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The Role of RNA Processing and Metabolism in Tumors
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The Role of RNA Processing and Metabolism in Tumors

A special issue of Genes (ISSN 2073-4425). This special issue belongs to the section "RNA".

Deadline for manuscript submissions: closed (20 August 2022) | Viewed by 18083

Special Issue Editors

Prof. Dr. Chunjiang He

E-Mail Website
Guest Editor
College of Biomedicine and Health, Huazhong Agricultural University, Wuhan 430070, China
Interests: RNA regulation; circRNA; leukemia
Special Issues, Collections and Topics in MDPI journals
Dr. Ke Chen

E-Mail Website
Guest Editor
Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China
Interests: non-coding RNA; metastasis; renal cell carcinoma; signaling pathways
Dr. Xiang Zhou

E-Mail Website
Guest Editor
1. Fudan University Shanghai Cancer Center, Fudan University, Shanghai 200032, China
2. Institutes of Biomedical Sciences, Fudan University, Shanghai 200032, China
Interests: p53; circular RNA; cancer metabolism; drug resistance
Special Issues, Collections and Topics in MDPI journals

Special Issue Information

Dear Colleagues,

RNA metabolism includes the transcription, splicing, modification, transportation, translation, and degradation of RNA molecules. Defects of RNA metabolism cause many human diseases, including cancer. The complete sequence of the human genome provided quite a surprise to many by revealing that more than 98% of the transcriptional output represents non-protein coding RNAs (ncRNAs). In addition to housekeeping ncRNAs (rRNAs, tRNAs, etc.), small regulatory RNAs (microRNAs, piRNAs, etc.), long noncoding RNAs (lncRNAs, >200nt), and circular RNAs are emerging as major population of eukaryotic transcripts with both reported and yet undiscovered roles in gene regulation. This special issue focuses on understanding how genetic/environmental factors affect RNA metabolism in humans and why dysregulation of this process causes cancer. Areas of interest include, but are not limited to:

1) Roles of noncoding RNAs in cancer development and therapy

2) Roles of noncoding RNAs in cancer metabolism and tumour microenvironment

3) Noncoding RNAs as novel therapeutic targets

4) Biogenesis and new action modes of lncRNAs and circular RNAs

5) Epigenetic regulation of noncoding RNAs

6) Nucleolar stress and cancer therapy

7) Identification of new RNA species in cancer

Prof. Dr. Chunjiang He
Dr. Ke Chen
Dr. Xiang Zhou
Guest Editors

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

  • noncoding RNA
  • metabolism
  • tumor microenvironment
  • cancer therapy

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Published Papers (5 papers)

