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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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2
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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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3
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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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Hashimoto M, Kojima Y, Sakamoto T, Ozato Y, Nakano Y, Abe T, Hosoda K, Saito H, Higuchi S, Hisamatsu Y, Toshima T, Yonemura Y, Masuda T, Hata T, Nagayama S, Kagawa K, Goto Y, Utou M, Gamachi A, Imamura K, Kuze Y, Zenkoh J, Suzuki A, Takahashi K, Niida A, Hirose H, Hayashi S, Koseki J, Fukuchi S, Murakami K, Yoshizumi T, Kadomatsu K, Tobo T, Oda Y, Uemura M, Eguchi H, Doki Y, Mori M, Oshima M, Shibata T, Suzuki Y, Shimamura T, Mimori K. Spatial and single-cell colocalisation analysis reveals MDK-mediated immunosuppressive environment with regulatory T cells in colorectal carcinogenesis. EBioMedicine 2024; 103:105102. [PMID: 38614865 PMCID: PMC11121171 DOI: 10.1016/j.ebiom.2024.105102] [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: 10/18/2023] [Revised: 03/19/2024] [Accepted: 03/20/2024] [Indexed: 04/15/2024] Open
Abstract
BACKGROUND Cell-cell interaction factors that facilitate the progression of adenoma to sporadic colorectal cancer (CRC) remain unclear, thereby hindering patient survival. METHODS We performed spatial transcriptomics on five early CRC cases, which included adenoma and carcinoma, and one advanced CRC. To elucidate cell-cell interactions within the tumour microenvironment (TME), we investigated the colocalisation network at single-cell resolution using a deep generative model for colocalisation analysis, combined with a single-cell transcriptome, and assessed the clinical significance in CRC patients. FINDINGS CRC cells colocalised with regulatory T cells (Tregs) at the adenoma-carcinoma interface. At early-stage carcinogenesis, cell-cell interaction inference between colocalised adenoma and cancer epithelial cells and Tregs based on the spatial distribution of single cells highlighted midkine (MDK) as a prominent signalling molecule sent from tumour epithelial cells to Tregs. Interaction between MDK-high CRC cells and SPP1+ macrophages and stromal cells proved to be the mechanism underlying immunosuppression in the TME. Additionally, we identified syndecan4 (SDC4) as a receptor for MDK associated with Treg colocalisation. Finally, clinical analysis using CRC datasets indicated that increased MDK/SDC4 levels correlated with poor overall survival in CRC patients. INTERPRETATION MDK is involved in the immune tolerance shown by Tregs to tumour growth. MDK-mediated formation of the TME could be a potential target for early diagnosis and treatment of CRC. FUNDING Japan Society for the Promotion of Science (JSPS) Grant-in-Aid for Science Research; OITA Cancer Research Foundation; AMED under Grant Number; Japan Science and Technology Agency (JST); Takeda Science Foundation; The Princess Takamatsu Cancer Research Fund.
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Affiliation(s)
- Masahiro Hashimoto
- Department of Surgery, Kyushu University Beppu Hospital, Beppu, 874-0838, Japan; Department of Gastroenterological Surgery, Osaka University Graduate School of Medicine, Suita, 565-0871, Japan
| | - Yasuhiro Kojima
- Division of Computational Bioscience, National Cancer Center Research Institute, Tokyo, 104-0045, Japan
| | - Takeharu Sakamoto
- Department of Cancer Biology, Institute of Biomedical Science, Kansai Medical University, Hirakata, 573-1010, Japan.
| | - Yuki Ozato
- Department of Surgery, Kyushu University Beppu Hospital, Beppu, 874-0838, Japan; Department of Gastroenterological Surgery, Osaka University Graduate School of Medicine, Suita, 565-0871, Japan
| | - Yusuke Nakano
- Department of Surgery, Kyushu University Beppu Hospital, Beppu, 874-0838, Japan; Department of Gastroenterological Surgery, Osaka University Graduate School of Medicine, Suita, 565-0871, Japan
| | - Tadashi Abe
- Department of Surgery, Kyushu University Beppu Hospital, Beppu, 874-0838, Japan
| | - Kiyotaka Hosoda
- Department of Surgery, Kyushu University Beppu Hospital, Beppu, 874-0838, Japan
| | - Hideyuki Saito
- Department of Surgery, Kyushu University Beppu Hospital, Beppu, 874-0838, Japan; Department of General Surgical Science, Gastroenterological Surgery, Gunma University Graduate School of Medicine, Maebashi, 371-8511, Japan
| | - Satoshi Higuchi
- Department of Surgery, Kyushu University Beppu Hospital, Beppu, 874-0838, Japan; Department of Gastroenterological Surgery, Osaka University Graduate School of Medicine, Suita, 565-0871, Japan
| | - Yuichi Hisamatsu
- Department of Surgery, Kyushu University Beppu Hospital, Beppu, 874-0838, Japan
| | - Takeo Toshima
- Department of Surgery, Kyushu University Beppu Hospital, Beppu, 874-0838, Japan
| | - Yusuke Yonemura
- Department of Surgery, Kyushu University Beppu Hospital, Beppu, 874-0838, Japan
| | - Takaaki Masuda
- Department of Surgery, Kyushu University Beppu Hospital, Beppu, 874-0838, Japan
| | - Tsuyoshi Hata
- Department of Gastroenterological Surgery, Osaka University Graduate School of Medicine, Suita, 565-0871, Japan
| | - Satoshi Nagayama
- Department of Surgery, Uji-Tokushukai Medical Center, Uji, 611-0041, Japan
| | - Koichi Kagawa
- Department of Gastroenterology, Shin Beppu Hospital, Beppu, 874-8538, Japan
| | - Yasuhiro Goto
- Department of Gastroenterology, Shin Beppu Hospital, Beppu, 874-8538, Japan
| | - Mitsuaki Utou
- Department of Pathology, Kyushu University Beppu Hospital, Beppu, 874-0838, Japan
| | - Ayako Gamachi
- Department of Pathology, Oita Oka Hospital, Oita, 870-0192, Japan
| | - Kiyomi Imamura
- Laboratory of Systems Genomics, Department of Computational Biology and Medical Sciences, Graduate School of Frontier Sciences, The University of Tokyo, Kashiwa, 277-8561, Japan
| | - Yuta Kuze
- Laboratory of Systems Genomics, Department of Computational Biology and Medical Sciences, Graduate School of Frontier Sciences, The University of Tokyo, Kashiwa, 277-8561, Japan
| | - Junko Zenkoh
- Laboratory of Systems Genomics, Department of Computational Biology and Medical Sciences, Graduate School of Frontier Sciences, The University of Tokyo, Kashiwa, 277-8561, Japan
| | - Ayako Suzuki
- Laboratory of Systems Genomics, Department of Computational Biology and Medical Sciences, Graduate School of Frontier Sciences, The University of Tokyo, Kashiwa, 277-8561, Japan
| | - Kazuki Takahashi
- Laboratory of Molecular Medicine, Human Genome Center, The Institute of Medical Science, The University of Tokyo, Tokyo, 108-8639, Japan
| | - Atsushi Niida
- Laboratory of Molecular Medicine, Human Genome Center, The Institute of Medical Science, The University of Tokyo, Tokyo, 108-8639, Japan
| | - Haruka Hirose
- Division of Systems Biology, Nagoya University Graduate School of Medicine, Nagoya, 466-8550, Japan
| | - Shuto Hayashi
- Division of Systems Biology, Nagoya University Graduate School of Medicine, Nagoya, 466-8550, Japan
| | - Jun Koseki
- Division of Systems Biology, Nagoya University Graduate School of Medicine, Nagoya, 466-8550, Japan
| | - Satoshi Fukuchi
- Department of Gastroenterological Medicine, Almeida Memorial Hospital, Oita, 870-1195, Japan
| | - Kazunari Murakami
- Department of Gastroenterology, Oita University Hospital, Yufu, 879-5593, Japan
| | - Tomoharu Yoshizumi
- Department of Surgery and Science, Graduate School of Medical Sciences, Kyushu University, Fukuoka, 812-8582, Japan
| | - Kenji Kadomatsu
- Department of Biochemistry, Nagoya University Graduate School of Medicine, Nagoya, 466-8550, Japan
| | - Taro Tobo
- Department of Pathology, Kyushu University Beppu Hospital, Beppu, 874-0838, Japan
| | - Yoshinao Oda
- Department of Anatomic Pathology, Kyushu University Hospital, Fukuoka, 812-8582, Japan
| | - Mamoru Uemura
- Department of Gastroenterological Surgery, Osaka University Graduate School of Medicine, Suita, 565-0871, Japan
| | - Hidetoshi Eguchi
- Department of Gastroenterological Surgery, Osaka University Graduate School of Medicine, Suita, 565-0871, Japan
| | - Yuichiro Doki
- Department of Gastroenterological Surgery, Osaka University Graduate School of Medicine, Suita, 565-0871, Japan
| | - Masaki Mori
- Tokai University School of Medicine, Isehara, 259-1193, Japan
| | - Masanobu Oshima
- Division of Genetics, Cancer Research Institute, Kanazawa University, Kanazawa, 920-1192, Japan
| | - Tatsuhiro Shibata
- Laboratory of Molecular Medicine, Human Genome Center, The Institute of Medical Science, The University of Tokyo, Tokyo, 108-8639, Japan
| | - Yutaka Suzuki
- Laboratory of Systems Genomics, Department of Computational Biology and Medical Sciences, Graduate School of Frontier Sciences, The University of Tokyo, Kashiwa, 277-8561, Japan
| | - Teppei Shimamura
- Division of Systems Biology, Nagoya University Graduate School of Medicine, Nagoya, 466-8550, Japan; Department of Computational and Systems Biology, Medical Research Insitute, Tokyo Medical and Dental University, Bunkyo-ku, Tokyo 113-0034, Japan.
| | - Koshi Mimori
- Department of Surgery, Kyushu University Beppu Hospital, Beppu, 874-0838, Japan.
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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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Gao F, You X, Yang L, Zou X, Sui B. Boosting immune responses in lung tumor immune microenvironment: A comprehensive review of strategies and adjuvants. Int Rev Immunol 2024:1-29. [PMID: 38525925 DOI: 10.1080/08830185.2024.2333275] [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: 11/05/2023] [Accepted: 03/15/2024] [Indexed: 03/26/2024]
Abstract
The immune system has a substantial impact on the growth and expansion of lung malignancies. Immune cells are encompassed by a stroma comprising an extracellular matrix (ECM) and different cells like stromal cells, which are known as the tumor immune microenvironment (TIME). TME is marked by the presence of immunosuppressive factors, which inhibit the function of immune cells and expand tumor growth. In recent years, numerous strategies and adjuvants have been developed to extend immune responses in the TIME, to improve the efficacy of immunotherapy. In this comprehensive review, we outline the present knowledge of immune evasion mechanisms in lung TIME, explain the biology of immune cells and diverse effectors on these components, and discuss various approaches for overcoming suppressive barriers. We highlight the potential of novel adjuvants, including toll-like receptor (TLR) agonists, cytokines, phytochemicals, nanocarriers, and oncolytic viruses, for enhancing immune responses in the TME. Ultimately, we provide a summary of ongoing clinical trials investigating these strategies and adjuvants in lung cancer patients. This review also provides a broad overview of the current state-of-the-art in boosting immune responses in the TIME and highlights the potential of these approaches for improving outcomes in lung cancer patients.
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Affiliation(s)
- Fei Gao
- Department of Oncology, The First Affiliated Hospital of Heilongjiang University of Chinese Medicine, Harbin, Heilongjiang Province, China
| | - Xiaoqing You
- Heilongjiang University of Chinese Medicine, Harbin, Heilongjiang Province, China
| | - Liu Yang
- Department of Oncology, Da Qing Long Nan Hospital, Daqing, Heilongjiang Province, China
| | - Xiangni Zou
- Department of Nursing, The First Affiliated Hospital of Heilongjiang University of Chinese Medicine, Harbin, Heilongjiang Province, China
| | - Bowen Sui
- Department of Oncology, The First Affiliated Hospital of Heilongjiang University of Chinese Medicine, Harbin, Heilongjiang Province, China
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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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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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Feng J, Province M, Li G, Payne PR, Chen Y, Li F. PathFinder: a novel graph transformer model to infer multi-cell intra- and inter-cellular signaling pathways and communications. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.01.13.575534. [PMID: 38293243 PMCID: PMC10827077 DOI: 10.1101/2024.01.13.575534] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/01/2024]
Abstract
Recently, large-scale scRNA-seq datasets have been generated to understand the complex and poorly understood signaling mechanisms within microenvironment of Alzheimer's Disease (AD), which are critical for identifying novel therapeutic targets and precision medicine. Though a set of targets have been identified, however, it remains a challenging to infer the core intra- and inter-multi-cell signaling communication networks using the scRNA-seq data, considering the complex and highly interactive background signaling network. Herein, we introduced a novel graph transformer model, PathFinder, to infer multi-cell intra- and inter-cellular signaling pathways and signaling communications among multi-cell types. Compared with existing models, the novel and unique design of PathFinder is based on the divide-and-conquer strategy, which divides the complex signaling networks into signaling paths, and then score and rank them using a novel graph transformer architecture to infer the intra- and inter-cell signaling communications. We evaluated PathFinder using scRNA-seq data of APOE4-genotype specific AD mice models and identified novel APOE4 altered intra- and inter-cell interaction networks among neurons, astrocytes, and microglia. PathFinder is a general signaling network inference model and can be applied to other omics data-driven signaling network inference.
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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, USA
- Department of Computer Science and Engineering, Washington University School of Medicine, Washington University in St. Louis, St. Louis, MO, USA
| | - Michael Province
- Division of Statistical Genomics, Department of Genetics, Washington University School of Medicine, Washington University in St. Louis, St. Louis, MO, USA
| | - Guangfu Li
- Department of Surgery, University of Missouri-Columbia, Columbia, MO, 65212, USA
- Department of Molecular Microbiology and Immunology, University of Missouri-Columbia, Columbia, MO, 65212, USA
- NextGen Precision Health Institute, University of Missouri-Columbia, Columbia, MO, 65212, USA
| | - Philip R.O. Payne
- Institute for Informatics (I2), Washington University School of Medicine, Washington University in St. Louis, St. Louis, MO, USA
| | - Yixin Chen
- Department of Computer Science and Engineering, Washington University School of Medicine, Washington University in St. Louis, St. Louis, MO, USA
| | - Fuhai Li
- Institute for Informatics (I2), Washington University School of Medicine, Washington University in St. Louis, St. Louis, MO, USA
- Department of Pediatrics, Washington University School of Medicine, Washington University in St. Louis, St. Louis, MO, USA
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Feng J, Goedegebuure SP, Zeng A, Bi Y, Wang T, Payne P, Ding L, DeNardo D, Hawkins W, Fields RC, Li F. sc2MeNetDrug: A computational tool to uncover inter-cell signaling targets and identify relevant drugs based on single cell RNA-seq data. PLoS Comput Biol 2024; 20:e1011785. [PMID: 38181047 PMCID: PMC10796047 DOI: 10.1371/journal.pcbi.1011785] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/07/2023] [Revised: 01/18/2024] [Accepted: 12/23/2023] [Indexed: 01/07/2024] Open
Abstract
Single-cell RNA sequencing (scRNA-seq) is a powerful technology to investigate the transcriptional programs in stromal, immune, and disease cells, like tumor cells or neurons within the Alzheimer's Disease (AD) brain or tumor microenvironment (ME) or niche. Cell-cell communications within ME play important roles in disease progression and immunotherapy response and are novel and critical therapeutic targets. Though many tools of scRNA-seq analysis have been developed to investigate the heterogeneity and sub-populations of cells, few were designed for uncovering cell-cell communications of ME and predicting the potentially effective drugs to inhibit the communications. Moreover, the data analysis processes of discovering signaling communication networks and effective drugs using scRNA-seq data are complex and involve a set of critical analysis processes and external supportive data resources, which are difficult for researchers who have no strong computational background and training in scRNA-seq data analysis. To address these challenges, in this study, we developed a novel open-source computational tool, sc2MeNetDrug (https://fuhaililab.github.io/sc2MeNetDrug/). It was specifically designed using scRNA-seq data to identify cell types within disease MEs, uncover the dysfunctional signaling pathways within individual cell types and interactions among different cell types, and predict effective drugs that can potentially disrupt cell-cell signaling communications. sc2MeNetDrug provided a user-friendly graphical user interface to encapsulate the data analysis modules, which can facilitate the scRNA-seq data-based discovery of novel inter-cell signaling communications and novel therapeutic regimens.
