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Kumaran G, Carroll L, Muirhead N, Bottomley MJ. How Can Spatial Transcriptomic Profiling Advance Our Understanding of Skin Diseases? J Invest Dermatol 2024:S0022-202X(24)01926-2. [PMID: 39177547 DOI: 10.1016/j.jid.2024.07.006] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/01/2024] [Revised: 05/23/2024] [Accepted: 07/04/2024] [Indexed: 08/24/2024]
Abstract
Spatial transcriptomic (ST) profiling is the mapping of gene expression within cell populations with preservation of positional context and represents an exciting new approach to develop our understanding of local and regional influences upon skin biology in health and disease. With the ability to probe from a few hundred transcripts to the entire transcriptome, multiple ST approaches are now widely available. In this paper, we review the ST field and discuss its application to dermatology. Its potential to advance our understanding of skin biology in health and disease is highlighted through the illustrative examples of 3 research areas: cutaneous aging, tumorigenesis, and psoriasis.
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Affiliation(s)
- Girishkumar Kumaran
- Chinese Academy of Medical Sciences Oxford Institute, Nuffield Department of Medicine, University of Oxford, Oxford, United Kingdom
| | - Liam Carroll
- Chinese Academy of Medical Sciences Oxford Institute, Nuffield Department of Medicine, University of Oxford, Oxford, United Kingdom
| | | | - Matthew J Bottomley
- Chinese Academy of Medical Sciences Oxford Institute, Nuffield Department of Medicine, University of Oxford, Oxford, United Kingdom.
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2
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Vicari M, Mirzazadeh R, Nilsson A, Shariatgorji R, Bjärterot P, Larsson L, Lee H, Nilsson M, Foyer J, Ekvall M, Czarnewski P, Zhang X, Svenningsson P, Käll L, Andrén PE, Lundeberg J. Spatial multimodal analysis of transcriptomes and metabolomes in tissues. Nat Biotechnol 2024; 42:1046-1050. [PMID: 37667091 PMCID: PMC11251988 DOI: 10.1038/s41587-023-01937-y] [Citation(s) in RCA: 9] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/19/2022] [Accepted: 08/08/2023] [Indexed: 09/06/2023]
Abstract
We present a spatial omics approach that combines histology, mass spectrometry imaging and spatial transcriptomics to facilitate precise measurements of mRNA transcripts and low-molecular-weight metabolites across tissue regions. The workflow is compatible with commercially available Visium glass slides. We demonstrate the potential of our method using mouse and human brain samples in the context of dopamine and Parkinson's disease.
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Affiliation(s)
- Marco Vicari
- Department of Gene Technology, KTH Royal Institute of Technology, Science for Life Laboratory, Stockholm, Sweden
| | - Reza Mirzazadeh
- Department of Gene Technology, KTH Royal Institute of Technology, Science for Life Laboratory, Stockholm, Sweden
| | - Anna Nilsson
- Department of Pharmaceutical Biosciences, Spatial Mass Spectrometry, Science for Life Laboratory, Uppsala University, Uppsala, Sweden
| | - Reza Shariatgorji
- Department of Pharmaceutical Biosciences, Spatial Mass Spectrometry, Science for Life Laboratory, Uppsala University, Uppsala, Sweden
| | - Patrik Bjärterot
- Department of Pharmaceutical Biosciences, Spatial Mass Spectrometry, Science for Life Laboratory, Uppsala University, Uppsala, Sweden
| | - Ludvig Larsson
- Department of Gene Technology, KTH Royal Institute of Technology, Science for Life Laboratory, Stockholm, Sweden
| | - Hower Lee
- Department of Biochemistry and Biophysics, Stockholm University, Science for Life Laboratory, Stockholm, Sweden
| | - Mats Nilsson
- Department of Biochemistry and Biophysics, Stockholm University, Science for Life Laboratory, Stockholm, Sweden
| | - Julia Foyer
- Department of Gene Technology, KTH Royal Institute of Technology, Science for Life Laboratory, Stockholm, Sweden
| | - Markus Ekvall
- Department of Gene Technology, KTH Royal Institute of Technology, Science for Life Laboratory, Stockholm, Sweden
| | - Paulo Czarnewski
- Department of Gene Technology, KTH Royal Institute of Technology, Science for Life Laboratory, Stockholm, Sweden
| | - Xiaoqun Zhang
- Department of Clinical Neuroscience, Section of Neurology, Karolinska Institutet, Stockholm, Sweden
| | - Per Svenningsson
- Department of Clinical Neuroscience, Section of Neurology, Karolinska Institutet, Stockholm, Sweden
- Basic and Clinical Neuroscience, King's College London, London, UK
| | - Lukas Käll
- Department of Gene Technology, KTH Royal Institute of Technology, Science for Life Laboratory, Stockholm, Sweden
| | - Per E Andrén
- Department of Pharmaceutical Biosciences, Spatial Mass Spectrometry, Science for Life Laboratory, Uppsala University, Uppsala, Sweden.
| | - Joakim Lundeberg
- Department of Gene Technology, KTH Royal Institute of Technology, Science for Life Laboratory, Stockholm, Sweden.
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3
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Hu X, van Sluijs B, García-Blay Ó, Stepanov Y, Rietrae K, Huck WTS, Hansen MMK. ARTseq-FISH reveals position-dependent differences in gene expression of micropatterned mESCs. Nat Commun 2024; 15:3918. [PMID: 38724524 PMCID: PMC11082235 DOI: 10.1038/s41467-024-48107-5] [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: 02/17/2023] [Accepted: 04/19/2024] [Indexed: 05/12/2024] Open
Abstract
Differences in gene-expression profiles between individual cells can give rise to distinct cell fate decisions. Yet how localisation on a micropattern impacts initial changes in mRNA, protein, and phosphoprotein abundance remains unclear. To identify the effect of cellular position on gene expression, we developed a scalable antibody and mRNA targeting sequential fluorescence in situ hybridisation (ARTseq-FISH) method capable of simultaneously profiling mRNAs, proteins, and phosphoproteins in single cells. We studied 67 (phospho-)protein and mRNA targets in individual mouse embryonic stem cells (mESCs) cultured on circular micropatterns. ARTseq-FISH reveals relative changes in both abundance and localisation of mRNAs and (phospho-)proteins during the first 48 hours of exit from pluripotency. We confirm these changes by conventional immunofluorescence and time-lapse microscopy. Chemical labelling, immunofluorescence, and single-cell time-lapse microscopy further show that cells closer to the edge of the micropattern exhibit increased proliferation compared to cells at the centre. Together these data suggest that while gene expression is still highly heterogeneous position-dependent differences in mRNA and protein levels emerge as early as 12 hours after LIF withdrawal.
