, CA, USA
| | - Raul Ramos
- The NSF-Simons Center for Multiscale Cell Fate Research, University of California, Irvine, Irvine, CA, USA
- Department of Developmental and Cell Biology, University of California, Irvine, Irvine, CA, USA
| | - Maksim V Plikus
- The NSF-Simons Center for Multiscale Cell Fate Research, University of California, Irvine, Irvine, CA, USA
- Department of Developmental and Cell Biology, University of California, Irvine, Irvine, CA, USA
| | - Scott X Atwood
- The NSF-Simons Center for Multiscale Cell Fate Research, University of California, Irvine, Irvine, CA, USA
- Department of Developmental and Cell Biology, University of California, Irvine, Irvine, CA, USA
| | - Qing Nie
- Department of Mathematics, University of California, Irvine, Irvine, CA, USA.
- The NSF-Simons Center for Multiscale Cell Fate Research, University of California, Irvine, Irvine, CA, USA.
- Department of Developmental and Cell Biology, University of California, Irvine, Irvine, CA, USA.
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35
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Ospina O, Soupir A, Fridley BL. A Primer on Preprocessing, Visualization, Clustering, and Phenotyping of Barcode-Based Spatial Transcriptomics Data. Methods Mol Biol 2023; 2629:115-140. [PMID: 36929076 DOI: 10.1007/978-1-0716-2986-4_7] [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] [Indexed: 03/18/2023]
Abstract
Recent developments in spatially resolved transcriptomics (ST) have resulted in a large number of studies characterizing the architecture of tissues, the spatial distribution of cell types, and their interactions. Furthermore, ST promises to enable the discovery of more accurate drug targets while also providing a better understanding of the etiology and evolution of complex diseases. The analysis of ST brings similar challenges as seen in other gene expression assays such as scRNA-seq; however, there is the additional spatial information that warrants the development of suitable algorithms for the quality control, preprocessing, visualization, and other discovery-enabling approaches (e.g., clustering, cell phenotyping). In this chapter, we review some of the existing algorithms to perform these analytical tasks and highlight some of the unmet analytical challenges in the analysis of ST data. Given the diversity of available ST technologies, we focus this chapter on the analysis of barcode-based RNA quantitation techniques.
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Affiliation(s)
- Oscar Ospina
- Department of Biostatistics and Bioinformatics, Moffitt Cancer Center, Tampa, FL, USA
| | - Alex Soupir
- Department of Biostatistics and Bioinformatics, Moffitt Cancer Center, Tampa, FL, USA
| | - Brooke L Fridley
- Department of Biostatistics and Bioinformatics, H. Lee Moffitt Cancer Center & Research Institute, Tampa, FL, USA.
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36
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Liu Z, Sun D, Wang C. Evaluation of cell-cell interaction methods by integrating single-cell RNA sequencing data with spatial information. Genome Biol 2022; 23:218. [PMID: 36253792 PMCID: PMC9575221 DOI: 10.1186/s13059-022-02783-y] [Citation(s) in RCA: 31] [Impact Index Per Article: 15.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/30/2022] [Accepted: 10/04/2022] [Indexed: 11/17/2022] Open
Abstract
Background Cell-cell interactions are important for information exchange between different cells, which are the fundamental basis of many biological processes. Recent advances in single-cell RNA sequencing (scRNA-seq) enable the characterization of cell-cell interactions using computational methods. However, it is hard to evaluate these methods since no ground truth is provided. Spatial transcriptomics (ST) data profiles the relative position of different cells. We propose that the spatial distance suggests the interaction tendency of different cell types, thus could be used for evaluating cell-cell interaction tools. Results We benchmark 16 cell-cell interaction methods by integrating scRNA-seq with ST data. We characterize cell-cell interactions into short-range and long-range interactions using spatial distance distributions between ligands and receptors. Based on this classification, we define the distance enrichment score and apply an evaluation workflow to 16 cell-cell interaction tools using 15 simulated and 5 real scRNA-seq and ST datasets. We also compare the consistency of the results from single tools with the commonly identified interactions. Our results suggest that the interactions predicted by different tools are highly dynamic, and the statistical-based methods show overall better performance than network-based methods and ST-based methods. Conclusions Our study presents a comprehensive evaluation of cell-cell interaction tools for scRNA-seq. CellChat, CellPhoneDB, NicheNet, and ICELLNET show overall better performance than other tools in terms of consistency with spatial tendency and software scalability. We recommend using results from at least two methods to ensure the accuracy of identified interactions. We have packaged the benchmark workflow with detailed documentation at GitHub (https://github.com/wanglabtongji/CCI). Supplementary Information The online version contains supplementary material available at 10.1186/s13059-022-02783-y.
