TRNA level in HeLa, CFBE41o- and primary HBE cells
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ABSTRACT:
ORGANISM(S): Homo sapiens
PROVIDER: GSE53991 | GEO | 2017/05/24
SECONDARY ACCESSION(S): PRJNA234294
REPOSITORIES: GEO
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Project description:Cystic fibrosis (CF) is characterized by chronic inflammation and excessive cytokines secretion in the lung. Isogenic human CF bronchial epithelial (CFBE41o-) cell lines stably expressing wt-CFTR (WTBE) or F508del mutant (CFBE) are widely used tools in understanding responses to stimuli or drugs and CF pathogenesis in vitro. However, their intrinsic cellular differences in culture are unknown. Hence, we performed integrative analyses at protein, mRNA and chromatin levels on these isogenic cell lines cultured in submerged and transwell condition. CFBE and WTBE cells displayed different secretion patterns on IL-6, IL-8, CXCL1, CXCL10, and CCL5 . The ALI culture dramatically increased cytokines secretion in both cells. ATAC-seq results showed that CFBE cells exhibited higher genome-wide chromatin accessibility than WTBE cells in both culture methods, but the relative openness of cytokine genes between two cells varied individually. Differentially expressed genes between two cell lines from mRNA sequencing were highly concentrated in immunity-related pathways. While the mRNA stability of CXCL10 and CXCL1 exhibited the most significant differences between cell lines in SUB culture, most cytokines had comparable mRNA stabilities within same culture method. Moreover, polarization of cells via transwell culture remodeled the chromatin accessibility and transcriptome. This multilayered studies presents a comprehensive baseline activities of CFBE and WTBE cells, further facilitating their usage and data interpretation as CF cell models.
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Project description:Rationale:Cultured human bronchial epithelia (HBE) are the gold standard model for assessing the efficacy of small molecule therapies in cystic fibrosis (CF). However, these cells are difficult to access, especially in young children. Human nasal epithelia (HNE) are used as a surrogate model although it is unknown whether HNE recapitulate the gene expression properties of HBE Objective: To investigate the similarities and differences in gene expression genome-wide between HBE and HNE with a focus on CF lung disease modifier genes. Methods: RNA-sequencing was conducted on paired cultured and naïve HNE and HBE (n=71 samples) collected from 21 patients with CF who underwent lung transplantation. Gene expression was first compared across cultured and naïve samples to assess the impact of the culturing process, then compared between cultured HNE and HBE. Co-expression relationships of CF modifier genes were compared between cultured HNE and HBE. Results: The culturing process had little impact on the expression level of CF lung disease modifier genes. These genes also showed significant equivalent expression between cultured HNE and HBE. Their co-expression relationships in cultured HNE and HBE overlapped significantly, suggesting the corresponding biological processes are consistent across the two tissues. Conclusions: CF lung disease modifier genes have similar expression profiles across cultured HNE and HBE. This supports the use of HNE as a surrogate airway model to investigate CF lung disease, modifier genes and enable investigation of CF precision medicine.
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Project description:To identify miRNAs involved in ST-induced cell transformation, we used microarray chips containing 856 miRNA probes to define miRNA expression profiles in 16HBE,16HBER and 16HBERST cells. we created HBE cells at different stages of the cell transformation process (Pang et al., 2008). In brief, primary human bronchial epithelial cells were immortalized by expressing SV40 LT and hTERT (named as HBELH cells). HBER cells were created by introduction of an oncogenic version of H-Ras into HBELH cells. In agreement with previous studies, the expression of the oncogene H-Ras led to an increase in cell proliferation; however these cells (HBER) were unable to grow in soft agar or form tumors in immunodeficient mice. Subsequently, HBERST cells generated by the additional introduction of SV40 ST into HBER cells grew in an anchorage independent fashion and formed tumors in immunodeficient mice. Therefore, these cell lines represent distinct stages of immortalized cells (HBELH), pre-transformed cells (HBER) and transformed cells (HBERST). And then, the different miRNA expression profiles of HBE cells at different stages were assayed by miRNA microarray.
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