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Affiliation(s)
- Xinyu Hu
- Institute for Molecules and Materials, Radboud University, Heyendaalseweg 135, 6525 AJ, Nijmegen, the Netherlands
- Oncode Institute, Nijmegen, The Netherlands
| | - Bob van Sluijs
- Institute for Molecules and Materials, Radboud University, Heyendaalseweg 135, 6525 AJ, Nijmegen, the Netherlands
| | - Óscar García-Blay
- Institute for Molecules and Materials, Radboud University, Heyendaalseweg 135, 6525 AJ, Nijmegen, the Netherlands
- Oncode Institute, Nijmegen, The Netherlands
| | - Yury Stepanov
- Institute for Molecules and Materials, Radboud University, Heyendaalseweg 135, 6525 AJ, Nijmegen, the Netherlands
| | - Koen Rietrae
- Institute for Molecules and Materials, Radboud University, Heyendaalseweg 135, 6525 AJ, Nijmegen, the Netherlands
| | - Wilhelm T S Huck
- Institute for Molecules and Materials, Radboud University, Heyendaalseweg 135, 6525 AJ, Nijmegen, the Netherlands.
| | - Maike M K Hansen
- Institute for Molecules and Materials, Radboud University, Heyendaalseweg 135, 6525 AJ, Nijmegen, the Netherlands.
- Oncode Institute, Nijmegen, The Netherlands.
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4
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Fujiwara N, Kimura G, Nakagawa H. Emerging Roles of Spatial Transcriptomics in Liver Research. Semin Liver Dis 2024; 44:115-132. [PMID: 38574750 DOI: 10.1055/a-2299-7880] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 04/06/2024]
Abstract
Spatial transcriptomics, leveraging sequencing- and imaging-based techniques, has emerged as a groundbreaking technology for mapping gene expression within the complex architectures of tissues. This approach provides an in-depth understanding of cellular and molecular dynamics across various states of healthy and diseased livers. Through the integration of sophisticated bioinformatics strategies, it enables detailed exploration of cellular heterogeneity, transitions in cell states, and intricate cell-cell interactions with remarkable precision. In liver research, spatial transcriptomics has been particularly revelatory, identifying distinct zonated functions of hepatocytes that are crucial for understanding the metabolic and detoxification processes of the liver. Moreover, this technology has unveiled new insights into the pathogenesis of liver diseases, such as the role of lipid-associated macrophages in steatosis and endothelial cell signals in liver regeneration and repair. In the domain of liver cancer, spatial transcriptomics has proven instrumental in delineating intratumor heterogeneity, identifying supportive microenvironmental niches and revealing the complex interplay between tumor cells and the immune system as well as susceptibility to immune checkpoint inhibitors. In conclusion, spatial transcriptomics represents a significant advance in hepatology, promising to enhance our understanding and treatment of liver diseases.
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Affiliation(s)
- Naoto Fujiwara
- Department of Gastroenterology and Hepatology, Graduate School of Medicine, Mie University, Mie, Japan
| | - Genki Kimura
- Department of Gastroenterology and Hepatology, Graduate School of Medicine, Mie University, Mie, Japan
| | - Hayato Nakagawa
- Department of Gastroenterology and Hepatology, Graduate School of Medicine, Mie University, Mie, Japan
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5
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Chen J, Ke R. Spatial analysis toolkits for RNA in situ sequencing. WILEY INTERDISCIPLINARY REVIEWS. RNA 2024; 15:e1842. [PMID: 38605484 DOI: 10.1002/wrna.1842] [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: 12/15/2023] [Revised: 03/13/2024] [Accepted: 03/14/2024] [Indexed: 04/13/2024]
Abstract
Spatial transcriptomics (ST) is featured by high-throughput gene expression profiling within their native cell and tissue context, offering a means to investigate gene regulatory networks in tissue microenvironment. In situ sequencing (ISS) is an imaging-based ST technology that simultaneously detects hundreds to thousands of genes at subcellular resolution. As a highly reproducible and robust technique, ISS has been widely adapted and undergone a series of technical iterations. As the interest in ISS-based spatial transcriptomic analysis grows, scalable and integrated data analysis workflows are needed to facilitate the applications of ISS in different research fields. This review presents the state-of-the-art bioinformatic toolkits for ISS data analysis, which covers the upstream and downstream analysis workflows, including image analysis, cell segmentation, clustering, functional enrichment, detection of spatially variable genes and cell clusters, spatial cell-cell interactions, and trajectory inference. To assist the community in choosing the right tools for their research, the application of each tool and its compatibility with ISS data are reviewed in detailed. Finally, future perspectives and challenges concerning how to integrate heterogeneous tools into a user-friendly analysis pipeline are discussed. This article is categorized under: RNA Methods > RNA Analyses In Vitro and In Silico.
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Affiliation(s)
- Jiayu Chen
- School of Medicine, Huaqiao University, Xiamen, Fujian, China
| | - Rongqin Ke
- School of Medicine, Huaqiao University, Xiamen, Fujian, China
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6
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Pang JMB, Byrne DJ, Bergin ART, Caramia F, Loi S, Gorringe KL, Fox SB. Spatial transcriptomics and the anatomical pathologist: Molecular meets morphology. Histopathology 2024; 84:577-586. [PMID: 37991396 DOI: 10.1111/his.15093] [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: 06/18/2023] [Revised: 10/23/2023] [Accepted: 10/26/2023] [Indexed: 11/23/2023]
Abstract
In recent years anatomical pathology has been revolutionised by the incorporation of molecular findings into routine diagnostic practice, and in some diseases the presence of specific molecular alterations are now essential for diagnosis. Spatial transcriptomics describes a group of technologies that provide up to transcriptome-wide expression profiling while preserving the spatial origin of the data, with many of these technologies able to provide these data using a single tissue section. Spatial transcriptomics allows expression profiling of highly specific areas within a tissue section potentially to subcellular resolution, and allows correlation of expression data with morphology, tissue type and location relative to other structures. While largely still research laboratory-based, several spatial transcriptomics methods have now achieved compatibility with formalin-fixed paraffin-embedded tissue (FFPE), allowing their use in diagnostic tissue samples, and with further development potentially leading to their incorporation in routine anatomical pathology practice. This mini review provides an overview of spatial transcriptomics methods, with an emphasis on platforms compatible with FFPE tissue, approaches to assess the data and potential applications in anatomical pathology practice.