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Affiliation(s)
- Zhaoyang Liu
- Key Laboratory of Spine and Spinal Cord Injury Repair and Regeneration of Ministry of Education, Department of Orthopedics, Tongji Hospital, School of Life Science and Technology, Tongji University, Shanghai, 200092, China.,Frontier Science Center for Stem Cells, School of Life Sciences and Technology, Tongji University, Shanghai, 200092, China
| | - Dongqing Sun
- Key Laboratory of Spine and Spinal Cord Injury Repair and Regeneration of Ministry of Education, Department of Orthopedics, Tongji Hospital, School of Life Science and Technology, Tongji University, Shanghai, 200092, China.,Frontier Science Center for Stem Cells, School of Life Sciences and Technology, Tongji University, Shanghai, 200092, China
| | - Chenfei Wang
- Key Laboratory of Spine and Spinal Cord Injury Repair and Regeneration of Ministry of Education, Department of Orthopedics, Tongji Hospital, School of Life Science and Technology, Tongji University, Shanghai, 200092, China. .,Frontier Science Center for Stem Cells, School of Life Sciences and Technology, Tongji University, Shanghai, 200092, China.
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37
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Ke M, Elshenawy B, Sheldon H, Arora A, Buffa FM. Single cell RNA-sequencing: A powerful yet still challenging technology to study cellular heterogeneity. Bioessays 2022; 44:e2200084. [PMID: 36068142 DOI: 10.1002/bies.202200084] [Citation(s) in RCA: 21] [Impact Index Per Article: 10.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/29/2022] [Revised: 08/18/2022] [Accepted: 08/19/2022] [Indexed: 11/11/2022]
Abstract
Almost all biomedical research to date has relied upon mean measurements from cell populations, however it is well established that what it is observed at this macroscopic level can be the result of many interactions of several different single cells. Thus, the observable macroscopic 'average' cannot outright be used as representative of the 'average cell'. Rather, it is the resulting emerging behaviour of the actions and interactions of many different cells. Single-cell RNA sequencing (scRNA-Seq) enables the comparison of the transcriptomes of individual cells. This provides high-resolution maps of the dynamic cellular programmes allowing us to answer fundamental biological questions on their function and evolution. It also allows to address medical questions such as the role of rare cell populations contributing to disease progression and therapeutic resistance. Furthermore, it provides an understanding of context-specific dependencies, namely the behaviour and function that a cell has in a specific context, which can be crucial to understand some complex diseases, such as diabetes, cardiovascular disease and cancer. Here, we provide an overview of scRNA-Seq, including a comparative review of emerging technologies and computational pipelines. We discuss the current and emerging applications and focus on tumour heterogeneity a clear example of how scRNA-Seq can provide new understanding of a complex disease. Additionally, we review the limitations and highlight the need of powerful computational pipelines and reproducible protocols for the broader acceptance of this technique in basic and clinical research.
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Affiliation(s)
- May Ke
- Department of Oncology, Medical Sciences Division, University of Oxford, Oxford, UK
| | - Badran Elshenawy
- Department of Oncology, Medical Sciences Division, University of Oxford, Oxford, UK
| | - Helen Sheldon
- Department of Oncology, Medical Sciences Division, University of Oxford, Oxford, UK
| | - Anjali Arora
- Department of Oncology, Medical Sciences Division, University of Oxford, Oxford, UK
| | - Francesca M Buffa
- Department of Oncology, Medical Sciences Division, University of Oxford, Oxford, UK.,Department of Computing Sciences, Bocconi University, Milano, Italy.,Institute for Data Science and Analytics, Bocconi University, Milano, Italy
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38
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Xiong A, Zhang J, Chen Y, Zhang Y, Yang F. Integrated single-cell transcriptomic analyses reveal that GPNMB-high macrophages promote PN-MES transition and impede T cell activation in GBM. EBioMedicine 2022; 83:104239. [PMID: 36054938 PMCID: PMC9437813 DOI: 10.1016/j.ebiom.2022.104239] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/03/2022] [Revised: 08/10/2022] [Accepted: 08/11/2022] [Indexed: 10/27/2022] Open
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39
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Tebani A, Bekri S. [The promise of omics in the precision medicine era]. Rev Med Interne 2022; 43:649-660. [PMID: 36041909 DOI: 10.1016/j.revmed.2022.07.009] [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: 06/10/2022] [Accepted: 07/12/2022] [Indexed: 10/15/2022]
Abstract
The rise of omics technologies that simultaneously measure thousands of molecules in a complex biological sample represents the core of systems biology. These technologies have profoundly impacted biomarkers and therapeutic targets discovery in the precision medicine era. Systems biology aims to perform a systematic probing of complex interactions in biological systems. Powered by high-throughput omics technologies and high-performance computing, systems biology provides relevant, resolving, and multi-scale overviews from cells to populations. Precision medicine takes advantage of these conceptual and technological developments and is based on two main pillars: the generation of multimodal data and their subsequent modeling. High-throughput omics technologies enable the comprehensive and holistic extraction of biological information, while computational capabilities enable multidimensional modeling and, as a result, offer an intuitive and intelligible visualization. Despite their promise, translating these technologies into clinically actionable tools has been slow. In this contribution, we present the most recent multi-omics data generation and analysis strategies and their clinical deployment in the post-genomic era. Furthermore, medical application challenges of omics-based biomarkers are discussed.