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Affiliation(s)
- Jiarui Feng
- Institute for Informatics (I2), Washington University School of Medicine, Washington University in St. Louis, St. Louis, Missouri, United States of America
- Department of Computer Science and Engineering, Washington University in St. Louis, St. Louis, Missouri, United States of America
| | - S. Peter Goedegebuure
- Department of Surgery, Washington University in St. Louis, St. Louis, Missouri, United States of America
- Siteman Cancer Center, Washington University in St. Louis, St. Louis, Missouri, United States of America
| | - Amanda Zeng
- Department of Computer Science and Engineering, Washington University in St. Louis, St. Louis, Missouri, United States of America
| | - Ye Bi
- Department of Surgery, Washington University in St. Louis, St. Louis, Missouri, United States of America
| | - Ting Wang
- Department of Genetics, Washington University in St. Louis, St. Louis, Missouri, United States of America
- McDonnell Genome Institute, Washington University in St. Louis, St. Louis, Missouri, United States of America
| | - Philip Payne
- Institute for Informatics (I2), Washington University School of Medicine, Washington University in St. Louis, St. Louis, Missouri, United States of America
| | - Li Ding
- Siteman Cancer Center, Washington University in St. Louis, St. Louis, Missouri, United States of America
- Department of Genetics, Washington University in St. Louis, St. Louis, Missouri, United States of America
- McDonnell Genome Institute, Washington University in St. Louis, St. Louis, Missouri, United States of America
- Department of Medicine, Washington University in St. Louis, St. Louis, Missouri, United States of America
| | - David DeNardo
- Department of Surgery, Washington University in St. Louis, St. Louis, Missouri, United States of America
- Siteman Cancer Center, Washington University in St. Louis, St. Louis, Missouri, United States of America
| | - William Hawkins
- Department of Surgery, Washington University in St. Louis, St. Louis, Missouri, United States of America
- Siteman Cancer Center, Washington University in St. Louis, St. Louis, Missouri, United States of America
| | - Ryan C. Fields
- Department of Surgery, Washington University in St. Louis, St. Louis, Missouri, United States of America
- Siteman Cancer Center, Washington University in St. Louis, St. Louis, Missouri, United States of America
| | - Fuhai Li
- Institute for Informatics (I2), Washington University School of Medicine, Washington University in St. Louis, St. Louis, Missouri, United States of America
- Department of Pediatrics, Washington University School of Medicine, Washington University in St. Louis, St. Louis, Missouri, United States of America
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11
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LaMarche NM, Hegde S, Park MD, Maier BB, Troncoso L, Le Berichel J, Hamon P, Belabed M, Mattiuz R, Hennequin C, Chin T, Reid AM, Reyes-Torres I, Nemeth E, Zhang R, Olson OC, Doroshow DB, Rohs NC, Gomez JE, Veluswamy R, Hall N, Venturini N, Ginhoux F, Liu Z, Buckup M, Figueiredo I, Roudko V, Miyake K, Karasuyama H, Gonzalez-Kozlova E, Gnjatic S, Passegué E, Kim-Schulze S, Brown BD, Hirsch FR, Kim BS, Marron TU, Merad M. An IL-4 signalling axis in bone marrow drives pro-tumorigenic myelopoiesis. Nature 2024; 625:166-174. [PMID: 38057662 PMCID: PMC11189607 DOI: 10.1038/s41586-023-06797-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/10/2023] [Accepted: 10/30/2023] [Indexed: 12/08/2023]
Abstract
Myeloid cells are known to suppress antitumour immunity1. However, the molecular drivers of immunosuppressive myeloid cell states are not well defined. Here we used single-cell RNA sequencing of human and mouse non-small cell lung cancer (NSCLC) lesions, and found that in both species the type 2 cytokine interleukin-4 (IL-4) was predicted to be the primary driver of the tumour-infiltrating monocyte-derived macrophage phenotype. Using a panel of conditional knockout mice, we found that only deletion of the IL-4 receptor IL-4Rα in early myeloid progenitors in bone marrow reduced tumour burden, whereas deletion of IL-4Rα in downstream mature myeloid cells had no effect. Mechanistically, IL-4 derived from bone marrow basophils and eosinophils acted on granulocyte-monocyte progenitors to transcriptionally programme the development of immunosuppressive tumour-promoting myeloid cells. Consequentially, depletion of basophils profoundly reduced tumour burden and normalized myelopoiesis. We subsequently initiated a clinical trial of the IL-4Rα blocking antibody dupilumab2-5 given in conjunction with PD-1/PD-L1 checkpoint blockade in patients with relapsed or refractory NSCLC who had progressed on PD-1/PD-L1 blockade alone (ClinicalTrials.gov identifier NCT05013450 ). Dupilumab supplementation reduced circulating monocytes, expanded tumour-infiltrating CD8 T cells, and in one out of six patients, drove a near-complete clinical response two months after treatment. Our study defines a central role for IL-4 in controlling immunosuppressive myelopoiesis in cancer, identifies a novel combination therapy for immune checkpoint blockade in humans, and highlights cancer as a systemic malady that requires therapeutic strategies beyond the primary disease site.
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Affiliation(s)
- Nelson M LaMarche
- Marc and Jennifer Lipschultz Precision Immunology Institute, Icahn School of Medicine at Mount Sinai, New York, NY, USA
- The Tisch Cancer Institute, Icahn School of Medicine at Mount Sinai, New York, NY, USA
- Department of Immunology and Immunotherapy, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Samarth Hegde
- Marc and Jennifer Lipschultz Precision Immunology Institute, Icahn School of Medicine at Mount Sinai, New York, NY, USA
- The Tisch Cancer Institute, Icahn School of Medicine at Mount Sinai, New York, NY, USA
- Department of Immunology and Immunotherapy, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Matthew D Park
- Marc and Jennifer Lipschultz Precision Immunology Institute, Icahn School of Medicine at Mount Sinai, New York, NY, USA
- The Tisch Cancer Institute, Icahn School of Medicine at Mount Sinai, New York, NY, USA
- Department of Immunology and Immunotherapy, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Barbara B Maier
- Marc and Jennifer Lipschultz Precision Immunology Institute, Icahn School of Medicine at Mount Sinai, New York, NY, USA
- The Tisch Cancer Institute, Icahn School of Medicine at Mount Sinai, New York, NY, USA
- Department of Immunology and Immunotherapy, Icahn School of Medicine at Mount Sinai, New York, NY, USA
- CeMM Research Center for Molecular Medicine of the Austrian Academy of Sciences, Vienna, Austria
| | - Leanna Troncoso
- Marc and Jennifer Lipschultz Precision Immunology Institute, Icahn School of Medicine at Mount Sinai, New York, NY, USA
- The Tisch Cancer Institute, Icahn School of Medicine at Mount Sinai, New York, NY, USA
- Department of Immunology and Immunotherapy, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Jessica Le Berichel
- Marc and Jennifer Lipschultz Precision Immunology Institute, Icahn School of Medicine at Mount Sinai, New York, NY, USA
- The Tisch Cancer Institute, Icahn School of Medicine at Mount Sinai, New York, NY, USA
- Department of Immunology and Immunotherapy, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Pauline Hamon
- Marc and Jennifer Lipschultz Precision Immunology Institute, Icahn School of Medicine at Mount Sinai, New York, NY, USA
- The Tisch Cancer Institute, Icahn School of Medicine at Mount Sinai, New York, NY, USA
- Department of Immunology and Immunotherapy, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Meriem Belabed
- Marc and Jennifer Lipschultz Precision Immunology Institute, Icahn School of Medicine at Mount Sinai, New York, NY, USA
- The Tisch Cancer Institute, Icahn School of Medicine at Mount Sinai, New York, NY, USA
- Department of Immunology and Immunotherapy, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Raphaël Mattiuz
- Marc and Jennifer Lipschultz Precision Immunology Institute, Icahn School of Medicine at Mount Sinai, New York, NY, USA
- The Tisch Cancer Institute, Icahn School of Medicine at Mount Sinai, New York, NY, USA
- Department of Immunology and Immunotherapy, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Clotilde Hennequin
- Marc and Jennifer Lipschultz Precision Immunology Institute, Icahn School of Medicine at Mount Sinai, New York, NY, USA
- The Tisch Cancer Institute, Icahn School of Medicine at Mount Sinai, New York, NY, USA
- Department of Immunology and Immunotherapy, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Theodore Chin
- Marc and Jennifer Lipschultz Precision Immunology Institute, Icahn School of Medicine at Mount Sinai, New York, NY, USA
- The Tisch Cancer Institute, Icahn School of Medicine at Mount Sinai, New York, NY, USA
- Department of Immunology and Immunotherapy, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Amanda M Reid
- Marc and Jennifer Lipschultz Precision Immunology Institute, Icahn School of Medicine at Mount Sinai, New York, NY, USA
- The Tisch Cancer Institute, Icahn School of Medicine at Mount Sinai, New York, NY, USA
- Department of Immunology and Immunotherapy, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Iván Reyes-Torres
- Marc and Jennifer Lipschultz Precision Immunology Institute, Icahn School of Medicine at Mount Sinai, New York, NY, USA
- The Tisch Cancer Institute, Icahn School of Medicine at Mount Sinai, New York, NY, USA
- Department of Immunology and Immunotherapy, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Erika Nemeth
- Marc and Jennifer Lipschultz Precision Immunology Institute, Icahn School of Medicine at Mount Sinai, New York, NY, USA
- The Tisch Cancer Institute, Icahn School of Medicine at Mount Sinai, New York, NY, USA
- Department of Immunology and Immunotherapy, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Ruiyuan Zhang
- Columbia Stem Cell Initiative, Department of Genetics and Development, Columbia University, New York, NY, USA
| | - Oakley C Olson
- Columbia Stem Cell Initiative, Department of Genetics and Development, Columbia University, New York, NY, USA
| | - Deborah B Doroshow
- The Tisch Cancer Institute, Icahn School of Medicine at Mount Sinai, New York, NY, USA
- Division of Hematology/Oncology, Icahn School of Medicine at Mount Sinai, New York, NY, USA
- Center for Thoracic Oncology, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Nicholas C Rohs
- The Tisch Cancer Institute, Icahn School of Medicine at Mount Sinai, New York, NY, USA
- Division of Hematology/Oncology, Icahn School of Medicine at Mount Sinai, New York, NY, USA
- Center for Thoracic Oncology, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Jorge E Gomez
- The Tisch Cancer Institute, Icahn School of Medicine at Mount Sinai, New York, NY, USA
- Division of Hematology/Oncology, Icahn School of Medicine at Mount Sinai, New York, NY, USA
- Center for Thoracic Oncology, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Rajwanth Veluswamy
- The Tisch Cancer Institute, Icahn School of Medicine at Mount Sinai, New York, NY, USA
- Division of Hematology/Oncology, Icahn School of Medicine at Mount Sinai, New York, NY, USA
- Center for Thoracic Oncology, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Nicole Hall
- The Tisch Cancer Institute, Icahn School of Medicine at Mount Sinai, New York, NY, USA
- Division of Hematology/Oncology, Icahn School of Medicine at Mount Sinai, New York, NY, USA
- Center for Thoracic Oncology, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Nicholas Venturini
- Marc and Jennifer Lipschultz Precision Immunology Institute, Icahn School of Medicine at Mount Sinai, New York, NY, USA
- The Tisch Cancer Institute, Icahn School of Medicine at Mount Sinai, New York, NY, USA
- Department of Immunology and Immunotherapy, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Florent Ginhoux
- Singapore Immunology Network (SIgN), Agency for Science, Technology and Research (A*STAR), BIOPOLIS, Singapore, Singapore
- INSERM U1015, Gustave Roussy Cancer Campus, Villejuif, France
- Shanghai Institute of Immunology, Shanghai Jiao Tong University School of Medicine, Shanghai, China
- SingHealth Duke-NUS Academic Medical Centre, Translational Immunology Institute, Singapore, Singapore
| | - Zhaoyuan Liu
- Shanghai Institute of Immunology, Shanghai Jiao Tong University School of Medicine, Shanghai, China
| | - Mark Buckup
- Marc and Jennifer Lipschultz Precision Immunology Institute, Icahn School of Medicine at Mount Sinai, New York, NY, USA
- The Tisch Cancer Institute, Icahn School of Medicine at Mount Sinai, New York, NY, USA
- Department of Immunology and Immunotherapy, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Igor Figueiredo
- Marc and Jennifer Lipschultz Precision Immunology Institute, Icahn School of Medicine at Mount Sinai, New York, NY, USA
- The Tisch Cancer Institute, Icahn School of Medicine at Mount Sinai, New York, NY, USA
- Department of Immunology and Immunotherapy, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Vladimir Roudko
- Marc and Jennifer Lipschultz Precision Immunology Institute, Icahn School of Medicine at Mount Sinai, New York, NY, USA
- Human Immune Monitoring Center, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Kensuke Miyake
- Inflammation, Infection and Immunity Laboratory, Advanced Research Institute, Tokyo Medical and Dental University (TMDU), Tokyo, Japan
| | - Hajime Karasuyama
- Inflammation, Infection and Immunity Laboratory, Advanced Research Institute, Tokyo Medical and Dental University (TMDU), Tokyo, Japan
| | - Edgar Gonzalez-Kozlova
- Marc and Jennifer Lipschultz Precision Immunology Institute, Icahn School of Medicine at Mount Sinai, New York, NY, USA
- The Tisch Cancer Institute, Icahn School of Medicine at Mount Sinai, New York, NY, USA
- Department of Immunology and Immunotherapy, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Sacha Gnjatic
- Marc and Jennifer Lipschultz Precision Immunology Institute, Icahn School of Medicine at Mount Sinai, New York, NY, USA
- The Tisch Cancer Institute, Icahn School of Medicine at Mount Sinai, New York, NY, USA
- Department of Immunology and Immunotherapy, Icahn School of Medicine at Mount Sinai, New York, NY, USA
- Division of Hematology/Oncology, Icahn School of Medicine at Mount Sinai, New York, NY, USA
- Human Immune Monitoring Center, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Emmanuelle Passegué
- Columbia Stem Cell Initiative, Department of Genetics and Development, Columbia University, New York, NY, USA
| | - Seunghee Kim-Schulze
- Marc and Jennifer Lipschultz Precision Immunology Institute, Icahn School of Medicine at Mount Sinai, New York, NY, USA
- Human Immune Monitoring Center, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Brian D Brown
- Marc and Jennifer Lipschultz Precision Immunology Institute, Icahn School of Medicine at Mount Sinai, New York, NY, USA
- The Tisch Cancer Institute, Icahn School of Medicine at Mount Sinai, New York, NY, USA
- Department of Immunology and Immunotherapy, Icahn School of Medicine at Mount Sinai, New York, NY, USA
- Icahn Genomics Institute, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Fred R Hirsch
- The Tisch Cancer Institute, Icahn School of Medicine at Mount Sinai, New York, NY, USA
- Division of Hematology/Oncology, Icahn School of Medicine at Mount Sinai, New York, NY, USA
- Center for Thoracic Oncology, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Brian S Kim
- Marc and Jennifer Lipschultz Precision Immunology Institute, Icahn School of Medicine at Mount Sinai, New York, NY, USA
- Kimberly and Eric J. Waldman Department of Dermatology, Icahn School of Medicine at Mount Sinai, New York City, NY, USA
- Mark Lebwohl Center for Neuroinflammation and Sensation, Icahn School of Medicine at Mount Sinai, New York City, NY, USA
- Friedman Brain Institute, Icahn School of Medicine at Mount Sinai, New York City, NY, USA
| | - Thomas U Marron
- Marc and Jennifer Lipschultz Precision Immunology Institute, Icahn School of Medicine at Mount Sinai, New York, NY, USA
- The Tisch Cancer Institute, Icahn School of Medicine at Mount Sinai, New York, NY, USA
- Department of Immunology and Immunotherapy, Icahn School of Medicine at Mount Sinai, New York, NY, USA
- Division of Hematology/Oncology, Icahn School of Medicine at Mount Sinai, New York, NY, USA
- Center for Thoracic Oncology, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Miriam Merad
- Marc and Jennifer Lipschultz Precision Immunology Institute, Icahn School of Medicine at Mount Sinai, New York, NY, USA.
- The Tisch Cancer Institute, Icahn School of Medicine at Mount Sinai, New York, NY, USA.
- Department of Immunology and Immunotherapy, Icahn School of Medicine at Mount Sinai, New York, NY, USA.
- Division of Hematology/Oncology, Icahn School of Medicine at Mount Sinai, New York, NY, USA.
- Center for Thoracic Oncology, Icahn School of Medicine at Mount Sinai, New York, NY, USA.
- Human Immune Monitoring Center, Icahn School of Medicine at Mount Sinai, New York, NY, USA.
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12
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Quach HT, Skovgard MS, Villena-Vargas J, Bellis RY, Chintala NK, Amador-Molina A, Bai Y, Banerjee S, Saini J, Xiong Y, Vista WR, Byun AJ, De Biasi A, Zeltsman M, Mayor M, Morello A, Mittal V, Gomez DR, Rimner A, Jones DR, Adusumilli PS. Tumor-Targeted Nonablative Radiation Promotes Solid Tumor CAR T-cell Therapy Efficacy. Cancer Immunol Res 2023; 11:1314-1331. [PMID: 37540803 PMCID: PMC10592183 DOI: 10.1158/2326-6066.cir-22-0840] [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: 10/28/2022] [Revised: 04/18/2023] [Accepted: 08/02/2023] [Indexed: 08/06/2023]
Abstract
Infiltration of tumor by T cells is a prerequisite for successful immunotherapy of solid tumors. In this study, we investigate the influence of tumor-targeted radiation on chimeric antigen receptor (CAR) T-cell therapy tumor infiltration, accumulation, and efficacy in clinically relevant models of pleural mesothelioma and non-small cell lung cancers. We use a nonablative dose of tumor-targeted radiation prior to systemic administration of mesothelin-targeted CAR T cells to assess infiltration, proliferation, antitumor efficacy, and functional persistence of CAR T cells at primary and distant sites of tumor. A tumor-targeted, nonablative dose of radiation promotes early and high infiltration, proliferation, and functional persistence of CAR T cells. Tumor-targeted radiation promotes tumor-chemokine expression and chemokine-receptor expression in infiltrating T cells and results in a subpopulation of higher-intensity CAR-expressing T cells with high coexpression of chemokine receptors that further infiltrate distant sites of disease, enhancing CAR T-cell antitumor efficacy. Enhanced CAR T-cell efficacy is evident in models of both high-mesothelin-expressing mesothelioma and mixed-mesothelin-expressing lung cancer-two thoracic cancers for which radiotherapy is part of the standard of care. Our results strongly suggest that the use of tumor-targeted radiation prior to systemic administration of CAR T cells may substantially improve CAR T-cell therapy efficacy for solid tumors. Building on our observations, we describe a translational strategy of "sandwich" cell therapy for solid tumors that combines sequential metastatic site-targeted radiation and CAR T cells-a regional solution to overcome barriers to systemic delivery of CAR T cells.