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Affiliation(s)
- Jia-Min B Pang
- Peter MacCallum Cancer Centre, Melbourne, VIC, Australia
| | - David J Byrne
- Peter MacCallum Cancer Centre, Melbourne, VIC, Australia
| | - Alice R T Bergin
- Peter MacCallum Cancer Centre, Melbourne, VIC, Australia
- Sir Peter MacCallum Department of Oncology, University of Melbourne, Melbourne, VIC, Australia
| | - Franco Caramia
- Peter MacCallum Cancer Centre, Melbourne, VIC, Australia
- Sir Peter MacCallum Department of Oncology, University of Melbourne, Melbourne, VIC, Australia
| | - Sherene Loi
- Peter MacCallum Cancer Centre, Melbourne, VIC, Australia
- Sir Peter MacCallum Department of Oncology, University of Melbourne, Melbourne, VIC, Australia
| | - Kylie L Gorringe
- Peter MacCallum Cancer Centre, Melbourne, VIC, Australia
- Sir Peter MacCallum Department of Oncology, University of Melbourne, Melbourne, VIC, Australia
| | - Stephen B Fox
- Peter MacCallum Cancer Centre, Melbourne, VIC, Australia
- Sir Peter MacCallum Department of Oncology, University of Melbourne, Melbourne, VIC, Australia
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Wu H, Dixon EE, Xuanyuan Q, Guo J, Yoshimura Y, Debashish C, Niesnerova A, Xu H, Rouault M, Humphreys BD. High resolution spatial profiling of kidney injury and repair using RNA hybridization-based in situ sequencing. Nat Commun 2024; 15:1396. [PMID: 38360882 PMCID: PMC10869771 DOI: 10.1038/s41467-024-45752-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/08/2023] [Accepted: 02/02/2024] [Indexed: 02/17/2024] Open
Abstract
Emerging spatially resolved transcriptomics technologies allow for the measurement of gene expression in situ at cellular resolution. We apply direct RNA hybridization-based in situ sequencing (dRNA HybISS, Cartana part of 10xGenomics) to compare male and female healthy mouse kidneys and the male kidney injury and repair timecourse. A pre-selected panel of 200 genes is used to identify cell state dynamics patterns during injury and repair. We develop a new computational pipeline, CellScopes, for the rapid analysis, multi-omic integration and visualization of spatially resolved transcriptomic datasets. The resulting dataset allows us to resolve 13 kidney cell types within distinct kidney niches, dynamic alterations in cell state over the course of injury and repair and cell-cell interactions between leukocytes and kidney parenchyma. At late timepoints after injury, C3+ leukocytes are enriched near pro-inflammatory, failed-repair proximal tubule cells. Integration of snRNA-seq dataset from the same injury and repair samples also allows us to impute the spatial localization of genes not directly measured by dRNA HybISS.
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Affiliation(s)
- Haojia Wu
- Division of Nephrology, Department of Medicine, Washington University in St. Louis School of Medicine, St. Louis, MO, USA
| | - Eryn E Dixon
- Division of Nephrology, Department of Medicine, Washington University in St. Louis School of Medicine, St. Louis, MO, USA
| | - Qiao Xuanyuan
- Division of Nephrology, Department of Medicine, Washington University in St. Louis School of Medicine, St. Louis, MO, USA
| | - Juanru Guo
- Division of Nephrology, Department of Medicine, Washington University in St. Louis School of Medicine, St. Louis, MO, USA
| | - Yasuhiro Yoshimura
- Division of Nephrology, Department of Medicine, Washington University in St. Louis School of Medicine, St. Louis, MO, USA
| | | | | | - Hao Xu
- 10X Genomics, Pleasanton, CA, USA
- Aplex Bio AB, Solna, Sweden
| | | | - Benjamin D Humphreys
- Division of Nephrology, Department of Medicine, Washington University in St. Louis School of Medicine, St. Louis, MO, USA.
- Department of Developmental Biology, Washington University in St. Louis School of Medicine, St. Louis, MO, USA.
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8
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Carow B, Muliadi V, Skålén K, Yokota C, Kathamuthu GR, Setiabudiawan TP, Lange C, Scheu K, Gaede KI, Goldmann T, Pandita A, Masood KI, Pervez S, Grunewald J, Hasan Z, Levin M, Rottenberg ME. Immune mapping of human tuberculosis and sarcoidosis lung granulomas. Front Immunol 2024; 14:1332733. [PMID: 38385142 PMCID: PMC10879604 DOI: 10.3389/fimmu.2023.1332733] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/03/2023] [Accepted: 12/18/2023] [Indexed: 02/23/2024] Open
Abstract
Tuberculosis (TB) and sarcoidosis are both granulomatous diseases. Here, we compared the immunological microenvironments of granulomas from TB and sarcoidosis patients using in situ sequencing (ISS) transcriptomic analysis and multiplexed immunolabeling of tissue sections. TB lesions consisted of large necrotic and cellular granulomas, whereas "multifocal" granulomas with macrophages or epitheloid cell core and a T-cell rim were observed in sarcoidosis samples. The necrotic core in TB lesions was surrounded by macrophages and encircled by a dense T-cell layer. Within the T-cell layer, compact B-cell aggregates were observed in most TB samples. These B-cell clusters were vascularized and could contain defined B-/T-cell and macrophage-rich areas. The ISS of 40-60 immune transcripts revealed the enriched expression of transcripts involved in homing or migration to lymph nodes, which formed networks at single-cell distances in lymphoid areas of the TB lesions. Instead, myeloid-annotated regions were enriched in CD68, CD14, ITGAM, ITGAX, and CD4 mRNA. CXCL8 and IL1B mRNA were observed in granulocytic areas in which M. tuberculosis was also detected. In line with ISS data indicating tertiary lymphoid structures, immune labeling of TB sections expressed markers of high endothelial venules, follicular dendritic cells, follicular helper T cells, and lymph-node homing receptors on T cells. Neither ISS nor immunolabeling showed evidence of tertiary lymphoid aggregates in sarcoidosis samples. Together, our finding suggests that despite their heterogeneity, the formation of tertiary immune structures is a common feature in granulomas from TB patients.
