Regulatory role of FOXQ1 gene and its target genes in colorectal cancer

Yuxiang Zou; Jialong Qi; Hui Tang; Yuxiang Zou; Jialong Qi; Hui Tang

doi:10.3934/medsci.2024018

AIMS Medical Science

2024, Volume 11, Issue 3: 232-247. doi: 10.3934/medsci.2024018

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Theory article

Regulatory role of FOXQ1 gene and its target genes in colorectal cancer

1.
Medical School, Kunming University of Science and Technology, Kunming, 650500, P. R. China
2.
Department of Gastroenterology, The First People's Hospital of Yunnan Province, Kunming, P. R. China

Received: 19 February 2024 Revised: 30 June 2024 Accepted: 18 July 2024 Published: 24 July 2024

Forkhead box Q1 (FOXQ1) is a nuclear transcription factor that controls the transcriptional activity of downstream genes to exert biological effects. Since its regulatory role in colorectal cancer (CRC) is unknown, we correlated RNA-seq and ATAC-seq sequencing data from the Cancer Genome Atlas Program (TCGA), the Gene Expression Omnibus (GEO), and other databases with FOXQ1 knockdown data from our group and normal DLD1-CRC cell lines. First, we analyzed FOXQ1 gene expression across multiple databases and datasets and found significant differences in FOXQ1 gene expression in most tumors. In addition, we performed an extension analysis of the FOXQ1 gene at different levels and found a close relationship between the FOXQ1 gene and immunity. Then, based on the FOXQ1 gene, we collected its target genes and obtained a total of 107 genes that met the regulatory trend. After a series of target gene analyses, we obtained three key genes (SERPINA1, MYL9, and CFTR). Moreover, an enrichment analysis, an independent prognostic analysis, and an immune-related analysis were performed around FOXQ1 and its target genes. After knocking down FOXQ1 protein in SW480 cells, the SERPINA1 and MYL9 proteins were significantly altered, though the CFTR protein was not significantly changed. These results provide bioinformatics data that support studying and exploring the FOXQ1 gene and its target genes in CRC.
- FOXQ1,
- RNA-seq2,
- ATAC-seq3,
- pan-cancer4,
- immunity5,
- survival6,
- colorectal cancer
Citation: Yuxiang Zou, Jialong Qi, Hui Tang. Regulatory role of FOXQ1 gene and its target genes in colorectal cancer[J]. AIMS Medical Science, 2024, 11(3): 232-247. doi: 10.3934/medsci.2024018

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Abstract

Forkhead box Q1 (FOXQ1) is a nuclear transcription factor that controls the transcriptional activity of downstream genes to exert biological effects. Since its regulatory role in colorectal cancer (CRC) is unknown, we correlated RNA-seq and ATAC-seq sequencing data from the Cancer Genome Atlas Program (TCGA), the Gene Expression Omnibus (GEO), and other databases with FOXQ1 knockdown data from our group and normal DLD1-CRC cell lines. First, we analyzed FOXQ1 gene expression across multiple databases and datasets and found significant differences in FOXQ1 gene expression in most tumors. In addition, we performed an extension analysis of the FOXQ1 gene at different levels and found a close relationship between the FOXQ1 gene and immunity. Then, based on the FOXQ1 gene, we collected its target genes and obtained a total of 107 genes that met the regulatory trend. After a series of target gene analyses, we obtained three key genes (SERPINA1, MYL9, and CFTR). Moreover, an enrichment analysis, an independent prognostic analysis, and an immune-related analysis were performed around FOXQ1 and its target genes. After knocking down FOXQ1 protein in SW480 cells, the SERPINA1 and MYL9 proteins were significantly altered, though the CFTR protein was not significantly changed. These results provide bioinformatics data that support studying and exploring the FOXQ1 gene and its target genes in CRC.

Acknowledgments

We acknowledge TCGA and GEO database for providing their platforms and contributors for uploading their meaningful datasets.

Availability of data and materials

The datasets generated and/or analyzed during the current study are available in the TCGA and GEO repository, https://portal.gdc.cancer.gov/ and https://www.ncbi.nlm.nih.gov/gds.

Ethics approval of research and informed consent

The studies involving human participants were reviewed and approved by TCGA and GEO. The patients/participants provided their written informed consent to participate in this study.

Conflict of interest

The authors declare no conflict of interest.

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