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Affiliation(s)
- A Tebani
- UNIROUEN, Inserm U1245, Department of Metabolic Biochemistry, Normandie University, CHU Rouen, 76000 Rouen, France.
| | - S Bekri
- UNIROUEN, Inserm U1245, Department of Metabolic Biochemistry, Normandie University, CHU Rouen, 76000 Rouen, France
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40
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Knowledge-graph-based cell-cell communication inference for spatially resolved transcriptomic data with SpaTalk. Nat Commun 2022; 13:4429. [PMID: 35908020 PMCID: PMC9338929 DOI: 10.1038/s41467-022-32111-8] [Citation(s) in RCA: 30] [Impact Index Per Article: 15.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/20/2022] [Accepted: 07/18/2022] [Indexed: 12/19/2022] Open
Abstract
Spatially resolved transcriptomics provides genetic information in space toward elucidation of the spatial architecture in intact organs and the spatially resolved cell-cell communications mediating tissue homeostasis, development, and disease. To facilitate inference of spatially resolved cell-cell communications, we here present SpaTalk, which relies on a graph network and knowledge graph to model and score the ligand-receptor-target signaling network between spatially proximal cells by dissecting cell-type composition through a non-negative linear model and spatial mapping between single-cell transcriptomic and spatially resolved transcriptomic data. The benchmarked performance of SpaTalk on public single-cell spatial transcriptomic datasets is superior to that of existing inference methods. Then we apply SpaTalk to STARmap, Slide-seq, and 10X Visium data, revealing the in-depth communicative mechanisms underlying normal and disease tissues with spatial structure. SpaTalk can uncover spatially resolved cell-cell communications for single-cell and spot-based spatially resolved transcriptomic data universally, providing valuable insights into spatial inter-cellular tissue dynamics. Cell-cell communication is a vital feature involving numerous biological processes. Here, the authors develop SpaTalk, a cell-cell communication inference method using knowledge graph for spatially resolved transcriptomic data, providing valuable insights into spatial intercellular tissue dynamics.
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41
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Karikomi M, Zhou P, Nie Q. DURIAN: an integrative deconvolution and imputation method for robust signaling analysis of single-cell transcriptomics data. Brief Bioinform 2022; 23:6609525. [PMID: 35709795 PMCID: PMC9294432 DOI: 10.1093/bib/bbac223] [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: 03/09/2022] [Revised: 04/29/2022] [Accepted: 05/11/2022] [Indexed: 01/31/2023] Open
Abstract
Single-cell RNA sequencing trades read-depth for dimensionality, often leading to loss of critical signaling gene information that is typically present in bulk data sets. We introduce DURIAN (Deconvolution and mUltitask-Regression-based ImputAtioN), an integrative method for recovery of gene expression in single-cell data. Through systematic benchmarking, we demonstrate the accuracy, robustness and empirical convergence of DURIAN using both synthetic and published data sets. We show that use of DURIAN improves single-cell clustering, low-dimensional embedding, and recovery of intercellular signaling networks. Our study resolves several inconsistent results of cell-cell communication analysis using single-cell or bulk data independently. The method has broad application in biomarker discovery and cell signaling analysis using single-cell transcriptomics data sets.
