Single-cell RNA sequencing analysis of T helper cell differentiation and heterogeneity

Jaroušek, Radim; Mikulová, Antónia; Daďová, Petra; Tauš, Petr; Kurucová, Terézia; Plevová, Karla; Tichý, Boris; Kubala, Lukáš

doi:10.1016/j.bbamcr.2022.119321

Cited by 7 publications

(1 citation statement)

References 81 publications

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“…Differentially expressed proteins (DEPs) were defined based on a significance threshold of P value < 0.05 and a fold change (FC) greater than 1 [ 45 ]. The relative protein abundance in gastric tissues was depicted through the creation of heatmaps and bar graphs using ggplot2 in R software [ 46 ].…”

Section: Methodsmentioning

confidence: 99%

Revealing the pathogenesis of gastric intestinal metaplasia based on the mucosoid air-liquid interface

Liu,

Wen,

et al. 2024

J Transl Med

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Background Gastric intestinal metaplasia (GIM) is an essential precancerous lesion. Although the reversal of GIM is challenging, it potentially brings a state-to-art strategy for gastric cancer therapeutics (GC). The lack of the appropriate in vitro model limits studies of GIM pathogenesis, which is the issue this work aims to address for further studies. Method The air-liquid interface (ALI) model was adopted for the long-term culture of GIM cells in the present work. This study conducted Immunofluorescence (IF), quantitative real-time polymerase chain reaction (qRT-PCR), transcriptomic sequencing, and mucoproteomic sequencing (MS) techniques to identify the pathways for differential expressed genes (DEGs) enrichment among different groups, furthermore, to verify novel biomarkers of GIM cells. Result Our study suggests that GIM-ALI model is analog to the innate GIM cells, which thus can be used for mucus collection and drug screening. We found genes MUC17, CDA, TRIM15, TBX3, FLVCR2, ONECUT2, ACY3, NMUR2, and MAL2 were highly expressed in GIM cells, while GLDN, SLC5A5, MAL, and MALAT1 showed down-regulated, which can be used as potential biomarkers for GIM cells. In parallel, these genes that highly expressed in GIM samples were mainly involved in cancer-related pathways, such as the MAPK signal pathway and oxidative phosphorylation signal pathway. Conclusion The ALI model is validated for the first time for the in vitro study of GIM. GIM-ALI model is a novel in vitro model that can mimic the tissue micro-environment in GIM patients and further provide an avenue for studying the characteristics of GIM mucus. Our study identified new markers of GIM as well as pathways associated with GIM, which provides outstanding insight for exploring GIM pathogenesis and potentially other related conditions.

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Section: Methodsmentioning

confidence: 99%