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Research

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10 pages, 1428 KiB  
Article
Identification of Long Non-Coding RNA MIR4435-2HG as a Prognostic Biomarker in Bladder Cancer
by Zhiquan Hu, Siquan Ma, Yi Sun, Gongwei Long and Ke Chen
Genes 2022, 13(8), 1462; https://doi.org/10.3390/genes13081462 - 17 Aug 2022
Cited by 3 | Viewed by 2329
Abstract
The abnormal expression of long non-coding RNAs(lncRNAs) is closely related to the prognosis of patients. This finding may indicate a new target for the treatment of malignant tumors. Non-muscle invasive bladder cancer (NMIBC) is the most common subtype of bladder cancer, and BCG [...] Read more.
The abnormal expression of long non-coding RNAs(lncRNAs) is closely related to the prognosis of patients. This finding may indicate a new target for the treatment of malignant tumors. Non-muscle invasive bladder cancer (NMIBC) is the most common subtype of bladder cancer, and BCG intravesical therapy is the first-line treatment for NMIBC, but about half of NMIBC patients relapse within two years after BCG treatment. Therefore, it is necessary to screen out lncRNAs related to the prognosis and treatment of BGC-resistant patients. Here, we performed differential expression analysis of lncRNAs in the Cancer Genome Atlas (TCGA) and Gene Expression Omnibus (GEO) datasets, and screened MIR4435-2HG as the only BCG-response-related lncRNA. Then, the prognosis value of MIR4435-2HG was validated in several publicly available cohorts, and confirmed its prognostic value in bladder cancer of different stages. In addition, we also analyzed its genetic alterations, clinical relevance, function enrichment, and association with other biomarkers. Further validation of the expression of MIR4435-2HG might be helpful to instruct NMIBC prognosis and treatment. Full article
(This article belongs to the Special Issue The Role of RNA Processing and Metabolism in Tumors)
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23 pages, 9090 KiB  
Article
Integrated Analysis of a Ferroptosis-Related LncRNA Signature for Evaluating the Prognosis of Patients with Colorectal Cancer
by Shaohua Xu, Yanjie Zhou, Junyun Luo, Su Chen, Jiahui Xie, Hui Liu, Yirong Wang and Zhaoyong Li
Genes 2022, 13(6), 1094; https://doi.org/10.3390/genes13061094 - 19 Jun 2022
Cited by 11 | Viewed by 3310
Abstract
LncRNAs have been well known for their multiple functions in the tumorigenesis, development, and relapse of colorectal cancer (CRC). Accumulating studies demonstrated that the expression of lncRNAs can be regulated by ferroptosis, a biological process that has been revealed to suppress CRC progression. [...] Read more.
LncRNAs have been well known for their multiple functions in the tumorigenesis, development, and relapse of colorectal cancer (CRC). Accumulating studies demonstrated that the expression of lncRNAs can be regulated by ferroptosis, a biological process that has been revealed to suppress CRC progression. However, the functions and clinical implications of ferroptosis-associated lncRNAs in CRC remain largely unknown. We, herein, aim to construct a prognostic signature with ferroptosis-related lncRNAs for the prognostic estimation of CRC patients. Firstly, we identified the lncRNAs related to ferroptosis based on the RNA-Seq data of CRC from the TCGA database. The univariate and multivariate Cox analyses were then performed to establish a prognostic signature composed of eight ferroptosis-related lncRNAs (AL161729.4, AC010973.2, CCDC144NL-AS1, AC009549.1, LINC01857, AP003555.1, AC099850.3, and AC008494.3). Furthermore, we divided the CRC patients into high- and low-risk groups based on the signature and found the overall survival (OS) of patients in the high-risk group was significantly shorter than that in the low-risk group (p = 3.31 × 10−11). Moreover, the patients in the high-risk groups had shorter recurrence-free survival (RFS) (p = 6.5 × 10−3) and disease-free survival (DFS) (p = 4.27 × 10−4), as well as higher tumor recurrence rate. Additionally, we found that the oncogenic pathways were enriched in the high-risk group, whereas the ferroptosis pathway that probably repressed CRC development was enriched in the low-risk group. In summary, our signature may provide a theoretical foundation for not only accurate judgment for prognosis but also evaluation for recurrence and metastasis in CRC patients. Full article
(This article belongs to the Special Issue The Role of RNA Processing and Metabolism in Tumors)
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13 pages, 2440 KiB  
Article
G-Protein Subunit Gamma 4 as a Potential Biomarker for Predicting the Response of Chemotherapy and Immunotherapy in Bladder Cancer
by Lianhui Duan, Xuefei Liu, Ziwei Luo, Chen Zhang, Chun Wu, Weiping Mu, Zhixiang Zuo, Xiaoqing Pei and Tian Shao
Genes 2022, 13(4), 693; https://doi.org/10.3390/genes13040693 - 14 Apr 2022
Cited by 5 | Viewed by 3006
Abstract
Background: GNG4, a member of the G-protein γ family, is a marker of poor overall survival (OS) rates in some malignancies. However, the potential role of GNG4 in bladder cancer (BLCA) is unknown. It is also unclear whether GNG4 may be utilized as [...] Read more.
Background: GNG4, a member of the G-protein γ family, is a marker of poor overall survival (OS) rates in some malignancies. However, the potential role of GNG4 in bladder cancer (BLCA) is unknown. It is also unclear whether GNG4 may be utilized as a marker to guide chemotherapy or immunotherapy. Methods: Single-cell RNA sequencing data were used to explore the expression of GNG4 in tumor microenvironment of BLCA. Bulk RNA sequencing data from TCGA were used to evaluate the relationship between GNG4 expression and biological features, such as immune cell infiltrations and gene mutations. The associations between GNG4 expression and survival in BLCA patients under or not under immunotherapy were evaluated using seven BLCA cohorts. Results: GNG4 was specifically expressed in exhausted CD4+ T cells. And the high expression of the GNG4 was associated with high level of immune cell infiltration. The high-GNG4-expression group displayed a better response to immunotherapy, whereas patients in the low-GNG4-expression group often benefited from chemotherapy. Moreover, the high-GNG4 group was more similar to the basal group, whereas the low-GNG4 group was similar to the luminal group. Conclusions: GNG4 may be a potential biomarker for the prediction of the response to therapy in BLCA. Higher GNG4 expression can be used as a predictor of response to immunotherapy, and lower GNG4 expression can be used as a predictor of response to chemotherapy. Full article
(This article belongs to the Special Issue The Role of RNA Processing and Metabolism in Tumors)
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12 pages, 4427 KiB  
Article
Circular RNA circYPEL2: A Novel Biomarker in Cervical Cancer
by Xinyang Zhang, Siqi Yang, Wenbo Chen, Xin Dong, Rongyu Zhang, Haidong Ye, Xiangfei Mei, Huan Liu, Yu Fang and Chunjiang He
Genes 2022, 13(1), 38; https://doi.org/10.3390/genes13010038 - 23 Dec 2021
Cited by 7 | Viewed by 3129
Abstract
Cervical cancer (CC) is one of the most threatening diseases in women. Circular RNAs (circRNAs) have been reported to be cancer hallmarks, but typical circRNAs in CC were rarely indicated. Through high-throughput sequencing in CC and normal cervix tissues, circYPEL2 (hsa_circ_0005600) was proposed [...] Read more.
Cervical cancer (CC) is one of the most threatening diseases in women. Circular RNAs (circRNAs) have been reported to be cancer hallmarks, but typical circRNAs in CC were rarely indicated. Through high-throughput sequencing in CC and normal cervix tissues, circYPEL2 (hsa_circ_0005600) was proposed as a candidate circRNA. CircYPEL2 exhibited significantly high expression in CC tissue and strong stability in CC cell lines. Furthermore, knockdown and overexpression of circYPEL2 indicated the potential involvement in CC proliferation, migration and invasion. Finally, the downstream regulatory genes of circYPEL2 were investigated by knockdown experiment in CC cell lines with high-throughput sequencing. In summary, our work identified circYPEL2 as a potential biomarker for clinical research of cervical cancer. Full article
(This article belongs to the Special Issue The Role of RNA Processing and Metabolism in Tumors)
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Review

