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Cancer Bioinformatics
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Cancer Bioinformatics

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

Deadline for manuscript submissions: closed (15 June 2023) | Viewed by 4077

Special Issue Editors

Prof. Dr. Shuhui Song

E-Mail Website
Guest Editor
1. China National Center for Bioinformation, Beijing 100029, China
2. National Genomics Data Center, Beijing Institute of Genomics, Chinese Academy of Sciences (CAS), Beijing 100029, China
Interests: cancer bioinformatics; RNA-omics; bioinformatics; genomic variation; data integration and analytics
Dr. Liye Zhang

E-Mail Website
Guest Editor
School of Life Science and Technology, ShanghaiTech University, Shanghai 201210, China
Interests: bioinformatics; genomics; precision medicine
Dr. Liguo Wang

E-Mail Website
Guest Editor
Mayo Medical School, Rochester, MN 55905, USA
Interests: bioinformatics; genomics; precision medicine

Special Issue Information

Dear Colleagues,

In addition to the application of multiple omics technologies in cancer studies, the field of cancer bioinformatics represents a dynamic and expanding field of cancer genetic research. In recent years, aided by TCGA projects, the increased knowledge in genetics, biochemistry, and molecular biology, together with technological advancements, especially in genomic sequencing and artificial intelligence, has animated researchers and clinicians who are dealing with the complexity of various cancers. In particular, the areas of discovery of molecular markers for early cancer diagnosis, discovery of precise therapeutic targets, and different types of cancer and molecular mechanisms must be noted.

This Special Issue on cancer bioinformatics will provide an updated overview, novel insights, and critical perspectives on the diagnosis and treatment of different cancers. Given the complexity and broadness of these topics, contributions from experts in the field through research papers and reviews are welcome.

Prof. Dr. Shuhui Song
Dr. Liye Zhang
Dr. Liguo Wang
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

  • databases for cancers
  • multiple omics data integration
  • algorithms and tools
  • single cell
  • data-informed clinical decision-making and precision medicine

Published Papers (2 papers)

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Research

15 pages, 3993 KiB  
Article
A Pan-Cancer Analysis of Prognostic and Immunological Roles for Cell Death Genes
by Ye Hong, Yan Yuan, Zekun Liu, Zexian Liu and Yizhuo Zhang
Genes 2023, 14(6), 1178; https://doi.org/10.3390/genes14061178 - 28 May 2023
Viewed by 1775
Abstract
The dysregulation of cell death is closely associated with the development, progression, tumor microenvironment (TME), and prognosis of cancer. However, there is no study that comprehensively explores the prognostic and immunological role of cell death in human pan-cancer. We used published human pan-cancer [...] Read more.
The dysregulation of cell death is closely associated with the development, progression, tumor microenvironment (TME), and prognosis of cancer. However, there is no study that comprehensively explores the prognostic and immunological role of cell death in human pan-cancer. We used published human pan-cancer RNA-sequencing and clinical data to explore the prognostic and immunological roles of programmed cell death, which included apoptosis, autophagy, ferroptosis, necroptosis, and pyroptosis. A total of 9925 patients were included for bioinformatic analysis, with 6949 and 2976 patients in the training cohort and validation cohort, respectively. Five-hundred and ninety-nine genes were defined as programmed-cell-death-related genes. In the training cohort, 75 genes were identified to define PAGscore by survival analysis. According to the median value of PAGscore, patients were divided into high- and low-risk groups, and subsequent analyses demonstrated that the high-risk group had a higher level of genomic mutation frequency, hypoxia score, immuneScore, expression of immune genes, activity of malignant signaling pathways, and cancer immunity cycle. Most anti-tumor and pro-tumor components of the TME showed greater activity in high-risk patients. Scores of malignant cell properties were also higher in high-risk patients. These findings were confirmed in the validation cohort and external cohort. Our study constructed a reliable gene signature to distinguish prognosis-favorable and prognosis-unfavorable patients and demonstrated that cell death was significantly associated with cancer prognosis and the TME. Full article
(This article belongs to the Special Issue Cancer Bioinformatics)
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23 pages, 14527 KiB  
Article
A Comprehensive Pan-Cancer Analysis of the Regulation and Prognostic Effect of Coat Complex Subunit Zeta 1
by Ye Hong, Zengfei Xia, Yuting Sun, Yingxia Lan, Tian Di, Jing Yang, Jian Sun, Miaozhen Qiu, Qiuyun Luo and Dajun Yang
Genes 2023, 14(4), 889; https://doi.org/10.3390/genes14040889 - 10 Apr 2023
Cited by 1 | Viewed by 1853
Abstract
The Coatomer protein complex Zeta 1 (COPZ1) has been reported to play an essential role in maintaining the survival of some types of tumors. In this study, we sought to explore the molecular characteristics of COPZ1 and its clinical prognostic value through a [...] Read more.
The Coatomer protein complex Zeta 1 (COPZ1) has been reported to play an essential role in maintaining the survival of some types of tumors. In this study, we sought to explore the molecular characteristics of COPZ1 and its clinical prognostic value through a pan-cancers bioinformatic analysis. We found that COPZ1 was extremely prevalent in a variety of cancer types, and high expression of COPZ1 was linked to poor overall survival in many cancers, while low expression in LAML and PADC was correlated with tumorigenesis. Besides, the CRISPR Achilles’ knockout analysis revealed that COPZ1 was vital for many tumor cells’ survival. We further demonstrated that the high expression level of COPZ1 in tumors was regulated in multi-aspects, including abnormal CNV, DNA-methylation, transcription factor and microRNAs. As for the functional exploration of COPZ1, we found a positive relationship between COPZ1’s expression and stemness and hypoxia signature, especially the contribution of COPZ1 on EMT ability in SARC. GSEA analysis revealed that COPZ1 was associated with many immune response pathways. Further investigation demonstrated that COPZ expression was negatively correlated with immune score and stromal score, and low expression of COPZ1 has been associated to more antitumor immune cell infiltration and pro-inflammatory cytokines. The further analysis of COPZ1 expression and anti-inflammatory M2 cells showed a consistent result. Finally, we verified the expression of COPZ1 in HCC cells, and proved its ability of sustaining tumor growth and invasion with biological experiments. Our study provides a multi-dimensional pan-cancer analysis of COPZ and demonstrates that COPZ1 can serve as both a prospective target for the treatment of cancer and a prognostic marker for a variety of cancer types. Full article
(This article belongs to the Special Issue Cancer Bioinformatics)
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