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Affiliation(s)
- Hue Tu Quach
- Thoracic Service, Department of Surgery, Memorial Sloan Kettering Cancer Center; New York, NY, USA
| | - Matthew S. Skovgard
- Thoracic Service, Department of Surgery, Memorial Sloan Kettering Cancer Center; New York, NY, USA
| | - Jonathan Villena-Vargas
- Thoracic Service, Department of Surgery, Memorial Sloan Kettering Cancer Center; New York, NY, USA
| | - Rebecca Y. Bellis
- Thoracic Service, Department of Surgery, Memorial Sloan Kettering Cancer Center; New York, NY, USA
| | - Navin K. Chintala
- Thoracic Service, Department of Surgery, Memorial Sloan Kettering Cancer Center; New York, NY, USA
| | - Alfredo Amador-Molina
- Thoracic Service, Department of Surgery, Memorial Sloan Kettering Cancer Center; New York, NY, USA
| | - Yang Bai
- Department of Cardiothoracic Surgery, Weill Cornell Medicine; New York, NY, USA
- Meyer Cancer Center, Weill Cornell Medicine; New York, NY, USA
| | - Srijita Banerjee
- Thoracic Service, Department of Surgery, Memorial Sloan Kettering Cancer Center; New York, NY, USA
| | - Jasmeen Saini
- Thoracic Service, Department of Surgery, Memorial Sloan Kettering Cancer Center; New York, NY, USA
| | - Yuquan Xiong
- Thoracic Service, Department of Surgery, Memorial Sloan Kettering Cancer Center; New York, NY, USA
| | - William-Ray Vista
- Thoracic Service, Department of Surgery, Memorial Sloan Kettering Cancer Center; New York, NY, USA
| | - Alexander J. Byun
- Thoracic Service, Department of Surgery, Memorial Sloan Kettering Cancer Center; New York, NY, USA
| | - Andreas De Biasi
- Thoracic Service, Department of Surgery, Memorial Sloan Kettering Cancer Center; New York, NY, USA
| | - Masha Zeltsman
- Thoracic Service, Department of Surgery, Memorial Sloan Kettering Cancer Center; New York, NY, USA
| | - Marissa Mayor
- Thoracic Service, Department of Surgery, Memorial Sloan Kettering Cancer Center; New York, NY, USA
| | - Aurore Morello
- Thoracic Service, Department of Surgery, Memorial Sloan Kettering Cancer Center; New York, NY, USA
| | - Vivek Mittal
- Department of Cardiothoracic Surgery, Weill Cornell Medicine; New York, NY, USA
- Meyer Cancer Center, Weill Cornell Medicine; New York, NY, USA
| | - Daniel R. Gomez
- Thoracic Radiation Oncology, Memorial Sloan Kettering Cancer Center; New York, NY, USA
| | - Andreas Rimner
- Thoracic Radiation Oncology, Memorial Sloan Kettering Cancer Center; New York, NY, USA
| | - David R. Jones
- Thoracic Service, Department of Surgery, Memorial Sloan Kettering Cancer Center; New York, NY, USA
| | - Prasad S. Adusumilli
- Thoracic Service, Department of Surgery, Memorial Sloan Kettering Cancer Center; New York, NY, USA
- Center for Cell Engineering, Memorial Sloan Kettering Cancer Center; New York, NY, USA
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13
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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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14
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Peng L, Yuan R, Han C, Han G, Tan J, Wang Z, Chen M, Chen X. CellEnBoost: A Boosting-Based Ligand-Receptor Interaction Identification Model for Cell-to-Cell Communication Inference. IEEE Trans Nanobioscience 2023; 22:705-715. [PMID: 37216267 DOI: 10.1109/tnb.2023.3278685] [Citation(s) in RCA: 6] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/24/2023]
Abstract
Cell-to-cell communication (CCC) plays important roles in multicellular organisms. The identification of communication between cancer cells themselves and one between cancer cells and normal cells in tumor microenvironment helps understand cancer genesis, development and metastasis. CCC is usually mediated by Ligand-Receptor Interactions (LRIs). In this manuscript, we developed a Boosting-based LRI identification model (CellEnBoost) for CCC inference. First, potential LRIs are predicted by data collection, feature extraction, dimensional reduction, and classification based on an ensemble of Light gradient boosting machine and AdaBoost combining convolutional neural network. Next, the predicted LRIs and known LRIs are filtered. Third, the filtered LRIs are applied to CCC elucidation by combining CCC strength measurement and single-cell RNA sequencing data. Finally, CCC inference results are visualized using heatmap view, Circos plot view, and network view. The experimental results show that CellEnBoost obtained the best AUCs and AUPRs on the collected four LRI datasets. Case study in human head and neck squamous cell carcinoma (HNSCC) tissues demonstrates that fibroblasts were more likely to communicate with HNSCC cells, which is in accord with the results from iTALK. We anticipate that this work can contribute to the diagnosis and treatment of cancers.
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15
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Zhang C, Tan G, Zhang Y, Zhong X, Zhao Z, Peng Y, Cheng Q, Xue K, Xu Y, Li X, Li F, Zhang Y. Comprehensive analyses of brain cell communications based on multiple scRNA-seq and snRNA-seq datasets for revealing novel mechanism in neurodegenerative diseases. CNS Neurosci Ther 2023; 29:2775-2786. [PMID: 37269061 PMCID: PMC10493674 DOI: 10.1111/cns.14280] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/17/2022] [Revised: 04/24/2023] [Accepted: 05/16/2023] [Indexed: 06/04/2023] Open
Abstract
AIMS Complex cellular communications between glial cells and neurons are critical for brain normal function and disorders, and single-cell level RNA-sequencing datasets display more advantages for analyzing cell communications. Therefore, it is necessary to systematically explore brain cell communications when considering factors such as sex and brain region. METHODS We extracted a total of 1,039,459 cells derived from 28 brain single-cell RNA-sequencing (scRNA-seq) or single-nucleus RNA-sequencing (snRNA-seq) datasets from the GEO database, including 12 human and 16 mouse datasets. These datasets were further divided into 71 new sub-datasets when considering disease, sex, and region conditions. In the meanwhile, we integrated four methods to evaluate ligand-receptor interaction score among six major brain cell types (microglia, neuron, astrocyte, oligodendrocyte, OPC, and endothelial cell). RESULTS For Alzheimer's disease (AD), disease-specific ligand-receptor pairs when compared with normal sub-datasets, such as SEMA4A-NRP1, were identified. Furthermore, we explored the sex- and region-specific cell communications and identified that WNT5A-ROR1 among microglia cells displayed close communications in male, and SPP1-ITGAV displayed close communications in the meninges region from microglia to neurons. Furthermore, based on the AD-specific cell communications, we constructed a model for AD early prediction and confirmed the predictive performance using multiple independent datasets. Finally, we developed an online platform for researchers to explore brain condition-specific cell communications. CONCLUSION This research provided a comprehensive study to explore brain cell communications, which could reveal novel biological mechanisms involved in normal brain function and neurodegenerative diseases such as AD.
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Affiliation(s)
- Chunlong Zhang
- College of Bioinformatics Science and TechnologyHarbin Medical UniversityHarbinChina
| | - Guiyuan Tan
- College of Bioinformatics Science and TechnologyHarbin Medical UniversityHarbinChina
| | - Yuxi Zhang
- College of Bioinformatics Science and TechnologyHarbin Medical UniversityHarbinChina
| | - Xiaoling Zhong
- College of Bioinformatics Science and TechnologyHarbin Medical UniversityHarbinChina
| | - Ziyan Zhao
- College of Bioinformatics Science and TechnologyHarbin Medical UniversityHarbinChina
| | - Yunyi Peng
- College of Bioinformatics Science and TechnologyHarbin Medical UniversityHarbinChina
| | - Qian Cheng
- College of Bioinformatics Science and TechnologyHarbin Medical UniversityHarbinChina
| | - Ke Xue
- College of Bioinformatics Science and TechnologyHarbin Medical UniversityHarbinChina
| | - Yanjun Xu
- College of Bioinformatics Science and TechnologyHarbin Medical UniversityHarbinChina
| | - Xia Li
- College of Bioinformatics Science and TechnologyHarbin Medical UniversityHarbinChina
| | - Feng Li
- College of Bioinformatics Science and TechnologyHarbin Medical UniversityHarbinChina
| | - Yunpeng Zhang
- College of Bioinformatics Science and TechnologyHarbin Medical UniversityHarbinChina
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16
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Sahni S, Wang B, Wu D, Dhruba SR, Nagy M, Patkar S, Ferreira I, Wang K, Ruppin E. Deactivation of ligand-receptor interactions enhancing lymphocyte infiltration drives melanoma resistance to Immune Checkpoint Blockade. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.09.20.558683. [PMID: 37886558 PMCID: PMC10602042 DOI: 10.1101/2023.09.20.558683] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 10/28/2023]
Abstract
Immune checkpoint blockade (ICB) is a promising cancer therapy; however, resistance often develops. To learn more about ICB resistance mechanisms, we developed IRIS (Immunotherapy Resistance cell-cell Interaction Scanner), a machine learning model aimed at identifying candidate ligand-receptor interactions (LRI) that are likely to mediate ICB resistance in the tumor microenvironment (TME). We developed and applied IRIS to identify resistance-mediating cell-type-specific ligand-receptor interactions by analyzing deconvolved transcriptomics data of the five largest melanoma ICB therapy cohorts. This analysis identifies a set of specific ligand-receptor pairs that are deactivated as tumors develop resistance, which we refer to as resistance deactivated interactions (RDI). Quite strikingly, the activity of these RDIs in pre-treatment samples offers a markedly stronger predictive signal for ICB therapy response compared to those that are activated as tumors develop resistance. Their predictive accuracy surpasses the state-of-the-art published transcriptomics biomarker signatures across an array of melanoma ICB datasets. Many of these RDIs are involved in chemokine signaling. Indeed, we further validate on an independent large melanoma patient cohort that their activity is associated with CD8+ T cell infiltration and enriched in hot/brisk tumors. Taken together, this study presents a new strongly predictive ICB response biomarker signature, showing that following ICB treatment resistant tumors turn inhibit lymphocyte infiltration by deactivating specific key ligand-receptor interactions.
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Affiliation(s)
- Sahil Sahni
- Cancer Data Science Laboratory (CDSL), Center for Cancer Research (CCR), National Cancer Institute (NCI), National Institutes of Health (NIH), Bethesda, MD USA
| | - Binbin Wang
- Cancer Data Science Laboratory (CDSL), Center for Cancer Research (CCR), National Cancer Institute (NCI), National Institutes of Health (NIH), Bethesda, MD USA
| | - Di Wu
- Laboratory of Pathology, Center for Cancer Research (CCR), National Cancer Institute (NCI), National Institutes of Health (NIH), Bethesda, MD USA
| | - Saugato Rahman Dhruba
- Cancer Data Science Laboratory (CDSL), Center for Cancer Research (CCR), National Cancer Institute (NCI), National Institutes of Health (NIH), Bethesda, MD USA
| | - Matthew Nagy
- Cancer Data Science Laboratory (CDSL), Center for Cancer Research (CCR), National Cancer Institute (NCI), National Institutes of Health (NIH), Bethesda, MD USA
| | - Sushant Patkar
- Artificial Intelligence Resource, Molecular Imaging Branch, National Cancer Institute (NCI), National Institutes of Health (NIH), Bethesda, MD USA
| | - Ingrid Ferreira
- Experimental Cancer Genetics, Wellcome Sanger Institute, Wellcome Genome Campus, Hinxton, Cambridge UK
| | - Kun Wang
- Cancer Data Science Laboratory (CDSL), Center for Cancer Research (CCR), National Cancer Institute (NCI), National Institutes of Health (NIH), Bethesda, MD USA
| | - Eytan Ruppin
- Cancer Data Science Laboratory (CDSL), Center for Cancer Research (CCR), National Cancer Institute (NCI), National Institutes of Health (NIH), Bethesda, MD USA
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17
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Markowitz GJ, Ban Y, Tavarez DA, Yoffe L, Podaza E, He Y, Martin MT, Crowley MJP, Sandoval TA, Gao D, Martin ML, Elemento O, Cubillos-Ruiz JR, McGraw TE, Altorki NK, Mittal V. Deficiency of metabolic regulator PKM2 activates the pentose phosphate pathway and generates TCF1+ progenitor CD8+ T cells to improve checkpoint blockade. RESEARCH SQUARE 2023:rs.3.rs-3356477. [PMID: 37790365 PMCID: PMC10543315 DOI: 10.21203/rs.3.rs-3356477/v1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 10/05/2023]
Abstract
TCF1high progenitor CD8+ T cells mediate the efficacy of PD-1 blockade, however the mechanisms that govern their generation and maintenance are poorly understood. Here, we show that targeting glycolysis through deletion of pyruvate kinase muscle 2 (PKM2) results in elevated pentose phosphate pathway (PPP) activity, leading to enrichment of a TCF1high central memory-like phenotype and increased responsiveness to PD-1 blockade in vivo. PKM2KO CD8+ T cells showed reduced glycolytic flux, accumulation of glycolytic intermediates and PPP metabolites, and increased PPP cycling as determined by 1,2 13C glucose carbon tracing. Small molecule agonism of the PPP without acute glycolytic impairment skewed CD8+ T cells towards a TCF1high population, generated a unique transcriptional landscape, enhanced tumor control in mice in combination with PD-1 blockade, and promoted tumor killing in patient-derived tumor organoids. Our study demonstrates a new metabolic reprogramming that contributes to a progenitor-like T cell state amenable to checkpoint blockade.
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18
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Ennis S, Ó Broin P, Szegezdi E. CCPlotR: an R package for the visualization of cell-cell interactions. BIOINFORMATICS ADVANCES 2023; 3:vbad130. [PMID: 37767186 PMCID: PMC10521630 DOI: 10.1093/bioadv/vbad130] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 08/19/2023] [Revised: 09/01/2023] [Accepted: 09/18/2023] [Indexed: 09/29/2023]
Abstract
Summary We present CCPlotR-an R package that generates visualizations of cell-cell interactions. CCPlotR is designed to work with the output of tools that predict cell-cell interactions from single-cell gene expression data and requires only a table of predicted interactions as input. The package can generate a comprehensive set of publication-ready figures such as heatmaps, dotplots, circos plots and network diagrams, providing a useful resource for researchers working on cell-cell interactions. Availability and implementation CCPlotR is available to download and install from GitHub (https://github.com/Sarah145/CCPlotR) and comes with a toy dataset to demonstrate the different functions. Support for users will be provided via the GitHub issues tracker (https://github.com/Sarah145/CCPlotR/issues).
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Affiliation(s)
- Sarah Ennis
- The SFI Centre for Research Training in Genomics Data Science, Galway, H91 TK33, Ireland
- Discipline of Bioinformatics, School of Mathematical & Statistical Sciences, University of Galway, Galway, H91 TK33, Ireland
- Apoptosis Research Centre, School of Biological & Chemical Sciences, University of Galway, Galway, H91 TK33, Ireland
| | - Pilib Ó Broin
- The SFI Centre for Research Training in Genomics Data Science, Galway, H91 TK33, Ireland
- Discipline of Bioinformatics, School of Mathematical & Statistical Sciences, University of Galway, Galway, H91 TK33, Ireland
| | - Eva Szegezdi
- The SFI Centre for Research Training in Genomics Data Science, Galway, H91 TK33, Ireland
- Apoptosis Research Centre, School of Biological & Chemical Sciences, University of Galway, Galway, H91 TK33, Ireland
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19
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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: 6] [Impact Index Per Article: 6.0] [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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20
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Sun J, Hu L, Bok S, Yallowitz AR, Cung M, McCormick J, Zheng LJ, Debnath S, Niu Y, Tan AY, Lalani S, Morse KW, Shinn D, Pajak A, Hammad M, Suhardi VJ, Li Z, Li N, Wang L, Zou W, Mittal V, Bostrom MPG, Xu R, Iyer S, Greenblatt MB. A vertebral skeletal stem cell lineage driving metastasis. Nature 2023; 621:602-609. [PMID: 37704733 PMCID: PMC10829697 DOI: 10.1038/s41586-023-06519-1] [Citation(s) in RCA: 10] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/26/2022] [Accepted: 08/04/2023] [Indexed: 09/15/2023]
Abstract
Vertebral bone is subject to a distinct set of disease processes from long bones, including a much higher rate of solid tumour metastases1-4. The basis for this distinct biology of vertebral bone has so far remained unknown. Here we identify a vertebral skeletal stem cell (vSSC) that co-expresses ZIC1 and PAX1 together with additional cell surface markers. vSSCs display formal evidence of stemness, including self-renewal, label retention and sitting at the apex of their differentiation hierarchy. vSSCs are physiologic mediators of vertebral bone formation, as genetic blockade of the ability of vSSCs to generate osteoblasts results in defects in the vertebral neural arch and body. Human counterparts of vSSCs can be identified in vertebral endplate specimens and display a conserved differentiation hierarchy and stemness features. Multiple lines of evidence indicate that vSSCs contribute to the high rates of vertebral metastatic tropism observed in breast cancer, owing in part to increased secretion of the novel metastatic trophic factor MFGE8. Together, our results indicate that vSSCs are distinct from other skeletal stem cells and mediate the unique physiology and pathology of vertebrae, including contributing to the high rate of vertebral metastasis.
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Affiliation(s)
- Jun Sun
- Department of Pathology and Laboratory Medicine, Weill Cornell Medicine, New York, NY, USA
| | - Lingling Hu
- Department of Pathology and Laboratory Medicine, Weill Cornell Medicine, New York, NY, USA
- Department of Spine Surgery, Hospital for Special Surgery, New York, NY, USA
| | - Seoyeon Bok
- Department of Pathology and Laboratory Medicine, Weill Cornell Medicine, New York, NY, USA
| | - Alisha R Yallowitz
- Department of Pathology and Laboratory Medicine, Weill Cornell Medicine, New York, NY, USA
| | - Michelle Cung
- Department of Pathology and Laboratory Medicine, Weill Cornell Medicine, New York, NY, USA
| | - Jason McCormick
- Flow Cytometry Core Facility, Weill Cornell Medicine, New York, NY, USA
| | - Ling J Zheng
- Department of Pathology and Laboratory Medicine, Weill Cornell Medicine, New York, NY, USA
| | - Shawon Debnath
- Department of Pathology and Laboratory Medicine, Weill Cornell Medicine, New York, NY, USA
| | - Yuzhe Niu
- Department of Pathology and Laboratory Medicine, Weill Cornell Medicine, New York, NY, USA
| | - Adrian Y Tan
- Genomics Resources Core Facility, Weill Cornell Medicine, New York, NY, USA
| | - Sarfaraz Lalani
- Department of Pathology and Laboratory Medicine, Weill Cornell Medicine, New York, NY, USA
| | - Kyle W Morse
- Department of Spine Surgery, Hospital for Special Surgery, New York, NY, USA
| | - Daniel Shinn
- Department of Spine Surgery, Hospital for Special Surgery, New York, NY, USA
- Weill Cornell Medical College, New York, NY, USA
| | - Anthony Pajak
- Department of Spine Surgery, Hospital for Special Surgery, New York, NY, USA
| | - Mohammed Hammad
- Research Division, Hospital for Special Surgery, New York, NY, USA
| | - Vincentius Jeremy Suhardi
- Research Division, Hospital for Special Surgery, New York, NY, USA
- Department of Orthopedic Surgery, Hospital for Special Surgery, New York, NY, USA
| | - Zan Li
- Department of Pathology and Laboratory Medicine, Weill Cornell Medicine, New York, NY, USA
| | - Na Li
- State Key Laboratory of Cellular Stress Biology, School of Medicine, Xiamen University, Xiamen, China
| | - Lijun Wang
- Institute of Microsurgery on Extremities, Shanghai Jiao Tong University Affiliated Sixth People's Hospital, Shanghai, China
| | - Weiguo Zou
- Institute of Microsurgery on Extremities, Shanghai Jiao Tong University Affiliated Sixth People's Hospital, Shanghai, China
- State Key Laboratory of Cell Biology, Shanghai Institute of Biochemistry and Cell Biology, Center for Excellence in Molecular Cell Science, Chinese Academy of Sciences, University of Chinese Academy of Sciences, Shanghai, China
| | - Vivek Mittal
- Department of Cardiothoracic Surgery, Weill Cornell Medicine, New York, NY, USA
| | - Mathias P G Bostrom
- Research Division, Hospital for Special Surgery, New York, NY, USA
- Department of Orthopedic Surgery, Hospital for Special Surgery, New York, NY, USA
- Department of Orthopedic Surgery, Weill Cornell Medicine, New York, NY, USA
| | - Ren Xu
- State Key Laboratory of Cellular Stress Biology, School of Medicine, Xiamen University, Xiamen, China
| | - Sravisht Iyer
- Department of Spine Surgery, Hospital for Special Surgery, New York, NY, USA
| | - Matthew B Greenblatt
- Department of Pathology and Laboratory Medicine, Weill Cornell Medicine, New York, NY, USA.