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Affiliation(s)
| | - Peijie Zhou
- Corresponding authors: Peijie Zhou, 540P Rowland Hall, University of California Irvine, Irvine CA 92697, USA. Tel: 949-824-5530; Fax: 949-8247993; ; Qing Nie, 540F Rowland Hall, University of California Irvine, Irvine CA 92697, USA. Tel: 949-824-5530; Fax: 949-8247993;
| | - Qing Nie
- Corresponding authors: Peijie Zhou, 540P Rowland Hall, University of California Irvine, Irvine CA 92697, USA. Tel: 949-824-5530; Fax: 949-8247993; ; Qing Nie, 540F Rowland Hall, University of California Irvine, Irvine CA 92697, USA. Tel: 949-824-5530; Fax: 949-8247993;
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42
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Koh L, Novera W, Lim SW, Chong YK, Pang QY, Low D, Ang BT, Tang C. Integrative multi-omics approach to targeted therapy for glioblastoma. Pharmacol Res 2022; 182:106308. [PMID: 35714825 DOI: 10.1016/j.phrs.2022.106308] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 03/30/2022] [Revised: 05/19/2022] [Accepted: 06/10/2022] [Indexed: 11/30/2022]
Abstract
This review describes recent technological advances applied to glioblastoma (GBM), a brain tumor with dismal prognosis. International consortial efforts suggest the presence of molecular subtypes within histologically identical GBM tumors. This emphasizes that future treatment decisions should no longer be made based solely on morphological analyses, but must now take into consideration such molecular and cellular heterogeneity. The use of single-cell technologies has advanced our understanding and assignation of functional subtypes revealing therapeutic vulnerabilities. Our team has developed stratification approaches in the past few years, and we have been able to identify patient cohorts enriched for various signaling pathways. Importantly, our Glioportal brain tumor resource has been established under the National Neuroscience Institute Tissue Bank in 2021. This resource offers preclinical capability to validate working hypotheses established from patient clinical datasets. This review highlights recent developments with the ultimate goal of assigning functional meaning to molecular subtypes, revealing therapeutic vulnerabilities.
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Affiliation(s)
- Lynnette Koh
- Department of Research, National Neuroscience Institute, Singapore.
| | - Wisna Novera
- Department of Research, National Neuroscience Institute, Singapore
| | - See Wee Lim
- Department of Research, National Neuroscience Institute, Singapore
| | - Yuk Kien Chong
- Department of Research, National Neuroscience Institute, Singapore
| | - Qing You Pang
- Department of Research, National Neuroscience Institute, Singapore
| | - David Low
- Department of Neurosurgery, National Neuroscience Institute, Singapore; Duke-National University of Singapore, Singapore
| | - Beng Ti Ang
- Department of Neurosurgery, National Neuroscience Institute, Singapore; Duke-National University of Singapore, Singapore
| | - Carol Tang
- Department of Research, National Neuroscience Institute, Singapore; Duke-National University of Singapore, Singapore; School of Biological Sciences, Nanyang Technological University, Singapore.
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43
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Liu Q, Hsu CY, Li J, Shyr Y. Dysregulated ligand-receptor interactions from single-cell transcriptomics. Bioinformatics 2022; 38:3216-3221. [PMID: 35482476 PMCID: PMC9191214 DOI: 10.1093/bioinformatics/btac294] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/16/2021] [Revised: 03/29/2022] [Accepted: 04/21/2022] [Indexed: 11/13/2022] Open
Abstract
MOTIVATION Intracellular communication is crucial to many biological processes, such as differentiation, development, homeostasis and inflammation. Single-cell transcriptomics provides an unprecedented opportunity for studying cell-cell communications mediated by ligand-receptor interactions. Although computational methods have been developed to infer cell type-specific ligand-receptor interactions from one single-cell transcriptomics profile, there is lack of approaches considering ligand and receptor simultaneously to identifying dysregulated interactions across conditions from multiple single-cell profiles. RESULTS We developed scLR, a statistical method for examining dysregulated ligand-receptor interactions between two conditions. scLR models the distribution of the product of ligands and receptors expressions and accounts for inter-sample variances and small sample sizes. scLR achieved high sensitivity and specificity in simulation studies. scLR revealed important cytokine signaling between macrophages and proliferating T cells during severe acute COVID-19 infection, and activated TGF-β signaling from alveolar type II cells in the pathogenesis of pulmonary fibrosis. AVAILABILITY AND IMPLEMENTATION scLR is freely available at https://github.com/cyhsuTN/scLR. SUPPLEMENTARY INFORMATION Supplementary data are available at Bioinformatics online.