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Affiliation(s)
- Berit Carow
- Department of Microbiology, Tumor and Cell Biology, Karolinska Institutet, Stockholm, Sweden
| | - Victoria Muliadi
- Department of Microbiology, Tumor and Cell Biology, Karolinska Institutet, Stockholm, Sweden
| | - Kristina Skålén
- Department of Molecular and Clinical Medicine/Wallenberg Laboratory, Institute of Medicine, Sahlgrenska Academy, University of Gothenburg, Gothenburg, Sweden
| | - Chika Yokota
- Science for Life Laboratory, Department of Biochemistry and Biophysics, Stockholm University, Stockholm, Sweden
| | - Gokul Raj Kathamuthu
- Department of Microbiology, Tumor and Cell Biology, Karolinska Institutet, Stockholm, Sweden
| | | | - Christoph Lange
- Research Center Borstel, Leibniz Lung Center, Borstel, Germany
| | - Katrin Scheu
- Research Center Borstel, Leibniz Lung Center, Borstel, Germany
| | - Karoline I Gaede
- German Center for Lung Research (DZL), Airway Research Center North (ARCN), Borstel, Germany
- BioMaterialBank North, Research Center Borstel, Leibniz Lung Center, Borstel, Germany
| | - Torsten Goldmann
- Research Center Borstel, Leibniz Lung Center, Borstel, Germany
- German Center for Lung Research (DZL), Airway Research Center North (ARCN), Borstel, Germany
| | - Ankur Pandita
- Department of Molecular and Clinical Medicine/Wallenberg Laboratory, Institute of Medicine, Sahlgrenska Academy, University of Gothenburg, Gothenburg, Sweden
- Department of Oncology, Institute of Clinical Sciences, Sahlgrenska Academy, University of Gothenburg, Gothenburg, Sweden
- Department of Oncology, Sahlgrenska University Hospital, Gothenburg, Sweden
| | - Kiran Iqbal Masood
- Department of Pathology and Laboratory Medicine, The Aga Khan University, Karachi, Pakistan
| | - Shahid Pervez
- Department of Pathology and Laboratory Medicine, The Aga Khan University, Karachi, Pakistan
| | - Johan Grunewald
- Respiratory Medicine Division, Department of Medicine Solna, Karolinska Institutet, Stockholm, Sweden
| | - Zahra Hasan
- Department of Pathology and Laboratory Medicine, The Aga Khan University, Karachi, Pakistan
| | - Max Levin
- Department of Molecular and Clinical Medicine/Wallenberg Laboratory, Institute of Medicine, Sahlgrenska Academy, University of Gothenburg, Gothenburg, Sweden
- Department of Oncology, Institute of Clinical Sciences, Sahlgrenska Academy, University of Gothenburg, Gothenburg, Sweden
- Department of Oncology, Sahlgrenska University Hospital, Gothenburg, Sweden
| | - Martin E Rottenberg
- Department of Microbiology, Tumor and Cell Biology, Karolinska Institutet, Stockholm, Sweden
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9
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Shin S, Kim YJ, Yun HG, Chung H, Cho H, Choi S. 3D Amplified Single-Cell RNA and Protein Imaging Identifies Oncogenic Transcript Subtypes in B-Cell Acute Lymphoblastic Leukemia. ACS NANO 2024. [PMID: 38320154 DOI: 10.1021/acsnano.3c10421] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/08/2024]
Abstract
Simultaneous in situ detection of transcript and protein markers at the single-cell level is essential for gaining a better understanding of tumor heterogeneity and for predicting and monitoring treatment responses. However, the limited accessibility to advanced 3D imaging techniques has hindered their rapid implementation. Here, we present a 3D single-cell imaging technique, termed 3D digital rolling circle amplification (4DRCA), capable of the multiplexed and amplified simultaneous digital quantification of single-cell RNAs and proteins using standard fluorescence microscopy and off-the-shelf reagents. We generated spectrally distinguishable DNA amplicons from molecular markers through an integrative protocol combining single-cell RNA and protein assays and directly enumerated the amplicons by leveraging an open-source algorithm for 3D deconvolution with a custom-built automatic gating algorithm. With 4DRCA, we were able to simultaneously quantify surface protein markers and cytokine transcripts in T-lymphocytes. We also show that 4DRCA can distinguish BCR-ABL1 fusion transcript positive B-cell acute lymphoblastic leukemia cells with or without CD19 protein expression. The accessibility and extensibility of 4DRCA render it broadly applicable to other cell-based diagnostic workflows, enabling sensitive and accurate single-cell RNA and protein profiling.
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Affiliation(s)
- Suyeon Shin
- Department of Electronic Engineering, Hanyang University, Seoul 04763, Republic of Korea
| | - Yoon-Jin Kim
- Department of Electronic Engineering, Hanyang University, Seoul 04763, Republic of Korea
| | - Hyo Geun Yun
- Department of Electronic Engineering, Hanyang University, Seoul 04763, Republic of Korea
| | - Haerim Chung
- Division of Hematology, Department of Internal Medicine, Yonsei University College of Medicine, Seoul 03722, Republic of Korea
| | - Hyunsoo Cho
- Division of Hematology, Department of Internal Medicine, Yonsei University College of Medicine, Seoul 03722, Republic of Korea
| | - Sungyoung Choi
- Department of Electronic Engineering, Hanyang University, Seoul 04763, Republic of Korea
- Department of Biomedical Engineering, Hanyang University, Seoul 04763, Republic of Korea
- Department of Healthcare Digital Engineering, Hanyang University, Seoul 04763, Republic of Korea
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10
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Lee S, Kim G, Lee J, Lee AC, Kwon S. Mapping cancer biology in space: applications and perspectives on spatial omics for oncology. Mol Cancer 2024; 23:26. [PMID: 38291400 PMCID: PMC10826015 DOI: 10.1186/s12943-024-01941-z] [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: 06/19/2023] [Accepted: 01/12/2024] [Indexed: 02/01/2024] Open
Abstract
Technologies to decipher cellular biology, such as bulk sequencing technologies and single-cell sequencing technologies, have greatly assisted novel findings in tumor biology. Recent findings in tumor biology suggest that tumors construct architectures that influence the underlying cancerous mechanisms. Increasing research has reported novel techniques to map the tissue in a spatial context or targeted sampling-based characterization and has introduced such technologies to solve oncology regarding tumor heterogeneity, tumor microenvironment, and spatially located biomarkers. In this study, we address spatial technologies that can delineate the omics profile in a spatial context, novel findings discovered via spatial technologies in oncology, and suggest perspectives regarding therapeutic approaches and further technological developments.
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Affiliation(s)
- Sumin Lee
- Department of Electrical and Computer Engineering, Seoul National University, Seoul, 08826, Republic of Korea
- Meteor Biotech,, Co. Ltd, Seoul, 08826, Republic of Korea
| | - Gyeongjun Kim
- Interdisciplinary Program in Bioengineering, Seoul National University, Seoul, 08826, Republic of Korea
| | - JinYoung Lee
- Division of Engineering Science, University of Toronto, Toronto, Ontario, ON, M5S 3H6, Canada
| | - Amos C Lee
- Meteor Biotech,, Co. Ltd, Seoul, 08826, Republic of Korea.
- Bio-MAX Institute, Seoul National University, Seoul, 08826, Republic of Korea.
| | - Sunghoon Kwon
- Department of Electrical and Computer Engineering, Seoul National University, Seoul, 08826, Republic of Korea.
- Interdisciplinary Program in Bioengineering, Seoul National University, Seoul, 08826, Republic of Korea.
- Bio-MAX Institute, Seoul National University, Seoul, 08826, Republic of Korea.
- Institutes of Entrepreneurial BioConvergence, Seoul National University, Seoul, 08826, Republic of Korea.
- Cancer Research Institute, Seoul National University College of Medicine, Seoul, 03080, Republic of Korea.
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11
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Kiessling P, Kuppe C. Spatial multi-omics: novel tools to study the complexity of cardiovascular diseases. Genome Med 2024; 16:14. [PMID: 38238823 PMCID: PMC10795303 DOI: 10.1186/s13073-024-01282-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/15/2023] [Accepted: 01/02/2024] [Indexed: 01/22/2024] Open
Abstract
Spatial multi-omic studies have emerged as a promising approach to comprehensively analyze cells in tissues, enabling the joint analysis of multiple data modalities like transcriptome, epigenome, proteome, and metabolome in parallel or even the same tissue section. This review focuses on the recent advancements in spatial multi-omics technologies, including novel data modalities and computational approaches. We discuss the advancements in low-resolution and high-resolution spatial multi-omics methods which can resolve up to 10,000 of individual molecules at subcellular level. By applying and integrating these techniques, researchers have recently gained valuable insights into the molecular circuits and mechanisms which govern cell biology along the cardiovascular disease spectrum. We provide an overview of current data analysis approaches, with a focus on data integration of multi-omic datasets, highlighting strengths and weaknesses of various computational pipelines. These tools play a crucial role in analyzing and interpreting spatial multi-omics datasets, facilitating the discovery of new findings, and enhancing translational cardiovascular research. Despite nontrivial challenges, such as the need for standardization of experimental setups, data analysis, and improved computational tools, the application of spatial multi-omics holds tremendous potential in revolutionizing our understanding of human disease processes and the identification of novel biomarkers and therapeutic targets. Exciting opportunities lie ahead for the spatial multi-omics field and will likely contribute to the advancement of personalized medicine for cardiovascular diseases.