- Research Division, Hospital for Special Surgery, New York, NY, USA.
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21
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Maffuid K, Cao Y. Decoding the Complexity of Immune-Cancer Cell Interactions: Empowering the Future of Cancer Immunotherapy. Cancers (Basel) 2023; 15:4188. [PMID: 37627216 PMCID: PMC10453128 DOI: 10.3390/cancers15164188] [Citation(s) in RCA: 6] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/15/2023] [Revised: 08/16/2023] [Accepted: 08/16/2023] [Indexed: 08/27/2023] Open
Abstract
The tumor and tumor microenvironment (TME) consist of a complex network of cells, including malignant, immune, fibroblast, and vascular cells, which communicate with each other. Disruptions in cell-cell communication within the TME, caused by a multitude of extrinsic and intrinsic factors, can contribute to tumorigenesis, hinder the host immune system, and enable tumor evasion. Understanding and addressing intercellular miscommunications in the TME are vital for combating these processes. The effectiveness of immunotherapy and the heterogeneous response observed among patients can be attributed to the intricate cellular communication between immune cells and cancer cells. To unravel these interactions, various experimental, statistical, and computational techniques have been developed. These include ligand-receptor analysis, intercellular proximity labeling approaches, and imaging-based methods, which provide insights into the distorted cell-cell interactions within the TME. By characterizing these interactions, we can enhance the design of cancer immunotherapy strategies. In this review, we present recent advancements in the field of mapping intercellular communication, with a particular focus on immune-tumor cellular interactions. By modeling these interactions, we can identify critical factors and develop strategies to improve immunotherapy response and overcome treatment resistance.
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Affiliation(s)
- Kaitlyn Maffuid
- Division of Pharmacotherapy and Experimental Therapeutics, School of Pharmacy, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA;
| | - Yanguang Cao
- Division of Pharmacotherapy and Experimental Therapeutics, School of Pharmacy, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA;
- Lineberger Comprehensive Cancer Center, School of Medicine, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA
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22
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Pratt EC, Lopez-Montes A, Volpe A, Crowley MJ, Carter LM, Mittal V, Pillarsetty N, Ponomarev V, Udías JM, Grimm J, Herraiz JL. Simultaneous quantitative imaging of two PET radiotracers via the detection of positron-electron annihilation and prompt gamma emissions. Nat Biomed Eng 2023; 7:1028-1039. [PMID: 37400715 PMCID: PMC10810307 DOI: 10.1038/s41551-023-01060-y] [Citation(s) in RCA: 12] [Impact Index Per Article: 12.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/15/2022] [Accepted: 05/23/2023] [Indexed: 07/05/2023]
Abstract
In conventional positron emission tomography (PET), only one radiotracer can be imaged at a time, because all PET isotopes produce the same two 511 keV annihilation photons. Here we describe an image reconstruction method for the simultaneous in vivo imaging of two PET tracers and thereby the independent quantification of two molecular signals. This method of multiplexed PET imaging leverages the 350-700 keV range to maximize the capture of 511 keV annihilation photons and prompt γ-ray emission in the same energy window, hence eliminating the need for energy discrimination during reconstruction or for signal separation beforehand. We used multiplexed PET to track, in mice with subcutaneous tumours, the biodistributions of intravenously injected [124I]I-trametinib and 2-deoxy-2-[18F]fluoro-D-glucose, [124I]I-trametinib and its nanoparticle carrier [89Zr]Zr-ferumoxytol, and the prostate-specific membrane antigen (PSMA) and infused PSMA-targeted chimaeric antigen receptor T cells after the systemic administration of [68Ga]Ga-PSMA-11 and [124I]I. Multiplexed PET provides more information depth, gives new uses to prompt γ-ray-emitting isotopes, reduces radiation burden by omitting the need for an additional computed-tomography scan and can be implemented on preclinical and clinical systems without any modifications in hardware or image acquisition software.
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Affiliation(s)
- Edwin C Pratt
- Department of Pharmacology, Weill Cornell Graduate School, New York, NY, USA
- Molecular Pharmacology, Memorial Sloan Kettering Cancer Center, New York, NY, USA
- Department of Radiology, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Alejandro Lopez-Montes
- Nuclear Physics Group, EMFTEL and IPARCOS, Complutense University of Madrid, Madrid, Spain
- Department of Biomedical Engineering, Johns Hopkins University, Baltimore, MD, USA
| | - Alessia Volpe
- Department of Radiology, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Michael J Crowley
- Department of Cell and Developmental Biology, Weill Cornell Graduate School, New York, NY, USA
| | - Lukas M Carter
- Department of Radiology, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Vivek Mittal
- Department of Cell and Developmental Biology, Weill Cornell Graduate School, New York, NY, USA
- Department of Cardiothoracic Surgery, Weill Cornell Medicine, New York, USA
- Neuberger Berman Lung Cancer Center, Weill Cornell Medicine, New York, USA
- Sandra and Edward Meyer Cancer Center, Weill Cornell Medicine, New York, USA
| | | | - Vladimir Ponomarev
- Molecular Pharmacology, Memorial Sloan Kettering Cancer Center, New York, NY, USA
- Department of Radiology, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Jose M Udías
- Nuclear Physics Group, EMFTEL and IPARCOS, Complutense University of Madrid, Madrid, Spain
- Instituto de Investigación Sanitaria Hospital Clínico San Carlos, Madrid, Spain
| | - Jan Grimm
- Department of Pharmacology, Weill Cornell Graduate School, New York, NY, USA.
- Molecular Pharmacology, Memorial Sloan Kettering Cancer Center, New York, NY, USA.
- Department of Radiology, Memorial Sloan Kettering Cancer Center, New York, NY, USA.
| | - Joaquin L Herraiz
- Nuclear Physics Group, EMFTEL and IPARCOS, Complutense University of Madrid, Madrid, Spain.
- Instituto de Investigación Sanitaria Hospital Clínico San Carlos, Madrid, Spain.
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23
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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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24
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Li C, Zhang B, Schaafsma E, Reuben A, Wang L, Turk MJ, Zhang J, Cheng C. TimiGP: Inferring cell-cell interactions and prognostic associations in the tumor immune microenvironment through gene pairs. Cell Rep Med 2023; 4:101121. [PMID: 37467716 PMCID: PMC10394258 DOI: 10.1016/j.xcrm.2023.101121] [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: 12/02/2022] [Revised: 04/11/2023] [Accepted: 06/21/2023] [Indexed: 07/21/2023]
Abstract
Determining the prognostic association of different immune cell types in the tumor microenvironment is critical for understanding cancer biology and developing new therapeutic strategies. However, this is challenging in certain cancer types, where the abundance of different immune subsets is highly correlated. In this study, we develop a computational method named TimiGP to overcome this challenge. Based on bulk gene expression and survival data, TimiGP infers cell-cell interactions that reveal the association between immune cell relative abundance and prognosis. As demonstrated in metastatic melanoma, TimiGP prioritizes immune cells critical in prognosis based on the identified cell-cell interactions. Highly consistent results are obtained by TimiGP when applied to seven independent melanoma datasets and when different cell-type marker sets are used as inputs. Additionally, TimiGP can leverage single-cell RNA sequencing data to delineate the tumor immune microenvironment at high resolutions across a wide range of cancer types.
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Affiliation(s)
- Chenyang Li
- Department of Genomic Medicine, The University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA; Graduate School of Biomedical Sciences, The University of Texas MD Anderson Cancer Center UTHealth Houston, Houston, TX 77030, USA
| | - Baoyi Zhang
- Department of Chemical and Biomolecular Engineering, Rice University, Houston, TX 77030, USA
| | - Evelien Schaafsma
- Department of Microbiology and Immunology, Dartmouth College, Hanover, NH 03755, USA
| | - Alexandre Reuben
- Graduate School of Biomedical Sciences, The University of Texas MD Anderson Cancer Center UTHealth Houston, Houston, TX 77030, USA; Department of Thoracic/Head and Neck Medical Oncology, The University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA
| | - Linghua Wang
- Department of Genomic Medicine, The University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA; Graduate School of Biomedical Sciences, The University of Texas MD Anderson Cancer Center UTHealth Houston, Houston, TX 77030, USA
| | - Mary Jo Turk
- Department of Microbiology and Immunology, The Geisel School of Medicine at Dartmouth, Lebanon, NH 03756, USA; Norris Cotton Cancer Center, The Geisel School of Medicine at Dartmouth, Lebanon, NH 03756, USA
| | - Jianjun Zhang
- Department of Genomic Medicine, The University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA; Graduate School of Biomedical Sciences, The University of Texas MD Anderson Cancer Center UTHealth Houston, Houston, TX 77030, USA; Department of Thoracic/Head and Neck Medical Oncology, The University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA; Lung Cancer Genomics Program, The University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA; Lung Cancer Interception Program, The University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA.
| | - Chao Cheng
- Department of Medicine, Baylor College of Medicine, Houston, TX 77030, USA; Dan L. Duncan Comprehensive Cancer Center, Baylor College of Medicine, Houston, TX 77030, USA; The Institute for Clinical and Translational Research, Baylor College of Medicine, Houston, TX 77030, USA.
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25
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Jin J, Yu S, Lu P, Cao P. Deciphering plant cell-cell communications using single-cell omics data. Comput Struct Biotechnol J 2023; 21:3690-3695. [PMID: 37576747 PMCID: PMC10412842 DOI: 10.1016/j.csbj.2023.06.016] [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: 10/27/2022] [Revised: 06/16/2023] [Accepted: 06/16/2023] [Indexed: 08/15/2023] Open
Abstract
Plants have various cell types that respond to different environmental factors, and cell-cell communication is the fundamental process that controls these plant responses. The emergence of single-cell techniques provides opportunities to explore features unique to each cell type and construct a comprehensive cell-cell communication (CCC) network. Although the most current successes of CCC inference were achieved in animal research, computational methods can also be directly applied to plants. This review describes the current major models for cell-cell communication inference and summarizes the computational tools based on single-cell omics datasets. In addition, we discuss the limitations of plant cell-cell communication research and propose new directions to expand the field in meaningful ways.
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Affiliation(s)
- Jingjing Jin
- China Tobacco Gene Research Center, Zhengzhou Tobacco Research Institute of CNTC, Zhengzhou 450001, China
| | - Shizhou Yu
- Molecular Genetics Key Laboratory of China Tobacco, Guizhou Academy of Tobacco Science, Guiyang 550081, China
| | - Peng Lu
- China Tobacco Gene Research Center, Zhengzhou Tobacco Research Institute of CNTC, Zhengzhou 450001, China
| | - Peijian Cao
- China Tobacco Gene Research Center, Zhengzhou Tobacco Research Institute of CNTC, Zhengzhou 450001, China
- School of Agricultural Sciences, Zhengzhou University, Zhengzhou 450001, China
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26
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Ma S, Ji D, Wang X, Yang Y, Shi Y, Chen Y. Transcriptomic Analysis Reveals Candidate Ligand-Receptor Pairs and Signaling Networks Mediating Intercellular Communication between Hair Matrix Cells and Dermal Papilla Cells from Cashmere Goats. Cells 2023; 12:1645. [PMID: 37371115 DOI: 10.3390/cells12121645] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/08/2023] [Revised: 05/16/2023] [Accepted: 05/23/2023] [Indexed: 06/29/2023] Open
Abstract
Hair fiber growth is determined by the spatiotemporally controlled proliferation, differentiation, and apoptosis of hair matrix cells (HMCs) inside the hair follicle (HF); however, dermal papilla cells (DPCs), the cell population surrounded by HMCs, manipulate the above processes via intercellular crosstalk with HMCs. Therefore, exploring how the mutual commutations between the cells are molecularly achieved is vital to understanding the mechanisms underlying hair growth. Here, based on our previous successes in cultivating HMCs and DPCs from cashmere goats, we combined a series of techniques, including in vitro cell coculture, transcriptome sequencing, and bioinformatic analysis, to uncover ligand-receptor pairs and signaling networks mediating intercellular crosstalk. Firstly, we found that direct cellular interaction significantly alters cell cycle distribution patterns and changes the gene expression profiles of both cells at the global level. Next, we constructed the networks of ligand-receptor pairs mediating intercellular autocrine or paracrine crosstalk between the cells. A few pairs, such as LEP-LEPR, IL6-EGFR, RSPO1-LRP6, and ADM-CALCRL, are found to have known or potential roles in hair growth by acting as bridges linking cells. Further, we inferred the signaling axis connecting the cells from transcriptomic data with the advantage of CCCExplorer. Certain pathways, including INHBA-ACVR2A/ACVR2B-ACVR1/ACVR1B-SMAD3, were predicted as the axis mediating the promotive effect of INHBA on hair growth via paracrine crosstalk between DPCs and HMCs. Finally, we verified that LEP-LEPR and IL1A-IL1R1 are pivotal ligand-receptor pairs involved in autocrine and paracrine communication of DPCs and HMCs to DPCs, respectively. Our study provides a comprehensive landscape of intercellular crosstalk between key cell types inside HF at the molecular level, which is helpful for an in-depth understanding of the mechanisms related to hair growth.
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Affiliation(s)
- Sen Ma
- College of Animal Science and Technology, Henan Agricultural University, Zhengzhou 450002, China
- Henan Key Laboratory of Innovation and Utilization of Grassland Resources, Zhengzhou 450002, China
- Henan Engineering Research Center for Forage, Zhengzhou 450002, China
| | - Dejun Ji
- Key Laboratory for Animal Genetics and Molecular Breeding of Jiangsu Province, College of Animal Science and Technology, Yangzhou University, Yangzhou 225009, China
| | - Xiaolong Wang
- Key Laboratory of Animal Genetics, Breeding and Reproduction of Shaanxi Province, College of Animal Science and Technology, Northwest A&F University, Yangling 712100, China
| | - Yuxin Yang
- Key Laboratory of Animal Genetics, Breeding and Reproduction of Shaanxi Province, College of Animal Science and Technology, Northwest A&F University, Yangling 712100, China
| | - Yinghua Shi
- College of Animal Science and Technology, Henan Agricultural University, Zhengzhou 450002, China
- Henan Key Laboratory of Innovation and Utilization of Grassland Resources, Zhengzhou 450002, China
- Henan Engineering Research Center for Forage, Zhengzhou 450002, China
| | - Yulin Chen
- Key Laboratory of Animal Genetics, Breeding and Reproduction of Shaanxi Province, College of Animal Science and Technology, Northwest A&F University, Yangling 712100, China
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27
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Villemin JP, Bassaganyas L, Pourquier D, Boissière F, Cabello-Aguilar S, Crapez E, Tanos R, Cornillot E, Turtoi A, Colinge J. Inferring ligand-receptor cellular networks from bulk and spatial transcriptomic datasets with BulkSignalR. Nucleic Acids Res 2023:7152875. [PMID: 37144485 DOI: 10.1093/nar/gkad352] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/17/2022] [Revised: 03/24/2023] [Accepted: 04/22/2023] [Indexed: 05/06/2023] Open
Abstract
The study of cellular networks mediated by ligand-receptor interactions has attracted much attention recently owing to single-cell omics. However, rich collections of bulk data accompanied with clinical information exists and continue to be generated with no equivalent in single-cell so far. In parallel, spatial transcriptomic (ST) analyses represent a revolutionary tool in biology. A large number of ST projects rely on multicellular resolution, for instance the Visium™ platform, where several cells are analyzed at each location, thus producing localized bulk data. Here, we describe BulkSignalR, a R package to infer ligand-receptor networks from bulk data. BulkSignalR integrates ligand-receptor interactions with downstream pathways to estimate statistical significance. A range of visualization methods complement the statistics, including functions dedicated to spatial data. We demonstrate BulkSignalR relevance using different datasets, including new Visium liver metastasis ST data, with experimental validation of protein colocalization. A comparison with other ST packages shows the significantly higher quality of BulkSignalR inferences. BulkSignalR can be applied to any species thanks to its built-in generic ortholog mapping functionality.
