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Transcriptome analysis upon PHF14 and HMG20A knockdown in MDA-MB-231 cells

ABSTRACT: High mobility group proteins are chromatin regulators with essential functions in development, cell differentiation and cell proliferation. We have shown that the high mobility group protein HMG20A copurifies with the histone reader PHF14. To understand the common functions of HMG20A and PHF14 proteins in regulating the transcriptome, we have performed RNA-Seq expression analysis following depletion of each protein in the triple-negative breast cancer cell line MDA-MB-231. Results indicate that genes regulated by PHF14 largely overlap with those regulated by HMG20A.

ORGANISM(S): Homo sapiens

PROVIDER: GSE193476 | GEO | 2022/09/05

REPOSITORIES: GEO

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Project description:High mobility group proteins are chromatin regulators with essential functions in development, cell differentiation and cell proliferation. The protein HMG20A contains three well defined domains: an amino terminal intrinsically distorted domain, a high mobility group box with higher affinity for double stranded four-way-junction DNA than for lineal DNA and a long coiled-coil domain. Here we have found by a proteomic study that HMG20A copurify with the histone reader protein PHF14. Deletion analysis of the interaction domains and structural modeling by using AlphaFold2 software indicated that HMG20A forms a complex with PHF14 through the establishment of a two-stranded alpha-helical coiled-coil. Furthermore, PHF14 was essential for the stability and the chromatin localization of HMG20A. Transcriptomic analysis of triple negative human breast cancer cells demonstrated that PHF14 and HMG20A share a large subset of targets. PHF14 or HMG20A deficiency increased epithelial markers such as E-cadherin or p63 and components of the Hippo pathway and impaired mesenchymal phenotypes including cell migration, and invasion. Expression of mesenchymal adhesion molecules involved in metastasis such as L1CAM and LRRC15 were downregulated in PHF14 or HMG20A depleted cells in agreement with a decreased homotypic cell-cell adhesion ability. Inducible CRISPR inactivation of PHF14 or HMG20A genes impaired normal TGFβ-trigged epithelial to mesenchymal transition in mouse normal breast epithelial cells. Finally, we performed a meta-analysis of PHF14 and HMG20A genes in cancer databases. PHF14 gene is often amplified in different cancers which is associated to poor prognosis. In fact, high levels of PHF14 mRNA are associated to poor prognosis in many types of cancers. High expression of HMG20A and PHF14 are commonly associated to poor prognosis in sarcoma, colon and pancreas adenocarcinomas. In these tumors we found a clear correlation between the mRNA levels of both factors and also similar patterns of co-expressed genes with HMG20A and PHF14, indicating similar functions.

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Transcriptome analysis upon PHF14 and HMG20A knockdown in MDA-MB-231 cells

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