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Affiliation(s)
- Paul Kiessling
- Department of Nephrology, Rheumatology, and Clinical Immunology, University Hospital RWTH Aachen, Aachen, Germany
| | - Christoph Kuppe
- Department of Nephrology, Rheumatology, and Clinical Immunology, University Hospital RWTH Aachen, Aachen, Germany.
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12
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Wu Z, Yin H, Guo Y, Yin H, Li Y. Detection of cell-type-enriched long noncoding RNAs in atherosclerosis using single-cell techniques: A brief review. Life Sci 2023; 333:122138. [PMID: 37805167 DOI: 10.1016/j.lfs.2023.122138] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/15/2023] [Revised: 09/20/2023] [Accepted: 09/29/2023] [Indexed: 10/09/2023]
Abstract
Cardiovascular diseases are the leading causes of mortality and morbidity worldwide. Atherosclerotic plaque underlies the predominant factors and is composed of various cell types, including structure cells, such as endothelial and smooth muscle cells, and immune cells, such as macrophages and T cells. Single-cell RNA sequencing (scRNA-seq) has been extensively applied to decipher these cellular heterogeneities to expand our understanding on the mechanisms of atherosclerosis (AS) and to facilitate identifying cell-type-specific long noncoding RNAs (LncRNAs). LncRNAs have been demonstrated to deeply regulate biological activities at the transcriptional and post-transcriptional levels. A group of well-documented functional lncRNAs in AS have been studied. In our review, we selectively described several lncRNAs involved in the critical process of AS. We highlighted four novel lncRNAs (lncRNA CARMN, LINC00607, PCAT19, LINC01235) detected in scRNA-seq datasets and their functions in AS. We also reviewed open web source and bioinformatic tools, as well as the latest methods to perform an in-depth study of lncRNAs. It is fundamental to annotate functional lncRNAs in the various biological activities of AS, as lncRNAs may represent promising targets in the future for treatment and diagnosis in clinical practice.
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Affiliation(s)
- Zhiyuan Wu
- Department of Vascular Surgery, Beijing Hospital, National Center of Gerontology, Institute of Geriatric Medicine, Chinese Academy of Medical Sciences, 100730 Beijing, PR China
| | - Huarun Yin
- Department of Pathology, Institute of Basic Medical Sciences Chinese Academy of Medical Sciences, School of Basic Medicine Peking Union Medical College, 100730 Beijing, PR China
| | - Yongsheng Guo
- Peking University Health Science Center, 100191 Beijing, PR China
| | - Hongchao Yin
- Department of Pathology, Institute of Basic Medical Sciences Chinese Academy of Medical Sciences, School of Basic Medicine Peking Union Medical College, 100730 Beijing, PR China
| | - Yongjun Li
- Department of Vascular Surgery, Beijing Hospital, National Center of Gerontology, Institute of Geriatric Medicine, Chinese Academy of Medical Sciences, 100730 Beijing, PR China; Peking University Health Science Center, 100191 Beijing, PR China; Graduate School of Peking Union Medical College, Chinese Academy of Medical Sciences, 100730 Beijing, PR China
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13
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Alexandrov T, Saez‐Rodriguez J, Saka SK. Enablers and challenges of spatial omics, a melting pot of technologies. Mol Syst Biol 2023; 19:e10571. [PMID: 37842805 PMCID: PMC10632737 DOI: 10.15252/msb.202110571] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/16/2021] [Revised: 07/31/2023] [Accepted: 08/03/2023] [Indexed: 10/17/2023] Open
Abstract
Spatial omics has emerged as a rapidly growing and fruitful field with hundreds of publications presenting novel methods for obtaining spatially resolved information for any omics data type on spatial scales ranging from subcellular to organismal. From a technology development perspective, spatial omics is a highly interdisciplinary field that integrates imaging and omics, spatial and molecular analyses, sequencing and mass spectrometry, and image analysis and bioinformatics. The emergence of this field has not only opened a window into spatial biology, but also created multiple novel opportunities, questions, and challenges for method developers. Here, we provide the perspective of technology developers on what makes the spatial omics field unique. After providing a brief overview of the state of the art, we discuss technological enablers and challenges and present our vision about the future applications and impact of this melting pot.
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Affiliation(s)
- Theodore Alexandrov
- Structural and Computational Biology UnitEuropean Molecular Biology LaboratoryHeidelbergGermany
- Molecular Medicine Partnership UnitEuropean Molecular Biology LaboratoryHeidelbergGermany
- BioInnovation InstituteCopenhagenDenmark
| | - Julio Saez‐Rodriguez
- Molecular Medicine Partnership UnitEuropean Molecular Biology LaboratoryHeidelbergGermany
- Faculty of Medicine and Heidelberg University Hospital, Institute for Computational BiomedicineHeidelberg UniversityHeidelbergGermany
| | - Sinem K Saka
- Genome Biology UnitEuropean Molecular Biology LaboratoryHeidelbergGermany
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14
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Robles-Remacho A, Sanchez-Martin RM, Diaz-Mochon JJ. Spatial Transcriptomics: Emerging Technologies in Tissue Gene Expression Profiling. Anal Chem 2023; 95:15450-15460. [PMID: 37814884 PMCID: PMC10603609 DOI: 10.1021/acs.analchem.3c02029] [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: 05/10/2023] [Accepted: 09/21/2023] [Indexed: 10/11/2023]
Abstract
In this Perspective, we discuss the current status and advances in spatial transcriptomics technologies, which allow high-resolution mapping of gene expression in intact cell and tissue samples. Spatial transcriptomics enables the creation of high-resolution maps of gene expression patterns within their native spatial context, adding an extra layer of information to the bulk sequencing data. Spatial transcriptomics has expanded significantly in recent years and is making a notable impact on a range of fields, including tissue architecture, developmental biology, cancer, and neurodegenerative and infectious diseases. The latest advancements in spatial transcriptomics have resulted in the development of highly multiplexed methods, transcriptomic-wide analysis, and single-cell resolution utilizing diverse technological approaches. In this Perspective, we provide a detailed analysis of the molecular foundations behind the main spatial transcriptomics technologies, including methods based on microdissection, in situ sequencing, single-molecule FISH, spatial capturing, selection of regions of interest, and single-cell or nuclei dissociation. We contextualize the detection and capturing efficiency, strengths, limitations, tissue compatibility, and applications of these techniques as well as provide information on data analysis. In addition, this Perspective discusses future directions and potential applications of spatial transcriptomics, highlighting the importance of the continued development to promote widespread adoption of these techniques within the research community.
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Affiliation(s)
- Agustín Robles-Remacho
- GENYO.