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Affiliation(s)
- Jean-Philippe Villemin
- Institut de Recherche en Cancérologie de Montpellier (IRCM), Inserm U 1194, Montpellier, France
- Université de Montpellier, Montpellier, France
- Institut régional du Cancer Montpellier (ICM), Montpellier, France
| | - Laia Bassaganyas
- Institut de Recherche en Cancérologie de Montpellier (IRCM), Inserm U 1194, Montpellier, France
- Université de Montpellier, Montpellier, France
- Institut régional du Cancer Montpellier (ICM), Montpellier, France
| | - Didier Pourquier
- Institut de Recherche en Cancérologie de Montpellier (IRCM), Inserm U 1194, Montpellier, France
- Institut régional du Cancer Montpellier (ICM), Montpellier, France
| | | | - Simon Cabello-Aguilar
- Institut de Recherche en Cancérologie de Montpellier (IRCM), Inserm U 1194, Montpellier, France
- Université de Montpellier, Montpellier, France
- Institut régional du Cancer Montpellier (ICM), Montpellier, France
| | - Evelyne Crapez
- Institut de Recherche en Cancérologie de Montpellier (IRCM), Inserm U 1194, Montpellier, France
- Institut régional du Cancer Montpellier (ICM), Montpellier, France
| | - Rita Tanos
- Institut régional du Cancer Montpellier (ICM), Montpellier, France
| | - Emmanuel Cornillot
- Institut de Recherche en Cancérologie de Montpellier (IRCM), Inserm U 1194, Montpellier, France
- Université de Montpellier, Montpellier, France
- Institut régional du Cancer Montpellier (ICM), Montpellier, France
- Faculté de Pharmacie, Université de Montpellier, Montpellier, France
| | - Andrei Turtoi
- Institut de Recherche en Cancérologie de Montpellier (IRCM), Inserm U 1194, Montpellier, France
- Université de Montpellier, Montpellier, France
- Institut régional du Cancer Montpellier (ICM), Montpellier, France
| | - Jacques Colinge
- Institut de Recherche en Cancérologie de Montpellier (IRCM), Inserm U 1194, Montpellier, France
- Université de Montpellier, Montpellier, France
- Institut régional du Cancer Montpellier (ICM), Montpellier, France
- Faculté de Médecine, Université de Montpellier, Montpellier, France
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28
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Ferri-Borgogno S, Zhu Y, Sheng J, Burks JK, Gomez JA, Wong KK, Wong ST, Mok SC. Spatial Transcriptomics Depict Ligand-Receptor Cross-talk Heterogeneity at the Tumor-Stroma Interface in Long-Term Ovarian Cancer Survivors. Cancer Res 2023; 83:1503-1516. [PMID: 36787106 PMCID: PMC10159916 DOI: 10.1158/0008-5472.can-22-1821] [Citation(s) in RCA: 21] [Impact Index Per Article: 21.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/07/2022] [Revised: 12/06/2022] [Accepted: 02/10/2023] [Indexed: 02/15/2023]
Abstract
Advanced high-grade serous ovarian cancer (HGSC) is an aggressive disease that accounts for 70% of all ovarian cancer deaths. Nevertheless, 15% of patients diagnosed with advanced HGSC survive more than 10 years. The elucidation of predictive markers of these long-term survivors (LTS) could help identify therapeutic targets for the disease, and thus improve patient survival rates. To investigate the stromal heterogeneity of the tumor microenvironment (TME) in ovarian cancer, we used spatial transcriptomics to generate spatially resolved transcript profiles in treatment-naïve advanced HGSC from LTS and short-term survivors (STS) and determined the association between cancer-associated fibroblasts (CAF) heterogeneity and survival in patients with advanced HGSC. Spatial transcriptomics and single-cell RNA-sequencing data were integrated to distinguish tumor and stroma regions, and a computational method was developed to investigate spatially resolved ligand-receptor interactions between various tumor and CAF subtypes in the TME. A specific subtype of CAFs and its spatial location relative to a particular ovarian cancer cell subtype in the TME correlated with long-term survival in patients with advanced HGSC. Also, increased APOE-LRP5 cross-talk occurred at the stroma-tumor interface in tumor tissues from STS compared with LTS. These findings were validated using multiplex IHC. Overall, this spatial transcriptomics analysis revealed spatially resolved CAF-tumor cross-talk signaling networks in the ovarian TME that are associated with long-term survival of patients with HGSC. Further studies to confirm whether such cross-talk plays a role in modulating the malignant phenotype of HGSC and could serve as a predictive biomarker of patient survival are warranted. SIGNIFICANCE Generation of spatially resolved gene expression patterns in tumors from patients with ovarian cancer surviving more than 10 years allows the identification of novel predictive biomarkers and therapeutic targets for better patient management. See related commentary by Kelliher and Lengyel, p. 1383.
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Affiliation(s)
- Sammy Ferri-Borgogno
- Department of Gynecologic Oncology and Reproductive Medicine, The University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA
| | - Ying Zhu
- Systems Medicine and Bioengineering Department, Houston Methodist Cancer Center, Houston Methodist Hospital, Houston, TX 77030, USA
- Departments of Pathology and Laboratory Medicine and Radiology, Houston Methodist Hospital, Weill Cornell Medicine, Houston, TX 77030, USA
| | - Jianting Sheng
- Systems Medicine and Bioengineering Department, Houston Methodist Cancer Center, Houston Methodist Hospital, Houston, TX 77030, USA
- Departments of Pathology and Laboratory Medicine and Radiology, Houston Methodist Hospital, Weill Cornell Medicine, Houston, TX 77030, USA
| | - Jared K. Burks
- Department of Leukemia, The University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA
| | - Javier A. Gomez
- Department of Leukemia, The University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA
| | - Kwong Kwok Wong
- Department of Gynecologic Oncology and Reproductive Medicine, The University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA
| | - Stephen T.C. Wong
- Systems Medicine and Bioengineering Department, Houston Methodist Cancer Center, Houston Methodist Hospital, Houston, TX 77030, USA
- Departments of Pathology and Laboratory Medicine and Radiology, Houston Methodist Hospital, Weill Cornell Medicine, Houston, TX 77030, USA
| | - Samuel C. Mok
- Department of Gynecologic Oncology and Reproductive Medicine, The University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA
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29
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Groppa E, Martini P, Derakhshan N, Theret M, Ritso M, Tung LW, Wang YX, Soliman H, Hamer MS, Stankiewicz L, Eisner C, Erwan LN, Chang C, Yi L, Yuan JH, Kong S, Weng C, Adams J, Chang L, Peng A, Blau HM, Romualdi C, Rossi FMV. Spatial compartmentalization of signaling imparts source-specific functions on secreted factors. Cell Rep 2023; 42:112051. [PMID: 36729831 DOI: 10.1016/j.celrep.2023.112051] [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: 10/04/2020] [Revised: 09/08/2022] [Accepted: 01/16/2023] [Indexed: 02/03/2023] Open
Abstract
Efficient regeneration requires multiple cell types acting in coordination. To better understand the intercellular networks involved and how they change when regeneration fails, we profile the transcriptome of hematopoietic, stromal, myogenic, and endothelial cells over 14 days following acute muscle damage. We generate a time-resolved computational model of interactions and identify VEGFA-driven endothelial engagement as a key differentiating feature in models of successful and failed regeneration. In addition, the analysis highlights that the majority of secreted signals, including VEGFA, are simultaneously produced by multiple cell types. To test whether the cellular source of a factor determines its function, we delete VEGFA from two cell types residing in close proximity: stromal and myogenic progenitors. By comparing responses to different types of damage, we find that myogenic and stromal VEGFA have distinct functions in regeneration. This suggests that spatial compartmentalization of signaling plays a key role in intercellular communication networks.
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Affiliation(s)
- Elena Groppa
- School of Biomedical Engineering, University of British Columbia, 2222 Health Sciences Mall, Vancouver, BC, Canada; Borea Therapeutics, Scuola Internazionale Superiore di Studi Avanzati, Via Bonomea 265, Trieste, Italy
| | - Paolo Martini
- Department of Molecular and Translational Medicine, University of Brescia, Brescia, Italy; Department of Biology, University of Padova, via U. Bassi 58B, Padova, Italy
| | - Nima Derakhshan
- School of Biomedical Engineering, University of British Columbia, 2222 Health Sciences Mall, Vancouver, BC, Canada
| | - Marine Theret
- School of Biomedical Engineering, University of British Columbia, 2222 Health Sciences Mall, Vancouver, BC, Canada
| | - Morten Ritso
- School of Biomedical Engineering, University of British Columbia, 2222 Health Sciences Mall, Vancouver, BC, Canada
| | - Lin Wei Tung
- School of Biomedical Engineering, University of British Columbia, 2222 Health Sciences Mall, Vancouver, BC, Canada
| | - Yu Xin Wang
- Baxter Laboratory for Stem Cell Biology, Department of Microbiology and Immunology, Stanford University School of Medicine, Stanford, CA, USA
| | - Hesham Soliman
- School of Biomedical Engineering, University of British Columbia, 2222 Health Sciences Mall, Vancouver, BC, Canada; Faculty of Pharmaceutical Sciences, Minia University, Minia, Egypt; Aspect Biosystems, 1781 W 75th Avenue, Vancouver, BC, Canada
| | - Mark Stephen Hamer
- School of Biomedical Engineering, University of British Columbia, 2222 Health Sciences Mall, Vancouver, BC, Canada
| | - Laura Stankiewicz
- School of Biomedical Engineering, University of British Columbia, 2222 Health Sciences Mall, Vancouver, BC, Canada
| | - Christine Eisner
- School of Biomedical Engineering, University of British Columbia, 2222 Health Sciences Mall, Vancouver, BC, Canada
| | - Le Nevé Erwan
- Department of Pediatrics, Université Laval, Laval, QC, Canada
| | - Chihkai Chang
- School of Biomedical Engineering, University of British Columbia, 2222 Health Sciences Mall, Vancouver, BC, Canada
| | - Lin Yi
- School of Biomedical Engineering, University of British Columbia, 2222 Health Sciences Mall, Vancouver, BC, Canada
| | - Jack H Yuan
- School of Biomedical Engineering, University of British Columbia, 2222 Health Sciences Mall, Vancouver, BC, Canada
| | - Sunny Kong
- School of Biomedical Engineering, University of British Columbia, 2222 Health Sciences Mall, Vancouver, BC, Canada
| | - Curtis Weng
- School of Biomedical Engineering, University of British Columbia, 2222 Health Sciences Mall, Vancouver, BC, Canada
| | - Josephine Adams
- School of Biomedical Engineering, University of British Columbia, 2222 Health Sciences Mall, Vancouver, BC, Canada
| | - Lucas Chang
- School of Biomedical Engineering, University of British Columbia, 2222 Health Sciences Mall, Vancouver, BC, Canada
| | - Anne Peng
- School of Biomedical Engineering, University of British Columbia, 2222 Health Sciences Mall, Vancouver, BC, Canada
| | - Helen M Blau
- Baxter Laboratory for Stem Cell Biology, Department of Microbiology and Immunology, Stanford University School of Medicine, Stanford, CA, USA
| | - Chiara Romualdi
- Department of Biology, University of Padova, via U. Bassi 58B, Padova, Italy
| | - Fabio M V Rossi
- School of Biomedical Engineering, University of British Columbia, 2222 Health Sciences Mall, Vancouver, BC, Canada.
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30
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Crowley MJP, Bhinder B, Markowitz GJ, Martin M, Verma A, Sandoval TA, Chae CS, Yomtoubian S, Hu Y, Chopra S, Tavarez DA, Giovanelli P, Gao D, McGraw TE, Altorki NK, Elemento O, Cubillos-Ruiz JR, Mittal V. Tumor-intrinsic IRE1α signaling controls protective immunity in lung cancer. Nat Commun 2023; 14:120. [PMID: 36624093 PMCID: PMC9829901 DOI: 10.1038/s41467-022-35584-9] [Citation(s) in RCA: 12] [Impact Index Per Article: 12.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/24/2021] [Accepted: 12/13/2022] [Indexed: 01/11/2023] Open
Abstract
IRE1α-XBP1 signaling is emerging as a central orchestrator of malignant progression and immunosuppression in various cancer types. Employing a computational XBP1s detection method applied to TCGA datasets, we demonstrate that expression of the XBP1s mRNA isoform predicts poor survival in non-small cell lung cancer (NSCLC) patients. Ablation of IRE1α in malignant cells delays tumor progression and extends survival in mouse models of NSCLC. This protective effect is accompanied by alterations in intratumoral immune cell subsets eliciting durable adaptive anti-cancer immunity. Mechanistically, cancer cell-intrinsic IRE1α activation sustains mPGES-1 expression, enabling production of the immunosuppressive lipid mediator prostaglandin E2. Accordingly, restoring mPGES-1 expression in IRE1αKO cancer cells rescues normal tumor progression. We have developed an IRE1α gene signature that predicts immune cell infiltration and overall survival in human NSCLC. Our study unveils an immunoregulatory role for cancer cell-intrinsic IRE1α activation and suggests that targeting this pathway may help enhance anti-tumor immunity in NSCLC.
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Affiliation(s)
- Michael J P Crowley
- Department of Cardiothoracic Surgery, Weill Cornell Medicine, 525 East 68th street, New York, NY, 10065, USA
- Neuberger Berman Lung Cancer Center, Weill Cornell Medicine, 525 East 68th street, New York, NY, 10065, USA
- Weill Cornell Graduate School of Medical Sciences, Weill Cornell Medicine, 525 East 68th street, New York, NY, 10065, USA
| | - Bhavneet Bhinder
- Caryl and Israel Englander Institute for Precision Medicine, Weill Cornell Medicine, 413 East 69th street, New York, NY, 10065, USA
- HRH Prince Alwaleed Bin Talal Bin Abdulaziz Alsaud Institute for Computational Biomedicine, Department of Physiology and Biophysics, Weill Cornell Medicine, 525 East 68th street, New York, NY, 10065, USA
| | - Geoffrey J Markowitz
- Department of Cardiothoracic Surgery, Weill Cornell Medicine, 525 East 68th street, New York, NY, 10065, USA
- Neuberger Berman Lung Cancer Center, Weill Cornell Medicine, 525 East 68th street, New York, NY, 10065, USA
- Department of Cell and Developmental Biology, Weill Cornell Medicine, 525 East 68th street, New York, NYk, 10065, USA
| | - Mitchell Martin
- Department of Cardiothoracic Surgery, Weill Cornell Medicine, 525 East 68th street, New York, NY, 10065, USA
- Neuberger Berman Lung Cancer Center, Weill Cornell Medicine, 525 East 68th street, New York, NY, 10065, USA
- Weill Cornell Graduate School of Medical Sciences, Weill Cornell Medicine, 525 East 68th street, New York, NY, 10065, USA
| | - Akanksha Verma
- Weill Cornell Graduate School of Medical Sciences, Weill Cornell Medicine, 525 East 68th street, New York, NY, 10065, USA
- Caryl and Israel Englander Institute for Precision Medicine, Weill Cornell Medicine, 413 East 69th street, New York, NY, 10065, USA
- HRH Prince Alwaleed Bin Talal Bin Abdulaziz Alsaud Institute for Computational Biomedicine, Department of Physiology and Biophysics, Weill Cornell Medicine, 525 East 68th street, New York, NY, 10065, USA
- Volastra Therapeutics, New York, NY, 10027, USA
| | - Tito A Sandoval
- Sandra and Edward Meyer Cancer Center, Weill Cornell Medicine, 413 East 69th street, New York, NY, 10065, USA
- Department of Obstetrics and Gynecology, Weill Cornell Medicine, 525 East 68th street, New York, NY, 10065, USA
| | - Chang-Suk Chae
- Sandra and Edward Meyer Cancer Center, Weill Cornell Medicine, 413 East 69th street, New York, NY, 10065, USA
- Department of Obstetrics and Gynecology, Weill Cornell Medicine, 525 East 68th street, New York, NY, 10065, USA
| | - Shira Yomtoubian
- Department of Cardiothoracic Surgery, Weill Cornell Medicine, 525 East 68th street, New York, NY, 10065, USA
- Neuberger Berman Lung Cancer Center, Weill Cornell Medicine, 525 East 68th street, New York, NY, 10065, USA
- Weill Cornell Graduate School of Medical Sciences, Weill Cornell Medicine, 525 East 68th street, New York, NY, 10065, USA
- Salk Institute for Biological Studies, San Diego, CA, USA
| | - Yang Hu
- Caryl and Israel Englander Institute for Precision Medicine, Weill Cornell Medicine, 413 East 69th street, New York, NY, 10065, USA
- HRH Prince Alwaleed Bin Talal Bin Abdulaziz Alsaud Institute for Computational Biomedicine, Department of Physiology and Biophysics, Weill Cornell Medicine, 525 East 68th street, New York, NY, 10065, USA
| | - Sahil Chopra
- Weill Cornell Graduate School of Medical Sciences, Weill Cornell Medicine, 525 East 68th street, New York, NY, 10065, USA
- Department of Obstetrics and Gynecology, Weill Cornell Medicine, 525 East 68th street, New York, NY, 10065, USA
- Vertex Ventures HC, 345 California Avenue, Palo Alto, CA, 94306, USA
| | - Diamile A Tavarez
- Department of Cardiothoracic Surgery, Weill Cornell Medicine, 525 East 68th street, New York, NY, 10065, USA
- Neuberger Berman Lung Cancer Center, Weill Cornell Medicine, 525 East 68th street, New York, NY, 10065, USA
- Regeneron Pharmaceuticals, 777 Old Saw Mill River Rd, Tarrytown, NY, 10591, USA
| | - Paolo Giovanelli
- Weill Cornell Graduate School of Medical Sciences, Weill Cornell Medicine, 525 East 68th street, New York, NY, 10065, USA
- Immunology and Microbial Pathogenesis Program, Weill Cornell Medicine, 525 East 68th street, New York, NY, 10065, USA
| | - Dingcheng Gao
- Department of Cardiothoracic Surgery, Weill Cornell Medicine, 525 East 68th street, New York, NY, 10065, USA
- Neuberger Berman Lung Cancer Center, Weill Cornell Medicine, 525 East 68th street, New York, NY, 10065, USA
- Department of Cell and Developmental Biology, Weill Cornell Medicine, 525 East 68th street, New York, NYk, 10065, USA
| | - Timothy E McGraw
- Department of Cardiothoracic Surgery, Weill Cornell Medicine, 525 East 68th street, New York, NY, 10065, USA
- Neuberger Berman Lung Cancer Center, Weill Cornell Medicine, 525 East 68th street, New York, NY, 10065, USA
- Weill Cornell Graduate School of Medical Sciences, Weill Cornell Medicine, 525 East 68th street, New York, NY, 10065, USA
- Sandra and Edward Meyer Cancer Center, Weill Cornell Medicine, 413 East 69th street, New York, NY, 10065, USA
- Department of Biochemistry, Weill Cornell Medicine, 525 East 68th street, New York, NY, 10065, USA
| | - Nasser K Altorki
- Department of Cardiothoracic Surgery, Weill Cornell Medicine, 525 East 68th street, New York, NY, 10065, USA
- Neuberger Berman Lung Cancer Center, Weill Cornell Medicine, 525 East 68th street, New York, NY, 10065, USA
- Caryl and Israel Englander Institute for Precision Medicine, Weill Cornell Medicine, 413 East 69th street, New York, NY, 10065, USA
- Sandra and Edward Meyer Cancer Center, Weill Cornell Medicine, 413 East 69th street, New York, NY, 10065, USA
| | - Olivier Elemento
- Caryl and Israel Englander Institute for Precision Medicine, Weill Cornell Medicine, 413 East 69th street, New York, NY, 10065, USA
- HRH Prince Alwaleed Bin Talal Bin Abdulaziz Alsaud Institute for Computational Biomedicine, Department of Physiology and Biophysics, Weill Cornell Medicine, 525 East 68th street, New York, NY, 10065, USA
- Sandra and Edward Meyer Cancer Center, Weill Cornell Medicine, 413 East 69th street, New York, NY, 10065, USA
| | - Juan R Cubillos-Ruiz
- Weill Cornell Graduate School of Medical Sciences, Weill Cornell Medicine, 525 East 68th street, New York, NY, 10065, USA.
