Evaluating methods for integrating single-cell data and genetics to understand inflammatory disease complexity
BackgroundUnderstanding genetic underpinnings of immune-mediated inflammatory diseases is crucial to improve treatments. Single-cell RNA sequencing (scRNA-seq) identifies cell states expanded in disease, but often overlooks genetic causality due to cost and small genotyping cohorts. Conversely, larg...
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Frontiers Media S.A.
2024-12-01
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| author | Hope A. Townsend Hope A. Townsend Kaylee J. Rosenberger Kaylee J. Rosenberger Lauren A. Vanderlinden Lauren A. Vanderlinden Jun Inamo Jun Inamo Fan Zhang Fan Zhang Fan Zhang |
| author_facet | Hope A. Townsend Hope A. Townsend Kaylee J. Rosenberger Kaylee J. Rosenberger Lauren A. Vanderlinden Lauren A. Vanderlinden Jun Inamo Jun Inamo Fan Zhang Fan Zhang Fan Zhang |
| author_sort | Hope A. Townsend |
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| description | BackgroundUnderstanding genetic underpinnings of immune-mediated inflammatory diseases is crucial to improve treatments. Single-cell RNA sequencing (scRNA-seq) identifies cell states expanded in disease, but often overlooks genetic causality due to cost and small genotyping cohorts. Conversely, large genome-wide association studies (GWAS) are commonly accessible.MethodsWe present a 3-step robust benchmarking analysis of integrating GWAS and scRNA-seq to identify genetically relevant cell states and genes in inflammatory diseases. First, we applied and compared the results of three recent algorithms, based on pathways (scGWAS), single-cell disease scores (scDRS), or both (scPagwas), according to accuracy/sensitivity and interpretability. While previous studies focused on coarse cell types, we used disease-specific, fine-grained single-cell atlases (183,742 and 228,211 cells) and GWAS data (Ns of 97,173 and 45,975) for rheumatoid arthritis (RA) and ulcerative colitis (UC). Second, given the lack of scRNA-seq for many diseases with GWAS, we further tested the tools’ resolution limits by differentiating between similar diseases with only one fine-grained scRNA-seq atlas. Lastly, we provide a novel evaluation of noncoding SNP incorporation methods by testing which enabled the highest sensitivity/accuracy of known cell-state calls.ResultsWe first found that single-cell based tools scDRS and scPagwas called superior numbers of supported cell states that were overlooked by scGWAS. While scGWAS and scPagwas were advantageous for gene exploration, scDRS effectively accounted for batch effect and captured cellular heterogeneity of disease-relevance without single-cell genotyping. For noncoding SNP integration, we found a key trade-off between statistical power and confidence with positional (e.g. MAGMA) and non-positional approaches (e.g. chromatin-interaction, eQTL). Even when directly incorporating noncoding SNPs through 5’ scRNA-seq measures of regulatory elements, non disease-specific atlases gave misleading results by not containing disease-tissue specific transcriptomic patterns. Despite this criticality of tissue-specific scRNA-seq, we showed that scDRS enabled deconvolution of two similar diseases with a single fine-grained scRNA-seq atlas and separate GWAS. Indeed, we identified supported and novel genetic-phenotype linkages separating RA and ankylosing spondylitis, and UC and crohn’s disease. Overall, while noting evolving single-cell technologies, our study provides key findings for integrating expanding fine-grained scRNA-seq, GWAS, and noncoding SNP resources to unravel the complexities of inflammatory diseases. |
| format | Article |
| id | doaj-art-dcec6853bea04b8aaf82df055ac850a5 |
| institution | OA Journals |
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| spelling | doaj-art-dcec6853bea04b8aaf82df055ac850a52025-08-20T02:18:55ZengFrontiers Media S.A.Frontiers in Immunology1664-32242024-12-011510.3389/fimmu.2024.14542631454263Evaluating methods for integrating single-cell data and genetics to understand inflammatory disease complexityHope A. Townsend0Hope A. Townsend1Kaylee J. Rosenberger2Kaylee J. Rosenberger3Lauren A. Vanderlinden4Lauren A. Vanderlinden5Jun Inamo6Jun Inamo7Fan Zhang8Fan Zhang9Fan Zhang10Biofrontiers Institute, University of Colorado Boulder, Boulder, CO, United StatesDepartment of Molecular, Cellular, Developmental Biology, University of Colorado Boulder, Boulder, CO, United StatesBiofrontiers Institute, University of Colorado Boulder, Boulder, CO, United StatesDepartment of Ecology and Evolutionary Biology, University of Colorado Boulder, Boulder, CO, United StatesDepartment of Medicine, Division of Rheumatology, University of Colorado Anschutz Medical Campus, Denver, CO, United StatesDepartment of Biomedical Informatics, Center