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Affiliation(s)
- Qi Liu
- Department of Biostatistics, Vanderbilt University Medical Center, Nashville, TN 37232, USA
- Department of Biostatistics, Vanderbilt University Medical Center, Nashville, TN 37232, USA
| | - Chih-Yuan Hsu
- Department of Biostatistics, Vanderbilt University Medical Center, Nashville, TN 37232, USA
- Department of Biostatistics, Vanderbilt University Medical Center, Nashville, TN 37232, USA
| | - Jia Li
- Department of Biostatistics, Vanderbilt University Medical Center, Nashville, TN 37232, USA
- Department of Biostatistics, Vanderbilt University Medical Center, Nashville, TN 37232, USA
| | - Yu Shyr
- Department of Biostatistics, Vanderbilt University Medical Center, Nashville, TN 37232, USA
- Department of Biostatistics, Vanderbilt University Medical Center, Nashville, TN 37232, USA
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44
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Dimitrov D, Türei D, Garrido-Rodriguez M, Burmedi PL, Nagai JS, Boys C, Ramirez Flores RO, Kim H, Szalai B, Costa IG, Valdeolivas A, Dugourd A, Saez-Rodriguez J. Comparison of methods and resources for cell-cell communication inference from single-cell RNA-Seq data. Nat Commun 2022; 13:3224. [PMID: 35680885 PMCID: PMC9184522 DOI: 10.1038/s41467-022-30755-0] [Citation(s) in RCA: 142] [Impact Index Per Article: 71.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/17/2021] [Accepted: 05/17/2022] [Indexed: 12/18/2022] Open
Abstract
The growing availability of single-cell data, especially transcriptomics, has sparked an increased interest in the inference of cell-cell communication. Many computational tools were developed for this purpose. Each of them consists of a resource of intercellular interactions prior knowledge and a method to predict potential cell-cell communication events. Yet the impact of the choice of resource and method on the resulting predictions is largely unknown. To shed light on this, we systematically compare 16 cell-cell communication inference resources and 7 methods, plus the consensus between the methods’ predictions. Among the resources, we find few unique interactions, a varying degree of overlap, and an uneven coverage of specific pathways and tissue-enriched proteins. We then examine all possible combinations of methods and resources and show that both strongly influence the predicted intercellular interactions. Finally, we assess the agreement of cell-cell communication methods with spatial colocalisation, cytokine activities, and receptor protein abundance and find that predictions are generally coherent with those data modalities. To facilitate the use of the methods and resources described in this work, we provide LIANA, a LIgand-receptor ANalysis frAmework as an open-source interface to all the resources and methods. Multiple methods to infer cell-cell communication (CCC) from single cell data are currently available. Here, the authors systematically compare 16 CCC inference resources and 7 methods, and develop the LIANA framework as an interface to use and compare all these approaches.
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Affiliation(s)
- Daniel Dimitrov
- Heidelberg University, Faculty of Medicine, and Heidelberg University Hospital, Institute for Computational Biomedicine, BioQuant, Heidelberg, Germany
| | - Dénes Türei
- Heidelberg University, Faculty of Medicine, and Heidelberg University Hospital, Institute for Computational Biomedicine, BioQuant, Heidelberg, Germany
| | - Martin Garrido-Rodriguez
- Heidelberg University, Faculty of Medicine, and Heidelberg University Hospital, Institute for Computational Biomedicine, BioQuant, Heidelberg, Germany
| | - Paul L Burmedi
- Heidelberg University, Faculty of Medicine, and Heidelberg University Hospital, Institute for Computational Biomedicine, BioQuant, Heidelberg, Germany
| | - James S Nagai
- Institute for Computational Genomics, Faculty of Medicine, RWTH Aachen University, Aachen, 52074, Germany.,Joint Research Center for Computational Biomedicine, RWTH Aachen University Hospital, Aachen, Germany
| | - Charlotte Boys
- Heidelberg University, Faculty of Medicine, and Heidelberg University Hospital, Institute for Computational Biomedicine, BioQuant, Heidelberg, Germany
| | - Ricardo O Ramirez Flores
- Heidelberg University, Faculty of Medicine, and Heidelberg University Hospital, Institute for Computational Biomedicine, BioQuant, Heidelberg, Germany
| | - Hyojin Kim
- Heidelberg University, Faculty of Medicine, and Heidelberg University Hospital, Institute for Computational Biomedicine, BioQuant, Heidelberg, Germany
| | - Bence Szalai
- Faculty of Medicine, Department of Physiology, Semmelweis University, Budapest, Hungary
| | - Ivan G Costa
- Institute for Computational Genomics, Faculty of Medicine, RWTH Aachen University, Aachen, 52074, Germany.,Joint Research Center for Computational Biomedicine, RWTH Aachen University Hospital, Aachen, Germany
| | - Alberto Valdeolivas
- Roche Pharma Research and Early Development, Pharmaceutical Sciences, Roche Innovation Center Basel, Basel, Switzerland
| | - Aurélien Dugourd
- Heidelberg University, Faculty of Medicine, and Heidelberg University Hospital, Institute for Computational Biomedicine, BioQuant, Heidelberg, Germany
| | - Julio Saez-Rodriguez
- Heidelberg University, Faculty of Medicine, and Heidelberg University Hospital, Institute for Computational Biomedicine, BioQuant, Heidelberg, Germany.