- Sandra and Edward Meyer Cancer Center, Weill Cornell Medicine, 413 East 69th street, New York, NY, 10065, USA.
- Department of Obstetrics and Gynecology, Weill Cornell Medicine, 525 East 68th street, New York, NY, 10065, USA.
- Immunology and Microbial Pathogenesis Program, Weill Cornell Medicine, 525 East 68th street, New York, NY, 10065, USA.
| | - Vivek Mittal
- Department of Cardiothoracic Surgery, Weill Cornell Medicine, 525 East 68th street, New York, NY, 10065, USA.
- Neuberger Berman Lung Cancer Center, Weill Cornell Medicine, 525 East 68th street, New York, NY, 10065, USA.
- Weill Cornell Graduate School of Medical Sciences, Weill Cornell Medicine, 525 East 68th street, New York, NY, 10065, USA.
- Caryl and Israel Englander Institute for Precision Medicine, Weill Cornell Medicine, 413 East 69th street, New York, NY, 10065, USA.
- Department of Cell and Developmental Biology, Weill Cornell Medicine, 525 East 68th street, New York, NYk, 10065, USA.
- Sandra and Edward Meyer Cancer Center, Weill Cornell Medicine, 413 East 69th street, New York, NY, 10065, USA.
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31
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Hyrossova P, Milosevic M, Alghadi AY, Kucera L, Prochazka J, Sedlacek R, Rohlena J, Rohlenova K. Spatial Analysis of Nucleotide Metabolism: From CRISPR Knockout Cancer Cells to MALDI Imaging of Tumors. Methods Mol Biol 2023; 2675:297-308. [PMID: 37258772 DOI: 10.1007/978-1-0716-3247-5_22] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/02/2023]
Abstract
Cancer cells depend on nucleotides for proliferation. Inhibition of nucleotide metabolism by antimetabolites is a well-established anticancer therapy. However, resistance and toxicity to antimetabolite treatments reduce their effectiveness. Here, we focus on the pyrimidine de novo synthesis pathway, which is crucial for cancer cell proliferation, yet its pharmacological targeting in cancer has been without much clinical success so far. Hence, it is important to understand how cancer cells cope with the insufficiency of this pathway. Here, we describe a procedure to prepare subcutaneous tumor model deficient in de novo pyrimidine synthesis. For examination of metabolic responses to de novo synthesis blockade in tumors, we propose application of MALDI imaging that allows spatially resolved examination of metabolic responses to de novo synthesis blockade in tumors.
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Affiliation(s)
- Petra Hyrossova
- Laboratory of Cellular Metabolism, Institute of Biotechnology of the Czech Academy of Sciences, Vestec, Czech Republic
| | - Mirko Milosevic
- Laboratory of Cellular Metabolism, Institute of Biotechnology of the Czech Academy of Sciences, Vestec, Czech Republic
- Faculty of Science, Charles University, Prague, Czech Republic
| | - Ahmad Y Alghadi
- Laboratory of Cellular Metabolism, Institute of Biotechnology of the Czech Academy of Sciences, Vestec, Czech Republic
| | - Lukas Kucera
- Czech Center for Phenogenomics, Institute of Molecular Genetics of the Czech Academy of Sciences, Prague, Czech Republic
| | - Jan Prochazka
- Czech Center for Phenogenomics, Institute of Molecular Genetics of the Czech Academy of Sciences, Prague, Czech Republic
| | - Radislav Sedlacek
- Czech Center for Phenogenomics, Institute of Molecular Genetics of the Czech Academy of Sciences, Prague, Czech Republic
| | - Jakub Rohlena
- Laboratory of Cellular Metabolism, Institute of Biotechnology of the Czech Academy of Sciences, Vestec, Czech Republic
| | - Katerina Rohlenova
- Laboratory of Cellular Metabolism, Institute of Biotechnology of the Czech Academy of Sciences, Vestec, Czech Republic.
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Su M, Pan T, Chen QZ, Zhou WW, Gong Y, Xu G, Yan HY, Li S, Shi QZ, Zhang Y, He X, Jiang CJ, Fan SC, Li X, Cairns MJ, Wang X, Li YS. Data analysis guidelines for single-cell RNA-seq in biomedical studies and clinical applications. Mil Med Res 2022; 9:68. [PMID: 36461064 PMCID: PMC9716519 DOI: 10.1186/s40779-022-00434-8] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 09/27/2022] [Accepted: 11/18/2022] [Indexed: 12/03/2022] Open
Abstract
The application of single-cell RNA sequencing (scRNA-seq) in biomedical research has advanced our understanding of the pathogenesis of disease and provided valuable insights into new diagnostic and therapeutic strategies. With the expansion of capacity for high-throughput scRNA-seq, including clinical samples, the analysis of these huge volumes of data has become a daunting prospect for researchers entering this field. Here, we review the workflow for typical scRNA-seq data analysis, covering raw data processing and quality control, basic data analysis applicable for almost all scRNA-seq data sets, and advanced data analysis that should be tailored to specific scientific questions. While summarizing the current methods for each analysis step, we also provide an online repository of software and wrapped-up scripts to support the implementation. Recommendations and caveats are pointed out for some specific analysis tasks and approaches. We hope this resource will be helpful to researchers engaging with scRNA-seq, in particular for emerging clinical applications.
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Affiliation(s)
- Min Su
- State Key Laboratory of Reproductive Medicine, Nanjing Medical University, Nanjing, 211166, China
| | - Tao Pan
- College of Biomedical Information and Engineering, the First Affiliated Hospital of Hainan Medical University, Hainan Medical University, Haikou, 571199, Hainan, China
| | - Qiu-Zhen Chen
- State Key Laboratory of Reproductive Medicine, Nanjing Medical University, Nanjing, 211166, China
| | - Wei-Wei Zhou
- College of Bioinformatics Science and Technology, Harbin Medical University, Harbin, 150081, Heilongjiang, China
| | - Yi Gong
- State Key Laboratory of Reproductive Medicine, Nanjing Medical University, Nanjing, 211166, China.,Department of Immunology, Nanjing Medical University, Nanjing, 211166, China
| | - Gang Xu
- College of Biomedical Information and Engineering, the First Affiliated Hospital of Hainan Medical University, Hainan Medical University, Haikou, 571199, Hainan, China
| | - Huan-Yu Yan
- State Key Laboratory of Reproductive Medicine, Nanjing Medical University, Nanjing, 211166, China
| | - Si Li
- College of Biomedical Information and Engineering, the First Affiliated Hospital of Hainan Medical University, Hainan Medical University, Haikou, 571199, Hainan, China
| | - Qiao-Zhen Shi
- State Key Laboratory of Reproductive Medicine, Nanjing Medical University, Nanjing, 211166, China
| | - Ya Zhang
- College of Biomedical Information and Engineering, the First Affiliated Hospital of Hainan Medical University, Hainan Medical University, Haikou, 571199, Hainan, China
| | - Xiao He
- Department of Laboratory Medicine, Women and Children's Hospital of Chongqing Medical University, Chongqing, 401174, China
| | | | - Shi-Cai Fan
- Shenzhen Institute for Advanced Study, University of Electronic Science and Technology of China, Shenzhen, 518110, Guangdong, China
| | - Xia Li
- College of Bioinformatics Science and Technology, Harbin Medical University, Harbin, 150081, Heilongjiang, China.
| | - Murray J Cairns
- School of Biomedical Sciences and Pharmacy, Faculty of Health and Medicine, the University of Newcastle, University Drive, Callaghan, NSW, 2308, Australia. .,Precision Medicine Research Program, Hunter Medical Research Institute, New Lambton Heights, NSW, 2305, Australia.
| | - Xi Wang
- State Key Laboratory of Reproductive Medicine, Nanjing Medical University, Nanjing, 211166, China.
| | - Yong-Sheng Li
- College of Biomedical Information and Engineering, the First Affiliated Hospital of Hainan Medical University, Hainan Medical University, Haikou, 571199, Hainan, China.
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Integrated proteomic and transcriptomic landscape of macrophages in mouse tissues. Nat Commun 2022; 13:7389. [PMID: 36450731 PMCID: PMC9712610 DOI: 10.1038/s41467-022-35095-7] [Citation(s) in RCA: 11] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/22/2021] [Accepted: 11/18/2022] [Indexed: 12/03/2022] Open
Abstract
Macrophages are involved in tissue homeostasis and are critical for innate immune responses, yet distinct macrophage populations in different tissues exhibit diverse gene expression patterns and biological processes. While tissue-specific macrophage epigenomic and transcriptomic profiles have been reported, proteomes of different macrophage populations remain poorly characterized. Here we use mass spectrometry and bulk RNA sequencing to assess the proteomic and transcriptomic patterns, respectively, of 10 primary macrophage populations from seven mouse tissues, bone marrow-derived macrophages and the cell line RAW264.7. The results show distinct proteomic landscape and protein copy numbers between tissue-resident and recruited macrophages. Construction of a hierarchical regulatory network finds cell-type-specific transcription factors of macrophages serving as hubs for denoting tissue and functional identity of individual macrophage subsets. Finally, Il18 is validated to be essential in distinguishing molecular signatures and cellular function features between tissue-resident and recruited macrophages in the lung and liver. In summary, these deposited datasets and our open proteome server ( http://macrophage.mouseprotein.cn ) integrating all information will provide a valuable resource for future functional and mechanistic studies of mouse macrophages.
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Yamazaki M, Hosokawa M, Matsunaga H, Arikawa K, Takamochi K, Suzuki K, Hayashi T, Kambara H, Takeyama H. Integrated spatial analysis of gene mutation and gene expression for understanding tumor diversity in formalin-fixed paraffin-embedded lung adenocarcinoma. Front Oncol 2022; 12:936190. [PMID: 36505794 PMCID: PMC9731154 DOI: 10.3389/fonc.2022.936190] [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: 05/04/2022] [Accepted: 10/31/2022] [Indexed: 11/26/2022] Open
Abstract
Introduction A deeper understanding of intratumoral heterogeneity is essential for prognosis prediction or accurate treatment plan decisions in clinical practice. However, due to the cross-links and degradation of biomolecules within formalin-fixed paraffin-embedded (FFPE) specimens, it is challenging to analyze them. In this study, we aimed to optimize the simultaneous extraction of mRNA and DNA from microdissected FFPE tissues (φ = 100 µm) and apply the method to analyze tumor diversity in lung adenocarcinoma before and after erlotinib administration. Method Two magnetic beads were used for the simultaneous extraction of mRNA and DNA. The decross-linking conditions were evaluated for gene mutation and gene expression analyses of microdissected FFPE tissues. Lung lymph nodes before treatment and lung adenocarcinoma after erlotinib administration were collected from the same patient and were preserved as FFPE specimens for 4 years. Gene expression and gene mutations between histologically classified regions of lung adenocarcinoma (pre-treatment tumor in lung lymph node biopsies and post-treatment tumor, normal lung, tumor stroma, and remission stroma, in resected lung tissue) were compared in a microdissection-based approach. Results Using the optimized simultaneous extraction of DNA and mRNA and whole-genome amplification, we detected approximately 4,000-10,000 expressed genes and the epidermal growth factor receptor (EGFR) driver gene mutations from microdissected FFPE tissues. We found the differences in the highly expressed cancer-associated genes and the positive rate of EGFR exon 19 deletions among the tumor before and after treatment and tumor stroma, even though they were collected from tumors of the same patient or close regions of the same specimen. Conclusion Our integrated spatial analysis method would be applied to various FFPE pathology specimens providing area-specific gene expression and gene mutation information.
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Affiliation(s)
- Miki Yamazaki
- Department of Life Science and Medical Bioscience, Waseda University, Tokyo, Japan,Computational Bio Big-Data Open Innovation Laboratory, National Institute of Advanced Industrial Science and Technology, Tokyo, Japan
| | - Masahito Hosokawa
- Department of Life Science and Medical Bioscience, Waseda University, Tokyo, Japan,Computational Bio Big-Data Open Innovation Laboratory, National Institute of Advanced Industrial Science and Technology, Tokyo, Japan,Research Organization for Nano and Life Innovation, Waseda University, Tokyo, Japan,Institute for Advanced Research of Biosystem Dynamics, Waseda Research Institute for Science and Engineering, Waseda University, Tokyo, Japan
| | - Hiroko Matsunaga
- Research Organization for Nano and Life Innovation, Waseda University, Tokyo, Japan
| | - Koji Arikawa
- Research Organization for Nano and Life Innovation, Waseda University, Tokyo, Japan
| | - Kazuya Takamochi
- Department of Thoracic Surgery, Juntendo University School of Medicine, Tokyo, Japan
| | - Kenji Suzuki
- Department of Thoracic Surgery, Juntendo University School of Medicine, Tokyo, Japan
| | - Takuo Hayashi
- Department of Human Pathology, Graduate School of Medicine, Juntendo University, Tokyo, Japan
| | - Hideki Kambara
- Research Organization for Nano and Life Innovation, Waseda University, Tokyo, Japan,Frontier BioSystems Inc., Tokyo, Japan
| | - Haruko Takeyama
- Department of Life Science and Medical Bioscience, Waseda University, Tokyo, Japan,Computational Bio Big-Data Open Innovation Laboratory, National Institute of Advanced Industrial Science and Technology, Tokyo, Japan,Research Organization for Nano and Life Innovation, Waseda University, Tokyo, Japan,Institute for Advanced Research of Biosystem Dynamics, Waseda Research Institute for Science and Engineering, Waseda University, Tokyo, Japan,*Correspondence: Haruko Takeyama,
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Armingol E, Ghaddar A, Joshi CJ, Baghdassarian H, Shamie I, Chan J, Her HL, Berhanu S, Dar A, Rodriguez-Armstrong F, Yang O, O’Rourke EJ, Lewis NE. Inferring a spatial code of cell-cell interactions across a whole animal body. PLoS Comput Biol 2022; 18:e1010715. [PMID: 36395331 PMCID: PMC9714814 DOI: 10.1371/journal.pcbi.1010715] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/01/2022] [Revised: 12/01/2022] [Accepted: 11/07/2022] [Indexed: 11/18/2022] Open
Abstract
Cell-cell interactions shape cellular function and ultimately organismal phenotype. Interacting cells can sense their mutual distance using combinations of ligand-receptor pairs, suggesting the existence of a spatial code, i.e., signals encoding spatial properties of cellular organization. However, this code driving and sustaining the spatial organization of cells remains to be elucidated. Here we present a computational framework to infer the spatial code underlying cell-cell interactions from the transcriptomes of the cell types across the whole body of a multicellular organism. As core of this framework, we introduce our tool cell2cell, which uses the coexpression of ligand-receptor pairs to compute the potential for intercellular interactions, and we test it across the Caenorhabditis elegans' body. Leveraging a 3D atlas of C. elegans' cells, we also implement a genetic algorithm to identify the ligand-receptor pairs most informative of the spatial organization of cells across the whole body. Validating the spatial code extracted with this strategy, the resulting intercellular distances are negatively correlated with the inferred cell-cell interactions. Furthermore, for selected cell-cell and ligand-receptor pairs, we experimentally confirm the communicatory behavior inferred with cell2cell and the genetic algorithm. Thus, our framework helps identify a code that predicts the spatial organization of cells across a whole-animal body.
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Affiliation(s)
- Erick Armingol
- Bioinformatics and Systems Biology Graduate Program, University of California, San Diego, La Jolla, California, United States of America
- Department of Pediatrics, University of California, San Diego, La Jolla, California, United States of America
| | - Abbas Ghaddar
- Department of Biology, University of Virginia, Charlottesville, Virginia, United States of America
| | - Chintan J. Joshi
- Department of Pediatrics, University of California, San Diego, La Jolla, California, United States of America
| | - Hratch Baghdassarian
- Bioinformatics and Systems Biology Graduate Program, University of California, San Diego, La Jolla, California, United States of America
- Department of Pediatrics, University of California, San Diego, La Jolla, California, United States of America
| | - Isaac Shamie
- Bioinformatics and Systems Biology Graduate Program, University of California, San Diego, La Jolla, California, United States of America
- Department of Pediatrics, University of California, San Diego, La Jolla, California, United States of America
| | - Jason Chan
- Poway High School, Poway, California, United States of America
| | - Hsuan-Lin Her
- Bioinformatics and Systems Biology Graduate Program, University of California, San Diego, La Jolla, California, United States of America
| | - Samuel Berhanu
- Department of Biology, University of Virginia, Charlottesville, Virginia, United States of America
| | - Anushka Dar
- Department of Biology, University of Virginia, Charlottesville, Virginia, United States of America
| | | | - Olivia Yang
- Department of Biology, University of Virginia, Charlottesville, Virginia, United States of America
| | - Eyleen J. O’Rourke
- Department of Biology, University of Virginia, Charlottesville, Virginia, United States of America
- Department of Cell Biology, School of Medicine of University of Virginia, Charlottesville, Virginia, United States of America
| | - Nathan E. Lewis
- Department of Pediatrics, University of California, San Diego, La Jolla, California, United States of America
- Department of Bioengineering, University of California, San Diego, La Jolla, California, United States of America
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36
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Chen M, Xu C, Xu Z, He W, Zhang H, Su J, Song Q. Uncovering the dynamic effects of DEX treatment on lung cancer by integrating bioinformatic inference and multiscale modeling of scRNA-seq and proteomics data. Comput Biol Med 2022; 149:105999. [PMID: 35998480 DOI: 10.1016/j.compbiomed.2022.105999] [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: 03/27/2022] [Revised: 06/16/2022] [Accepted: 08/14/2022] [Indexed: 11/18/2022]
Abstract
Lung cancer is one of the leading causes of cancer-related death, with a five-year survival rate of 18%. It is a priority for us to understand the underlying mechanisms affecting lung cancer therapeutics' implementation and effectiveness. In this study, we combine the power of Bioinformatics and Systems Biology to comprehensively uncover functional and signaling pathways of drug treatment using bioinformatics inference and multiscale modeling of both scRNA-seq data and proteomics data. Based on a time series of lung adenocarcinoma derived A549 cells after DEX treatment, we first identified the differentially expressed genes (DEGs) in those lung cancer cells. Through the interrogation of regulatory network of those DEGs, we identified key hub genes including TGFβ, MYC, and SMAD3 varied underlie DEX treatment. Further gene set enrichment analysis revealed the TGFβ signaling pathway as the top enriched term. Those genes involved in the TGFβ pathway and their crosstalk with the ERBB pathway presented a strong survival prognosis in clinical lung cancer samples. With the basis of biological validation and literature-based curation, a multiscale model of tumor regulation centered on both TGFβ-induced and ERBB-amplified signaling pathways was developed to characterize the dynamic effects of DEX therapy on lung cancer cells. Our simulation results were well matched to available data of SMAD2, FOXO3, TGFβ1, and TGFβR1 over the time course. Moreover, we provided predictions of different doses to illustrate the trend and therapeutic potential of DEX treatment. The innovative and cross-disciplinary approach can be further applied to other computational studies in tumorigenesis and oncotherapy. We released the approach as a user-friendly tool named BIMM (Bioinformatic Inference and Multiscale Modeling), with all the key features available at https://github.com/chenm19/BIMM.
