Complex Analysis of Single-Cell RNA Sequencing Data

Khozyainova, Anna A.; Valyaeva, Anna A.; Arbatsky, Mikhail; Isaev, Sergey; Iamshchikov, Pavel; Volchkov, Egor; Sabirov, Marat; Zainullina, Viktoria R.; Chechekhin, Vadim; Vorobev, Rostislav; Menyailo, Maxim E.; Tyurin‐Kuzmin, Pyotr A.; Denisov, Evgeny V.

doi:10.1134/s0006297923020074

Cited by 14 publications

(13 citation statements)

References 151 publications

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“…The epithelial and mesenchymal clusters were isolated by the Subset function and then prefiltered, renormalized and reclustered with the following cutoffs and parameters: mesenchymal cluster: 200 < nFeature_RNA < 7000, percent.mt < 10, percent.Hba < 0.2, percent.Hbb < 0.2, UMAP resolution = 0.3; epithelial cluster: 200 < nFeature_RNA < 8000, percent.mt < 20, percent.Hba < 0.4, percent.Hbb < 0.4, UMAP resolution = 0.1. Top2a + proliferating cells were excluded for eliminating the effects of different cell cycle states on reclustering and analysis of differentially expressed gene 17,18 . CellChat R package 19 was used to deduce ligand‐receptor interactions between mesenchymal and epithelium cells.…”

Section: Methodsmentioning

confidence: 99%

“…Top2a+ proliferating cells were excluded for eliminating the effects of different cell cycle states on reclustering and analysis of differentially expressed gene. 17,18 CellChat R package 19 was used to deduce ligand-receptor interactions between mesenchymal and epithelium cells. Average gene expression per cell cluster was calculated by using "computeCommuProb" function with the "truncat-edMean" method by setting the trim value as 0.05 (5%) for communication probabilities inferring.…”

Section: Endothelial Cells 5%mentioning

confidence: 99%

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Single‐cell transcriptomic profiling of the neonatal oviduct and uterus reveals new insights into upper Müllerian duct regionalization

Jia,

Zhao

2024

The FASEB Journal

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The upper Müllerian duct (MD) is patterned and specified into two morphologically and functionally distinct organs, the oviduct and uterus. It is known that this regionalization process is instructed by inductive signals from the adjacent mesenchyme. However, the interaction landscape between epithelium and mesenchyme during upper MD development remains largely unknown. Here, we performed single‐cell transcriptomic profiling of mouse neonatal oviducts and uteri at the initiation of MD epithelial differentiation (postnatal day 3). We identified major cell types including epithelium, mesenchyme, pericytes, mesothelium, endothelium, and immune cells in both organs with established markers. Moreover, we uncovered region‐specific epithelial and mesenchymal subpopulations and then deduced region‐specific ligand‐receptor pairs mediating mesenchymal‐epithelial interactions along the craniocaudal axis. Unexpectedly, we discovered a mesenchymal subpopulation marked by neurofilaments with specific localizations at the mesometrial pole of both the neonatal oviduct and uterus. Lastly, we analyzed and revealed organ‐specific signature genes of pericytes and mesothelial cells. Taken together, our study enriches our knowledge of upper MD development, and provides a manageable list of potential genes, pathways, and region‐specific cell subtypes for future functional studies.

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Section: Methodsmentioning

confidence: 99%

Section: Endothelial Cells 5%mentioning

confidence: 99%

Single‐cell transcriptomic profiling of the neonatal oviduct and uterus reveals new insights into upper Müllerian duct regionalization

Jia,

Zhao

2024

The FASEB Journal

View full text Add to dashboard Cite

show abstract

“…The epithelial and mesenchymal clusters were isolated by the Subset function and then prefiltered, renormalized and reclustered with the following cutoffs and parameters: mesenchymal cluster: 200 < nFeature_RNA < 7000, percent.mt < 10, percent.Hba < 0.2, percent.Hbb < 0.2, UMAP resolution= 0.3; epithelial cluster: 200 < nFeature_RNA < 8000, percent.mt < 20, percent.Hba < 0.4, percent.Hbb < 0.4, UMAP resolution= 0.1. Top2a + proliferating cells were excluded for eliminating the effects of different cell cycle states on reclustering and analysis of differentially expressed gene (89, 90). CellChat R package(40) was used to deduce ligand-receptor interactions between mesenchymal and epithelium cells.…”