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45
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Bridges K, Miller-Jensen K. Mapping and Validation of scRNA-Seq-Derived Cell-Cell Communication Networks in the Tumor Microenvironment. Front Immunol 2022; 13:885267. [PMID: 35572582 PMCID: PMC9096838 DOI: 10.3389/fimmu.2022.885267] [Citation(s) in RCA: 14] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/27/2022] [Accepted: 03/25/2022] [Indexed: 01/25/2023] Open
Abstract
Recent advances in single-cell technologies, particularly single-cell RNA-sequencing (scRNA-seq), have permitted high throughput transcriptional profiling of a wide variety of biological systems. As scRNA-seq supports inference of cell-cell communication, this technology has and continues to anchor groundbreaking studies into the efficacy and mechanism of novel immunotherapies for cancer treatment. In this review, we will highlight methods developed to infer inter- and intracellular signaling from scRNA-seq and discuss how they have contributed to studies of immunotherapeutic intervention in the tumor microenvironment (TME). However, a central challenge remains in validating the hypothesized cell-cell interactions. Therefore, this review will also cover strategies for integration of these scRNA-seq-derived interaction networks with existing experimental and computational approaches. Integration of these networks with imaging, protein secretion measurements, and network analysis and mathematical modeling tools addresses challenges that remain with scRNA-seq to enhance studies of immunosuppressive and immunotherapy-altered signaling in the TME.
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Affiliation(s)
- Kate Bridges
- Department of Biomedical Engineering, Yale University, New Haven, CT, United States
| | - Kathryn Miller-Jensen
- Department of Biomedical Engineering, Yale University, New Haven, CT, United States
- Department of Molecular, Cellular, and Developmental Biology, Yale University, New Haven, CT, United States
- Systems Biology Institute, Yale University, New Haven, CT, United States
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46
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Baruzzo G, Cesaro G, Di Camillo B. Identify, quantify and characterize cellular communication from single-cell RNA sequencing data with scSeqComm. Bioinformatics 2022; 38:1920-1929. [PMID: 35043939 DOI: 10.1093/bioinformatics/btac036] [Citation(s) in RCA: 13] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/07/2021] [Revised: 01/11/2022] [Accepted: 01/14/2022] [Indexed: 02/03/2023] Open
Abstract
MOTIVATION Recently, single-cell RNA-seq (scRNA-seq) data have been used to study cellular communication. Most bioinformatics methods infer only the intercellular signaling between groups of cells, mainly exploiting ligand-receptor expression levels. Only few methods consider the entire intercellular + intracellular signaling, mainly inferring lists/networks of signaling involved genes. RESULTS Here, we present scSeqComm, a computational method to identify and quantify the evidence of ongoing intercellular and intracellular signaling from scRNA-seq data, and at the same time providing a functional characterization of the inferred cellular communication. The possibility to quantify the evidence of ongoing communication assists the prioritization of the results, while the combined evidence of both intercellular and intracellular signaling increase the reliability of inferred communication. The application to a scRNA-seq dataset of tumor microenvironment, the agreement with independent bioinformatics analysis, the validation using spatial transcriptomics data and the comparison with state-of-the-art intercellular scoring schemes confirmed the robustness and reliability of the proposed method. AVAILABILITY AND IMPLEMENTATION scSeqComm R package is freely available at https://gitlab.com/sysbiobig/scseqcomm and https://sysbiobig.dei.unipd.it/software/#scSeqComm. Submitted software version and test data are available in Zenodo, at https://dx.doi.org/10.5281/zenodo.5833298. SUPPLEMENTARY INFORMATION Supplementary data are available at Bioinformatics online.