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Affiliation(s)
- Minghan Chen
- Department of Computer Science, Wake Forest University, Winston-Salem, NC, USA
| | - Chunrui Xu
- Genetics, Bioinformatics, and Computational Biology, Virginia Tech, Blacksburg, VA, USA
| | - Ziang Xu
- Department of Computer Science, Wake Forest University, Winston-Salem, NC, USA; Department of Chemistry, Wake Forest University, Winston-Salem, NC, USA
| | - Wei He
- Genetics, Bioinformatics, and Computational Biology, Virginia Tech, Blacksburg, VA, USA
| | - Haorui Zhang
- Department of Mathematics and Statistics, Wake Forest University, Winston-Salem, NC, USA
| | - Jing Su
- Department of Biostatistics and Health Data Science, Indiana University School of Medicine, Indianapolis, IN, USA
| | - Qianqian Song
- Center for Cancer Genomics and Precision Oncology, Wake Forest Baptist Comprehensive Cancer Center, Wake Forest Baptist Medical Center, Winston Salem, NC, USA; Department of Cancer Biology, Wake Forest School of Medicine, Winston Salem, NC, USA.
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Wang S, Zheng H, Choi JS, Lee JK, Li X, Hu H. A systematic evaluation of the computational tools for ligand-receptor-based cell-cell interaction inference. Brief Funct Genomics 2022; 21:339-356. [PMID: 35822343 PMCID: PMC9479691 DOI: 10.1093/bfgp/elac019] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/02/2022] [Revised: 06/13/2022] [Accepted: 06/16/2022] [Indexed: 11/13/2022] Open
Abstract
Cell-cell interactions (CCIs) are essential for multicellular organisms to coordinate biological processes and functions. One classical type of CCI interaction is between secreted ligands and cell surface receptors, i.e. ligand-receptor (LR) interactions. With the recent development of single-cell technologies, a large amount of single-cell ribonucleic acid (RNA) sequencing (scRNA-Seq) data has become widely available. This data availability motivated the single-cell-resolution study of CCIs, particularly LR-based CCIs. Dozens of computational methods and tools have been developed to predict CCIs by identifying LR-based CCIs. Many of these tools have been theoretically reviewed. However, there is little study on current LR-based CCI prediction tools regarding their performance and running results on public scRNA-Seq datasets. In this work, to fill this gap, we tested and compared nine of the most recent computational tools for LR-based CCI prediction. We used 15 well-studied scRNA-Seq samples that correspond to approximately 100K single cells under different experimental conditions for testing and comparison. Besides briefing the methodology used in these nine tools, we summarized the similarities and differences of these tools in terms of both LR prediction and CCI inference between cell types. We provided insight into using these tools to make meaningful discoveries in understanding cell communications.
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Affiliation(s)
| | | | | | | | - Xiaoman Li
- Corresponding authors: Haiyan Hu, Department of Computer Science, University of Central Florida, Orlando, FL, USA. Tel.: +1-4078820134; Fax: +1-4078235835; E-mail: ; Xiaoman Li, Burnett School of Biomedical Science, University of Central Florida, Orlando, FL, USA. Tel.: +1-4078234811; Fax: +1-4078235835; E-mail:
| | - Haiyan Hu
- Corresponding authors: Haiyan Hu, Department of Computer Science, University of Central Florida, Orlando, FL, USA. Tel.: +1-4078820134; Fax: +1-4078235835; E-mail: ; Xiaoman Li, Burnett School of Biomedical Science, University of Central Florida, Orlando, FL, USA. Tel.: +1-4078234811; Fax: +1-4078235835; E-mail:
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Xin Y, Lyu P, Jiang J, Zhou F, Wang J, Blackshaw S, Qian J. LRLoop: a method to predict feedback loops in cell-cell communication. Bioinformatics 2022; 38:4117-4126. [PMID: 35788263 PMCID: PMC9438954 DOI: 10.1093/bioinformatics/btac447] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/22/2022] [Revised: 06/24/2022] [Accepted: 07/03/2022] [Indexed: 12/24/2022] Open
Abstract
MOTIVATION Intercellular communication (i.e. cell-cell communication) plays an essential role in multicellular organisms coordinating various biological processes. Previous studies discovered that feedback loops between two cell types are a widespread and vital signaling motif regulating development, regeneration and cancer progression. While many computational methods have been developed to predict cell-cell communication based on gene expression datasets, these methods often predict one-directional ligand-receptor interactions from sender to receiver cells and are not suitable to identify feedback loops. RESULTS Here, we describe ligand-receptor loop (LRLoop), a new method for analyzing cell-cell communication based on bi-directional ligand-receptor interactions, where two pairs of ligand-receptor interactions are identified that are responsive to each other and thereby form a closed feedback loop. We first assessed LRLoop using bulk datasets and found our method significantly reduces the false positive rate seen with existing methods. Furthermore, we developed a new strategy to assess the performance of these methods in single-cell datasets. We used the between-tissue interactions as an indicator of potential false-positive prediction and found that LRLoop produced a lower fraction of between-tissue interactions than traditional methods. Finally, we applied LRLoop to the single-cell datasets obtained from retinal development. We discovered many new bi-directional ligand-receptor interactions among individual cell types that potentially control proliferation, neurogenesis and/or cell fate specification. AVAILABILITY AND IMPLEMENTATION An R package is available at https://github.com/Pinlyu3/LRLoop. The source code can be found at figshare (https://doi.org/10.6084/m9.figshare.20126138.v1). The datasets can be found at figshare (https://doi.org/10.6084/m9.figshare.20126021.v1). SUPPLEMENTARY INFORMATION Supplementary data are available at Bioinformatics online.
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Affiliation(s)
| | | | - Junyao Jiang
- CAS Key Laboratory of Regenerative Biology, Guangdong Provincial Key Laboratory of Stem Cell and Regenerative Medicine, Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences, Guangzhou 510530, China
| | - Fengquan Zhou
- Department of Orthopedic Surgery, Johns Hopkins University School of Medicine, Baltimore, MD 21287, USA,Solomon H. Snyder Department of Neuroscience, Johns Hopkins University School of Medicine, Baltimore, MD 21287, USA
| | - Jie Wang
- CAS Key Laboratory of Regenerative Biology, Guangdong Provincial Key Laboratory of Stem Cell and Regenerative Medicine, Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences, Guangzhou 510530, China
| | - Seth Blackshaw
- Department of Ophthalmology, Johns Hopkins University School of Medicine, Baltimore, MD 21287, USA,Solomon H. Snyder Department of Neuroscience, Johns Hopkins University School of Medicine, Baltimore, MD 21287, USA
| | - Jiang Qian
- To whom correspondence should be addressed.
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39
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Peng L, Wang F, Wang Z, Tan J, Huang L, Tian X, Liu G, Zhou L. Cell-cell communication inference and analysis in the tumour microenvironments from single-cell transcriptomics: data resources and computational strategies. Brief Bioinform 2022; 23:6618236. [PMID: 35753695 DOI: 10.1093/bib/bbac234] [Citation(s) in RCA: 34] [Impact Index Per Article: 17.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/14/2022] [Revised: 05/15/2022] [Accepted: 05/19/2022] [Indexed: 12/12/2022] Open
Abstract
Carcinomas are complex ecosystems composed of cancer, stromal and immune cells. Communication between these cells and their microenvironments induces cancer progression and causes therapy resistance. In order to improve the treatment of cancers, it is essential to quantify crosstalk between and within various cell types in a tumour microenvironment. Focusing on the coordinated expression patterns of ligands and cognate receptors, cell-cell communication can be inferred through ligand-receptor interactions (LRIs). In this manuscript, we carry out the following work: (i) introduce pipeline for ligand-receptor-mediated intercellular communication estimation from single-cell transcriptomics and list a few available LRI-related databases and visualization tools; (ii) demonstrate seven classical intercellular communication scoring strategies, highlight four types of representative intercellular communication inference methods, including network-based approaches, machine learning-based approaches, spatial information-based approaches and other approaches; (iii) summarize the evaluation and validation avenues for intercellular communication inference and analyze the advantages and limitations for the above four types of cell-cell communication methods; (iv) comment several major challenges while provide further research directions for intercellular communication analysis in the tumour microenvironments. We anticipate that this work helps to better understand intercellular crosstalk and to further develop powerful cell-cell communication estimation tools for tumor-targeted therapy.
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Affiliation(s)
- Lihong Peng
- School of Computer Science, Hunan University of Technology, 412007, Hunan, China.,College of Life Sciences and Chemistry, Hunan University of Technology, 412007, Hunan, China
| | - Feixiang Wang
- School of Computer Science, Hunan University of Technology, 412007, Hunan, China
| | - Zhao Wang
- School of Computer Science, Hunan University of Technology, 412007, Hunan, China
| | - Jingwei Tan
- School of Computer Science, Hunan University of Technology, 412007, Hunan, China
| | - Li Huang
- Academy of Arts and Design, Tsinghua University, 10084, Beijing, China.,The Future Laboratory, Tsinghua University, 10084, Beijing, China
| | - Xiongfei Tian
- School of Computer Science, Hunan University of Technology, 412007, Hunan, China
| | - Guangyi Liu
- School of Computer Science, Hunan University of Technology, 412007, Hunan, China
| | - Liqian Zhou
- School of Computer Science, Hunan University of Technology, 412007, Hunan, China
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40
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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: 125] [Impact Index Per Article: 62.5] [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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41
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Xiao Y, Wang Z, Zhao M, Deng Y, Yang M, Su G, Yang K, Qian C, Hu X, Liu Y, Geng L, Xiao Y, Zou Y, Tang X, Liu H, Xiao H, Fan R. Single-Cell Transcriptomics Revealed Subtype-Specific Tumor Immune Microenvironments in Human Glioblastomas. Front Immunol 2022; 13:914236. [PMID: 35669791 PMCID: PMC9163377 DOI: 10.3389/fimmu.2022.914236] [Citation(s) in RCA: 18] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/06/2022] [Accepted: 04/20/2022] [Indexed: 12/12/2022] Open
Abstract
Human glioblastoma (GBM), the most aggressive brain tumor, comprises six major subtypes of malignant cells, giving rise to both inter-patient and intra-tumor heterogeneity. The interaction between different tumor subtypes and non-malignant cells to collectively shape a tumor microenvironment has not been systematically characterized. Herein, we sampled the cellular milieu of surgically resected primary tumors from 7 GBM patients using single-cell transcriptome sequencing. A lineage relationship analysis revealed that a neural-progenitor-2-like (NPC2-like) state with high metabolic activity was associated with the tumor cells of origin. Mesenchymal-1-like (MES1-like) and mesenchymal-2-like (MES2-like) tumor cells correlated strongly with immune infiltration and chronic hypoxia niche responses. We identified four subsets of tumor-associated macrophages/microglia (TAMs), among which TAM-1 co-opted both acute and chronic hypoxia-response signatures, implicated in tumor angiogenesis, invasion, and poor prognosis. MES-like GBM cells expressed the highest number of M2-promoting ligands compared to other cellular states while all six states were associated with TAM M2-type polarization and immunosuppression via a set of 10 ligand–receptor signaling pathways. Our results provide new insights into the differential roles of GBM cell subtypes in the tumor immune microenvironment that may be deployed for patient stratification and personalized treatment.
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Affiliation(s)
- Yong Xiao
- Department of Biomedical Engineering, Yale University, New Haven, CT, United States
- Department of Neurosurgery, Nanjing Brain Hospital Affiliated to Nanjing Medical University, Nanjing, China
- Department of Neuro-Psychiatric Institute, Nanjing Brain Hospital Affiliated to Nanjing Medical University, Nanjing, China
| | - Zhen Wang
- Department of Neurosurgery, Nanjing Brain Hospital Affiliated to Nanjing Medical University, Nanjing, China
- Department of Neuro-Psychiatric Institute, Nanjing Brain Hospital Affiliated to Nanjing Medical University, Nanjing, China
| | - Mengjie Zhao
- Department of Neuro-Psychiatric Institute, Nanjing Brain Hospital Affiliated to Nanjing Medical University, Nanjing, China
| | - Yanxiang Deng
- Department of Biomedical Engineering, Yale University, New Haven, CT, United States
| | - Mingyu Yang
- Department of Biomedical Engineering, Yale University, New Haven, CT, United States
| | - Graham Su
- Department of Biomedical Engineering, Yale University, New Haven, CT, United States
| | - Kun Yang
- Department of Neurosurgery, Nanjing Brain Hospital Affiliated to Nanjing Medical University, Nanjing, China
| | - Chunfa Qian
- Department of Neurosurgery, Nanjing Brain Hospital Affiliated to Nanjing Medical University, Nanjing, China
| | - Xinhua Hu
- Department of Neurosurgery, Nanjing Brain Hospital Affiliated to Nanjing Medical University, Nanjing, China
| | - Yong Liu
- Department of Neurosurgery, Nanjing Brain Hospital Affiliated to Nanjing Medical University, Nanjing, China
| | - Liangyuan Geng
- Department of Neurosurgery, Nanjing Brain Hospital Affiliated to Nanjing Medical University, Nanjing, China
| | - Yang Xiao
- Department of Biomedical Engineering, Yale University, New Haven, CT, United States
| | - Yuanjie Zou
- Department of Neurosurgery, Nanjing Brain Hospital Affiliated to Nanjing Medical University, Nanjing, China
| | - Xianglong Tang
- Department of Neuro-Psychiatric Institute, Nanjing Brain Hospital Affiliated to Nanjing Medical University, Nanjing, China
| | - Hongyi Liu
- Department of Neurosurgery, Nanjing Brain Hospital Affiliated to Nanjing Medical University, Nanjing, China
- *Correspondence: Hongyi Liu, ; Hong Xiao, ; Rong Fan,
| | - Hong Xiao
- Department of Neuro-Psychiatric Institute, Nanjing Brain Hospital Affiliated to Nanjing Medical University, Nanjing, China
- *Correspondence: Hongyi Liu, ; Hong Xiao, ; Rong Fan,
| | - Rong Fan
- Department of Biomedical Engineering, Yale University, New Haven, CT, United States
- Yale Stem Cell Center and Yale Cancer Center, Yale School of Medicine, New Haven, CT, United States
- Human and Translational Immunology Program, Yale School of Medicine, New Haven, CT, United States
- *Correspondence: Hongyi Liu, ; Hong Xiao, ; Rong Fan,
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42
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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: 5] [Impact Index Per Article: 2.5] [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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43
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Yu A, Li Y, Li I, Ozawa MG, Yeh C, Chiou AE, Trope WL, Taylor J, Shrager J, Plevritis SK. Reconstructing codependent cellular cross-talk in lung adenocarcinoma using REMI. SCIENCE ADVANCES 2022; 8:eabi4757. [PMID: 35302849 PMCID: PMC8932661 DOI: 10.1126/sciadv.abi4757] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 03/25/2021] [Accepted: 01/27/2022] [Indexed: 06/14/2023]
Abstract
Cellular cross-talk in tissue microenvironments is fundamental to normal and pathological biological processes. Global assessment of cell-cell interactions (CCIs) is not yet technically feasible, but computational efforts to reconstruct these interactions have been proposed. Current computational approaches that identify CCI often make the simplifying assumption that pairwise interactions are independent of one another, which can lead to reduced accuracy. We present REMI (REgularized Microenvironment Interactome), a graph-based algorithm that predicts ligand-receptor (LR) interactions by accounting for LR dependencies on high-dimensional, small-sample size datasets. We apply REMI to reconstruct the human lung adenocarcinoma (LUAD) interactome from a bulk flow-sorted RNA sequencing dataset, then leverage single-cell transcriptomics data to increase the cell type resolution and identify LR prognostic signatures among tumor-stroma-immune subpopulations. We experimentally confirmed colocalization of CTGF:LRP6 among malignant cell subtypes as an interaction predicted to be associated with LUAD progression. Our work presents a computational approach to reconstruct interactomes and identify clinically relevant CCIs.
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Affiliation(s)
- Alice Yu
- Department of Biomedical Data Science, Stanford University, Stanford, CA, USA
| | - Yuanyuan Li
- Department of Biomedical Data Science, Stanford University, Stanford, CA, USA
- Department of Radiology, Stanford University, Stanford, CA, USA
| | - Irene Li
- Cancer Biology Interdepartmental, Program Stanford University, Stanford, CA, USA
| | | | - Christine Yeh
- Department of Biomedical Data Science, Stanford University, Stanford, CA, USA
| | - Aaron E. Chiou
- Department of Biomedical Data Science, Stanford University, Stanford, CA, USA
- Department of Radiology, Stanford University, Stanford, CA, USA
| | - Winston L. Trope
- Department of Cardiothoracic Surgery, Stanford University, Stanford, CA, USA
| | - Jonathan Taylor
- Department of Statistics, Stanford University, Stanford, CA, USA
| | - Joseph Shrager
- Department of Cardiothoracic Surgery, Stanford University, Stanford, CA, USA
| | - Sylvia K. Plevritis
- Department of Biomedical Data Science, Stanford University, Stanford, CA, USA
- Department of Radiology, Stanford University, Stanford, CA, USA
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44
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Wennerberg E, Mukherjee S, Spada S, Hung C, Agrusa CJ, Chen C, Valeta-Magara A, Rudqvist NP, Van Nest SJ, Kamel MK, Nasar A, Narula N, Mittal V, Markowitz GJ, Zhou XK, Adusumilli PS, Borczuk AC, White TE, Khan AG, Balderes PJ, Lorenz IC, Altorki N, Demaria S, McGraw TE, Stiles BM. Expression of the mono-ADP-ribosyltransferase ART1 by tumor cells mediates immune resistance in non-small cell lung cancer. Sci Transl Med 2022; 14:eabe8195. [PMID: 35294260 DOI: 10.1126/scitranslmed.abe8195] [Citation(s) in RCA: 14] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/29/2023]
Abstract
Most patients with non-small cell lung cancer (NSCLC) do not achieve durable clinical responses from immune checkpoint inhibitors, suggesting the existence of additional resistance mechanisms. Nicotinamide adenine dinucleotide (NAD)-induced cell death (NICD) of P2X7 receptor (P2X7R)-expressing T cells regulates immune homeostasis in inflamed tissues. This process is mediated by mono-adenosine 5'-diphosphate (ADP)-ribosyltransferases (ARTs). We found an association between membranous expression of ART1 on tumor cells and reduced CD8 T cell infiltration. Specifically, we observed a reduction in the P2X7R+ CD8 T cell subset in human lung adenocarcinomas. In vitro, P2X7R+ CD8 T cells were susceptible to ART1-mediated ADP-ribosylation and NICD, which was exacerbated upon blockade of the NAD+-degrading ADP-ribosyl cyclase CD38. Last, in murine NSCLC and melanoma models, we demonstrate that genetic and antibody-mediated ART1 inhibition slowed tumor growth in a CD8 T cell-dependent manner. This was associated with increased infiltration of activated P2X7R+CD8 T cells into tumors. In conclusion, we describe ART1-mediated NICD as a mechanism of immune resistance in NSCLC and provide preclinical evidence that antibody-mediated targeting of ART1 can improve tumor control, supporting pursuit of this approach in clinical studies.