for Health AI, University of Colorado Anschutz Medical Campus, Denver, CO, United StatesDepartment of Medicine, Division of Rheumatology, University of Colorado Anschutz Medical Campus, Denver, CO, United StatesDepartment of Biomedical Informatics, Center for Health AI, University of Colorado Anschutz Medical Campus, Denver, CO, United StatesBiofrontiers Institute, University of Colorado Boulder, Boulder, CO, United StatesDepartment of Medicine, Division of Rheumatology, University of Colorado Anschutz Medical Campus, Denver, CO, United StatesDepartment of Biomedical Informatics, Center for Health AI, University of Colorado Anschutz Medical Campus, Denver, CO, United StatesBackgroundUnderstanding genetic underpinnings of immune-mediated inflammatory diseases is crucial to improve treatments. Single-cell RNA sequencing (scRNA-seq) identifies cell states expanded in disease, but often overlooks genetic causality due to cost and small genotyping cohorts. Conversely, large genome-wide association studies (GWAS) are commonly accessible.MethodsWe present a 3-step robust benchmarking analysis of integrating GWAS and scRNA-seq to identify genetically relevant cell states and genes in inflammatory diseases. First, we applied and compared the results of three recent algorithms, based on pathways (scGWAS), single-cell disease scores (scDRS), or both (scPagwas), according to accuracy/sensitivity and interpretability. While previous studies focused on coarse cell types, we used disease-specific, fine-grained single-cell atlases (183,742 and 228,211 cells) and GWAS data (Ns of 97,173 and 45,975) for rheumatoid arthritis (RA) and ulcerative colitis (UC). Second, given the lack of scRNA-seq for many diseases with GWAS, we further tested the tools’ resolution limits by differentiating between similar diseases with only one fine-grained scRNA-seq atlas. Lastly, we provide a novel evaluation of noncoding SNP incorporation methods by testing which enabled the highest sensitivity/accuracy of known cell-state calls.ResultsWe first found that single-cell based tools scDRS and scPagwas called superior numbers of supported cell states that were overlooked by scGWAS. While scGWAS and scPagwas were advantageous for gene exploration, scDRS effectively accounted for batch effect and captured cellular heterogeneity of disease-relevance without single-cell genotyping. For noncoding SNP integration, we found a key trade-off between statistical power and confidence with positional (e.g. MAGMA) and non-positional approaches (e.g. chromatin-interaction, eQTL). Even when directly incorporating noncoding SNPs through 5’ scRNA-seq measures of regulatory elements, non disease-specific atlases gave misleading results by not containing disease-tissue specific transcriptomic patterns. Despite this criticality of tissue-specific scRNA-seq, we showed that scDRS enabled deconvolution of two similar diseases with a single fine-grained scRNA-seq atlas and separate GWAS. Indeed, we identified supported and novel genetic-phenotype linkages separating RA and ankylosing spondylitis, and UC and crohn’s disease. Overall, while noting evolving single-cell technologies, our study provides key findings for integrating expanding fine-grained scRNA-seq, GWAS, and noncoding SNP resources to unravel the complexities of inflammatory diseases.https://www.frontiersin.org/articles/10.3389/fimmu.2024.1454263/fullscRNA-seqGWASSNP-gene linkingautoimmune diseasesbenchmarkingomics |
| spellingShingle | Hope A. Townsend Hope A. Townsend Kaylee J. Rosenberger Kaylee J. Rosenberger Lauren A. Vanderlinden Lauren A. Vanderlinden Jun Inamo Jun Inamo Fan Zhang Fan Zhang Fan Zhang Evaluating methods for integrating single-cell data and genetics to understand inflammatory disease complexity Frontiers in Immunology scRNA-seq GWAS SNP-gene linking autoimmune diseases benchmarking omics |
| title | Evaluating methods for integrating single-cell data and genetics to understand inflammatory disease complexity |
| title_full | Evaluating methods for integrating single-cell data and genetics to understand inflammatory disease complexity |
| title_fullStr | Evaluating methods for integrating single-cell data and genetics to understand inflammatory disease complexity |
| title_full_unstemmed | Evaluating methods for integrating single-cell data and genetics to understand inflammatory disease complexity |
| title_short | Evaluating methods for integrating single-cell data and genetics to understand inflammatory disease complexity |
| title_sort | evaluating methods for integrating single cell data and genetics to understand inflammatory disease complexity |
| topic | scRNA-seq GWAS SNP-gene linking autoimmune diseases benchmarking omics |
| url | https://www.frontiersin.org/articles/10.3389/fimmu.2024.1454263/full |
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