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Affiliation(s)
- Giacomo Baruzzo
- Department of Information Engineering, University of Padova, Padova, Italy
| | - Giulia Cesaro
- Department of Information Engineering, University of Padova, Padova, Italy
| | - Barbara Di Camillo
- Department of Information Engineering, University of Padova, Padova, Italy.,Department of Comparative Biomedicine and Food Science, University of Padova, Padova, Italy.,CRIBI Innovative Biotechnology Center, University of Padova, Padova, Italy
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47
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Malhi NK, Luo Y, Tang X, Sriram K, Calandrelli R, Zhong S, Chen ZB. Isolation and Profiling of Human Primary Mesenteric Arterial Endothelial Cells at the Transcriptome Level. J Vis Exp 2022:10.3791/63307. [PMID: 35343966 PMCID: PMC9180814 DOI: 10.3791/63307] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/29/2023] Open
Abstract
Endothelial cells (ECs) are crucial for vascular and whole-body function through their dynamic response to environmental cues. Elucidating the transcriptome and epigenome of ECs is paramount to understanding their roles in development, health, and disease, but is limited in the availability of isolated primary cells. Recent technologies have enabled the high-throughput profiling of EC transcriptome and epigenome, leading to the identification of previously unknown EC cell subpopulations and developmental trajectories. While EC cultures are a useful tool in the exploration of EC function and dysfunction, the culture conditions and multiple passages can introduce external variables that alter the properties of native EC, including morphology, epigenetic state, and gene expression program. To overcome this limitation, the present paper demonstrates a method of isolating human primary ECs from donor mesenteric arteries aiming to capture their native state. ECs in the intimal layer are dissociated mechanically and biochemically with the use of particular enzymes. The resultant cells can be directly used for bulk RNA or single-cell RNA-sequencing or plated for culture. In addition, a workflow is described for the preparation of human arterial tissue for spatial transcriptomics, specifically for a commercially available platform, although this method is also suitable for other spatial transcriptome profiling techniques. This methodology can be applied to different vessels collected from a variety of donors in health or disease states to gain insights into EC transcriptional and epigenetic regulation, a pivotal aspect of endothelial cell biology.
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Affiliation(s)
| | - Yingjun Luo
- Department of Diabetes Complications and Metabolism, City of Hope
| | - Xiaofang Tang
- Department of Diabetes Complications and Metabolism, City of Hope
| | - Kiran Sriram
- Department of Diabetes Complications and Metabolism, City of Hope; Irell and Manella Graduate School of Biological Sciences, City of Hope
| | | | - Sheng Zhong
- Department of Bioengineering, University of California San Diego
| | - Zhen Bouman Chen
- Department of Diabetes Complications and Metabolism, City of Hope; Irell and Manella Graduate School of Biological Sciences, City of Hope;
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48
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Catozzi S, Ternet C, Gourrege A, Wynne K, Oliviero G, Kiel C. Reconstruction and analysis of a large-scale binary Ras-effector signaling network. Cell Commun Signal 2022; 20:24. [PMID: 35246154 PMCID: PMC8896392 DOI: 10.1186/s12964-022-00823-5] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/16/2021] [Accepted: 12/18/2021] [Indexed: 12/27/2022] Open
Abstract
BACKGROUND Ras is a key cellular signaling hub that controls numerous cell fates via multiple downstream effector pathways. While pathways downstream of effectors such as Raf, PI3K and RalGDS are extensively described in the literature, how other effectors signal downstream of Ras is often still enigmatic. METHODS A comprehensive and unbiased Ras-effector network was reconstructed downstream of 43 effector proteins (converging onto 12 effector classes) using public pathway and protein-protein interaction (PPI) databases. The output is an oriented graph of pairwise interactions defining a 3-layer signaling network downstream of Ras. The 2290 proteins comprising the network were studied for their implication in signaling crosstalk and feedbacks, their subcellular localizations, and their cellular functions. RESULTS The final Ras-effector network consists of 2290 proteins that are connected via 19,080 binary PPIs, increasingly distributed across the downstream layers, with 441 PPIs in layer 1, 1660 in layer 2, and 16,979 in layer 3. We identified a high level of crosstalk among proteins of the 12 effector classes. A class-specific Ras sub-network was generated in CellDesigner (.xml file) and a functional enrichment analysis thereof shows that 58% of the processes have previously been associated to a respective effector pathway, with the remaining providing insights into novel and unexplored functions of specific effector pathways. CONCLUSIONS Our large-scale and cell general Ras-effector network is a crucial steppingstone towards defining the network boundaries. It constitutes a 'reference interactome' and can be contextualized for specific conditions, e.g. different cell types or biopsy material obtained from cancer patients. Further, it can serve as a basis for elucidating systems properties, such as input-output relationships, crosstalk, and pathway redundancy. Video Abstract.
