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Genes
Special Issues
Gene Regulation and Transcription Factors in Cancer
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Gene Regulation and Transcription Factors in Cancer

A special issue of Genes (ISSN 2073-4425). This special issue belongs to the section "Molecular Genetics and Genomics".

Deadline for manuscript submissions: closed (10 March 2024) | Viewed by 1991

Special Issue Editor

Prof. Dr. Yihui Fan

E-Mail
Guest Editor
Department of Pathogenic Biology, School of Medicine, Nantong University, Nantong, China
Interests: enhancer; super-enhancer; transcriptional regulation; DNA regulatory elements
Special Issues, Collections and Topics in MDPI journals

Special Issue Information

Dear Colleagues,

Precise spatiotemporal expression of genes and specific gene expression profiling in each cell type at different stages are crucial for maintaining normal cell function. However, the gene regulation program in cancer cells is significantly disrupted, leading to the promotion of cancer hallmarks. Cancers can activate DNA regulatory elements such as super-enhancers or regulatory factors such as transcription factors to induce abnormal gene expression. This Special Issue invites papers that aim to uncover the mechanisms underlying abnormal gene regulation in cancer.

Prof. Dr. Yihui Fan
Guest Editor

Manuscript Submission Information

Manuscripts should be submitted online at www.mdpi.com by registering and logging in to this website. Once you are registered, click here to go to the submission form. Manuscripts can be submitted until the deadline. All submissions that pass pre-check are peer-reviewed. Accepted papers will be published continuously in the journal (as soon as accepted) and will be listed together on the special issue website. Research articles, review articles as well as short communications are invited. For planned papers, a title and short abstract (about 100 words) can be sent to the Editorial Office for announcement on this website.

Submitted manuscripts should not have been published previously, nor be under consideration for publication elsewhere (except conference proceedings papers). All manuscripts are thoroughly refereed through a single-blind peer-review process. A guide for authors and other relevant information for submission of manuscripts is available on the Instructions for Authors page. Genes is an international peer-reviewed open access monthly journal published by MDPI.

Please visit the Instructions for Authors page before submitting a manuscript. The Article Processing Charge (APC) for publication in this open access journal is 2600 CHF (Swiss Francs). Submitted papers should be well formatted and use good English. Authors may use MDPI's English editing service prior to publication or during author revisions.

Keywords

  • gene regulation
  • cancer
  • epigenetics
  • transcription
  • enhancer
  • super-enhancer
  • transcription factors

Published Papers (1 paper)

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Research

17 pages, 3976 KiB  
Article
The 3′ Non-Coding Sequence Negatively Regulates PD-L1 Expression, and Its Regulators Are Systematically Identified in Pan-Cancer
by Zike Chen, Hui Pi, Wen Zheng, Xiaohong Guo, Conglin Shi, Zhiyang Wang, Jie Zhang, Xuanhao Qu, Lehan Liu, Haoliang Shen, Yang Lu, Miaomiao Chen, Weibing Zhang, Rong Sun and Yihui Fan
Genes 2023, 14(8), 1620; https://doi.org/10.3390/genes14081620 - 13 Aug 2023
Viewed by 1621
Abstract
The 3′-untranslated region (3′-UTR) of PD-L1 is significantly longer than the coding sequences (CDSs). However, its role and regulators have been little studied. We deleted whole 3′-UTR region by CRISPR-Cas9. Prognostic analysis was performed using online tools. Immune infiltration analysis was performed using [...] Read more.
The 3′-untranslated region (3′-UTR) of PD-L1 is significantly longer than the coding sequences (CDSs). However, its role and regulators have been little studied. We deleted whole 3′-UTR region by CRISPR-Cas9. Prognostic analysis was performed using online tools. Immune infiltration analysis was performed using the Timer and Xcell packages. Immunotherapy response prediction and Cox regression was performed using the R software. MicroRNA network analysis was conducted by the Cytoscape software. The level of PD-L1 was significantly and dramatically up-regulated in cells after deleting the 3′-UTR. Additionally, we discovered a panel of 43 RNA-binding proteins (RBPs) whose expression correlates with PD-L1 in the majority of cancer cell lines and tumor tissues. Among these RBPs, PARP14 is widely associated with immune checkpoints, the tumor microenvironment, and immune-infiltrating cells in various cancer types. We also identified 38 microRNAs whose individual expressions are associated with PD-L1 across different cancers. Notably, miR-3139, miR-4761, and miR-15a-5p showed significant associations with PD-L1 in most cancer types. Furthermore, we revealed 21 m6A regulators that strongly correlate with PD-L1. Importantly, by combining the identified RBP and m6A regulators, we established an immune signature consisting of RBMS1, QKI, ZC3HAV1, and RBM38. This signature can be used to predict the responsiveness of cancer patients to immune checkpoint blockade treatment. We demonstrated the critical role of the 3′-UTR in the regulation of PD-L1 and identified a significant number of potential PD-L1 regulators across various types of cancer. The biomarker signature generated from our findings shows promise in predicting patient prognosis. However, further biological investigation is necessary to explore the potential of these PD-L1 regulators. Full article
(This article belongs to the Special Issue Gene Regulation and Transcription Factors in Cancer)
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