Single-cell meta-analysis of inflammatory bowel disease with scIBD

Nie, Hongtao; Lin, Peter H.; Zhang, Y.; Wan, Yihong; Li, Jiesheng; Yin, Chenghong; Zhang, Lei

doi:10.1038/s43588-023-00464-9

Cited by 11 publications

(2 citation statements)

References 55 publications

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“…This platform enabled the recognition of different cell types and IBD-associated genes. The meta-analysis corroborated the greater prevalence of Tregs in both UC and CD compared to healthy tissues, consistent with prior findings ( 72 ).…”

Section: Regulatory T Cellssupporting

confidence: 89%

Single cell RNA-sequencing profiling to improve the translation between human IBD and in vivo models

Karmele,

Moldoveanu,

Kaymak

et al. 2023

Front. Immunol.

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Inflammatory bowel disease (IBD) is an umbrella term for two conditions (Crohn’s Disease and Ulcerative Colitis) that is characterized by chronic inflammation of the gastrointestinal tract. The use of pre-clinical animal models has been invaluable for the understanding of potential disease mechanisms. However, despite promising results of numerous therapeutics in mouse colitis models, many of these therapies did not show clinical benefits in patients with IBD. Single cell RNA-sequencing (scRNA-seq) has recently revolutionized our understanding of complex interactions between the immune system, stromal cells, and epithelial cells by mapping novel cell subpopulations and their remodeling during disease. This technology has not been widely applied to pre-clinical models of IBD. ScRNA-seq profiling of murine models may provide an opportunity to increase the translatability into the clinic, and to choose the most appropriate model to test hypotheses and novel therapeutics. In this review, we have summarized some of the key findings at the single cell transcriptomic level in IBD, how specific signatures have been functionally validated in vivo, and highlighted the similarities and differences between scRNA-seq findings in human IBD and experimental mouse models. In each section of this review, we highlight the importance of utilizing this technology to find the most suitable or translational models of IBD based on the cellular therapeutic target.

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Section: Regulatory T Cellssupporting

confidence: 89%

Single cell RNA-sequencing profiling to improve the translation between human IBD and in vivo models

Karmele,

Moldoveanu,

Kaymak

et al. 2023

Front. Immunol.

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“…These studies involved 440 samples, revealing distinct cell lineages that contribute to IBD. Using these datasets, the scIBD platform [ 222 ] has been constructed to integrate large‐scale datasets and further systematic investigation of IBD. The scIBD framework facilitates comparative studies of different single‐cell datasets in a holistic manner, encompassing various aspects, such as the investigating intestinal microenvironment, exploring disease‐associated immune and nonimmune cell subsets, unraveling the cell‐type specificity of GWAS‐risk genes, and examining the cell‐type specificity of drug targets for IBD.…”

Section: Single‐cell Atlases In Disease Biologymentioning

confidence: 99%

Mapping Cell Atlases at the Single‐Cell Level

Ye,

Wang,

et al. 2023

Advanced Science

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Recent advancements in single‐cell technologies have led to rapid developments in the construction of cell atlases. These atlases have the potential to provide detailed information about every cell type in different organisms, enabling the characterization of cellular diversity at the single‐cell level. Global efforts in developing comprehensive cell atlases have profound implications for both basic research and clinical applications. This review provides a broad overview of the cellular diversity and dynamics across various biological systems. In addition, the incorporation of machine learning techniques into cell atlas analyses opens up exciting prospects for the field of integrative biology.

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