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Affiliation(s)
- Simona Catozzi
- Systems Biology Ireland, School of Medicine, University College Dublin, Belfield, Dublin 4, Ireland.,UCD Charles Institute of Dermatology, School of Medicine, University College Dublin, Belfield, Dublin 4, Ireland
| | - Camille Ternet
- Systems Biology Ireland, School of Medicine, University College Dublin, Belfield, Dublin 4, Ireland.,UCD Charles Institute of Dermatology, School of Medicine, University College Dublin, Belfield, Dublin 4, Ireland
| | - Alize Gourrege
- Systems Biology Ireland, School of Medicine, University College Dublin, Belfield, Dublin 4, Ireland.,UCD Charles Institute of Dermatology, School of Medicine, University College Dublin, Belfield, Dublin 4, Ireland
| | - Kieran Wynne
- Systems Biology Ireland, School of Medicine, University College Dublin, Belfield, Dublin 4, Ireland.,Conway Institute of Biomolecular and Biomedical Research, University College Dublin, Dublin 4, Ireland
| | - Giorgio Oliviero
- Systems Biology Ireland, School of Medicine, University College Dublin, Belfield, Dublin 4, Ireland.,UCD Charles Institute of Dermatology, School of Medicine, University College Dublin, Belfield, Dublin 4, Ireland
| | - Christina Kiel
- Systems Biology Ireland, School of Medicine, University College Dublin, Belfield, Dublin 4, Ireland. .,UCD Charles Institute of Dermatology, School of Medicine, University College Dublin, Belfield, Dublin 4, Ireland. .,Department of Molecular Medicine, University of Pavia, 27100, Pavia, Italy.
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49
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Computational exploration of cellular communication in skin from emerging single-cell and spatial transcriptomic data. Biochem Soc Trans 2022; 50:297-308. [PMID: 35191953 PMCID: PMC9022991 DOI: 10.1042/bst20210863] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/28/2021] [Revised: 01/29/2022] [Accepted: 02/01/2022] [Indexed: 12/28/2022]
Abstract
Tissue development and homeostasis require coordinated cell–cell communication. Recent advances in single-cell sequencing technologies have emerged as a revolutionary method to reveal cellular heterogeneity with unprecedented resolution. This offers a great opportunity to explore cell–cell communication in tissues systematically and comprehensively, and to further identify signaling mechanisms driving cell fate decisions and shaping tissue phenotypes. Using gene expression information from single-cell transcriptomics, several computational tools have been developed for inferring cell–cell communication, greatly facilitating analysis and interpretation. However, in single-cell transcriptomics, spatial information of cells is inherently lost. Given that most cell signaling events occur within a limited distance in tissues, incorporating spatial information into cell–cell communication analysis is critical for understanding tissue organization and function. Spatial transcriptomics provides spatial location of cell subsets along with their gene expression, leading to new directions for leveraging spatial information to develop computational approaches for cell–cell communication inference and analysis. These computational approaches have been successfully applied to uncover previously unrecognized mechanisms of intercellular communication within various contexts and across organ systems, including the skin, a formidable model to study mechanisms of cell–cell communication due to the complex interactions between the different cell populations that comprise it. Here, we review emergent cell–cell communication inference tools using single-cell transcriptomics and spatial transcriptomics, and highlight the biological insights gained by applying these computational tools to exploring cellular communication in skin development, homeostasis, disease and aging, as well as discuss future potential research avenues.
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50
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Jackson CA, Vogel C. New horizons in the stormy sea of multimodal single-cell data integration. Mol Cell 2022; 82:248-259. [PMID: 35063095 PMCID: PMC8830781 DOI: 10.1016/j.molcel.2021.12.012] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/11/2021] [Revised: 12/08/2021] [Accepted: 12/13/2021] [Indexed: 01/22/2023]
Abstract
While measurements of RNA expression have dominated the world of single-cell analyses, new single-cell techniques increasingly allow collection of different data modalities, measuring different molecules, structural connections, and intermolecular interactions. Integrating the resulting multimodal single-cell datasets is a new bioinformatics challenge. Equally important, it is a new experimental design challenge for the bench scientist, who is not only choosing from a myriad of techniques for each data modality but also faces new challenges in experimental design. The ultimate goal is to design, execute, and analyze multimodal single-cell experiments that are more than just descriptive but enable the learning of new causal and mechanistic biology. This objective requires strict consideration of the goals behind the analysis, which might range from mapping the heterogeneity of a cellular population to assembling system-wide causal networks that can further our understanding of cellular functions and eventually lead to models of tissues and organs. We review steps and challenges toward this goal. Single-cell transcriptomics is now a mature technology, and methods to measure proteins, lipids, small-molecule metabolites, and other molecular phenotypes at the single-cell level are rapidly developing. Integrating these single-cell readouts so that each cell has measurements of multiple types of data, e.g., transcriptomes, proteomes, and metabolomes, is expected to allow identification of highly specific cellular subpopulations and to provide the basis for inferring causal biological mechanisms.
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Affiliation(s)
- Christopher A Jackson
- New York University, Department of Biology, Center for Genomics and Systems Biology, New York NY, USA
| | - Christine Vogel
- New York University, Department of Biology, Center for Genomics and Systems Biology, New York NY, USA
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