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21 pages, 2856 KiB  
Review
USP10 as a Potential Therapeutic Target in Human Cancers
by Li Tao, Xiao Liu, Xinya Jiang, Kun Zhang, Yijing Wang, Xiumin Li, Shulong Jiang and Tao Han
Genes 2022, 13(5), 831; https://doi.org/10.3390/genes13050831 - 6 May 2022
Cited by 26 | Viewed by 5001
Abstract
Deubiquitination is a major form of post-translational protein modification involved in the regulation of protein homeostasis and various cellular processes. Deubiquitinating enzymes (DUBs), comprising about five subfamily members, are key players in deubiquitination. USP10 is a USP-family DUB featuring the classic USP domain, [...] Read more.
Deubiquitination is a major form of post-translational protein modification involved in the regulation of protein homeostasis and various cellular processes. Deubiquitinating enzymes (DUBs), comprising about five subfamily members, are key players in deubiquitination. USP10 is a USP-family DUB featuring the classic USP domain, which performs deubiquitination. Emerging evidence has demonstrated that USP10 is a double-edged sword in human cancers. However, the precise molecular mechanisms underlying its different effects in tumorigenesis remain elusive. A possible reason is dependence on the cell context. In this review, we summarize the downstream substrates and upstream regulators of USP10 as well as its dual role as an oncogene and tumor suppressor in various human cancers. Furthermore, we summarize multiple pharmacological USP10 inhibitors, including small-molecule inhibitors, such as spautin-1, and traditional Chinese medicines. Taken together, the development of specific and efficient USP10 inhibitors based on USP10’s oncogenic role and for different cancer types could be a promising therapeutic strategy. Full article
(This article belongs to the Special Issue The Role of RNA Processing and Metabolism in Tumors)
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