Centre for Genomics and Oncological Research, Pfizer/University of Granada/Andalusian Regional Government, PTS Granada, Avenida de la Ilustracion,
114. 18016 Granada, Spain
- Department
of Medicinal and Organic Chemistry, School of Pharmacy, University of Granada, Campus Cartuja s/n, 18071 Granada, Spain
- Instituto
de Investigación Biosanitaria ibs.GRANADA, 18012 Granada, Spain
| | - Rosario M. Sanchez-Martin
- GENYO.
Centre for Genomics and Oncological Research, Pfizer/University of Granada/Andalusian Regional Government, PTS Granada, Avenida de la Ilustracion,
114. 18016 Granada, Spain
- Department
of Medicinal and Organic Chemistry, School of Pharmacy, University of Granada, Campus Cartuja s/n, 18071 Granada, Spain
- Instituto
de Investigación Biosanitaria ibs.GRANADA, 18012 Granada, Spain
| | - Juan J. Diaz-Mochon
- GENYO.
Centre for Genomics and Oncological Research, Pfizer/University of Granada/Andalusian Regional Government, PTS Granada, Avenida de la Ilustracion,
114. 18016 Granada, Spain
- Department
of Medicinal and Organic Chemistry, School of Pharmacy, University of Granada, Campus Cartuja s/n, 18071 Granada, Spain
- Instituto
de Investigación Biosanitaria ibs.GRANADA, 18012 Granada, Spain
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15
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Gray S, Ottensmeier CH. Advancing Understanding of Non-Small Cell Lung Cancer with Multiplexed Antibody-Based Spatial Imaging Technologies. Cancers (Basel) 2023; 15:4797. [PMID: 37835491 PMCID: PMC10571797 DOI: 10.3390/cancers15194797] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/21/2023] [Revised: 09/22/2023] [Accepted: 09/27/2023] [Indexed: 10/15/2023] Open
Abstract
Non-small cell lung cancer (NSCLC) remains a cause of significant morbidity and mortality, despite significant advances made in its treatment using immune checkpoint inhibitors (ICIs) over the last decade; while a minority experience prolonged responses with ICIs, benefit is limited for most patients. The development of multiplexed antibody-based (MAB) spatial tissue imaging technologies has revolutionised analysis of the tumour microenvironment (TME), enabling identification of a wide range of cell types and subtypes, and analysis of the spatial relationships and interactions between them. Such study has the potential to translate into a greater understanding of treatment susceptibility and resistance, factors influencing prognosis and recurrence risk, and identification of novel therapeutic approaches and rational treatment combinations to improve patient outcomes in the clinic. Herein we review studies that have leveraged MAB technologies to deliver novel insights into the TME of NSCLC.
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Affiliation(s)
- Simon Gray
- Department of Molecular and Clinical Cancer Medicine, Faculty of Health and Life Sciences, University of Liverpool, Ashton St., Liverpool L69 3GB, UK
- Department of Medical Oncology, The Clatterbridge Cancer Centre NHS Foundation Trust, Pembroke Pl., Liverpool L7 8YA, UK
| | - Christian H. Ottensmeier
- Department of Molecular and Clinical Cancer Medicine, Faculty of Health and Life Sciences, University of Liverpool, Ashton St., Liverpool L69 3GB, UK
- Department of Medical Oncology, The Clatterbridge Cancer Centre NHS Foundation Trust, Pembroke Pl., Liverpool L7 8YA, UK
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16
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Tang X, Chen J, Zhang X, Liu X, Xie Z, Wei K, Qiu J, Ma W, Lin C, Ke R. Improved in situ sequencing for high-resolution targeted spatial transcriptomic analysis in tissue sections. J Genet Genomics 2023; 50:652-660. [PMID: 36796537 DOI: 10.1016/j.jgg.2023.02.004] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/03/2022] [Revised: 01/30/2023] [Accepted: 02/02/2023] [Indexed: 02/17/2023]
Abstract
Spatial transcriptomics enables the study of localization-indexed gene expression activity in tissues, providing the transcriptional landscape that in turn indicates the potential regulatory networks of gene expression. In situ sequencing (ISS) is a targeted spatial transcriptomic technique, based on padlock probe and rolling circle amplification combined with next-generation sequencing chemistry, for highly multiplexed in situ gene expression profiling. Here, we present improved in situ sequencing (IISS) that exploits a new probing and barcoding approach, combined with advanced image analysis pipelines for high-resolution targeted spatial gene expression profiling. We develop an improved combinatorial probe anchor ligation chemistry using a 2-base encoding strategy for barcode interrogation. The new encoding strategy results in higher signal intensity as well as improved specificity for in situ sequencing, while maintaining a streamlined analysis pipeline for targeted spatial transcriptomics. We show that IISS can be applied to both fresh frozen tissue and formalin-fixed paraffin-embedded tissue sections for single-cell level spatial gene expression analysis, based on which the developmental trajectory and cell-cell communication networks can also be constructed.
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Affiliation(s)
- Xinbin Tang
- School of Medicine and School of Biomedical Sciences, Huaqiao University, Quanzhou, Fujian 362021, China
| | - Jiayu Chen
- School of Medicine and School of Biomedical Sciences, Huaqiao University, Quanzhou, Fujian 362021, China
| | - Xinya Zhang
- School of Medicine and School of Biomedical Sciences, Huaqiao University, Quanzhou, Fujian 362021, China
| | - Xuzhu Liu
- School of Medicine and School of Biomedical Sciences, Huaqiao University, Quanzhou, Fujian 362021, China
| | - Zhaoxiang Xie
- School of Medicine and School of Biomedical Sciences, Huaqiao University, Quanzhou, Fujian 362021, China
| | - Kaipeng Wei
- Department of Pathology, The 910 Hospital, Quanzhou, Fujian 362000, China
| | - Jianlong Qiu
- Department of Pathology, The 910 Hospital, Quanzhou, Fujian 362000, China
| | - Weiyan Ma
- School of Medicine and School of Biomedical Sciences, Huaqiao University, Quanzhou, Fujian 362021, China
| | - Chen Lin
- School of Medicine and School of Biomedical Sciences, Huaqiao University, Quanzhou, Fujian 362021, China.
| | - Rongqin Ke
- School of Medicine and School of Biomedical Sciences, Huaqiao University, Quanzhou, Fujian 362021, China.
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17
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Magoulopoulou A, Salas SM, Tiklová K, Samuelsson ER, Hilscher MM, Nilsson M. Padlock Probe-Based Targeted In Situ Sequencing: Overview of Methods and Applications. Annu Rev Genomics Hum Genet 2023; 24:133-150. [PMID: 37018847 DOI: 10.1146/annurev-genom-102722-092013] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 04/07/2023]
Abstract
Elucidating spatiotemporal changes in gene expression has been an essential goal in studies of health, development, and disease. In the emerging field of spatially resolved transcriptomics, gene expression profiles are acquired with the tissue architecture maintained, sometimes at cellular resolution. This has allowed for the development of spatial cell atlases, studies of cell-cell interactions, and in situ cell typing. In this review, we focus on padlock probe-based in situ sequencing, which is a targeted spatially resolved transcriptomic method. We summarize recent methodological and computational tool developments and discuss key applications. We also discuss compatibility with other methods and integration with multiomic platforms for future applications.
