The 30 Non-Coding Sequence Negatively Regulates PD-L1 Expression, and Its Regulators Are Systematically Identified in Pan-Cancer

Sep 24, 2026

Uploaded by Bintang

The 30-untranslated region (30-UTR) of PD-L1 is substantially longer than its coding sequences, yet its function and regulatory network remain insufficiently characterized. Whole 30-UTR deletion was performed using CRISPR-Cas9, followed by prognostic assessment with online tools, immune infiltration evaluation with Timer and Xcell, and immunotherapy response prediction via R and Cox regression. PD-L1 levels increased markedly after 30-UTR removal. A panel of 43 RNA-binding proteins (RBPs) correlated with PD-L1 across most cancer cell lines and tumor tissues, including PARP14. The study further identified 38 microRNAs linked to PD-L1 and 21 m6A regulators strongly associated with PD-L1. Combining RBPs and m6A regulators produced an immune signature (RBMS1, QKI, ZC3HAV1, RBM38) for predicting patient responsiveness to immune checkpoint blockade and prognosis, though further experimental validation is needed.

LanguageEnglish

CategoryHealthcare

FormatPDF

Pages17

Reading Time43 min

AccessFree to download

Abstract

Introduction

PD-1/PD-L1 immunotherapy background

Article The 30 Non-Coding Sequence Negatively Regulates PD-L1 Expression, and Its Regulators Are Systematically Identiﬁed in Pan-Cancer Zike Chen 1,†, Hui Pi 2,†, Wen Zheng 3, Xiaohong Guo 3, Conglin Shi 3, Zhiyang Wang 1, Jie Zhang 1, Xuanhao Qu 1, Lehan Liu 1, Haoliang Shen 4, Yang Lu 4, Miaomiao Chen 1, Weibing Zhang 5, Rong Sun 1,* and Yihui Fan 1,3, * Citation: Chen, Z.; Pi, H.; Zheng, W.; Guo, X.; Shi, C.; Wang, Z.; Zhang, J.; Qu, X.; Liu, L.; Shen, H.; et al. The 30 Non-Coding Sequence Negatively Regulates PD-L1 Expression, and Its Regulators Are Systematically Identiﬁed in Pan-Cancer. Genes 2023, 14, 1620. [https://doi.org/10.3390/](https://doi.org/10.3390/)[ ](https://doi.org/10.3390/)genes14081620 Academic Editor: Albert Jeltsch Received: 15 July 2023 Revised: 9 August 2023 Accepted: 10 August 2023 Published: 13 August 2023 Copyright: © 2023 by the authors. Licensee MDPI, Basel, Switzerland. This article is an open access article distributed under the terms and conditions of the Creative Commons Attribution (CC BY) license ([https://](https://)[ ](https://)[creativecommons.org/licenses/by/](creativecommons.org/licenses/by/)[ ](creativecommons.org/licenses/by/)[4.0/](4.0/)) . 1 Laboratory of Medical Science, School of Medicine, Nantong University, Nantong 226001, China; [2031110148@stmail.ntu.edu.cn](2031110148@stmail.ntu.edu.cn) (Z.C.); [1910110206@stmail.ntu.edu.cn](1910110206@stmail.ntu.edu.cn) (Z.W.); [vk7ujc@163.com](vk7ujc@163.com) (J.Z.); [qxh011005@163.com](qxh011005@163.com) (X.Q.); [liukun@ntu.edu.cn](liukun@ntu.edu.cn) (L.L.); [chenmm1024@ntu.edu.cn](chenmm1024@ntu.edu.cn) (M.C.) 2 Department of Pathophysiology, School of Medicine, Nantong University, Nantong 226001, China; [pihui514@163.com](pihui514@163.com) 3 Department of Pathogenic Biology, School of Medicine, Nantong University, Nantong 226001, China; [z0107w@163.com](z0107w@163.com) (W.Z.); [gxh9606@163.com](gxh9606@163.com) (X.G.); [sclynne@163.com](sclynne@163.com) (C.S.) 4 The Intensive Care Unit, Afﬁliated Hospital of Nantong University, Nantong 226001, China; [shenhaoliang2006@126.com](shenhaoliang2006@126.com) (H.S.); [marineluyang@ntu.edu.cn](marineluyang@ntu.edu.cn) (Y.L.) 5 Nantong Center for Disease Control and Prevention, Nantong 226001, China; [ntzwb71@163.com](ntzwb71@163.com) * Correspondence: [sun891604@ntu.edu.cn](sun891604@ntu.edu.cn) (R.S.); [fanyihui@ntu.edu.cn](fanyihui@ntu.edu.cn) (Y.F.)† These authors are contributed equally to this work. Abstract: The 30-untranslated region (30-UTR) of PD-L1 is signiﬁcantly longer than the coding sequences (CDSs) . However, its role and regulators have been little studied. We deleted whole 30-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 30-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 treatme

FAQs

How was the PD-L1 30-UTR function tested in this study?

The researchers deleted the entire PD-L1 30-UTR region using CRISPR-Cas9 and then measured downstream effects, including changes in PD-L1 expression.

What major biomolecular groups were identified as PD-L1 regulators?

The study identified 43 RNA-binding proteins, 38 microRNAs, and 21 m6A regulators whose expression levels correlated with PD-L1 across cancers.

What is the immune signature and what is it used for?

By combining the identified RBPs and m6A regulators, the study built an immune signature consisting of RBMS1, QKI, ZC3HAV1, and RBM38 to predict responsiveness to immune checkpoint blockade and patient prognosis.

Sep 24, 2026

Uploaded by Bintang