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Affiliation(s)
- Erik Wennerberg
- Department of Radiation Oncology, Weill Cornell Medicine, New York, NY 10065, USA.,Division of Radiotherapy and Imaging, Institute of Cancer Research, London SM2 5NG, UK
| | - Sumit Mukherjee
- Department of Cardiothoracic Surgery, Weill Cornell Medicine, New York, NY 10065, USA.,Department of Cardiothoracic and Vascular Surgery, Albert Einstein College of Medicine, Bronx, NY 10461, USA
| | - Sheila Spada
- Department of Radiation Oncology, Weill Cornell Medicine, New York, NY 10065, USA
| | - Clarey Hung
- Department of Cardiothoracic Surgery, Weill Cornell Medicine, New York, NY 10065, USA
| | - Christopher J Agrusa
- Department of Cardiothoracic Surgery, Weill Cornell Medicine, New York, NY 10065, USA
| | - Chuang Chen
- Department of Cardiothoracic Surgery, Weill Cornell Medicine, New York, NY 10065, USA
| | - Amanda Valeta-Magara
- Department of Cardiothoracic Surgery, Weill Cornell Medicine, New York, NY 10065, USA
| | - Nils-Petter Rudqvist
- Department of Radiation Oncology, Weill Cornell Medicine, New York, NY 10065, USA
| | - Samantha J Van Nest
- Department of Radiation Oncology, Weill Cornell Medicine, New York, NY 10065, USA
| | - Mohamed K Kamel
- Department of Surgery, Central Michigan University College of Medicine, Saginaw, MI 48602, USA
| | - Abu Nasar
- Department of Cardiothoracic Surgery, Weill Cornell Medicine, New York, NY 10065, USA
| | - Navneet Narula
- Department of Pathology, New York University, New York, NY 10016, USA
| | - Vivek Mittal
- Department of Cardiothoracic Surgery, Weill Cornell Medicine, New York, NY 10065, USA.,Department of Cell and Developmental Biology, Weill Cornell Medicine, New York, NY 10021, USA
| | - Geoffrey J Markowitz
- Department of Cardiothoracic Surgery, Weill Cornell Medicine, New York, NY 10065, USA
| | - Xi Kathy Zhou
- Division of Biostatistics, Department of Population Health Sciences, Weill Cornell Medicine, New York, NY 10065, USA
| | - Prasad S Adusumilli
- Division of Thoracic Surgery, Department of Surgery, Memorial Sloan-Kettering Cancer Center, New York, NY 10065, USA
| | - Alain C Borczuk
- Department of Pathology and Laboratory Medicine, Weill Cornell Medicine, New York, NY 10021, USA
| | - Thomas E White
- Tri-Institutional Therapeutics Discovery Institute, New York, NY 10021, USA
| | - Abdul G Khan
- Tri-Institutional Therapeutics Discovery Institute, New York, NY 10021, USA
| | - Paul J Balderes
- Tri-Institutional Therapeutics Discovery Institute, New York, NY 10021, USA
| | - Ivo C Lorenz
- Tri-Institutional Therapeutics Discovery Institute, New York, NY 10021, USA
| | - Nasser Altorki
- Department of Cardiothoracic Surgery, Weill Cornell Medicine, New York, NY 10065, USA
| | - Sandra Demaria
- Department of Radiation Oncology, Weill Cornell Medicine, New York, NY 10065, USA.,Department of Pathology and Laboratory Medicine, Weill Cornell Medicine, New York, NY 10021, USA
| | - Timothy E McGraw
- Department of Cardiothoracic Surgery, Weill Cornell Medicine, New York, NY 10065, USA.,Department of Biochemistry, Weill Cornell Medicine, New York, NY 10065, USA
| | - Brendon M Stiles
- Department of Cardiothoracic Surgery, Weill Cornell Medicine, New York, NY 10065, USA.,Department of Cardiothoracic and Vascular Surgery, Albert Einstein College of Medicine, Bronx, NY 10461, USA
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Wahiduzzaman M, Liu Y, Huang T, Wei W, Li Y. Cell-cell communication analysis for single-cell RNA sequencing and its applications in carcinogenesis and COVID-19. BIOSAFETY AND HEALTH 2022. [DOI: 10.1016/j.bsheal.2022.03.001] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022] Open
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46
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p53 Signaling on Microenvironment and Its Contribution to Tissue Chemoresistance. MEMBRANES 2022; 12:membranes12020202. [PMID: 35207121 PMCID: PMC8877489 DOI: 10.3390/membranes12020202] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 12/31/2021] [Revised: 01/31/2022] [Accepted: 02/04/2022] [Indexed: 02/06/2023]
Abstract
Chemoresistance persists as a significant, unresolved clinical challenge in many cancer types. The tumor microenvironment, in which cancer cells reside and interact with non-cancer cells and tissue structures, has a known role in promoting every aspect of tumor progression, including chemoresistance. However, the molecular determinants of microenvironment-driven chemoresistance are mainly unknown. In this review, we propose that the TP53 tumor suppressor, found mutant in over half of human cancers, is a crucial regulator of cancer cell-microenvironment crosstalk and a prime candidate for the investigation of microenvironment-specific modulators of chemoresistance. Wild-type p53 controls the secretion of factors that inhibit the tumor microenvironment, whereas altered secretion or mutant p53 interfere with p53 function to promote chemoresistance. We highlight resistance mechanisms promoted by mutant p53 and enforced by the microenvironment, such as extracellular matrix remodeling and adaptation to hypoxia. Alterations of wild-type p53 extracellular function may create a cascade of spatial amplification loops in the tumor tissue that can influence cellular behavior far from the initial oncogenic mutation. We discuss the concept of chemoresistance as a multicellular/tissue-level process rather than intrinsically cellular. Targeting p53-dependent crosstalk mechanisms between cancer cells and components of the tumor environment might disrupt the waves of chemoresistance that spread across the tumor tissue, increasing the efficacy of chemotherapeutic agents.
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Olesch C, Brunn D, Aktay-Cetin Ö, Sirait-Fischer E, Pullamsetti SS, Grimminger F, Seeger W, Brüne B, Weigert A, Savai R. Picturing of the Lung Tumor Cellular Composition by Multispectral Flow Cytometry. Front Immunol 2022; 13:827719. [PMID: 35145525 PMCID: PMC8821098 DOI: 10.3389/fimmu.2022.827719] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/02/2021] [Accepted: 01/05/2022] [Indexed: 11/13/2022] Open
Abstract
The lung tumor microenvironment plays a critical role in the tumorigenesis and metastasis of lung cancer, resulting from the crosstalk between cancer cells and microenvironmental cells. Therefore, comprehensive identification and characterization of cell populations in the complex lung structure is crucial for development of novel targeted anti-cancer therapies. Here, a hierarchical clustering approach with multispectral flow cytometry was established to delineate the cellular landscape of murine lungs under steady-state and cancer conditions. Fluorochromes were used multiple times to be able to measure 24 cell surface markers with only 13 detectors, yielding a broad picture for whole-lung phenotyping. Primary and metastatic murine lung tumor models were included to detect major cell populations in the lung, and to identify alterations to the distribution patterns in these models. In the primary tumor models, major altered populations included CD324+ epithelial cells, alveolar macrophages, dendritic cells, and blood and lymph endothelial cells. The number of fibroblasts, vascular smooth muscle cells, monocytes (Ly6C+ and Ly6C–) and neutrophils were elevated in metastatic models of lung cancer. Thus, the proposed clustering approach is a promising method to resolve cell populations from complex organs in detail even with basic flow cytometers.
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Affiliation(s)
- Catherine Olesch
- Institute of Biochemistry I, Goethe-University Frankfurt, Frankfurt, Germany
| | - David Brunn
- Max Planck Institute for Heart and Lung Research, Member of the German Center for Lung Research (DZL), Member of the Cardio-Pulmonary Institute (CPI), Bad Nauheim, Germany
| | - Öznur Aktay-Cetin
- Max Planck Institute for Heart and Lung Research, Member of the German Center for Lung Research (DZL), Member of the Cardio-Pulmonary Institute (CPI), Bad Nauheim, Germany
| | | | - Soni Savai Pullamsetti
- Max Planck Institute for Heart and Lung Research, Member of the German Center for Lung Research (DZL), Member of the Cardio-Pulmonary Institute (CPI), Bad Nauheim, Germany
- Institute for Lung Health (ILH), Justus Liebig University, Giessen, Germany
| | - Friedrich Grimminger
- Institute for Lung Health (ILH), Justus Liebig University, Giessen, Germany
- Department of Internal Medicine, Justus Liebig University Giessen, Member of the DZL, Member of CPI, Giessen, Germany
| | - Werner Seeger
- Max Planck Institute for Heart and Lung Research, Member of the German Center for Lung Research (DZL), Member of the Cardio-Pulmonary Institute (CPI), Bad Nauheim, Germany
- Institute for Lung Health (ILH), Justus Liebig University, Giessen, Germany
- Department of Internal Medicine, Justus Liebig University Giessen, Member of the DZL, Member of CPI, Giessen, Germany
| | - Bernhard Brüne
- Institute of Biochemistry I, Goethe-University Frankfurt, Frankfurt, Germany
- Frankfurt Cancer Institute (FCI), Goethe University, Frankfurt am Main, Germany
- German Cancer Consortium (DKTK), Frankfurt, Germany
| | - Andreas Weigert
- Institute of Biochemistry I, Goethe-University Frankfurt, Frankfurt, Germany
- Frankfurt Cancer Institute (FCI), Goethe University, Frankfurt am Main, Germany
- German Cancer Consortium (DKTK), Frankfurt, Germany
- *Correspondence: Andreas Weigert, ; Rajkumar Savai, ;
| | - Rajkumar Savai
- Max Planck Institute for Heart and Lung Research, Member of the German Center for Lung Research (DZL), Member of the Cardio-Pulmonary Institute (CPI), Bad Nauheim, Germany
- Institute for Lung Health (ILH), Justus Liebig University, Giessen, Germany
- Department of Internal Medicine, Justus Liebig University Giessen, Member of the DZL, Member of CPI, Giessen, Germany
- Frankfurt Cancer Institute (FCI), Goethe University, Frankfurt am Main, Germany
- *Correspondence: Andreas Weigert, ; Rajkumar Savai, ;
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The use of machine learning to discover regulatory networks controlling biological systems. Mol Cell 2022; 82:260-273. [PMID: 35016036 PMCID: PMC8905511 DOI: 10.1016/j.molcel.2021.12.011] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/21/2021] [Revised: 12/06/2021] [Accepted: 12/13/2021] [Indexed: 01/22/2023]
Abstract
Biological systems are composed of a vast web of multiscale molecular interactors and interactions. High-throughput technologies, both bulk and single cell, now allow for investigation of the properties and quantities of these interactors. Computational algorithms and machine learning methods then provide the tools to derive meaningful insights from the resulting data sets. One such approach is graphical network modeling, which provides a computational framework to explicitly model the molecular interactions within and between the cells comprising biological systems. These graphical networks aim to describe a putative chain of cause and effect between interacting molecules. This feature allows for determination of key molecules in a biological process, accelerated generation of mechanistic hypotheses, and simulation of experimental outcomes. We review the computational concepts and applications of graphical network models across molecular scales for both intracellular and intercellular regulatory biology, examples of successful applications, and the future directions needed to overcome current limitations.
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49
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Uddin MN, Wang X. Identification of key tumor stroma-associated transcriptional signatures correlated with survival prognosis and tumor progression in breast cancer. Breast Cancer 2022; 29:541-561. [PMID: 35020130 DOI: 10.1007/s12282-022-01332-6] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/20/2021] [Accepted: 01/05/2022] [Indexed: 12/21/2022]
Abstract
BACKGROUND The aberrant expression of stromal gene signatures in breast cancer has been widely studied. However, the association of stromal gene signatures with tumor immunity, progression, and clinical outcomes remains lacking. METHODS Based on eight breast tumor stroma (BTS) transcriptomics datasets, we identified differentially expressed genes (DEGs) between BTS and normal breast stroma. Based on the DEGs, we identified dysregulated pathways and prognostic hub genes, hub oncogenes, hub protein kinases, and other key marker genes associated with breast cancer. Moreover, we compared the enrichment levels of stromal and immune signatures between breast cancer patients with bad and good clinical outcomes. We also investigated the association between tumor stroma-related genes and breast cancer progression. RESULTS The DEGs included 782 upregulated and 276 downregulated genes in BTS versus normal breast stroma. The pathways significantly associated with the DEGs included cytokine-cytokine receptor interaction, chemokine signaling, T cell receptor signaling, cell adhesion molecules, focal adhesion, and extracellular matrix-receptor interaction. Protein-protein interaction network analysis identified the stromal hub genes with prognostic value in breast cancer, including two oncogenes (COL1A1 and IL21R), two protein kinases encoding genes (PRKACA and CSK), and a growth factor encoding gene (PLAU). Moreover, we observed that the patients with bad clinical outcomes were less enriched in stromal and antitumor immune signatures (CD8 + T cells and tumor-infiltrating lymphocytes) but more enriched in tumor cells and immunosuppressive signatures (MDSCs and CD4 + regulatory T cells) compared with the patients with good clinical outcomes. The ratios of CD8 + /CD4 + regulatory T cells were lower in the patients with bad clinical outcomes. Furthermore, we identified the tumor stroma-related genes, including MCM4, SPECC1, IMPA2, and AGO2, which were gradually upregulated through grade I, II, and III breast cancers. In contrast, COL14A1, ESR1, SLIT2, IGF1, CH25H, PRR5L, ABCA6, CEP126, IGDCC4, LHFP, MFAP3, PCSK5, RAB37, RBMS3, SETBP1, and TSPAN11 were gradually downregulated through grade I, II, and III breast cancers. It suggests that the expression of these stromal genes has an association with the progression of breast cancers. These progression-associated genes also displayed an expression association with recurrence-free survival in breast cancer patients. CONCLUSIONS This study identified tumor stroma-associated biomarkers correlated with deregulated pathways, tumor immunity, tumor progression, and clinical outcomes in breast cancer. Our findings provide new insights into the pathogenesis of breast cancer.
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Affiliation(s)
- Md Nazim Uddin
- Biomedical Informatics Research Lab, School of Basic Medicine and Clinical Pharmacy, China Pharmaceutical University, Nanjing, 211198, China
- Cancer Genomics Research Center, School of Basic Medicine and Clinical Pharmacy, China Pharmaceutical University, Nanjing, 211198, China
- Big Data Research Institute, China Pharmaceutical University, Nanjing, 211198, China
- Institute of Food Science and Technology, Bangladesh Council of Scientific and Industrial Research (BCSIR), Dhaka, 1205, Bangladesh
| | - Xiaosheng Wang
- Biomedical Informatics Research Lab, School of Basic Medicine and Clinical Pharmacy, China Pharmaceutical University, Nanjing, 211198, China.
- Cancer Genomics Research Center, School of Basic Medicine and Clinical Pharmacy, China Pharmaceutical University, Nanjing, 211198, China.
- Big Data Research Institute, China Pharmaceutical University, Nanjing, 211198, China.
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50
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Interlandi M, Kerl K, Dugas M. InterCellar enables interactive analysis and exploration of cell-cell communication in single-cell transcriptomic data. Commun Biol 2022; 5:21. [PMID: 35017628 PMCID: PMC8752611 DOI: 10.1038/s42003-021-02986-2] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/31/2021] [Accepted: 12/16/2021] [Indexed: 12/03/2022] Open
Abstract
Deciphering cell-cell communication is a key step in understanding the physiology and pathology of multicellular systems. Recent advances in single-cell transcriptomics have contributed to unraveling the cellular composition of tissues and enabled the development of computational algorithms to predict cellular communication mediated by ligand-receptor interactions. Despite the existence of various tools capable of inferring cell-cell interactions from single-cell RNA sequencing data, the analysis and interpretation of the biological signals often require deep computational expertize. Here we present InterCellar, an interactive platform empowering lab-scientists to analyze and explore predicted cell-cell communication without requiring programming skills. InterCellar guides the biological interpretation through customized analysis steps, multiple visualization options, and the possibility to link biological pathways to ligand-receptor interactions. Alongside convenient data exploration features, InterCellar implements data-driven analyses including the possibility to compare cell-cell communication from multiple conditions. By analyzing COVID-19 and melanoma cell-cell interactions, we show that InterCellar resolves data-driven patterns of communication and highlights molecular signals through the integration of biological functions and pathways. We believe our user-friendly, interactive platform will help streamline the analysis of cell-cell communication and facilitate hypothesis generation in diverse biological systems.
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Affiliation(s)
- Marta Interlandi
- Institute of Medical Informatics, University of Münster, Münster, Germany.
- Department of Pediatric Hematology and Oncology, University Children's Hospital Münster, Münster, Germany.
| | - Kornelius Kerl
- Department of Pediatric Hematology and Oncology, University Children's Hospital Münster, Münster, Germany
| | - Martin Dugas
- Institute of Medical Informatics, University of Münster, Münster, Germany
- Institute of Medical Informatics, Heidelberg University Hospital, Heidelberg, Germany
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