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Affiliation(s)
- Anastasia Magoulopoulou
- Department of Biochemistry and Biophysics, Science for Life Laboratory, Stockholm University, Solna, Sweden; , , , , ,
| | - Sergio Marco Salas
- Department of Biochemistry and Biophysics, Science for Life Laboratory, Stockholm University, Solna, Sweden; , , , , ,
| | - Katarína Tiklová
- Department of Biochemistry and Biophysics, Science for Life Laboratory, Stockholm University, Solna, Sweden; , , , , ,
| | - Erik Reinhold Samuelsson
- Department of Biochemistry and Biophysics, Science for Life Laboratory, Stockholm University, Solna, Sweden; , , , , ,
| | - Markus M Hilscher
- Department of Biochemistry and Biophysics, Science for Life Laboratory, Stockholm University, Solna, Sweden; , , , , ,
| | - Mats Nilsson
- Department of Biochemistry and Biophysics, Science for Life Laboratory, Stockholm University, Solna, Sweden; , , , , ,
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18
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Park H, Jo SH, Lee RH, Macks CP, Ku T, Park J, Lee CW, Hur JK, Sohn CH. Spatial Transcriptomics: Technical Aspects of Recent Developments and Their Applications in Neuroscience and Cancer Research. ADVANCED SCIENCE (WEINHEIM, BADEN-WURTTEMBERG, GERMANY) 2023; 10:e2206939. [PMID: 37026425 PMCID: PMC10238226 DOI: 10.1002/advs.202206939] [Citation(s) in RCA: 13] [Impact Index Per Article: 13.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/25/2022] [Revised: 03/10/2023] [Indexed: 06/04/2023]
Abstract
Spatial transcriptomics is a newly emerging field that enables high-throughput investigation of the spatial localization of transcripts and related analyses in various applications for biological systems. By transitioning from conventional biological studies to "in situ" biology, spatial transcriptomics can provide transcriptome-scale spatial information. Currently, the ability to simultaneously characterize gene expression profiles of cells and relevant cellular environment is a paradigm shift for biological studies. In this review, recent progress in spatial transcriptomics and its applications in neuroscience and cancer studies are highlighted. Technical aspects of existing technologies and future directions of new developments (as of March 2023), computational analysis of spatial transcriptome data, application notes in neuroscience and cancer studies, and discussions regarding future directions of spatial multi-omics and their expanding roles in biomedical applications are emphasized.
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Affiliation(s)
- Han‐Eol Park
- Center for NanomedicineInstitute for Basic ScienceYonsei UniversitySeoul03722Republic of Korea
- Graduate Program in Nanobiomedical EngineeringAdvanced Science InstituteYonsei UniversitySeoul03722Republic of Korea
- School of Biological SciencesSeoul National UniversitySeoul08826Republic of Korea
| | - Song Hyun Jo
- Graduate School of Medical Science and EngineeringKorea Advanced Institute of Science and Technology (KAIST)Daejeon34141Republic of Korea
| | - Rosalind H. Lee
- School of Life SciencesGwangju Institute of Science and Technology (GIST)Gwangju61005Republic of Korea
| | - Christian P. Macks
- Center for NanomedicineInstitute for Basic ScienceYonsei UniversitySeoul03722Republic of Korea
- Graduate Program in Nanobiomedical EngineeringAdvanced Science InstituteYonsei UniversitySeoul03722Republic of Korea
| | - Taeyun Ku
- Graduate School of Medical Science and EngineeringKorea Advanced Institute of Science and Technology (KAIST)Daejeon34141Republic of Korea
| | - Jihwan Park
- School of Life SciencesGwangju Institute of Science and Technology (GIST)Gwangju61005Republic of Korea
| | - Chung Whan Lee
- Department of ChemistryGachon UniversitySeongnamGyeonggi‐do13120Republic of Korea
| | - Junho K. Hur
- Department of GeneticsCollege of MedicineHanyang UniversitySeoul04763Republic of Korea
| | - Chang Ho Sohn
- Center for NanomedicineInstitute for Basic ScienceYonsei UniversitySeoul03722Republic of Korea
- Graduate Program in Nanobiomedical EngineeringAdvanced Science InstituteYonsei UniversitySeoul03722Republic of Korea
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19
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Linares A, Brighi C, Espinola S, Bacchi F, Crevenna ÁH. Structured Illumination Microscopy Improves Spot Detection Performance in Spatial Transcriptomics. Cells 2023; 12:cells12091310. [PMID: 37174710 PMCID: PMC10177490 DOI: 10.3390/cells12091310] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/28/2023] [Revised: 04/28/2023] [Accepted: 05/01/2023] [Indexed: 05/15/2023] Open
Abstract
Spatial biology is a rapidly growing research field that focuses on the transcriptomic or proteomic profiling of single cells within tissues with preserved spatial information. Imaging-based spatial transcriptomics uses epifluorescence microscopy, which has shown remarkable results for the identification of multiple targets in situ. Nonetheless, the number of genes that can be reliably visualized is limited by the diffraction of light. Here, we investigate the effect of structured illumination (SIM), a super-resolution microscopy approach, on the performance of single-gene transcript detection in spatial transcriptomics experiments. We performed direct mRNA-targeted hybridization in situ sequencing for multiple genes in mouse coronal brain tissue sections. We evaluated spot detection performance in widefield and confocal images versus those with SIM in combination with 20×, 25× and 60× objectives. In general, SIM increases the detection efficiency of gene transcript spots compared to widefield and confocal modes. For each case, the specific fold increase in localizations is dependent on gene transcript density and the numerical aperture of the objective used, which has been shown to play an important role, especially for densely clustered spots. Taken together, our results suggest that SIM has the capacity to improve spot detection and overall data quality in spatial transcriptomics.