Section: Methodsmentioning

confidence: 99%

Single-cell transcriptomic profiling of the neonatal oviduct and uterus reveals new insights into upper Müllerian duct regionalization

Jia,

Zhao

2023

Preprint

View full text Add to dashboard Cite

The upper Müllerian duct (MD) is patterned and specified into two morphologically and functionally distinct organs, the oviduct and uterus. It is known that this regionalization process is instructed by inductive signals from the adjacent mesenchyme. However, the interaction landscape between epithelium and mesenchyme during upper MD development remains largely unknown. Here, we performed single-cell transcriptomic profiling of mouse neonatal oviducts and uteri at the initiation of MD epithelial differentiation (postnatal day 3). We identified major cell types including epithelium, mesenchyme, pericytes, mesothelium, endothelium, and immune cells in both organs with established markers. Moreover, we uncovered region-specific epithelial and mesenchymal subpopulations and then deduced region-specific ligand-receptor pairs mediating mesenchymal-epithelial interactions along the craniocaudal axis. Unexpectedly, we discovered a mesenchymal subpopulation marked by neurofilaments with specific localizations at the mesometrial pole of both the neonatal oviduct and uterus. Lastly, we analyzed and revealed organ-specific signature genes of pericytes and mesothelial cells. Taken together, our study enriches our knowledge of upper Müllerian duct development, and provides a manageable list of potential genes, pathways, and region-specific cell subtypes for future functional studies.

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“…In particular, single‐cell RNA sequencing (scRNA‐seq) can be utilised to measure variations in gene expression between samples. Furthermore, the dynamic pathways involved in cell development can be reestablished based on the similarity and heterogeneity of cell expression patterns mined from scRNA‐seq data, and unusual T‐cell subtypes and their differentiation status can be detected 22 . Specifically, scRNA‐seq‐based findings of different metabolic pathways have revealed that abnormal lipid buildup induces exhaustion in Teffs, causing high‐level lipid metabolism in both Teffs and Texs 23 .…”

Section: Introductionmentioning

confidence: 99%

Unlocking the potential of T‐cell metabolism reprogramming: Advancing single‐cell approaches for precision immunotherapy in tumour immunity

Huang,

Li,

Zhang

et al. 2024

Clinical & Translational Med

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As single‐cell RNA sequencing enables the detailed clustering of T‐cell subpopulations and facilitates the analysis of T‐cell metabolic states and metabolite dynamics, it has gained prominence as the preferred tool for understanding heterogeneous cellular metabolism. Furthermore, the synergistic or inhibitory effects of various metabolic pathways within T cells in the tumour microenvironment are coordinated, and increased activity of specific metabolic pathways generally corresponds to increased functional activity, leading to diverse T‐cell behaviours related to the effects of tumour immune cells, which shows the potential of tumour‐specific T cells to induce persistent immune responses. A holistic understanding of how metabolic heterogeneity governs the immune function of specific T‐cell subsets is key to obtaining field‐level insights into immunometabolism. Therefore, exploring the mechanisms underlying the interplay between T‐cell metabolism and immune functions will pave the way for precise immunotherapy approaches in the future, which will empower us to explore new methods for combating tumours with enhanced efficacy.

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Complex Analysis of Single-Cell RNA Sequencing Data

Cited by 14 publications

References 151 publications

Single‐cell transcriptomic profiling of the neonatal oviduct and uterus reveals new insights into upper Müllerian duct regionalization

Single‐cell transcriptomic profiling of the neonatal oviduct and uterus reveals new insights into upper Müllerian duct regionalization

Single-cell transcriptomic profiling of the neonatal oviduct and uterus reveals new insights into upper Müllerian duct regionalization

Unlocking the potential of T‐cell metabolism reprogramming: Advancing single‐cell approaches for precision immunotherapy in tumour immunity

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