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Affiliation(s)
- Alejandro Linares
- Epigenetics and Neurobiology Unit, European Molecular Biology Laboratory, 00015 Rome, Italy
| | | | - Sergio Espinola
- Epigenetics and Neurobiology Unit, European Molecular Biology Laboratory, 00015 Rome, Italy
| | | | - Álvaro H Crevenna
- Epigenetics and Neurobiology Unit, European Molecular Biology Laboratory, 00015 Rome, Italy
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20
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Sountoulidis A, Marco Salas S, Braun E, Avenel C, Bergenstråhle J, Theelke J, Vicari M, Czarnewski P, Liontos A, Abalo X, Andrusivová Ž, Mirzazadeh R, Asp M, Li X, Hu L, Sariyar S, Martinez Casals A, Ayoglu B, Firsova A, Michaëlsson J, Lundberg E, Wählby C, Sundström E, Linnarsson S, Lundeberg J, Nilsson M, Samakovlis C. A topographic atlas defines developmental origins of cell heterogeneity in the human embryonic lung. Nat Cell Biol 2023; 25:351-365. [PMID: 36646791 PMCID: PMC9928586 DOI: 10.1038/s41556-022-01064-x] [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: 03/18/2022] [Accepted: 11/23/2022] [Indexed: 01/18/2023]
Abstract
The lung contains numerous specialized cell types with distinct roles in tissue function and integrity. To clarify the origins and mechanisms generating cell heterogeneity, we created a comprehensive topographic atlas of early human lung development. Here we report 83 cell states and several spatially resolved developmental trajectories and predict cell interactions within defined tissue niches. We integrated single-cell RNA sequencing and spatially resolved transcriptomics into a web-based, open platform for interactive exploration. We show distinct gene expression programmes, accompanying sequential events of cell differentiation and maturation of the secretory and neuroendocrine cell types in proximal epithelium. We define the origin of airway fibroblasts associated with airway smooth muscle in bronchovascular bundles and describe a trajectory of Schwann cell progenitors to intrinsic parasympathetic neurons controlling bronchoconstriction. Our atlas provides a rich resource for further research and a reference for defining deviations from homeostatic and repair mechanisms leading to pulmonary diseases.
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Affiliation(s)
- Alexandros Sountoulidis
- grid.452834.c0000 0004 5911 2402Science for Life Laboratory, Solna, Sweden ,grid.10548.380000 0004 1936 9377Department of Molecular Biosciences, Wenner-Gren Institute, Stockholm University, Stockholm, Sweden
| | - Sergio Marco Salas
- grid.452834.c0000 0004 5911 2402Science for Life Laboratory, Solna, Sweden ,grid.10548.380000 0004 1936 9377Department of Biochemistry and Biophysics, Stockholm University, Stockholm, Sweden
| | - Emelie Braun
- grid.4714.60000 0004 1937 0626Division of Molecular Neurobiology, Department of Medical Biochemistry and Biophysics, Karolinska Institute, Stockholm, Sweden
| | - Christophe Avenel
- grid.8993.b0000 0004 1936 9457Department of Information Technology, Uppsala University, Uppsala, Sweden ,grid.452834.c0000 0004 5911 2402BioImage Informatics Facility, Science for Life Laboratory, SciLifeLab, Sweden
| | - Joseph Bergenstråhle
- grid.5037.10000000121581746Science for Life Laboratory, Department of Gene Technology, KTH Royal Institute of Technology, Stockholm, Sweden
| | - Jonas Theelke
- grid.452834.c0000 0004 5911 2402Science for Life Laboratory, Solna, Sweden ,grid.10548.380000 0004 1936 9377Department of Molecular Biosciences, Wenner-Gren Institute, Stockholm University, Stockholm, Sweden
| | - Marco Vicari
- grid.5037.10000000121581746Science for Life Laboratory, Department of Gene Technology, KTH Royal Institute of Technology, Stockholm, Sweden
| | - Paulo Czarnewski
- grid.5037.10000000121581746Science for Life Laboratory, Department of Gene Technology, KTH Royal Institute of Technology, Stockholm, Sweden
| | - Andreas Liontos
- grid.452834.c0000 0004 5911 2402Science for Life Laboratory, Solna, Sweden ,grid.10548.380000 0004 1936 9377Department of Molecular Biosciences, Wenner-Gren Institute, Stockholm University, Stockholm, Sweden
| | - Xesus Abalo
- grid.5037.10000000121581746Science for Life Laboratory, Department of Gene Technology, KTH Royal Institute of Technology, Stockholm, Sweden
| | - Žaneta Andrusivová
- grid.5037.10000000121581746Science for Life Laboratory, Department of Gene Technology, KTH Royal Institute of Technology, Stockholm, Sweden
| | - Reza Mirzazadeh
- grid.5037.10000000121581746Science for Life Laboratory, Department of Gene Technology, KTH Royal Institute of Technology, Stockholm, Sweden
| | - Michaela Asp
- grid.5037.10000000121581746Science for Life Laboratory, Department of Gene Technology, KTH Royal Institute of Technology, Stockholm, Sweden
| | - Xiaofei Li
- grid.4714.60000 0004 1937 0626Department of Neurobiology, Care Sciences and Society, Karolinska Institutet, Stockholm, Sweden
| | - Lijuan Hu
- grid.4714.60000 0004 1937 0626Division of Molecular Neurobiology, Department of Medical Biochemistry and Biophysics, Karolinska Institute, Stockholm, Sweden
| | - Sanem Sariyar
- grid.5037.10000000121581746Science for Life Laboratory, School of Engineering Sciences in Chemistry, Biotechnology and Health, KTH - Royal Institute of Technology, Stockholm, Sweden
| | - Anna Martinez Casals
- grid.5037.10000000121581746Science for Life Laboratory, School of Engineering Sciences in Chemistry, Biotechnology and Health, KTH - Royal Institute of Technology, Stockholm, Sweden
| | - Burcu Ayoglu
- grid.5037.10000000121581746Science for Life Laboratory, School of Engineering Sciences in Chemistry, Biotechnology and Health, KTH - Royal Institute of Technology, Stockholm, Sweden
| | - Alexandra Firsova
- grid.452834.c0000 0004 5911 2402Science for Life Laboratory, Solna, Sweden ,grid.10548.380000 0004 1936 9377Department of Molecular Biosciences, Wenner-Gren Institute, Stockholm University, Stockholm, Sweden
| | - Jakob Michaëlsson
- grid.4714.60000 0004 1937 0626Center for Infectious Medicine, Department of Medicine Huddinge, Karolinska Institutet, Stockholm, Sweden
| | - Emma Lundberg
- grid.5037.10000000121581746Science for Life Laboratory, School of Engineering Sciences in Chemistry, Biotechnology and Health, KTH - Royal Institute of Technology, Stockholm, Sweden
| | - Carolina Wählby
- grid.8993.b0000 0004 1936 9457Department of Information Technology, Uppsala University, Uppsala, Sweden ,grid.452834.c0000 0004 5911 2402BioImage Informatics Facility, Science for Life Laboratory, SciLifeLab, Sweden
| | - Erik Sundström
- grid.4714.60000 0004 1937 0626Department of Neurobiology, Care Sciences and Society, Karolinska Institutet, Stockholm, Sweden
| | - Sten Linnarsson
- grid.4714.60000 0004 1937 0626Division of Molecular Neurobiology, Department of Medical Biochemistry and Biophysics, Karolinska Institute, Stockholm, Sweden
| | - Joakim Lundeberg
- grid.5037.10000000121581746Science for Life Laboratory, Department of Gene Technology, KTH Royal Institute of Technology, Stockholm, Sweden
| | - Mats Nilsson
- Science for Life Laboratory, Solna, Sweden. .,Department of Biochemistry and Biophysics, Stockholm University, Stockholm, Sweden.
| | - Christos Samakovlis
- Science for Life Laboratory, Solna, Sweden. .,Department of Molecular Biosciences, Wenner-Gren Institute, Stockholm University, Stockholm, Sweden. .,Molecular Pneumology, Cardiopulmonary Institute, Justus Liebig University, Giessen, Germany.
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